Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold487
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 574485
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 4 of 4
Found at i:442934 original size:127 final size:128
Alignment explanation
Indices: 442708--442957 Score: 358
Period size: 127 Copynumber: 2.0 Consensus size: 128
442698 AACCATCACA
* * ** * ** *
442708 TCAAATAGGAATGAAAAGACATTTGACTAGGGCGAGAACCATTATGTCAAATAGGAATGAAAAGA
1 TCAAACAGGAATGAAAAAACATTTGACTAGAACGAGAACCATCACATCAAACAGGAATGAAAAGA
* * *
442773 TGTTTGACAAGGGCGAGAACCATTATGTCAAATAGG-AATGAAAAGAGTTTGACCAGGTATAG
66 TATTTGACAAGGGCGAGAACCATCATGTCAAATAGGAAATGAAAAAAGTTTGACCAGGTATAG
** *
442835 TCAAACAGGAATGAAAAAATGTTTGACTAGAACGAGAACCATCACATCAAACAGGAATGAAAAGG
1 TCAAACAGGAATGAAAAAACATTTGACTAGAACGAGAACCATCACATCAAACAGGAATGAAAAGA
*
442900 TATTTGACAAGGGTGAGAACCATCATGTCAAATAGGAAATGAAAAAAGTTTGACCAGG
66 TATTTGACAAGGGCGAGAACCATCATGTCAAATAGGAAATGAAAAAAGTTTGACCAGG
442958 GCAAGAACTA
Statistics
Matches: 107, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
127 87 0.81
128 20 0.19
ACGTcount: A:0.44, C:0.12, G:0.24, T:0.20
Consensus pattern (128 bp):
TCAAACAGGAATGAAAAAACATTTGACTAGAACGAGAACCATCACATCAAACAGGAATGAAAAGA
TATTTGACAAGGGCGAGAACCATCATGTCAAATAGGAAATGAAAAAAGTTTGACCAGGTATAG
Found at i:442944 original size:265 final size:265
Alignment explanation
Indices: 442487--443128 Score: 697
Period size: 265 Copynumber: 2.4 Consensus size: 265
442477 TAGTCAAACG
*
442487 GGAATGAAAAGATGTTTGACCAAGGCGAGAACCATTACGTCAAAT-GGTAATGAAAAGAGTTTGA
1 GGAATGAAAAGATGTTTGACCAAGGCGAGAACCATTATGTCAAATAGG-AATGAAAAGAGTTTGA
* * * * * ***
442551 CCAGGACAAGAACCATCACTCAAACAAGAATGAAAAGATGTTTGACCAGGGTGAGAACCATCACA
65 CCA-G----G---TAT-AATCAAACAGGAATGAAAAAATGTTTGACTAGAACGAGAACCATCACA
* * * *
442616 TCAAATAAGAAATGAAAAAAGTTTGACCAGGATGAGAACCATCACATCAAATCGGATATGAAAAG
121 TCAAATAAGAAATGAAAAAAGTTTGACAAGGATGAGAACCATCACATCAAATAGGAAATGAAAAA
* **
442681 AGTTTGACGAAAGTGAGAACCATCACATCAAATAGGA-ATGAAAAGACATTTGACTAGGGCGAGA
186 AGTTTGACCAAAGCAAGAACCATCACATCAAATAGGATATGAAAAGA-ATTTGACTAGGGCGAGA
* *
442745 ACCATTATGTCAAATA
250 ACCATCACGTCAAATA
442761 GGAATGAAAAGATGTTTGA-CAAGGGCGAGAACCATTATGTCAAATAGGAATGAAAAGAGTTTGA
1 GGAATGAAAAGATGTTTGACCAA-GGCGAGAACCATTATGTCAAATAGGAATGAAAAGAGTTTGA
* *
442825 CCAGGTATAGTCAAACAGGAATGAAAAAATGTTTGACTAGAACGAGAACCATCACATCAAA-CAG
65 CCAGGTATAATCAAACAGGAATGAAAAAATGTTTGACTAGAACGAGAACCATCACATCAAATAAG
* * * **
442889 GAATG-AAAAGGTATTTGACAAGGGTGAGAACCATCATGTCAAATAGGAAATGAAAAAAGTTTGA
130 AAATGAAAAAAG--TTTGACAAGGATGAGAACCATCACATCAAATAGGAAATGAAAAAAGTTTGA
** * * * * * *
442953 CCAGGGCAAGAACTATCACGTCAAATTGGATATGAAAAGAGTTTGACTAGGGTGAGAGCCATCAC
193 CCAAAGCAAGAACCATCACATCAAATAGGATATGAAAAGAATTTGACTAGGGCGAGAACCATCAC
*
443018 GTCAAATC
258 GTCAAATA
* * * * *
443026 GAATATGAAAAGA-GTTTGACCAAGGAGAGAACCATCATGTCAAACAGTAATGAAAAGAGTTTGA
1 GGA-ATGAAAAGATGTTTGACCAAGGCGAGAACCATTATGTCAAATAGGAATGAAAAGAGTTTGA
* * *
443090 CTAGGTACAATCAAAC-GAGAAT-AAAAAGATGTTTAACTA
65 CCAGGTATAATCAAACAG-GAATGAAAAA-ATGTTTGACTA
443129 AATACAGTAA
Statistics
Matches: 317, Mismatches: 42, Indels: 27
0.82 0.11 0.07
Matches are distributed among these distances:
263 5 0.02
264 12 0.04
265 211 0.67
266 23 0.07
269 1 0.00
273 4 0.01
274 59 0.19
275 2 0.01
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.20
Consensus pattern (265 bp):
GGAATGAAAAGATGTTTGACCAAGGCGAGAACCATTATGTCAAATAGGAATGAAAAGAGTTTGAC
CAGGTATAATCAAACAGGAATGAAAAAATGTTTGACTAGAACGAGAACCATCACATCAAATAAGA
AATGAAAAAAGTTTGACAAGGATGAGAACCATCACATCAAATAGGAAATGAAAAAAGTTTGACCA
AAGCAAGAACCATCACATCAAATAGGATATGAAAAGAATTTGACTAGGGCGAGAACCATCACGTC
AAATA
Found at i:447740 original size:21 final size:19
Alignment explanation
Indices: 447709--447755 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
447699 GTTTGGCTTA
447709 TTTTTTC-TATTTTCTCTTT
1 TTTTTTCTTATTTTC-CTTT
447728 TTTTTTCTTTATTTTCCTTT
1 TTTTTTC-TTATTTTCCTTT
*
447748 CTTTTTCT
1 TTTTTTCT
447756 CTCCCTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 8 0.32
20 10 0.40
21 7 0.28
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTTCTTATTTTCCTTT
Found at i:447747 original size:20 final size:21
Alignment explanation
Indices: 447716--447755 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
447706 TTATTTTTTC
*
447716 TATTTTCTCTTTTTTTTTCTT
1 TATTTTCTCTTTCTTTTTCTT
447737 TATTTTC-CTTTCTTTTTCT
1 TATTTTCTCTTTCTTTTTCT
447756 CTCCCTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (21 bp):
TATTTTCTCTTTCTTTTTCTT
Found at i:449801 original size:93 final size:91
Alignment explanation
Indices: 449331--449895 Score: 488
Period size: 88 Copynumber: 6.2 Consensus size: 91
449321 TTTGTGATCA
* * ** * *
449331 TGTGATGCATCAATACCATTTAGTGGCTT-GAAAAAAAGG-TATGATTGGGAATGAGTGGT-TAG
1 TGTGATGCATCAATACCATCTAATGG-TTGGATGAAAGGGATATGATTGGGAATGAGTGGTCGA-
* * *
449393 GATATCCTTGCCCTAAGGAAATCAAGTTT
64 GATATCCTT-CCCTAAGAAAATCAGGCTT
* * * **
449422 TATAATGCATCAATACCATCTAATGGTTGGATGAAAGGGATATGGTTGGGAATGAGTGGT-TTG-
1 TGTGATGCATCAATACCATCTAATGGTTGGATGAAAGGGATATGATTGGGAATGAGTGGTCGAGA
* * *
449485 CA-CCTTCCCCAAGAAAATCAGGTTT
66 TATCCTTCCCTAAGAAAATCAGGCTT
* * * * **
449510 TGTGATGCATTAATACCATTTAATGGTTTGATGAAGGGGATATGATCAGGAATGTA-TGGT--AT
1 TGTGATGCATCAATACCATCTAATGGTTGGATGAAAGGGATATGATTGGGAATG-AGTGGTCGA-
* * * * *
449572 G-CA-CCCTCCCCAAGGAAATCAAGCTT
64 GATATCCTTCCCTAAGAAAATCAGGCTT
* * ** * * * * *
449598 TGTGATGCATCAATACCATCTAGTGGCTAAAAGAAAAGGATATGATTGGGAATAATTGATCGAGA
1 TGTGATGCATCAATACCATCTAATGGTTGGATGAAAGGGATATGATTGGGAATGAGTGGTCGAGA
* *
449663 TATCCTTACCCTGAGAAAATTAGGCTT
66 TATCCTT-CCCTAAGAAAATCAGGCTT
* * * * * *
449690 TGTGATGCATCAACACCATCTAGTGATTGGATGGAAGGGGACATGATTGGGAATGAGTGGTCGGG
1 TGTGATGCATCAATACCATCTAATGGTTGGAT-GAAAGGGATATGATTGGGAATGAGTGGTCGAG
* *
449755 ATATCCTTGCCCTAAGAAAAACAGGTTT
65 ATATCCTT-CCCTAAGAAAATCAGGCTT
* *
449783 TGTGATGCATCAATACCATTTAATGGTTGGATG-AAGGGATATGATCGGGAATGAGTGGTCGAGA
1 TGTGATGCATCAATACCATCTAATGGTTGGATGAAAGGGATATGATTGGGAATGAGTGGTCGAGA
** * *
449847 TATCCTTATCTCGAGGAAATCAGGCTT
66 TATCCTTCCCT-AAGAAAATCAGGCTT
449874 TGTGATGCATCAATACCATCTA
1 TGTGATGCATCAATACCATCTA
449896 GGAGTTGAAA
Statistics
Matches: 382, Mismatches: 80, Indels: 24
0.79 0.16 0.05
Matches are distributed among these distances:
87 1 0.00
88 132 0.35
89 6 0.02
90 7 0.02
91 99 0.26
92 61 0.16
93 76 0.20
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (91 bp):
TGTGATGCATCAATACCATCTAATGGTTGGATGAAAGGGATATGATTGGGAATGAGTGGTCGAGA
TATCCTTCCCTAAGAAAATCAGGCTT
Found at i:450762 original size:51 final size:51
Alignment explanation
Indices: 450701--450869 Score: 187
Period size: 51 Copynumber: 3.3 Consensus size: 51
450691 AAATAACGGG
** *
450701 GTTGGAGTATCCCTAATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGAGAAAAATTGGTGTTTTGGAAATAAAATCGGA
* ** * ** *
450752 GTTGGAGTATCCCCGATTGCGGTAAATCGGTACTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGAGAAAAATTGGTGTTTTGGAAATAAAATCGGA
* * * * *
450803 GTTGGAGTATCCCCGATTAAGAAAATTTGATGTTTTGGAAATGAAACCGG-
1 GTTGGAGTATCCCCGATTGAGAAAAATTGGTGTTTTGGAAATAAAATCGGA
450853 GATTGGAGTATCCCCGA
1 G-TTGGAGTATCCCCGA
450870 GATGAAAAAT
Statistics
Matches: 96, Mismatches: 21, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
50 1 0.01
51 95 0.99
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGAGAAAAATTGGTGTTTTGGAAATAAAATCGGA
Found at i:453192 original size:13 final size:13
Alignment explanation
Indices: 453174--453199 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
453164 TGCCTGAATA
453174 TATCGATACAATG
1 TATCGATACAATG
453187 TATCGATACAATG
1 TATCGATACAATG
453200 CAAAATGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:453250 original size:13 final size:13
Alignment explanation
Indices: 453232--453259 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
453222 GTAAACCCAT
453232 AATGTATCGATAC
1 AATGTATCGATAC
453245 AATGTATCGATAC
1 AATGTATCGATAC
453258 AA
1 AA
453260 ATTGTGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:454377 original size:21 final size:21
Alignment explanation
Indices: 454359--454399 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
454349 AAGGTGATAT
454359 TTATTCATTTTATTTTGATTA
1 TTATTCATTTTATTTTGATTA
*
454380 TTATTTATTTTA-TTTGATTA
1 TTATTCATTTTATTTTGATTA
454400 AAAATCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.68
Consensus pattern (21 bp):
TTATTCATTTTATTTTGATTA
Found at i:454409 original size:20 final size:21
Alignment explanation
Indices: 454363--454409 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 21
454353 TGATATTTAT
** *
454363 TCATTTTATTTTGATTATTAT
1 TCATTTTATTTTGATTAAAAA
*
454384 TTATTTTA-TTTGATTAAAAA
1 TCATTTTATTTTGATTAAAAA
454404 TCATTT
1 TCATTT
454410 CGTACCCGAT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (21 bp):
TCATTTTATTTTGATTAAAAA
Found at i:455538 original size:19 final size:17
Alignment explanation
Indices: 455510--455547 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 17
455500 GGCTAAAAGC
455510 TTTTTCTTTTTTTTAATT
1 TTTTTCTTTTTTTT-ATT
455528 TTTTGTCTTTTTTTTATT
1 TTTT-TCTTTTTTTTATT
455546 TT
1 TT
455548 CATTTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.08, C:0.05, G:0.03, T:0.84
Consensus pattern (17 bp):
TTTTTCTTTTTTTTATT
Found at i:455547 original size:24 final size:25
Alignment explanation
Indices: 455509--455555 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
455499 TGGCTAAAAG
*
455509 CTTTTTCTTTTTTTTAATTTTTTGT
1 CTTTTTCTTTATTTTAATTTTTTGT
*
455534 CTTTTT-TTTATTTTCATTTTTT
1 CTTTTTCTTTATTTTAATTTTTT
455556 TTGCCATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.09, C:0.09, G:0.02, T:0.81
Consensus pattern (25 bp):
CTTTTTCTTTATTTTAATTTTTTGT
Found at i:455547 original size:25 final size:25
Alignment explanation
Indices: 455509--455556 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
455499 TGGCTAAAAG
*
455509 CTTTTTCTTTTTTTTAATTTTTTGT
1 CTTTTTCTTTTTTTCAATTTTTTGT
*
455534 CTTTTT-TTTATTTTCATTTTTTT
1 CTTTTTCTTT-TTTTCAATTTTTT
455557 TGCCATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 3 0.15
25 17 0.85
ACGTcount: A:0.08, C:0.08, G:0.02, T:0.81
Consensus pattern (25 bp):
CTTTTTCTTTTTTTCAATTTTTTGT
Found at i:456020 original size:26 final size:26
Alignment explanation
Indices: 456000--456049 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
455990 CTAAATAGGT
456000 TGATGTTTATGAAAGAATAAACACGC
1 TGATGTTTATGAAAGAATAAACACGC
*
456026 TGATGTTTATGAAAGAATTAACAC
1 TGATGTTTATGAAAGAATAAACAC
456050 AAATCAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.42, C:0.10, G:0.18, T:0.30
Consensus pattern (26 bp):
TGATGTTTATGAAAGAATAAACACGC
Found at i:456404 original size:13 final size:13
Alignment explanation
Indices: 456386--456415 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
456376 ACAATTCTTC
*
456386 ATGTATCGATATA
1 ATGTATCGATACA
456399 ATGTATCGATACA
1 ATGTATCGATACA
456412 ATGT
1 ATGT
456416 CCCATGTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:456422 original size:33 final size:33
Alignment explanation
Indices: 456363--456428 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
456353 GCTGTTGGGC
* *
456363 ATAATGTATCGATACAATTCTTCATGTATCGAT
1 ATAATGTATCGATACAATTCTCCATGTAACGAT
456396 ATAATGTATCGATACAATGTC-CCATGTAACGAT
1 ATAATGTATCGATACAAT-TCTCCATGTAACGAT
456429 GCATTTCACA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Consensus pattern (33 bp):
ATAATGTATCGATACAATTCTCCATGTAACGAT
Found at i:456501 original size:19 final size:19
Alignment explanation
Indices: 456460--456530 Score: 115
Period size: 19 Copynumber: 3.7 Consensus size: 19
456450 CTGCCAGTTT
* *
456460 CATGTATCAATACAATTGAG
1 CATGTATCGATACAA-GGAG
456480 CATGTATCGATACAAGGAG
1 CATGTATCGATACAAGGAG
456499 CATGTATCGATACAAGGAG
1 CATGTATCGATACAAGGAG
456518 CATGTATCGATAC
1 CATGTATCGATAC
456531 TAGGCACAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
19 35 0.71
20 14 0.29
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (19 bp):
CATGTATCGATACAAGGAG
Found at i:456504 original size:39 final size:38
Alignment explanation
Indices: 456460--456551 Score: 123
Period size: 39 Copynumber: 2.4 Consensus size: 38
456450 CTGCCAGTTT
*
456460 CATGTATCAATACAATTGAGCATGTATCGATACAAGG-A
1 CATGTATCAATACAA-GGAGCATGTATCGATACAAGGCA
* *
456498 GCATGTATCGATACAAGGAGCATGTATCGATACTAGGCA
1 -CATGTATCAATACAAGGAGCATGTATCGATACAAGGCA
456537 CAATGTATCAATACA
1 C-ATGTATCAATACA
456552 TCTGGATATT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
38 20 0.43
39 27 0.57
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (38 bp):
CATGTATCAATACAAGGAGCATGTATCGATACAAGGCA
Found at i:460412 original size:13 final size:13
Alignment explanation
Indices: 460394--460418 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
460384 ATCACTTAAA
460394 TGTATCGATACAT
1 TGTATCGATACAT
460407 TGTATCGATACA
1 TGTATCGATACA
460419 CTGACCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:460483 original size:52 final size:52
Alignment explanation
Indices: 460427--460555 Score: 206
Period size: 52 Copynumber: 2.5 Consensus size: 52
460417 CACTGACCTT
*
460427 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
460479 TGTATCGAT-CTATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATAC-ATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
460531 TGTATCGATACATCCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
460556 TCATATTTCG
Statistics
Matches: 71, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
51 1 0.01
52 69 0.97
53 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:473081 original size:52 final size:51
Alignment explanation
Indices: 473003--473151 Score: 235
Period size: 52 Copynumber: 2.9 Consensus size: 51
472993 CGAAATATGA
473003 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
473055 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
**
473107 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
473152 ATGTATCGAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 85 0.96
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:473158 original size:13 final size:13
Alignment explanation
Indices: 473140--473164 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
473130 CAAAGATCAG
473140 TGTATCGATACAA
1 TGTATCGATACAA
473153 TGTATCGATACA
1 TGTATCGATACA
473165 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:473232 original size:20 final size:20
Alignment explanation
Indices: 473203--473260 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
473193 GCAGTAGCTT
473203 AAAT-TGTATCGATACAAAA
