Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold127
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: 3416254
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 147187 characters in sequence are not A, C, G, or T
File 3 of 10
Found at i:751277 original size:35 final size:35
Alignment explanation
Indices: 751239--751354 Score: 135
Period size: 35 Copynumber: 3.3 Consensus size: 35
751229 CTCTAGTTGG
*
751239 ATAAACCAACAAAATTTGTGCCCAGTGCTAGTCAG
1 ATAAACCAACAAAATTTGTGCCCAGTGCTAGTCAA
* * * *
751274 ATAAACCGAC-GAATATGTGCCCAGCGCTAGTCAA
1 ATAAACCAACAAAATTTGTGCCCAGTGCTAGTCAA
** * *
751308 ATAAACTGACAAAAGTTGCGCCCAGTGCTAGTCAA
1 ATAAACCAACAAAATTTGTGCCCAGTGCTAGTCAA
*
751343 ATGAACCAACAA
1 ATAAACCAACAA
751355 TATCAATTAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
34 29 0.44
35 37 0.56
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (35 bp):
ATAAACCAACAAAATTTGTGCCCAGTGCTAGTCAA
Found at i:751277 original size:75 final size:75
Alignment explanation
Indices: 751109--751288 Score: 206
Period size: 75 Copynumber: 2.4 Consensus size: 75
751099 CAGAAGTTGC
* * * *
751109 GCCCAGTGCTAGTCGGATAAA-CAGACGAATAATTAGTTAGCGCAGCTCTAGTTGGATAAAGCAA
1 GCCCAGTGCTAGTCGGATAAACCAGACAAATAAATAGTGAGCGCAGCTCTAGTTGGATAAACCAA
***
751173 CGTTATTTGT
66 CAAAATTTGT
* * *
751183 GCCCAGTGCTATTTGGATAAACCA-ACAAAATAAATGGTGAGC-CTAGCTCTAGTTGGATAAACC
1 GCCCAGTGCTAGTCGGATAAACCAGAC-AAATAAATAGTGAGCGC-AGCTCTAGTTGGATAAACC
751246 AACAAAATTTGT
64 AACAAAATTTGT
* *
751258 GCCCAGTGCTAGTCAGATAAACC-GACGAATA
1 GCCCAGTGCTAGTCGGATAAACCAGACAAATA
751289 TGTGCCCAGC
Statistics
Matches: 88, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
74 26 0.30
75 62 0.70
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.24
Consensus pattern (75 bp):
GCCCAGTGCTAGTCGGATAAACCAGACAAATAAATAGTGAGCGCAGCTCTAGTTGGATAAACCAA
CAAAATTTGT
Found at i:751445 original size:37 final size:37
Alignment explanation
Indices: 751399--751582 Score: 359
Period size: 37 Copynumber: 5.0 Consensus size: 37
751389 ATTTCATAAT
*
751399 CTCAATATCACATTCACTTCAATTATCTATTAATCAA
1 CTCAGTATCACATTCACTTCAATTATCTATTAATCAA
751436 CTCAGTATCACATTCACTTCAATTATCTATTAATCAA
1 CTCAGTATCACATTCACTTCAATTATCTATTAATCAA
751473 CTCAGTATCACATTCACTTCAATTATCTATTAATCAA
1 CTCAGTATCACATTCACTTCAATTATCTATTAATCAA
751510 CTCAGTATCACATTCACTTCAATTATCTATTAATCAA
1 CTCAGTATCACATTCACTTCAATTATCTATTAATCAA
751547 CTCAGTATCACATTCACTTCAATTATCTATTAATCA
1 CTCAGTATCACATTCACTTCAATTATCTATTAATCA
751583 TTCATTAATT
Statistics
Matches: 146, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
37 146 1.00
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.38
Consensus pattern (37 bp):
CTCAGTATCACATTCACTTCAATTATCTATTAATCAA
Found at i:753672 original size:22 final size:22
Alignment explanation
Indices: 753647--753694 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
753637 GCATTTGTAT
753647 CAGTAAATTTATGGTTTACTTG
1 CAGTAAATTTATGGTTTACTTG
753669 CAGTAAATTTATGGTTTACTTG
1 CAGTAAATTTATGGTTTACTTG
753691 CAGT
1 CAGT
753695 TCAATTGTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.44
Consensus pattern (22 bp):
CAGTAAATTTATGGTTTACTTG
Found at i:756185 original size:25 final size:25
Alignment explanation
Indices: 756157--756213 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
756147 CCCTCTCTCT
**
756157 AGCCATATAACGAT-AAGCTCATGTG
1 AGCCATATAAC-ATGAAGCTCATAAG
*
756182 AGCCATGTAACATGAAGCTCATAAG
1 AGCCATATAACATGAAGCTCATAAG
756207 AGCCATA
1 AGCCATA
756214 ATCGGGAAGC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 2 0.07
25 25 0.93
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (25 bp):
AGCCATATAACATGAAGCTCATAAG
Found at i:763382 original size:27 final size:27
Alignment explanation
Indices: 763347--763413 Score: 107
Period size: 27 Copynumber: 2.4 Consensus size: 27
763337 ATTAGAGCAC
* *
763347 ATAATCGGGAAGTCCTCTCTCGAGCCAT
1 ATAA-CGGGAAGCCCTCTCTCAAGCCAT
763375 ATAACGGGAAGCCCTCTCTCAAGCCAT
1 ATAACGGGAAGCCCTCTCTCAAGCCAT
763402 ATAACGGGAAGC
1 ATAACGGGAAGC
763414 TCATGTGAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
27 33 0.89
28 4 0.11
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.19
Consensus pattern (27 bp):
ATAACGGGAAGCCCTCTCTCAAGCCAT
Found at i:763435 original size:25 final size:25
Alignment explanation
Indices: 763368--763480 Score: 95
Period size: 25 Copynumber: 4.5 Consensus size: 25
763358 GTCCTCTCTC
*
763368 GAGCCATATAACGGGAAGCCCTC-TCT
1 GAGCCATATAACGGGAAG--CTCATGT
*
763394 CAAGCCATATAACGGGAAGCTCATGT
1 -GAGCCATATAACGGGAAGCTCATGT
* * * *
763420 GAGCCATGTAATGGGAAGCTTATCT
1 GAGCCATATAACGGGAAGCTCATGT
* ** *
763445 GGGCTGTATAACGGGAAGCTCATGC
1 GAGCCATATAACGGGAAGCTCATGT
763470 GAGCCA-ATAAC
1 GAGCCATATAAC
763481 ATGTAGCTTC
Statistics
Matches: 67, Mismatches: 18, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
24 5 0.07
25 43 0.64
26 2 0.03
27 17 0.25
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.20
Consensus pattern (25 bp):
GAGCCATATAACGGGAAGCTCATGT
Found at i:765610 original size:12 final size:12
Alignment explanation
Indices: 765595--765619 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
765585 ATTTTTAAGA
765595 ATTTAATTTTTT
1 ATTTAATTTTTT
765607 ATTTAATTTTTT
1 ATTTAATTTTTT
765619 A
1 A
765620 GATTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
ATTTAATTTTTT
Found at i:765619 original size:28 final size:27
Alignment explanation
Indices: 765561--765617 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
765551 TTTTCATAAA
*
765561 TTTAAAATTTAATATTTTACTTTTATT
1 TTTAAAATTTAATATTTTACTTTAATT
*
765588 TTTAAGAATTTAATTTTTTA-TTTAATT
1 TTTAA-AATTTAATATTTTACTTTAATT
765615 TTT
1 TTT
765618 TAGATTTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 14 0.52
28 13 0.48
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (27 bp):
TTTAAAATTTAATATTTTACTTTAATT
Found at i:771463 original size:22 final size:21
Alignment explanation
Indices: 771434--771476 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
771424 TTTTTCCCAC
**
771434 GTTAGGTTTTTGGTTTTTAGG
1 GTTAGGTTTAGGGTTTTTAGG
771455 GTTAGGGTTTAGGGTTTTTAGG
1 GTTA-GGTTTAGGGTTTTTAGG
771477 ATTTTTAGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.12, C:0.00, G:0.37, T:0.51
Consensus pattern (21 bp):
GTTAGGTTTAGGGTTTTTAGG
Found at i:771792 original size:126 final size:125
Alignment explanation
Indices: 771567--771881 Score: 481
Period size: 126 Copynumber: 2.5 Consensus size: 125
771557 GATAAAATCA
* * *
771567 AAGCAGGATGCTTTCTGAGAAGAATATGTGAAATCGCGCCCTCGTAGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTAGACGCGCTTTTGCTACAGC
771632 AGGTCCTGGAAAAAATAATTTCGAGTTGACATTTCTGAGAAAATAGTATAAAAAACGCTTC
66 AGGTCCTGGAAAAAATAATTTCGAGTTGACATTTCTGAGAAAATAGTAT-AAAAACGCTTC
* * *
771693 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGTGTCCTCGT-GAACGTGCTTTTGCTACAG
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTAG-ACGCGCTTTTGCTACAG
*
771757 CAGGTCCTGGAAAAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAAACGCTTC
65 CAGGTCCTGGAAAAAATAATTTCGAGTTGACATTTCTGAGAAAATAGTATAAAAACGCTTC
* * * * *
771818 AAGCATGATGCTTTATCAGAAAAATTTGTGAAATCGCGCCCACGTGGACGC-CTTTTTGCTACAG
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTAGACGCGC-TTTTGCTACAG
771882 TAGCATGTTT
Statistics
Matches: 172, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
124 1 0.01
125 65 0.38
126 106 0.62
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (125 bp):
AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTAGACGCGCTTTTGCTACAGC
AGGTCCTGGAAAAAATAATTTCGAGTTGACATTTCTGAGAAAATAGTATAAAAACGCTTC
Found at i:773245 original size:26 final size:26
Alignment explanation
Indices: 773208--773259 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
773198 AATATACTCG
*
773208 GTTTATAGGTGTTTCACAAGATCATC
1 GTTTATAAGTGTTTCACAAGATCATC
773234 GTTTATAAGTGTTTCACAAGATCATC
1 GTTTATAAGTGTTTCACAAGATCATC
773260 CCAAGATGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.38
Consensus pattern (26 bp):
GTTTATAAGTGTTTCACAAGATCATC
Found at i:775043 original size:22 final size:21
Alignment explanation
Indices: 775012--775146 Score: 149
Period size: 22 Copynumber: 6.6 Consensus size: 21
775002 GGTTAGGGTT
775012 AGGGTTAGGGTTTTTAAGTTA
1 AGGGTTAGGGTTTTTAAGTTA
775033 AGGGTTTAGGGTTTTTAAGTTA
1 AGGG-TTAGGGTTTTTAAGTTA
775055 AGGGTTAGGG--TTT-AG---
1 AGGGTTAGGGTTTTTAAGTTA
* *
775070 -GGTTTAAGGTTTTTAAGTTA
1 AGGGTTAGGGTTTTTAAGTTA
*
775090 AGGGTTTAGGGTTTTTAACTTA
1 AGGG-TTAGGGTTTTTAAGTTA
*
775112 AGGGTTAGGTTTTTTAAGTTA
1 AGGGTTAGGGTTTTTAAGTTA
*
775133 AGGATTTAGGGTTT
1 AGG-GTTAGGGTTT
775147 GTCAATTAAA
Statistics
Matches: 95, Mismatches: 9, Indels: 19
0.77 0.07 0.15
Matches are distributed among these distances:
14 7 0.07
16 3 0.03
17 2 0.02
18 2 0.02
19 3 0.03
21 30 0.32
22 48 0.51
ACGTcount: A:0.23, C:0.01, G:0.32, T:0.44
Consensus pattern (21 bp):
AGGGTTAGGGTTTTTAAGTTA
Found at i:775060 original size:43 final size:42
Alignment explanation
Indices: 775012--775155 Score: 151
Period size: 43 Copynumber: 3.5 Consensus size: 42
775002 GGTTAGGGTT
775012 AGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTA
1 AGGGTTAGGGTTTTTAA-TTAAGGGTTTAGGGTTTTTAAGTTA
*
775055 AGGGTTAGGG----T--TT-AGGGTTTAAGGTTTTTAAGTTA
1 AGGGTTAGGGTTTTTAATTAAGGGTTTAGGGTTTTTAAGTTA
*
775090 AGGGTTTAGGGTTTTTAACTTAAGGG-TTAGGTTTTTTAAGTTA
1 AGGG-TTAGGGTTTTTAA-TTAAGGGTTTAGGGTTTTTAAGTTA
* *
775133 AGGATTTAGGGTTTGTCAATTAA
1 AGG-GTTAGGGTTT-TTAATTAA
775156 ATTATACATT
Statistics
Matches: 85, Mismatches: 5, Indels: 22
0.76 0.04 0.20
Matches are distributed among these distances:
