Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 17 of 344
Found at i:6013277 original size:19 final size:20
Alignment explanation
Indices: 6013253--6013296 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
6013243 CGTGAAAGTC
* *
6013253 TAATGCATATG-ATGCAATG
1 TAATGCAAATGCATGAAATG
6013272 TAATGCAAATGCATGAAATG
1 TAATGCAAATGCATGAAATG
6013292 -AATGC
1 TAATGC
6013297 CAAAAGAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.27
Consensus pattern (20 bp):
TAATGCAAATGCATGAAATG
Found at i:6022653 original size:16 final size:16
Alignment explanation
Indices: 6022632--6022662 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6022622 ACAATTATGT
*
6022632 AAATAATATTAAAATC
1 AAATAATAGTAAAATC
6022648 AAATAATAGTAAAAT
1 AAATAATAGTAAAAT
6022663 TATTGAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (16 bp):
AAATAATAGTAAAATC
Found at i:6035880 original size:17 final size:17
Alignment explanation
Indices: 6035858--6035892 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
6035848 TAAAAGTTAA
6035858 ATATAAAATTAGTACCC
1 ATATAAAATTAGTACCC
6035875 ATATAAAATTAGTACCC
1 ATATAAAATTAGTACCC
6035892 A
1 A
6035893 AATTTGTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.17, G:0.06, T:0.29
Consensus pattern (17 bp):
ATATAAAATTAGTACCC
Found at i:6038340 original size:20 final size:21
Alignment explanation
Indices: 6038311--6038349 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6038301 AATTTTTTAA
6038311 CTTTAAAA-TTTTTATAATTT
1 CTTTAAAATTTTTTATAATTT
*
6038331 CTTTACAATTTTTTATAAT
1 CTTTAAAATTTTTTATAAT
6038350 GTTTATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (21 bp):
CTTTAAAATTTTTTATAATTT
Found at i:6050170 original size:4 final size:5
Alignment explanation
Indices: 6050107--6050167 Score: 52
Period size: 5 Copynumber: 11.4 Consensus size: 5
6050097 TATTAAAAGG
**
6050107 AAATA AAATA AAATA AAA-A AAATA ATTTCA AAATA TAGAGATAA AAATA
1 AAATA AAATA AAATA AAATA AAATA AAAT-A AAATA -A-A-AT-A AAATA
6050156 AAATA AAATA AA
1 AAATA AAATA AA
6050168 TAATAGATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
4 4 0.09
5 30 0.65
6 6 0.13
7 2 0.04
8 3 0.07
9 1 0.02
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:6057368 original size:44 final size:44
Alignment explanation
Indices: 6057285--6057368 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 44
6057275 TTCATTTTTA
*
6057285 TTTCTATTTTGGGAAAACCACATCATTTTCAAATGATTTTATTT
1 TTTCTATTTTGGGAAAACCAAATCATTTTCAAATGATTTTATTT
* *
6057329 TTTC-ATTTTGGAGAAAACCATAATTATTTTTAAAT-ATTTT
1 TTTCTATTTTGG-GAAAACCA-AATCATTTTCAAATGATTTT
6057369 TCATTTCTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
43 7 0.20
44 17 0.49
45 11 0.31
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.49
Consensus pattern (44 bp):
TTTCTATTTTGGGAAAACCAAATCATTTTCAAATGATTTTATTT
Found at i:6063263 original size:12 final size:12
Alignment explanation
Indices: 6063237--6063280 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
6063227 CTTTTTCCAG
*
6063237 TTTTCTTCTTCTT
1 TTTTCTT-TTTTT
6063250 TTTTCTTTTTTT
1 TTTTCTTTTTTT
*
6063262 TTTTCCTTTTTT
1 TTTTCTTTTTTT
6063274 TTTTCTT
1 TTTTCTT
6063281 CTCTCACTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 21 0.75
13 7 0.25
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTCTTTTTTT
Found at i:6081539 original size:118 final size:118
Alignment explanation
Indices: 6081327--6081572 Score: 431
Period size: 118 Copynumber: 2.1 Consensus size: 118
6081317 AATATTCTTC
6081327 TTGA-TTTTTGTGGAGAGGGAGCAATCATACTTACGTAACTAGCCATGCTTGTCTTTATGCCTAT
1 TTGATTTTTTGTGGAGAGGGAGCAATCATACTTACGTAACTAGCCATGCTTGTCTTTATGCCTAT
6081391 AAGCAGAGCCTAGAACTCAAACTAATTGATGCATTAATTGCCCAAAGCAGACA
66 AAGCAGAGCCTAGAACTCAAACTAATTGATGCATTAATTGCCCAAAGCAGACA
* * *
6081444 TTGATTTTTTGTGGGGAGGGAGCAATTATACTTATGTAACTAGCCATGCTTGTCTTTATGCCTAT
1 TTGATTTTTTGTGGAGAGGGAGCAATCATACTTACGTAACTAGCCATGCTTGTCTTTATGCCTAT
* *
6081509 AAGCAGAGCTTCGAACTCAAACTAATTGATGCATTAATTGCCCAAAGCAGACA
66 AAGCAGAGCCTAGAACTCAAACTAATTGATGCATTAATTGCCCAAAGCAGACA
6081562 TTGATCTTTTT
1 TTGAT-TTTTT
6081573 TTCTTTTTCT
Statistics
Matches: 122, Mismatches: 5, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
117 4 0.03
118 113 0.93
119 5 0.04
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Consensus pattern (118 bp):
TTGATTTTTTGTGGAGAGGGAGCAATCATACTTACGTAACTAGCCATGCTTGTCTTTATGCCTAT
AAGCAGAGCCTAGAACTCAAACTAATTGATGCATTAATTGCCCAAAGCAGACA
Found at i:6084850 original size:17 final size:16
Alignment explanation
Indices: 6084804--6084851 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
6084794 TCTCAAATAG
* *
6084804 AAAATAAAAGGAAAAC
1 AAAAAAAAAGAAAAAC
* *
6084820 AAATAACAAGAAAAAC
1 AAAAAAAAAGAAAAAC
6084836 AAAAAAAATAGAAAAA
1 AAAAAAAA-AGAAAAA
6084852 AACCCAAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
16 18 0.72
17 7 0.28
ACGTcount: A:0.79, C:0.06, G:0.08, T:0.06
Consensus pattern (16 bp):
AAAAAAAAAGAAAAAC
Found at i:6085422 original size:22 final size:21
Alignment explanation
Indices: 6085397--6085460 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 21
6085387 TTAAGTATTC
6085397 TTTTTATATTTGAAATTTAATA
1 TTTTTAT-TTTGAAATTTAATA
* **
6085419 TTTTTATTTTAGAAGTTTGGTA
1 TTTTTATTTT-GAAATTTAATA
* *
6085441 CTTTTATTTTTCAAATTTAA
1 TTTTTA-TTTTGAAATTTAA
6085461 AAATTCAAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
21 3 0.09
22 25 0.78
23 4 0.12
ACGTcount: A:0.30, C:0.03, G:0.08, T:0.59
Consensus pattern (21 bp):
TTTTTATTTTGAAATTTAATA
Found at i:6088454 original size:9 final size:9
Alignment explanation
Indices: 6088442--6088529 Score: 74
Period size: 9 Copynumber: 9.4 Consensus size: 9
6088432 ATTAAATATG
6088442 AAAAATTAT
1 AAAAATTAT
6088451 AAAAATTCCAT
1 AAAAATT--AT
*
6088462 AAAAAGTAT
1 AAAAATTAT
6088471 AAAAATT-T
1 AAAAATTAT
6088479 AAAAAAGTTAT
1 -AAAAA-TTAT
6088490 AAATAATTAT
1 AAA-AATTAT
*
6088500 -AAAATAAT
1 AAAAATTAT
*
6088508 AAAAATTAC
1 AAAAATTAT
6088517 AAGAAA-TAT
1 AA-AAATTAT
6088526 AAAA
1 AAAA
6088530 TACATTAAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
8 8 0.12
9 34 0.52
10 12 0.18
11 11 0.17
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.27
Consensus pattern (9 bp):
AAAAATTAT
Found at i:6088465 original size:20 final size:18
Alignment explanation
Indices: 6088442--6088529 Score: 74
Period size: 20 Copynumber: 4.7 Consensus size: 18
6088432 ATTAAATATG
6088442 AAAAATTATAAAAATTCCAT
1 AAAAATTATAAAAATT--AT
*
6088462 AAAAAGTATAAAAATT-T
1 AAAAATTATAAAAATTAT
6088479 AAAAAAGTTATAAATAATTAT
1 -AAAAA-TTATAAA-AATTAT
* *
6088500 -AAAATAATAAAAATTAC
1 AAAAATTATAAAAATTAT
6088517 AAGAAA-TATAAAA
1 AA-AAATTATAAAA
6088530 TACATTAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 14
0.75 0.07 0.18
Matches are distributed among these distances:
17 6 0.11
18 18 0.32
19 13 0.23
20 19 0.33
21 1 0.02
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.27
Consensus pattern (18 bp):
AAAAATTATAAAAATTAT
Found at i:6088984 original size:21 final size:20
Alignment explanation
Indices: 6088960--6089004 Score: 72
Period size: 21 Copynumber: 2.2 Consensus size: 20
6088950 TCGTTATTAA
*
6088960 TTTTATAATCTTTTTAAATAG
1 TTTTACAATCTTTTT-AATAG
6088981 TTTTACAATCTTTTTAATAG
1 TTTTACAATCTTTTTAATAG
6089001 TTTT
1 TTTT
6089005 GATGTAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTTACAATCTTTTTAATAG
Found at i:6110642 original size:47 final size:47
Alignment explanation
Indices: 6110588--6110683 Score: 174
Period size: 47 Copynumber: 2.0 Consensus size: 47
6110578 GTTAACAAGA
*
6110588 AAAGATGCCTGAGTTTCAGTTCATTTAATGAACTTTAATGCCAAGCT
