Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013530.1 Kokia drynarioides strain JFW-HI SEQ_128556, whole genome shotgun sequence
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: 335120
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 315 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:474 original size:9 final size:9
Alignment explanation
Indices: 460--546 Score: 55
Period size: 9 Copynumber: 10.1 Consensus size: 9
450 GCAAATGATT
460 TTAAAATTA
1 TTAAAATTA
469 TTAAAATTA
1 TTAAAATTA
478 TT----TT-
1 TTAAAATTA
*
482 TTAAAAATA
1 TTAAAATTA
*
491 -TAAAATTT
1 TTAAAATTA
499 TTAAAATTAA
1 TTAAAATT-A
509 TTTAAAA-TA
1 -TTAAAATTA
518 -TAAAATTA
1 TTAAAATTA
*
526 TTTAAATTA
1 TTAAAATTA
535 TTTTAAAATTA
1 --TTAAAATTA
546 T
1 T
547 AATCATTATG
Statistics
Matches: 60, Mismatches: 6, Indels: 24
0.67 0.07 0.27
Matches are distributed among these distances:
4 2 0.03
5 2 0.03
7 5 0.08
8 9 0.15
9 27 0.45
10 1 0.02
11 14 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
TTAAAATTA
Found at i:480 original size:20 final size:20
Alignment explanation
Indices: 452--546 Score: 78
Period size: 20 Copynumber: 4.9 Consensus size: 20
442 CCATGTCAGC
*
452 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
*
472 AAATTATTTTTTAAAAATA-TA
1 AAATTA--TTTTAAAATTATTA
493 AAA-T-TTTTAAAATTAATTTA
1 AAATTATTTTAAAATT-A-TTA
*
513 AAA-TA---TAAAATTATTT
1 AAATTATTTTAAAATTATTA
529 AAATTATTTTAAAATTAT
1 AAATTATTTTAAAATTAT
547 AATCATTATG
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
16 5 0.08
17 12 0.20
18 8 0.13
20 21 0.34
21 5 0.08
22 10 0.16
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:523 original size:27 final size:27
Alignment explanation
Indices: 461--548 Score: 106
Period size: 27 Copynumber: 3.1 Consensus size: 27
451 CAAATGATTT
*
461 TAAAATTATTAAAATTATTTTTTAAAAATA
1 TAAAATTTTTAAAATTA--TTTT-AAAATA
*
491 TAAAATTTTTAAAATTAATTTAAAATA
1 TAAAATTTTTAAAATTATTTTAAAATA
518 TAAAATTATTT-AAATTATTTTAAAATTA
1 TAAAATT-TTTAAAATTATTTTAAAA-TA
546 TAA
1 TAA
549 TCATTATGTC
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
27 26 0.49
28 11 0.21
30 16 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
TAAAATTTTTAAAATTATTTTAAAATA
Found at i:738 original size:14 final size:14
Alignment explanation
Indices: 719--745 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
709 AGCAAATGAA
719 TTTTTTATTTTGAG
1 TTTTTTATTTTGAG
733 TTTTTTATTTTGA
1 TTTTTTATTTTGA
746 TTTCCACCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.11, T:0.74
Consensus pattern (14 bp):
TTTTTTATTTTGAG
Found at i:1142 original size:27 final size:28
Alignment explanation
Indices: 1076--1151 Score: 82
Period size: 27 Copynumber: 2.7 Consensus size: 28
1066 CAAAGCAACA
1076 CTAACCCAAAATCTCCAAGATCAGAAACC
1 CTAACCCAAAATCTCCAA-ATCAGAAACC
* * *
1105 CTAAACAAAAATCTCCAAATCA-AAACT
1 CTAACCCAAAATCTCCAAATCAGAAACC
* * *
1132 TTTACCCAAAATCCCCAAAT
1 CTAACCCAAAATCTCCAAAT
1152 TCAACAACCT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 19 0.49
28 4 0.10
29 16 0.41
ACGTcount: A:0.47, C:0.32, G:0.03, T:0.18
Consensus pattern (28 bp):
CTAACCCAAAATCTCCAAATCAGAAACC
Found at i:1165 original size:23 final size:24
Alignment explanation
Indices: 1139--1188 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
1129 ACTTTTACCC
1139 AAAATCCCCAAATTCAACAACC-T
1 AAAATCCCCAAATTCAACAACCAT
* *
1162 AAAATCTCCAAATTCGACAACCAT
1 AAAATCCCCAAATTCAACAACCAT
1186 AAA
1 AAA
1189 CAATTCATGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.50, C:0.30, G:0.02, T:0.18
Consensus pattern (24 bp):
AAAATCCCCAAATTCAACAACCAT
Found at i:20561 original size:135 final size:132
Alignment explanation
Indices: 20313--20582 Score: 371
Period size: 135 Copynumber: 2.0 Consensus size: 132
20303 CTCCAAGAAA
* * * * *
20313 TGCACGGTTTGTTTCCTCACCAAAGCAACTACTGCTAATTTTAAGGTGACTACTATCACCGTTTT
1 TGCACAGTTTGTTTCCTCACCAAAGCAACTACTGCCAACTTTAACGTGACTACTATCACCATTTT
* *
20378 CAGGAAAAGTGCTTCTCGGATCCATGCATTCTAGAAGTACATTAGGAACAGATTGGCAAAGACTA
66 CAGGAAAAGTGCTTCTCAGATCCATGCATTCTAGAAGTACATTAGGAACAGATTGGCAAAGACCA
20443 GT
131 GT
* *
20445 TGCACAGTTTGTTTCCTCACCAAAGCAACTACTGCCAACTTTAACGTGACTTTTTCTATCATCAT
1 TGCACAGTTTGTTTCCTCACCAAAGCAACTACTGCCAACTTTAACGTGAC---TACTATCACCAT
* * * * *
20510 TTTTAGGAAGAGTGC-TCATCAGATCCATGCATTCTAGAAGTCCTTTAGGAACAGATTGGTAAAG
63 TTTCAGGAAAAGTGCTTC-TCAGATCCATGCATTCTAGAAGTACATTAGGAACAGATTGGCAAAG
20574 ACCAGT
127 ACCAGT
20580 TGC
1 TGC
20583 TTGGTGCATT
Statistics
Matches: 120, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
132 46 0.38
134 2 0.02
135 72 0.60
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.31
Consensus pattern (132 bp):
TGCACAGTTTGTTTCCTCACCAAAGCAACTACTGCCAACTTTAACGTGACTACTATCACCATTTT
CAGGAAAAGTGCTTCTCAGATCCATGCATTCTAGAAGTACATTAGGAACAGATTGGCAAAGACCA
GT
Found at i:27007 original size:10 final size:10
Alignment explanation
Indices: 26964--27068 Score: 58
Period size: 10 Copynumber: 10.6 Consensus size: 10
26954 ATATTTAAAA
26964 TTTTATAACT
1 TTTTATAACT
26974 TTTTA-ATACT
1 TTTTATA-ACT
* *
26984 TTTAATAATTT
1 TTTTATAA-CT
26995 TTTTATAACT
1 TTTTATAACT
* * *
27005 TTTAAAATATT
1 TTTTATA-ACT
**
27016 TTTTATAGGT
1 TTTTATAACT
*
27026 TTTTACAA--
1 TTTTATAACT
27034 -TTT-TAACT
1 TTTTATAACT
*
27042 TTTATATAATT
1 TTT-TATAACT
27053 TTTTATAACT
1 TTTTATAACT
27063 TTTTAT
1 TTTTAT
27069 TATTATTTTT
Statistics
Matches: 70, Mismatches: 16, Indels: 18
0.67 0.15 0.17
Matches are distributed among these distances:
6 2 0.03
7 3 0.04
9 3 0.04
10 39 0.56
11 23 0.33
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (10 bp):
TTTTATAACT
Found at i:27021 original size:21 final size:21
Alignment explanation
Indices: 26964--27081 Score: 74
Period size: 21 Copynumber: 5.9 Consensus size: 21
26954 ATATTTAAAA
* *
26964 TTTT-ATAACTTTTTAAT-AC
1 TTTTAATAATTTTTTTATAAC
26983 TTTTAATAATTTTTTTATAAC
1 TTTTAATAATTTTTTTATAAC
**
27004 TTTTAA-AATATTTTTTATAGG
1 TTTTAATAAT-TTTTTTATAAC
* *
27025 TTTTTACAA----TTT-TAAC
1 TTTTAATAATTTTTTTATAAC
27041 TTTTATATAA-TTTTTTATAAC
1 TTTTA-ATAATTTTTTTATAAC
* *
27062 TTTTTATTATTATTTTTATA
1 TTTTAATAATT-TTTTTATA
27082 TTTAAAAAAA
Statistics
Matches: 77, Mismatches: 11, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
16 6 0.08
17 6 0.08
19 4 0.05
20 20 0.26
21 31 0.40
22 10 0.13
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (21 bp):
TTTTAATAATTTTTTTATAAC
Found at i:27240 original size:20 final size:20
Alignment explanation
Indices: 27194--27240 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
27184 AAGCTAAAGT
*
27194 AATTAAAAATAAATTAAACCC
1 AATT-AAAATAAATTAAAACC
*
27215 ATTTAAAAT-AATTAAAAACC
1 AATTAAAATAAATT-AAAACC
27235 AATTAA
1 AATTAA
27241 TCCCTCATGC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 4 0.18
20 15 0.68
21 3 0.14
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.28
Consensus pattern (20 bp):
AATTAAAATAAATTAAAACC
Found at i:29976 original size:35 final size:35
Alignment explanation
Indices: 29914--29982 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 35
29904 TCCAGATTTT
*** *
29914 AAGATTTCCTCTTTCCTTGATCAAAAAAAAAAAAA
1 AAGATTTCCTCTTTCCCAAAACAAAAAAAAAAAAA
* *
29949 AAGATTTCCTCTTTCCCAAAACTAAAAACAAAAA
1 AAGATTTCCTCTTTCCCAAAACAAAAAAAAAAAA
29983 TTTAATTGTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.49, C:0.20, G:0.04, T:0.26
Consensus pattern (35 bp):
AAGATTTCCTCTTTCCCAAAACAAAAAAAAAAAAA
Found at i:31651 original size:27 final size:28
Alignment explanation
Indices: 31611--31673 Score: 83
Period size: 27 Copynumber: 2.2 Consensus size: 28
31601 CAATTAATTA
*
31611 ATTTTTTAAAATTTTAAATACTAAAAAAT
1 ATTTTTT-AAATTTAAAATACTAAAAAAT
*
31640 ATTTTTT-AATTTAAAATATTAAAAAAT
1 ATTTTTTAAATTTAAAATACTAAAAAAT
*
31667 GTTTTTT
1 ATTTTTT
31674 TATAATTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 24 0.77
29 7 0.23
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (28 bp):
ATTTTTTAAATTTAAAATACTAAAAAAT
Found at i:31730 original size:25 final size:27
Alignment explanation
Indices: 31697--31752 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
31687 CTGTTTAAGG
31697 AATTTTT-AATTTTT-AAAAAATAATT
1 AATTTTTAAATTTTTGAAAAAATAATT
*
31722 AATTTTTAAATTTTTGAAAAATTAATT
1 AATTTTTAAATTTTTGAAAAAATAATT
31749 AATT
1 AATT
31753 GTTGATGCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 7 0.25
26 7 0.25
27 14 0.50
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (27 bp):
AATTTTTAAATTTTTGAAAAAATAATT
Found at i:44952 original size:3 final size:3
Alignment explanation
Indices: 44944--44980 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
44934 AAAAGTACAT
44944 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
44981 AAGGACTGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:47889 original size:12 final size:12
Alignment explanation
Indices: 47872--47943 Score: 53
Period size: 12 Copynumber: 6.2 Consensus size: 12
47862 CTTTTGTTTA
47872 ATGTTCATGAAC
1 ATGTTCATGAAC
*
47884 ATGTTCATTTAAC
1 ATGTTCA-TGAAC
* *
47897 ---TTAATCGAAT
1 ATGTTCAT-GAAC
*
47907 ATGTTCACGAAC
1 ATGTTCATGAAC
*
47919 AT-TTAATGAAC
1 ATGTTCATGAAC
47930 ATGTTCATGAAC
1 ATGTTCATGAAC
47942 AT
1 AT
47944 ATAATTGAAC
Statistics
Matches: 44, Mismatches: 10, Indels: 12
0.67 0.15 0.18
Matches are distributed among these distances:
9 1 0.02
10 5 0.11
11 9 0.20
12 22 0.50
13 7 0.16
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (12 bp):
ATGTTCATGAAC
Found at i:47933 original size:23 final size:23
Alignment explanation
Indices: 47897--47977 Score: 90
Period size: 24 Copynumber: 3.3 Consensus size: 23
47887 TTCATTTAAC
*
47897 TTAATCGAATATGTTCACGAACAT
1 TTAAT-GAACATGTTCACGAACAT
*
47921 TTAATGAACATGTTCATGAACAT
1 TTAATGAACATGTTCACGAACAT
* *
47944 ATAATTGAACATGTTCACTAACAAT
1 TTAA-TGAACATGTTCACGAAC-AT
47969 GTTAATGAA
1 -TTAATGAA
47978 TAAAAAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
23 19 0.40
24 20 0.42
25 6 0.12
26 3 0.06
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (23 bp):
TTAATGAACATGTTCACGAACAT