35 25 0.29
36 8 0.09
39 1 0.01
40 1 0.01
43 43 0.51
44 7 0.08
ACGTcount: A:0.24, C:0.01, G:0.31, T:0.44
Consensus pattern (42 bp):
AGGGTTAGGGTTTTTAATTAAGGGTTTAGGGTTTTTAAGTTA
Found at i:775075 original size:35 final size:36
Alignment explanation
Indices: 775033--775103 Score: 126
Period size: 35 Copynumber: 2.0 Consensus size: 36
775023 TTTTAAGTTA
*
775033 AGGGTTTAGGGTTTTTAAGTTAAGGG-TTAGGGTTT
1 AGGGTTTAAGGTTTTTAAGTTAAGGGTTTAGGGTTT
775068 AGGGTTTAAGGTTTTTAAGTTAAGGGTTTAGGGTTT
1 AGGGTTTAAGGTTTTTAAGTTAAGGGTTTAGGGTTT
775104 TTAACTTAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 25 0.74
36 9 0.26
ACGTcount: A:0.21, C:0.00, G:0.35, T:0.44
Consensus pattern (36 bp):
AGGGTTTAAGGTTTTTAAGTTAAGGGTTTAGGGTTT
Found at i:775089 original size:57 final size:55
Alignment explanation
Indices: 774999--775120 Score: 208
Period size: 57 Copynumber: 2.2 Consensus size: 55
774989 AGTACCAGTC
* *
774999 AAGGGTTAGGGTTAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTT
1 AAGGGTTAGGGTTAGGGTTAAGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAACTT
775054 AAGGGTTAGGGTTTAGGGTTTAAGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAACTT
1 AAGGGTTAGGG-TTAGGG-TTAAGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAACTT
775111 AAGGGTTAGG
1 AAGGGTTAGG
775121 TTTTTTAAGT
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
55 11 0.17
56 6 0.10
57 46 0.73
ACGTcount: A:0.23, C:0.01, G:0.35, T:0.41
Consensus pattern (55 bp):
AAGGGTTAGGGTTAGGGTTAAGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAACTT
Found at i:775654 original size:18 final size:18
Alignment explanation
Indices: 775628--775669 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
775618 GACTCAGAAA
* *
775628 AGGAAACATATAAGGGTT
1 AGGAAACATAAAAGGGCT
*
775646 AGGATACATAAAAGGGCT
1 AGGAAACATAAAAGGGCT
775664 AGGAAA
1 AGGAAA
775670 TGCACCTGGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.29, T:0.17
Consensus pattern (18 bp):
AGGAAACATAAAAGGGCT
Found at i:776328 original size:7 final size:7
Alignment explanation
Indices: 776318--776343 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
776308 TTATATACAT
776318 AATACTA
1 AATACTA
776325 AATACTA
1 AATACTA
776332 AATACTA
1 AATACTA
776339 AATAC
1 AATAC
776344 CAATCGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:776553 original size:20 final size:20
Alignment explanation
Indices: 776516--776553 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
776506 ATTATTTTTA
*
776516 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
776536 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
776554 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:777454 original size:22 final size:22
Alignment explanation
Indices: 777424--777505 Score: 87
Period size: 22 Copynumber: 3.7 Consensus size: 22
777414 TAGGGATTTA
*
777424 AGAGAAATTTAAGAGGAAATTG
1 AGAGAAATTTGAGAGGAAATTG
* *
777446 AGAGCAATTTGAGAGCAAATTG
1 AGAGAAATTTGAGAGGAAATTG
*
777468 AGAGGTAA-TTGAGAGGAAATTG
1 AGA-GAAATTTGAGAGGAAATTG
777490 AGA-AAATAATTGAGAG
1 AGAGAAAT--TTGAGAG
777506 ATGATTAGTT
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
20 2 0.04
22 38 0.76
23 10 0.20
ACGTcount: A:0.46, C:0.02, G:0.29, T:0.22
Consensus pattern (22 bp):
AGAGAAATTTGAGAGGAAATTG
Found at i:777468 original size:11 final size:11
Alignment explanation
Indices: 777435--777492 Score: 80
Period size: 11 Copynumber: 5.3 Consensus size: 11
777425 GAGAAATTTA
777435 AGAGGAAATTG
1 AGAGGAAATTG
* *
777446 AGAGCAATTTG
1 AGAGGAAATTG
*
777457 AGAGCAAATTG
1 AGAGGAAATTG
*
777468 AGAGGTAATTG
1 AGAGGAAATTG
777479 AGAGGAAATTG
1 AGAGGAAATTG
777490 AGA
1 AGA
777493 AAATAATTGA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 41 1.00
ACGTcount: A:0.43, C:0.03, G:0.33, T:0.21
Consensus pattern (11 bp):
AGAGGAAATTG
Found at i:782422 original size:25 final size:25
Alignment explanation
Indices: 782385--782434 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
782375 ATCCTAAATA
782385 TCTCTTTAAGTTAAATTTGTTTACC
1 TCTCTTTAAGTTAAATTTGTTTACC
*
782410 TCTCTTTAGGTTAAATTTGTTTACC
1 TCTCTTTAAGTTAAATTTGTTTACC
782435 CCATATGGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.22, C:0.16, G:0.10, T:0.52
Consensus pattern (25 bp):
TCTCTTTAAGTTAAATTTGTTTACC
Found at i:786453 original size:28 final size:29
Alignment explanation
Indices: 786415--786479 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 29
786405 ATTTGTACAT
* * *
786415 GATGGGTTCTGAA-AAATAGTTTTGAGGG
1 GATGGGTTCTGAAGAAATAATTTTGACGA
786443 GATGGGTTCTGAAGAAATAATTTTGACGA
1 GATGGGTTCTGAAGAAATAATTTTGACGA
786472 GATGGGTT
1 GATGGGTT
786480 GAGTTTTGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 13 0.39
29 20 0.61
ACGTcount: A:0.29, C:0.05, G:0.34, T:0.32
Consensus pattern (29 bp):
GATGGGTTCTGAAGAAATAATTTTGACGA
Found at i:788796 original size:20 final size:20
Alignment explanation
Indices: 788738--788812 Score: 84
Period size: 20 Copynumber: 3.8 Consensus size: 20
788728 GCTTATGCTC
788738 AGTAAATGGAATGG-AAGGTA
1 AGTAAATGGAATGGTAA-GTA
*
788758 AGTTAAT-GACAT-GTAAAGTA
1 AGTAAATGGA-ATGGT-AAGTA
788778 AGTAAATGGAATGGTAAGTA
1 AGTAAATGGAATGGTAAGTA
*
788798 AGTAAATGGAGTGGT
1 AGTAAATGGAATGGT
788813 TCATAGTCTT
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
19 3 0.06
20 38 0.81
21 6 0.13
ACGTcount: A:0.43, C:0.01, G:0.31, T:0.25
Consensus pattern (20 bp):
AGTAAATGGAATGGTAAGTA
Found at i:790545 original size:16 final size:16
Alignment explanation
Indices: 790524--790558 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
790514 TAGAAATTGA
790524 AGAAGTTCAGAAAAAT
1 AGAAGTTCAGAAAAAT
*
790540 AGAAGTTCAGAAGAAT
1 AGAAGTTCAGAAAAAT
790556 AGA
1 AGA
790559 GGTTGGGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.54, C:0.06, G:0.23, T:0.17
Consensus pattern (16 bp):
AGAAGTTCAGAAAAAT
Found at i:793438 original size:19 final size:19
Alignment explanation
Indices: 793414--793451 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
793404 CTAAAAAAGT
793414 TGAGAGAATGATGA-ATGAG
1 TGAGAG-ATGATGAGATGAG
793433 TGAGAGATGATGAGATGAG
1 TGAGAGATGATGAGATGAG
793452 GGATGATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.39, C:0.00, G:0.39, T:0.21
Consensus pattern (19 bp):
TGAGAGATGATGAGATGAG
Found at i:799790 original size:27 final size:27
Alignment explanation
Indices: 799752--799805 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
799742 ATGATTATAA
799752 CTTACTCCTCCCTTGCTAAAATTTCTT
1 CTTACTCCTCCCTTGCTAAAATTTCTT
799779 CTTACTCCTCCCTTGCTAAAATTTCTT
1 CTTACTCCTCCCTTGCTAAAATTTCTT
799806 TCTCAACTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.19, C:0.33, G:0.04, T:0.44
Consensus pattern (27 bp):
CTTACTCCTCCCTTGCTAAAATTTCTT
Found at i:805448 original size:19 final size:19
Alignment explanation
Indices: 805424--805461 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
805414 CTAAAAAAGT
805424 TGAGAGAATGATGA-ATGAG
1 TGAGAG-ATGATGAGATGAG
805443 TGAGAGATGATGAGATGAG
1 TGAGAGATGATGAGATGAG
805462 GGATAATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.39, C:0.00, G:0.39, T:0.21
Consensus pattern (19 bp):
TGAGAGATGATGAGATGAG
Found at i:809597 original size:12 final size:12
Alignment explanation
Indices: 809580--809606 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
809570 GGAACAGCCT
809580 AAGCTTAAACTA
1 AAGCTTAAACTA
809592 AAGCTTAAACTA
1 AAGCTTAAACTA
809604 AAG
1 AAG
809607 GTACTTCCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.15, G:0.11, T:0.22
Consensus pattern (12 bp):
AAGCTTAAACTA
Found at i:828354 original size:94 final size:94
Alignment explanation
Indices: 828245--828729 Score: 537
Period size: 94 Copynumber: 5.2 Consensus size: 94
828235 CTACAGTTTT
* * ** * * *
828245 TATACCCCTGAAGTTGCAGTAGGTTAGAATGAAACTACAATGGTGAATCTTATCTCCCTGAAGTT
1 TATACCCCTAAAGTTGCAGTAGGTTAGATTGAAGTTACCATAGCGAATCTTATCTCCCTGAAGTT
* * * * *
828310 ACAATGGAGTAAGATGAAGTTATAAATCC
66 GCAGTGGAGCAAGATGAAGCTACAAATCC
* * *
828339 TATACCCCTAAAGTTGCAGTGGGTTAGATTGAAGCTACCATAGCGAATCTTATCTCCTTGAAGTT
1 TATACCCCTAAAGTTGCAGTAGGTTAGATTGAAGTTACCATAGCGAATCTTATCTCCCTGAAGTT
* *
828404 GCAATGGAGTAAGATGAAGCTACAAATCC
66 GCAGTGGAGCAAGATGAAGCTACAAATCC
* * * *
828433 TATACCCCTGAAGTTGCAGCAGG-TCGCATTGAAGTTACCATAGCGAATCTTAGT-TACCTGAAG
1 TATACCCCTAAAGTTGCAGTAGGTTAG-ATTGAAGTTACCATAGCGAATCTTA-TCTCCCTGAAG
*
828496 TTACAGTGGAGCAAGATGAAGCTACAAATCC
64 TTGCAGTGGAGCAAGATGAAGCTACAAATCC
* * * * * * * * * * *
828527 TATGCCCCTAAAGCTGTAATGGGTCAGAATGAAGTTACTAT-GCTGAATTTTATCTCCCTAAATT
1 TATACCCCTAAAGTTGCAGTAGGTTAGATTGAAGTTACCATAGC-GAATCTTATCTCCCTGAAGT
828591 TGCAGTGGAGCAAGATGAAGCTACAAATCC
65 TGCAGTGGAGCAAGATGAAGCTACAAATCC
* * * * * *
828621 TATGCCCCTAAAGTTGCAGT-GGTCAGATTTAAGTTACCATAGCAAATCTTATCTCCTTAAAGTT
1 TATACCCCTAAAGTTGCAGTAGGTTAGATTGAAGTTACCATAGCGAATCTTATCTCCCTGAAGTT
* *
828685 GTAGTGGAGCAAGATGAAGCTCCAAATCC
66 GCAGTGGAGCAAGATGAAGCTACAAATCC
*
828714 TATACCCCTGAAGTTG
1 TATACCCCTAAAGTTG
828730 TAGTGGAGTA
Statistics
Matches: 334, Mismatches: 51, Indels: 13
0.84 0.13 0.03
Matches are distributed among these distances:
93 80 0.24
94 252 0.75
95 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (94 bp):
TATACCCCTAAAGTTGCAGTAGGTTAGATTGAAGTTACCATAGCGAATCTTATCTCCCTGAAGTT
GCAGTGGAGCAAGATGAAGCTACAAATCC
Found at i:828424 original size:50 final size:48
Alignment explanation
Indices: 828289--828751 Score: 137
Period size: 44 Copynumber: 9.9 Consensus size: 48
828279 CTACAATGGT
* *
828289 GAATCTTATCTCCCTGAAGTTACAATGGAGTAAGATGAAG-T--TATA
1 GAATCTTATCTCCCTGAAGTTGCAATGGAGTAAGATGAAGCTACCATA
* * * *