1 AAATATGTATCGATACAAAA
*
473222 AAATATGTATCGATACAACA
1 AAATATGTATCGATACAAAA
***
473242 CTTTATGTATCGATACAAA
1 AAATATGTATCGATACAAA
473261 TCGTTGAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (20 bp):
AAATATGTATCGATACAAAA
Found at i:474138 original size:52 final size:51
Alignment explanation
Indices: 474082--474271 Score: 227
Period size: 52 Copynumber: 3.8 Consensus size: 51
474072 GTTAAAGATG
* *
474082 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATAGGACTTAAGGATGACA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAGG-TGACA
474134 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT---G-G---
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAGGTGACA
* * *
474178 -AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGT-ACCA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AAGGTGA-CA
* *
474229 AAGGCGCCAATATGCTGATTCAAGGCTAGCGATATTGGACTTA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA
474272 GAAGAAGACG
Statistics
Matches: 118, Mismatches: 10, Indels: 21
0.79 0.07 0.14
Matches are distributed among these distances:
43 38 0.32
47 2 0.02
49 1 0.01
51 1 0.01
52 76 0.64
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (51 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAGGTGACA
Found at i:474196 original size:43 final size:43
Alignment explanation
Indices: 474135--474218 Score: 141
Period size: 43 Copynumber: 2.0 Consensus size: 43
474125 AGGATGACAA
*
474135 AGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTGG
1 AGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTGG
* *
474178 AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
474219 AAAGGTACCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (43 bp):
AGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTGG
Found at i:474246 original size:95 final size:95
Alignment explanation
Indices: 474083--474270 Score: 299
Period size: 95 Copynumber: 2.0 Consensus size: 95
474073 TTAAAGATGA
* *
474083 AGGTGCCAATGTGCTGATTCAAGGCCAGCGATATAGGACTTAAGGATGACAAAGGTGCCAATATG
1 AGGTGCCAATGTGCTGATTCAAGGCCAGCGACATAGGACTTAAGGATGACAAAGGCGCCAATATG
474148 CTGATTCAAGGCCAGCGATATTGGACTTGG
66 CTGATTCAAGGCCAGCGATATTGGACTTGG
* *
474178 AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGG-T-ACCAAAGGCGCCAATA
1 AGGTGCCAATGTGCTGATTCAAGGCCAGCGACATAGGACTT-AAGGATGA-CAAAGGCGCCAATA
*
474241 TGCTGATTCAAGGCTAGCGATATTGGACTT
64 TGCTGATTCAAGGCCAGCGATATTGGACTT
474271 AGAAGAAGAC
Statistics
Matches: 86, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
94 1 0.01
95 81 0.94
96 4 0.05
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (95 bp):
AGGTGCCAATGTGCTGATTCAAGGCCAGCGACATAGGACTTAAGGATGACAAAGGCGCCAATATG
CTGATTCAAGGCCAGCGATATTGGACTTGG
Found at i:474351 original size:28 final size:28
Alignment explanation
Indices: 474319--474475 Score: 179
Period size: 28 Copynumber: 5.4 Consensus size: 28
474309 GATTGCATCA
*
474319 ACTTGTGTGCTTTTGAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
* *
474347 ACTTGTGGGCTTTTAAAGATTGCCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
*
474375 ACTTGTGGGCTTTTAAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
* * *
474403 AGTTGTGGGCTTTTGAAAAGAGATGCCACTA
1 ACTTGTGGGCTTTTG--AAG-GTTGCCACTG
* * *
474434 ACTTGTGGGATTTTGAAAAGGGTGCCACTA
1 ACTTGTGGGCTTTTG--AAGGTTGCCACTG
474464 ACTTGTGGGCTT
1 ACTTGTGGGCTT
474476 AAAAGGAAAA
Statistics
Matches: 114, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
28 65 0.57
30 23 0.20
31 26 0.23
ACGTcount: A:0.21, C:0.16, G:0.29, T:0.34
Consensus pattern (28 bp):
ACTTGTGGGCTTTTGAAGGTTGCCACTG
Found at i:474394 original size:56 final size:57
Alignment explanation
Indices: 474293--474475 Score: 219
Period size: 56 Copynumber: 3.2 Consensus size: 57
474283 CACCAACTTG
* *
474293 TGTGGGCTTTTAAAAGGATTG-CA-TCAACTTGTGTGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTAAAA-GATTGCCACT-AACTTGTGGGCTTTTAAAGGTTGCCACTGACT
* *
474350 TGTGGGCTTTT-AAAGATTGCCACTGACTTGTGGGCTTTTAAAGGTTGCCACTGAGT
1 TGTGGGCTTTTAAAAGATTGCCACTAACTTGTGGGCTTTTAAAGGTTGCCACTGACT
* * * *
474406 TGTGGGCTTTTGAAAAGAGATGCCACTAACTTGTGGGATTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTT-AAAAGA-TTGCCACTAACTTGTGGGCTTTT--AAAGGTTGCCACTGACT
474467 TGTGGGCTT
1 TGTGGGCTT
474476 AAAAGGAAAA
Statistics
Matches: 109, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
55 5 0.05
56 44 0.40
57 12 0.11
58 5 0.05
59 20 0.18
61 23 0.21
ACGTcount: A:0.22, C:0.15, G:0.28, T:0.34
Consensus pattern (57 bp):
TGTGGGCTTTTAAAAGATTGCCACTAACTTGTGGGCTTTTAAAGGTTGCCACTGACT
Found at i:474462 original size:30 final size:30
Alignment explanation
Indices: 474319--474753 Score: 322
Period size: 30 Copynumber: 14.6 Consensus size: 30
474309 GATTGCATCA
* *
474319 ACTTGTGTGCTTTTG--AAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
**
474347 ACTTGTGGGCTTTT--AAAGATTGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
*
474375 ACTTGTGGGCTTTT--AAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
* * *
474403 AGTTGTGGGCTTTTGAAAAGAGATGCCACTA
1 ACTTGTGGGCTTTTGAAAAG-GGTGCCACTG
* *
474434 ACTTGTGGGATTTTGAAAAGGGTGCCACTA
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
** * *
474464 ACTTGTGGGCTTAAAAGGAAAAAGAGTGCTA-TAG
1 ACTTGTGGGCTT---TTG-AAAAGGGTGCCACT-G
* * ** *
474498 AGTTGTGAGCTTACAAAAGAAAAAGAGTGCCAC-G
1 ACTTGTGGGCTT----TTG-AAAAGGGTGCCACTG
* * * * *
474532 AAGTTGTGGACTTTGGAAAA-GATGCCACCG
1 -ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
**
474562 ACTTGTGGGCTTCGGAAAAGGGTGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
* * * *
474592 ATTTGTGGGC-TTTGAAAAAGATGCCACCG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
**
474621 ACTTGTGGGCTTCGGAAAAGGGTGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
* * * *
474651 ATTTATGGGC-TTTG--AAGGTTGCCACCG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
*
474678 ATTTGTGGGCTTTTGAAAAGGGTGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
*
474708 ACTTGTGGGC-TTTGAAAAGGATGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
474737 ACTTGTGGGCTTTTGAA
1 ACTTGTGGGCTTTTGAA
474754 GGGTGAGGAA
Statistics
Matches: 334, Mismatches: 54, Indels: 36
0.79 0.13 0.08
Matches are distributed among these distances:
27 20 0.06
28 69 0.21
29 75 0.22
30 94 0.28
31 27 0.08
33 2 0.01
34 21 0.06
35 26 0.08
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.29
Consensus pattern (30 bp):
ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
Found at i:474537 original size:35 final size:34
Alignment explanation
Indices: 474449--474539 Score: 103
Period size: 35 Copynumber: 2.6 Consensus size: 34
474439 TGGGATTTTG
* * * *
474449 AAAAGGGTGCCACTAACTTGTGGGCTTAAAAGGA
1 AAAAGAGTGCCACTAAGTTGTGAGCTTAAAAAGA
*
474483 AAAAGAGTGCTA-TAGAGTTGTGAGCTTACAAAAGA
1 AAAAGAGTGCCACTA-AGTTGTGAGCTTA-AAAAGA
*
474518 AAAAGAGTGCCACGAAGTTGTG
1 AAAAGAGTGCCACTAAGTTGTG
474540 GACTTTGGAA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
33 2 0.04
34 21 0.45
35 23 0.49
36 1 0.02
ACGTcount: A:0.38, C:0.12, G:0.29, T:0.21
Consensus pattern (34 bp):
AAAAGAGTGCCACTAAGTTGTGAGCTTAAAAAGA
Found at i:474567 original size:29 final size:30
Alignment explanation
Indices: 474535--474749 Score: 235
Period size: 29 Copynumber: 7.4 Consensus size: 30
474525 TGCCACGAAG
*
474535 TTGTGGACTTTGGAAAA-GATGCCACCGAC
1 TTGTGGGCTTTGGAAAAGGATGCCACCGAC
* * * *
474564 TTGTGGGCTTCGGAAAAGGGTGCCACTGAT
1 TTGTGGGCTTTGGAAAAGGATGCCACCGAC
*
474594 TTGTGGGCTTT-GAAAAAGATGCCACCGAC
1 TTGTGGGCTTTGGAAAAGGATGCCACCGAC
* * * *
474623 TTGTGGGCTTCGGAAAAGGGTGCCACTGAT
1 TTGTGGGCTTTGGAAAAGGATGCCACCGAC
* * *
474653 TTATGGGCTTT-G--AAGGTTGCCACCGAT
1 TTGTGGGCTTTGGAAAAGGATGCCACCGAC
* * *
474680 TTGTGGGCTTTTGAAAAGGGTGCCACTGAC
1 TTGTGGGCTTTGGAAAAGGATGCCACCGAC
*
474710 TTGTGGGCTTT-GAAAAGGATGCCACTGAC
1 TTGTGGGCTTTGGAAAAGGATGCCACCGAC
474739 TTGTGGGCTTT
1 TTGTGGGCTTT
474750 TGAAGGGTGA
Statistics
Matches: 157, Mismatches: 24, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
27 23 0.15
28 1 0.01
29 68 0.43
30 65 0.41
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (30 bp):
TTGTGGGCTTTGGAAAAGGATGCCACCGAC
Found at i:474598 original size:59 final size:58
Alignment explanation
Indices: 474334--474748 Score: 327
Period size: 59 Copynumber: 6.9 Consensus size: 58
474324 TGTGCTTTTG
* * * * **
474334 AAGGTTGCCACTGACTTGTGGGCTTT-TAAAGATTGCCACTGACTTGTGGGCTT--TTA
1 AAGGGTGCCACTGATTTGTGGGCTTTGAAAAGA-TGCCACCGACTTGTGGGCTTCGGAA
* * ** * **
474390 AAGGTTGCCACTGAGTTGTGGGCTTTTGAAAAGAGATGCCACTAACTTGTGGGATTTTGAA
1 AAGGGTGCCACTGATTTGTGGGC-TTTG-AAA-AGATGCCACCGACTTGTGGGCTTCGGAA
* * * * ** * *
474451 AAGGGTGCCACTAACTTGTGGGCTTAAAAGGAAAAAGAGTGCTATAGAGTTGTGAGCTTACAAAA
1 AAGGGTGCCACTGATTTGTGGGCTT----TG-AAAAGA-TGCCACCGACTTGTGGGCTT-C----
*
474516 GAAA
55 GGAA
* * *
474520 AAGAGTGCCAC-GAAGTTGTGGACTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGGAA
1 AAGGGTGCCACTG-ATTTGTGGGCTTT-GAAAAGATGCCACCGACTTGTGGGCTTCGGAA
474579 AAGGGTGCCACTGATTTGTGGGCTTTGAAAAAGATGCCACCGACTTGTGGGCTTCGGAA
1 AAGGGTGCCACTGATTTGTGGGCTTTG-AAAAGATGCCACCGACTTGTGGGCTTCGGAA
* * * * **
474638 AAGGGTGCCACTGATTTATGGGCTTTG-AAGGTTGCCACCGATTTGTGGGCTTTTGAA
1 AAGGGTGCCACTGATTTGTGGGCTTTGAAAAGATGCCACCGACTTGTGGGCTTCGGAA
* *
474695 AAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTT
1 AAGGGTGCCACTGATTTGTGGGCTTTGAAAA-GATGCCACCGACTTGTGGGCTT
474749 TTGAAGGGTG
Statistics
Matches: 291, Mismatches: 46, Indels: 41
0.77 0.12 0.11
Matches are distributed among these distances:
56 22 0.08
57 53 0.18
58 3 0.01
59 120 0.41
60 6 0.02
61 21 0.07
63 4 0.01
64 33 0.11
65 6 0.02
66 1 0.00
69 22 0.08
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (58 bp):
AAGGGTGCCACTGATTTGTGGGCTTTGAAAAGATGCCACCGACTTGTGGGCTTCGGAA
Found at i:476196 original size:1 final size:1
Alignment explanation
Indices: 476190--476289 Score: 65
Period size: 1 Copynumber: 100.0 Consensus size: 1
476180 TCCGGACCCC
* * * ** * * * **
476190 TTTTTTTTGTTTTTGTTTTTTTGTTTTCCTTTTTTTTTGTTTTTATTTTTTTTATTTTTAATTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * *
476255 TTTTTGTTTTGTTGTTTTTTTGTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
476290 GTGGAGGACG
Statistics
Matches: 73, Mismatches: 26, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 73 1.00
ACGTcount: A:0.04, C:0.02, G:0.09, T:0.85
Consensus pattern (1 bp):
T
Found at i:476209 original size:16 final size:16
Alignment explanation
Indices: 476190--476289 Score: 102
Period size: 16 Copynumber: 6.4 Consensus size: 16
476180 TCCGGACCCC
476190 TTTTTTTTGTTTTTG-
1 TTTTTTTTGTTTTTGT
**
476205 -TTTTTTTGTTTTCCT
1 TTTTTTTTGTTTTTGT
*
476220 TTTTTTTTGTTTTTAT
1 TTTTTTTTGTTTTTGT
**
476236 TTTTTTTAT-TTTTAAT
1 TTTTTTT-TGTTTTTGT
476252 TTTTTTTTG-TTTTGT
1 TTTTTTTTGTTTTTGT
476267 TGTTTTTTTG-TTTTGT
1 T-TTTTTTTGTTTTTGT
476283 TTTTTTT
1 TTTTTTT
476290 GTGGAGGACG
Statistics
Matches: 73, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
14 12 0.16
15 12 0.16
16 48 0.66
17 1 0.01
ACGTcount: A:0.04, C:0.02, G:0.09, T:0.85
Consensus pattern (16 bp):
TTTTTTTTGTTTTTGT
Found at i:476291 original size:30 final size:30
Alignment explanation
Indices: 476190--476289 Score: 114
Period size: 32 Copynumber: 3.2 Consensus size: 30
476180 TCCGGACCCC
*
476190 TTTTTTTTG-TTTTTGTTTTTTTGTTTTCCT
1 TTTTTTTTGTTTTTTGTTTTTTTGTTTT-AT
*
476220 TTTTTTTTGTTTTTAT-TTTTTTTATTTTTAAT
1 TTTTTTTTGTTTTT-TGTTTTTTT-GTTTT-AT
*
476252 TTTTTTTTGTTTTGTTGTTTTTTTGTTTTGT
1 TTTTTTTTGTTTT-TTGTTTTTTTGTTTTAT
476283 TTTTTTT
1 TTTTTTT
476290 GTGGAGGACG
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
30 9 0.15
31 19 0.32
32 24 0.40
33 8 0.13
ACGTcount: A:0.04, C:0.02, G:0.09, T:0.85
Consensus pattern (30 bp):
TTTTTTTTGTTTTTTGTTTTTTTGTTTTAT
Found at i:486059 original size:33 final size:33
Alignment explanation
Indices: 486000--486062 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
485990 ACCGTTGGGC
*
486000 ATAATGTATCGATACAATTCTTCATGTATCAAT
1 ATAATGTATCGATACAATTCTCCATGTATCAAT
486033 ATAATGTATCGATACAATGTC-CCATGTATC
1 ATAATGTATCGATACAAT-TCTCCATGTATC
486063 GATACGTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (33 bp):
ATAATGTATCGATACAATTCTCCATGTATCAAT
Found at i:486136 original size:13 final size:13
Alignment explanation
Indices: 486118--486142 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
486108 AGAATTGAGC
486118 ATGTATCGATACA
1 ATGTATCGATACA
486131 ATGTATCGATAC
1 ATGTATCGATAC
486143 TAGGCATAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:488517 original size:22 final size:19
Alignment explanation
Indices: 488482--488531 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
488472 TTTTTATGAA
488482 GATTTTG-ATGAAAAACAGAT
1 GATTTTGAATG-AAAA-AGAT
488502 GATTTTGATATGAAAAAGAT
1 GATTTTGA-ATGAAAAAGAT
488522 GAATTTTGAA
1 G-ATTTTGAA
488532 AAGGATTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 13 0.48
21 11 0.41
22 3 0.11
ACGTcount: A:0.44, C:0.02, G:0.20, T:0.34
Consensus pattern (19 bp):
GATTTTGAATGAAAAAGAT
Found at i:488668 original size:13 final size:13
Alignment explanation
Indices: 488650--488688 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
488640 TAGTAACCAC
*
488650 TATATCGATATAT
1 TATATCGATATAA
*
488663 TATATCGATACAA
1 TATATCGATATAA
*
488676 TGTATCGATATAA
1 TATATCGATATAA
488689 AAAACATTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.38
Consensus pattern (13 bp):
TATATCGATATAA
Found at i:496056 original size:20 final size:20
Alignment explanation
Indices: 496033--496070 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
496023 ACATGAAAAT
496033 TTTAAGAAA-AAAATGAAACA
1 TTTAAGAAATAAAA-GAAACA
*
496053 TTTATGAAATAAAAGAAA
1 TTTAAGAAATAAAAGAAA
496071 GTTTTTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.63, C:0.03, G:0.11, T:0.24
Consensus pattern (20 bp):
TTTAAGAAATAAAAGAAACA
Found at i:496109 original size:165 final size:163
Alignment explanation
Indices: 495617--496121 Score: 444
Period size: 166 Copynumber: 3.1 Consensus size: 163
495607 GACAATGTTA
* * * * *
495617 GATGAAATTTAAAAATTTTAAATCT-AGAAAAAT-AT-CCTGAAAACATTTAAGGAA-TAGAAAA
1 GATGAATTTTAAAAATTATAAA-CTAAGAAAAATCCTCCCCGAAAACATTT-ACGAAGTAGAAAA
* ** * *
495678 -CTTGATTTTTCACAAAA-AAGGGAATTTCAAAGAAAAATGAAAAACTTATGAACATAAATA-AA
64 CCTT-ATATTTCA-AAAATAA-AAAAATTCAAAAAAAAATG-AAAACTTATGAA-ATAAA-AGAA
* *
495740 ATTTTCAAAACTGATTTACTATGGATCAAATGATGATATTT
123 ATTTTTAAAACTGATTTACTATGAATCAAATGATGATATTT
* *
495781 GAT-AATTTTTAAAAATTATAAACTAAGAAAAATCCTCCCCGAAAATATTTTCGAAGTAGAAAAC
1 GATGAA-TTTTAAAAATTATAAACTAAGAAAAATCCTCCCCGAAAACATTTACGAAGTAGAAAAC