1 AAAGATGCCTGAGTTTCAGTTCATTTAACGAACTTTAATGCCAAGCT
*
6110635 AAAGATGCCTGAGTTTCAGTTTATTTAACGAACTTTAATGCCAAGCT
1 AAAGATGCCTGAGTTTCAGTTCATTTAACGAACTTTAATGCCAAGCT
6110682 AA
1 AA
6110684 CTGAATTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (47 bp):
AAAGATGCCTGAGTTTCAGTTCATTTAACGAACTTTAATGCCAAGCT
Found at i:6123287 original size:20 final size:20
Alignment explanation
Indices: 6123258--6123367 Score: 71
Period size: 20 Copynumber: 5.5 Consensus size: 20
6123248 TGATAAATTC
* * *
6123258 AAAATTTTAGTTATTTTGTT
1 AAAATATTAGATATTTTGGT
6123278 AAAATATTAGATATTTTGGT
1 AAAATATTAGATATTTTGGT
* * * * *
6123298 -AAATTTATAAAAATATTAG-
1 AAAATAT-TAGATATTTTGGT
* * *
6123317 CAAATCAATAGATATGTTGGT
1 AAAAT-ATTAGATATTTTGGT
*
6123338 AAAATATTAGATATTTTGAT
1 AAAATATTAGATATTTTGGT
6123358 AAAAATATTA
1 -AAAATATTA
6123368 ACTATATTGG
Statistics
Matches: 67, Mismatches: 18, Indels: 9
0.71 0.19 0.10
Matches are distributed among these distances:
19 5 0.07
20 49 0.73
21 13 0.19
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.43
Consensus pattern (20 bp):
AAAATATTAGATATTTTGGT
Found at i:6123438 original size:40 final size:40
Alignment explanation
Indices: 6123353--6123575 Score: 144
Period size: 40 Copynumber: 5.7 Consensus size: 40
6123343 ATTAGATATT
* * * *
6123353 TTGATAAAAATATTA-ACTATATTGGCAAATCTTTAGC-AATT
1 TTGAT-AAATTATTAGA-TATATTAGTAAATCTTTA-CAAATA
** *
6123394 TTGATAAATCGTTAGATATATTAGTAAATCTTTAAAAATA
1 TTGATAAATTATTAGATATATTAGTAAATCTTTACAAATA
* * * * * *
6123434 TTGATATATAATTAAAAATATCAAT-AA--TTT-----T-
1 TTGATAAATTATTAGATATATTAGTAAATCTTTACAAATA
* *
6123465 TTGGTAAATTATTAGATATATTAGTAAATCCTTACAAATA
1 TTGATAAATTATTAGATATATTAGTAAATCTTTACAAATA
*
6123505 TTGATATATATTATTAGATATATTAGTAAATCCTTACAAATA
1 TTGATA-A-ATTATTAGATATATTAGTAAATCTTTACAAATA
* * * *
6123547 TTGATATATTGTTAGAAATATTGGTAAAT
1 TTGATAAATTATTAGATATATTAGTAAAT
6123576 TCTTAAATGT
Statistics
Matches: 142, Mismatches: 27, Indels: 27
0.72 0.14 0.14
Matches are distributed among these distances:
31 18 0.13
32 3 0.02
34 2 0.01
37 3 0.02
39 3 0.02
40 67 0.47
41 7 0.05
42 39 0.27
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (40 bp):
TTGATAAATTATTAGATATATTAGTAAATCTTTACAAATA
Found at i:6123493 original size:20 final size:20
Alignment explanation
Indices: 6123468--6123535 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 20
6123458 TAATTTTTTG
6123468 GTAAATTATTAGATATATTA
1 GTAAATTATTAGATATATTA
** * *
6123488 GTAAATCCTTACAAATATT-
1 GTAAATTATTAGATATATTA
6123507 GATATATATTATTAGATATATTA
1 G-TA-A-ATTATTAGATATATTA
6123530 GTAAAT
1 GTAAAT
6123536 CCTTACAAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
19 1 0.03
20 19 0.53
21 2 0.06
22 13 0.36
23 1 0.03
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (20 bp):
GTAAATTATTAGATATATTA
Found at i:6123520 original size:42 final size:40
Alignment explanation
Indices: 6123472--6123580 Score: 164
Period size: 42 Copynumber: 2.7 Consensus size: 40
6123462 TTTTTGGTAA
6123472 ATTATTAGATATATTAGTAAATCCTTACAAATATTGATATAT
1 ATTATTAGATATATTAGTAAATCCTTACAAATATTG--ATAT
6123514 ATTATTAGATATATTAGTAAATCCTTACAAATATTGATAT
1 ATTATTAGATATATTAGTAAATCCTTACAAATATTGATAT
* * * *
6123554 ATTGTTAGAAATATTGGTAAATTCTTA
1 ATTATTAGATATATTAGTAAATCCTTA
6123581 AATGTTTTGG
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
40 27 0.43
42 36 0.57
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.43
Consensus pattern (40 bp):
ATTATTAGATATATTAGTAAATCCTTACAAATATTGATAT
Found at i:6123547 original size:22 final size:22
Alignment explanation
Indices: 6123480--6123547 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
6123470 AAATTATTAG
6123480 ATATATTAGTAAATCCTTACAA
1 ATATATTAGTAAATCCTTACAA
* * * * *
6123502 ATAT-TGA-TATAT-ATTATTAG
1 ATATATTAGTAAATCCTTA-CAA
6123522 ATATATTAGTAAATCCTTACAA
1 ATATATTAGTAAATCCTTACAA
6123544 ATAT
1 ATAT
6123548 TGATATATTG
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
19 3 0.09
20 9 0.28
21 4 0.12
22 13 0.41
23 3 0.09
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (22 bp):
ATATATTAGTAAATCCTTACAA
Found at i:6123924 original size:21 final size:23
Alignment explanation
Indices: 6123882--6123932 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
6123872 TTTGAACATT
6123882 TTTTTTTATTCTTCTAACTTTC-
1 TTTTTTTATTCTTCTAACTTTCA
* **
6123904 TTTTTTTGTTCTT-TATTTTTCA
1 TTTTTTTATTCTTCTAACTTTCA
6123926 TTTTTTT
1 TTTTTTT
6123933 TTTTGCTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.10, C:0.12, G:0.02, T:0.76
Consensus pattern (23 bp):
TTTTTTTATTCTTCTAACTTTCA
Found at i:6124972 original size:24 final size:26
Alignment explanation
Indices: 6124944--6125002 Score: 77
Period size: 24 Copynumber: 2.3 Consensus size: 26
6124934 ATGGAGAAGG
6124944 AAAGAAAATAGAAAG-AG-AAAAAAA
1 AAAGAAAATAGAAAGAAGAAAAAAAA
*
6124968 AAAGAGAATAGAAAGTAAAGAAAAAAAA
1 AAAGAAAATAGAAAG--AAGAAAAAAAA
6124996 AAAGAAA
1 AAAGAAA
6125003 GTTCAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 14 0.48
27 2 0.07
28 13 0.45
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (26 bp):
AAAGAAAATAGAAAGAAGAAAAAAAA
Found at i:6125044 original size:23 final size:23
Alignment explanation
Indices: 6125014--6125059 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
6125004 TTCAAAGAAC
*
6125014 ATGGGTACATTCATCCATATTTG
1 ATGGGTACACTCATCCATATTTG
6125037 ATGGGTACACTCATCCATATTTG
1 ATGGGTACACTCATCCATATTTG
6125060 TGGTTGATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (23 bp):
ATGGGTACACTCATCCATATTTG
Found at i:6157067 original size:22 final size:23
Alignment explanation
Indices: 6157042--6157087 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
6157032 CAACCAAATC
6157042 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
6157064 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
6157087 A
1 A
6157088 CGTTATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:6157803 original size:41 final size:41
Alignment explanation
Indices: 6157715--6157830 Score: 164
Period size: 41 Copynumber: 2.9 Consensus size: 41
6157705 AATAGGGTTT
* * * *
6157715 TAGCGGCGTTTTTGTTAACAA-GCCGCTAAAA-ACAGAGTAA
1 TAGCGGCGCTTTTGGTAA-AACGCCGCTAAAAGTCAGAGCAA
6157755 TAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCAGAGCAA
1 TAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCAGAGCAA
*
6157796 TAGCGGCGCTTTTAGTAAAACGCCGCTAAAAGTCA
1 TAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCA
6157831 TATAACCCCT
Statistics
Matches: 69, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
39 2 0.03
40 26 0.38
41 41 0.59
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (41 bp):
TAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCAGAGCAA
Found at i:6158736 original size:7 final size:7
Alignment explanation
Indices: 6158726--6158788 Score: 108
Period size: 7 Copynumber: 8.7 Consensus size: 7
6158716 ACTCAAAAAA
6158726 TAAAATT
1 TAAAATT
6158733 TAAAAATT
1 T-AAAATT
6158741 TAAAAATT
1 T-AAAATT
6158749 TAAAATT
1 TAAAATT
6158756 TAAAATT
1 TAAAATT
6158763 TAAAATT
1 TAAAATT
6158770 TAAAATT
1 TAAAATT
6158777 TAAAATT
1 TAAAATT
6158784 TAAAA
1 TAAAA
6158789 ATAAAAAAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
7 40 0.73
8 15 0.27
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
TAAAATT
Found at i:6158737 original size:14 final size:14
Alignment explanation
Indices: 6158706--6158814 Score: 67
Period size: 14 Copynumber: 7.6 Consensus size: 14
6158696 TAAACTGAAA
*
6158706 TAAAAAAT-AAACT
1 TAAAAAATAAAATT
*
6158719 CAAAAAATAAAATT
1 TAAAAAATAAAATT
*
6158733 TAAAAATTTAAAAATT
1 TAAAAA-AT-AAAATT