828334 -AATCCTATAC-CCCTAAAGTTGCAGTGG-GTTAGATTGAAGCTACCATA
1 GAATCTTAT-CTCCCTGAAGTTGCAATGGAGTAAGA-TGAAGCTACCATA
*
828381 GCGAATCTTATCTCCTTGAAGTTGCAATGGAGTAAGATGAAGCTA-C--A
1 --GAATCTTATCTCCCTGAAGTTGCAATGGAGTAAGATGAAGCTACCATA
* * * *
828428 -AATCCTATAC-CCCTGAAGTTGC-A-GCAGGT-CGCATTGAAGTTACCATA
1 GAATCTTAT-CTCCCTGAAGTTGCAATGGA-GTAAG-A-TGAAGCTACCATA
* * * *
828475 GCGAATCTTAGT-TACCTGAAGTTACAGTGGAGCAAGATGAAGCTA-C--A
1 --GAATCTTA-TCTCCCTGAAGTTGCAATGGAGTAAGATGAAGCTACCATA
* * * * * * * *
828522 -AATCCTATGC-CCCTAAAGCTGTAATGG-GTCAGAATGAAGTTACTATGCT
1 GAATCTTAT-CTCCCTGAAGTTGCAATGGAGTAAG-ATGAAGCTACCAT--A
* * * * *
828571 GAATTTTATCTCCCTAAATTTGCAGTGGAGCAAGATGAAGCTA-C--A
1 GAATCTTATCTCCCTGAAGTTGCAATGGAGTAAGATGAAGCTACCATA
* * * * * *
828616 -AATCCTATGC-CCCTAAAGTTGCAGT-G-GTCAGATTTAAGTTACCATA
1 GAATCTTAT-CTCCCTGAAGTTGCAATGGAGTAAGA-TGAAGCTACCATA
* * * * *
828662 GCAAATCTTATCTCCTTAAAGTTGTAGTGGAGCAAGATGAAGCT-CC--A
1 G--AATCTTATCTCCCTGAAGTTGCAATGGAGTAAGATGAAGCTACCATA
* * *
828709 -AATCCTATAC-CCCTGAAGTTGTAGTGGAGTAAGATGAAGCTAC
1 GAATCTTAT-CTCCCTGAAGTTGCAATGGAGTAAGATGAAGCTAC
828752 AAATCCTATA
Statistics
Matches: 304, Mismatches: 65, Indels: 98
0.65 0.14 0.21
Matches are distributed among these distances:
42 7 0.02
43 20 0.07
44 132 0.43
45 7 0.02
46 1 0.00
47 7 0.02
48 1 0.00
49 26 0.09
50 85 0.28
51 15 0.05
52 3 0.01
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (48 bp):
GAATCTTATCTCCCTGAAGTTGCAATGGAGTAAGATGAAGCTACCATA
Found at i:828442 original size:138 final size:138
Alignment explanation
Indices: 828300--828869 Score: 386
Period size: 138 Copynumber: 4.1 Consensus size: 138
828290 AATCTTATCT
* * * *
828300 CCCTGAAGTTACAATGGAGTAAGATGAAGTTATAAATCCTATACCCCTAAAGTTGCAGTGGGTTA
1 CCCTGAAGTTGCAATGGAGTAAGATGAAGCTACAAATCCTATACCCCTAAAGTTGCAGTGGGTCA
* * *
828365 GATTGAAGCTACCATAGCGAATCTTATCTCCTTGAAGTTGCAATGGAGTAAGATGAAGCTACAAA
66 GATTGAAGCTACCATAGCAAATCTTATCTCCTTAAAGTTGCAATGGAGCAAGATGAAGCTACAAA
828430 TCCTATAC
131 TCCTATAC
* * * * *
828438 CCCTGAAGTTGC-A-GCAGGT-CGCATTGAAGTTACCATAGCGAATCTTAGTTA--CCTGAAGTT
1 CCCTGAAGTTGCAATGGA-GTAAG-A-TGAAG----C-TA-CAAATCCTA--TACCCCTAAAGTT
* * * * *
828498 ACAGTGGAG-CAAGA-TGAAG----C-TA-CAAATCCTATGC-CCCTAAAGCTGTAATGG-GTC-
55 GCAGTGG-GTC-AGATTGAAGCTACCATAGCAAATCTTAT-CTCCTTAAAGTTGCAATGGAG-CA
* * *
828552 AGAATGAAGTTAC-TATGCTGAATTTTATC
116 AG-ATGAAGCTACAAATCCT--A---TA-C
* * * * *
828581 TCCCTAAATTTGCAGTGGAGCAAGATGAAGCTACAAATCCTATGCCCCTAAAGTTGCAGT-GGTC
1 -CCCTGAAGTTGCAATGGAGTAAGATGAAGCTACAAATCCTATACCCCTAAAGTTGCAGTGGGTC
* * * * *
828645 AGATTTAAGTTACCATAGCAAATCTTATCTCCTTAAAGTTGTAGTGGAGCAAGATGAAGCTCCAA
65 AGATTGAAGCTACCATAGCAAATCTTATCTCCTTAAAGTTGCAATGGAGCAAGATGAAGCTACAA
828710 ATCCTATAC
130 ATCCTATAC
* * * * * * * *
828719 CCCTGAAGTTGTAGTGGAGTAAGATGAAGCTACAAATCCTATATCCCTGAATTTGTAATGGGTCG
1 CCCTGAAGTTGCAATGGAGTAAGATGAAGCTACAAATCCTATACCCCTAAAGTTGCAGTGGGTCA
* * * * * *
828784 GATTGAAGTTATCATAACAAATCTTATCT-CTCTAAAGTTGCAGTGGAGCCAGATGAAGTTACAA
66 GATTGAAGCTACCATAGCAAATCTTATCTCCT-TAAAGTTGCAATGGAGCAAGATGAAGCTACAA
828848 ATCCTATAC
130 ATCCTATAC
*
828857 CCTTGAAGTTGCA
1 CCCTGAAGTTGCA
828870 GTGGGTCGGA
Statistics
Matches: 330, Mismatches: 60, Indels: 84
0.70 0.13 0.18
Matches are distributed among these distances:
136 8 0.02
137 68 0.21
138 144 0.44
139 8 0.02
140 2 0.01
141 1 0.00
142 6 0.02
143 35 0.11
144 47 0.14
145 6 0.02
146 5 0.02
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (138 bp):
CCCTGAAGTTGCAATGGAGTAAGATGAAGCTACAAATCCTATACCCCTAAAGTTGCAGTGGGTCA
GATTGAAGCTACCATAGCAAATCTTATCTCCTTAAAGTTGCAATGGAGCAAGATGAAGCTACAAA
TCCTATAC
Found at i:828729 original size:44 final size:44
Alignment explanation
Indices: 828680--828873 Score: 160
Period size: 44 Copynumber: 4.3 Consensus size: 44
828670 TATCTCCTTA
*
828680 AAGTTGTAGTGGAGCAAGATGAAGCTCCAAATCCTATACCCCTG
1 AAGTTGTAGTGGAGCAAGATGAAGCTACAAATCCTATACCCCTG
* *
828724 AAGTTGTAGTGGAGTAAGATGAAGCTACAAATCCTATATCCCTG
1 AAGTTGTAGTGGAGCAAGATGAAGCTACAAATCCTATACCCCTG
* * * * * *
828768 AATTTGTAATGG-GTC-GGATTGAAGTTATCATAACAAATCTTAT-CTCTCTA
1 AAGTTGTAGTGGAG-CAAGA-TGAAG----C-T-ACAAATCCTATAC-CCCTG
* * * *
828818 AAGTTGCAGTGGAGCCAGATGAAGTTACAAATCCTATACCCTTG
1 AAGTTGTAGTGGAGCAAGATGAAGCTACAAATCCTATACCCCTG
*
828862 AAGTTGCAGTGG
1 AAGTTGTAGTGG
828874 GTCGGATTGA
Statistics
Matches: 118, Mismatches: 20, Indels: 24
0.73 0.12 0.15
Matches are distributed among these distances:
43 3 0.03
44 80 0.68
45 2 0.02
48 1 0.01
49 1 0.01
50 28 0.24
51 3 0.03
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (44 bp):
AAGTTGTAGTGGAGCAAGATGAAGCTACAAATCCTATACCCCTG
Found at i:828891 original size:138 final size:137
Alignment explanation
Indices: 828590--828873 Score: 390
Period size: 138 Copynumber: 2.1 Consensus size: 137
828580 CTCCCTAAAT
* * * *
828590 TTGCAGTGGAGCAAGATGAAGCTACAAATCCTATGCCCCTAAAGTTGCAGTGGTCAGATTTAAGT
1 TTGCAGTGGAGTAAGATGAAGCTACAAATCCTATACCCCTAAAGTTGCAATGGTCAGATTGAAGT
* * *
828655 TACCATAGCAAATCTTATCTCCTTAAAGTTGTAGTGGAGCAAGATGAAGCTCCAAATCCTATACC
66 TACCATAACAAATCTTATCTCCTTAAAGTTGCAGTGGAGCAAGATGAAGCTACAAATCCTATACC
828720 CCTGAAG
131 CCTGAAG
* * * * * *
828727 TTGTAGTGGAGTAAGATGAAGCTACAAATCCTATATCCCTGAATTTGTAATGGGTCGGATTGAAG
1 TTGCAGTGGAGTAAGATGAAGCTACAAATCCTATACCCCTAAAGTTGCAAT-GGTCAGATTGAAG
* * *
828792 TTATCATAACAAATCTTATCT-CTCTAAAGTTGCAGTGGAGCCAGATGAAGTTACAAATCCTATA
65 TTACCATAACAAATCTTATCTCCT-TAAAGTTGCAGTGGAGCAAGATGAAGCTACAAATCCTATA
*
828856 CCCTTGAAG
129 CCCCTGAAG
828865 TTGCAGTGG
1 TTGCAGTGG
828874 GTCGGATTGA
Statistics
Matches: 127, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
137 45 0.35
138 82 0.65
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.29
Consensus pattern (137 bp):
TTGCAGTGGAGTAAGATGAAGCTACAAATCCTATACCCCTAAAGTTGCAATGGTCAGATTGAAGT
TACCATAACAAATCTTATCTCCTTAAAGTTGCAGTGGAGCAAGATGAAGCTACAAATCCTATACC
CCTGAAG
Found at i:828919 original size:50 final size:50
Alignment explanation
Indices: 828859--828954 Score: 174
Period size: 50 Copynumber: 1.9 Consensus size: 50
828849 TCCTATACCC
* *
828859 TTGAAGTTGCAGTGGGTCGGATTGAAACTACAATAACAAATCTTATTTAA
1 TTGAAGTTGCAGTGGGTCAGATTGAAACTACAACAACAAATCTTATTTAA
828909 TTGAAGTTGCAGTGGGTCAGATTGAAACTACAACAACAAATCTTAT
1 TTGAAGTTGCAGTGGGTCAGATTGAAACTACAACAACAAATCTTAT
828955 CTTCTCGAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (50 bp):
TTGAAGTTGCAGTGGGTCAGATTGAAACTACAACAACAAATCTTATTTAA
Found at i:828941 original size:94 final size:94
Alignment explanation
Indices: 828721--828941 Score: 261
Period size: 94 Copynumber: 2.4 Consensus size: 94
828711 TCCTATACCC
* * * *
828721 CTGAAGTTGTAGTGGAGTAAGATGAAGCTACAAATCCTATATCCCTGAATTTGTAATGGGTCGGA
1 CTGAAGTTGCAGTGGAGTCAGATGAAGCTACAAATCCTATATCCCTGAAGTTGCAATGGGTCGGA
** *
828786 TTGAAGTTATCATAACAAATCTTATCTCT
66 TTGAAACTATCATAACAAATCTTATCTAT
* * * *
828815 CTAAAGTTGCAGTGGAGCCAGATGAAGTTACAAATCCTATA-CCCTTGAAGTTGCAGTGGGTCGG
1 CTGAAGTTGCAGTGGAGTCAGATGAAGCTACAAATCCTATATCCC-TGAAGTTGCAATGGGTCGG
*
828879 ATTGAAACTA-CAATAACAAATCTTATTTAAT
65 ATTGAAACTATC-ATAACAAATCTTATCT-AT
*
828910 -TGAAGTTGCAGTGG-GTCAGATTGAAACTACAA
1 CTGAAGTTGCAGTGGAGTCAGA-TGAAGCTACAA
828942 CAACAAATCT
Statistics
Matches: 107, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
93 9 0.08
94 97 0.91
95 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.30
Consensus pattern (94 bp):
CTGAAGTTGCAGTGGAGTCAGATGAAGCTACAAATCCTATATCCCTGAAGTTGCAATGGGTCGGA
TTGAAACTATCATAACAAATCTTATCTAT
Found at i:828965 original size:50 final size:50
Alignment explanation
Indices: 828861--828969 Score: 166
Period size: 50 Copynumber: 2.2 Consensus size: 50
828851 CTATACCCTT
* * *
828861 GAAGTTGCAGTGGGTCGGATTGAAACTACAATAACAAATCTTATTTAATT
1 GAAGTTGCAGTGGGTCAGATTGAAACTACAACAACAAATCTTATTTAATC
*
828911 GAAGTTGCAGTGGGTCAGATTGAAACTACAACAACAAATCTTATCTT-CTC
1 GAAGTTGCAGTGGGTCAGATTGAAACTACAACAACAAATCTTAT-TTAATC
828961 GAAGTTGCA
1 GAAGTTGCA
828970 ATGGAGCAAG
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
50 52 0.96
51 2 0.04
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (50 bp):
GAAGTTGCAGTGGGTCAGATTGAAACTACAACAACAAATCTTATTTAATC
Found at i:829306 original size:15 final size:16
Alignment explanation
Indices: 829281--829315 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
829271 CCCAAATACA
829281 AAAACCCTAAAAGCCC
1 AAAACCCTAAAAGCCC
829297 AAAA-CCTAAAAGCCC
1 AAAACCCTAAAAGCCC
829312 AAAA
1 AAAA
829316 TTTAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.57, C:0.31, G:0.06, T:0.06
Consensus pattern (16 bp):
AAAACCCTAAAAGCCC
Found at i:830535 original size:29 final size:30
Alignment explanation
Indices: 830497--830553 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
830487 AGTCCTTTAC
* *
830497 TTATTTAATTTC-ACCCCTTTTATTTTTTG
1 TTATTCAATTTCTACCCCTTTTAATTTTTG
*
830526 TTATTCAATTTCTAGCCCTTTTAATTTT
1 TTATTCAATTTCTACCCCTTTTAATTTT
830554 CTTAATTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.19, C:0.18, G:0.04, T:0.60
Consensus pattern (30 bp):
TTATTCAATTTCTACCCCTTTTAATTTTTG
Found at i:835112 original size:84 final size:88
Alignment explanation
Indices: 835011--835178 Score: 227
Period size: 84 Copynumber: 2.0 Consensus size: 88
835001 GGGAGACAGG
* * *
835011 ATCTACAATTTTTAACCTACTCCACTGCTGCTCA-GGA-AGAGGA-CAAGTTTTCAATCTGCTTC
1 ATCTACAATCTTCAACCTACTCCACTACTGCTCAGGGAGAGAGGACCAAGTTTTCAATCTGCTTC
*
835073 ACTGCC-AGTACAGGAAGACAAA
66 ACTGCCTAGTACAAGAAGACAAA
* * ** *
835095 ATCTACAATCTTCAACCTACTCCACTACTGCTCAGGGAGATAGGACCAATTTTTTTATCTGTTTC
1 ATCTACAATCTTCAACCTACTCCACTACTGCTCAGGGAGAGAGGACCAAGTTTTCAATCTGCTTC
835160 ACTGCCTAGTACAAGAAGA
66 ACTGCCTAGTACAAGAAGA
835179 TGAGATATGT