* *
495845 CTTATATTTCAAAAATAAAAAAAATTCAAATAAAAATGGAAAACTTATGAAAATAAATG-AATTT
65 CTTATATTTCAAAAAT-AAAAAAATTCAAAAAAAAAT-GAAAACTTATG-AAATAAAAGAAATTT
**
495909 TTCAAAGTTGATTTACTATGAATCAAATGATGATATTT
127 TT-AAAACTGATTTACTATGAATCAAATGATGATATTT
* ** *
495947 GATGAATTTTAAAAATTGTAAACTAAGAAAAATCC-CCTTGAAAGCATTTAC-AGAGTAGAAAAC
1 GATGAATTTTAAAAATTATAAACTAAGAAAAATCCTCCCCGAAAACATTTACGA-AGTAGAAAAC
* * * * *
496010 TCTGTAT-TTT-AGAACAT-GAAAATTTTAAGAAAAAAATGAAACATTTATGAAATAAAAGAAAG
65 -CT-TATATTTCA-AAAATAAAAAAATTCAA-AAAAAAATGAAA-ACTTATGAAATAAAAGAAA-
* * *
496072 TTTTTAAAACTGATTTAATGTGAATTAAATGATGATATTT
124 TTTTTAAAACTGATTTACTATGAATCAAATGATGATATTT
* *
496112 AAAGAATTTT
1 GATGAATTTT
496122 GAAGTTAAAA
Statistics
Matches: 283, Mismatches: 37, Indels: 41
0.78 0.10 0.11
Matches are distributed among these distances:
163 4 0.01
164 46 0.16
165 89 0.31
166 131 0.46
167 13 0.05
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (163 bp):
GATGAATTTTAAAAATTATAAACTAAGAAAAATCCTCCCCGAAAACATTTACGAAGTAGAAAACC
TTATATTTCAAAAATAAAAAAATTCAAAAAAAAATGAAAACTTATGAAATAAAAGAAATTTTTAA
AACTGATTTACTATGAATCAAATGATGATATTT
Found at i:496541 original size:10 final size:11
Alignment explanation
Indices: 496512--496540 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
496502 CCTAAATTTT
496512 TCAAAAAATTC
1 TCAAAAAATTC
496523 TCAAAAAATTC
1 TCAAAAAATTC
496534 TCAAAAA
1 TCAAAAA
496541 TAGAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.59, C:0.17, G:0.00, T:0.24
Consensus pattern (11 bp):
TCAAAAAATTC
Found at i:496954 original size:47 final size:46
Alignment explanation
Indices: 496851--496954 Score: 118
Period size: 46 Copynumber: 2.2 Consensus size: 46
496841 AAGCCAACGG
* * **
496851 GAATGAAAAGGGTTTGACTAGAGTGATAACTGATGTAGTCAAACAA
1 GAATGAAAAAGGTTTGACTAGAGTGATAACTAATACAGTCAAACAA
* * * * *
496897 GGATGAAAAAGGTTTGGCTAGGGTGGTAACTAATACAGTCAAACTA
1 GAATGAAAAAGGTTTGACTAGAGTGATAACTAATACAGTCAAACAA
496943 GAATGGAAAAAG
1 GAAT-GAAAAAG
496955 TTTAACCATG
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
46 40 0.85
47 7 0.15
ACGTcount: A:0.41, C:0.09, G:0.28, T:0.22
Consensus pattern (46 bp):
GAATGAAAAAGGTTTGACTAGAGTGATAACTAATACAGTCAAACAA
Found at i:496979 original size:47 final size:46
Alignment explanation
Indices: 496928--497230 Score: 194
Period size: 47 Copynumber: 6.4 Consensus size: 46
496918 GGTGGTAACT
* ** *
496928 AATACAGTCAAACTAGAATGGAAAAAGTTTAACCATGTCCTAATGCC
1 AATACAGTCAAACGAGGGTGGAAAAAGTTTAACCA-GTCCTAACGCC
* * * * * * *
496975 AATACTGTCAAACGCGGGTGTAAAGAGTTTGACTAGATCCTAACGTC
1 AATACAGTCAAACGAGGGTGGAAAAAGTTTAACCAG-TCCTAACGCC
497022 AATACAGTCAAACGAGGGTGGAAAAAGTTTAACCAAGTCCTAACGCC
1 AATACAGTCAAACGAGGGTGGAAAAAGTTTAACC-AGTCCTAACGCC
* * * * * * ** *
497069 AATACAATCAAATGAGGGCGAAAAAGAGTTTGACTAGGACTAACGCT
1 AATACAGTCAAACGAGGGTGGAAAA-AGTTTAACCAGTCCTAACGCC
* * * * * * * *
497116 AATATAGTCAAATGAAGTTAAGAAAAAGTTTGACTAGGTCCTAATGCC
1 AATACAGTCAAACGAGGGT-GGAAAAAGTTTAACCA-GTCCTAACGCC
* * * * * * *
497164 AAAATAATCAAACGAGGGTGAAAAAGAGTTTGACCAAG-ACTAACACC
1 AATACAGTCAAACGAGGGTGGAAAA-AGTTTAACC-AGTCCTAACGCC
* *
497211 AATACAATCAAATGAGGGTG
1 AATACAGTCAAACGAGGGTG
497231 AAGAGAGTTT
Statistics
Matches: 197, Mismatches: 52, Indels: 14
0.75 0.20 0.05
Matches are distributed among these distances:
46 1 0.01
47 152 0.77
48 43 0.22
49 1 0.01
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.21
Consensus pattern (46 bp):
AATACAGTCAAACGAGGGTGGAAAAAGTTTAACCAGTCCTAACGCC
Found at i:497033 original size:94 final size:95
Alignment explanation
Indices: 496928--497197 Score: 273
Period size: 94 Copynumber: 2.9 Consensus size: 95
496918 GGTGGTAACT
* * * ** *
496928 AATACAGTCAAACTAGAATGGAAAAAGTTTAACCATGTCCTAATGCCAATACTGTCAAACGCGGG
1 AATACAGTCAAACGAGAATGGAAAAAGTTTAACCAAGTCCTAACGCCAATACAATCAAACGAGGG
* *
496993 TG-TAAAGAGTTTGACTAGATCCTAACGTC
66 CGAAAAAGAGTTTGACTAGATCCTAACGTC
** *
497022 AATACAGTCAAACGAGGGTGGAAAAAGTTTAACCAAGTCCTAACGCCAATACAATCAAATGAGGG
1 AATACAGTCAAACGAGAATGGAAAAAGTTTAACCAAGTCCTAACGCCAATACAATCAAACGAGGG
497087 CGAAAAAGAGTTTGACTAGGA--CTAACG-C
66 CGAAAAAGAGTTTGACTA-GATCCTAACGTC
* * * * * * * *
497115 TAATATAGTCAAATGAAGTTAA--GAAAAAGTTTGACTAGGTCCTAATGCCAAAATAATCAAACG
1 -AATACAGTCAAACG-AG--AATGGAAAAAGTTTAACCAAGTCCTAACGCCAATACAATCAAACG
*
497178 AGGGTGAAAAAGAGTTTGAC
62 AGGGCGAAAAAGAGTTTGAC
497198 CAAGACTAAC
Statistics
Matches: 147, Mismatches: 23, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
93 1 0.01
94 75 0.51
95 69 0.47
96 2 0.01
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (95 bp):
AATACAGTCAAACGAGAATGGAAAAAGTTTAACCAAGTCCTAACGCCAATACAATCAAACGAGGG
CGAAAAAGAGTTTGACTAGATCCTAACGTC
Found at i:497158 original size:95 final size:95
Alignment explanation
Indices: 496948--497225 Score: 247
Period size: 95 Copynumber: 2.9 Consensus size: 95
496938 AACTAGAATG
* * * ** * * * *
496948 GAAAAAGTTTAACCATGTCCTAATGCCAATACTGTCAAACGCGGGTG-TAAAGAGTTTGA-CTAG
1 GAAAAAGTTTAACCAAGTCCTAACGCCAAAACAATCAAACGAGGGCGAAAAAGAGTTTGACCAAG
** * * * * *
497011 ATCCTAACGTCAATACAGTCAAACGAGGGT-G
66 A--CTAACACCAATACAATCAAATGAAGTTAA
* * * *
497042 GAAAAAGTTTAACCAAGTCCTAACGCCAATACAATCAAATGAGGGCGAAAAAGAGTTTGACTAGG
1 GAAAAAGTTTAACCAAGTCCTAACGCCAAAACAATCAAACGAGGGCGAAAAAGAGTTTGACCAAG
* * * *
497107 ACTAACGCTAATATAGTCAAATGAAGTTAA
66 ACTAACACCAATACAATCAAATGAAGTTAA
* * * * * *
497137 GAAAAAGTTTGACTAGGTCCTAATGCCAAAATAATCAAACGAGGGTGAAAAAGAGTTTGACCAAG
1 GAAAAAGTTTAACCAAGTCCTAACGCCAAAACAATCAAACGAGGGCGAAAAAGAGTTTGACCAAG
497202 ACTAACACCAATACAATCAAATGA
66 ACTAACACCAATACAATCAAATGA
497226 GGGTGAAGAG
Statistics
Matches: 149, Mismatches: 32, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
94 61 0.41
95 86 0.58
96 2 0.01
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.21
Consensus pattern (95 bp):
GAAAAAGTTTAACCAAGTCCTAACGCCAAAACAATCAAACGAGGGCGAAAAAGAGTTTGACCAAG
ACTAACACCAATACAATCAAATGAAGTTAA
Found at i:497231 original size:47 final size:47
Alignment explanation
Indices: 496996--497260 Score: 214
Period size: 47 Copynumber: 5.6 Consensus size: 47
496986 ACGCGGGTGT
* * * * *
496996 AAAGAGTTTGACTA-GATCCTAACGTCAATACAGTCAAACGAGGGTGGA
1 AAAGAGTTTGACCAGGA--CTAACGCCAATACAATCAAATGAGGGTGAA
* ** *
497044 AAA-AGTTTAACCAAGTCCTAACGCCAATACAATCAAATGAGGGCGAA
1 AAAGAGTTTGACC-AGGACTAACGCCAATACAATCAAATGAGGGTGAA
* * * * * *
497091 AAAGAGTTTGACTAGGACTAACGCTAATATAGTCAAATGA-AGTTAA
1 AAAGAGTTTGACCAGGACTAACGCCAATACAATCAAATGAGGGTGAA
* * * * * * *
497137 GAAAAAGTTTGACTAGGTCCTAATGCCAAAATAATCAAACGAGGGTGAA
1 -AAAGAGTTTGACCAGG-ACTAACGCCAATACAATCAAATGAGGGTGAA
* *
497186 AAAGAGTTTGACCAAGACTAACACCAATACAATCAAATGAGGGTG-A
1 AAAGAGTTTGACCAGGACTAACGCCAATACAATCAAATGAGGGTGAA
* * *
497232 AGAGAGTTTGAACAGGACTAATGCCAATA
1 AAAGAGTTTGACCAGGACTAACGCCAATA
497261 AAACCAAACA
Statistics
Matches: 169, Mismatches: 42, Indels: 14
0.75 0.19 0.06
Matches are distributed among these distances:
46 28 0.17
47 95 0.56
48 42 0.25
49 4 0.02
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (47 bp):
AAAGAGTTTGACCAGGACTAACGCCAATACAATCAAATGAGGGTGAA
Found at i:497323 original size:45 final size:45
Alignment explanation
Indices: 497265--497360 Score: 129
Period size: 45 Copynumber: 2.1 Consensus size: 45
497255 CCAATAAAAC
* * * **
497265 CAAACAAAGGAAGATAGTTTGACTAGGTCCTAACGCTGAGATAGT
1 CAAACAAAAGAAGATAGTTTAACCAGGTCCTAACGCCAAGATAGT
* *
497310 CAAACAAAAGAAGATAGTTTAACCAGGTCCTAATGCCAATATAGT
1 CAAACAAAAGAAGATAGTTTAACCAGGTCCTAACGCCAAGATAGT
497355 CAAACA
1 CAAACA
497361 TAATTGAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.21
Consensus pattern (45 bp):
CAAACAAAAGAAGATAGTTTAACCAGGTCCTAACGCCAAGATAGT
Found at i:499610 original size:9 final size:10
Alignment explanation
Indices: 499597--499624 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
499587 ATTTTTCTTT
499597 TTTTTTTCAA
1 TTTTTTTCAA
499607 TTTTTTTCAA
1 TTTTTTTCAA
499617 TTTTTTTC
1 TTTTTTTC
499625 TTCTTTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTTTTCAA
Found at i:499642 original size:10 final size:10
Alignment explanation
Indices: 499584--499641 Score: 52
Period size: 10 Copynumber: 6.2 Consensus size: 10
499574 ACTCAATTTC
*
499584 TTCATTTTTC
1 TTCATTTTTT
499594 TT--TTTTTT
1 TTCATTTTTT
*
499602 TTCAATTTTT
1 TTCATTTTTT
*
499612 TTCAATTTTT
1 TTCATTTTTT
*
499622 TTC-TTCTTT
1 TTCATTTTTT
499631 TTC-TTTTTT
1 TTCATTTTTT
499640 TT
1 TT
499642 TTTAAAAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
8 7 0.17
9 14 0.34
10 20 0.49
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (10 bp):
TTCATTTTTT
Found at i:504719 original size:23 final size:23
Alignment explanation
Indices: 504693--504743 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
504683 TTTCCTAAAA
*
504693 ACTTCATGAAA-AGTCTATTTTAC
1 ACTTCATGAAATAGCCT-TTTTAC
**
504716 ACTTTTTGAAATAGCCTTTTTAC
1 ACTTCATGAAATAGCCTTTTTAC
504739 ACTTC
1 ACTTC
504744 TGAGAATTCC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.29, C:0.20, G:0.08, T:0.43
Consensus pattern (23 bp):
ACTTCATGAAATAGCCTTTTTAC
Found at i:505215 original size:28 final size:28
Alignment explanation
Indices: 505184--505266 Score: 89
Period size: 28 Copynumber: 2.9 Consensus size: 28
505174 ATTAAAAAAT
*
505184 AAGAAAGATCAAGGAAGTGAAAATCAA-C
1 AAGAAATATCAAGGAAGTG-AAATCAAGC
* *
505212 AAGAAATATGAAAGGAAATGAAAT-AAGC
1 AAGAAATAT-CAAGGAAGTGAAATCAAGC
*
505240 AAGAAATATCAAAGGAAGAGAAATCAA
1 AAGAAATATC-AAGGAAGTGAAATCAA
505267 TGAAGAGGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
27 2 0.04
28 33 0.73
29 10 0.22
ACGTcount: A:0.60, C:0.07, G:0.20, T:0.12
Consensus pattern (28 bp):
AAGAAATATCAAGGAAGTGAAATCAAGC
Found at i:505825 original size:19 final size:19
Alignment explanation
Indices: 505793--505842 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
505783 ATCGATACAA
* *
505793 TGTATGGATTCATAAGTGT
1 TGTATCGATACATAAGTGT
*
505812 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAGTGT
505831 TGTATCGATACA
1 TGTATCGATACA
505843 ATGTATCGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:505913 original size:13 final size:13
Alignment explanation
Indices: 505895--505922 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
505885 ATTACTCAAA
505895 TGTATCGATACAT
1 TGTATCGATACAT
505908 TGTATCGATACAT
1 TGTATCGATACAT
505921 TG
1 TG
505923 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:512924 original size:1 final size:1
Alignment explanation
Indices: 512920--512993 Score: 58
Period size: 1 Copynumber: 74.0 Consensus size: 1
512910 AAAAATGATG
* * * * * * * * *
512920 AAAAAAAACAAACAAAACAAAACAAAAAACAAAAAAAAAACAAAAAACAACAAAAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
512985 CAAAAAAAA
1 AAAAAAAAA
512994 GAGAGAGTGC
Statistics
Matches: 53, Mismatches: 20, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:512936 original size:10 final size:9
Alignment explanation
Indices: 512923--512993 Score: 83
Period size: 9 Copynumber: 7.6 Consensus size: 9
512913 AATGATGAAA
512923 AAAAACAAAC
1 AAAAA-AAAC
512933 AAAACAAAAC
1 AAAA-AAAAC
512943 AAAAAACAA-
1 AAAAAA-AAC
512952 AAAAAAAAC
1 AAAAAAAAC
512961 AAAAAACAAC
1 AAAAAA-AAC
512971 AAAAAAAAC
1 AAAAAAAAC
512980 AAAAACAAA-
1 AAAAA-AAAC
512989 AAAAA
1 AAAAA
512994 GAGAGAGTGC
Statistics
Matches: 56, Mismatches: 0, Indels: 11
0.84 0.00 0.16
Matches are distributed among these distances:
8 2 0.04
9 27 0.48
10 26 0.46
11 1 0.02
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:512954 original size:18 final size:18
Alignment explanation
Indices: 512922--512993 Score: 101
Period size: 18 Copynumber: 3.8 Consensus size: 18
512912 AAATGATGAA
512922 AAAAAACAAACAAAACAAAAC
1 AAAAAAC-AA-AAAA-AAAAC
512943 AAAAAACAAAAAAAAAAC
1 AAAAAACAAAAAAAAAAC
512961 AAAAAACAACAAAAAAAAC
1 AAAAAACAA-AAAAAAAAC
512980 -AAAAACAAAAAAAA
1 AAAAAACAAAAAAAA
512994 GAGAGAGTGC
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.12
18 22 0.44
19 13 0.26
20 2 0.04
21 7 0.14
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (18 bp):
AAAAAACAAAAAAAAAAC
Found at i:512956 original size:30 final size:29
Alignment explanation
Indices: 512920--512993 Score: 100
Period size: 28 Copynumber: 2.6 Consensus size: 29
512910 AAAAATGATG
512920 AAAAAAAACAAACAAAACAA-AACAAAAAA
1 AAAAAAAACAAACAAAA-AACAACAAAAAA
*
512949 CAAAAAAA-AAACAAAAAACAACAAAAAA
1 AAAAAAAACAAACAAAAAACAACAAAAAA
*
512977 AACAAAAACAAA-AAAAA
1 AAAAAAAACAAACAAAAA
512994 GAGAGAGTGC
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
27 2 0.05
28 28 0.70
29 10 0.25
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (29 bp):
AAAAAAAACAAACAAAAAACAACAAAAAA
Found at i:512966 original size:25 final size:25
Alignment explanation
Indices: 512920--512991 Score: 85
Period size: 25 Copynumber: 2.8 Consensus size: 25
512910 AAAAATGATG
*
512920 AAAAAAAACAAACAAA-ACAAAACAA-
1 AAAAAAAA-AAA-AAACAAAAAACAAC
512945 AAAACAAAAAAAAAACAAAAAACAAC
1 AAAA-AAAAAAAAAACAAAAAACAAC
*
512971 AAAAAAAACAAAAACAAAAAA
1 AAAAAAAAAAAAAACAAAAAA
512992 AAGAGAGAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
24 3 0.07
25 31 0.74
26 8 0.19
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (25 bp):
AAAAAAAAAAAAAACAAAAAACAAC
Found at i:514356 original size:61 final size:61
Alignment explanation
Indices: 514281--514454 Score: 255
Period size: 61 Copynumber: 2.9 Consensus size: 61
514271 ATACCTTCTT
*
514281 AAAGTCCACGACTCAGTGGCAATCTCTTC-TCAAAGCCCACGACTCAGTGGCAT-T-TTGTCCC
1 AAAGTCCACGACTCAGTGGC-ATCTTTTCTTCAAAGCCCACGACTCAGTGGCATCTCTT-T-CC
*
514342 AAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACGACTCAGTGGCATCTCTTTCC
1 AAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGCCCACGACTCAGTGGCATCTCTTTCC
* * *
514403 AAAGACCACGACTCAGTGGCATCTTTTCTTCAAAGCCCACAACTCCGTGGCA
1 AAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGCCCACGACTCAGTGGCA
514455 CCTTTTTCTT
Statistics
Matches: 104, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
60 7 0.07
61 93 0.89
62 2 0.02
63 2 0.02
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.25
Consensus pattern (61 bp):
AAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGCCCACGACTCAGTGGCATCTCTTTCC
Found at i:514460 original size:31 final size:31
Alignment explanation
Indices: 514276--514460 Score: 220
Period size: 31 Copynumber: 6.1 Consensus size: 31
514266 TTCAAATACC
* *
514276 TTCTT-AAAGTCCACGACTCAGTGGCAATCTC
1 TTCTTCAAAGCCCACGACTCAGTGGC-ATCTT
514307 TTC-TCAAAGCCCACGACTCAGTGGCAT-TT
1 TTCTTCAAAGCCCACGACTCAGTGGCATCTT
* *
514336 TGTC-CCAAAGTCCACGACTCAGTGGCATCTT
1 T-TCTTCAAAGCCCACGACTCAGTGGCATCTT