**
6158749 TAAAATTTAAAATT
1 TAAAAAATAAAATT
**
6158763 TAAAATTTAAAATT
1 TAAAAAATAAAATT
** *
6158777 TAAAATTTAAAAAT
1 TAAAAAATAAAATT
*
6158791 AAAAAAATACAAAATT
1 TAAAAAAT--AAAATT
*
6158807 TTAAAAAT
1 TAAAAAAT
6158815 TTGATATTTA
Statistics
Matches: 79, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
13 7 0.09
14 47 0.59
15 3 0.04
16 22 0.28
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (14 bp):
TAAAAAATAAAATT
Found at i:6158740 original size:8 final size:8
Alignment explanation
Indices: 6158727--6158816 Score: 100
Period size: 8 Copynumber: 11.9 Consensus size: 8
6158717 CTCAAAAAAT
6158727 AAAATTTA
1 AAAATTTA
6158735 AAAATTTA
1 AAAATTTA
6158743 AAAATTT-
1 AAAATTTA
6158750 AAAATTT-
1 AAAATTTA
6158757 AAAATTT-
1 AAAATTTA
6158764 AAAATTT-
1 AAAATTTA
6158771 AAAATTT-
1 AAAATTTA
6158778 AAAATTTA
1 AAAATTTA
**
6158786 AAAATAAA
1 AAAATTTA
**
6158794 AAAATACA
1 AAAATTTA
*
6158802 AAATTTTA
1 AAAATTTA
6158810 AAAATTT
1 AAAATTT
6158817 GATATTTAAT
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
7 35 0.47
8 39 0.53
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (8 bp):
AAAATTTA
Found at i:6158795 original size:21 final size:21
Alignment explanation
Indices: 6158720--6158795 Score: 107
Period size: 21 Copynumber: 3.5 Consensus size: 21
6158710 AAATAAACTC
*
6158720 AAAAAATAAAATTTAAAAATTT
1 AAAAATTAAAATTT-AAAATTT
6158742 AAAAATTTAAAATTTAAAATTT
1 AAAAA-TTAAAATTTAAAATTT
*
6158764 AAAATTTAAAATTTAAAATTT
1 AAAAATTAAAATTTAAAATTT
*
6158785 AAAAATAAAAA
1 AAAAATTAAAA
6158796 AATACAAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
21 25 0.51
22 16 0.33
23 8 0.16
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAAATTAAAATTTAAAATTT
Found at i:6158910 original size:18 final size:17
Alignment explanation
Indices: 6158889--6158927 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 17
6158879 TTCAAAAGAG
6158889 AAAAATAAAAAAAATGTT
1 AAAAATAAAAAAAAT-TT
6158907 AAAAATAAAAAAAATTT
1 AAAAATAAAAAAAATTT
6158924 AAAA
1 AAAA
6158928 TTAATCAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (17 bp):
AAAAATAAAAAAAATTT
Found at i:6164516 original size:19 final size:19
Alignment explanation
Indices: 6164494--6164534 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
6164484 TTTATTGATA
6164494 TTTTTA-TATTTAATCTAG
1 TTTTTATTATTTAATCTAG
* *
6164512 TTTTTATTATTTATTTTAG
1 TTTTTATTATTTAATCTAG
6164531 TTTT
1 TTTT
6164535 GATTCTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTTTATTATTTAATCTAG
Found at i:6168544 original size:27 final size:26
Alignment explanation
Indices: 6168496--6168589 Score: 89
Period size: 26 Copynumber: 3.6 Consensus size: 26
6168486 AAAGTAAACA
*
6168496 ATAAAACAATTTAAAATGAATAATAC
1 ATAAAACAATTTAAAATAAATAATAC
**
6168522 ATAAAACAAGTTTAAAATAAATAATGT
1 ATAAAACAA-TTTAAAATAAATAATAC
* * **
6168549 ATAAAGCATTTTAAAATTTATAATAC
1 ATAAAACAATTTAAAATAAATAATAC
* * *
6168575 ACAAAGCAAATTAAA
1 ATAAAACAATTTAAA
6168590 GAATGACATA
Statistics
Matches: 55, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
26 34 0.62
27 21 0.38
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.29
Consensus pattern (26 bp):
ATAAAACAATTTAAAATAAATAATAC
Found at i:6168626 original size:26 final size:27
Alignment explanation
Indices: 6168597--6168652 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
6168587 AAAGAATGAC
* *
6168597 ATATATGAA-TAATTTTAAAATAAATA
1 ATATATAAATTAATTTAAAAATAAATA
*
6168623 ATATATAAATTAATTTAAAAATAATTA
1 ATATATAAATTAATTTAAAAATAAATA
6168650 ATA
1 ATA
6168653 AGAAGTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (27 bp):
ATATATAAATTAATTTAAAAATAAATA
Found at i:6168784 original size:17 final size:17
Alignment explanation
Indices: 6168762--6168801 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
6168752 TGAAATATAT
*
6168762 AATATACAATAACTTAA
1 AATATAAAATAACTTAA
* *
6168779 AATATAAAATAATTTGA
1 AATATAAAATAACTTAA
6168796 AATATA
1 AATATA
6168802 TATATATAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.33
Consensus pattern (17 bp):
AATATAAAATAACTTAA
Found at i:6170678 original size:25 final size:26
Alignment explanation
Indices: 6170623--6170679 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
6170613 TTTAATTTCA
*
6170623 TATATTTATATATTTAAATTTTTATT
1 TATATTTATATATGTAAATTTTTATT
*
6170649 T-TATTTATA-GTGTAAATTATTT-TT
1 TATATTTATATATGTAAATT-TTTATT
6170673 TATATTT
1 TATATTT
6170680 CAATTTTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 10 0.37
25 16 0.59
26 1 0.04
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.65
Consensus pattern (26 bp):
TATATTTATATATGTAAATTTTTATT
Found at i:6174112 original size:9 final size:9
Alignment explanation
Indices: 6174095--6174128 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
6174085 AGATATTGGC
6174095 GGAGGTGGA
1 GGAGGTGGA
*
6174104 GGCGGTGGA
1 GGAGGTGGA
6174113 GGAGGTGGA
1 GGAGGTGGA
*
6174122 GGTGGTG
1 GGAGGTG
6174129 AAGCTGGTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.15, C:0.03, G:0.68, T:0.15
Consensus pattern (9 bp):
GGAGGTGGA
Found at i:6175564 original size:19 final size:19
Alignment explanation
Indices: 6175527--6175564 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
6175517 TTTATACACT
*
6175527 AAAATGATTATTTTGTTAA
1 AAAATGATTAATTTGTTAA
6175546 AAAATTGATTAATTT-TTAA
1 AAAA-TGATTAATTTGTTAA
6175565 TTTTAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (19 bp):
AAAATGATTAATTTGTTAA
Found at i:6175865 original size:15 final size:15
Alignment explanation
Indices: 6175847--6175879 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
6175837 TTTTAAAAAG
*
6175847 ATATTTTATTAATTA
1 ATATTTTATAAATTA
6175862 ATATTTTATAAATTA
1 ATATTTTATAAATTA
6175877 ATA
1 ATA
6175880 GCGAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATATTTTATAAATTA
Found at i:6181128 original size:104 final size:104
Alignment explanation
Indices: 6180948--6181171 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
6180938 TGTATATAAA
** * *
6180948 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
6181013 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
6181052 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCG-TGATCCACCATATCT
6181116 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
6181156 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
6181172 GATATCCATT
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:6181223 original size:71 final size:72
Alignment explanation
Indices: 6181090--6181241 Score: 252
Period size: 71 Copynumber: 2.1 Consensus size: 72
6181080 TCATTGGTGG
* *
6181090 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
6181155 GAGGGGT
66 GAGGGGT
***
6181162 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
6181226 GAGGGGT
66 GAGGGGT
6181233 TGCTAAGTG
1 TGCTAAGTG
6181242 ATGATTCCCC
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 45 0.60
72 30 0.40
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (72 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
GAGGGGT
Found at i:6184579 original size:52 final size:52
Alignment explanation
Indices: 6184508--6184855 Score: 459
Period size: 52 Copynumber: 6.9 Consensus size: 52
6184498 ATCAAGTGAC
* **
6184508 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
* *
6184560 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
* *
6184612 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC------
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
* **
6184658 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
* *
6184710 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC------