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
84 31 0.44
85 3 0.04
86 5 0.07
87 21 0.30
88 11 0.15
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (88 bp):
ATCTACAATCTTCAACCTACTCCACTACTGCTCAGGGAGAGAGGACCAAGTTTTCAATCTGCTTC
ACTGCCTAGTACAAGAAGACAAA
Found at i:835282 original size:89 final size:89
Alignment explanation
Indices: 835189--835373 Score: 232
Period size: 89 Copynumber: 2.1 Consensus size: 89
835179 TGAGATATGT
* *
835189 TATCTTCAGACTACTCCGCTGCAAACTCAGGGAGG-CAAGGCTGGCGTCTTCGATCTAC-TTCGC
1 TATCTTCAGACTACTCCGCTGCAAACTCAGGGAGGTC-AGGCCGACGTCTTCGATCTACATT-GC
* *
835252 TGCCAATGCA-GAATGACAAGATCTGC
64 TACCAATACAGGAA-GACAAGATCTGC
* * * * *
835278 TATCTTTAGTCTGCTCCGCTGCAAACTCAGGGAGGTCAGGCCGATGTCTTTGATCTACATTGCTA
1 TATCTTCAGACTACTCCGCTGCAAACTCAGGGAGGTCAGGCCGACGTCTTCGATCTACATTGCTA
*
835343 CCAGTACAGGAAGACAAGATCTGC
66 CCAATACAGGAAGACAAGATCTGC
835367 TATCTTC
1 TATCTTC
835374 TTTAATCCAT
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
89 76 0.93
90 6 0.07
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.26
Consensus pattern (89 bp):
TATCTTCAGACTACTCCGCTGCAAACTCAGGGAGGTCAGGCCGACGTCTTCGATCTACATTGCTA
CCAATACAGGAAGACAAGATCTGC
Found at i:836351 original size:97 final size:97
Alignment explanation
Indices: 836218--836439 Score: 356
Period size: 97 Copynumber: 2.3 Consensus size: 97
836208 AACAAAGCTC
*
836218 AATTAATCAAGATAGCAAACTTTT-CTAGGATAAGATGAAAAAGATTATCACAATGGATAAGATG
1 AATTAATCAAGATAGCAAA-TTTTGCTAAGATAAGATGAAAAAGATTATCACAATGGATAAGATG
*
836282 AAATTTTATTGAGAGCACAGCTTGAAATAAATA
65 AAATTTTATTGAGAGCACAGCTCGAAATAAATA
* * *
836315 AATTAATCAAGATATCATATTTTGCTAAGATAAGATGAAAAATATTATCACAATGGATAAGATGA
1 AATTAATCAAGATAGCAAATTTTGCTAAGATAAGATGAAAAAGATTATCACAATGGATAAGATGA
*
836380 AATTTTATTGAGAGCACAGCTCGAAATGAATA
66 AATTTTATTGAGAGCACAGCTCGAAATAAATA
* *
836412 AATTAATTAAGATAGAAAATTTTGCTAA
1 AATTAATCAAGATAGCAAATTTTGCTAA
836440 TATGAAAACA
Statistics
Matches: 114, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
96 4 0.04
97 110 0.96
ACGTcount: A:0.46, C:0.09, G:0.15, T:0.30
Consensus pattern (97 bp):
AATTAATCAAGATAGCAAATTTTGCTAAGATAAGATGAAAAAGATTATCACAATGGATAAGATGA
AATTTTATTGAGAGCACAGCTCGAAATAAATA
Found at i:836739 original size:1 final size:1
Alignment explanation
Indices: 836735--836783 Score: 53
Period size: 1 Copynumber: 49.0 Consensus size: 1
836725 ATTTTTCTTC
* * * * *
836735 TTTTTTTTTCTTTTCTTTTTTATTTTTTCTTTTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
836784 AACATTCTTT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.02, C:0.06, G:0.02, T:0.90
Consensus pattern (1 bp):
T
Found at i:836740 original size:11 final size:10
Alignment explanation
Indices: 836708--836782 Score: 80
Period size: 10 Copynumber: 7.6 Consensus size: 10
836698 TTGGCCTCTC
836708 TTTTTTCTTT
1 TTTTTTCTTT
* * *
836718 TTCTTCCATT
1 TTTTTTCTTT
*
836728 TTTCTTCTTT
1 TTTTTTCTTT
836738 TTTTTTCTTT
1 TTTTTTCTTT
* *
836748 TCTTTT-TTA
1 TTTTTTCTTT
836757 TTTTTTCTTT
1 TTTTTTCTTT
*
836767 TTTTTTGTTT
1 TTTTTTCTTT
836777 TTTTTT
1 TTTTTT
836783 TAACATTCTT
Statistics
Matches: 51, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
9 7 0.14
10 44 0.86
ACGTcount: A:0.03, C:0.12, G:0.01, T:0.84
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:836744 original size:30 final size:30
Alignment explanation
Indices: 836708--836778 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
836698 TTGGCCTCTC
836708 TTTTTTCTTTTTCTTCCATT-TTTCTTCTTT
1 TTTTTTCTTTTTCTT-CATTATTTCTTCTTT
** *
836738 TTTTTTC-TTTTCTTTTTTATTTTTTCTTT
1 TTTTTTCTTTTTCTTCATTATTTCTTCTTT
*
836767 TTTTTTGTTTTT
1 TTTTTTCTTTTT
836779 TTTTTAACAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 2 0.06
29 22 0.63
30 11 0.31
ACGTcount: A:0.03, C:0.13, G:0.01, T:0.83
Consensus pattern (30 bp):
TTTTTTCTTTTTCTTCATTATTTCTTCTTT
Found at i:836762 original size:24 final size:24
Alignment explanation
Indices: 836708--836783 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
836698 TTGGCCTCTC
*
836708 TTTTTTCTTTTTC-TTCCATTTTTCT
1 TTTTTTCTTTTTCTTTTC-TTTTT-T
*
836733 TCTTTT-TTTTTCTTTTCTTTTTT
1 TTTTTTCTTTTTCTTTTCTTTTTT
*
836756 ATTTTTTCTTTTT-TTTTGTTTTTT
1 -TTTTTTCTTTTTCTTTTCTTTTTT
836780 TTTT
1 TTTT
836784 AACATTCTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
23 5 0.11
24 26 0.59
25 13 0.30
ACGTcount: A:0.03, C:0.12, G:0.01, T:0.84
Consensus pattern (24 bp):
TTTTTTCTTTTTCTTTTCTTTTTT
Found at i:836781 original size:19 final size:19
Alignment explanation
Indices: 836735--836781 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
836725 ATTTTTCTTC
836735 TTTTTTTTTCTTTTCTTTT
1 TTTTTTTTTCTTTTCTTTT
*
836754 TTATTTTTTCTTTT-TTTT
1 TTTTTTTTTCTTTTCTTTT
836772 TGTTTTTTTT
1 T-TTTTTTTT
836782 TTAACATTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 5 0.20
19 20 0.80
ACGTcount: A:0.02, C:0.06, G:0.02, T:0.89
Consensus pattern (19 bp):
TTTTTTTTTCTTTTCTTTT
Found at i:836782 original size:29 final size:30
Alignment explanation
Indices: 836727--836784 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
836717 TTTCTTCCAT
836727 TTTTCTTCTTTTTTTTTCTTTTCTTTTTTA
1 TTTTCTTCTTTTTTTTTCTTTTCTTTTTTA
*
836757 TTTT-TTCTTTTTTTTTGTTTT-TTTTTTA
1 TTTTCTTCTTTTTTTTTCTTTTCTTTTTTA
836785 ACATTCTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 7 0.26
29 16 0.59
30 4 0.15
ACGTcount: A:0.03, C:0.09, G:0.02, T:0.86
Consensus pattern (30 bp):
TTTTCTTCTTTTTTTTTCTTTTCTTTTTTA
Found at i:841425 original size:20 final size:18
Alignment explanation
Indices: 841400--841451 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
841390 TGCATGAATA
841400 ATAATAGATTAATAACATAT
1 ATAATA-ATTAATAACAT-T
841420 ATAATAATGATAATAACATT
1 ATAATAAT--TAATAACATT
*
841440 AAAATAATTAAT
1 ATAATAATTAAT
841452 TAAATAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
18 4 0.14
19 2 0.07
20 14 0.48
21 9 0.31
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (18 bp):
ATAATAATTAATAACATT
Found at i:841427 original size:23 final size:20
Alignment explanation
Indices: 841397--841447 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 20
841387 AAGTGCATGA
841397 ATAATAATAGATTAATAACATAT
1 ATAATAAT-GA-TAATAACAT-T
841420 ATAATAATGATAATAACATT
1 ATAATAATGATAATAACATT
*
841440 AAAATAAT
1 ATAATAAT
841448 TAATTAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 8 0.30
21 9 0.33
22 2 0.07
23 8 0.30
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (20 bp):
ATAATAATGATAATAACATT
Found at i:843988 original size:4 final size:4
Alignment explanation
Indices: 843979--844011 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
843969 TAAATAGACG
843979 CATA CATA CATA CATA CATA CATA CATA CATA C
1 CATA CATA CATA CATA CATA CATA CATA CATA C
844012 CTAACTTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:847761 original size:20 final size:20
Alignment explanation
Indices: 847736--847833 Score: 76
Period size: 20 Copynumber: 4.9 Consensus size: 20
847726 TATGGGATTG
*
847736 CACTTCGGTGCCTCTGTTTA
1 CACTTCAGTGCCTCTGTTTA
* * *
847756 CACTTCAGTGTCTCTATTCA
1 CACTTCAGTGCCTCTGTTTA
* * *
847776 CAC-TAAGGTGCCTCTGGTTG
1 CACTTCA-GTGCCTCTGTTTA
*
847796 CA-TAATC-GTGCCTCTGTTTG
1 CACT--TCAGTGCCTCTGTTTA
847816 CACTTCAGTGCCTCTGTT
1 CACTTCAGTGCCTCTGTT
847834 ACGCATTTAT
Statistics
Matches: 60, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
19 4 0.07
20 54 0.90
21 1 0.02
22 1 0.02
ACGTcount: A:0.14, C:0.29, G:0.19, T:0.38
Consensus pattern (20 bp):
CACTTCAGTGCCTCTGTTTA
Found at i:852361 original size:207 final size:204
Alignment explanation
Indices: 851977--852379 Score: 585
Period size: 207 Copynumber: 2.0 Consensus size: 204
851967 GATTTCTGCT
* * * *
851977 GATATTCGACCATTTAAAGTTGCTGCAATTAGTTAGAAATTGACCAAAAAGCTTGCTGCTATCTA
1 GATATTCGACCATTTAAAGTTACTGCAACTAGTTAGAAATTGACCAAAAAGCTTACTGCTATATA
* * * *
852042 GTTAAAAATATTCACATAGTTTTATCTTTTGACAAGAGTTGTTTCAACTAGATATTGTCAAGATG
66 GTTAAAAATAGTCACATAGTTCTATCTTTTGACAAGAGTTGTTTCAACTAGATACTGCCAAGATG
* * *
852107 ATTCTAACATTTTCTTATTTAAGTTGATGATGATATGTTTTCAGATTAGGAAAAAATAGAAAAGC
131 ATTCTAACATTTGCTTATTTAAGTTAATGATGATATGTTTCCAGATTAGGAAAAAATAGAAAAGC
852172 ACTACTACG
196 ACTACTACG
* *
852181 GATATTCGACCATTTAAAGTTACTGGAACTAGTTATAAATTGACCAGAAAA-CTTACTGCTATAT
1 GATATTCGACCATTTAAAGTTACTGCAACTAGTTAGAAATTGACCA-AAAAGCTTACTGCTATAT
* * * *
852245 AGTTCAAAATAGTCAGATCGTTAGTTCTATCTTTTGCCAAGAGTTGTTTCAACTAGTTACTGCCA
65 AGTTAAAAATAGTC--A-C-ATAGTTCTATCTTTTGACAAGAGTTGTTTCAACTAGATACTGCCA
*
852310 A-ATGATTCTAACATTTGCTTATTTAAGTTAATGATGTTATGTTTCCAGATTAGGAAAAAATAGA
126 AGATGATTCTAACATTTGCTTATTTAAGTTAATGATGATATGTTTCCAGATTAGGAAAAAATAGA
852374 AAAGCA
191 AAAGCA
852380 TATAGAGAAG
Statistics
Matches: 176, Mismatches: 18, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
204 65 0.37
205 4 0.02
206 1 0.01
207 66 0.38
208 40 0.23
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (204 bp):
GATATTCGACCATTTAAAGTTACTGCAACTAGTTAGAAATTGACCAAAAAGCTTACTGCTATATA
GTTAAAAATAGTCACATAGTTCTATCTTTTGACAAGAGTTGTTTCAACTAGATACTGCCAAGATG
ATTCTAACATTTGCTTATTTAAGTTAATGATGATATGTTTCCAGATTAGGAAAAAATAGAAAAGC
ACTACTACG
Found at i:868427 original size:26 final size:27
Alignment explanation
Indices: 868371--868429 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
868361 ATATATGTTT
** *
868371 TTTATTTTTAAAATACTTTTTTATTTT
1 TTTATTTTTAAAATACTTTTTTAGGTG
868398 TTTATTTTTAAAATA-TATTTTT-GGTG
1 TTTATTTTTAAAATACT-TTTTTAGGTG
868424 TTTATT
1 TTTATT
868430 AAAAAAAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 8 0.29
27 20 0.71
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (27 bp):