*
514367 TTCTTCAAAGTCCACGACTCAGTGGCATCTCT
1 TTCTTCAAAGCCCACGACTCAGTGGCATCT-T
*
514399 TTC--CAAAGACCACGACTCAGTGGCATCTT
1 TTCTTCAAAGCCCACGACTCAGTGGCATCTT
* * *
514428 TTCTTCAAAGCCCACAACTCCGTGGCACCTT
1 TTCTTCAAAGCCCACGACTCAGTGGCATCTT
514459 TT
1 TT
514461 TCTTTTTAAA
Statistics
Matches: 137, Mismatches: 10, Indels: 14
0.85 0.06 0.09
Matches are distributed among these distances:
29 6 0.04
30 53 0.39
31 74 0.54
32 4 0.03
ACGTcount: A:0.24, C:0.32, G:0.16, T:0.28
Consensus pattern (31 bp):
TTCTTCAAAGCCCACGACTCAGTGGCATCTT
Found at i:514585 original size:49 final size:49
Alignment explanation
Indices: 514525--515486 Score: 953
Period size: 49 Copynumber: 19.9 Consensus size: 49
514515 GGCATCTTCT
* * * *
514525 TTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATC
** *
514574 TTTAAAACCAATGTCGCTGGCCTTGAATCAGCATATTGGCA-C-----C
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATC
* * * * *
514617 TTTAAGTCTAATATCGCTGGCCTTGAATTAGCATATTGGCACCTTTGTC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATC
* * *
514666 TTTTTAGACCAATGTCGCTAGCCTTGAATCAGCACATTGGCA-C-----C
1 -TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATC
* * *
514710 TTTAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCACC-TTATC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATC
*
514758 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-C-----C
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATC
* * * *
514801 TTTAAGTCCAATATCACTGGCCTTGAATCAGCAGATTGGCACCTTTGTC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATC
*
514850 TTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-C-----C
1 -TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATC
* * * *
514894 TTTAAGTCCAATATCGCTGACCTTGAATCAGCATATTGGCACC-TCATC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATC
* *
514942 TGTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-----C
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATC
* * *
514986 -TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATC
* *
515034 TTTAAGTCCAATGTCGTTGGGCTTGAATCAGCACATTGGCACCTTTATC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATC
*
515083 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATC
* * *
515132 TTTAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTTGTCATC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-TT-T-ATC
* * * *
515184 TGTAAGTCCAATGTTGTTGGCCTTGAATCAGCACATTGGCACCTTCATC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATC
* * * *
515233 TTTAAGTCCAATATCGCTGGCCTTGACTCAGCATATTGGCGCCTTTGTCATC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-TT-T-ATC
* * *
515285 TTTTAAGTCCAATGTTGCTAGCCTTGAATCAGCACATTGGCACCTTCATC
1 -TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATC
* * * *
515335 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTAGCGCCTTCATCATC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT--T-ATC
** * * * *
515387 TTTAAAACCCAATGTTGTTGGCCTTAAATCAGCACATTGGCATTCTTCTCATC
1 TTT-AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CCTT-T-ATC
* * ** * *
515440 TTCAAGTCTAATGTCGCTAACCATGAATCAGCACATTGACATCCTTT
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CCTTT
515487 TTCTCATCTT
Statistics
Matches: 761, Mismatches: 110, Indels: 82
0.80 0.12 0.09
Matches are distributed among these distances:
43 185 0.24
44 7 0.01
47 1 0.00
48 79 0.10
49 249 0.33
50 78 0.10
51 3 0.00
52 83 0.11
53 73 0.10
54 3 0.00
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (49 bp):
TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATC
Found at i:514802 original size:21 final size:21
Alignment explanation
Indices: 514778--514845 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
514768 ATGTCGCTGG
514778 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
* ** *
514799 CCTTTAAGTCCAATATCACTGG--
1 CCTTGAA-T-CAGCA-CATTGGCA
*
514821 CCTTGAATCAGCAGATTGGCA
1 CCTTGAATCAGCACATTGGCA
514842 CCTT
1 CCTT
514846 TGTCTTTTAA
Statistics
Matches: 33, Mismatches: 9, Indels: 10
0.63 0.17 0.19
Matches are distributed among these distances:
19 4 0.12
20 3 0.09
21 11 0.33
22 7 0.21
23 3 0.09
24 5 0.15
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (21 bp):
CCTTGAATCAGCACATTGGCA
Found at i:514842 original size:184 final size:184
Alignment explanation
Indices: 514525--515367 Score: 1051
Period size: 184 Copynumber: 4.4 Consensus size: 184
514515 GGCATCTTCT
* * *
514525 TTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAAACCAATGTCG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTATCTTTAAGACCAATGTCG
* * *
514590 CTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCTAATATCGCTGGCCTTGAATTAGCATATTG
65 CTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
* *
514655 GCACCTTTGTCTTTTTAGACCAATGTCGCTAGCCTTGAATCAGCACATTGGCA-CC
130 GCACCTTTGTC-TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCC
*
514710 TTTAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGC
* *
514775 TGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCACTGGCCTTGAATCAGCAGATTGG
66 TGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
514840 CACCTTTGTCTTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CC
131 CACCTTTGTC-TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCC
* * *
514894 TTTAAGTCCAATATCGCTGACCTTGAATCAGCATATTGGCACCTCATCTGTAAGACCAATGTCGC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGC
*
514959 TGGCCTTGAATCAGCACATTGGCACCCTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
66 TGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
* * *
515024 CACCTTTGTCTTTAAGTCCAATGTCGTTGGGCTTGAATCAGCACATTGGCACCTTTATC
131 CACCTTTGTCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-----C
* * * * *
515083 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCA
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-ATCTTTAAGACCAATGTCG
* * * *
515148 CTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTGTAAGTCCAATGTTGTTGGCCTTGAATC
65 CTGGCCTTGAATCAGCACATTGGCA-C-----C-T-T-TAAGTCCAATATCGCTGGCCTTGAATC
* ** * * * * *
515213 AGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGACTCAGCATATTGGCGCCTT
121 AGCATATTGGCACCTTTGTCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGC-AC--
515278 TGTCATC
183 ---C--C
* * * * * *
515285 TTTTAAGTCCAATGTTGCTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATC
1 -TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-ATCTTTAAGACCAATGTC
515350 GCTGGCCTTGAATCAGCA
64 GCTGGCCTTGAATCAGCA
515368 TATTAGCGCC
Statistics
Matches: 589, Mismatches: 46, Indels: 28
0.89 0.07 0.04
Matches are distributed among these distances:
183 38 0.06
184 266 0.45
185 41 0.07
189 42 0.07
190 39 0.07
191 1 0.00
196 1 0.00
198 1 0.00
199 76 0.13
200 1 0.00
202 3 0.01
203 79 0.13
205 1 0.00
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (184 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGC
TGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
CACCTTTGTCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCC
Found at i:515348 original size:102 final size:101
Alignment explanation
Indices: 514986--515428 Score: 631
Period size: 102 Copynumber: 4.4 Consensus size: 101
514976 ATTGGCACCC
* * * ** * *
514986 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGTCCAATGTCGT
1 TTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGC
* *
515051 TGGGCTTGAATCAGCACATTGGCACC-TT-T-ATCT
66 TGGCCTTGAATCAGCATATTGGCACCTTTGTCATCT
* *
515084 TTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCAC
1 TTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGC
515149 TGGCCTTGAATCAGCATATTGGCACCTTTGTCATCT
66 TGGCCTTGAATCAGCATATTGGCACCTTTGTCATCT
* *
515185 GTAAGTCCAATGTTGTTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGC
1 TTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGC
* *
515250 TGGCCTTGACTCAGCATATTGGCGCCTTTGTCATCTT
66 TGGCCTTGAATCAGCATATTGGCACCTTTGTCATC-T
*
515287 TTAAGTCCAATGTTGCTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGC
1 TTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGC
* * **
515352 TGGCCTTGAATCAGCATATTAGCGCCTTCATCATCT
66 TGGCCTTGAATCAGCATATTGGCACCTTTGTCATCT
** * *
515388 TTAAAACCCAATGTTGTTGGCCTTAAATCAGCACATTGGCA
1 TT-AAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCA
515429 TTCTTCTCAT
Statistics
Matches: 313, Mismatches: 27, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
98 82 0.26
99 2 0.01
100 1 0.00
101 101 0.32
102 127 0.41
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (101 bp):
TTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGC
TGGCCTTGAATCAGCATATTGGCACCTTTGTCATCT
Found at i:516236 original size:20 final size:21
Alignment explanation
Indices: 516187--516243 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
516177 ACTGCCAAGG
516187 AAATGTATCGATACATTACTC
1 AAATGTATCGATACATTACTC
*
516208 AAATGTATCGATACATTGCTC
1 AAATGTATCGATACATTACTC
**
516229 -TTTGTATCGATACAT
1 AAATGTATCGATACAT
516244 ATTAGGGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 13 0.39
21 20 0.61
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (21 bp):
AAATGTATCGATACATTACTC
Found at i:531218 original size:79 final size:79
Alignment explanation
Indices: 531028--531612 Score: 632
Period size: 79 Copynumber: 7.4 Consensus size: 79
531018 TATTTTTTAG
* * * * ** *
531028 ATAAAAACGGGGTCGAAGTA-CCCCTTCAGAAATAACGGGGTTGGAGTATCCCCAATGGTGG-AA
1 ATAAAACCGGGGTTGGAGTATCCCC-TCAGAAATAACGAGGTTGGAGTATCCCTGATTGTGGAAA
* *
531091 ATCGATGTTTTGAAA
65 ATTGGTGTTTTGAAA
* * * * *
531106 ATAAAATCGAGGTTAGAGTATCCCTTC-GAAAATAACGAGGTTAGAGTATCCCTGATTGTGGAAA
1 ATAAAACCGGGGTTGGAGTATCCCCTCAG-AAATAACGAGGTTGGAGTATCCCTGATTGTGGAAA
531170 ATTGGTGTTTTGAAA
65 ATTGGTGTTTTGAAA
* * *
531185 ATAAAATCGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTAGAGTA-CCCTGATTGTGGAAAA
1 ATAAAACCGGGGTTGGAGTATCCCCTCAGAAATAACGAGGTTGGAGTATCCCTGATTGTGGAAAA
*
531249 TTGGTGTTTTGGAA
66 TTGGTGTTTTGAAA
** * * * * * *
531263 ATAAAATTGGGGTTGGAGTATCCCATCAAAAATAACGAGGTTAGAGTATCTCTGATTATGAAAAA
1 ATAAAACCGGGGTTGGAGTATCCCCTCAGAAATAACGAGGTTGGAGTATCCCTGATTGTGGAAAA
* *
531328 CTGGTGTTTTGGAA
66 TTGGTGTTTTGAAA
* **
531342 ATAAAACCGGGGTTGGAGTAT-CCCTCGGAAATAAC-AGGGTTGGAGTATCCCCAATTGT-GAAA
1 ATAAAACCGGGGTTGGAGTATCCCCTCAGAAATAACGA-GGTTGGAGTATCCCTGATTGTGGAAA
531404 ATTTGGTGTTTTGGAAA
65 A-TTGGTGTTTT-GAAA
* * *
531421 A-AAAACCGGGGTTGGAGTATCCCCTCAAAAATAATG-GCGTTGGAGTATCCCTGATTGTGAAAA
1 ATAAAACCGGGGTTGGAGTATCCCCTCAGAAATAACGAG-GTTGGAGTATCCCTGATTGTGGAAA
* *
531484 ACTGGTGTTTTGGAA
65 ATTGGTGTTTTGAAA
* * * * ** *
531499 ATAAAACCAGGGTTGGAGTATCTCCTCGGAAATAACGTGGTTGGAGTATCCCCAATTGTGAAAAA
1 ATAAAACCGGGGTTGGAGTATCCCCTCAGAAATAACGAGGTTGGAGTATCCCTGATTGTGGAAAA
*
531564 TTAGTGTTTTGAAA
66 TTGGTGTTTTGAAA
*
531578 ATAAAACCAGGGG-TGGAGTATCTCCTCAGAAATAA
1 ATAAAACC-GGGGTTGGAGTATCCCCTCAGAAATAA
531613 AAACATGATT
Statistics
Matches: 433, Mismatches: 59, Indels: 29
0.83 0.11 0.06
Matches are distributed among these distances:
77 6 0.01
78 177 0.41
79 241 0.56
80 9 0.02
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.28
Consensus pattern (79 bp):
ATAAAACCGGGGTTGGAGTATCCCCTCAGAAATAACGAGGTTGGAGTATCCCTGATTGTGGAAAA
TTGGTGTTTTGAAA
Found at i:531318 original size:157 final size:158
Alignment explanation
Indices: 531028--531612 Score: 738
Period size: 157 Copynumber: 3.7 Consensus size: 158
531018 TATTTTTTAG
* * * *
531028 ATAAAAACGGGGTCGAAGTA-CCCCTTCAGAAATAACGGGGTTGGAGTATCCCCAATGGTGG-AA
1 ATAAAACCGGGGTTGGAGTATCCCC-TCAGAAATAACGGGGTTGGAGTATCCCCAATTGTGGAAA
* * * * * *
531091 ATCGATGTTTTGAAAATAAAATCGAGGTTAGAGTATCCCTTCGAAAATAACGAGGTTAGAGTATC
65 ATTGGTGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCATCAAAAATAACGAGGTTAGAGTATC
* * *
531156 CCTGATTGTGGAAAATTGGTGTTTTGAAA
130 CCTGATTGTGAAAAACTGGTGTTTTGGAA
* * **
531185 ATAAAATCGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTAGAGTA-CCCTGATTGTGGAAAA
1 ATAAAACCGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCAATTGTGGAAAA
* * *
531249 TTGGTGTTTTGGAAATAAAATTGGGGTTGGAGTATCCCATCAAAAATAACGAGGTTAGAGTATCT
66 TTGGTGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCATCAAAAATAACGAGGTTAGAGTATCC
*
531314 CTGATTATGAAAAACTGGTGTTTTGGAA
131 CTGATTGTGAAAAACTGGTGTTTTGGAA
* *
531342 ATAAAACCGGGGTTGGAGTAT-CCCTCGGAAATAACAGGGTTGGAGTATCCCCAATTGT-GAAAA
1 ATAAAACCGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCAATTGTGGAAAA
* * * *
531405 TTTGGTGTTTTGGAAAA-AAAACCGGGGTTGGAGTATCCCCTCAAAAATAATG-GCGTTGGAGTA
66 -TTGGTGTTTT-GAAAATAAAATCGGGGTTGGAGTATCCCATCAAAAATAACGAG-GTTAGAGTA
531468 TCCCTGATTGTGAAAAACTGGTGTTTTGGAA
128 TCCCTGATTGTGAAAAACTGGTGTTTTGGAA
* * * * *
531499 ATAAAACCAGGGTTGGAGTATCTCCTCGGAAATAACGTGGTTGGAGTATCCCCAATTGTGAAAAA
1 ATAAAACCGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCAATTGTGGAAAA
* * *
531564 TTAGTGTTTTGAAAATAAAACCAGGGG-TGGAGTATCTCC-TCAGAAATAA
66 TTGGTGTTTTGAAAATAAAATC-GGGGTTGGAGTATC-CCATCAAAAATAA
531613 AAACATGATT
Statistics
Matches: 376, Mismatches: 41, Indels: 21
0.86 0.09 0.05
Matches are distributed among these distances:
156 38 0.10
157 253 0.67
158 75 0.20
159 10 0.03
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.28
Consensus pattern (158 bp):
ATAAAACCGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCAATTGTGGAAAA
TTGGTGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCATCAAAAATAACGAGGTTAGAGTATCC
CTGATTGTGAAAAACTGGTGTTTTGGAA
Found at i:533968 original size:13 final size:13
Alignment explanation
Indices: 533950--533979 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
533940 TAAAACCCAG
533950 AATGTATCGATAC
1 AATGTATCGATAC
*
533963 AATGTATCGATAT
1 AATGTATCGATAC
533976 AATG
1 AATG
533980 AACAATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:533986 original size:20 final size:20
Alignment explanation
Indices: 533961--534016 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
533951 ATGTATCGAT
* *
533961 ACAATGTATCGATATAATGA
1 ACAATGTATCGATACAATAA
*
533981 ACAATGTATCGATGCAATAA
1 ACAATGTATCGATACAATAA
*
534001 ATAATGTATCGATACA
1 ACAATGTATCGATACA
534017 TCTGGGTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (20 bp):
ACAATGTATCGATACAATAA
Found at i:534726 original size:35 final size:33
Alignment explanation
Indices: 534687--534827 Score: 120
Period size: 35 Copynumber: 3.8 Consensus size: 33
534677 AAAAGGAAGT
534687 GTCCTGCTTCTTGAGGACAAAGTGAAAAAGAGTAC
1 GTCCTGC-TCTTGAGGACAAAG-GAAAAAGAGTAC
**
534722 GTCCTGCTCTTCGAGGACAAAGGAAAAAAGGAAATGAAATGT
1 GTCCTGCTCTT-GAGGACAAAGG-AAAAA-G--A-G---TAC
534764 GTCCTGCTTCTTGAGGACAAAGTGAAAAAGAGTAC