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
*
6184756 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
** * *
6184808 AAAGTGATAAGTGATAGCTTTAGTTACACTTATCTGATCAAGAGACAA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
6184856 AGTGATAAGT
Statistics
Matches: 263, Mismatches: 21, Indels: 24
0.85 0.07 0.08
Matches are distributed among these distances:
46 85 0.32
52 178 0.68
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (52 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
Found at i:6184630 original size:98 final size:98
Alignment explanation
Indices: 6184508--6184866 Score: 511
Period size: 98 Copynumber: 3.6 Consensus size: 98
6184498 ATCAAGTGAC
** ** * *
6184508 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTA
1 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC------AAAGTGATAAGTG
*
6184573 ATAGCTTCGGCTATACTTATCTGATCAAGTGACAAGTGG
60 ATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
*
6184612 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCT
1 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCT
**
6184677 TTAGCTACACTTATCTGATCAAGTGACAAGTGG
66 TCGGCTACACTTATCTGATCAAGTGACAAGTGG
6184710 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCT
1 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCT
*
6184775 TCGGCTACACTTATCTGATCAAGTGACAAGTGA
66 TCGGCTACACTTATCTGATCAAGTGACAAGTGG
* ** * * *
6184808 AAAGTGATAAGTGATAGCTTTAGTTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGTG
6184867 GCTACACTTA
Statistics
Matches: 235, Mismatches: 20, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
98 194 0.83
104 41 0.17
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.29
Consensus pattern (98 bp):
AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCT
TCGGCTACACTTATCTGATCAAGTGACAAGTGG
Found at i:6184714 original size:150 final size:144
Alignment explanation
Indices: 6184494--6184855 Score: 571
Period size: 150 Copynumber: 2.4 Consensus size: 144
6184484 TTTGAGTACT
6184494 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
6184559 GAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGT
66 GAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC------AAAGTGATAAGT
*
6184624 AATAGCTTCGGCTATACTTA
125 AATAGCTTCGGCTACACTTA
6184644 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
6184709 GAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGC
66 GAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGTAATAGC
6184774 TTCGGCTACACTTA
131 TTCGGCTACACTTA
* * *
6184788 TCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTTAGTTACACTTATCTGATCAAGAGA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGA
6184853 CAA
60 CAA
6184856 AGTGATAAGT
Statistics
Matches: 201, Mismatches: 5, Indels: 12
0.92 0.02 0.06
Matches are distributed among these distances:
144 44 0.22
150 157 0.78
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (144 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
GAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGTAATAGC
TTCGGCTACACTTA
Found at i:6184876 original size:37 final size:37
Alignment explanation
Indices: 6184832--6185049 Score: 377
Period size: 37 Copynumber: 5.9 Consensus size: 37
6184822 TAGCTTTAGT
*
6184832 TACACTTATCTGATCAAGAGACAAAGTGATAAGTGGC
1 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGC
6184869 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGC
1 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGC
*
6184906 TACACTTATCTGATCAAGAAACAAAGTGATAGGTGGC
1 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGC
6184943 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGC
1 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGC
*
6184980 TACACTTATCTGATCAAGAAACAAAGTGATAGGTGGC
1 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGC
**
6185017 TACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 TACACTTATCTGATCAAGAAACAAAGTGATAAGTG
6185050 ATCATACGTA
Statistics
Matches: 174, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
35 11 0.06
36 4 0.02
37 159 0.91
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (37 bp):
TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGC
Found at i:6186380 original size:58 final size:58
Alignment explanation
Indices: 6186303--6186470 Score: 237
Period size: 58 Copynumber: 3.0 Consensus size: 58
6186293 CATGTGAACA
6186303 TGTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
1 TGTGA-TATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
6186362 TGTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATA--
1 TGTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
* * *
6186418 TGTG--A--T--TT-CGTGTAAGACCATAGTTGGGCTATGGCATCGGTATGTGATTTG
1 TGTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
6186469 TG
1 TG
6186471 ATTACGTGTA
Statistics
Matches: 104, Mismatches: 3, Indels: 12
0.87 0.03 0.10
Matches are distributed among these distances:
49 38 0.37
50 2 0.02
51 2 0.02
52 1 0.01
54 1 0.01
56 4 0.04
58 51 0.49
59 5 0.05
ACGTcount: A:0.23, C:0.13, G:0.31, T:0.33
Consensus pattern (58 bp):
TGTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
Found at i:6186412 original size:28 final size:28
Alignment explanation
Indices: 6186322--6186412 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 28
6186312 GTGATTCCGT
6186322 GTAAGACCATAGCTGGGCTATGGCATCG
1 GTAAGACCATAGCTGGGCTATGGCATCG
** * *
6186350 GTAAG-TGATATG-TGTGATATGTG-ATTCCG
1 GTAAGACCATA-GCTGGGCTATG-GCA-T-CG
6186379 TGTAAGACCATAGCTGGGCTATGGCATCG
1 -GTAAGACCATAGCTGGGCTATGGCATCG
6186408 GTAAG
1 GTAAG
6186413 TGATATGTGA
Statistics
Matches: 47, Mismatches: 8, Indels: 16
0.66 0.11 0.23
Matches are distributed among these distances:
27 11 0.23
28 13 0.28
29 4 0.09
30 8 0.17
31 11 0.23
ACGTcount: A:0.25, C:0.15, G:0.32, T:0.27
Consensus pattern (28 bp):
GTAAGACCATAGCTGGGCTATGGCATCG
Found at i:6186435 original size:49 final size:49
Alignment explanation
Indices: 6186363--6186505 Score: 232
Period size: 49 Copynumber: 2.9 Consensus size: 49
6186353 AGTGATATGT
* *
6186363 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
1 GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
* *
6186412 GTGATATGTGATTTCGTGTAAGACCATAGTTGGGCTATGGCATCGGTAT
1 GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
* *
6186461 GTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCG
1 GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCG
6186506 AGAAAACGAA
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 88 1.00
ACGTcount: A:0.24, C:0.14, G:0.30, T:0.32
Consensus pattern (49 bp):
GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
Found at i:6189712 original size:46 final size:45
Alignment explanation
Indices: 6189687--6189948 Score: 210
Period size: 46 Copynumber: 5.4 Consensus size: 45
6189677 GATCAAGTGA
* * *
6189687 CAAGTGGA-AAGTGATAAGTAATAGCT-TCGGCTATACTTATCTGAT
1 CAAGT-GACAAGTGATAAGTGATAGCTAT-AGCTACACTTATCTGAT
* *
6189732 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1 CAAGTGAC-AAGTGATAAGTGATAGCTATAGCTACACTTATCTGAT
*
6189778 CAAGTGACAAGTGGA-AAGTGATAAG-TAATAGCTTCGGCTATACTTATCTGAT
1 CAAGTGACAAGT-GATAAGTGAT-AGCT-ATA------GCTACACTTATCTGAT
*
6189830 CAAGTGACAAAGTGATAAGTGATAGCT-TCGGCTACACTTATCTGAT
1 CAAGTGAC-AAGTGATAAGTGATAGCTAT-AGCTACACTTATCTGAT
*
6189876 CAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGAT
1 CAAGTGAC-------AAGTGATAAGTGATAGCTATAGCTACACTTATCTGAT
*
6189928 CAAGAGACAAAGTGATAAGTG
1 CAAGTGAC-AAGTGATAAGTG
6189949 GCTACACTTA
Statistics
Matches: 183, Mismatches: 11, Indels: 45
0.77 0.05 0.19