Found at i:47957 original size:24 final size:23
Alignment explanation
Indices: 47879--47960 Score: 87
Period size: 23 Copynumber: 3.5 Consensus size: 23
47869 TTAATGTTCA
*
47879 TGAACATGTTCATTTAAC-TTAAT
1 TGAACATGTTCA-TGAACATTAAT
* * *
47902 CGAATATGTTCACGAACATTTAA-
1 TGAACATGTTCATGAACA-TTAAT
47925 TGAACATGTTCATGAACATATAAT
1 TGAACATGTTCATGAACAT-TAAT
47949 TGAACATGTTCA
1 TGAACATGTTCA
47961 CTAACAATGT
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
22 4 0.08
23 28 0.58
24 16 0.33
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (23 bp):
TGAACATGTTCATGAACATTAAT
Found at i:48260 original size:16 final size:17
Alignment explanation
Indices: 48239--48274 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
48229 TTATTAATTT
48239 TTGATTAAAAATTT-AA
1 TTGATTAAAAATTTCAA
48255 TTGATTAAAAATTTCAA
1 TTGATTAAAAATTTCAA
48272 TTG
1 TTG
48275 TTTTGTAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (17 bp):
TTGATTAAAAATTTCAA
Found at i:49934 original size:96 final size:96
Alignment explanation
Indices: 49749--49940 Score: 239
Period size: 96 Copynumber: 2.0 Consensus size: 96
49739 TTTTTGGGAA
* *
49749 AAGGATATTAGATTATCTCGATTTGAAGAAAGATTGCACCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTAGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
*
49814 GAATCGAAGATAAGGAAACATTGCCTCGATT
66 GAATCGAAGATAAAGAAACATTGCCTCGATT
* * * * *
49845 AAGGGTATTCGATTATTTCGATTTGAGGAAAAAATTGCACCTAGTGAGTTAAGGCACAA-ATTTT
1 AAGGATATTAGATTATCTCGATTTGAAG-AAAAATTGCACCTAGTAAGTTAAGGCACAATA-TTT
*
49909 C-GAAACTCGAA-ATAAAG-AATATTGCCTCGATT
64 CAG-AA-TCGAAGATAAAGAAACATTGCCTCGATT
49941 TTAAAGTTTT
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
96 40 0.48
97 38 0.46
98 5 0.06
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (96 bp):
AAGGATATTAGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
GAATCGAAGATAAAGAAACATTGCCTCGATT
Found at i:50233 original size:59 final size:59
Alignment explanation
Indices: 50164--50516 Score: 219
Period size: 59 Copynumber: 6.0 Consensus size: 59
50154 TTCGGATACC
50164 CGAGGGTAAAATGGTAA-TTTTGAGAAAATTCGGGGTTAAAAATGGGATTTTTGGAAG-TT
1 CGAGGGTAAAATGGTAATTTTTG-GAAAATTCGGGGTT-AAAATGGGATTTTTGGAAGTTT
* ** *
50223 CGAGGGTAAAAAT-ATAATTTTTGGAAGTTTTGGGGTTAAAATGGGATTTTTGGAAGTTT
1 CGAGGGT-AAAATGGTAATTTTTGGAAAATTCGGGGTTAAAATGGGATTTTTGGAAGTTT
* * * ** * ** ** **
50282 CGAGGTTAAAATGG-GATTTTTAGAAGTTTAGGGGTGGAAA-GTAAATTTTTAAAAGTTT
1 CGAGGGTAAAATGGTAATTTTTGGAAAATTCGGGGTTAAAATG-GGATTTTTGGAAGTTT
* * * * * *
50340 CGAGGTTAAAAATAGG--ATTTTCGGAAATTTGGGGGTGAAAATGGAATTTTTGGAAGTTT
1 CGAGGGT-AAAAT-GGTAATTTTTGGAAAATTCGGGGTTAAAATGGGATTTTTGGAAGTTT
* * * *
50399 C-AGGGTTAAAAATGG-GATTTTTGG-AAGTTCGAGGGTGAAAATGGAATTTTTGGAAGTTT
1 CGAGGG-T-AAAATGGTAATTTTTGGAAAATTCG-GGGTTAAAATGGGATTTTTGGAAGTTT
* * * * * *
50458 TG-GGGTTAAAAATGG-GATTTTTGG-AAGTTCGAGGGTAAAAACGGAATTTTTGGAAGTTT
1 CGAGGG-T-AAAATGGTAATTTTTGGAAAATTCG-GGGTTAAAATGGGATTTTTGGAAGTTT
50517 AAGGACTTTC
Statistics
Matches: 252, Mismatches: 30, Indels: 24
0.82 0.10 0.08
Matches are distributed among these distances:
57 1 0.00
58 74 0.29
59 164 0.65
60 13 0.05
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (59 bp):
CGAGGGTAAAATGGTAATTTTTGGAAAATTCGGGGTTAAAATGGGATTTTTGGAAGTTT
Found at i:50234 original size:29 final size:29
Alignment explanation
Indices: 50164--50515 Score: 270
Period size: 29 Copynumber: 12.0 Consensus size: 29
50154 TTCGGATACC
* * *
50164 CGAGGGT-AAAATGGTAATTTTGAGAAAATT
1 CGAGGGTAAAAATGGGATTTTTG-G-AAGTT
50194 CG-GGGTTAAAAATGGGATTTTTGGAAGTT
1 CGAGGG-TAAAAATGGGATTTTTGGAAGTT
***
50223 CGAGGGTAAAAATATAATTTTTGGAAGTTT
1 CGAGGGTAAAAATGGGATTTTTGGAAG-TT
* *
50253 TG-GGGTTAAAATGGGATTTTTGGAAGTTT
1 CGAGGGTAAAAATGGGATTTTTGGAAG-TT
* *
50282 CGA-GGTTAAAATGGGATTTTTAGAAGTT
1 CGAGGGTAAAAATGGGATTTTTGGAAGTT
* ** ** **
50310 -TAGGGGTGGAAA-GTAAATTTTTAAAAGTTT
1 CGA-GGGTAAAAATG-GGATTTTTGGAAG-TT
* * * *
50340 CGAGGTTAAAAATAGGATTTTCGGAAATT
1 CGAGGGTAAAAATGGGATTTTTGGAAGTT
* * * *
50369 TGGGGGTGAAAATGGAATTTTTGGAAGTTT
1 CGAGGGTAAAAATGGGATTTTTGGAAG-TT
50399 C-AGGGTTAAAAATGGGATTTTTGGAAGTT
1 CGAGGG-TAAAAATGGGATTTTTGGAAGTT
* *
50428 CGAGGGTGAAAATGGAATTTTTGGAAGTTT
1 CGAGGGTAAAAATGGGATTTTTGGAAG-TT
*
50458 TG-GGGTTAAAAATGGGATTTTTGGAAGTT
1 CGAGGG-TAAAAATGGGATTTTTGGAAGTT
* *
50487 CGAGGGTAAAAACGGAATTTTTGGAAGTT
1 CGAGGGTAAAAATGGGATTTTTGGAAGTT
50516 TAAGGACTTT
Statistics
Matches: 255, Mismatches: 50, Indels: 35
0.75 0.15 0.10
Matches are distributed among these distances:
27 1 0.00
28 3 0.01
29 162 0.64
30 75 0.29
31 14 0.05
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (29 bp):
CGAGGGTAAAAATGGGATTTTTGGAAGTT
Found at i:52343 original size:17 final size:18
Alignment explanation
Indices: 52321--52433 Score: 81
Period size: 17 Copynumber: 6.4 Consensus size: 18
52311 GGCTTTATTT
**
52321 ATTTTAAATTT-ATGATA
1 ATTTTAAATTTGAAAATA
52338 ATTTTAAATTTGAAAATA
1 ATTTTAAATTTGAAAATA
* *
52356 ATTTTAAACTT-AAATTA
1 ATTTTAAATTTGAAAATA
*
52373 AATTTAAATTT-AAAATAA
1 ATTTTAAATTTGAAAAT-A
* ** *
52391 ATTTAAAATTTTTAAACA
1 ATTTTAAATTTGAAAATA
* *
52409 AATTT-AATTTTAAAATA
1 ATTTTAAATTTGAAAATA
*
52426 AATTTAAA
1 ATTTTAAA
52434 AGGAGTATGG
Statistics
Matches: 77, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
17 44 0.57
18 30 0.39
19 3 0.04
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTTTAAATTTGAAAATA
Found at i:52362 original size:35 final size:34
Alignment explanation
Indices: 52340--52433 Score: 100
Period size: 35 Copynumber: 2.7 Consensus size: 34
52330 TTATGATAAT
52340 TTTAAATTTGAAAATAATTTTAAACTTAAATTAAA
1 TTTAAATTT-AAAATAATTTTAAACTTAAATTAAA
* * *
52375 TTTAAATTTAAAATAAATTTAAAATTTTTAAA-CAAA
1 TTTAAATTTAAAAT-AATTTTAAA--CTTAAATTAAA
* *
52411 TTTAATTTTAAAATAAATTTAAA
1 TTTAAATTTAAAATAATTTTAAA
52434 AGGAGTATGG
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
34 5 0.10
35 24 0.48
36 16 0.32
37 5 0.10
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (34 bp):
TTTAAATTTAAAATAATTTTAAACTTAAATTAAA
Found at i:52391 original size:11 final size:11
Alignment explanation
Indices: 52342--52399 Score: 55
Period size: 11 Copynumber: 5.1 Consensus size: 11
52332 ATGATAATTT
52342 TAAATTTGAAAA
1 TAAATTT-AAAA
* *
52354 TAATTTTAAACT
1 TAAATTTAAA-A
*
52366 TAAA-TTAAATT
1 TAAATTTAAA-A
52377 TAAATTTAAAA
1 TAAATTTAAAA
52388 TAAATTTAAAA
1 TAAATTTAAAA
52399 T
1 T
52400 TTTTAAACAA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
11 25 0.64
12 14 0.36
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:52433 original size:6 final size:6
Alignment explanation
Indices: 52340--52397 Score: 50
Period size: 6 Copynumber: 10.0 Consensus size: 6
52330 TTATGATAAT
* * *
52340 TTTAAA TTTGAAA -ATAAT TTTAAA CTTAAA -TTAAA TTTAAA TTTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
52387 -ATAAA TTTAAA
1 TTTAAA TTTAAA
52398 ATTTTTAAAC
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
5 11 0.27
6 27 0.66
7 3 0.07
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:53822 original size:6 final size:6
Alignment explanation
Indices: 53812--53887 Score: 86
Period size: 6 Copynumber: 13.0 Consensus size: 6
53802 CGGACTTTTT
* * *
53812 TTTAAT TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA -TT-AA TCTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA
*
53858 TTTAAA TTTAAA TTTAAT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
53888 AAAATTCAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
4 2 0.03
5 5 0.08
6 49 0.83
7 3 0.05
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:53838 original size:17 final size:17
Alignment explanation
Indices: 53816--53885 Score: 86
Period size: 17 Copynumber: 4.1 Consensus size: 17
53806 CTTTTTTTTA
*
53816 ATTTTAAATTTAGATTT
1 ATTTTAAATTTAAATTT
*
53833 ATTTTAAATTTAAATTA
1 ATTTTAAATTTAAATTT
*
53850 ATCTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
* *
53867 AAATTTAATTTTAAATTT
1 -ATTTTAAATTTAAATTT
53885 A
1 A
53886 AAAAAATTCA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
17 31 0.69
18 14 0.31
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:53839 original size:23 final size:23
Alignment explanation
Indices: 53813--53887 Score: 82
Period size: 23 Copynumber: 3.2 Consensus size: 23
53803 GGACTTTTTT
*
53813 TTAATTTTAAATTTAGATTT-ATT
1 TTAAATTTAAATTTA-ATTTAATT
*
53836 TTAAATTTAAATT-AATCTTAAAT
1 TTAAATTTAAATTTAAT-TTAATT
*
53859 TTAAATTTAAATTTAATTTTAAAT
1 TTAAATTTAAATTTAA-TTTAATT
53883 TTAAA
1 TTAAA
53888 AAAATTCAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
21 2 0.04
22 3 0.07
23 27 0.59
24 13 0.28
25 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (23 bp):
TTAAATTTAAATTTAATTTAATT
Found at i:54557 original size:9 final size:9
Alignment explanation
Indices: 54543--54608 Score: 53
Period size: 9 Copynumber: 7.0 Consensus size: 9
54533 TCAATAATTC
54543 TTAATAATA
1 TTAATAATA
54552 TTAATAAT-
1 TTAATAATA
**
54560 TGTTTTAATA
1 T-TAATAATA
*
54570 ATAATAATA
1 TTAATAATA
*
54579 ATAATAATA
1 TTAATAATA
54588 TTAATGATATCA
1 TTAAT-A-AT-A
54600 TTAATAATA
1 TTAATAATA
54609 AATAAGTTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
8 1 0.02
9 33 0.72
10 3 0.07
11 3 0.07
12 6 0.13
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.44
Consensus pattern (9 bp):
TTAATAATA
Found at i:54604 original size:27 final size:27
Alignment explanation
Indices: 54574--54672 Score: 85
Period size: 27 Copynumber: 3.5 Consensus size: 27
54564 TTAATAATAA
*
54574 TAATAATAATAATATTAATGATATCAT
1 TAATAATAATAATATTATTGATATCAT
* * *
54601 TAATAATAAATAAGTTTTTCTTAATATTCAT
1 TAATAAT-AATAA--TATTATTGATA-TCAT
*
54632 TAATAATAATAA-ATGTTTTGATAAT-AT
1 TAATAATAATAATAT-TATTGAT-ATCAT
54659 TAATAATAATAATA
1 TAATAATAATAATA
54673 AATAAATAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
27 22 0.38
28 12 0.21
29 1 0.02
30 12 0.21
31 11 0.19
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.43
Consensus pattern (27 bp):
TAATAATAATAATATTATTGATATCAT
Found at i:54632 original size:31 final size:32
Alignment explanation