1 GTCCTGC-TCTTGAGGACAAAG-GAAAAAGAGTAC
* *
534799 GTCCTGCTCATCGAGGATAAAGGAAAAAG
1 GTCCTGCTC-TTGAGGACAAAGGAAAAAG
534828 GAGAACGAAA
Statistics
Matches: 88, Mismatches: 6, Indels: 25
0.74 0.05 0.21
Matches are distributed among these distances:
34 14 0.16
35 40 0.45
36 1 0.01
38 2 0.02
39 2 0.02
41 1 0.01
42 23 0.26
43 5 0.06
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (33 bp):
GTCCTGCTCTTGAGGACAAAGGAAAAAGAGTAC
Found at i:534780 original size:77 final size:76
Alignment explanation
Indices: 534604--534868 Score: 286
Period size: 77 Copynumber: 3.4 Consensus size: 76
534594 AATGGAAGGG
* * *
534604 GTGTCCTGCTTTTTGAGGACAAAGGAAAAAAGAATGAAATAGGTCCTACTCCTT-GAGGACAAAG
1 GTGTCCTGCTTCTTGAGGACAAAGG-AAAAAG-A-G---TACGTCCTGCT-CTTCGAGGACAAAG
* * *
534668 GAAGAAAGAAAAAGGAA-
59 GAAAAAAGGAAAAGAAAT
534685 GTGTCCTGCTTCTTGAGGACAAAGTGAAAAAGAGTACGTCCTGCTCTTCGAGGACAAAGGAAAAA
1 GTGTCCTGCTTCTTGAGGACAAAG-GAAAAAGAGTACGTCCTGCTCTTCGAGGACAAAGGAAAAA
*
534750 AGGAAATGAAAT
65 AGGAAAAGAAAT
* *
534762 GTGTCCTGCTTCTTGAGGACAAAGTGAAAAAGAGTACGTCCTGCTCATCGAGGATAAAGG-AAAA
1 GTGTCCTGCTTCTTGAGGACAAAG-GAAAAAGAGTACGTCCTGCTCTTCGAGGACAAAGGAAAAA
*
534826 AGGAGAACGAAAT
65 AGGA-AAAGAAAT
** *
534839 ACGTCCTAC-TCTTTGAGGACAAAGGAAAAA
1 GTGTCCTGCTTC-TTGAGGACAAAGGAAAAA
534869 AGGAAATGAG
Statistics
Matches: 166, Mismatches: 13, Indels: 15
0.86 0.07 0.08
Matches are distributed among these distances:
75 3 0.02
76 48 0.29
77 83 0.50
79 1 0.01
80 1 0.01
81 29 0.17
82 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.26, T:0.20
Consensus pattern (76 bp):
GTGTCCTGCTTCTTGAGGACAAAGGAAAAAGAGTACGTCCTGCTCTTCGAGGACAAAGGAAAAAA
GGAAAAGAAAT
Found at i:534781 original size:42 final size:42
Alignment explanation
Indices: 534721--535000 Score: 239
Period size: 42 Copynumber: 6.8 Consensus size: 42
534711 AAAAAGAGTA
*
534721 CGTCCTGCTCTTCGAGGACAAAGGAAAAAAGGAAATGAAATG
1 CGTCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAATGAAATG
* *
534763 TGTCCTGCT-TCTTGAGGACAAAGTG-AAAAA-G--A-G---TA
1 CGTCCTGCTCT-TTGAGGACAAAG-GAAAAAAGGAAATGAAATG
* * * * *
534798 CGTCCTGCTCATCGAGGATAAAGG-AAAAAGGAGAACGAAATA
1 CGTCCTGCTCTTTGAGGACAAAGGAAAAAAGGA-AATGAAATG
* **
534840 CGTCCTACTCTTTGAGGACAAAGGAAAAAAGGAAATGAGGTG
1 CGTCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAATGAAATG
* *
534882 -TTCCCTGCTCTTTGAGGACATAGG-AAAAAGGAAA--AAATG
1 CGT-CCTGCTCTTTGAGGACAAAGGAAAAAAGGAAATGAAATG
*
534921 CATCCTGCTCTCTT-AGGACAAAAGGGAAAAAAAGGAAATGAAATG
1 CGTCCTGCTCT-TTGAGGAC-AAA-GG-AAAAAAGGAAATGAAATG
* *
534966 TGTCCTGCTCTTTGAGGACAAAGGAGAAAAGGAAA
1 CGTCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAA
535001 ATGCGTCATG
Statistics
Matches: 191, Mismatches: 25, Indels: 44
0.73 0.10 0.17
Matches are distributed among these distances:
34 6 0.03
35 20 0.10
38 2 0.01
39 18 0.09
40 5 0.03
41 15 0.08
42 80 0.42
43 21 0.11
44 5 0.03
45 19 0.10
ACGTcount: A:0.40, C:0.15, G:0.26, T:0.19
Consensus pattern (42 bp):
CGTCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAATGAAATG
Found at i:534974 original size:45 final size:43
Alignment explanation
Indices: 534906--534995 Score: 112
Period size: 45 Copynumber: 2.0 Consensus size: 43
534896 AGGACATAGG
534906 AAAAAGGAAAAAATGCATCCTGCTCTCTT-AGGACAAAAGG-GAA
1 AAAAAGGAAAAAATGCATCCTGCTCT-TTGAGGAC-AAAGGAGAA
**
534949 AAAAAGGAAATGAAATGTGTCCTGCTCTTTGAGGACAAAGGAGAA
1 AAAAAGGAAA--AAATGCATCCTGCTCTTTGAGGACAAAGGAGAA
534994 AA
1 AA
534996 GGAAAATGCG
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
43 10 0.24
44 7 0.17
45 24 0.59
ACGTcount: A:0.46, C:0.13, G:0.23, T:0.18
Consensus pattern (43 bp):
AAAAAGGAAAAAATGCATCCTGCTCTTTGAGGACAAAGGAGAA
Found at i:535028 original size:84 final size:83
Alignment explanation
Indices: 534864--535029 Score: 212
Period size: 84 Copynumber: 2.0 Consensus size: 83
534854 AGGACAAAGG
** * *
534864 AAAAAAGGAAATGAGGTGTTCCCTGCTCTTTGAGGACATAGGAAAAAGGAAAAAATGCATCCTGC
1 AAAAAAGGAAATGAAATGTTCCCTGCTCTTTGAGGACAAAGGAAAAAGG-AAAAATGCATCATGC
*
534929 TCTCTTAGGACAAAAGGGA
65 TCTCTTAAGACAAAAGGGA
*
534948 AAAAAAGGAAATGAAATGTGT-CCTGCTCTTTGAGGACAAAGGAGAAAAGG-AAAATGCGTCATG
1 AAAAAAGGAAATGAAATGT-TCCCTGCTCTTTGAGGACAAAGGA-AAAAGGAAAAATGCATCATG
535011 CTC-CTTAAAGACTAAAAGG
64 CTCTCTT-AAGAC-AAAAGG
535030 TGCCAGCAAC
Statistics
Matches: 72, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
82 3 0.04
83 18 0.25
84 44 0.61
85 7 0.10
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.20
Consensus pattern (83 bp):
AAAAAAGGAAATGAAATGTTCCCTGCTCTTTGAGGACAAAGGAAAAAGGAAAAATGCATCATGCT
CTCTTAAGACAAAAGGGA
Found at i:535154 original size:62 final size:62
Alignment explanation
Indices: 534991--536879 Score: 2185
Period size: 62 Copynumber: 30.6 Consensus size: 62
534981 GGACAAAGGA
* * * * * * * * * *
534991 GAAAAGGAAAATGCGTCATGCTCCTTAAAGACTAAAAGGTGCCAGCAACTCATGTAGGCTTT
1 GAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT
* * * * *
535053 G-AAA-AAAAAGGCATCCTACTCTTTGAGGACTAAAAGGTGCCACCAAATCGTGTAGGCTTT
1 GAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT
* *
535113 GAAAAGAAAAAGGCGTCCTACTCTTTGAGGACTAAAGGGTGCCACCAAATCGTGTGGGCTTT
1 GAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT
* *
535175 GAAAAAAAAAAGGCATCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT
1 GAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT
* * * * *
535237 GAAAAGAAAAAGACATCCTACTCTTTGAGCACTAAAGGGTGCCACCAACTCGTGTGGGTTTT
1 GAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT
** * * * * *
535299 GAAAAGAAAAAGATGCCCTGTTTTTTAAGGACTAAAGGGTGCTACCAACTCGTGTGGGCTTT
1 GAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT
*
535361 GAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCCTGTGGGCTTT
1 GAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT
*** * * *
535423 GAAAAGAAAAAGATATCCTGCTTTTTTGAGGACTAAAAGGTGCCACCAACTCCTGTGGGCTTT
1 GAAAAGAAAAAGGCGTCCTGC-TCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT
* * *
535486 GAAAAGAAAAAGGCATCCTGCTCTTTGA-GAGCAAAAGGGTGCCATCAACTC------GCTTT
1 GAAAAGAAAAAGGCGTCCTGCTCTTTGAGGA-CTAAAGGGTGCCACCAACTCGTGTGGGCTTT
* * * *
535542 GAAAAGAAAAAGGCGTCATGCTCTTTAAGGACTAAAGGGAGCCACCAACTCATGTGGGCTTT
1 GAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT
* * *
535604 GAAAAGAAAAAGTCGTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGACTTT
1 GAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT
* * * **
535666 GAAAAGGAAAAGGCATCCTGCTCTTTGAGGACTAAGGGGTGCCACCAACTCGTGTGCACTTT
1 GAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT
* * * * ** *
535728 AAAAAG-GAAAGGCATCCTACTCTTTGAGGACTAAAAAAGTGCCACCAGCTCGTGTGGGCTTT
1 GAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACT-AAAGGGTGCCACCAACTCGTGTGGGCTTT
* * * ** *
535790 -AAAACGGAAAAGGCGTCCCGCTCTTTTAGGACTAAAGGGTGCCACCAACTTATGTGAGCTTT
1 GAAAA-GAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT
* * * * * *
535852 GAAAAGGAAAATGTGTCATGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGAGCCTT
1 GAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT
* * ** * * *
535914 AAAAAGGAAAAGAAGTCTTGCTCTTTGAGGACTAAAAGGTGCTACCAACTCGTGTGGGCTTT
1 GAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT
*
535976 GAAAAGAAAAAGGCATCCTAG-TCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT
1 GAAAAGAAAAAGGCGTCCT-GCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT
* * *
536038 GGAAAGAAAAAGGCGTCCTGCTCTTTCAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTT
1 GAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT
* * * ** * * * *
536100 GAAAAGGAAAAGGTGACCTATTTTTTGAGGACTAAAGGGTGCCACTAACTCATGTGGGTTTT
1 GAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT
* * * * *
536162 GAAATGGAAAAGGCATCCTGCTTTTTAAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT
1 GAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT
* * * * ** * *
536224 AAAAAG-GAAAGGTGTCCTGCTCTTTAAGGACTAAAAATGTGCCACCAGCTCATGTGGGCTTT
1 GAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACT-AAAGGGTGCCACCAACTCGTGTGGGCTTT
* * * *
536286 AAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGAGCTTT
1 GAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT
* * *
536348 GAAAAGGAAAAA-GCGTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTCATATGGGCTTT
1 GAAAA-GAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT
* ** *
536410 AAAAAGAAAAAGAAGTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT
1 GAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT
* * * * * *
536472 GAAAAGAAAAAGGAGTCCTGCTCTTTAAAGAGTAAAGAGTGCCACCAACTCGCGTGGGCTTT
1 GAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT
* * * * * ** * *
536534 AAAAAG-GAAAGGCATCTTGCTC-TTGATGACTAAAAATGTGCCACCAGCTCGTGTAGGCTTT
1 GAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACT-AAAGGGTGCCACCAACTCGTGTGGGCTTT
* * * * *
536595 AAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTATGGGCTTT
1 GAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT
* * * * * *
536657 GAAAAGGAAAAGGCGTCTTGTTTTTTGAGGACTAAAGGGTGGCACCAACTCGTGTGGGCTGT
1 GAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT
* * **
536719 AAAAAGGAAAAGAAG-CCATGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT
1 GAAAAGAAAAAGGCGTCC-TGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT
* * * *
536781 GAAAAGAAAAATGTGTCCTACTCTTTGAGGACTGAA-GGTGCCACCAACTCGTGTGGGCTTT
1 GAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT
* * * *
536842 AAAAAGAAAAAGACGTCTTGCTCTTTAAGGACTAAAGG
1 GAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGG
536880 AAAATAAGGA
Statistics
Matches: 1565, Mismatches: 235, Indels: 54
0.84 0.13 0.03
Matches are distributed among these distances:
56 47 0.03
57 2 0.00
60 52 0.03
61 161 0.10
62 1181 0.75
63 122 0.08
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (62 bp):
GAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT
Found at i:543134 original size:79 final size:79
Alignment explanation
Indices: 543059--543447 Score: 408
Period size: 79 Copynumber: 4.9 Consensus size: 79
543049 ACCCTCTTAG
* * * * * *
543059 AAATAACGGGGTTGGAGTATCCCCAATGGTGGAAAATCGATGTTTTGAAAATAAAATCAGGGTTG
1 AAATAACGGGGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTGAAAATAAAACCGGGGTTG
543124 GAGTAT-CCTCTCGA
66 GAGTATCCCT-TCGA
*** * * * * * *
543138 AAATAATATGATTAGAGTATCCCCAATTATGGAAAATTAGTGTTTTAAAAATAAAACCGGGGTTG
1 AAATAACGGGGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTGAAAATAAAACCGGGGTTG
* *
543203 GTGTATCCCCTCGA
66 GAGTATCCCTTCGA
* * * * ** *
543217 AAATAACGGGGTTGGAGTAT-CCTGATTGTGGAAAATTGGTATTTGGGAAATAAAATTGGGGTTA
1 AAATAACGGGGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTGAAAATAAAACCGGGGTTG
* *
543281 GAGTATCCCCTCGG
66 GAGTATCCCTTCGA
* * * *
543295 AAATAACGGGGTTGAAGTATCCCTGATTGT-GAAAATTTGGTGTTTT-AGAAATAATACCGAGGT
1 AAATAACGGGGTTGGAGTATCCCCGATTGTGGAAAA-TTGGTGTTTTGA-AAATAAAACCGGGGT
*
543358 TGGAGTATTCCTTCGA
64 TGGAGTATCCCTTCGA
* * * *
543374 AAATAACGGGGTTGGAGTATCCCCGTTTGTGAAAAATTGGTGTTTTGGAAATAAAACCGGGGTCG
1 AAATAACGGGGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTGAAAATAAAACCGGGGTTG
543439 GAGTATCCC
66 GAGTATCCC
543448 CGATTGTGAA
Statistics
Matches: 250, Mismatches: 54, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
78 69 0.28
79 175 0.70
80 6 0.02
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (79 bp):
AAATAACGGGGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTGAAAATAAAACCGGGGTTG
GAGTATCCCTTCGA
Found at i:543317 original size:157 final size:158
Alignment explanation
Indices: 543059--543448 Score: 462
Period size: 157 Copynumber: 2.5 Consensus size: 158
543049 ACCCTCTTAG
* * * * * *
543059 AAATAACGGGGTTGGAGTATCCCCAATGGTGGAAAATCGATGTTTTGAAAATAAAATCAGGGTTG
1 AAATAACGGGGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTGGAAATAAAATCGGGGTTG
* * *
543124 GAGTATCCTCTCGAAAATAATATGATTAGAGTATCCCCAATTATGGAAAA-TTAGTGTTTTAAAA
66 GAGTATCCCCTCGAAAATAACAGGATTAGAGTATCCCCAATTAT-GAAAATTTAGTGTTTTAAAA
* *
543188 ATAAAACCGGGGTTGGTGTATCCCCTCGA
130 ATAAAACCGAGGTTGGAGTATCCCCTCGA
* * * * *
543217 AAATAACGGGGTTGGAGTAT-CCTGATTGTGGAAAATTGGTATTTGGGAAATAAAATTGGGGTTA
1 AAATAACGGGGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTGGAAATAAAATCGGGGTTG
* * * ** * * *
543281 GAGTATCCCCTCGGAAATAACGGGGTT-GAAGTATCCCTGATTGTGAAAATTTGGTGTTTTAGAA
66 GAGTATCCCCTCGAAAATAACAGGATTAG-AGTATCCCCAATTATGAAAATTTAGTGTTTTAAAA
* * *
543345 ATAATACCGAGGTTGGAGTATTCCTTCGA
130 ATAAAACCGAGGTTGGAGTATCCCCTCGA
* * * *
543374 AAATAACGGGGTTGGAGTATCCCCGTTTGTGAAAAATTGGTGTTTTGGAAATAAAACCGGGGTCG
1 AAATAACGGGGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTGGAAATAAAATCGGGGTTG
543439 GAGTATCCCC
66 GAGTATCCCC
543449 GATTGTGAAA
Statistics
Matches: 193, Mismatches: 36, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
156 6 0.03
157 122 0.63
158 65 0.34
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (158 bp):
AAATAACGGGGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTGGAAATAAAATCGGGGTTG
GAGTATCCCCTCGAAAATAACAGGATTAGAGTATCCCCAATTATGAAAATTTAGTGTTTTAAAAA
TAAAACCGAGGTTGGAGTATCCCCTCGA
Found at i:543447 original size:51 final size:51
Alignment explanation
Indices: 543380--543550 Score: 279
Period size: 51 Copynumber: 3.4 Consensus size: 51
543370 TCGAAAATAA
*
543380 CGGGGTTGGAGTATCCCCGTTTGTGAAAAATTGGTGTTTTGGAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAAC
*
543431 CGGGGTCGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAAC
* * *
543482 CGGGGTTAGAGTATCCCCAATTGTGAAAAATTGATGTTTTGGAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAAC
* *
543533 CAGGATTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
543551 TCGAAAATAA
Statistics
Matches: 111, Mismatches: 9, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
51 111 1.00
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAAC
Found at i:543507 original size:181 final size:181
Alignment explanation
Indices: 543301--543629 Score: 491
Period size: 181 Copynumber: 1.8 Consensus size: 181
543291 TCGGAAATAA
** * * *
543301 CGGGGTTGAAGTATCCCTGATTGTGAAAATTTGGTGTTTTAGAAATAATACCGAGG-TTGGAGTA
1 CGGGGTTGAAGTATCCCCAATTGTGAAAAATTGATGTTTTAGAAATAAAACC-AGGATTGGAGTA
* * ** * *
543365 TTCCTTCGAAAATAACGGGGTTGGAGTATCCCCGTTTGTGAAAAATTGGTGTTTTGGAAATAAAA
65 TCCCCTCGAAAATAACGGGGTTGGAGTATCCCCCATTGTGAAAAATTAGTGTTTTCGAAATAAAA
*
543430 CCGGGGTCGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAAC
130 CCAGGGTCGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAAC
*
543482 CGGGGTT-AGAGTATCCCCAATTGTGAAAAATTGATGTTTTGGAAATAAAACCAGGATTGGAGTA
1 CGGGGTTGA-AGTATCCCCAATTGTGAAAAATTGATGTTTTAGAAATAAAACCAGGATTGGAGTA