Matches are distributed among these distances:
44 2 0.01
45 16 0.09
46 81 0.44
47 1 0.01
51 1 0.01
52 69 0.38
53 13 0.07
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (45 bp):
CAAGTGACAAGTGATAAGTGATAGCTATAGCTACACTTATCTGAT
Found at i:6189713 original size:52 final size:51
Alignment explanation
Indices: 6189642--6189948 Score: 382
Period size: 52 Copynumber: 6.1 Consensus size: 51
6189632 ATCAAGTGAC
* *
6189642 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGT-G
* * *
6189694 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC-----
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* *
6189740 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGT-G
* * *
6189792 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC-----
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
*
6189838 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* *
6189889 AAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGTG
1 -AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC-AAGTG
6189942 ATAAGTG
1 A-AAGTG
6189949 GCTACACTTA
Statistics
Matches: 221, Mismatches: 20, Indels: 27
0.82 0.07 0.10
Matches are distributed among these distances:
46 85 0.38
52 126 0.57
53 10 0.05
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (51 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
Found at i:6189748 original size:98 final size:98
Alignment explanation
Indices: 6189628--6189949 Score: 563
Period size: 98 Copynumber: 3.3 Consensus size: 98
6189618 TTTGAGTACT
6189628 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
6189693 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
6189726 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
6189791 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* **
6189824 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
* * ** *
6189889 AAAAGTGATAAGTGATAGCTTTAGCTACACTTA
66 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
*
6189922 TCTGATCAAGAGACAAAGTGATAAGTGG
1 TCTGATCAAGTGACAAAGTGATAAGTGG
6189950 CTACACTTAT
Statistics
Matches: 214, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 214 1.00
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:6189956 original size:37 final size:37
Alignment explanation
Indices: 6189912--6190131 Score: 381
Period size: 37 Copynumber: 6.0 Consensus size: 37
6189902 GATAGCTTTA
*
6189912 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
6189949 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
6189986 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
6190023 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
6190060 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
6190097 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
6190132 ATCATACGTA
Statistics
Matches: 176, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
35 11 0.06
36 4 0.02
37 161 0.91
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:6195651 original size:104 final size:104
Alignment explanation
Indices: 6195529--6195752 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
6195519 AATGGATATC
6195529 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
6195594 GGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GGATCA-CGCACATAGCACCACCAATAAACCGGGGAATCA
6195633 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
6195698 GGATCACGCACATAGCACCACCCATAAATCGGGGAATCA
66 GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
**
6195737 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
6195753 TTTATATACA
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (104 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:6196114 original size:29 final size:29
Alignment explanation
Indices: 6196081--6196144 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
6196071 TAATCCACCA
6196081 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
6196110 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
6196140 CCCAA
1 CCCAA
6196145 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:6196118 original size:30 final size:30
Alignment explanation
Indices: 6196088--6196144 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
6196078 CCACCCAACT
6196088 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
6196117 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
6196145 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:6199918 original size:29 final size:29
Alignment explanation
Indices: 6199886--6200004 Score: 88
Period size: 29 Copynumber: 4.1 Consensus size: 29
6199876 TTTAATATAT
*
6199886 TATTGCTATTATTATTATGTTTCTATTTA
1 TATTTCTATTATTATTATGTTTCTATTTA
* * *
6199915 TATTTATTTTGTTATTCCAATGTTAT-T-TTTA
1 TATTTCTATTATTATT---ATGTT-TCTATTTA
6199946 T-TTATCTA--ATTATTAT-TTATCTATTTA
1 TATT-TCTATTATTATTATGTT-TCTATTTA
* *
6199973 TATTTCTACTATTATTATATTTCTATTTA
1 TATTTCTATTATTATTATGTTTCTATTTA
6200002 TAT
1 TAT
6200005 ACTAATATTA
Statistics
Matches: 72, Mismatches: 7, Indels: 22
0.71 0.07 0.22
Matches are distributed among these distances:
25 4 0.06
26 3 0.04
27 9 0.12
28 2 0.03
29 36 0.50
30 4 0.06
31 7 0.10
32 6 0.08
33 1 0.01
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (29 bp):
TATTTCTATTATTATTATGTTTCTATTTA
Found at i:6199963 original size:15 final size:15
Alignment explanation
Indices: 6199943--6199990 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
6199933 AATGTTATTT
6199943 TTATTTATCTAATTA
1 TTATTTATCTAATTA
*
6199958 TTATTTATCTATTTA
1 TTATTTATCTAATTA
*
6199973 -TATTTCTACT-ATTA
1 TTATTTAT-CTAATTA
6199987 TTAT
1 TTAT
6199991 ATTTCTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 9 0.32
15 19 0.68
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATTTATCTAATTA
Found at i:6200028 original size:29 final size:30
Alignment explanation
Indices: 6199954--6200029 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 30
6199944 TATTTATCTA
* *
6199954 ATTATTAT-TTATCTATTTATATTTCTACT
1 ATTATTATATTATCTATTTATATTACTAAT
6199983 ATTATTATATT-TCTATTTATA-TACTAAT
1 ATTATTATATTATCTATTTATATTACTAAT
*
6200011 ATTATTTTCATTAT-TATTT
1 ATTATTAT-ATTATCTATTT
6200030 TTTTTTATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 12 0.29
29 26 0.63
30 3 0.07
ACGTcount: A:0.30, C:0.08, G:0.00, T:0.62
Consensus pattern (30 bp):
ATTATTATATTATCTATTTATATTACTAAT
Found at i:6200143 original size:3 final size:3
Alignment explanation
Indices: 6200135--6200263 Score: 95
Period size: 3 Copynumber: 42.3 Consensus size: 3
6200125 TTTAAAACTT
*
6200135 TTA TTA TTA TTA TTA TTA TTA -TA TT- TCTA TT- TATA TTTA TGTA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA T-TA -TTA T-TA TTA
* * * *
6200181 ATA TCA TTA TT- TTT TTA TATA TTA TTA TTA TTA TCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
6200226 CTA TTA GTA CTA TTA TTA TTT TCTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA T
6200264 ATTTATTTAT
Statistics
Matches: 100, Mismatches: 16, Indels: 20
0.74 0.12 0.15
Matches are distributed among these distances:
2 6 0.06
3 82 0.82
4 11 0.11
5 1 0.01
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:6209691 original size:46 final size:46
Alignment explanation
Indices: 6209641--6209816 Score: 210
Period size: 46 Copynumber: 3.8 Consensus size: 46
6209631 TGGTTGAGCA
*
6209641 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
*** * * ** *
6209687 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGC-AAACG
* *
6209734 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
6209780 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
6209817 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