TTTATTTTTAAAATACTTTTTTAGGTG
Found at i:873591 original size:27 final size:27
Alignment explanation
Indices: 873532--873598 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 27
873522 TACTCATCAG
*
873532 GCCCCATGTTTAATGTCCTAATAGACT
1 GCCCCGTGTTTAATGTCCTAATAGACT
** * * *
873559 TTCCCGTGTTTATTGTCCTAGTGGACT
1 GCCCCGTGTTTAATGTCCTAATAGACT
*
873586 GCCCCGTTTTTAA
1 GCCCCGTGTTTAA
873599 CGTCTTGACG
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (27 bp):
GCCCCGTGTTTAATGTCCTAATAGACT
Found at i:877192 original size:23 final size:22
Alignment explanation
Indices: 877160--877221 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
877150 TTTAAGTGGA
877160 TATGTT-GAAGGGTATATTGGT
1 TATGTTCGAAGGGTATATTGGT
*
877181 TATGGTTGGAA-GGTATACTTGGT
1 TAT-GTTCGAAGGGTATA-TTGGT
* *
877204 TGTGTTCGAAGGTTATAT
1 TATGTTCGAAGGGTATAT
877222 ATATATGGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
21 3 0.09
22 16 0.47
23 15 0.44
ACGTcount: A:0.23, C:0.03, G:0.32, T:0.42
Consensus pattern (22 bp):
TATGTTCGAAGGGTATATTGGT
Found at i:877240 original size:50 final size:46
Alignment explanation
Indices: 877167--877330 Score: 154
Period size: 50 Copynumber: 3.5 Consensus size: 46
877157 GGATATGTTG
* * * * *
877167 AAGGGTATAT-TGGTTATGGTTGGAAGGTATACTTGGTTGTGTTCG
1 AAGGATATATATGGTTGTGTTTGGAAGGTATAATTGGTTGTGTTCA
*
877212 AAGGTTATATATATATGGTTGTGTTTGGAAGGTATATTTGGTTGTGTTCA
1 AAGG----ATATATATGGTTGTGTTTGGAAGGTATAATTGGTTGTGTTCA
* * **
877262 AAGGATACATATGGTTGTGTTTGGAGGGTA-AATTGGTTGTGTTTG
1 AAGGATATATATGGTTGTGTTTGGAAGGTATAATTGGTTGTGTTCA
* *
877307 GAGGCTATGAT-TGGTTGTGTTTGG
1 AAGGATAT-ATATGGTTGTGTTTGG
877331 TGGGTGATAG
Statistics
Matches: 100, Mismatches: 13, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
45 34 0.34
46 26 0.26
49 5 0.05
50 35 0.35
ACGTcount: A:0.21, C:0.03, G:0.34, T:0.42
Consensus pattern (46 bp):
AAGGATATATATGGTTGTGTTTGGAAGGTATAATTGGTTGTGTTCA
Found at i:877253 original size:23 final size:23
Alignment explanation
Indices: 877170--877330 Score: 118
Period size: 23 Copynumber: 6.9 Consensus size: 23
877160 TATGTTGAAG
* *
877170 GGTATA-TTGGTTATGGTTGGAA
1 GGTATATTTGGTTGTGTTTGGAA
* *
877192 GGTATACTTGGTTGTG-TTCGAA
1 GGTATATTTGGTTGTGTTTGGAA
877214 GGTTATATATATATGGTTGTGTTTGGAA
1 GG---TATAT-T-TGGTTGTGTTTGGAA
**
877242 GGTATATTTGGTTGTG-TTCAAA
1 GGTATATTTGGTTGTGTTTGGAA
* * *
877264 GGATACATATGGTTGTGTTTGGAG
1 GG-TATATTTGGTTGTGTTTGGAA
*
877288 GGTA-AATTGGTTGTGTTTGG-A
1 GGTATATTTGGTTGTGTTTGGAA
877309 GGCTATGA-TTGGTTGTGTTTGG
1 GG-TAT-ATTTGGTTGTGTTTGG
877331 TGGGTGATAG
Statistics
Matches: 113, Mismatches: 14, Indels: 23
0.75 0.09 0.15
Matches are distributed among these distances:
21 2 0.02
22 35 0.31
23 44 0.39
24 7 0.06
25 9 0.08
26 1 0.01
27 8 0.07
28 7 0.06
ACGTcount: A:0.20, C:0.03, G:0.34, T:0.43
Consensus pattern (23 bp):
GGTATATTTGGTTGTGTTTGGAA
Found at i:879060 original size:32 final size:32
Alignment explanation
Indices: 879013--879075 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
879003 GCTAAATTTC
*
879013 TAATCAATCCCAATTTCTTCAAGGGTTTGTAT
1 TAATCAATCCCAATTTCTTCAAGGATTTGTAT
**
879045 TAATCAATCTTAATTTCTTCAAGGATTTGTA
1 TAATCAATCCCAATTTCTTCAAGGATTTGTA
879076 CTAAATCTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (32 bp):
TAATCAATCCCAATTTCTTCAAGGATTTGTAT
Found at i:884434 original size:17 final size:17
Alignment explanation
Indices: 884412--884445 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
884402 GACTAACCCC
*
884412 TATACATCACTTAGGTA
1 TATACATCACCTAGGTA
*
884429 TATACATTACCTAGGTA
1 TATACATCACCTAGGTA
884446 CATGCCACAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (17 bp):
TATACATCACCTAGGTA
Found at i:886499 original size:15 final size:15
Alignment explanation
Indices: 886471--886512 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
886461 GATTCGTCTC
* *
886471 TTCTATTCTGTTTCTT
1 TTCT-TTCTTTTTCTA
886487 TTCTTTCTTTTTCTA
1 TTCTTTCTTTTTCTA
886502 TTCTTTCTTTT
1 TTCTTTCTTTT
886513 GTTTTATGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 20 0.83
16 4 0.17
ACGTcount: A:0.05, C:0.19, G:0.02, T:0.74
Consensus pattern (15 bp):
TTCTTTCTTTTTCTA
Found at i:886536 original size:5 final size:5
Alignment explanation
Indices: 886522--886594 Score: 64
Period size: 5 Copynumber: 14.6 Consensus size: 5
886512 TGTTTTATGT
886522 ATATA TATATA ATATA ATATA ATAT- AT-TA ATAATA ATATA ATATA A-A-A
1 ATATA -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA ATATA ATATA
* *
886570 ACATA ATCATTA CTATA ATATA ATA
1 ATATA AT-A-TA ATATA ATATA ATA
886595 ATATTTTTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
3 3 0.05
4 6 0.11
5 34 0.60
6 11 0.19
7 3 0.05
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:886548 original size:19 final size:19
Alignment explanation
Indices: 886524--886566 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
886514 TTTTATGTAT
886524 ATATATATAAT-ATAATATA
1 ATATAT-TAATAATAATATA
886543 ATATATTAATAATAATATA
1 ATATATTAATAATAATATA
886562 ATATA
1 ATATA
886567 AAAACATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATATTAATAATAATATA
Found at i:886576 original size:24 final size:25
Alignment explanation
Indices: 886530--886595 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 25
886520 GTATATATAT
* *
886530 ATAATATAATATAATATATTAAT-A
1 ATAATATAATATAATAAAATAATCA
886554 ATAATATAATATAA-AAACATAATCA
1 ATAATATAATATAATAAA-ATAATCA
* *
886579 TTACTATAATATAATAA
1 ATAATATAATATAATAA
886596 TATTTTTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
23 2 0.06
24 18 0.51
25 13 0.37
26 2 0.06
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (25 bp):
ATAATATAATATAATAAAATAATCA
Found at i:887830 original size:23 final size:23
Alignment explanation
Indices: 887804--887877 Score: 112
Period size: 23 Copynumber: 3.2 Consensus size: 23
887794 TGATTTTTAA
* *
887804 ATTTTGAATTATTTAATGATAAT
1 ATTTAGAATTATTTAGTGATAAT
*
887827 ATTTACAATTATTTAGTGATAAT
1 ATTTAGAATTATTTAGTGATAAT
*
887850 ATTTAGGATTATTTAGTGATAAT
1 ATTTAGAATTATTTAGTGATAAT
887873 ATTTA
1 ATTTA
887878 TAAAAAATCT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.01, G:0.11, T:0.50
Consensus pattern (23 bp):
ATTTAGAATTATTTAGTGATAAT
Found at i:888784 original size:5 final size:5
Alignment explanation
Indices: 888774--888806 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
888764 TCAAATCTAT
888774 TTTTA TTTTA TTTTA TTTTA TTTT- TTTGTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTT-TA TTT
888807 CCTTATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 3 0.12
5 20 0.77
6 3 0.12
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:889536 original size:42 final size:43
Alignment explanation
Indices: 889489--889582 Score: 111
Period size: 41 Copynumber: 2.2 Consensus size: 43
889479 GTTTTTTGGT
* * *
889489 TTAGGGTTTTTAAGGTTAGTGTTTTGTTAAAATAATTT-AGGG
1 TTAGGGTTTTTAAGGGTAGGGTTTTGTAAAAATAATTTAAGGG
* * **
889531 TTAGGG-TTGTAGGGGTAGGGTTTTGTAAAAATAATTTAAGTT
1 TTAGGGTTTTTAAGGGTAGGGTTTTGTAAAAATAATTTAAGGG
889573 TTAGGGTTTT
1 TTAGGGTTTT
889583 AGGAATTTTA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
41 26 0.62
42 14 0.33
43 2 0.05
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.46
Consensus pattern (43 bp):
TTAGGGTTTTTAAGGGTAGGGTTTTGTAAAAATAATTTAAGGG
Found at i:896478 original size:22 final size:21
Alignment explanation
Indices: 896429--896487 Score: 77
Period size: 19 Copynumber: 2.8 Consensus size: 21
896419 AGGAAACTAA
896429 ATTAAAAAATAAAAAAATTAT
1 ATTAAAAAATAAAAAAATTAT
*
896450 ATT--AAAATAGAAAAATTAT
1 ATTAAAAAATAAAAAAATTAT
896469 ATTACAAAAATATAAAAAA
1 ATTA-AAAAATA-AAAAAA
896488 GATAAAATAG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 18 0.56
21 3 0.09
22 6 0.19
23 5 0.16
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (21 bp):
ATTAAAAAATAAAAAAATTAT
Found at i:896857 original size:22 final size:21
Alignment explanation
Indices: 896832--896872 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
896822 TTTTTTACTT
*
896832 TTTTTAAATTAATAAAAATACA
1 TTTTAAAATTAA-AAAAATACA
*
896854 TTTTAAAATTTAAAAAATA
1 TTTTAAAATTAAAAAAATA
896873 TGTATGAAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
TTTTAAAATTAAAAAAATACA
Found at i:898254 original size:22 final size:21
Alignment explanation
Indices: 898224--898264 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
898214 TTTTTTACTT
*
898224 TTTTTAAATTAATAAAAATACA
1 TTTTAAAATTAA-AAAAATACA
*
898246 TTTTAAAATTTAAAAAATA
1 TTTTAAAATTAAAAAAATA
898265 TGTATGAAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
TTTTAAAATTAAAAAAATACA
Found at i:901062 original size:93 final size:93
Alignment explanation
Indices: 900903--901088 Score: 372
Period size: 93 Copynumber: 2.0 Consensus size: 93
900893 AGCCTTTCAA
900903 CCATCATCGTTGCCCATGGTATTTATTTATCCTCCTTTTAGCAAGCATCTTAATGAGTAGATTAG
1 CCATCATCGTTGCCCATGGTATTTATTTATCCTCCTTTTAGCAAGCATCTTAATGAGTAGATTAG
900968 TGATTCAATCTACTATTTTACTTTATTT
66 TGATTCAATCTACTATTTTACTTTATTT
900996 CCATCATCGTTGCCCATGGTATTTATTTATCCTCCTTTTAGCAAGCATCTTAATGAGTAGATTAG
1 CCATCATCGTTGCCCATGGTATTTATTTATCCTCCTTTTAGCAAGCATCTTAATGAGTAGATTAG
901061 TGATTCAATCTACTATTTTACTTTATTT
66 TGATTCAATCTACTATTTTACTTTATTT
901089 TGTATAGGTT
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 93 1.00
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (93 bp):
CCATCATCGTTGCCCATGGTATTTATTTATCCTCCTTTTAGCAAGCATCTTAATGAGTAGATTAG
TGATTCAATCTACTATTTTACTTTATTT
Found at i:903860 original size:41 final size:41
Alignment explanation
Indices: 903758--903860 Score: 143
Period size: 41 Copynumber: 2.5 Consensus size: 41