543546 TCCCCTCGAAAATAACGGGGTTGGAGTATCCCCCATTGTGAAAAATTAGTGTTTTCGAAATAAAA
65 TCCCCTCGAAAATAACGGGGTTGGAGTATCCCCCATTGTGAAAAATTAGTGTTTTCGAAATAAAA
* *
543611 CCAGGGTTGTAGTATCCCC
130 CCAGGGTCGGAGTATCCCC
543630 TCGGAAATAA
Statistics
Matches: 131, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
180 4 0.03
181 127 0.97
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.29
Consensus pattern (181 bp):
CGGGGTTGAAGTATCCCCAATTGTGAAAAATTGATGTTTTAGAAATAAAACCAGGATTGGAGTAT
CCCCTCGAAAATAACGGGGTTGGAGTATCCCCCATTGTGAAAAATTAGTGTTTTCGAAATAAAAC
CAGGGTCGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAAC
Found at i:543552 original size:260 final size:258
Alignment explanation
Indices: 543223--543707 Score: 648
Period size: 260 Copynumber: 1.9 Consensus size: 258
543213 TCGAAAATAA
* ** * * *** *
543223 CGGGGTTGGAGTATCCTGATTGTGGAAAATTGGTATTTGGGAAATAAAATTGGGGTTAGAGTATC
1 CGGGGTTAGAGTATCCCAATTGTGAAAAATTGATATTTGGGAAATAAAACCAGGATTAGAGTATC
* ** * * *
543288 CCCTCGGAAATAACGGGGTTGAAGTATCCCTGATTGTGAAAATTTGGTGTTTTAGAAATAATACC
66 CCCTCGAAAATAACGGGGTTGAAGTATCCCCCATTGTGAAAAATTAGTGTTTTAGAAATAAAACC
* * * * * * *
543353 -GAGGTTGGAGTATTCCTTCGAAAATAACGGGGTTGGAGTATCCCCGTTTGTGAAAAATTGGTGT
131 AG-GGTTGGAGTATCCCCTCGAAAATAACAGGATTAGAGTATCCCCGATTGT-AAAAATTGGGGT
*
543417 TTTGGAAATAAAACCGGGGTCGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAAC
194 TTTGGAAATAAAACCGGGGTCAGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAAC
* * *
543482 CGGGGTTAGAGTATCCCCAATTGTGAAAAATTGATGTTTTGGAAATAAAACCAGGATTGGAGTAT
1 CGGGGTTAGAGTAT-CCCAATTGTGAAAAATTGATATTTGGGAAATAAAACCAGGATTAGAGTAT
* *
543547 CCCCTCGAAAATAACGGGGTTGGAGTATCCCCCATTGTGAAAAATTAGTGTTTTCGAAATAAAAC
65 CCCCTCGAAAATAACGGGGTTGAAGTATCCCCCATTGTGAAAAATTAGTGTTTTAGAAATAAAAC
* * *
543612 CAGGGTTGTAGTATCCCCTCGGAAATAATAGGATTAGAGTATCCCCGATTGTAAAAATTGGGGTT
130 CAGGGTTGGAGTATCCCCTCGAAAATAACAGGATTAGAGTATCCCCGATTGTAAAAATTGGGGTT
*
543677 TTGGAAATAAAACCGGGGTTAGAGTATCCCC
195 TTGGAAATAAAACCGGGGTCAGAGTATCCCC
543708 TCGAAAATAA
Statistics
Matches: 192, Mismatches: 32, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
259 54 0.28
260 137 0.71
261 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.29
Consensus pattern (258 bp):
CGGGGTTAGAGTATCCCAATTGTGAAAAATTGATATTTGGGAAATAAAACCAGGATTAGAGTATC
CCCTCGAAAATAACGGGGTTGAAGTATCCCCCATTGTGAAAAATTAGTGTTTTAGAAATAAAACC
AGGGTTGGAGTATCCCCTCGAAAATAACAGGATTAGAGTATCCCCGATTGTAAAAATTGGGGTTT
TGGAAATAAAACCGGGGTCAGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAAC
Found at i:543613 original size:79 final size:78
Alignment explanation
Indices: 543482--543717 Score: 321
Period size: 79 Copynumber: 3.0 Consensus size: 78
543472 GAAATAAAAC
*
543482 CGGGGTTAGAGTATCCCCAATTGTGAAAAATTGATGTTTTGGAAATAAAACCAGGATTGGAGTAT
1 CGGGGTTAGAGTATCCCCAATTGTGAAAAATTG-TGTTTTGGAAATAAAACCAGGGTTGGAGTAT
543547 CCCCTCGAAAATAA
65 CCCCTCGAAAATAA
* * * *
543561 CGGGGTTGGAGTATCCCCCATTGTGAAAAATTAGTGTTTTCGAAATAAAACCAGGGTTGTAGTAT
1 CGGGGTTAGAGTATCCCCAATTGTGAAAAATT-GTGTTTTGGAAATAAAACCAGGGTTGGAGTAT
*
543626 CCCCTCGGAAATAA
65 CCCCTCGAAAATAA
** * * * * *
543640 TAGGATTAGAGTATCCCCGATTGT-AAAAATTGGGGTTTTGGAAATAAAACCGGGGTTAGAGTAT
1 CGGGGTTAGAGTATCCCCAATTGTGAAAAATT-GTGTTTTGGAAATAAAACCAGGGTTGGAGTAT
543704 CCCCTCGAAAATAA
65 CCCCTCGAAAATAA
543718 AAATATGAAT
Statistics
Matches: 138, Mismatches: 18, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
78 47 0.34
79 90 0.65
80 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (78 bp):
CGGGGTTAGAGTATCCCCAATTGTGAAAAATTGTGTTTTGGAAATAAAACCAGGGTTGGAGTATC
CCCTCGAAAATAA
Found at i:544416 original size:21 final size:22
Alignment explanation
Indices: 544390--544431 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
544380 CTCTTTGAGG
544390 GAAAAAT-ATCTTGAAATTTTA
1 GAAAAATCATCTTGAAATTTTA
* *
544411 GAAAAATCATTTTGAATTTTT
1 GAAAAATCATCTTGAAATTTT
544432 TACATAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.43
Consensus pattern (22 bp):
GAAAAATCATCTTGAAATTTTA
Found at i:546958 original size:67 final size:68
Alignment explanation
Indices: 546836--546962 Score: 175
Period size: 67 Copynumber: 1.9 Consensus size: 68
546826 ATTGGGTTTT
* * * *
546836 AAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCTAGCAATATTGGACTTAAAGATGAAGATG
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
546901 AGA
66 AGA
* * * *
546904 AAAG-TGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGA
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGA
546963 GAAAAAGGAT
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
67 47 0.92
68 4 0.08
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.25
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
AGA
Found at i:547046 original size:52 final size:55
Alignment explanation
Indices: 546915--547065 Score: 191
Period size: 52 Copynumber: 2.8 Consensus size: 55
546905 AAGTGATAAA
* * * * *
546915 GATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAG
1 GATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAGAAAAAG
* * * * *
546970 GATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG-G-AATAG
1 GATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAGAAAAAG
547023 G-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 GATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
547066 GTGATGAGGA
Statistics
Matches: 82, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
52 38 0.46
53 5 0.06
54 1 0.01
55 38 0.46
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (55 bp):
GATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAGAAAAAG
Found at i:547382 original size:400 final size:400
Alignment explanation
Indices: 546623--547468 Score: 1521
Period size: 400 Copynumber: 2.1 Consensus size: 400
546613 GTTTTGCAAT
* * * * * * * *
546623 GTGCCACTATGCAGATACAAGGCCTGCCACACTGGACTTAAAGATGATGAGGATGAAGAGTGGTA
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGATGAGGATGAAGAGTGGTA
*
546688 AAAGGACCAATACGTTGATTCACAGCCAACAATATTGGGTCTAGAGATGAGAAAAAGGATAAAGG
66 AAAGGACCAATACGTTGATTCACAGCCAACAATATTAGGTCTAGAGATGAGAAAAAGGATAAAGG
546753 AGCCAATATGCGACTAGCGATATTAGGCTCGAAGATGCGAAAAATGACAATGTGCTGATTCATGA
131 AGCCAATATGCGACTAGCGATATTAGGCTCGAAGATGCGAAAAATGACAATGTGCTGATTCATGA
*
546818 CCAGCGTCATTGGGTTTTAAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCTAGCAATATTG
196 CCAGCGTCATTGGGTTTTAAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTG
*
546883 GACTTAAAGATGAAGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATAT
261 GACTTAAAGATGAAGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCACGGCCAACGATAT
* *
546948 TGGGCTTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
326 TGGGCTTAAAGATGAGAAAAAGGATGTAAATGTGCTAATTCAAGGCCAGCTACATTGAACTTAAA
*
547013 GATGGAATAG
391 GATGGAAAAG
547023 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGATGAGGATGAAGAGTGGTA
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGATGAGGATGAAGAGTGGTA
* *
547088 AAAGGACCAATACGTTGATTCACAGCCAACGATATTAGGTCTAGTGATGAGAAAAAGGATAAAGG
66 AAAGGACCAATACGTTGATTCACAGCCAACAATATTAGGTCTAGAGATGAGAAAAAGGATAAAGG
547153 AGCCAATATGCGACTAGCGATATTAGGCTCGAAGATGCGAAAAATGACAATGTGCTGATTCATGA
131 AGCCAATATGCGACTAGCGATATTAGGCTCGAAGATGCGAAAAATGACAATGTGCTGATTCATGA
* *
547218 CCATCGTCATTGGGTTTTAAAGATGATGAAGGTTCCAATATGCTGATTCAAGGCCAGCAATATTG
196 CCAGCGTCATTGGGTTTTAAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTG
547283 GACTTAAAGATGAAGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCACGGCCAACGATAT
261 GACTTAAAGATGAAGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCACGGCCAACGATAT
547348 TGGGCTTAAAGATGAGAAAAAGGATGTAAATGTGCTAATTCAAGGCCAGCTACATTGAACTTAAA
326 TGGGCTTAAAGATGAGAAAAAGGATGTAAATGTGCTAATTCAAGGCCAGCTACATTGAACTTAAA
547413 GATGGAAAAG
391 GATGGAAAAG
*
547423 GTACCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTG
547469 CCAATGTGCT
Statistics
Matches: 427, Mismatches: 19, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
400 427 1.00
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.24
Consensus pattern (400 bp):
GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGATGAGGATGAAGAGTGGTA
AAAGGACCAATACGTTGATTCACAGCCAACAATATTAGGTCTAGAGATGAGAAAAAGGATAAAGG
AGCCAATATGCGACTAGCGATATTAGGCTCGAAGATGCGAAAAATGACAATGTGCTGATTCATGA
CCAGCGTCATTGGGTTTTAAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTG
GACTTAAAGATGAAGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCACGGCCAACGATAT
TGGGCTTAAAGATGAGAAAAAGGATGTAAATGTGCTAATTCAAGGCCAGCTACATTGAACTTAAA
GATGGAAAAG
Found at i:547535 original size:49 final size:49
Alignment explanation
Indices: 547376--548833 Score: 1868
Period size: 49 Copynumber: 30.9 Consensus size: 49
547366 AAAGGATGTA
* * * *
547376 AATGTGCTAATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTACC
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---AGAAGGTGCC
* *
547428 AATATGCTGATTCAAGGCCAGCTATATTGGACTT-----A-AAGGTGCC
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
547471 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
* * *
547520 AATATGCTGATTCAAGGCCAGCAATATTGGACTT--A-AAG-A--TGCC
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
*
547563 AATGTGCTGATTCAAGGCTAGCTACATTGGACTTAAAGAAGAAGGTGCC
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
* * *
547612 AATATGCTGATTCAAGGCCAGCGATATTGGACTT--A-AAG-A--TGCC
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
* * *
547655 AATGTGCTAATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCC
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
* * * *
547704 AATATGCTGATTCAAGGCCAGC--GA-T--A-TT-GAGCATGAAGGTGCC
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG-AAGAAGGTGCC
547747 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
* * *
547796 AATGTGGTAATTCAAGGCCAGCTACATTAGACTTAAAGAAGAAGGTGCC
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
547845 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
* *
547894 AATATGCTGATTCAAGGCCAGCTATATTGGACTT-----A-AAGGTGCC
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
*
547937 AATGTGCTGATTCAAGGCCAACTACATTGGACTTAAAGAAGAAGGTGCC
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
547986 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
* * *
548035 AATATGCTGATTCAAGGCCAGCGATATTGGACTT-----A-AAGGTGCC
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
*
548078 AATGTGATGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
*
548127 AATGTGCTGATTCAAGGCCAGCTACATAGGACTTAAAGAAGAAGGTGCC
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
** * *
548176 AATACGCTGATTCAAGGCCAGCGATATTGGACTT-----A-AAGGTGCC
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
548219 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
*
548268 AATGTGCTGATTCAAGGCCAACTACATTGGACTTAAAGAAGAAGGTGCC
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
* * *
548317 AATATGCTGATTCAAGGCCAGCGATATTGGACTT-----A-AAGGTGCC
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
548360 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
548409 AATGTGCTGATTCCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
1 AATGTGCTGATT-CAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
* * * * * *
548459 AATATGCTAATTCAAGGCTAGCGATATTGAACTTAAAGAAGAAGGTGCC
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
* * *
548508 AATATGCTGATTCAAGGCCAGCGATATTGGACTT--A-AAG-A--TGCC
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
548551 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
548600 AATGTGCTGATTCCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
1 AATGTGCTGATT-CAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
* * * * * *
548650 AATATGCTAATTCAAGGCTAGCGATATTGAACTTAAAGAAGAAGGTGCC
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
* * *
548699 AATATGCTGATTCAAGGCCAGCGATATTGGACTT--A-AAG-A--TGCC
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
* *
548742 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGTC
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
* * *
548791 AATATGCTGATTCAAGGCCAACTATATTGGACTTAAAGGAAGA
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA-GAAGA
548834 TGCCATCAAC
Statistics
Matches: 1241, Mismatches: 100, Indels: 132
0.84 0.07 0.09
Matches are distributed among these distances:
42 2 0.00
43 364 0.29
44 6 0.00
45 9 0.01
46 24 0.02
47 9 0.01
48 6 0.00
49 691 0.56
50 100 0.08
52 30 0.02
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (49 bp):
AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
Found at i:547550 original size:92 final size:94
Alignment explanation
Indices: 547376--548833 Score: 1721
Period size: 92 Copynumber: 15.4 Consensus size: 94
547366 AAAGGATGTA
* * * *
547376 AATGTGCTAATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTACCAATATGCTGATTC
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---AGAAGGTGCCAATATGCTGATTC
547441 AAGGCCAGCTATATTGGACTT-A-AAGGTGCC
63 AAGGCCAGCTATATTGGACTTAAGAAGGTGCC
547471 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAG
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAG
* *
547536 GCCAGCAATATTGGACTT-A-AAGATGCC
66 GCCAGCTATATTGGACTTAAGAAGGTGCC
*
547563 AATGTGCTGATTCAAGGCTAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAG
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAG
* *
547628 GCCAGCGATATTGGACTT-A-AAGATGCC
66 GCCAGCTATATTGGACTTAAGAAGGTGCC
* * *
547655 AATGTGCTAATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAG
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAG
* *
547720 GCCAGCGATATT-GAGC--ATGAAGGTGCC
66 GCCAGCTATATTGGA-CTTAAGAAGGTGCC
* * *
547747 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATGTGGTAATTCAAG
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAG
* *
547812 GCCAGCTACATTAGACTTAAAGAAGAAGGTGCC
66 GCCAGCTATATTGGACTT----AAGAAGGTGCC
547845 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAG
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAG
547910 GCCAGCTATATTGGACTT-A-AAGGTGCC
66 GCCAGCTATATTGGACTTAAGAAGGTGCC
* *
547937 AATGTGCTGATTCAAGGCCAACTACATTGGACTTAAAGAAGAAGGTGCCAATGTGCTGATTCAAG
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAG
*
548002 GCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
66 GCCAGCTATATTGGACTT----AAGAAGGTGCC
* * * * *
548035 AATATGCTGATTCAAGGCCAGCGATATTGGACTT-----A-AAGGTGCCAATGTGATGATTCAAG
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAG
*
548094 GCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
66 GCCAGCTATATTGGACTT----AAGAAGGTGCC
* *
548127 AATGTGCTGATTCAAGGCCAGCTACATAGGACTTAAAGAAGAAGGTGCCAATACGCTGATTCAAG