Indices: 54588--54679 Score: 98
Period size: 31 Copynumber: 2.8 Consensus size: 32
54578 AATAATAATA
*
54588 TTAATGATATCATTAATAATAAATAAGT-TTTTC
1 TTAAT-AT-TCATTAATAATAAATAAATGTTTTC
*
54621 TTAATATTCATTAATAAT-AATAAATGTTTTG
1 TTAATATTCATTAATAATAAATAAATGTTTTC
* *
54652 ATAATATTAATAATAATAATAAATAAAT
1 TTAATATTCAT--TAATAATAAATAAAT
54680 AAAAGGAGAC
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
30 6 0.12
31 24 0.47
32 2 0.04
33 12 0.24
34 7 0.14
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.43
Consensus pattern (32 bp):
TTAATATTCATTAATAATAAATAAATGTTTTC
Found at i:55682 original size:29 final size:30
Alignment explanation
Indices: 55630--56034 Score: 316
Period size: 30 Copynumber: 13.8 Consensus size: 30
55620 GGAGGTCCCT
** *
55630 AAACATTCCAAAAATTTTACTTTTAACCTCG
1 AAAC-TTCCAAAAATTCCATTTTTAACCTCG
* * *
55661 AAACTTCTAAAAATTCTATTTTTACCCTCG
1 AAACTTCCAAAAATTCCATTTTTAACCTCG
* * * *
55691 -AACTTCC-AAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTAACCTCG
* *
55719 AAACTTCCAAAAATTCTAATTTT-ACACTCG
1 AAACTTCCAAAAATTCCATTTTTAAC-CTCG
* *
55749 -AATTTCCAAAAATTCCA-TTTTAACCTCA
1 AAACTTCCAAAAATTCCATTTTTAACCTCG
* * *
55777 AAACTTCAAAAAAATT-CA-TTTT-ACCCCC
1 AAACTTC-CAAAAATTCCATTTTTAACCTCG
* * * *
55805 AAATTTCCAAAAAATCCATTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTTAACCTCG
* * * * *
55835 AAACATCTAAACATTTCATTTTTACCCTCG
1 AAACTTCCAAAAATTCCATTTTTAACCTCG
* * *
55865 -AATTTCCAAAAATCCCATTTTTAACCCCG
1 AAACTTCCAAAAATTCCATTTTTAACCTCG
* *
55894 AAACTTCCAAAAATTCCATTTTT-ACCCCT
1 AAACTTCCAAAAATTCCATTTTTAACCTCG
* * *
55923 AAATTTCCAAGAATCCCATTTTTAACC-CTG
1 AAACTTCCAAAAATTCCATTTTTAACCTC-G
*
55953 AAACTTCCAAAAATTCCATTTTTACCCTCG
1 AAACTTCCAAAAATTCCATTTTTAACCTCG
* *
55983 -AACTTCCAAAAA-TCTCATTTTTGACC-CTA
1 AAACTTCCAAAAATTC-CATTTTTAACCTC-G
*
56012 AAACTTACAAAAATTCCATTTTT
1 AAACTTCCAAAAATTCCATTTTT
56035 CCCTTAACCT
Statistics
Matches: 298, Mismatches: 59, Indels: 35
0.76 0.15 0.09
Matches are distributed among these distances:
27 6 0.02
28 37 0.12
29 115 0.39
30 133 0.45
31 7 0.02
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34
Consensus pattern (30 bp):
AAACTTCCAAAAATTCCATTTTTAACCTCG
Found at i:55731 original size:58 final size:59
Alignment explanation
Indices: 55650--56150 Score: 450
Period size: 59 Copynumber: 8.6 Consensus size: 59
55640 AAAATTTTAC
* * * * *
55650 TTTTAACCTCGAAACTTCTAAAAATTCTATTTTTACCCTCGAACTTCC-AAAATCCCAT
1 TTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCGAATTTCCAAAAATCCCAT
* * * * *
55708 TTTTGACCCCAAAACTTCCAAAAATTCTAATTTTACACTCGAATTTCCAAAAATTCCA-
1 TTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCGAATTTCCAAAAATCCCAT
* * * *
55766 TTTTAACCTCAAAACTTCAAAAAAATT-CA-TTTTACCCCCAAATTTCCAAAAAAT-CCAT
1 TTTTAACCCCAAAACTTC-CAAAAATTCCATTTTTACCCTCGAATTTCC-AAAAATCCCAT
* * * *
55824 TTTTAACCCCAAAACATCTAAACATTTCATTTTTACCCTCGAATTTCCAAAAATCCCAT
1 TTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCGAATTTCCAAAAATCCCAT
* * *
55883 TTTTAACCCCGAAACTTCCAAAAATTCCATTTTTACCC-CTAAATTTCCAAGAATCCCAT
1 TTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCTC-GAATTTCCAAAAATCCCAT
** * *
55942 TTTTAACCCTGAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCTCAT
1 TTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCGAATTTCCAAAAATCCCAT
* * * * **
56001 TTTTGACCCTAAAACTTACAAAAATTCCATTTTT-CCCT-TAACCTCC-AAAATCTCCAT
1 TTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCGAATTTCCAAAAATC-CCAT
** * * * * * * *
56058 TTTCGATCTCGAAAC-TCTCAAAATTTCC-CTTTTACTCC-CGAATGTCCAAAAATTCCAT
1 TTTTAACCCCAAAACTTC-CAAAAATTCCATTTTTAC-CCTCGAATTTCCAAAAATCCCAT
* ** *
56116 TTTTAAACCCCGAATTTTCCCAAAATTACCATTTT
1 TTTT-AACCCCAAAACTTCCAAAAATT-CCATTTT
56151 GCCTCGGATA
Statistics
Matches: 364, Mismatches: 60, Indels: 35
0.79 0.13 0.08
Matches are distributed among these distances:
56 11 0.03
57 53 0.15
58 107 0.29
59 185 0.51
60 5 0.01
61 3 0.01
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (59 bp):
TTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCGAATTTCCAAAAATCCCAT
Found at i:56017 original size:30 final size:28
Alignment explanation
Indices: 55626--56038 Score: 277
Period size: 29 Copynumber: 14.1 Consensus size: 28
55616 CCTTGGAGGT
* *
55626 CCCT-AAACATTCCAAAAATTTTACTTTTA
1 CCCTCAAAC-TTCCAAAAA-TTCATTTTTA
* *
55655 ACCTCGAAACTTCTAAAAATTCTATTTTTA
1 CCCTC-AAACTTCCAAAAATTC-ATTTTTA
* *
55685 CCCTCGAACTTCC-AAAATCCCATTTTTGA
1 CCCTCAAACTTCCAAAAAT-TCATTTTT-A
*
55714 CCC-CAAAACTTCCAAAAATTCTAATTTTA
1 CCCTC-AAACTTCCAAAAATTC-ATTTTTA
* * *
55743 CACTCGAATTTCCAAAAATTCCA-TTTTA
1 CCCTCAAACTTCCAAAAATT-CATTTTTA
* *
55771 ACCTCAAAACTTCAAAAAAATTCA-TTTTA
1 CCCTC-AAACTTC-CAAAAATTCATTTTTA
* * *
55800 CCCCCAAATTTCCAAAAAATCCATTTTTAA
1 CCCTCAAACTTCC-AAAAATTCATTTTT-A
* * *
55830 CCC-CAAAACATCTAAACATTTCATTTTTA
1 CCCTC-AAACTTCCAAA-AATTCATTTTTA
* * *
55859 CCCTCGAATTTCCAAAAATCCCATTTTTAA
1 CCCTCAAACTTCCAAAAAT-TCATTTTT-A
55889 CCC-CGAAACTTCCAAAAATTCCATTTTTA
1 CCCTC-AAACTTCCAAAAATT-CATTTTTA
* * *
55918 CCC-CTAAATTTCCAAGAATCCCATTTTTAA
1 CCCTC-AAACTTCCAAAAAT-TCATTTTT-A
*
55948 CCCTGAAACTTCCAAAAATTCCATTTTTA
1 CCCTCAAACTTCCAAAAATT-CATTTTTA
*
55977 CCCTCGAACTTCCAAAAATCTCATTTTTGA
1 CCCTCAAACTTCCAAAAAT-TCATTTTT-A
* *
56007 CCCTAAAACTTACAAAAATTCCATTTTT-
1 CCCTCAAACTTCCAAAAATT-CATTTTTA
56035 CCCT
1 CCCT
56039 TAACCTCCAA
Statistics
Matches: 304, Mismatches: 51, Indels: 59
0.73 0.12 0.14
Matches are distributed among these distances:
28 40 0.13
29 133 0.44
30 127 0.42
31 4 0.01
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.34
Consensus pattern (28 bp):
CCCTCAAACTTCCAAAAATTCATTTTTA
Found at i:56119 original size:29 final size:27
Alignment explanation
Indices: 55669--56150 Score: 213
Period size: 29 Copynumber: 16.5 Consensus size: 27
55659 CGAAACTTCT
*
55669 AAAAATTCTATTTTTACCCTCGAACTTCC
1 AAAAATTCCATTTTTACCC-CGAA-TTCC
* *
55698 -AAAATCCCATTTTTGACCCCAAAACTTCC
1 AAAAATTCCATTTTT-ACCCC-GAA-TTCC
* * *
55727 AAAAATTCTAATTTTACACTCGAATTTCC
1 AAAAATTCCATTTTTAC-CCCGAA-TTCC
* ** *
55756 AAAAATTCCATTTTAACCTCAAAACTTCAA
1 AAAAATTCCATTTTTACC-CCGAA-TTC-C
*
55786 AAAAATT-CA-TTTTACCCCCAAATTTCC
1 AAAAATTCCATTTTTA-CCCCGAA-TTCC
* * * *
55813 AAAAAATCCATTTTTAACCCCAAAACATCT
1 AAAAATTCCATTTTT-ACCCC-GAA-TTCC
* *
55843 AAACATTTCATTTTTACCCTCGAATTTCC
1 AAAAATTCCATTTTTACCC-CGAA-TTCC
*
55872 AAAAATCCCATTTTTAACCCCGAAACTTCC
1 AAAAATTCCATTTTT-ACCCCG-AA-TTCC
*
55902 AAAAATTCCATTTTTACCCCTAAATTTCC
1 AAAAATTCCATTTTTACCCC-GAA-TTCC
* * *
55931 AAGAATCCCATTTTTAACCCTGAAACTTCC
1 AAAAATTCCATTTTT-ACCCCG-AA-TTCC
55961 AAAAATTCCATTTTTACCCTCGAACTTCC
1 AAAAATTCCATTTTTACCC-CGAA-TTCC
** *
55990 AAAAA-TCTCATTTTTGACCCTAAAACTTAC
1 AAAAATTC-CATTTTT-ACCC-CGAA-TTCC
** *
56020 AAAAATTCCATTTTT-CCCTTAACCTCC
1 AAAAATTCCATTTTTACCCCGAA-TTCC
* * * *
56047 -AAAATCTCCATTTTCGATCTCGAAACTCTC
1 AAAAAT-TCCATTTT-TACCCCG-AATTC-C
* *
56077 AAAATTTCC-CTTTTACTCCCGAATGTCC
1 AAAAATTCCATTTTTAC-CCCGAAT-TCC
56105 AAAAATTCCATTTTTAAACCCCGAATTTTCC
1 AAAAATTCCATTTTT--ACCCCGAA--TTCC
*
56136 CAAAATTACCATTTT
1 AAAAATT-CCATTTT
56151 GCCTCGGATA
Statistics
Matches: 350, Mismatches: 68, Indels: 67
0.72 0.14 0.14
Matches are distributed among these distances:
26 5 0.01
27 19 0.05
28 44 0.13
29 135 0.39
30 122 0.35
31 17 0.05
32 8 0.02
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (27 bp):
AAAAATTCCATTTTTACCCCGAATTCC
Found at i:72014 original size:77 final size:77
Alignment explanation
Indices: 71881--72026 Score: 193
Period size: 77 Copynumber: 1.9 Consensus size: 77
71871 GCCAAAACAA
* * * * *
71881 AAACACGCAAATCTAATTGCAACGATATTATTGTCAATATAAGAGGACGTGAGATTAAATATATT
1 AAACACGCAAATCTAACTGCAACGATATTATTATCAATATAAAAAGACATGAGATTAAATATATT
71946 GAAGCGTAGGAG
66 GAAGCGTAGGAG
* ** * * *
71958 AAACACGCTAATCTAACTGCATTGATATTATTATCAATGTAAAAAGACATGTGATTAAATATGTT
1 AAACACGCAAATCTAACTGCAACGATATTATTATCAATATAAAAAGACATGAGATTAAATATATT
72023 GAAG
66 GAAG
72027 TGTGAACCCC
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
77 58 1.00
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.29
Consensus pattern (77 bp):
AAACACGCAAATCTAACTGCAACGATATTATTATCAATATAAAAAGACATGAGATTAAATATATT
GAAGCGTAGGAG
Found at i:73446 original size:17 final size:17
Alignment explanation
Indices: 73424--73457 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
73414 TTTTTTTCTA
73424 TTTAAATTTAGTTCTTT
1 TTTAAATTTAGTTCTTT
73441 TTTAAATTTAGTTCTTT
1 TTTAAATTTAGTTCTTT
73458 ACTTACTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.65
Consensus pattern (17 bp):
TTTAAATTTAGTTCTTT
Found at i:76556 original size:88 final size:87
Alignment explanation
Indices: 76413--76580 Score: 239
Period size: 88 Copynumber: 1.9 Consensus size: 87
76403 AACTTTTTTT
* * * *
76413 AAAAAATAATTAAGTCCTTTTTTTTTTTACACTCAATTGAGCACTTGAACTTTCAAAATTCATAA
1 AAAAAATAATTAAGCCCTTTTTTTTTCTACACTAAATTGAGCACTTGAACTTTCAAAATGCATAA
*
76478 AAAA-ACCCCTCAAATTCCTTA
66 AAAATAACCCTCAAATTCCTTA
* * *
76499 AAAAAATAATTAAGCCCTTGCTTTTTTTCTCCATTAAATTGAGTACTTGAACTTTCAAAATGCAT
1 AAAAAATAATTAAGCCCTT--TTTTTTTCTACACTAAATTGAGCACTTGAACTTTCAAAATGCAT
76564 AAAAAATAACCCTCAAA
64 AAAAAATAACCCTCAAA
76581 AATTTTCAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
86 18 0.25
88 44 0.62
89 9 0.13
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.35
Consensus pattern (87 bp):
AAAAAATAATTAAGCCCTTTTTTTTTCTACACTAAATTGAGCACTTGAACTTTCAAAATGCATAA
AAAATAACCCTCAAATTCCTTA
Found at i:76979 original size:18 final size:18
Alignment explanation
Indices: 76948--76984 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
76938 AGTTTTATAA
76948 ATTTTTTACGAATTTTAT
1 ATTTTTTACGAATTTTAT
76966 ATTTTCTTAC-AATTTTAT
1 ATTTT-TTACGAATTTTAT
76984 A
1 A
76985 AAAATTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.30, C:0.08, G:0.03, T:0.59
Consensus pattern (18 bp):
ATTTTTTACGAATTTTAT
Found at i:77062 original size:10 final size:10
Alignment explanation
Indices: 77020--77096 Score: 52
Period size: 10 Copynumber: 8.0 Consensus size: 10
77010 TATATATTAT
*
77020 ATAATTTTTT