903748 CCATTAGTGG
* * * *
903758 CGTTTTTTCCATAAACGTCACAAAAGATAAAGCAATAGCAG
1 CGTTTTTCCCATAAACGCCGCAAAAGATAAAGCAATAGCAA
* *
903799 CGTTTTTCCTATAAACGCCGCAAAAGGTAAAGCAATAGCAA
1 CGTTTTTCCCATAAACGCCGCAAAAGATAAAGCAATAGCAA
*
903840 CGTTTTTCCCATAAATGCCGC
1 CGTTTTTCCCATAAACGCCGC
903861 GAATTATTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (41 bp):
CGTTTTTCCCATAAACGCCGCAAAAGATAAAGCAATAGCAA
Found at i:905886 original size:51 final size:50
Alignment explanation
Indices: 905761--905956 Score: 205
Period size: 51 Copynumber: 3.9 Consensus size: 50
905751 GATGGTCATG
* ** * * **
905761 TGTGTAGTACTATGTGCAGGCTACTACGTTTACC-GAAATGATAGGTCACA
1 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATA-GTTTCGTCACA
*
905811 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGATCACG
1 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTTTCG-TCACA
* *** * * * * *
905862 TGTGTAGTACTATGTGTAGGCTACTACATGTATCGAATGGTAATAGTCACA
1 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-TTCGTCACA
905913 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTTTC
1 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTTTC
905957 NNNNNNNNNN
Statistics
Matches: 116, Mismatches: 27, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
50 35 0.30
51 79 0.68
52 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (50 bp):
TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGTCACA
Found at i:905939 original size:102 final size:101
Alignment explanation
Indices: 905760--905956 Score: 317
Period size: 102 Copynumber: 1.9 Consensus size: 101
905750 TGATGGTCAT
* *
905760 GTGTGTAGTACTATGTGCAGGCTACTACGTTTACCGAAATGATAGGTCACATGTGTAGTACTATG
1 GTGTGTAGTACTATGTGCAGGCTACTACATGTACCGAAATGATAGGTCACATGTGTAGTACTATG
905825 TGCAGGCTACTATGCGTACCGGATAGTTTCGATCAC
66 TGCAGGCTACTATGCGTACCGGATAGTTTCGATCAC
* *
905861 GTGTGTAGTACTATGTGTAGGCTACTACATGTATCG-AATGGTAATA-GTCACATGTGTAGTACT
1 GTGTGTAGTACTATGTGCAGGCTACTACATGTACCGAAAT-G--ATAGGTCACATGTGTAGTACT
905924 ATGTGCAGGCTACTATGCGTACCGGATAGTTTC
63 ATGTGCAGGCTACTATGCGTACCGGATAGTTTC
905957 NNNNNNNNNN
Statistics
Matches: 89, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
100 3 0.03
101 33 0.37
102 50 0.56
103 3 0.03
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (101 bp):
GTGTGTAGTACTATGTGCAGGCTACTACATGTACCGAAATGATAGGTCACATGTGTAGTACTATG
TGCAGGCTACTATGCGTACCGGATAGTTTCGATCAC
Found at i:912657 original size:16 final size:16
Alignment explanation
Indices: 912636--912668 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
912626 AATAATTTCT
*
912636 AAAAAAATGTATATGA
1 AAAAAAATGCATATGA
912652 AAAAAAATGCATATGA
1 AAAAAAATGCATATGA
912668 A
1 A
912669 TTAGAAAATG
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:0.64, C:0.03, G:0.12, T:0.21
Consensus pattern (16 bp):
AAAAAAATGCATATGA
Found at i:912954 original size:3 final size:3
Alignment explanation
Indices: 912946--912984 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
912936 ATAGGCGTAT
*
912946 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA TTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
912985 TCAATAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:916318 original size:133 final size:133
Alignment explanation
Indices: 916144--916472 Score: 597
Period size: 133 Copynumber: 2.5 Consensus size: 133
916134 CACTTCACTG
* *
916144 CCAGTATGGGAAGATAAGA-CATGTATATTTGATCCACTTCGCTACCGATATAGGAAGACAGGAC
1 CCAGTATGGGAAGACAAGATC-TGTATATTCGATCCACTTCGCTACCGATATAGGAAGACAGGAC
* *
916208 CTATTATCTTTGATCTACTTCACGCCAGTACATGAATATAAGATCTATTTTCTTCGATCTACTCC
65 CTATTATCTTTGATCTACTTCACGCCAGTACATGAAGATAAGATCTATTTTATTCGATCTACTCC
916273 ACCA
130 ACCA
916277 CCAGTATGGGAAGACAAGATCTGTATATTCGATCCACTTCGCTACCGATATAGGAAGACAGGACC
1 CCAGTATGGGAAGACAAGATCTGTATATTCGATCCACTTCGCTACCGATATAGGAAGACAGGACC
916342 TATTATCTTTGATCTACTTCACGCCAGTACATGAAGATAAGATCTATTTTATTCGATCTACTCCA
66 TATTATCTTTGATCTACTTCACGCCAGTACATGAAGATAAGATCTATTTTATTCGATCTACTCCA
916407 CCA
131 CCA
*
916410 CCAGTATGGGAAGACAAGATCTGTATATTCGATCCACTTCGCTACCAATATAGGAAGACAGGA
1 CCAGTATGGGAAGACAAGATCTGTATATTCGATCCACTTCGCTACCGATATAGGAAGACAGGA
916473 TCTGCTGCTT
Statistics
Matches: 190, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
133 189 0.99
134 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (133 bp):
CCAGTATGGGAAGACAAGATCTGTATATTCGATCCACTTCGCTACCGATATAGGAAGACAGGACC
TATTATCTTTGATCTACTTCACGCCAGTACATGAAGATAAGATCTATTTTATTCGATCTACTCCA
CCA
Found at i:916475 original size:89 final size:90
Alignment explanation
Indices: 916131--916475 Score: 220
Period size: 89 Copynumber: 3.9 Consensus size: 90
916121 TGTAATCTTT
** * * * * *
916131 GATC-ACTTCACTGCCAGTATGGGAAGATAAGA-C-ATGTATATTTGATCCACTTCGCTACCGAT
1 GATCTACTTCACCACCAGTATAGGAAGACAAGATCTA-GTATATTCGATCCACTTCACTACCAAT
* * * *
916193 ATAGGAAGACAGGACCTATTATCTTT
65 ATAGGAAGACAAGATCTATTATATTC
* * * * * * * * * * * *
916219 GATCTACTTCA-CGCCAGTACATGAATATAAGATCTATTTTCTTCGATCTACTCCACCACCAGTA
1 GATCTACTTCACCACCAGTATAGGAAGACAAGATCTAGTATATTCGATCCACTTCACTACCAATA
* *
916283 TGGGAAGACAAGATCT-GTATATTC
66 TAGGAAGACAAGATCTATTATATTC
* * * * * * * * * * *
916307 GATCCACTTCGCTACC-GATATAGGAAGACAGGACCTATTATCTTTGATCTACTTCAC-GCCAGT
1 GATCTACTTCACCACCAG-TATAGGAAGACAAGATCTAGTATATTCGATCCACTTCACTACCAAT
* * * *
916370 ACATGAAGATAAGATCTATTTTATTC
65 ATAGGAAGACAAGATCTATTATATTC
* * *
916396 GATCTACTCCACCACCAGTATGGGAAGACAAGATCT-GTATATTCGATCCACTTCGCTACCAATA
1 GATCTACTTCACCACCAGTATAGGAAGACAAGATCTAGTATATTCGATCCACTTCACTACCAATA
*
916460 TAGGAAGACAGGATCT
66 TAGGAAGACAAGATCT
916476 GCTGCTTTTC
Statistics
Matches: 190, Mismatches: 59, Indels: 15
0.72 0.22 0.06
Matches are distributed among these distances:
88 68 0.36
89 120 0.63
90 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (90 bp):
GATCTACTTCACCACCAGTATAGGAAGACAAGATCTAGTATATTCGATCCACTTCACTACCAATA
TAGGAAGACAAGATCTATTATATTC
Found at i:916476 original size:44 final size:44
Alignment explanation
Indices: 916114--916476 Score: 207
Period size: 44 Copynumber: 8.2 Consensus size: 44
916104 CTTAGGGAGG
* * * *
916114 CAAGATCTGTAATCTTTGAT-CACTTCACTGCCAGTATGGGAAGA
1 CAAGATCTGT-ATATTCGATCCACTTCACTACCAGTATAGGAAGA
* * *
916158 TAAGA-CATGTATATTTGATCCACTTCGCTACC-GATATAGGAAGA
1 CAAGATC-TGTATATTCGATCCACTTCACTACCAG-TATAGGAAGA
* * * * * * * * * *
916202 CAGGACCTATTATCTTTGATCTACTTCAC-GCCAGTACATGAATA
1 CAAGATCT-GTATATTCGATCCACTTCACTACCAGTATAGGAAGA
* * * * * * * *
916246 TAAGATCTATTTTCTTCGATCTACTCCACCACCAGTATGGGAAGA
1 CAAGATCT-GTATATTCGATCCACTTCACTACCAGTATAGGAAGA
*
916291 CAAGATCTGTATATTCGATCCACTTCGCTACC-GATATAGGAAGA
1 CAAGATCTGTATATTCGATCCACTTCACTACCAG-TATAGGAAGA
* * * * * * * * *
916335 CAGGACCTATTATCTTTGATCTACTTCAC-GCCAGTACATGAAGA
1 CAAGATCT-GTATATTCGATCCACTTCACTACCAGTATAGGAAGA
* * * * * * *
916379 TAAGATCTATTTTATTCGATCTACTCCACCACCAGTATGGGAAGA
1 CAAGATCT-GTATATTCGATCCACTTCACTACCAGTATAGGAAGA
* *
916424 CAAGATCTGTATATTCGATCCACTTCGCTACCAATATAGGAAGA
1 CAAGATCTGTATATTCGATCCACTTCACTACCAGTATAGGAAGA
*
916468 CAGGATCTG
1 CAAGATCTG
916477 CTGCTTTTCA
Statistics
Matches: 242, Mismatches: 66, Indels: 22
0.73 0.20 0.07
Matches are distributed among these distances:
43 11 0.05
44 162 0.67
45 69 0.29
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (44 bp):
CAAGATCTGTATATTCGATCCACTTCACTACCAGTATAGGAAGA
Found at i:927952 original size:18 final size:18
Alignment explanation
Indices: 927929--927966 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
927919 TTTTTAAAAC
927929 AAAATAA-AAAAAAGGAAA
1 AAAATAACAAAAAA-GAAA
*
927947 AAAATAACGAAAAAGAAA
1 AAAATAACAAAAAAGAAA
927965 AA
1 AA
927967 CAGAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.82, C:0.03, G:0.11, T:0.05
Consensus pattern (18 bp):
AAAATAACAAAAAAGAAA
Found at i:929042 original size:18 final size:17
Alignment explanation
Indices: 929009--929047 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
928999 TTTTGTAAAT
929009 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
929027 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
929044 TGTG
1 TGTG
929048 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:929297 original size:23 final size:23
Alignment explanation
Indices: 929284--929369 Score: 120
Period size: 23 Copynumber: 3.7 Consensus size: 23
929274 GTAGCTTTGG
929284 CTACATTTCAGTGGTAGCTACGA
1 CTACATTTCAGTGGTAGCTACGA
* * *
929307 CTACATATCAGTGGTAACTTCGA
1 CTACATTTCAGTGGTAGCTACGA
*
929330 CTACATTTCAGTGGTAGCTACGG
1 CTACATTTCAGTGGTAGCTACGA
929353 CTAC-TTATCAGTGGTAG
1 CTACATT-TCAGTGGTAG
929370 TTTCAGTTAT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
22 2 0.04
23 53 0.96
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (23 bp):
CTACATTTCAGTGGTAGCTACGA
Found at i:929820 original size:11 final size:10
Alignment explanation
Indices: 929794--929818 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
929784 TCTGACTTTG
929794 AAAAATTGTT
1 AAAAATTGTT
929804 AAAAATTGTT
1 AAAAATTGTT
929814 AAAAA
1 AAAAA
929819 ATAATTACGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (10 bp):
AAAAATTGTT
Found at i:937960 original size:5 final size:6
Alignment explanation
Indices: 937944--937968 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
937934 ATTAATTTTT
937944 TAAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA TAAAAA T
937969 TACTTTTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
TAAAAA
Found at i:940444 original size:21 final size:22
Alignment explanation
Indices: 940408--940458 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
940398 AAACTTGAAT
940408 TCTT-ACTTTCTCTCTTTAA-TC