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAG
*
548192 GCCAGCGATATTGGACTT-A-AAGGTGCC
66 GCCAGCTATATTGGACTTAAGAAGGTGCC
*
548219 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATGTGCTGATTCAAG
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAG
* *
548284 GCCAACTACATTGGACTTAAAGAAGAAGGTGCC
66 GCCAGCTATATTGGACTT----AAGAAGGTGCC
* * * *
548317 AATATGCTGATTCAAGGCCAGCGATATTGGACTT-----A-AAGGTGCCAATGTGCTGATTCAAG
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAG
*
548376 GCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
66 GCCAGCTATATTGGACTT----AAGAAGGTGCC
*
548409 AATGTGCTGATTCCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTAATTCAA
1 AATGTGCTGATT-CAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAA
* * *
548474 GGCTAGCGATATTGAACTTAAAGAAGAAGGTGCC
65 GGCCAGCTATATTGGACTT----AAGAAGGTGCC
* * * *
548508 AATATGCTGATTCAAGGCCAGCGATATTGGACTT--A-AAG-A--TGCCAATGTGCTGATTCAAG
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAG
*
548567 GCCAGCTACATTGGACTTAAAGAAGAAGGTGCC
66 GCCAGCTATATTGGACTT----AAGAAGGTGCC
*
548600 AATGTGCTGATTCCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTAATTCAA
1 AATGTGCTGATT-CAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAA
* * *
548665 GGCTAGCGATATTGAACTTAAAGAAGAAGGTGCC
65 GGCCAGCTATATTGGACTT----AAGAAGGTGCC
* * * *
548699 AATATGCTGATTCAAGGCCAGCGATATTGGACTT--A-AAG-A--TGCCAATGTGCTGATTCAAG
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAG
* *
548758 GCCAGCTACATTGGACTTAAAGATGAAGGTGTC
66 GCCAGCTATATTGGACTT--A-A-GAAGGTGCC
* * *
548791 AATATGCTGATTCAAGGCCAACTATATTGGACTTAAAGGAAGA
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA-GAAGA
548834 TGCCATCAAC
Statistics
Matches: 1219, Mismatches: 95, Indels: 96
0.86 0.07 0.07
Matches are distributed among these distances:
90 2 0.00
91 3 0.00
92 746 0.61
93 46 0.04
94 3 0.00
95 44 0.04
96 8 0.01
97 4 0.00
98 243 0.20
99 120 0.10
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (94 bp):
AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAG
GCCAGCTATATTGGACTTAAGAAGGTGCC
Found at i:548827 original size:141 final size:144
Alignment explanation
Indices: 547317--548833 Score: 1820
Period size: 141 Copynumber: 10.7 Consensus size: 144
547307 GTGATAAAGA
* * * * **
547317 TGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTAAATGTG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-GAG---AAGG-TGCCAATGTG
* * * * *
547382 CTAATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTACCAATATGCTGATTCAAGGCC
59 CTGATTCAAGGCCAGCTACATTGGACTTAAAGA---AGAAGGTGCCAATGTGCTGATTCAAGGCC
*
547447 AGCTATATTGGACTT-A-AAG--G
121 AGCTACATTGGACTTAAGAAGAAG
* * * *
547467 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG-AGAAGGTGCCAATGTGCTGATT
* * *
547532 CAAGGCCAGCAATATTGGACTT--A-AAG-A--TGCCAATGTGCTGATTCAAGGCTAGCTACATT
65 CAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATT
547591 GGACTTAAAGAAGAAGG
130 GGACTT-AAGAAGAA-G
*
547608 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-AG-A--TGCCAATGTGCTAATTC
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAGAAGGTGCCAATGTGCTGATTC
* * * * *
547668 AAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATT-
66 AAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTG
*
547732 GAGC--ATGAAG--G
131 GA-CTTAAGAAGAAG
* * * * *
547743 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATGTGGTAATT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG-AGAAGGTGCCAATGTGCTGATT
*
547808 CAAGGCCAGCTACATTAGACTTAAAGAAGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATT
65 CAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATT
547873 GGACTTAAAGAAGAAGG
130 GGACTT-AAGAAGAA-G
*
547890 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A-AAGGTGCCAATGTGCTGATTC
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAGAAGGTGCCAATGTGCTGATTC
*
547950 AAGGCCAACTACATTGGACTTAAAGAAGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTG
66 AAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTG
548015 GACTTAAAGAAGAAGG
131 GACTT-AAGAAGAA-G
*
548031 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A-AAGGTGCCAATGTGATGATTC
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAGAAGGTGCCAATGTGCTGATTC
*
548091 AAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATAG
66 AAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTG
548156 GACTTAAAGAAGAAGG
131 GACTT-AAGAAGAA-G
*
548172 TGCCAATACGCTGATTCAAGGCCAGCGATATTGGACTT----A-AAGGTGCCAATGTGCTGATTC
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAGAAGGTGCCAATGTGCTGATTC
*
548232 AAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATGTGCTGATTCAAGGCCAACTACATTG
66 AAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTG
548297 GACTTAAAGAAGAAGG
131 GACTT-AAGAAGAA-G
548313 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A-AAGGTGCCAATGTGCTGATTC
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAGAAGGTGCCAATGTGCTGATTC
548373 AAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATGTGCTGATTCCAAGGCCAGCTACATT
66 AAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATGTGCTGATT-CAAGGCCAGCTACATT
548438 GGACTTAAAGAAGAAGG
130 GGACTT-AAGAAGAA-G
* * * *
548455 TGCCAATATGCTAATTCAAGGCTAGCGATATTGAACTTAAAGAAGAAGGTGCCAATATGCTGATT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG-AGAAGGTGCCAATGTGCTGATT
* *
548520 CAAGGCCAGCGATATTGGACTT--A-AAG-A--TGCCAATGTGCTGATTCAAGGCCAGCTACATT
65 CAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATT
548579 GGACTTAAAGAAGAAGG
130 GGACTT-AAGAAGAA-G
* * * * *
548596 TGCCAATGTGCTGATTCCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTAAT
1 TGCCAATATGCTGATT-CAAGGCCAGCGATATTGGACTTAAAG-AGAAGGTGCCAATGTGCTGAT
* * * * * * *
548661 TCAAGGCTAGCGATATTGAACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATAT
64 TCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACAT
548726 TGGACTT-A-AAG-A-
129 TGGACTTAAGAAGAAG
* * * * *
548738 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGTCAATATGCTGATT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA-GAAGGTGCCAATGTGCTGATT
* *
548803 CAAGGCCAACTATATTGGACTTAAAGGAAGA
65 CAAGGCCAGCTACATTGGACTTAAA-GAAGA
548834 TGCCATCAAC
Statistics
Matches: 1241, Mismatches: 83, Indels: 94
0.88 0.06 0.07
Matches are distributed among these distances:
135 104 0.08
136 2 0.00
137 4 0.00
138 15 0.01
139 2 0.00
140 5 0.00
141 733 0.59
142 172 0.14
144 39 0.03
145 13 0.01
146 3 0.00
147 39 0.03
148 77 0.06
149 2 0.00
150 31 0.02
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.24
Consensus pattern (144 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAGAAGGTGCCAATGTGCTGATTC
AAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTG
GACTTAAGAAGAAG
Found at i:548979 original size:33 final size:32
Alignment explanation
Indices: 548842--548959 Score: 182
Period size: 33 Copynumber: 3.6 Consensus size: 32
548832 GATGCCATCA
*
548842 ACTTGTGTAGGCTTTTGAAAAAGGTTGCCACCG
1 ACTTGTGTGGGC-TTTGAAAAAGGTTGCCACCG
***
548875 ACTTGTGTGGGCTTTGAAGGGGGTTGCCACCG
1 ACTTGTGTGGGCTTTGAAAAAGGTTGCCACCG
548907 ACTTGTGTGGGCTTTAGAAAAAGGTTGCCACCG
1 ACTTGTGTGGGCTTT-GAAAAAGGTTGCCACCG
548940 ACTTGTGTGGGCTTTGAAAA
1 ACTTGTGTGGGCTTTGAAAA
548960 GAAGGTGCCA
Statistics
Matches: 77, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
32 37 0.48
33 40 0.52
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.30
Consensus pattern (32 bp):
ACTTGTGTGGGCTTTGAAAAAGGTTGCCACCG
Found at i:549056 original size:27 final size:27
Alignment explanation
Indices: 549026--549085 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
549016 TTTAAAGGAA
549026 AAAAGGGTGCCACGGAGTCGTGGACTT
1 AAAAGGGTGCCACGGAGTCGTGGACTT
* *
549053 AAAAGGGTGCCATGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTCGTGGACTT
549080 AAAAGG
1 AAAAGG
549086 AAAAAGAGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.30, C:0.13, G:0.37, T:0.20
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTCGTGGACTT
Found at i:549067 original size:62 final size:64
Alignment explanation
Indices: 548955--549109 Score: 201
Period size: 68 Copynumber: 2.4 Consensus size: 64
548945 TGTGGGCTTT
* *
548955 GAAAAGAA-GGTGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCATGGGGTTGTGGACTTT
1 GAAAA-AAGGGTGCCACGGAGTTGTGGACTTAAAAGG----AGGTGCCATGGAGTTGTGGACTTA
549019 AAAG
61 AAAG
*
549023 GAAAAAAGGGTGCCACGGAGTCGTGGACTTAAAA-G-GGTGCCATGGAGTTGTGGACTTAAAAG
1 GAAAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAGGTGCCATGGAGTTGTGGACTTAAAAG
*
549085 G-AAAAAGAGTGCCACGGAGTTGTGG
1 GAAAAAAGGGTGCCACGGAGTTGTGG
549110 GCTTTAGAGA
Statistics
Matches: 81, Mismatches: 5, Indels: 9
0.85 0.05 0.09
Matches are distributed among these distances:
61 22 0.27
62 26 0.32
67 3 0.04
68 30 0.37
ACGTcount: A:0.32, C:0.12, G:0.36, T:0.19
Consensus pattern (64 bp):
GAAAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAGGTGCCATGGAGTTGTGGACTTAAAAG
Found at i:550178 original size:16 final size:16
Alignment explanation
Indices: 550127--550178 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
550117 GTTTTTCCCC
550127 TTTTT-TTTTGTTT-T
1 TTTTTGTTTTGTTTCT
* *
550141 TTTTTCTTTTTTTTCT
1 TTTTTGTTTTGTTTCT
550157 TTTTTGTTTTGTTTCT
1 TTTTTGTTTTGTTTCT
550173 TTTTTG
1 TTTTTG
550179 GAAAAGAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 21 0.64
ACGTcount: A:0.00, C:0.06, G:0.08, T:0.87
Consensus pattern (16 bp):
TTTTTGTTTTGTTTCT
Found at i:557442 original size:52 final size:52
Alignment explanation
Indices: 557294--557422 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
557284 CGAAATATGA
557294 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
557346 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
*
557398 AAATTTGCCTACATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
557423 AAGATCAGTG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
Found at i:557449 original size:13 final size:13
Alignment explanation
Indices: 557431--557455 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
557421 CAAAGATCAG
557431 TGTATCGATACAA
1 TGTATCGATACAA
557444 TGTATCGATACA
1 TGTATCGATACA
557456 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:557522 original size:19 final size:18
Alignment explanation
Indices: 557498--557595 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
557488 TAGCTTATAT
557498 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
557517 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
557530 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
557549 TGTATCGATAC--A-TT-
1 TGTATCGATACAAACTTA
557563 T-TATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
557582 TGTATCGATACAAA
1 TGTATCGATACAAA
557596 TCGTTGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 20 0.30
14 2 0.03
15 2 0.03
16 4 0.06
18 3 0.05
19 24 0.36
20 11 0.17
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:557535 original size:13 final size:13
Alignment explanation
Indices: 557517--557573 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
557507 ACAAAACTTA
557517 TGTATCGATACAT
1 TGTATCGATACAT
557530 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
557548 ATGTATCGATACAT
1 -TGTATCGATACAT
*
557562 TTTATCGATACA
1 TGTATCGATACA
557574 ACACTTTATG
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 20 0.54
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:557537 original size:32 final size:32
Alignment explanation
Indices: 557496--557593 Score: 169
Period size: 32 Copynumber: 3.0 Consensus size: 32
557486 AGTAGCTTAT
*
557496 ATTGTATCGATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
557528 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
*
557560 ATTTTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACAC-TTATGTATCGATAC
557593 A
1 A
557594 AATCGTTGAA
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 48 0.76
33 15 0.24
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (32 bp):
ATTGTATCGATACAACACTTATGTATCGATAC
Found at i:559296 original size:20 final size:20
Alignment explanation
Indices: 559271--559325 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
559261 GTATTGATAC
*
559271 AATGTATCGATATAATGAAT
1 AATGTATCGATACAATGAAT
*
559291 AATGTATCAATACAATGAAT
1 AATGTATCGATACAATGAAT
559311 AATGTATCGATACAA
1 AATGTATCGATACAA
559326 ATTATGAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (20 bp):
AATGTATCGATACAATGAAT
Found at i:560269 original size:41 final size:40
Alignment explanation
Indices: 559987--560946 Score: 507
Period size: 42 Copynumber: 23.3 Consensus size: 40
559977 AGTACATCCA
*
559987 GCTCTTTGAGGACAAAGGAAGAAAA-GAAATGTAA-TGTGTCCT
1 GCTCTTTGAGGACAAAGGAA-AAAAGGAAA---AAGTGCGTCCT
* * * * *
560029 ACTTTTTGAGGATAAAGGAAAAAGGAGAACAAAATGCGTCCT
1 GCTCTTTGAGGACAAAGGAAAAAAG-GAA-AAAGTGCGTCCT
* *
560071 GCTCTTTGAGGACAAAGGAAAAAGAAGAATAAAGTGCATCCT
1 GCTCTTTGAGGACAAAGGAAAAA-AGGAA-AAAGTGCGTCCT
560113 GCTCTTTGAGGACATAAGGAAAAAGAAGGAAATGAAGTGCGTCCT
1 GCTCTTTGAGGACA-AAGG-AAAA-AAGGAAA--AAGTGCGTCCT
* * ** *
560158 ACTCTTTGAGGACAAAAGGGGGAAAGAAGGAAATGGTGTGTCCT
1 GCTCTTTGAGGAC-AAA---GGAAAAAAGGAAAAAGTGCGTCCT
* * * *
560202 GTTCTTTGAGGACAAAGGAGAAAAGGAAAATGTGCATCCT
1 GCTCTTTGAGGACAAAGGAAAAAAGGAAAAAGTGCGTCCT
* * * * *
560242 GCTTTTTAAGGACAAAGGAAAAGAAGGAAGTTAAGTGTGTCTT
1 GCTCTTTGAGGACAAAGGAAAA-AAGGAA--AAAGTGCGTCCT
* * *
560285 GCTCTTTGAGGACAAAGG-GAAAAGGAAATAGAGTGCATCTT
1 GCTCTTTGAGGACAAAGGAAAAAAGGAAA-A-AGTGCGTCCT
* *
560326 GCTCTTTGAGGACAAAGG-GAAAAGGAAATAGAGTGCGTCAT
1 GCTCTTTGAGGACAAAGGAAAAAAGGAAA-A-AGTGCGTCCT
* *
560367 ACTCTTTGAGGACAAAAGGGAAAGAAAGGAAATGAAGTACGTCCT
1 GCTCTTTGAGGAC-AAA-GGAAA-AAAGGAAA--AAGTGCGTCCT
* * *
560412 GGTCTTTGAGGACAAAGGAGAAAAGG-AAAAGT-CATCCT
1 GCTCTTTGAGGACAAAGGAAAAAAGGAAAAAGTGCGTCCT
* * *
560450 AC-CTTTTGAGGACTAAGG-GAAAAGG-AAAAGT-C-TCCT
1 GCTC-TTTGAGGACAAAGGAAAAAAGGAAAAAGTGCGTCCT
*
560486 GCTCTTTGAGGACAAAGG-AAAAAGGAAATAAAGTGTGTCCT
1 GCTCTTTGAGGACAAAGGAAAAAAGG-AA-AAAGTGCGTCCT
* * * * *
560527 ACTCTTTAAAGACAAAAAGGAAAAGAAGGAAATGTAGTGTGTCCT
1 GCTCTTTGAGGAC--AAAGGAAAA-AAGGAAA--AAGTGCGTCCT
* * *
560572 GCTCTTTGAGGACTAAGGGAAAAGAAGGAAATGAGGTGC-ACCAT
1 GCTCTTTGAGGAC-AAAGGAAAA-AAGGAAA--AAGTGCGTCC-T
* *
560616 GCTCTTTGAGGACAAAGGAAAAAA-GAAAATGAGGAAAGTGTCCT
1 GCTCTTTGAGGACAAAGGAAAAAAGGAAAA--A-G--TGCGTCCT
* * *
560660 GCTCCTTGAGGACAAAGGAAAAGA-GAATGAAA-TGGGTCCT
1 GCTCTTTGAGGACAAAGGAAAAAAGGAA--AAAGTGCGTCCT
* * * *
560700 GCTCCTTGAGGACAAAGGAAGAAA-GAAAAAGGAAAGTGTCCT
1 GCTCTTTGAGGACAAAGGAAAAAAGGAAAAA-G--TGCGTCCT
* * *
560742 ACT-TCTTGAGGACAAAATG-AAAAA-G----AGTACGTCCT