1 ATAATTTTTA
* *
77030 ACAATTTTTT
1 ATAATTTTTA
77040 AT-ATTTTT-
1 ATAATTTTTA
*
77048 CTAATTTTTA
1 ATAATTTTTA
77058 ATAATTTTTA
1 ATAATTTTTA
* **
77068 TTAAAATTTA
1 ATAATTTTTA
*
77078 ATAATATTT-
1 ATAATTTTTA
*
77087 ATAACTTTTA
1 ATAATTTTTA
77097 TTTATTTTAT
Statistics
Matches: 53, Mismatches: 11, Indels: 6
0.76 0.16 0.09
Matches are distributed among these distances:
8 1 0.02
9 19 0.36
10 33 0.62
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (10 bp):
ATAATTTTTA
Found at i:77240 original size:88 final size:87
Alignment explanation
Indices: 77139--77306 Score: 194
Period size: 89 Copynumber: 1.9 Consensus size: 87
77129 AAACGAAGGT
*** * * *
77139 TTAATTAC-ATTTTTGAAAAAAATTAGAAATTGTTTTTGATGCATTTTAAAAGTTCAAATATCCA
1 TTAATTACTATTTTTGAAAAAAATTA-AAAACCTTTTTAATGCATTTTAAAAATTCAAATACCCA
*
77203 ATTAAAAGAAAAAAAAATAAAAAC
65 ACT-AAAGAAAAAAAAATAAAAAC
* * * *
77227 TTAATTGCTTTTTTTTGAAAAAAATTAAAAACCTTTTTAATGTATTTTAAAAATTCAAGTACCCA
1 TTAATTAC-TATTTTTGAAAAAAATTAAAAACCTTTTTAATGCATTTTAAAAATTCAAATACCCA
*
77292 ACTAAATAAAAAAAA
65 ACTAAAGAAAAAAAA
77307 CTTAATTACT
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
88 18 0.27
89 32 0.48
90 16 0.24
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.36
Consensus pattern (87 bp):
TTAATTACTATTTTTGAAAAAAATTAAAAACCTTTTTAATGCATTTTAAAAATTCAAATACCCAA
CTAAAGAAAAAAAAATAAAAAC
Found at i:78394 original size:6 final size:6
Alignment explanation
Indices: 78385--78415 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
78375 ATATATGTAT
*
78385 AGTAGG AGTAGG AGTAGG AGTAGG AGAAGG A
1 AGTAGG AGTAGG AGTAGG AGTAGG AGTAGG A
78416 AGGTTTTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.48, T:0.13
Consensus pattern (6 bp):
AGTAGG
Found at i:78878 original size:26 final size:25
Alignment explanation
Indices: 78831--78879 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
78821 TAAATTAATT
78831 AATAATAATATATATACGATATTAA
1 AATAATAATATATATACGATATTAA
*
78856 AATAATATATATATATACTATATT
1 AATAATA-ATATATATACGATATT
78880 GTGAGTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (25 bp):
AATAATAATATATATACGATATTAA
Found at i:80679 original size:12 final size:11
Alignment explanation
Indices: 80651--80744 Score: 51
Period size: 10 Copynumber: 8.7 Consensus size: 11
80641 TTTTGAACTG
80651 AAATTA-TTAT
1 AAATTATTTAT
80661 AATATTATTTAT
1 AA-ATTATTTAT
80673 ATAATTATTTA-
1 A-AATTATTTAT
*
80684 AAA-GATATT-T
1 AAATTAT-TTAT
80694 AAA-TA-TTA-
1 AAATTATTTAT
80702 AAATTACTTTAT
1 AAATTA-TTTAT
*
80714 ATTAATTATTTAC
1 A--AATTATTTAT
*
80727 AAA-TATTTAA
1 AAATTATTTAT
80737 AAATTATT
1 AAATTATT
80745 CAATGTATCA
Statistics
Matches: 67, Mismatches: 4, Indels: 25
0.70 0.04 0.26
Matches are distributed among these distances:
8 5 0.07
9 4 0.06
10 19 0.28
11 14 0.21
12 14 0.21
13 6 0.09
14 5 0.07
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (11 bp):
AAATTATTTAT
Found at i:80713 original size:41 final size:42
Alignment explanation
Indices: 80655--80743 Score: 121
Period size: 41 Copynumber: 2.1 Consensus size: 42
80645 GAACTGAAAT
80655 TATTATAATATTATTTATA-TAATTATTTAAAAGATATTTAAA
1 TATTATAATATTATTTATATTAATTATTTAAAA-ATATTTAAA
*
80697 TATTA-AA-ATTACTTTATATTAATTATTTACAAATATTTAAA
1 TATTATAATATTA-TTTATATTAATTATTTAAAAATATTTAAA
*
80738 AATTAT
1 TATTAT
80744 TCAATGTATC
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
40 4 0.10
41 21 0.50
42 17 0.40
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.49
Consensus pattern (42 bp):
TATTATAATATTATTTATATTAATTATTTAAAAATATTTAAA
Found at i:81733 original size:31 final size:31
Alignment explanation
Indices: 81698--81776 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
81688 GGATATCAAA
* *
81698 AAGTTTAAATACCAACTTAAAAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAAAAAAAAGTGTC
* ** *
81729 AAGTTTAGGTACCAAATTAGGAAGAAGTGTC
1 AAGTTTAAGTACCAAATTAAAAAAAAGTGTC
*
81760 AAGTTCAAGTACCAAAT
1 AAGTTTAAGTACCAAAT
81777 AATATATTAA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.46, C:0.13, G:0.16, T:0.25
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAAAAAAAAGTGTC
Found at i:83984 original size:11 final size:12
Alignment explanation
Indices: 83955--83984 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
83945 TATTTTAGAA
83955 CAAAAAAGGTGT
1 CAAAAAAGGTGT
83967 CAAAAAAGGTGT
1 CAAAAAAGGTGT
83979 CGAAAA
1 C-AAAA
83985 TTTGAGAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.53, C:0.10, G:0.23, T:0.13
Consensus pattern (12 bp):
CAAAAAAGGTGT
Found at i:84533 original size:18 final size:18
Alignment explanation
Indices: 84512--84546 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
84502 AAAAAGAAGG
84512 AAAAT-AATAAAATAATAT
1 AAAATAAAT-AAATAATAT
84530 AAAATAAATAAATAATA
1 AAAATAAATAAATAATA
84547 AAAGGGGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAATAAATAAATAATAT
Found at i:88917 original size:17 final size:16
Alignment explanation
Indices: 88887--88920 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
88877 TGCTTTCAGG
*
88887 TTTTTTTATTTTTTAA
1 TTTTTTTATATTTTAA
88903 TTTTTTTAGTATTTTAA
1 TTTTTTTA-TATTTTAA
88920 T
1 T
88921 AATATTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTTTTTATATTTTAA
Found at i:93149 original size:6 final size:7
Alignment explanation
Indices: 93132--93165 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
93122 CAAAAAAATC
93132 TTTTTTA
1 TTTTTTA
93139 TTTTTTA
1 TTTTTTA
93146 -TTTTTA
1 TTTTTTA
93152 TTTTTTA
1 TTTTTTA
93159 TTTTTTA
1 TTTTTTA
93166 AATATTGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTTA
Found at i:93151 original size:13 final size:13
Alignment explanation
Indices: 93133--93163 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
93123 AAAAAAATCT
93133 TTTTTATTTTTTA
1 TTTTTATTTTTTA
93146 TTTTTATTTTTTA
1 TTTTTATTTTTTA
93159 TTTTT
1 TTTTT
93164 TAAATATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:95368 original size:15 final size:15
Alignment explanation
Indices: 95348--95379 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
95338 AATCATTGGG
95348 TTGAGCCTGAAAAGT
1 TTGAGCCTGAAAAGT
*
95363 TTGAGCCTGAAAGGT
1 TTGAGCCTGAAAAGT
95378 TT
1 TT
95380 ATGAACAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.31
Consensus pattern (15 bp):
TTGAGCCTGAAAAGT
Found at i:97252 original size:53 final size:50
Alignment explanation
Indices: 97184--97323 Score: 124
Period size: 53 Copynumber: 2.7 Consensus size: 50
97174 CCTAAAAAAA
* * * *
97184 TTTAC-TCCCCAAACCCTCAAAACTTTTTTCTTTTATTTTTCTCTCTAAAATT
1 TTTACTTCCTCAAACCC-CAAAACTTTTTTCTTTTACTTTTC-C-CCAAAACT
* * *
97236 TTTACTTCCTCAAACCCCCCTAAAC-TTTTCCTTTTACTTTTCCCCGAAACT
1 TTTACTTCCTCAAA--CCCCAAAACTTTTTTCTTTTACTTTTCCCCAAAACT
97287 TTTACTTCCTCCGAAACCCCAAAAACTTTTTT-TTTTA
1 TTTACTTCCT-C-AAACCCC-AAAACTTTTTTCTTTTA
97324 ATTTATGTCT
Statistics
Matches: 72, Mismatches: 9, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
51 19 0.26
52 16 0.22
53 29 0.40
54 5 0.07
55 3 0.04
ACGTcount: A:0.24, C:0.31, G:0.01, T:0.44
Consensus pattern (50 bp):
TTTACTTCCTCAAACCCCAAAACTTTTTTCTTTTACTTTTCCCCAAAACT
Found at i:97951 original size:57 final size:57
Alignment explanation
Indices: 97863--97976 Score: 131
Period size: 57 Copynumber: 2.0 Consensus size: 57
97853 CATTTTCAGG
* ** * *
97863 TCATTTTCATTTTGGAAAAAACCACGTTCATTTCCAAATGA-TTCCATTTCTCTATTT
1 TCATTTTCAATTTGGAAAAAACCACAATCATTTACAAAT-ATTTCCATTTCTCCATTT
* * * *
97920 TCATTTTCAATTTGGAGAAAACTATAATCATTTACAAATATTTTCATTTCTCCATTT
1 TCATTTTCAATTTGGAAAAAACCACAATCATTTACAAATATTTCCATTTCTCCATTT
97977 CACCATTTCT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
56 1 0.02
57 46 0.98
ACGTcount: A:0.31, C:0.18, G:0.06, T:0.45
Consensus pattern (57 bp):
TCATTTTCAATTTGGAAAAAACCACAATCATTTACAAATATTTCCATTTCTCCATTT
Found at i:104025 original size:15 final size:16
Alignment explanation
Indices: 103986--104029 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
103976 AGCTTATGAC
*
103986 CTTTTGTTAAAATTAA
1 CTTTTGTTAAAATCAA
* *
104002 ATATTGTTAAAA-CAA
1 CTTTTGTTAAAATCAA
104017 CTTTTGTTAAAAT
1 CTTTTGTTAAAAT
104030 AATGACACTT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (16 bp):
CTTTTGTTAAAATCAA
Found at i:104904 original size:28 final size:27
Alignment explanation
Indices: 104827--104904 Score: 66
Period size: 28 Copynumber: 2.8 Consensus size: 27
104817 TCAATTTTTA
* *
104827 TATATATTAGATTTTTTAATAAATAAT
1 TATATATTAGATTTTTAAATATATAAT
* * * ** *
104854 AATTTTTTAGAGTTTTTGCATATTTAATT
1 TATATATTAGA-TTTTTAAATATATAA-T
104883 TATATATTAGATTTTTAAATAT
1 TATATATTAGATTTTTAAATAT
104905 CTTTTAAAGT
Statistics
Matches: 37, Mismatches: 12, Indels: 3
0.71 0.23 0.06
Matches are distributed among these distances:
27 8 0.22
28 20 0.54
29 9 0.24
ACGTcount: A:0.37, C:0.01, G:0.06, T:0.55
Consensus pattern (27 bp):
TATATATTAGATTTTTAAATATATAAT
Found at i:110184 original size:24 final size:24
Alignment explanation
Indices: 110123--110185 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
110113 TAGACTAATA
* *
110123 AGAATTTAACTCAAACAACTAAAC
1 AGAATTTAACTGAAACAAATAAAC
*
110147 AGAATTTAATTGAAACAAATAAAC
1 AGAATTTAACTGAAACAAATAAAC
*
110171 AGAGTTTAACTGAAA
1 AGAATTTAACTGAAA
110186 GATTACTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.54, C:0.13, G:0.10, T:0.24
Consensus pattern (24 bp):
AGAATTTAACTGAAACAAATAAAC
Found at i:117053 original size:16 final size:17
Alignment explanation
Indices: 117020--117053 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
117010 TATTACGGAC
117020 ATAGTTATTCTCGAACA
1 ATAGTTATTCTCGAACA
*
117037 ATAGTTGTTCT-GAACA
1 ATAGTTATTCTCGAACA
117053 A
1 A
117054 CAACTATTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (17 bp):
ATAGTTATTCTCGAACA
Found at i:120179 original size:7 final size:7
Alignment explanation
Indices: 120167--120191 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
120157 CTCGCCTTGG
120167 ATTAATT
1 ATTAATT
120174 ATTAATT
1 ATTAATT
120181 ATTAATT
1 ATTAATT
120188 ATTA
1 ATTA
120192 GTTTTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