1 TCTTCACTTTCTCTC-TTAACTC
*
940429 TCTTCACTTTCT-TCTTAACTT
1 TCTTCACTTTCTCTCTTAACTC
940450 TCTTCACTT
1 TCTTCACTT
940459 CAATCTCCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 4 0.15
21 16 0.59
22 7 0.26
ACGTcount: A:0.14, C:0.29, G:0.00, T:0.57
Consensus pattern (22 bp):
TCTTCACTTTCTCTCTTAACTC
Found at i:945835 original size:40 final size:40
Alignment explanation
Indices: 945780--945987 Score: 265
Period size: 40 Copynumber: 5.2 Consensus size: 40
945770 ATTGAACATA
* * * *
945780 CCAGACAAAAGCTCATACGAGTTAATCCAATCGAAACACG
1 CCAGACAGAAGCTCATAAGAGCTAATCCAATCGAAACAAG
* * *
945820 CCAGACAGACGCTCATAAGAGCTAATCCAATTGAAACACG
1 CCAGACAGAAGCTCATAAGAGCTAATCCAATCGAAACAAG
* * * *
945860 CCAGACAGAATCTCATAAGAGTTAATCCAACCGAAACATG
1 CCAGACAGAAGCTCATAAGAGCTAATCCAATCGAAACAAG
* * *
945900 CTAGACAGAAGCTCATGAGAGCTAATCTAATCGAAACAAG
1 CCAGACAGAAGCTCATAAGAGCTAATCCAATCGAAACAAG
* *
945940 CCAGACAGAAGCTCATAAGAGCTAATACAACCGAAACAAG
1 CCAGACAGAAGCTCATAAGAGCTAATCCAATCGAAACAAG
945980 -CAGACAGA
1 CCAGACAGA
945988 GAGTATAACA
Statistics
Matches: 145, Mismatches: 23, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
39 8 0.06
40 137 0.94
ACGTcount: A:0.43, C:0.25, G:0.17, T:0.14
Consensus pattern (40 bp):
CCAGACAGAAGCTCATAAGAGCTAATCCAATCGAAACAAG
Found at i:953047 original size:9 final size:9
Alignment explanation
Indices: 953033--953062 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
953023 AAAATATCAT
953033 ATTAATTTA
1 ATTAATTTA
*
953042 ATTAATTTG
1 ATTAATTTA
953051 ATTAATTTA
1 ATTAATTTA
953060 ATT
1 ATT
953063 TTCCTTGTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (9 bp):
ATTAATTTA
Found at i:953141 original size:13 final size:13
Alignment explanation
Indices: 953125--953157 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
953115 TTTTTCAAGA
953125 AAATTCTTTAATC
1 AAATTCTTTAATC
953138 AAATTCTTTAATC
1 AAATTCTTTAATC
953151 AAATTCT
1 AAATTCT
953158 CTAGTTGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.39, C:0.15, G:0.00, T:0.45
Consensus pattern (13 bp):
AAATTCTTTAATC
Found at i:954260 original size:15 final size:15
Alignment explanation
Indices: 954240--954269 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
954230 CTATGCATGC
*
954240 AAAATATAAAAGACA
1 AAAATACAAAAGACA
954255 AAAATACAAAAGACA
1 AAAATACAAAAGACA
954270 TAACAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.73, C:0.10, G:0.07, T:0.10
Consensus pattern (15 bp):
AAAATACAAAAGACA
Found at i:962949 original size:14 final size:15
Alignment explanation
Indices: 962930--962960 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
962920 ATTTTTATAC
962930 TTTTAATAT-AAATT
1 TTTTAATATAAAATT
962944 TTTTAATATAAAATT
1 TTTTAATATAAAATT
962959 TT
1 TT
962961 CTATACAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTTAATATAAAATT
Found at i:963209 original size:26 final size:27
Alignment explanation
Indices: 963174--963235 Score: 90
Period size: 26 Copynumber: 2.3 Consensus size: 27
963164 CTTTTCCCCA
* *
963174 AAAAAATTTACTTCCTCCAAACCCC-C
1 AAAAATTTTACTTCCGCCAAACCCCTC
*
963200 AAAACTTTTACTTCCGCCAAACCCCTC
1 AAAAATTTTACTTCCGCCAAACCCCTC
963227 AAAAATTTT
1 AAAAATTTT
963236 TTTCCCTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 22 0.71
27 9 0.29
ACGTcount: A:0.37, C:0.34, G:0.02, T:0.27
Consensus pattern (27 bp):
AAAAATTTTACTTCCGCCAAACCCCTC
Found at i:969989 original size:41 final size:41
Alignment explanation
Indices: 969932--970035 Score: 181
Period size: 41 Copynumber: 2.5 Consensus size: 41
969922 TTTAACATAT
* *
969932 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
1 TCACCGGCACGTAGCCTGCTAGGCTTATAACCTGATTCAGA
*
969973 TCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACGTAGCCTGCTAGGCTTATAACCTGATTCAGA
970014 TCACCGGCACGTAGCCTGCTAG
1 TCACCGGCACGTAGCCTGCTAG
970036 NNNNNNNNNN
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.22, C:0.30, G:0.23, T:0.25
Consensus pattern (41 bp):
TCACCGGCACGTAGCCTGCTAGGCTTATAACCTGATTCAGA
Found at i:976070 original size:28 final size:29
Alignment explanation
Indices: 976024--976085 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 29
976014 TTGATTTATG
*
976024 TTATAAAAATATT-ATTTAA-TTAAAATA
1 TTATAAAAATATTAATTAAAGTTAAAATA
* *
976051 TTATAAATTATATTAATTAAAGTTAAGATA
1 TTATAAA-AATATTAATTAAAGTTAAAATA
976081 TTATA
1 TTATA
976086 TTATAGGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 7 0.24
28 5 0.17
29 5 0.17
30 12 0.41
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (29 bp):
TTATAAAAATATTAATTAAAGTTAAAATA
Found at i:976254 original size:19 final size:22
Alignment explanation
Indices: 976216--976258 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
976206 TTGTGAATAA
976216 AATATTATTATATGATTATTAT
1 AATATTATTATATGATTATTAT
*
976238 AATA-TATTATTATTATTATTA
1 AATATTATTA-TATGATTATTA
976259 ACTAATGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
AATATTATTATATGATTATTAT
Found at i:976306 original size:17 final size:18
Alignment explanation
Indices: 976284--976319 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
976274 GGAATAAAAT
*
976284 AAAAGAATAAA-AGAAAC
1 AAAAGAAGAAATAGAAAC
976301 AAAAGAAGAAATAGAAAC
1 AAAAGAAGAAATAGAAAC
976319 A
1 A
976320 GAATAGCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.75, C:0.06, G:0.14, T:0.06
Consensus pattern (18 bp):
AAAAGAAGAAATAGAAAC
Found at i:976764 original size:23 final size:22
Alignment explanation
Indices: 976737--976822 Score: 115
Period size: 21 Copynumber: 4.0 Consensus size: 22
976727 GCTTTACTGA
976737 TCAGGCACTTTATGTGTCGTAT
1 TCAGGCACTTTATGTGTCGTAT
976759 CTCAGGCACTTTATGTGTCGTA-
1 -TCAGGCACTTTATGTGTCGTAT
* * *
976781 TCAGGCACCTTGTGTGTCAT-T
1 TCAGGCACTTTATGTGTCGTAT
976802 TCAGGCAC-TTATGTGTCGTAT
1 TCAGGCACTTTATGTGTCGTAT
976823 ACTAATCAGG
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
20 9 0.16
21 26 0.46
23 21 0.38
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.38
Consensus pattern (22 bp):
TCAGGCACTTTATGTGTCGTAT
Found at i:976787 original size:44 final size:41
Alignment explanation
Indices: 976736--976822 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 41
976726 GGCTTTACTG
*
976736 ATCAGGCACTTTATGTGTCGTATCTCAGGCACTTTATGTGTCGT
1 ATCAGGCACCTTATGTGTC--ATCTCAGGCAC-TTATGTGTCGT
* *
976780 ATCAGGCACCTTGTGTGTCATTTCAGGCACTTATGTGTCGT
1 ATCAGGCACCTTATGTGTCATCTCAGGCACTTATGTGTCGT
976821 AT
1 AT
976823 ACTAATCAGG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
41 13 0.32
42 10 0.25
44 17 0.43
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.38
Consensus pattern (41 bp):
ATCAGGCACCTTATGTGTCATCTCAGGCACTTATGTGTCGT
Found at i:982874 original size:3 final size:3
Alignment explanation
Indices: 982866--982903 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
982856 GCAATCAGAC
982866 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
982904 GATTTAGTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:983366 original size:9 final size:10
Alignment explanation
Indices: 983325--983367 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
983315 GAAGTTTTTT
983325 AAAATTATTAA
1 AAAATTA-TAA
*
983336 ATAAATCATAA
1 A-AAATTATAA
983347 AAAATTATAA
1 AAAATTATAA
983357 AAAATT-TAA
1 AAAATTATAA
983366 AA
1 AA
983368 TACAATGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 5 0.17
10 14 0.48
11 5 0.17
12 5 0.17
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (10 bp):
AAAATTATAA
Found at i:987415 original size:21 final size:21
Alignment explanation
Indices: 987374--987412 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
987364 ATTCAATTTT
*
987374 TTTTATTTAATTTATTATTAA
1 TTTTATTTAATTTATGATTAA
*
987395 TTTTATTT-TTTTATGATT
1 TTTTATTTAATTTATGATT
987413 TAAAAATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (21 bp):
TTTTATTTAATTTATGATTAA
Found at i:987769 original size:21 final size:21
Alignment explanation
Indices: 987730--987770 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
987720 TTATTTAATT
987730 TAAATTTTTATGATATAAAAA
1 TAAATTTTTATGATATAAAAA
*
987751 TAAATATTTTAT-ATTTAAAA
1 TAAAT-TTTTATGATATAAAA
987771 TCCTAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
TAAATTTTTATGATATAAAAA
Found at i:988070 original size:13 final size:14
Alignment explanation
Indices: 988044--988081 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
988034 CTAAAAAAAT
988044 TAAATA-TATAATAA
1 TAAATATTATAAT-A
988058 TATAATATTATAATA
1 TA-AATATTATAATA
988073 TAAATATTA
1 TAAATATTA
988082 AAAGATTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 9 0.41
15 7 0.32
16 6 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TAAATATTATAATA
Found at i:989462 original size:34 final size:35
Alignment explanation
Indices: 989418--989484 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
989408 CAGTAAAATG
*
989418 TTTTCCGTAAAATGATTT-CTGGAAAATATTTTAC
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
*
989452 TTTTCTGTAAAATGATTTACTAGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTT
989485 CTACTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
Found at i:989554 original size:20 final size:20
Alignment explanation
Indices: 989529--989580 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 20
989519 GAAAAAGTTG
989529 TTTTTACATATATT-AATAAA
1 TTTTTACATATATTAAAT-AA
* *
989549 TTTTT--ATATTTTAAATTA
1 TTTTTACATATATTAAATAA
989567 TTTTTACATATATT
1 TTTTTACATATATT
989581 GCAATGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
18 12 0.46
19 3 0.12
20 11 0.42
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTTACATATATTAAATAA
Found at i:991595 original size:11 final size:11