46 72 0.67
47 35 0.33
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:6209797 original size:93 final size:93
Alignment explanation
Indices: 6209638--6209808 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
6209628 GGATGGTTGA
* *
6209638 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
6209703 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* * *
6209731 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
6209796 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
6209809 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:6213642 original size:21 final size:21
Alignment explanation
Indices: 6213616--6213656 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6213606 ATCTGCTCAA
* *
6213616 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
6213637 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
6213657 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:6217355 original size:33 final size:33
Alignment explanation
Indices: 6217315--6217380 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
6217305 AATTTGAGAG
6217315 AAAAATTTATTATTATACAAATAAAAATTATAT
1 AAAAATTTATTATTATACAAATAAAAATTATAT
6217348 AAAAATTTATTATTATACAAATAAAAATTATAT
1 AAAAATTTATTATTATACAAATAAAAATTATAT
6217381 GCAATTGCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (33 bp):
AAAAATTTATTATTATACAAATAAAAATTATAT
Found at i:6217377 original size:18 final size:18
Alignment explanation
Indices: 6217323--6217378 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
6217313 AGAAAAATTT
6217323 ATTATTATACAAATAAAA
1 ATTATTATACAAATAAAA
***
6217341 ATTA-TATA-AAA-ATTT
1 ATTATTATACAAATAAAA
6217356 ATTATTATACAAATAAAA
1 ATTATTATACAAATAAAA
6217374 ATTAT
1 ATTAT
6217379 ATGCAATTGC
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
15 5 0.17
16 7 0.24
17 7 0.24
18 10 0.34
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (18 bp):
ATTATTATACAAATAAAA
Found at i:6223462 original size:37 final size:37
Alignment explanation
Indices: 6223377--6223469 Score: 107
Period size: 37 Copynumber: 2.5 Consensus size: 37
6223367 AGTACACAAG
* * * *
6223377 TAATCCAACTGA-AACACGTCAATCGCTCACAAGAGG
1 TAATCCAACCGATAACACGCCAAACGCTCACAAGAGC
* * * *
6223413 TACTCCACCCGATAACATGCCAAACGCTCATAAGAGC
1 TAATCCAACCGATAACACGCCAAACGCTCACAAGAGC
6223450 TAATCCAACCGATAACACGC
1 TAATCCAACCGATAACACGC
6223470 TATGATACTA
Statistics
Matches: 45, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
36 9 0.20
37 36 0.80
ACGTcount: A:0.38, C:0.32, G:0.14, T:0.16
Consensus pattern (37 bp):
TAATCCAACCGATAACACGCCAAACGCTCACAAGAGC
Found at i:6227078 original size:30 final size:30
Alignment explanation
Indices: 6227034--6227096 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
6227024 GCTTAACAAG
6227034 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
6227064 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
6227094 CAA
1 CAA
6227097 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:6227152 original size:22 final size:22
Alignment explanation
Indices: 6227127--6227169 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
6227117 TATCCAAACA
6227127 ATAACAATAAAATAGTAGCAAC
1 ATAACAATAAAATAGTAGCAAC
* * *
6227149 ATAATAGTAAAATGGTAGCAA
1 ATAACAATAAAATAGTAGCAA
6227170 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.09, G:0.14, T:0.21
Consensus pattern (22 bp):
ATAACAATAAAATAGTAGCAAC
Found at i:6229548 original size:28 final size:26
Alignment explanation
Indices: 6229495--6229548 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 26
6229485 AAAAAATATT
*
6229495 TTAATAATTTTAAAATTAAATTAATA
1 TTAATAATTTTAAAATTAAATCAATA
* *
6229521 TTAATTAATTTTTAATATTAACTCAATA
1 TTAA-TAA-TTTTAAAATTAAATCAATA
6229549 AAACACTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 4 0.17
27 3 0.13
28 16 0.70
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (26 bp):
TTAATAATTTTAAAATTAAATCAATA
Found at i:6240371 original size:20 final size:21
Alignment explanation
Indices: 6240346--6240390 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
6240336 AGAGTATATT
6240346 AAAAAATATGAGGAAATA-CAA
1 AAAAAAT-TGAGGAAATACCAA
*
6240367 AAAAAATTGAGGGAATACCAA
1 AAAAAATTGAGGAAATACCAA
6240388 AAA
1 AAA
6240391 TCATAACTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.64, C:0.07, G:0.16, T:0.13
Consensus pattern (21 bp):
AAAAAATTGAGGAAATACCAA
Found at i:6240590 original size:20 final size:20
Alignment explanation
Indices: 6240547--6240937 Score: 136
Period size: 20 Copynumber: 19.9 Consensus size: 20
6240537 ACCAAGAGTA
* * * *
6240547 ATGAGAAAGTACCAAAATTT
1 ATGAGGAAGTACAAAAAATC
* * *
6240567 ATGATGATGTATAAAAAATC
1 ATGAGGAAGTACAAAAAATC
6240587 ATGAGGAAGTACAAAAAAAT-
1 ATGAGGAAGTAC-AAAAAATC
* *
6240607 ACGAGGAAGTACAAAAAATT
1 ATGAGGAAGTACAAAAAATC
* *
6240627 ATGAGGGAGTAC-CAAAA-C
1 ATGAGGAAGTACAAAAAATC
* * *
6240645 -TTA-GATGTATAAAAAATC
1 ATGAGGAAGTACAAAAAATC
*
6240663 ATGAGGAAATACTAAAAAAT-
1 ATGAGGAAGTAC-AAAAAATC
*
6240683 ATGAGGAAGTACAAAAAATT
1 ATGAGGAAGTACAAAAAATC
* *
6240703 ACGAGGGA-TACCAAAAAAT-
1 ATGAGGAAGTA-CAAAAAATC
* * * *
6240722 ACGAGGATGCACAAAAAATT
1 ATGAGGAAGTACAAAAAATC
* * * *
6240742 ATGAAGATGTAC-AAAACTT
1 ATGAGGAAGTACAAAAAATC
*
6240761 ATGA-GATAATACAAAAAAT-
1 ATGAGGA-AGTACAAAAAATC
6240780 ATGAGGGAA-TACTAAAAAA--
1 ATGA-GGAAGTAC-AAAAAATC
* * *
6240799 ATGA-TAAGTACAGAAAATT
1 ATGAGGAAGTACAAAAAATC
* *
6240818 ATGAGAGAA-TATTATAAAATC
1 ATGAG-GAAGTA-CAAAAAATC
* * *
6240839 A-GAGAAAGTATAAAAAATG
1 ATGAGGAAGTACAAAAAATC
* * * *
6240858 AAGAAGGATGTACTAAAAATT
1 ATG-AGGAAGTACAAAAAATC
* * **
6240879 ATAAGGATGTATCAAAATGT-
1 ATGAGGAAGTA-CAAAAAATC
* *
6240899 ACGAGGAAGTACAAAAAATT
1 ATGAGGAAGTACAAAAAATC
6240919 ATGAGAGAA-TACAGAAAAA
1 ATGAG-GAAGTACA-AAAAA
6240938 AAAAGAAGAG
Statistics
Matches: 280, Mismatches: 62, Indels: 57
0.70 0.16 0.14
Matches are distributed among these distances:
16 4 0.01
17 13 0.05
18 6 0.02
19 80 0.29
20 126 0.45
21 51 0.18
ACGTcount: A:0.54, C:0.07, G:0.18, T:0.20
Consensus pattern (20 bp):
ATGAGGAAGTACAAAAAATC
Found at i:6240667 original size:76 final size:75
Alignment explanation
Indices: 6240572--6240718 Score: 249
Period size: 76 Copynumber: 1.9 Consensus size: 75
6240562 AATTTATGAT
* *
6240572 GATGTATAAAAAATCATGAGGAAGTACAAAAAAATACGAGGAAGTACAAAAAATTATGAGGGAGT
1 GATGTATAAAAAATCATGAGGAAATACAAAAAAATACGAGGAAGTACAAAAAATTACGAGGGA-T
6240637 ACCAAAACTTA
65 ACCAAAACTTA
* *
6240648 GATGTATAAAAAATCATGAGGAAATACTAAAAAATATGAGGAAGTACAAAAAATTACGAGGGATA
1 GATGTATAAAAAATCATGAGGAAATACAAAAAAATACGAGGAAGTACAAAAAATTACGAGGGATA
6240713 CCAAAA
66 CCAAAA
6240719 AATACGAGGA
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
75 8 0.12
76 59 0.88
ACGTcount: A:0.54, C:0.09, G:0.19, T:0.18
Consensus pattern (75 bp):
GATGTATAAAAAATCATGAGGAAATACAAAAAAATACGAGGAAGTACAAAAAATTACGAGGGATA
CCAAAACTTA
Found at i:6240719 original size:39 final size:39
Alignment explanation
Indices: 6240579--6240745 Score: 153
Period size: 39 Copynumber: 4.3 Consensus size: 39
6240569 GATGATGTAT
* * *
6240579 AAAAAATCATGAGGAAGTACAAAAAAATACGAGGAAGTAC
1 AAAAAATTATGAGGGA-TACCAAAAAATACGAGGAAGTAC
* * * *
6240619 AAAAAATTATGAGGGAGTACC-AAAACT--TA-GATGTAT
1 AAAAAATTATGAGGGA-TACCAAAAAATACGAGGAAGTAC
* * * *
6240655 AAAAAATCATGAGGAAATACTAAAAAATATGAGGAAGTAC
1 AAAAAATTATGAGG-GATACCAAAAAATACGAGGAAGTAC
* * *
6240695 AAAAAATTACGAGGGATACCAAAAAATACGAGGATGCAC
1 AAAAAATTATGAGGGATACCAAAAAATACGAGGAAGTAC
6240734 AAAAAATTATGA
1 AAAAAATTATGA
6240746 AGATGTACAA
Statistics
Matches: 100, Mismatches: 22, Indels: 11
0.75 0.17 0.08