ATTAATT
Found at i:121887 original size:13 final size:11
Alignment explanation
Indices: 121860--121902 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
121850 AGTTAAATAT
121860 TATTTTATTAA
1 TATTTTATTAA
121871 TATTTTACTTAA
1 TATTTTA-TTAA
*
121883 -ATATTTATTAT
1 TAT-TTTATTAA
121894 TATTTTATT
1 TATTTTATT
121903 TAGAAAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:122161 original size:20 final size:22
Alignment explanation
Indices: 122119--122161 Score: 54
Period size: 20 Copynumber: 2.0 Consensus size: 22
122109 TTTTGAAGAA
* *
122119 AGAAAATAGTAGATGAAAGAGG
1 AGAAAATAGTAGAAGAAAAAGG
122141 AGAAAAT-G-AGAAGAAAAAGG
1 AGAAAATAGTAGAAGAAAAAGG
122161 A
1 A
122162 AGGAAAGTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 11 0.58
21 1 0.05
22 7 0.37
ACGTcount: A:0.60, C:0.00, G:0.30, T:0.09
Consensus pattern (22 bp):
AGAAAATAGTAGAAGAAAAAGG
Found at i:131167 original size:6 final size:6
Alignment explanation
Indices: 131156--131183 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
131146 TTAAATGAGT
131156 CTATTC CTATTC CTATTC CTATTC CTAT
1 CTATTC CTATTC CTATTC CTATTC CTAT
131184 ACACATCCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.32, G:0.00, T:0.50
Consensus pattern (6 bp):
CTATTC
Found at i:134296 original size:59 final size:59
Alignment explanation
Indices: 134127--134317 Score: 199
Period size: 60 Copynumber: 3.2 Consensus size: 59
134117 TTAATATAAC
134127 ATTTGGTACCTGAACTTGATATTTTTT--TTAATTTGGTATACCTAAACTTTTTTTGACTCA
1 ATTTGGTACCTGAACTTGATATTTTTTCCTT-ATTTGGTAT--CTAAACTTTTTTTGACTCA
* * * * * * * *
134187 ATTTGATTCTTGAACTTGACACTTTTTCCTAATTTGATACCTAAACTTTTTTTGGAC-CAA
1 ATTTGGTACCTGAACTTGATATTTTTTCCTTATTTGGTATCTAAACTTTTTTT-GACTC-A
** * *
134247 ATTTGGTACCTGAACTTGATATTTTTTCCTTATTTGGTATCTAAGTTTTTTTTAGATTTA
1 ATTTGGTACCTGAACTTGATATTTTTTCCTTATTTGGTATCTAAACTTTTTTT-GACTCA
134307 ATTTGGTACCT
1 ATTTGGTACCT
134318 AAATTTATTA
Statistics
Matches: 105, Mismatches: 21, Indels: 10
0.77 0.15 0.07
Matches are distributed among these distances:
59 14 0.13
60 83 0.79
61 7 0.07
62 1 0.01
ACGTcount: A:0.24, C:0.14, G:0.12, T:0.50
Consensus pattern (59 bp):
ATTTGGTACCTGAACTTGATATTTTTTCCTTATTTGGTATCTAAACTTTTTTTGACTCA
Found at i:134592 original size:31 final size:31
Alignment explanation
Indices: 134523--134604 Score: 112
Period size: 30 Copynumber: 2.7 Consensus size: 31
134513 GGACCCTAAA
* * *
134523 AAGTTTAAGTACCAATTTAAAAAAAAATGTT
1 AAGTTTAAGTACCAAATTAAAAAAAAATATC
*
134554 AA-ATTAAGTACCAAATTAAAAAAAAATATC
1 AAGTTTAAGTACCAAATTAAAAAAAAATATC
*
134584 AAGTTTAAGTACGAAATTAAA
1 AAGTTTAAGTACCAAATTAAA
134605 CCAAAAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
30 26 0.59
31 18 0.41
ACGTcount: A:0.56, C:0.07, G:0.09, T:0.28
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAAAAAAAAATATC
Found at i:135134 original size:11 final size:11
Alignment explanation
Indices: 135118--135164 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
135108 CCTCAAAAAA
135118 TTATAAAATAT
1 TTATAAAATAT
135129 TTATAAAATAT
1 TTATAAAATAT
*
135140 TTTTCCAAAA-AT
1 TTAT--AAAATAT
135152 TTAT-AAATAT
1 TTATAAAATAT
135162 TTA
1 TTA
135165 AATTCAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
9 3 0.10
10 5 0.16
11 14 0.45
12 5 0.16
13 4 0.13
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (11 bp):
TTATAAAATAT
Found at i:136673 original size:172 final size:173
Alignment explanation
Indices: 136387--136735 Score: 655
Period size: 172 Copynumber: 2.0 Consensus size: 173
136377 AGAATGTTCA
* * *
136387 TTTTCTTAGTATACTATGTGGTTGCAGCATTATTTAATCTTTCATATCAGTAAAGAAATTTTCAC
1 TTTTCTTAGTATACTATGTGGTTGCAGCATTATCTAATCTTCCATATCAATAAAGAAATTTTCAC
*
136452 TATTGGAGATTATTCGTGGTTGTTCAATTACTGGATATAAGTATAGTTGTGTGAAAGTGCATGTC
66 TATTGGAGATTATTCGTGGTTGTTCAATTACTGGATATAAGTATAGTTGTATGAAAGTGCATGTC
136517 TAGGAAAAGTTTTAGCTAGGAAGGCTTGGTATTTAAAAGTGT-
131 TAGGAAAAGTTTTAGCTAGGAAGGCTTGGTATTTAAAAGTGTC
136559 TTTTCTTAGTATACTATGTGGTTGCAGCATTATCTAATCTTCCATATCAATAAAGAAATTTTCAC
1 TTTTCTTAGTATACTATGTGGTTGCAGCATTATCTAATCTTCCATATCAATAAAGAAATTTTCAC
136624 TATTGGAGATTATTCGTGGTTGTTCAATTACTGGATATAAGTATAGTTGTATGAAAGTGCATGTC
66 TATTGGAGATTATTCGTGGTTGTTCAATTACTGGATATAAGTATAGTTGTATGAAAGTGCATGTC
136689 TAGGAAAAGTTTTAGCTAGGAAGGCTTGGTATTTAAAAGTGTC
131 TAGGAAAAGTTTTAGCTAGGAAGGCTTGGTATTTAAAAGTGTC
136732 TTTT
1 TTTT
136736 TACCCAACTC
Statistics
Matches: 172, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
172 168 0.98
173 4 0.02
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (173 bp):
TTTTCTTAGTATACTATGTGGTTGCAGCATTATCTAATCTTCCATATCAATAAAGAAATTTTCAC
TATTGGAGATTATTCGTGGTTGTTCAATTACTGGATATAAGTATAGTTGTATGAAAGTGCATGTC
TAGGAAAAGTTTTAGCTAGGAAGGCTTGGTATTTAAAAGTGTC
Found at i:149470 original size:80 final size:80
Alignment explanation
Indices: 149337--149488 Score: 259
Period size: 80 Copynumber: 1.9 Consensus size: 80
149327 AACCAAATTT
* **
149337 GTCAATTCATGACACCCAGTGCCTAGCGGATAAACCGTGATAAGTGAGCCCAGCTCTAGTTGGAT
1 GTCAATTCATGACACCCAATGCCTAGCGGATAAACCGCAATAAGTGAGCCCAGCTCTAGTTGGAT
149402 TAACCAATGAAATCC
66 TAACCAATGAAATCC
* *
149417 GTCAATTCATGGCACCCAATGCCTAGCGGATAAACTGCAATAAGTGAGCCCAGCTCTAGTTGGAT
1 GTCAATTCATGACACCCAATGCCTAGCGGATAAACCGCAATAAGTGAGCCCAGCTCTAGTTGGAT
149482 TAACCAA
66 TAACCAA
149489 CGATTCTGCG
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
80 67 1.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (80 bp):
GTCAATTCATGACACCCAATGCCTAGCGGATAAACCGCAATAAGTGAGCCCAGCTCTAGTTGGAT
TAACCAATGAAATCC
Found at i:158689 original size:90 final size:87
Alignment explanation
Indices: 158539--158717 Score: 286
Period size: 90 Copynumber: 2.0 Consensus size: 87
158529 TTATTAATCT
* *
158539 AACGAGTGGTTTCAGTGGTAAAAAAGATGTTTATTTTAAGAGATTCAGGTTCGAGCACTTGTGTG
1 AACGAGTGGTTTCAGTGGTAAAAAAGATGTTTATTCTAAGAGATTCAGGTTCAAGCACTTGTGTG
* *
158604 TGCAAGGTGTGTGTGCCTTGTC
66 TGCAAGGTGTGTGTGACTTATC
*
158626 AACGAGTGGTTTCAGTGGTAAAAAAGATGTTGTTTATTCTAAGATATTCAGGTTCAAGCACTTGT
1 AACGAGTGGTTTCAGTGGTAAAAAAGA---TGTTTATTCTAAGAGATTCAGGTTCAAGCACTTGT
158691 GTGTGCAAGGTGTGTGTGACTTATC
63 GTGTGCAAGGTGTGTGTGACTTATC
158716 AA
1 AA
158718 AGGACTAAAA
Statistics
Matches: 84, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
87 27 0.32
90 57 0.68
ACGTcount: A:0.26, C:0.11, G:0.28, T:0.35
Consensus pattern (87 bp):
AACGAGTGGTTTCAGTGGTAAAAAAGATGTTTATTCTAAGAGATTCAGGTTCAAGCACTTGTGTG
TGCAAGGTGTGTGTGACTTATC
Found at i:162827 original size:21 final size:20
Alignment explanation
Indices: 162803--162893 Score: 78
Period size: 20 Copynumber: 4.5 Consensus size: 20
162793 GCCCGAAGCT
162803 ATTTTGACTTGTTTGAAAAAC
1 ATTTTGACTTGTTT-AAAAAC
**
162824 ATTTTGAAGTG-TTAAAATA-
1 ATTTTGACTTGTTTAAAA-AC
* * *
162843 ATTTTGACTTGGTTGAAATC
1 ATTTTGACTTGTTTAAAAAC
* *
162863 ATTTTGCCTTATTTAAAAAC
1 ATTTTGACTTGTTTAAAAAC
*
162883 ATTTTAACTTG
1 ATTTTGACTTG
162894 ATTTTAAAAT
Statistics
Matches: 53, Mismatches: 14, Indels: 7
0.72 0.19 0.09
Matches are distributed among these distances:
19 13 0.25
20 31 0.58
21 9 0.17
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (20 bp):
ATTTTGACTTGTTTAAAAAC
Found at i:165141 original size:16 final size:16
Alignment explanation
Indices: 165120--165152 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
165110 AAGTAATTTT
165120 TTAAAATTTTAAAAAA
1 TTAAAATTTTAAAAAA
*
165136 TTAAAATTTTTAAAAA
1 TTAAAATTTTAAAAAA
165152 T
1 T
165153 CATTGAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTAAAATTTTAAAAAA
Found at i:166580 original size:21 final size:22
Alignment explanation
Indices: 166548--166589 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
166538 ACAAGTAATA
166548 TTAAAAATTA-TTATCTATTTTT
1 TTAAAAATTATTTAT-TATTTTT
166570 TTAAAAA-TATTTATTATTTT
1 TTAAAAATTATTTATTATTTT
166590 AATATTTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
TTAAAAATTATTTATTATTTTT
Found at i:166700 original size:29 final size:31
Alignment explanation
Indices: 166640--166700 Score: 72
Period size: 29 Copynumber: 2.0 Consensus size: 31
166630 AAATATTTAT
* *
166640 AAAAATTTTAAAATTTATTTTTAAAAAAATA
1 AAAAATTCTAAAATTTATTTCTAAAAAAATA
* *
166671 AAAAATTCT-AAATTT-TTTCTGAAATAATA
1 AAAAATTCTAAAATTTATTTCTAAAAAAATA
166700 A
1 A
166701 TTTTGGGATC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 12 0.46
30 6 0.23
31 8 0.31
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (31 bp):
AAAAATTCTAAAATTTATTTCTAAAAAAATA
Found at i:167613 original size:11 final size:11
Alignment explanation
Indices: 167597--167642 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
167587 AAAATTTCAT
*
167597 AATTATAATTA
1 AATTATAAATA
167608 AATTATTAAAT-
1 AATTA-TAAATA
167619 AATTA-AAATTA
1 AATTATAAA-TA
167630 AATTATAAATA
1 AATTATAAATA
167641 AA
1 AA
167643 AAAATAGGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
9 3 0.10
10 1 0.03
11 19 0.63
12 7 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
AATTATAAATA
Found at i:167621 original size:22 final size:21
Alignment explanation
Indices: 167595--167641 Score: 76
Period size: 22 Copynumber: 2.2 Consensus size: 21
167585 TTAAAATTTC
*
167595 ATAATTATAATTAAATTATTAA
1 ATAATTAAAATTAAATTA-TAA
167617 ATAATTAAAATTAAATTATAA
1 ATAATTAAAATTAAATTATAA
167638 ATAA
1 ATAA
167642 AAAAATAGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATAATTAAAATTAAATTATAA
Found at i:171755 original size:28 final size:28
Alignment explanation
Indices: 171675--171740 Score: 132
Period size: 28 Copynumber: 2.4 Consensus size: 28
171665 CACGGTTTGG
171675 ACACACGGGCGTGTGCCACACCGTGGGC
1 ACACACGGGCGTGTGCCACACCGTGGGC
171703 ACACACGGGCGTGTGCCACACCGTGGGC
1 ACACACGGGCGTGTGCCACACCGTGGGC
171731 ACACACGGGC
1 ACACACGGGC
171741 TGGCACACGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.20, C:0.36, G:0.35, T:0.09
Consensus pattern (28 bp):
ACACACGGGCGTGTGCCACACCGTGGGC
Found at i:172811 original size:23 final size:22
Alignment explanation
Indices: 172757--172811 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
172747 TTATTTCATT
*