Alignment explanation
Indices: 991579--991604 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
991569 TATATAGGTA
991579 AATATTAAATT
1 AATATTAAATT
991590 AATATTAAATT
1 AATATTAAATT
991601 AATA
1 AATA
991605 AAATATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
AATATTAAATT
Found at i:991628 original size:31 final size:30
Alignment explanation
Indices: 991590--991694 Score: 97
Period size: 31 Copynumber: 3.4 Consensus size: 30
991580 ATATTAAATT
*
991590 AATATTAAATTAATAAAATATTATATAGGTA
1 AATATTAAATTAATAAAATACTATATA-GTA
** * *
991621 AATATTAAATTAAATTTAAT-GTATCATA-TT
1 AATATTAAATT-AATAAAATACTAT-ATAGTA
* *
991651 AATATTAATTTAATAAAATACTATTTAGATA
1 AATATTAAATTAATAAAATACTATATAG-TA
991682 AATATTAAATTAA
1 AATATTAAATTAA
991695 ATTTAATATC
Statistics
Matches: 58, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
29 8 0.14
30 14 0.24
31 27 0.47
32 9 0.16
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (30 bp):
AATATTAAATTAATAAAATACTATATAGTA
Found at i:991657 original size:61 final size:61
Alignment explanation
Indices: 991587--991727 Score: 210
Period size: 61 Copynumber: 2.3 Consensus size: 61
991577 TAAATATTAA
* * *
991587 ATTAATATTAAATTAATAAAATATTATATAGGTAAATATTAAATTAAATTTAATGTATCAT
1 ATTAATATTAAATTAATAAAATACTATATAGATAAATATTAAATTAAATTTAATATATCAT
* * *
991648 ATTAATATTAATTTAATAAAATACTATTTAGATAAATATTAAATTAAATTTAATATCTCAT
1 ATTAATATTAAATTAATAAAATACTATATAGATAAATATTAAATTAAATTTAATATATCAT
*
991709 ATTAATATCTAAATAAATA
1 ATTAATAT-TAAATTAATA
991728 TTAAATTCAT
Statistics
Matches: 71, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
61 63 0.89
62 8 0.11
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.43
Consensus pattern (61 bp):
ATTAATATTAAATTAATAAAATACTATATAGATAAATATTAAATTAAATTTAATATATCAT
Found at i:993081 original size:50 final size:50
Alignment explanation
Indices: 993027--993248 Score: 322
Period size: 50 Copynumber: 4.4 Consensus size: 50
993017 GATGGTCACG
*
993027 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGGTCGCA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAATGATAGGTCGCA
* * * * * * * *
993077 TGTGTAGTACTATGTGCAGGCTACTATGCGT-TTCGGATA-GTTTCGATCACG
1 TGTGTAGTACTATGTGCAGGCTACTA--CGTGTACCGAAATG-ATAGGTCGCA
993128 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAATGATAGGTCGCA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAATGATAGGTCGCA
993178 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAATGATAGGTCGCA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAATGATAGGTCGCA
993228 TGTGTAGTACTATGTGCAGGC
1 TGTGTAGTACTATGTGCAGGC
993249 CCATCATTGA
Statistics
Matches: 150, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
49 3 0.02
50 108 0.72
51 36 0.24
52 3 0.02
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (50 bp):
TGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAATGATAGGTCGCA
Found at i:993142 original size:101 final size:101
Alignment explanation
Indices: 993022--993203 Score: 355
Period size: 101 Copynumber: 1.8 Consensus size: 101
993012 AAAGTGATGG
*
993022 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAATGATAGGTCGCATGTGTAGTAC
993087 TATGTGCAGGCTACTATGCGTTTCGGATAGTTTCGA
66 TATGTGCAGGCTACTATGCGTTTCGGATAGTTTCGA
993123 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAATGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAATGATAGGTCGCATGTGTAGTAC
993188 TATGTGCAGGCTACTA
66 TATGTGCAGGCTACTA
993204 CGTGTACCGA
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
101 80 1.00
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAATGATAGGTCGCATGTGTAGTAC
TATGTGCAGGCTACTATGCGTTTCGGATAGTTTCGA
Found at i:1002785 original size:94 final size:95
Alignment explanation
Indices: 1002665--1002853 Score: 337
Period size: 94 Copynumber: 2.0 Consensus size: 95
1002655 AGTTGAGCAA
* *
1002665 GTTGAAACCTCGTTTAATTTAAAAGACCCTTAATTTTT-TTCCTTTTTATTTTTAATAAATGACA
1 GTTGAAACCTCGTTTAATTTAAAAGACCCTTAATTTTTCAT-ATTTTTATTTTTAATAAATGACA
1002729 TACTTAGAAATTAATTTTCTTGAATTAATAC
65 TACTTAGAAATTAATTTTCTTGAATTAATAC
1002760 GTTGAAACCT-GTTTAATTTAAAAGACCCTTAATTTTTCATATTTTTATTTTTAATAAATGACAT
1 GTTGAAACCTCGTTTAATTTAAAAGACCCTTAATTTTTCATATTTTTATTTTTAATAAATGACAT
1002824 ACTTAGAAATTAATTTTCTTGAATTAATAC
66 ACTTAGAAATTAATTTTCTTGAATTAATAC
1002854 ATTAAATTAA
Statistics
Matches: 91, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
94 80 0.88
95 11 0.12
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.46
Consensus pattern (95 bp):
GTTGAAACCTCGTTTAATTTAAAAGACCCTTAATTTTTCATATTTTTATTTTTAATAAATGACAT
ACTTAGAAATTAATTTTCTTGAATTAATAC
Found at i:1008950 original size:13 final size:13
Alignment explanation
Indices: 1008934--1008958 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1008924 TTTAGTTCAT
1008934 TTATTTATTTTTG
1 TTATTTATTTTTG
1008947 TTATTTATTTTT
1 TTATTTATTTTT
1008959 TTCCTCTTAA
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:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (13 bp):
TTATTTATTTTTG
Found at i:1015695 original size:5 final size:5
Alignment explanation
Indices: 1015685--1015713 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1015675 AGCCACTTAG
1015685 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
1015714 GTCAGTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:1016053 original size:6 final size:6
Alignment explanation
Indices: 1016042--1016073 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
1016032 AGAATTAGGA
1016042 TTTGAG TTTGAG TTTGAG TTTGAG TTTGAG TT
1 TTTGAG TTTGAG TTTGAG TTTGAG TTTGAG TT
1016074 AGTTGACTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.31, T:0.53
Consensus pattern (6 bp):
TTTGAG
Found at i:1020467 original size:24 final size:24
Alignment explanation
Indices: 1020435--1020575 Score: 90
Period size: 25 Copynumber: 5.7 Consensus size: 24
1020425 CTATGTAACA
1020435 GGAAGCTCATAAGAGCCATATTCG
1 GGAAGCTCATAAGAGCCATATTCG
**
1020459 GGAAGCTCATGCGAGCCCATATT-G
1 GGAAGCTCATAAGAG-CCATATTCG
* *
1020483 GGAAGCTC-TAGAGAGCCATTAATCA
1 GGAAGCTCATA-AGAGCCA-TATTCG
* * * *
1020508 GGAAACTCATGAAAGAGCCTTTAATCA
1 GGAAGCTCAT--AAGAGCC-ATATTCG
* *
1020535 AGAAGCTC-TGGAGAGCCATATATCG
1 GGAAGCTCAT-AAGAGCCATAT-TCG
*
1020560 GGATGCTCATAAGAGC
1 GGAAGCTCATAAGAGC
1020576 TACGGTGTGT
Statistics
Matches: 89, Mismatches: 18, Indels: 19
0.71 0.14 0.15
Matches are distributed among these distances:
23 4 0.04
24 30 0.34
25 33 0.37
26 3 0.03
27 18 0.20
28 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.21
Consensus pattern (24 bp):
GGAAGCTCATAAGAGCCATATTCG
Found at i:1020702 original size:24 final size:24
Alignment explanation
Indices: 1020675--1020728 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1020665 AGAAGCTCAA
*
1020675 GAGAGCCAATAACTGGATGCTCTT
1 GAGAGCCAATAACGGGATGCTCTT
* * *
1020699 GAGAGCTATTATCGGGATGCTCTT
1 GAGAGCCAATAACGGGATGCTCTT
*
1020723 GTGAGC
1 GAGAGC
1020729 TGTGCTGTGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.28
Consensus pattern (24 bp):
GAGAGCCAATAACGGGATGCTCTT
Found at i:1029492 original size:24 final size:23
Alignment explanation
Indices: 1029438--1029506 Score: 59
Period size: 24 Copynumber: 2.9 Consensus size: 23
1029428 AGCCATGTAA
*
1029438 TAGGAAGCTCATAAGATCCATAT
1 TAGGAAGCTCATAAGAGCCATAT
* **
1029461 TCGAGAAGCTCATGCGAGCCAATAT
1 TAG-GAAGCTCATAAGAGCC-ATAT
*
1029486 TAGGAAGGTC-TAGAGAGCCAT
1 TAGGAAGCTCATA-AGAGCCAT
1029507 TAATCGAGAA
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
23 5 0.14
24 24 0.69
25 6 0.17
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.22
Consensus pattern (23 bp):
TAGGAAGCTCATAAGAGCCATAT
Found at i:1042081 original size:26 final size:26
Alignment explanation
Indices: 1041956--1042082 Score: 123
Period size: 26 Copynumber: 4.9 Consensus size: 26
1041946 CTGTTATATA
* * *
1041956 AATCATCAACTCAAAGCCTACTAACT
1 AATCACCAGCTCAAAGCCTGCTAACT
* * *
1041982 AATCATCGGCTCAAAGCCGGCTAACT
1 AATCACCAGCTCAAAGCCTGCTAACT
* *
1042008 AATCA-CTGACTCAAAGCCTACTAA-T
1 AATCACCAG-CTCAAAGCCTGCTAACT
* * *
1042033 CAGTCACTAGCTCAAAGCTTGCTAACT
1 -AATCACCAGCTCAAAGCCTGCTAACT
1042060 AATCACCAGCTCAAAGCCTGCTA
1 AATCACCAGCTCAAAGCCTGCTA
1042083 TCAGTCACAT
Statistics
Matches: 82, Mismatches: 15, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
25 3 0.04
26 77 0.94
27 2 0.02
ACGTcount: A:0.35, C:0.31, G:0.12, T:0.22
Consensus pattern (26 bp):
AATCACCAGCTCAAAGCCTGCTAACT
Found at i:1044960 original size:9 final size:9
Alignment explanation
Indices: 1044946--1044976 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1044936 GTTAAACGAA
1044946 TCGAGTTAT
1 TCGAGTTAT
*
1044955 TCGAGTTAA
1 TCGAGTTAT
1044964 TCGAGTTAT
1 TCGAGTTAT
1044973 TCGA
1 TCGA
1044977 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:1045046 original size:9 final size:9
Alignment explanation
Indices: 1045029--1045065 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
1045019 TGAGCTTTCG
1045029 AATTCGAAT
1 AATTCGAAT
*
1045038 AACTCGAAT
1 AATTCGAAT
1045047 AATTCGAAT
1 AATTCGAAT
1045056 AATTCGAAT
1 AATTCGAAT
1045065 A
1 A
1045066 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:1045336 original size:30 final size:29
Alignment explanation
Indices: 1045280--1045336 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
1045270 AACCTTTTAT
*
1045280 TTTTCCCCAAAATTTTTACTCCCTTCCAC
1 TTTTCCCCAAAACTTTTACTCCCTTCCAC
* *
1045309 TTTTCCCCTAAAACTTTTATTCTCTTCC
1 TTTTCCCC-AAAACTTTTACTCCCTTCC
1045337 CATCCCACCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.19, C:0.35, G:0.00, T:0.46
Consensus pattern (29 bp):
TTTTCCCCAAAACTTTTACTCCCTTCCAC
Done.