Matches are distributed among these distances:
36 21 0.21
37 7 0.07
39 37 0.37
40 35 0.35
ACGTcount: A:0.54, C:0.10, G:0.19, T:0.17
Consensus pattern (39 bp):
AAAAAATTATGAGGGATACCAAAAAATACGAGGAAGTAC
Found at i:6240757 original size:39 final size:39
Alignment explanation
Indices: 6240579--6241146 Score: 170
Period size: 40 Copynumber: 14.3 Consensus size: 39
6240569 GATGATGTAT
*
6240579 AAAAAATCATGAGGAAGTACAAAAAAATACGAGGAAGTAC
1 AAAAAATTATGAGGAAGTAC-AAAAAATACGAGGAAGTAC
* * * * * *
6240619 AAAAAATTATGAGGGAGTACCAAAACT--TA-GATGTAT
1 AAAAAATTATGAGGAAGTACAAAAAATACGAGGAAGTAC
* * *
6240655 AAAAAATCATGAGGAAATACTAAAAAATATGAGGAAGTAC
1 AAAAAATTATGAGGAAGTAC-AAAAAATACGAGGAAGTAC
* * * *
6240695 AAAAAATTACGAGGGA-TACCAAAAAATACGAGGATGCAC
1 AAAAAATTATGAGGAAGTA-CAAAAAATACGAGGAAGTAC
* * ** * *
6240734 AAAAAATTATGAAGATGTACAAAACTTATGA-GATAATAC
1 AAAAAATTATGAGGAAGTACAAAAAATACGAGGA-AGTAC
* *
6240773 AAAAAA-TATGAGGGAA-TACTAAAAAA-ATGA-TAAGTAC
1 AAAAAATTATGA-GGAAGTAC-AAAAAATACGAGGAAGTAC
* * * * *
6240810 AGAAAATTATGAGAGAA-TATTATAAAAT-CAGAGAAAGTAT
1 AAAAAATTATGAG-GAAGTA-CAAAAAATAC-GAGGAAGTAC
* * * * ** *
6240850 AAAAAATGAAGAAGGATGTACTAAAAATTATAAGGATGTATC
1 AAAAAATTATG-AGGAAGTAC-AAAAAATACGAGGAAGTA-C
* *
6240892 --AAAATGTACGAGGAAGTACAAAAAATTATGAGAGAA-TAC
1 AAAAAAT-TATGAGGAAGTACAAAAAA-TACGAG-GAAGTAC
** * * * *
6240931 AGAAAAAAAAAGAAGAGAAAGTACCAAAAAATATGATGATGTATC
1 A-AAAAATTATG-AG-G-AAGTA-CAAAAAATACGAGGAAGTA-C
* * * *
6240976 -AAAAATTATGAAGATGTTCAAAAAACTATGAGAGAA-TATC
1 AAAAAATTATGAGGAAGTACAAAAAA-TACGAG-GAAGTA-C
* * * *
6241016 -AAAAATTACGAGGGAAAATTA-AAAAAATAAGAGGAAGTGC
1 AAAAAATTATGA-GG--AAGTACAAAAAATACGAGGAAGTAC
* * * * *
6241056 CAAAAATTATAAAAGAA-TACCATAAAATATGAGGAAGTATC
1 AAAAAATTAT-GAGGAAGTA-CAAAAAATACGAGGAAGTA-C
* * *
6241097 -AAAAATTATGAGGGAA-TACAAAAAAAAATGAGAAAGTAC
1 AAAAAATTATGA-GGAAGTAC-AAAAAATACGAGGAAGTAC
*
6241136 CAAAAATTATG
1 AAAAAATTATG
6241147 GAAGAATACC
Statistics
Matches: 390, Mismatches: 92, Indels: 92
0.68 0.16 0.16
Matches are distributed among these distances:
36 22 0.06
37 16 0.04
38 32 0.08
39 79 0.20
40 154 0.39
41 41 0.11
42 14 0.04
43 12 0.03
44 12 0.03
45 8 0.02
ACGTcount: A:0.55, C:0.07, G:0.18, T:0.20
Consensus pattern (39 bp):
AAAAAATTATGAGGAAGTACAAAAAATACGAGGAAGTAC
Found at i:6240784 original size:19 final size:19
Alignment explanation
Indices: 6240732--6240828 Score: 58
Period size: 19 Copynumber: 5.1 Consensus size: 19
6240722 ACGAGGATGC
*
6240732 ACAAAAAATTATGAAGAT-GT
1 ACAAAAAA-TATG-AGATAAT
**
6240752 ACAAAACTTATGAGATAAT
1 ACAAAAAATATGAGATAAT
**
6240771 ACAAAAAATATGAGGGAAT
1 ACAAAAAATATGAGATAAT
6240790 ACTAAAAAA-AT--GATAAGT
1 AC-AAAAAATATGAGATAA-T
* *
6240808 ACAGAAAATTATGAGAGAAT
1 ACA-AAAAATATGAGATAAT
6240828 A
1 A
6240829 TTATAAAATC
Statistics
Matches: 59, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
17 4 0.07
18 11 0.19
19 26 0.44
20 14 0.24
21 4 0.07
ACGTcount: A:0.57, C:0.06, G:0.15, T:0.22
Consensus pattern (19 bp):
ACAAAAAATATGAGATAAT
Found at i:6240978 original size:20 final size:19
Alignment explanation
Indices: 6240955--6241006 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
6240945 GAGAAAGTAC
*
6240955 CAAAAAATATGATGATGTAT
1 CAAAAAATATGAAGATGT-T
*
6240975 CAAAAATTATGAAGATGTT
1 CAAAAAATATGAAGATGTT
6240994 CAAAAAACTATGA
1 CAAAAAA-TATGA
6241007 GAGAATATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 7 0.25
20 21 0.75
ACGTcount: A:0.52, C:0.08, G:0.13, T:0.27
Consensus pattern (19 bp):
CAAAAAATATGAAGATGTT
Found at i:6241019 original size:20 final size:20
Alignment explanation
Indices: 6240972--6241159 Score: 77
Period size: 20 Copynumber: 9.3 Consensus size: 20
6240962 TATGATGATG
6240972 TATCAAAAATTATGA-AG-A
1 TATCAAAAATTATGAGAGAA
* *
6240990 TGTTCAAAAAACTATGAGAGAA
1 T-ATC-AAAAATTATGAGAGAA
* *
6241012 TATCAAAAATTACGAGGGAA
1 TATCAAAAATTATGAGAGAA
* * * *
6241032 AATTAAAAA-AATAAGAGGAA
1 TATCAAAAATTATGAGA-GAA
** * *
6241052 GTGCCAAAAATTATAAAAGAA
1 -TATCAAAAATTATGAGAGAA
*
6241073 TACCATAAAA-TATGAG-GAA
1 TATCA-AAAATTATGAGAGAA
*
6241092 GTATCAAAAATTATGAGGGAA
1 -TATCAAAAATTATGAGAGAA
**
6241113 TA-CAAAAAAAAATGAGA-AA
1 TATC-AAAAATTATGAGAGAA
*
6241132 GTACCAAAAATTATG-GAAGAA
1 -TATCAAAAATTATGAG-AGAA
*
6241153 TACCAAA
1 TATCAAA
6241160 CAACAAGAAA
Statistics
Matches: 127, Mismatches: 27, Indels: 30
0.69 0.15 0.16
Matches are distributed among these distances:
18 1 0.01
19 16 0.13
20 81 0.64
21 22 0.17
22 7 0.06
ACGTcount: A:0.56, C:0.08, G:0.16, T:0.20
Consensus pattern (20 bp):
TATCAAAAATTATGAGAGAA
Found at i:6241063 original size:81 final size:79
Alignment explanation
Indices: 6240975--6241159 Score: 196
Period size: 80 Copynumber: 2.3 Consensus size: 79
6240965 GATGATGTAT
** *
6240975 CAAAAATTAT-GAAGATGTTCAAAAAACTATGAGAGAA-TATCAAAAATTACGAGGGAAAATTAA
1 CAAAAATTATAGAAGAT-ACCAAAAAA-TATGAG-GAAGTATCAAAAATTACGAGGGAAAA-CAA
* *
6241038 AAAAATAA-GAGGAAGTGC
62 AAAAA-AATGAGAAAGTAC
* * * *
6241056 CAAAAATTATAAAAGAATACCATAAAATATGAGGAAGTATCAAAAATTATGAGGGAATACAAAAA
1 CAAAAATTATAGAAG-ATACCAAAAAATATGAGGAAGTATCAAAAATTACGAGGGAAAACAAAAA
6241121 AAAATGAGAAAGTAC
65 AAAATGAGAAAGTAC
*
6241136 CAAAAATTATGGAAGAATACCAAA
1 CAAAAATTATAGAAG-ATACCAAA
6241160 CAACAAGAAA
Statistics
Matches: 88, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
79 2 0.02
80 39 0.44
81 36 0.41
82 9 0.10
83 2 0.02
ACGTcount: A:0.57, C:0.08, G:0.16, T:0.19
Consensus pattern (79 bp):
CAAAAATTATAGAAGATACCAAAAAATATGAGGAAGTATCAAAAATTACGAGGGAAAACAAAAAA
AAATGAGAAAGTAC
Found at i:6241118 original size:19 final size:19
Alignment explanation
Indices: 6240996--6241159 Score: 78
Period size: 20 Copynumber: 8.2 Consensus size: 19
6240986 AAGATGTTCA
* *
6240996 AAAAACTATGAGAGAATATC
1 AAAAATTATGAG-GAATACC
* * **
6241016 AAAAATTACGAGGGAAAATTA
1 AAAAATTATGA-GGAATA-CC
* * *
6241037 AAAAAATAAGAGGAAGTGCC
1 AAAAATTATGAGGAA-TACC
* *
6241057 AAAAATTATAAAAGAATACC
1 AAAAATTAT-GAGGAATACC
*
6241077 ATAAAA-TATGAGGAAGTATC
1 A-AAAATTATGAGGAA-TACC
*
6241097 AAAAATTATGAGGGAATACA
1 AAAAATTATGA-GGAATACC
** *
6241117 AAAAAAAATGAGAAAGTACC
1 AAAAATTATGAGGAA-TACC
*
6241137 AAAAATTATGGAAGAATACC
1 AAAAATTAT-GAGGAATACC
6241157 AAA
1 AAA
6241160 CAACAAGAAA
Statistics
Matches: 106, Mismatches: 28, Indels: 20
0.69 0.18 0.13
Matches are distributed among these distances:
19 11 0.10
20 68 0.64
21 27 0.25
ACGTcount: A:0.58, C:0.08, G:0.16, T:0.18
Consensus pattern (19 bp):
AAAAATTATGAGGAATACC
Found at i:6241180 original size:80 final size:80
Alignment explanation
Indices: 6241015--6241195 Score: 179
Period size: 80 Copynumber: 2.2 Consensus size: 80
6241005 GAGAGAATAT
* * * * *
6241015 CAAAAATTACGAGGGAAAATTAAAAAAATAAGAGGAAGTGCCAAAAATTATAAAAGAATACCATA
1 CAAAAATTATGAGGGAATA-CAAAAAAATAAGAGAAAGTACCAAAAATTATAAAAGAATACCATA
* * * *
6241080 AAATATGAGGAAGTAT
65 AAACAAGAGAAAGTAC
**
6241096 CAAAAATTATGAGGGAATACAAAAAAA-AATGAGAAAGTACCAAAAATTATGGAAGAATACCA-A
1 CAAAAATTATGAGGGAATACAAAAAAATAA-GAGAAAGTACCAAAAATTATAAAAGAATACCATA
6241159 ACAACAAGA-AAAGATAC
65 A-AACAAGAGAAAG-TAC
* * *
6241176 CAAAATTTGTGAGGGGATAC
1 CAAAAATTATGAGGGAATAC
6241196 CAATTTTTGG
Statistics
Matches: 83, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
79 7 0.08
80 59 0.71
81 17 0.20
ACGTcount: A:0.56, C:0.09, G:0.18, T:0.17
Consensus pattern (80 bp):
CAAAAATTATGAGGGAATACAAAAAAATAAGAGAAAGTACCAAAAATTATAAAAGAATACCATAA
AACAAGAGAAAGTAC
Found at i:6252130 original size:16 final size:17
Alignment explanation
Indices: 6252109--6252144 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
6252099 AATTGGGTTG
6252109 AAAAAATT-ATTTAATT
1 AAAAAATTAATTTAATT
*