172757 AAATAAAATTAATTACAAATATA
1 AAAT-AAATTAAGTACAAATATA
* *
172780 AAATTAATTAAGTACTAATAATA
1 AAATAAATTAAGTACAAAT-ATA
*
172803 ACATAAATT
1 AAATAAATT
172812 CTATTATCCT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 12 0.46
23 14 0.54
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (22 bp):
AAATAAATTAAGTACAAATATA
Found at i:173738 original size:9 final size:9
Alignment explanation
Indices: 173726--173761 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
173716 AAAACCTAAA
173726 AAAAATAAT
1 AAAAATAAT
173735 AAAAATAAT
1 AAAAATAAT
*
173744 AAATAAAAAT
1 AAA-AATAAT
173754 AAAAATAA
1 AAAAATAA
173762 AATTCTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAAAATAAT
Found at i:173747 original size:16 final size:16
Alignment explanation
Indices: 173712--173762 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
173702 CAGACCCAAA
*
173712 AAATAAAACCTAAAAA-
1 AAATAAAA-ATAAAAAT
*
173728 AAATAATAAA-AATAAT
1 AAATAA-AAATAAAAAT
173744 AAATAAAAATAAAAAT
1 AAATAAAAATAAAAAT
173760 AAA
1 AAA
173763 ATTCTCAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 7 0.24
16 20 0.69
17 2 0.07
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.18
Consensus pattern (16 bp):
AAATAAAAATAAAAAT
Found at i:173753 original size:6 final size:6
Alignment explanation
Indices: 173710--173763 Score: 65
Period size: 6 Copynumber: 8.7 Consensus size: 6
173700 ACCAGACCCA
*
173710 AAAAAT AAAACCT AAAAA- AAATAAT AAAAAT AATAAAT AAAAAT AAAAAT
1 AAAAAT AAAA-AT AAAAAT AAA-AAT AAAAAT AA-AAAT AAAAAT AAAAAT
173760 AAAA
1 AAAA
173764 TTCTCAAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
5 3 0.07
6 25 0.60
7 14 0.33
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:173754 original size:19 final size:17
Alignment explanation
Indices: 173709--173763 Score: 65
Period size: 19 Copynumber: 3.0 Consensus size: 17
173699 GACCAGACCC
*
173709 AAAAAATAAAACCTAAAA
1 AAAAAATAAAA-ATAAAA
173727 AAAATAATAAAAATAATAA
1 AAAA-AATAAAAATAA-AA
173746 ATAAAAATAAAAATAAAA
1 A-AAAAATAAAAATAAAA
173764 TTCTCAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 9 0.27
19 21 0.64
20 3 0.09
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (17 bp):
AAAAAATAAAAATAAAA
Found at i:187243 original size:49 final size:49
Alignment explanation
Indices: 187190--187546 Score: 286
Period size: 49 Copynumber: 7.3 Consensus size: 49
187180 TGAAGACACA
* * *
187190 AAGGGAACGGTTTAAGTCGCAACGACGAACCTTATACCTCAAAAGCATG
1 AAGGGAAAGATTTAAGTCGCAACGGCGAACCTTATACCTCAAAAGCATG
* * * **
187239 AAGGGAAAGATTTAAGTTGCAACGGCGAATCC--AGTACCATGAAGA-CACA
1 AAGGGAAAGATTTAAGTCGCAACGGCGAA-CCTTA-TACC-TCAAAAGCATG
* * *
187288 AAGGGAATGATTTAAGTCGCAACGACGAACCTTGTACCTCAAAAGCATG
1 AAGGGAAAGATTTAAGTCGCAACGGCGAACCTTATACCTCAAAAGCATG
* * * * **
187337 AAGGGAAAGATTTAAGCCGTAACGGCGAATCC--AGTACCAC-GAAGACACA
1 AAGGGAAAGATTTAAGTCGCAACGGCGAA-CCTTA-TACCTCAAAAG-CATG
* * *
187386 AAGGGAACGATTTAAGTCGCAACGACGAACCTTGTACCTCAAAAGCATG
1 AAGGGAAAGATTTAAGTCGCAACGGCGAACCTTATACCTCAAAAGCATG
* * * * *
187435 ATGGGAAAGATTTAAGTCGCGACGGCGAATC-TAGTA--TTATAAAG-ATACA
1 AAGGGAAAGATTTAAGTCGCAACGGCGAACCTTA-TACCTCA-AAAGCAT--G
* * *
187484 AAGGGAAATG-TTTAAATTGCAATGGCGAACCTTATACCTCAAAAGCATG
1 AAGGGAAA-GATTTAAGTCGCAACGGCGAACCTTATACCTCAAAAGCATG
187533 AAGGGAAAGATTTA
1 AAGGGAAAGATTTA
187547 GGCCACAACG
Statistics
Matches: 236, Mismatches: 50, Indels: 44
0.72 0.15 0.13
Matches are distributed among these distances:
47 4 0.02
48 18 0.08
49 192 0.81
50 18 0.08
51 4 0.02
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.19
Consensus pattern (49 bp):
AAGGGAAAGATTTAAGTCGCAACGGCGAACCTTATACCTCAAAAGCATG
Found at i:187314 original size:98 final size:98
Alignment explanation
Indices: 187135--187546 Score: 601
Period size: 98 Copynumber: 4.2 Consensus size: 98
187125 AGGTTACATT
* * * *
187135 AGCAAGAAGAGAAAGATTTAAGTTGCAACGGCGAATCCAGTACCATGAAGACACAAAGGGAACGG
1 AGCATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACCATGAAGACACAAAGGGAACGA
187200 TTTAAGTCGCAACGACGAACCTTATACCTCAAA
66 TTTAAGTCGCAACGACGAACCTTATACCTCAAA
* *
187233 AGCATGAAGGGAAAGATTTAAGTTGCAACGGCGAATCCAGTACCATGAAGACACAAAGGGAATGA
1 AGCATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACCATGAAGACACAAAGGGAACGA
*
187298 TTTAAGTCGCAACGACGAACCTTGTACCTCAAA
66 TTTAAGTCGCAACGACGAACCTTATACCTCAAA
* * *
187331 AGCATGAAGGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCACGAAGACACAAAGGGAACGA
1 AGCATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACCATGAAGACACAAAGGGAACGA
*
187396 TTTAAGTCGCAACGACGAACCTTGTACCTCAAA
66 TTTAAGTCGCAACGACGAACCTTATACCTCAAA
* * * ** * * *
187429 AGCATGATGGGAAAGATTTAAGTCGCGACGGCGAATCTAGTATTATAAAGATACAAAGGGAAATG
1 AGCATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACCATGAAGACACAAAGGG-AACG
* * * *
187494 -TTTAAATTGCAATGGCGAACCTTATACCTCAAA
65 ATTTAAGTCGCAACGACGAACCTTATACCTCAAA
187527 AGCATGAAGGGAAAGATTTA
1 AGCATGAAGGGAAAGATTTA
187547 GGCCACAACG
Statistics
Matches: 286, Mismatches: 27, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
98 283 0.99
99 3 0.01
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.19
Consensus pattern (98 bp):
AGCATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACCATGAAGACACAAAGGGAACGA
TTTAAGTCGCAACGACGAACCTTATACCTCAAA
Found at i:188041 original size:9 final size:9
Alignment explanation
Indices: 188029--188064 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
188019 ATAAAACCCA
188029 AAAAATAAT
1 AAAAATAAT
188038 AAAAATAAT
1 AAAAATAAT
*
188047 AAATAAAAAT
1 AAA-AATAAT
188057 AAAAATAA
1 AAAAATAA
188065 AATTCTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAAAATAAT
Found at i:188047 original size:12 final size:12
Alignment explanation
Indices: 188028--188066 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
188018 AATAAAACCC
188028 AAAA-AATAATA
1 AAAATAATAATA
188039 AAAATAATAAATA
1 AAAATAAT-AATA
*
188052 AAAATAAAAATA
1 AAAATAATAATA
188064 AAA
1 AAA
188067 TTCTCAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 4 0.16
12 10 0.40
13 11 0.44
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (12 bp):
AAAATAATAATA
Found at i:188051 original size:13 final size:12
Alignment explanation
Indices: 188035--188066 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
188025 CCCAAAAAAT
188035 AATAAAAATAATA
1 AATAAAAATAA-A
188048 AATAAAAATAAA
1 AATAAAAATAAA
188060 AATAAAA
1 AATAAAA
188067 TTCTCAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (12 bp):
AATAAAAATAAA
Found at i:188056 original size:6 final size:6
Alignment explanation
Indices: 188035--188066 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
188025 CCCAAAAAAT
188035 AATAAA AATAATA AATAAA AATAAA AATAAA A
1 AATAAA AATAA-A AATAAA AATAAA AATAAA A
188067 TTCTCAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
AATAAA
Found at i:193496 original size:32 final size:32
Alignment explanation
Indices: 193455--193524 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
193445 TTAATACACC
*
193455 TATGGTTAGTTCTTTGGTTTTGTCAAAGGTTG
1 TATGGTTAGTTCTTTGGTTTTGTCAAAGGATG
193487 TATGGTTAGTTCTTTGGTTTTGTCAAAGGATG
1 TATGGTTAGTTCTTTGGTTTTGTCAAAGGATG
193519 TA-GGTT
1 TATGGTT
193525 CGCCAATGTC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 4 0.11
32 33 0.89
ACGTcount: A:0.17, C:0.06, G:0.29, T:0.49
Consensus pattern (32 bp):
TATGGTTAGTTCTTTGGTTTTGTCAAAGGATG
Found at i:196206 original size:16 final size:17
Alignment explanation
Indices: 196193--196237 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
196183 GCTTGTTCCA
196193 AACAT-GAGTTGTTCTC
1 AACATAGAGTTGTTCTC
* *
196209 AACATAGAGTTCTT-TG
1 AACATAGAGTTGTTCTC
196225 AACA-AGAGTTGTT
1 AACATAGAGTTGTT
196238 TTGTGACGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 8 0.32
16 10 0.40
17 7 0.28
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (17 bp):
AACATAGAGTTGTTCTC
Found at i:197646 original size:16 final size:16
Alignment explanation
Indices: 197625--197657 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
197615 ATAAGAGTCG
197625 TATCATCCAATGAAAA
1 TATCATCCAATGAAAA
197641 TATCATCCAATGAAAA
1 TATCATCCAATGAAAA
197657 T
1 T
197658 GTCAAATCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.18, G:0.06, T:0.27
Consensus pattern (16 bp):
TATCATCCAATGAAAA
Found at i:199772 original size:15 final size:15
Alignment explanation
Indices: 199752--199789 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
199742 TCATAAACGC
*
199752 CATTATTTTTAGTGG
1 CATTATTTTTAGCGG
*
199767 CATTATCTTTAGCGG
1 CATTATTTTTAGCGG
199782 CATT-TTTT
1 CATTATTTT
199790 GCGGTGCTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 3 0.15
15 17 0.85
ACGTcount: A:0.18, C:0.13, G:0.16, T:0.53
Consensus pattern (15 bp):
CATTATTTTTAGCGG
Found at i:202440 original size:12 final size:12
Alignment explanation
Indices: 202423--202450 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
202413 CAATTAAGGG
202423 TAGTAATTGACT
1 TAGTAATTGACT
202435 TAGTAATTGACT
1 TAGTAATTGACT
202447 TAGT
1 TAGT
202451 TGATAATTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.43
Consensus pattern (12 bp):
TAGTAATTGACT
Found at i:211533 original size:13 final size:13
Alignment explanation
Indices: 211517--211580 Score: 51
Period size: 13 Copynumber: 4.8 Consensus size: 13
211507 TGATTTAAGA
*
211517 TTTAGGGTTTGGG
1 TTTAAGGTTTGGG
211530 TTT-AGGTTTAGGG
1 TTTAAGGTTT-GGG
*
211543 -TCAATGGTTTGGG
1 TTTAA-GGTTTGGG
*
211556 ATTTTAAGTTTTGGG
1 --TTTAAGGTTTGGG
211571 TTTAAGGTTT
1 TTTAAGGTTT
211581 AATATTTTAG
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
12 6 0.15
13 19 0.47
14 5 0.12
15 7 0.17
16 3 0.08
ACGTcount: A:0.16, C:0.02, G:0.34, T:0.48
Consensus pattern (13 bp):
TTTAAGGTTTGGG
Found at i:212937 original size:13 final size:13
Alignment explanation
Indices: 212919--212943 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
212909 AAAAATATTA
212919 AAAATCATAAAAT
1 AAAATCATAAAAT
212932 AAAATCATAAAA
1 AAAATCATAAAA
212944 AATGCTTAAA