1 GCTCT-TTGAGGAC-AAAGGAAAAAAGGAAAAAGTGCGTCCT
* * * *
560777 GCTCTTCGAGGACAAAGGAAAAAATGAAATCAGGTGCGCCCT
1 GCTCTTTGAGGACAAAGGAAAAAAGGAAA--AAGTGCGTCCT
*
560819 ACTC-TTGAAGGACAAAGG----AA--AAAAA-TGCGTCCT
1 GCTCTTTG-AGGACAAAGGAAAAAAGGAAAAAGTGCGTCCT
* * *
560852 GCTCTCTGAGGACAAAAGGGAAAAGAAAGAAGTGAAA-TGTGTCCT
1 GCTCTTTGAGGAC-AAA-GGAAAA-AAGGAA---AAAGTGCGTCCT
*
560897 GCTCTTTGAGGACAAAGGAGAAAAGGAAAAA--G-GTCCT
1 GCTCTTTGAGGACAAAGGAAAAAAGGAAAAAGTGCGTCCT
*
560934 ACTCTTTGAGGAC
1 GCTCTTTGAGGAC
560947 TAAAAGGTGC
Statistics
Matches: 732, Mismatches: 111, Indels: 155
0.73 0.11 0.16
Matches are distributed among these distances:
33 15 0.02
34 10 0.01
35 21 0.03
36 29 0.04
37 34 0.05
38 26 0.04
39 13 0.02
40 70 0.10
41 98 0.13
42 132 0.18
43 65 0.09
44 103 0.14
45 100 0.14
46 11 0.02
47 3 0.00
48 2 0.00
ACGTcount: A:0.39, C:0.14, G:0.27, T:0.20
Consensus pattern (40 bp):
GCTCTTTGAGGACAAAGGAAAAAAGGAAAAAGTGCGTCCT
Found at i:560476 original size:37 final size:36
Alignment explanation
Indices: 560204--560513 Score: 172
Period size: 41 Copynumber: 7.7 Consensus size: 36
560194 TGTGTCCTGT
*
560204 TCTTTGAGGACAAAGGAGAAAAGGAAAATGTGCATCCTGC
1 TCTTTGAGGACAAAGG-GAAAAGGAAAA-GT-C-TCCTCC
* * * * * *
560244 TTTTTAAGGACAAAGGAAAAGAAGGAAGTTAAGTGTGTCTTGC
1 TCTTTGAGGACAAAGG-GAA-AAGGAA---AA--GTCTCCTCC
* *
560287 TCTTTGAGGACAAAGGGAAAAGGAAATAGAGTGCATCTTGC
1 TCTTTGAGGACAAAGGGAAAAGG-AA-A-AGT-C-TCCTCC
* *
560328 TCTTTGAGGACAAAGGGAAAAGGAAATAGAGTGCGTCATAC
1 TCTTTGAGGACAAAGGGAAAAGG-AA-A-AGT-C-TCCTCC
**
560369 TCTTTGAGGACAAAAGGGAAAGAAAGGAAATGAAGTACGTCCTGG
1 TCTTTGAGGAC-AAAGGG--A-AAAGG-AA--AAGT-C-TCCTCC
560414 TCTTTGAGGACAAAGGAGAAAAGGAAAAGTCATCCTACC
1 TCTTTGAGGACAAAGG-GAAAAGGAAAAGTC-TCCT-CC
* *
560453 T-TTTGAGGACTAAGGGAAAAGGAAAAGTCTCCTGC
1 TCTTTGAGGACAAAGGGAAAAGGAAAAGTCTCCTCC
*
560488 TCTTTGAGGACAAAGGAAAAAGGAAA
1 TCTTTGAGGACAAAGGGAAAAGGAAA
560514 TAAAGTGTGT
Statistics
Matches: 229, Mismatches: 24, Indels: 38
0.79 0.08 0.13
Matches are distributed among these distances:
35 2 0.01
36 26 0.11
37 14 0.06
38 18 0.08
39 7 0.03
40 19 0.08
41 68 0.30
42 15 0.07
43 20 0.09
44 8 0.03
45 31 0.14
46 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.28, T:0.21
Consensus pattern (36 bp):
TCTTTGAGGACAAAGGGAAAAGGAAAAGTCTCCTCC
Found at i:560532 original size:160 final size:164
Alignment explanation
Indices: 560289--560595 Score: 428
Period size: 160 Copynumber: 1.9 Consensus size: 164
560279 TGTCTTGCTC
* *
560289 TTTGAGGACAAAGGGAAAAGGAAATAGAGTGCATCTTGCTCTTTGAGGACAAAGGGAAAAGGAAA
1 TTTGAGGACAAAGGGAAAAGGAAATAGAGTGCATCCTGCTCTTTGAGGACAAAGGAAAAAGGAAA
* * * * *
560354 TAGAGTGCGTCATACTCTTTGAGGAC-AAAAGGGAAAGAAAGGAAATGAAGTACGTCCTGGTCTT
66 TAAAGTGCGTCATACTCTTTAAAGACAAAAAGGAAAAG-AAGGAAATGAAGTACGTCCTGCTCTT
560418 TGAGGACAAAGGAGAAAAGGAAAAGTCATCCTACCT
130 TGAGGACAAAGG-GAAAAGGAAAAGTCATCCTACCT
*
560454 TTTGAGGACTAAGGGAAAAGG-AA-A-AGT-C-TCCTGCTCTTTGAGGACAAAGGAAAAAGGAAA
1 TTTGAGGACAAAGGGAAAAGGAAATAGAGTGCATCCTGCTCTTTGAGGACAAAGGAAAAAGGAAA
* * * **
560514 TAAAGTGTGTCCTACTCTTTAAAGACAAAAAGGAAAAGAAGGAAATGTAGTGTGTCCTGCTCTTT
66 TAAAGTGCGTCATACTCTTTAAAGACAAAAAGGAAAAGAAGGAAATGAAGTACGTCCTGCTCTTT
*
560579 GAGGACTAAGGGAAAAG
131 GAGGACAAAGGGAAAAG
560596 AAGGAAATGA
Statistics
Matches: 127, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
159 6 0.05
160 84 0.66
161 11 0.09
162 3 0.02
163 1 0.01
164 2 0.02
165 20 0.16
ACGTcount: A:0.39, C:0.12, G:0.28, T:0.21
Consensus pattern (164 bp):
TTTGAGGACAAAGGGAAAAGGAAATAGAGTGCATCCTGCTCTTTGAGGACAAAGGAAAAAGGAAA
TAAAGTGCGTCATACTCTTTAAAGACAAAAAGGAAAAGAAGGAAATGAAGTACGTCCTGCTCTTT
GAGGACAAAGGGAAAAGGAAAAGTCATCCTACCT
Found at i:560713 original size:84 final size:84
Alignment explanation
Indices: 560565--560767 Score: 250
Period size: 88 Copynumber: 2.4 Consensus size: 84
560555 GAAATGTAGT
* * * *
560565 GTGTCCTGCTCTTTGAGGACTAAGGGAAAAGAAGGAAATGAGGTGCACCATGCTCTTTGAGGACA
1 GTGTCCTGCTCCTTGAGGACAAAGGAAAAAGAAGGAAATGAGGT--ACCATGCTCCTTGAGGACA
560630 AAGGAAAAAAGAAAATGAGGAAA
64 AAGGAAAAAAGAAAA--AGGAAA
*
560653 GTGTCCTGCTCCTTGAGGACAAAGGAAAAGAGAATGAAATG-GGT-CC-TGCTCCTTGAGGACAA
1 GTGTCCTGCTCCTTGAGGACAAAGGAAAA-AGAAGGAAATGAGGTACCATGCTCCTTGAGGACAA
*
560715 AGGAAGAAAGAAAAAGGAAA
65 AGGAAAAAAGAAAAAGGAAA
* * *
560735 GTGTCCTACTTCTTGAGGACAAAATGAAAAAGA
1 GTGTCCTGCTCCTTGAGGAC-AAAGGAAAAAGA
560768 GTACGTCCTG
Statistics
Matches: 104, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
82 27 0.26
83 8 0.08
84 28 0.27
85 2 0.02
88 29 0.28
89 10 0.10
ACGTcount: A:0.40, C:0.14, G:0.28, T:0.18
Consensus pattern (84 bp):
GTGTCCTGCTCCTTGAGGACAAAGGAAAAAGAAGGAAATGAGGTACCATGCTCCTTGAGGACAAA
GGAAAAAAGAAAAAGGAAA
Found at i:561018 original size:62 final size:62
Alignment explanation
Indices: 560916--561333 Score: 556
Period size: 62 Copynumber: 6.7 Consensus size: 62
560906 GGACAAAGGA
* *
560916 GAAAAGGAAAAAG--GTCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTT
1 GAAAA-GAAAAAGACGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTT
** *
560977 GAAAAGAAAAAGACGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGCGCTTT
1 GAAAAGAAAAAGACGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTT
*** * * *
561039 GAAAAGAAAAAGGTATCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTCGTATGGGCTTT
1 GAAAAGAAAAAGACGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTT
* * * *
561101 GAAAAGAAAAAGATGTCATGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTT
1 GAAAAGAAAAAGACGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTT
561163 GAAAAGAAAAAGA--TACCTTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTT
1 GAAAAGAAAAAGACGT-CC-TGCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTT
* * * * * *
561225 GAAAAGAAAAAGGCATCTTACTCTTTGAGGACTGAAGGGTGCCACCAAGTCATGTGGGCTTT
1 GAAAAGAAAAAGACGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTT
* * *
561287 GCAAAGAAAAAGACGTCATGCTCTTTGAGGACTAAAAAGGTGCCACC
1 GAAAAGAAAAAGACGTCCTGCTCTTTGAGGACT-AAAGGGTGCCACC
561334 TGCTCGTGTG
Statistics
Matches: 317, Mismatches: 33, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
60 8 0.03
61 6 0.02
62 290 0.91
63 12 0.04
64 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.23
Consensus pattern (62 bp):
GAAAAGAAAAAGACGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTT
Found at i:561249 original size:186 final size:185
Alignment explanation
Indices: 560935--561348 Score: 650
Period size: 186 Copynumber: 2.2 Consensus size: 185
560925 AAAGGTCCTA
*
560935 CTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGACGTCCTGCTC
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGAC-TCCTGCTC
** *
561000 TTTGAGGACTAAAGGGTGCCACCAACTTGTGTGCGCTTTGAAAAGAAAAAGGTATCCTACTCTTT
65 TTTGAGGACTAAAGGGTGCCACCAACTCATGTGCGCTTTGAAAAGAAAAAGGCATCCTACTCTTT
* *
561065 GAGGACTAAAGGGTGCCACCAACTCGTATGGGCTTTGAAAAGAAAAAGATGTCATG
130 GAGGACTAAAGGGTGCCACCAACTCATATGGGCTTTGAAAAGAAAAAGACGTCATG
561121 CTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGA-TACCTTGCT
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACT-CC-TGCT
* *
561185 CTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGGCATCTTACTCTT
64 CTTTGAGGACTAAAGGGTGCCACCAACTCATGTGCGCTTTGAAAAGAAAAAGGCATCCTACTCTT
* * * *
561250 TGAGGACTGAAGGGTGCCACCAAGTCATGTGGGCTTTGCAAAGAAAAAGACGTCATG
129 TGAGGACTAAAGGGTGCCACCAACTCATATGGGCTTTGAAAAGAAAAAGACGTCATG
** *
561307 CTCTTTGAGGACTAAAAAGGTGCCACCTGCTCGTGTGAGCTT
1 CTCTTTGAGGACT-AAAAGGTGCCACCAACTCGTGTGGGCTT
561349 CCAAATGGAA
Statistics
Matches: 210, Mismatches: 15, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
184 1 0.00
185 2 0.01
186 182 0.87
187 25 0.12
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.24
Consensus pattern (185 bp):
CTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACTCCTGCTCT
TTGAGGACTAAAGGGTGCCACCAACTCATGTGCGCTTTGAAAAGAAAAAGGCATCCTACTCTTTG
AGGACTAAAGGGTGCCACCAACTCATATGGGCTTTGAAAAGAAAAAGACGTCATG
Found at i:564040 original size:14 final size:13
Alignment explanation
Indices: 564010--564084 Score: 55
Period size: 14 Copynumber: 5.7 Consensus size: 13
564000 TCGCCATTTG
564010 TCAAGAAATAGTTA
1 TCAAGAAAT-GTTA
*
564024 TCAAGAAATTTTCA
1 TCAAGAAATGTT-A
* *
564038 TCAAGAACTTTTA
1 TCAAGAAATGTTA
*
564051 TCGAG-AATGTTCA
1 TCAAGAAATGTT-A
* *
564064 TC-AGAAAAGTTG
1 TCAAGAAATGTTA
564076 TCAAGAAAT
1 TCAAGAAAT
564085 TTTTGTCAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
12 8 0.16
13 20 0.41
14 21 0.43
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.31
Consensus pattern (13 bp):
TCAAGAAATGTTA
Found at i:564148 original size:28 final size:28
Alignment explanation
Indices: 564102--564709 Score: 685
Period size: 28 Copynumber: 21.6 Consensus size: 28
564092 AATATGACCT
*
564102 CTTTTCAAAGCCCACAAGTTAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
564130 CTTCTCAAAGCCCATAAGTCAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
*
564158 CTTCTCAAAGCCCACAAGTCAGTGGCAAC
1 CTTTTCAAAGCCCACAAGTCAGTGGC-AC
*
564187 ACTTTTCAAAGCCCACAAGTTAGTGGCAACC
1 -CTTTTCAAAGCCCACAAGTCAGTGGC-A-C
* * * **
564218 CTTTTCAAGGCCTATAAGTCAGTGGGGC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
564246 CTTCTCAAAGCCCACATGTTAGTGGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
564275 C-TTTCAAAGCCCACAAGTCAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
*
564302 CTTTTCAAAGCCCACAAGTTAGTGGCAACC
1 CTTTTCAAAGCCCACAAGTCAGTGGC-A-C
* * *
564332 CTTTTCAAGGCCCATAAG-CTAATGGCAC
1 CTTTTCAAAGCCCACAAGTC-AGTGGCAC
* * * * * *
564360 CTTCTCAAAGCCTACATGTTAATGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
564388 CTTTTCAAAGCCTACAAGTTAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
564416 CTTTTCAAAGCCCAC-A--CAGTGGCACC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
* *
564442 CCTTTCAAAGCCCACAAGTTAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
*
564470 CTTTTCAAAGCCCACAAGTCAGTGGTAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
*
564498 ATTTTCAAAG-CCACAAGTCAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
564525 CTTCTCAAAGCCCATAAGTCAATGGCACC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
* *
564554 CTTTTCAAAGCCCATAAGTTAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
*
564582 CTTCTT-AAAGCCCACAAGTCATTGGCAC
1 CTT-TTCAAAGCCCACAAGTCAGTGGCAC
*
564610 CTTTTCAAAACCCACAAGTCAGTGGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
* *
564639 C-TTTCAAAGCCCATAAGTCAGTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
*
564666 CTTTTCAAAGTCCACAAGTCAGTGGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
564695 C-TTTCAAAGCCCACA
1 CTTTTCAAAGCCCACA
564710 CAAGCCGGTG
Statistics
Matches: 493, Mismatches: 67, Indels: 40
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.01
26 15 0.03
27 31 0.06
28 327 0.66
29 43 0.09
30 69 0.14
31 1 0.00
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (28 bp):
CTTTTCAAAGCCCACAAGTCAGTGGCAC
Found at i:564363 original size:114 final size:114
Alignment explanation
Indices: 564102--564709 Score: 731
Period size: 114 Copynumber: 5.4 Consensus size: 114
564092 AATATGACCT
* *
564102 CTTTTCAAAGCCCACAAGTTAGTGGCACCTTCTCAAAGCCCATAAGTCAGTGGCA-CCTTCTCAA
1 CTTTTCAAAGCCCATAAGTTAGTGGCACCTTCTCAAAGCCCACAAGTCAGTGGCATCCTT-TCAA
*
564166 AGCCCACAAGTCAGTGGCAACACTTTTCAAAGCCCACAAGTTAGTGGCAACC
65 AGCCCACAAGTCAGTGGC-AC-CTTTTCAAAGCCCACAAGTCAGTGGCAACC
* * * ** * *
564218 CTTTTCAAGGCCTATAAGTCAGTGGGGCCTTCTCAAAGCCCACATGTTAGTGGCATCCTTTCAAA
1 CTTTTCAAAGCCCATAAGTTAGTGGCACCTTCTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAA
*
564283 GCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTTAGTGGCAACC
66 GCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCAACC
* * * * * * * *
564332 CTTTTCAAGGCCCATAAGCTAATGGCACCTTCTCAAAGCCTACATGTTAATGGCATCTTTTCAAA
1 CTTTTCAAAGCCCATAAGTTAGTGGCACCTTCTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAA
* *
564397 GCCTACAAGTTAGTGGCACCTTTTCAAAGCCCAC-A--CAGTGGC-ACC
66 GCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCAACC
* * *
564442 CCTTTCAAAGCCCACAAGTTAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGTACAT--TTTCA
1 CTTTTCAAAGCCCATAAGTTAGTGGCACCTTCTCAAAGCCCACAAGTCAGTGG--CATCCTTTCA
* * *
564505 AAG-CCACAAGTCAGTGGCACCTTCTCAAAGCCCATAAGTCAATGGC-ACC
64 AAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCAACC
* *
564554 CTTTTCAAAGCCCATAAGTTAGTGGCACCTTCTTAAAGCCCACAAGTCATTGGCA-CCTTTTCAA
1 CTTTTCAAAGCCCATAAGTTAGTGGCACCTTCTCAAAGCCCACAAGTCAGTGGCATCC-TTTCAA
* * *
564618 AACCCACAAGTCAGTGGCATCC-TTTCAAAGCCCATAAGTCAGTGGC-A-T
65 AGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGCAACC
* * *
564666 CTTTTCAAAGTCCACAAGTCAGTGGCATCCTT-TCAAAGCCCACA
1 CTTTTCAAAGCCCATAAGTTAGTGGCA-CCTTCTCAAAGCCCACA
564710 CAAGCCGGTG
Statistics
Matches: 431, Mismatches: 49, Indels: 28
0.85 0.10 0.06
Matches are distributed among these distances:
109 28 0.06
110 57 0.13
111 6 0.01
112 102 0.24
113 44 0.10
114 120 0.28
115 2 0.00
116 68 0.16
117 4 0.01
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (114 bp):
CTTTTCAAAGCCCATAAGTTAGTGGCACCTTCTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAA
GCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCAACC
Found at i:571237 original size:36 final size:36
Alignment explanation
Indices: 571147--571218 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
571137 CTTACAATAA
*
571147 ATTAGTTTATTTGAAATCCTTTTATTTCATTAATTT
1 ATTAGTTTATTTGAAATTCTTTTATTTCATTAATTT
571183 ATTAGTTTATTTGAAAATTC-TTTATTTCATTAATTT
1 ATTAGTTTATTTG-AAATTCTTTTATTTCATTAATTT
571219 TTCTTTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 29 0.85
37 5 0.15
ACGTcount: A:0.29, C:0.07, G:0.06, T:0.58
Consensus pattern (36 bp):
ATTAGTTTATTTGAAATTCTTTTATTTCATTAATTT
Found at i:572042 original size:22 final size:21
Alignment explanation
Indices: 572014--572057 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
572004 GCAGTAGAGA
* *
572014 AAAAAGAGAGAGAAAAAGAAAG
1 AAAAAGAAAGA-AAAAAAAAAG
572036 AAAAAGAAAGAAAAAAAAAAG
1 AAAAAGAAAGAAAAAAAAAAG
572057 A
1 A
572058 GAGAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (21 bp):
AAAAAGAAAGAAAAAAAAAAG
Found at i:572064 original size:10 final size:10
Alignment explanation
Indices: 572014--572050 Score: 56
Period size: 10 Copynumber: 3.5 Consensus size: 10
572004 GCAGTAGAGA
572014 AAAAAGAGAGAG
1 AAAAAGA-A-AG
572026 AAAAAGAAAG
1 AAAAAGAAAG
572036 AAAAAGAAAG
1 AAAAAGAAAG
572046 AAAAA
1 AAAAA
572051 AAAAAGAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 17 0.68
11 1 0.04
12 7 0.28
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Done.