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:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATCATAAAAT
Found at i:213700 original size:19 final size:20
Alignment explanation
Indices: 213669--213709 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
213659 TAATTTTTAA
213669 ATAATATAATTTAA-TTATT
1 ATAATATAATTTAATTTATT
213688 ATAAT-TAATTTTAATTTATT
1 ATAATATAA-TTTAATTTATT
213708 AT
1 AT
213710 TCGAATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 3 0.15
19 10 0.50
20 7 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATAATATAATTTAATTTATT
Found at i:213726 original size:24 final size:24
Alignment explanation
Indices: 213671--213727 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
213661 ATTTTTAAAT
*
213671 AATATAATTTAATTATTATAATTA
1 AATATAATTTAATTATTAGAATTA
* * *
213695 ATTTTAATTT-ATTATTCGAATTTA
1 AATATAATTTAATTATTAGAA-TTA
213719 AATATAATT
1 AATATAATT
213728 AAAATATATT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 8 0.31
24 18 0.69
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
AATATAATTTAATTATTAGAATTA
Found at i:223608 original size:117 final size:115
Alignment explanation
Indices: 223481--223793 Score: 280
Period size: 117 Copynumber: 2.7 Consensus size: 115
223471 TGGTCACTCC
* * *
223481 GGGGC-AAAATGATAATTTTGTAAAAGTTAAGGGTCAAAAATGGAATTTTTAGACA-TCCGGGGG
1 GGGGCTAAAATGGTAATTTTG-AAAAATT-GGGGTCAAAAATGGAATTTTTAGA-AGTCCGGGGG
* * *
223544 T-AAAATGGTACTTTTTGGAAGAATCGAGGTCAAAAATGGAATTTTTGGAAGTTT
63 TAAAAAT-ATAATTTTTGGAAAAATCGAGGT-AAAAATGGAATTTTTGGAAGTTT
* * * * * * **
223598 AGGGG-T-AAATGGTCTATTTTGAAAAAATCGGGGTAAAAAATGGAGTTCTTGGAAGTTTGGGGG
1 -GGGGCTAAAATGGT-AATTTTG-AAAAATTGGGGTCAAAAATGGAATTTTTAGAAGTCCGGGGG
* * *
223661 TAAAAATATAATTTTTGGAAAAATTGGGGTTAAAATGGAATTTTTGGAAGTTT
63 TAAAAATATAATTTTTGGAAAAATCGAGGTAAAAATGGAATTTTTGGAAGTTT
** * *
223714 GGGGCTAAAATGGTAATTTTGGAAAAATTGGGGTCAAAAAAAGAA-TTTTAGAATGTAC-GAGGT
1 GGGGCTAAAATGGTAATTTT-GAAAAATTGGGGTCAAAAATGGAATTTTTAGAA-GTCCGGGGGT
* *
223777 AAAAATGTAATTGTTGG
64 AAAAATATAATTTTTGG
223794 GAAGTTCAAG
Statistics
Matches: 156, Mismatches: 31, Indels: 19
0.76 0.15 0.09
Matches are distributed among these distances:
115 29 0.19
116 49 0.31
117 58 0.37
118 20 0.13
ACGTcount: A:0.37, C:0.04, G:0.27, T:0.31
Consensus pattern (115 bp):
GGGGCTAAAATGGTAATTTTGAAAAATTGGGGTCAAAAATGGAATTTTTAGAAGTCCGGGGGTAA
AAATATAATTTTTGGAAAAATCGAGGTAAAAATGGAATTTTTGGAAGTTT
Found at i:223637 original size:58 final size:58
Alignment explanation
Indices: 223540--223762 Score: 217
Period size: 58 Copynumber: 3.8 Consensus size: 58
223530 TAGACATCCG
* * *
223540 GGGGTAAAATGGTACT-TTTTGGAAGAATCGAGGTCAAAAATGGAATTTTTGGAAGTTT
1 GGGGTAAAATGGT-CTATTTTGGAAAAATCGGGGTAAAAAATGGAATTTTTGGAAGTTT
* * *
223598 AGGGGT-AAATGGTCTATTTTGAAAAAATCGGGGTAAAAAATGGAGTTCTTGGAAGTTT
1 -GGGGTAAAATGGTCTATTTTGGAAAAATCGGGGTAAAAAATGGAATTTTTGGAAGTTT
* * * *
223656 GGGGGTAAAAAT-AT-AATTTTTGGAAAAATTGGGGT-TAAAATGGAATTTTTGGAAGTTT
1 -GGGGT-AAAATGGTCTA-TTTTGGAAAAATCGGGGTAAAAAATGGAATTTTTGGAAGTTT
* * *
223714 GGGGCTAAAATGGT-AATTTTGGAAAAATTGGGGTCAAAAAA-AGAATTTT
1 GGGG-TAAAATGGTCTATTTTGGAAAAATCGGGGT-AAAAAATGGAATTTT
223763 AGAATGTACG
Statistics
Matches: 139, Mismatches: 17, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
57 29 0.21
58 80 0.58
59 26 0.19
60 4 0.03
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.32
Consensus pattern (58 bp):
GGGGTAAAATGGTCTATTTTGGAAAAATCGGGGTAAAAAATGGAATTTTTGGAAGTTT
Found at i:223665 original size:29 final size:29
Alignment explanation
Indices: 223511--223737 Score: 117
Period size: 29 Copynumber: 7.8 Consensus size: 29
223501 TAAAAGTTAA
* **
223511 GGGTCAAAAATGGAATTTTTAGACA-TCCGG
1 GGGT-AAAAATGGAATTTTTGGA-AGTTTGG
* ** *
223541 GGGT-AAAATGGTACTTTTTGGAAGAATCG
1 GGGTAAAAATGG-AATTTTTGGAAGTTTGG
* *
223570 AGGTCAAAAATGGAATTTTTGGAAGTTTAG
1 GGGT-AAAAATGGAATTTTTGGAAGTTTGG
** * *** *
223600 GGGT--AAATGGTCTATTTTGAAAAAATCG
1 GGGTAAAAATGGAAT-TTTTGGAAGTTTGG
* *
223628 GGGTAAAAAATGGAGTTCTTGGAAGTTTGG
1 GGGT-AAAAATGGAATTTTTGGAAGTTTGG
** **
223658 GGGTAAAAATATAATTTTTGGAAAAATT-G
1 GGGTAAAAATGGAATTTTTGG-AAGTTTGG
*
223687 GGGTTAAAATGGAATTTTTGGAAGTTTGG
1 GGGTAAAAATGGAATTTTTGGAAGTTTGG
*
223716 GGCT-AAAATGGTAA-TTTTGGAA
1 GGGTAAAAATGG-AATTTTTGGAA
223738 AAATTGGGGT
Statistics
Matches: 147, Mismatches: 39, Indels: 24
0.70 0.19 0.11
Matches are distributed among these distances:
27 7 0.05
28 40 0.27
29 50 0.34
30 36 0.24
31 14 0.10
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (29 bp):
GGGTAAAAATGGAATTTTTGGAAGTTTGG
Found at i:223744 original size:29 final size:29
Alignment explanation
Indices: 223670--223746 Score: 104
Period size: 28 Copynumber: 2.7 Consensus size: 29
223660 GTAAAAATAT
*
223670 AATTTTTGGAAAAATTGGGGTTAAAATGG
1 AATTTTTGGAAAAATTGGGGCTAAAATGG
**
223699 AATTTTTGG-AAGTTTGGGGCTAAAATGG
1 AATTTTTGGAAAAATTGGGGCTAAAATGG
223727 TAA-TTTTGGAAAAATTGGGG
1 -AATTTTTGGAAAAATTGGGG
223747 TCAAAAAAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 22 0.54
29 19 0.46
ACGTcount: A:0.34, C:0.01, G:0.30, T:0.35
Consensus pattern (29 bp):
AATTTTTGGAAAAATTGGGGCTAAAATGG
Found at i:225068 original size:20 final size:21
Alignment explanation
Indices: 225026--225081 Score: 87
Period size: 20 Copynumber: 2.7 Consensus size: 21
225016 TTTCCTTTTT
* *
225026 TATTTATTAATATTACCAAAA
1 TATTTATTATTATTACAAAAA
225047 TATTTATTATTATTA-AAAAA
1 TATTTATTATTATTACAAAAA
225067 TATTTATTATTATTA
1 TATTTATTATTATTA
225082 TTATTATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
20 19 0.58
21 14 0.42
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.52
Consensus pattern (21 bp):
TATTTATTATTATTACAAAAA
Found at i:225120 original size:3 final size:3
Alignment explanation
Indices: 225070--225105 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
225060 TAAAAAATAT
225070 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
225106 ATACATTCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:225841 original size:17 final size:17
Alignment explanation
Indices: 225819--225928 Score: 89
Period size: 17 Copynumber: 6.4 Consensus size: 17
225809 GGACATTTAG
* *
225819 TTTAAATTTAAAACCAT
1 TTTAAATTTAAAACAAA
* *
225836 TTTAAATCT-AAGCTAAA
1 TTTAAATTTAAAAC-AAA
*
225853 TTTAAATTTAAAACAAG
1 TTTAAATTTAAAACAAA
*
225870 TTTAAATTTAAATTCAGAA
1 TTTAAATTTAAA-ACA-AA
*
225889 -ATAAATTTAAAATCAAA
1 TTTAAATTTAAAA-CAAA
* *
225906 TTTAAATTTAATATAAA
1 TTTAAATTTAAAACAAA
225923 TTTAAA
1 TTTAAA
225929 AGTTTGATCC
Statistics
Matches: 73, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
16 3 0.04
17 42 0.58
18 27 0.37
19 1 0.01
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (17 bp):
TTTAAATTTAAAACAAA
Found at i:225860 original size:6 final size:6
Alignment explanation
Indices: 225849--225928 Score: 58
Period size: 6 Copynumber: 13.7 Consensus size: 6
225839 AAATCTAAGC
* * * * *
225849 TAAATT TAAATT TAAA-A CAAGTT TAAATT TAAATT CAGAA-A TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TA-AATT TAAATT
* * *
225896 TAAAAT CAAATT TAAATT T-AATA TAAATT TAAA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAA
225929 AGTTTGATCC
Statistics
Matches: 54, Mismatches: 16, Indels: 8
0.69 0.21 0.10
Matches are distributed among these distances:
5 8 0.15
6 44 0.81
7 2 0.04
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.39
Consensus pattern (6 bp):
TAAATT
Found at i:226462 original size:36 final size:36
Alignment explanation
Indices: 226412--226481 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
226402 GACTGGTTGA
* * *
226412 TGGTGACCTACCTCAGGTTTGAGGTAAGAGATCGAG
1 TGGTGACCTACCTCAAGCTCGAGGTAAGAGATCGAG
* * *
226448 TGGTGATCTGCCTCAAGCTCGGGGTAAGAGATCG
1 TGGTGACCTACCTCAAGCTCGAGGTAAGAGATCG
226482 GATGACTGCA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.24
Consensus pattern (36 bp):
TGGTGACCTACCTCAAGCTCGAGGTAAGAGATCGAG
Found at i:226558 original size:78 final size:78
Alignment explanation
Indices: 226451--226608 Score: 174
Period size: 78 Copynumber: 2.0 Consensus size: 78
226441 GATCGAGTGG
* * * ** *
226451 TGATCTGCCTCAAGCTCGGGGTAAGAGATCGGATGACTGCAATCTACCCCAGGCTC-AGGGTAGG
1 TGATCTGCCCCAAGCTAGGGGTAAAAGATCAAATGACTGCAATCTACCCCAGGCTCGA-GGTAAG
226515 AGATTGGTTGACGA
65 AGATTGGTTGACGA
* * ** * * *
226529 TGATCTGCCCCAGGCTATGGGTAAAAGATCAAATGGTTGCATTCTGCCCCAGGTTCGAGGTAAGA
1 TGATCTGCCCCAAGCTAGGGGTAAAAGATCAAATGACTGCAATCTACCCCAGGCTCGAGGTAAGA
*
226594 GATTGGTTGAGGA
66 GATTGGTTGACGA
226607 TG
1 TG
226609 TAACTTCACT
Statistics
Matches: 65, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
78 64 0.98
79 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.32, T:0.24
Consensus pattern (78 bp):
TGATCTGCCCCAAGCTAGGGGTAAAAGATCAAATGACTGCAATCTACCCCAGGCTCGAGGTAAGA
GATTGGTTGACGA
Found at i:226954 original size:48 final size:48
Alignment explanation
Indices: 226902--227024 Score: 201
Period size: 48 Copynumber: 2.6 Consensus size: 48
226892 GTACTAGGTT
* * * *
226902 CGCCATTGTGACTTAAACCTTTCCCTTGTGTCTTCGTGGTACTGGATC
1 CGCCATTGCGGCTTAGATCTTTCCCTTGTGTCTTCGTGGTACTGGATC
226950 CGCCATTGCGGCTTAGATCTTTCCCTTGTGTCTTCGTGGTACTGGATC
1 CGCCATTGCGGCTTAGATCTTTCCCTTGTGTCTTCGTGGTACTGGATC
*
226998 CACCATTGCGGCTTAGATCTTTCCCTT
1 CGCCATTGCGGCTTAGATCTTTCCCTT
227025 CATGCTTCTA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 70 1.00
ACGTcount: A:0.13, C:0.28, G:0.21, T:0.37
Consensus pattern (48 bp):
CGCCATTGCGGCTTAGATCTTTCCCTTGTGTCTTCGTGGTACTGGATC
Found at i:227091 original size:98 final size:98
Alignment explanation
Indices: 226970--227223 Score: 307
Period size: 98 Copynumber: 2.6 Consensus size: 98
226960 GCTTAGATCT
* * * *
226970 TTCCC-TTGTGTCTTCGTGGTACTGGATCCACCATTGCGGCTTAGATCTTTCCCTTCATGCTTCT
1 TTCCCTTTGTGTCTTTGCGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTCATGCTTCT
*
227034 AAGGTAGC-AGGTTC-TCTGTTGCTACTCAAACCC
66 AAGGTA-CAAGGTTCGTC-GTTGCGACTCAAACCC
* * * ** *
227067 TTCCCTTTGTGTCTTTGCAGTACTGGATCCGCTGTTACGGCTTAGATAATTCCCTTCATGCTTTT
1 TTCCCTTTGTGTCTTTGCGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTCATGCTTCT
* *
227132 GAGGTACAAGGTTCGTCGTTGCGACTTAAACCC
66 AAGGTACAAGGTTCGTCGTTGCGACTCAAACCC
* * * **
227165 TTCCCTTTGTGTCTTTGCGGTATTGGATTCGTCGTTGCATCTTAGATCTTTCCCTTCAT
1 TTCCCTTTGTGTCTTTGCGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTCAT
227224 ATCTCTGAGG
Statistics
Matches: 131, Mismatches: 23, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
97 6 0.05
98 123 0.94
99 2 0.02
ACGTcount: A:0.15, C:0.26, G:0.20, T:0.39
Consensus pattern (98 bp):
TTCCCTTTGTGTCTTTGCGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTCATGCTTCT
AAGGTACAAGGTTCGTCGTTGCGACTCAAACCC
Found at i:227233 original size:98 final size:97
Alignment explanation
Indices: 227008--227260 Score: 287
Period size: 98 Copynumber: 2.6 Consensus size: 97
226998 CACCATTGCG
* * *
227008 GCTTAGATCTTTCCCTTCATGCTTCTAAGGTAGCAGGTTC-TCTGTTGCTACTCAAACCCTTCCC
1 GCTTAGATCTTTCCCTTCATGCTTCTGAGGTA-CAGGTTCGTC-GTTGCGACTTAAACCCTTCCC
*
227072 TTTGTGTCTTTGCAGTACTGGATCCGCTGTTACG
64 TTTGTGTCTTTGCAGTACTGGATCCGCTGTTACA
** *
227106 GCTTAGATAATTCCCTTCATGCTTTTGAGGTACAAGGTTCGTCGTTGCGACTTAAACCCTTCCCT
1 GCTTAGATCTTTCCCTTCATGCTTCTGAGGTAC-AGGTTCGTCGTTGCGACTTAAACCCTTCCCT
* * * *
227171 TTGTGTCTTTGCGGTATTGGATTCG-TCGTTGCA
65 TTGTGTCTTTGCAGTACTGGATCCGCT-GTTACA
* * * * *
227204 TCTTAGATCTTTCCCTTCAT-ATCTCTGAGGTACTAGGTTCGCCATTGTGACTTAAAC
1 GCTTAGATCTTTCCCTTCATGCT-TCTGAGGTAC-AGGTTCGTCGTTGCGACTTAAAC
227261 TTCTCCCTCT
Statistics
Matches: 131, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
97 3 0.02
98 126 0.96
99 2 0.02
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.38
Consensus pattern (97 bp):
GCTTAGATCTTTCCCTTCATGCTTCTGAGGTACAGGTTCGTCGTTGCGACTTAAACCCTTCCCTT
TGTGTCTTTGCAGTACTGGATCCGCTGTTACA
Found at i:227268 original size:98 final size:98
Alignment explanation
Indices: 226950--227260 Score: 261
Period size: 98 Copynumber: 3.2 Consensus size: 98
226940 GTACTGGATC
* * * * * ** * ** * *
226950 CGCCATTGCGGCTTAGATCTTTCCC-TTGTGTCTTCGTGGTACTGGATCCACCATTGCGGCTTAG
1 CGCCATTGCGACTTAAACCCTTCCCTTTGTGTCTTTGCAGTACTGGATCCGCTGTTACAGCTTAG
** *
227014 ATCTTTCCCTTCATGCTTCTAAGGTAGC-AGGTT
66 ATAATTCCCTTCATGCTTCTGAGGTA-CAAGGTT
* ** * * *
227047 CTCTGTTGCTACTCAAACCCTTCCCTTTGTGTCTTTGCAGTACTGGATCCGCTGTTACGGCTTAG
1 CGCCATTGCGACTTAAACCCTTCCCTTTGTGTCTTTGCAGTACTGGATCCGCTGTTACAGCTTAG
*
227112 ATAATTCCCTTCATGCTTTTGAGGTACAAGGTT
66 ATAATTCCCTTCATGCTTCTGAGGTACAAGGTT
* * * * * * *
227145 CGTCGTTGCGACTTAAACCCTTCCCTTTGTGTCTTTGCGGTATTGGATTCG-TCGTTGCATCTTA
1 CGCCATTGCGACTTAAACCCTTCCCTTTGTGTCTTTGCAGTACTGGATCCGCT-GTTACAGCTTA
** * *
227209 GATCTTTCCCTTCAT-ATCTCTGAGGTACTAGGTT
65 GATAATTCCCTTCATGCT-TCTGAGGTACAAGGTT
*
227243 CGCCATTGTGACTTAAAC
1 CGCCATTGCGACTTAAAC
227261 TTCTCCCTCT
Statistics
Matches: 171, Mismatches: 39, Indels: 7
0.79 0.18 0.03
Matches are distributed among these distances:
97 19 0.11
98 152 0.89
ACGTcount: A:0.16, C:0.26, G:0.21, T:0.38
Consensus pattern (98 bp):
CGCCATTGCGACTTAAACCCTTCCCTTTGTGTCTTTGCAGTACTGGATCCGCTGTTACAGCTTAG
ATAATTCCCTTCATGCTTCTGAGGTACAAGGTT
Found at i:228172 original size:17 final size:15
Alignment explanation
Indices: 228152--228261 Score: 50
Period size: 17 Copynumber: 6.9 Consensus size: 15
228142 CCTCGACCTT
228152 TTTTTTTCTTTTTCTCG
1 TTTTTTTCTTTTT-T-G
228169 -TTTTTTCTATTTTTG
1 TTTTTTTCT-TTTTTG
228184 TTTTTCTTCTTGTTTT-
1 TTTTT-TTCTT-TTTTG
228200 TCCTCTTTTT-TTTTTTG
1 T--T-TTTTTCTTTTTTG
*
228217 TTTTTCCTCCTTTTTT-
1 TTTTT--TTCTTTTTTG
*
228233 TTCTTTTTCCTTTTT-
1 TT-TTTTTCTTTTTTG
* *
228248 TTCTTTTATTTTTT
1 TTTTTTTCTTTTTT
228262 TCTTCTTCTT
Statistics
Matches: 75, Mismatches: 6, Indels: 27
0.69 0.06 0.25
Matches are distributed among these distances:
14 12 0.16
15 11 0.15
16 22 0.29
17 24 0.32
18 3 0.04
19 3 0.04
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.79
Consensus pattern (15 bp):
TTTTTTTCTTTTTTG
Found at i:228188 original size:33 final size:33
Alignment explanation
Indices: 228151--228222 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
228141 ACCTCGACCT
* *
228151 TTTTTTTTCTT-TTTCTCGT-TTTTTCTATTTTTG
1 TTTTTCTTCTTGTTTCTCCTCTTTTT-T-TTTTTG
*
228184 TTTTTCTTCTTGTTTTTCCTCTTTTTTTTTTTG
1 TTTTTCTTCTTGTTTCTCCTCTTTTTTTTTTTG
228217 TTTTTC
1 TTTTTC
228223 CTCCTTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 22 0.65
34 7 0.21
35 5 0.15
ACGTcount: A:0.01, C:0.14, G:0.06, T:0.79
Consensus pattern (33 bp):
TTTTTCTTCTTGTTTCTCCTCTTTTTTTTTTTG
Found at i:228193 original size:27 final size:27
Alignment explanation
Indices: 228163--228215 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
228153 TTTTTTCTTT
*
228163 TTCTCGTTTTTTCTATTTTTGTTTTTC
1 TTCTCGTTTTTCCTATTTTTGTTTTTC
* * *
228190 TTCTTGTTTTTCCTCTTTTTTTTTTT
1 TTCTCGTTTTTCCTATTTTTGTTTTT
228216 GTTTTTCCTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.02, C:0.15, G:0.06, T:0.77
Consensus pattern (27 bp):
TTCTCGTTTTTCCTATTTTTGTTTTTC
Found at i:228198 original size:12 final size:12
Alignment explanation
Indices: 228181--228237 Score: 57
Period size: 12 Copynumber: 4.9 Consensus size: 12
228171 TTTTCTATTT
228181 TTGTTTTTCTTC
1 TTGTTTTTCTTC
*
228193 TTGTTTTTCCTC
1 TTGTTTTTCTTC
228205 TT-TTTTT-TT-
1 TTGTTTTTCTTC
*
228214 TTGTTTTTCCTCC
1 TTGTTTTT-CTTC
*
228227 TTTTTTTTCTT
1 TTGTTTTTCTT
228238 TTTCCTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
9 2 0.06
10 6 0.17
11 5 0.14
12 16 0.44
13 7 0.19
ACGTcount: A:0.00, C:0.18, G:0.05, T:0.77
Consensus pattern (12 bp):
TTGTTTTTCTTC
Found at i:228217 original size:21 final size:21
Alignment explanation
Indices: 228184--228260 Score: 79
Period size: 21 Copynumber: 3.8 Consensus size: 21
228174 TCTATTTTTG
* *
228184 TTTTTCTTCTTGTTTTTCCTC
1 TTTTTTTTTTTGTTTTTCCTC
228205 TTTTTTTTTTTGTTTTTCCTC
1 TTTTTTTTTTTGTTTTTCCTC
* *
228226 --CTTTTTTTTCTTTTTCCT-
1 TTTTTTTTTTTGTTTTTCCTC
* *
228244 TTTTTTCTTTTATTTTT
1 TTTTTTTTTTTGTTTTT
228261 TTCTTCTTCT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
19 16 0.34
20 12 0.26
21 19 0.40
ACGTcount: A:0.01, C:0.17, G:0.03, T:0.79
Consensus pattern (21 bp):
TTTTTTTTTTTGTTTTTCCTC
Found at i:228239 original size:24 final size:22
Alignment explanation
Indices: 228184--228239 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 22
228174 TCTATTTTTG
228184 TTTTTCTTCTTGTTTTTCCTCTT
1 TTTTTCTT-TTGTTTTTCCTCTT
228207 TTTTT-TTTTGTTTTTCCTCCTTT
1 TTTTTCTTTTGTTTTTCCT-C-TT
228230 TTTTTCTTTT
1 TTTTTCTTTT
228240 TCCTTTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
21 11 0.37
22 3 0.10
23 12 0.40
24 4 0.13
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.79
Consensus pattern (22 bp):
TTTTTCTTTTGTTTTTCCTCTT
Found at i:228247 original size:33 final size:31
Alignment explanation
Indices: 228170--228277 Score: 89
Period size: 33 Copynumber: 3.4 Consensus size: 31
228160 TTTTTCTCGT
*
228170 TTTTTCTATTTTTGTTTTTCTTCTTGTTTTTCCTC
1 TTTTTCT-TTTTTGTTTTTCTCCTT-TTTTT--TC
228205 TTTTT-TTTTTTGTTTTTCCTCCTTTTTTTTC
1 TTTTTCTTTTTTGTTTTT-CTCCTTTTTTTTC
*
228236 TTTTTCCTTTTTT-TCTTTTAT--TTTTTTCTTC
1 TTTTT-CTTTTTTGT-TTTTCTCCTTTTTT-TTC
*
228267 TTCTTCTTTTT
1 TTTTTCTTTTT
228278 CTTCTTTCTT
Statistics
Matches: 65, Mismatches: 3, Indels: 15
0.78 0.04 0.18
Matches are distributed among these distances:
30 12 0.18
31 14 0.22
32 2 0.03
33 26 0.40
34 6 0.09
35 5 0.08
ACGTcount: A:0.02, C:0.17, G:0.03, T:0.79
Consensus pattern (31 bp):
TTTTTCTTTTTTGTTTTTCTCCTTTTTTTTC
Found at i:228259 original size:19 final size:19
Alignment explanation
Indices: 228149--228292 Score: 70
Period size: 19 Copynumber: 7.6 Consensus size: 19
228139 TCACCTCGAC
228149 CTTTTTT-TTTCTTTTT-CT
1 CTTTTTTCTTT-TTTTTCCT
*
228167 CGTTTTTTCTATTTTTGT--T
1 C-TTTTTTCT-TTTTTTTCCT
* *
228186 -TTTCTTCTTGTTTTTCCT
1 CTTTTTTCTTTTTTTTCCT
*
228204 CTTTTTTTTTTTGTTTTTCCT
1 C-TTTTTTCTTT-TTTTTCCT
*
228225 CCTTTTTT-TTCTTTTTCCT
1 -CTTTTTTCTTTTTTTTCCT
**
228244 -TTTTTTCTTTTATTTTTTT
1 CTTTTTTCTTTT-TTTTCCT
* * *
228263 C-TTCTTCTTCTTTTTCTT
1 CTTTTTTCTTTTTTTTCCT
228281 CTTTCTTTCTTT
1 CTTT-TTTCTTT
228293 ATTGAATCCG
Statistics
Matches: 96, Mismatches: 16, Indels: 26
0.70 0.12 0.19
Matches are distributed among these distances:
16 5 0.05
17 13 0.14
18 12 0.12
19 30 0.31
20 19 0.20
21 16 0.17
22 1 0.01
ACGTcount: A:0.01, C:0.18, G:0.03, T:0.78
Consensus pattern (19 bp):
CTTTTTTCTTTTTTTTCCT
Found at i:228286 original size:22 final size:20
Alignment explanation
Indices: 228230--228288 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 20
228220 TTCCTCCTTT
*
228230 TTTTTCTTTTTCCTTTTTTTC
1 TTTTTCTTTTT-CTTTTCTTC
*
228251 TTTTATTTTTTTCTTCTTCTTC
1 TTTT-TCTTTTTCTT-TTCTTC
228273 TTTTTCTTCTTTCTTT
1 TTTTTCTT-TTTCTTT
228289 CTTTATTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
21 11 0.34
22 21 0.66
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTTCTTTTTCTTTTCTTC
Found at i:232851 original size:29 final size:27
Alignment explanation
Indices: 232819--232884 Score: 71
Period size: 29 Copynumber: 2.4 Consensus size: 27
232809 TAGACATTCG
232819 GGGGTTAAATGGTACTTTTTGGAAGAATT
1 GGGGTTAAATGG-ACTTTTTGGAAG-ATT
* * *
232848 GGGGTCAAAATGGAGTTTTTGGAAGTTT
1 GGGGT-TAAATGGACTTTTTGGAAGATT
232876 GGGG-TAAAT
1 GGGGTTAAAT
232885 TTTTAATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
26 4 0.12
28 6 0.19
29 16 0.50
30 6 0.19
ACGTcount: A:0.27, C:0.03, G:0.35, T:0.35
Consensus pattern (27 bp):
GGGGTTAAATGGACTTTTTGGAAGATT
Found at i:232924 original size:29 final size:29
Alignment explanation
Indices: 232892--232987 Score: 72
Period size: 30 Copynumber: 3.3 Consensus size: 29
232882 AATTTTTAAT
232892 TTTTGAAAAAATTAGGGTCAAAAATGGAA
1 TTTTGAAAAAATTAGGGTCAAAAATGGAA
* **
232921 TTTTTG-GAAGTTTAGGGGT--AAAATGGTAA
1 -TTTTGAAAAAATTA-GGGTCAAAAATGG-AA
* * * *
232950 TTTTGGAAAAATCAAGGTCAAAAATGCAA
1 TTTTGAAAAAATTAGGGTCAAAAATGGAA
232979 TTTTAGAAA
1 TTTT-GAAA
232988 GTTCGGGGGT
Statistics
Matches: 50, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
28 15 0.30
29 17 0.34
30 18 0.36
ACGTcount: A:0.43, C:0.04, G:0.22, T:0.31
Consensus pattern (29 bp):
TTTTGAAAAAATTAGGGTCAAAAATGGAA
Done.