6252125 AAAAAATTAATTTATTT
1 AAAAAATTAATTTAATT
6252142 AAA
1 AAA
6252145 TTAATTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAAAAATTAATTTAATT
Found at i:6252145 original size:14 final size:14
Alignment explanation
Indices: 6252128--6252171 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
6252118 TTTAATTAAA
6252128 AAATTAATTTATTT
1 AAATTAATTTATTT
*
6252142 AAATTAATTTA-AT
1 AAATTAATTTATTT
*
6252155 AAATAATATTTATTT
1 AAATTA-ATTTATTT
6252170 AA
1 AA
6252172 GGAAATAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 6 0.24
14 16 0.64
15 3 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AAATTAATTTATTT
Found at i:6263515 original size:64 final size:65
Alignment explanation
Indices: 6263404--6263532 Score: 197
Period size: 64 Copynumber: 2.0 Consensus size: 65
6263394 CATACAATAG
6263404 CACATCTAGTTAAGAGCATTTGATTTCATTTCAATCATAGCACCCTAATTATTTGACATAAGCAT
1 CACATCTAGTTAAGAGCATTTGATTTCATTTCAATCATAGCACCCTAATTATTTGACATAAGCAT
* * ** * *
6263469 CACATCTAGTTAGGAGTATTTGA-TTCATTTCGGTCATAGCATCCTAATTATTTGGCATAAGCAT
1 CACATCTAGTTAAGAGCATTTGATTTCATTTCAATCATAGCACCCTAATTATTTGACATAAGCAT
6263533 AGATATATGA
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
64 37 0.64
65 21 0.36
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (65 bp):
CACATCTAGTTAAGAGCATTTGATTTCATTTCAATCATAGCACCCTAATTATTTGACATAAGCAT
Found at i:6263894 original size:45 final size:45
Alignment explanation
Indices: 6263843--6263940 Score: 117
Period size: 45 Copynumber: 2.2 Consensus size: 45
6263833 GAAGTTGCAG
* * * *
6263843 GAAGCAGACCGAAGAT-TTCAGATATTATCTCCATGTATCGGTTAT
1 GAAGCAGACCAAAAATGATCAG-TATTATCTCCATGTATCGGCTAT
* * *
6263888 GAAGCAGATCAAAAATGATGAGTCTTATCTCCATGTATCGGCTAT
1 GAAGCAGACCAAAAATGATCAGTATTATCTCCATGTATCGGCTAT
6263933 GAAGCAGA
1 GAAGCAGA
6263941 TTTTAGCCAC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
45 42 0.93
46 3 0.07
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (45 bp):
GAAGCAGACCAAAAATGATCAGTATTATCTCCATGTATCGGCTAT
Found at i:6263904 original size:176 final size:176
Alignment explanation
Indices: 6263597--6264338 Score: 1056
Period size: 176 Copynumber: 4.2 Consensus size: 176
6263587 CGGTGAAGAT
* * * * * *
6263597 ACCAGCCTTATCTCTCTGAAGTTGCAGAGAGCAGGTTGAATATACAGGTCTTATCTTTCTGAAAT
1 ACCAGCCTTATCTCTCTGAAGTTACAGAGAGCAGGTCGAAGATACAAGTCTTATCTTCCTGAAGT
* * * * *
6263662 TGCAGGAAGTAGACCGAAGATTTCAGATCTTATCTCCATGTATCGGCTATGGAGAAGATAAAAAA
66 TGCAGGAAGCAGACCGAAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCAAAAA
*
6263727 TGGCGAGTCTTATCTCCATATATCGGCTATGGAGCAGATTTTAGCC
131 TGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCC
* * *
6263773 ACTAGCCTTATCTCTCTGAAGTTACAGAGAGCAGGTCGAAGATACAGGTCTTATCTTTCTGAAGT
1 ACCAGCCTTATCTCTCTGAAGTTACAGAGAGCAGGTCGAAGATACAAGTCTTATCTTCCTGAAGT
* * * * *
6263838 TGCAGGAAGCAGACCGAAGATTTCAGATATTATCTCCATGTATCGGTTATGAAGCAGATCAAAAA
66 TGCAGGAAGCAGACCGAAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCAAAAA
** *
6263903 TGATGAGTCTTATCTCCATGTATCGGCTATGAAGCAGATTTTAGCC
131 TGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCC
* * * *
6263949 ACCAGCCTTATCTCTCTGAAGTTGCAGTAAAGCAGGCTC-AATATGCAAGTCTTATCTTCCTGAA
1 ACCAGCCTTATCTCTCTGAAGTTACAG-AGAGCAGG-TCGAAGATACAAGTCTTATCTTCCTGAA
* * *
6264013 GTTGCAGGAAGCGGACGGAAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCGAA
64 GTTGCAGGAAGCAGACCGAAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCAAA
* *
6264078 GATGGCAAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCC
129 AATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCC
** *
6264126 ACCAGTTTTATCTCTCTGAAGTTACAGAGAGCAGGTTGAAGATACAAGTCTTATCTTCCTGAAGT
1 ACCAGCCTTATCTCTCTGAAGTTACAGAGAGCAGGTCGAAGATACAAGTCTTATCTTCCTGAAGT
* * * * *
6264191 TACAGGAAGCATACTGAAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCGAAGA
66 TGCAGGAAGCAGACCGAAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCAAAAA
*
6264256 TGGCGAGTCTTATCTCCATGTATCGACTATGGAGCAGATTTTAGCC
131 TGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCC
*
6264302 ACCAGCCTTATCTCTCTG-AGGTAGCAAGAGAGCAGGT
1 ACCAGCCTTATCTCTCTGAAGTTA-C-AGAGAGCAGGT
6264339 TGTGTATCGG
Statistics
Matches: 510, Mismatches: 51, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
175 5 0.01
176 340 0.67
177 163 0.32
178 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (176 bp):
ACCAGCCTTATCTCTCTGAAGTTACAGAGAGCAGGTCGAAGATACAAGTCTTATCTTCCTGAAGT
TGCAGGAAGCAGACCGAAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCAAAAA
TGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCC
Found at i:6264294 original size:353 final size:352
Alignment explanation
Indices: 6263597--6264320 Score: 1097
Period size: 353 Copynumber: 2.1 Consensus size: 352
6263587 CGGTGAAGAT
* * * * *
6263597 ACCAGCCTTATCTCTCTGAAGTTGCAGAGAGCAGGTTGAATATACAGGTCTTATCTTTCTGAAAT
1 ACCAGCCTTATCTCTCTGAAGTTGCAGAAAGCAGGCTCAATATACAAGTCTTATCTTCCTGAAAT
* * *
6263662 TGCAGGAAGTAGACCGAAGATTTCAGATCTTATCTCCATGTATCGGCTATGGAGAAGATAAAAAA
66 TGCAGGAAGCAGACCGAAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGAAGATAAAAAA
* *
6263727 TGGCGAGTCTTATCTCCATATATCGGCTATGGAGCAGATTTTAGCCACTAGCCTTATCTCTCTGA
131 TGGCAAGTCTTATCTCCATATATCGGCTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGA
* * * *
6263792 AGTTACAGAGAGCAGGTCGAAGATACAGGTCTTATCTTTCTGAAGTTGCAGGAAGCAGACCGAAG
196 AGTTACAGAGAGCAGGTCGAAGATACAAGTCTTATCTTCCTGAAGTTACAGGAAGCAGACCGAAA
* * *
6263857 ATTTCAGATATTATCTCCATGTATCGGTTATGAAGCAGATCAAAAATGATGAGTCTTATCTCCAT
261 ATTACAGATATTATCTCCATGTATCGGCTATGAAGCAGATCAAAAATGACGAGTCTTATCTCCAT
*
6263922 GTATCGGCTATGAAGCAGATTTTAGCC
326 GTATCGACTATGAAGCAGATTTTAGCC
* *
6263949 ACCAGCCTTATCTCTCTGAAGTTGCAGTAAAGCAGGCTCAATATGCAAGTCTTATCTTCCTGAAG
1 ACCAGCCTTATCTCTCTGAAGTTGCAG-AAAGCAGGCTCAATATACAAGTCTTATCTTCCTGAAA
* * * ** *
6264014 TTGCAGGAAGCGGACGGAAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCGAAG
65 TTGCAGGAAGCAGACCGAAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGAAGATAAAAA
* **
6264079 ATGGCAAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAGTTTTATCTCTCTG
130 ATGGCAAGTCTTATCTCCATATATCGGCTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTG
* * *
6264144 AAGTTACAGAGAGCAGGTTGAAGATACAAGTCTTATCTTCCTGAAGTTACAGGAAGCATACTGAA
195 AAGTTACAGAGAGCAGGTCGAAGATACAAGTCTTATCTTCCTGAAGTTACAGGAAGCAGACCGAA
* * * * *
6264209 AATTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCGAAGATGGCGAGTCTTATCTCCA
260 AATTACAGATATTATCTCCATGTATCGGCTATGAAGCAGATCAAAAATGACGAGTCTTATCTCCA
*
6264274 TGTATCGACTATGGAGCAGATTTTAGCC
325 TGTATCGACTATGAAGCAGATTTTAGCC
6264302 ACCAGCCTTATCTCTCTGA
1 ACCAGCCTTATCTCTCTGA
6264321 GGTAGCAAGA
Statistics
Matches: 333, Mismatches: 38, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
352 27 0.08
353 306 0.92
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (352 bp):
ACCAGCCTTATCTCTCTGAAGTTGCAGAAAGCAGGCTCAATATACAAGTCTTATCTTCCTGAAAT
TGCAGGAAGCAGACCGAAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGAAGATAAAAAA
TGGCAAGTCTTATCTCCATATATCGGCTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGA
AGTTACAGAGAGCAGGTCGAAGATACAAGTCTTATCTTCCTGAAGTTACAGGAAGCAGACCGAAA
ATTACAGATATTATCTCCATGTATCGGCTATGAAGCAGATCAAAAATGACGAGTCTTATCTCCAT
GTATCGACTATGAAGCAGATTTTAGCC
Found at i:6264382 original size:67 final size:67
Alignment explanation
Indices: 6264274--6264470 Score: 331
Period size: 67 Copynumber: 2.9 Consensus size: 67
6264264 CTTATCTCCA
6264274 TGTATCGACTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGT
1 TGTATCGACTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGT
6264339 TG
66 TG
* * *
6264341 TGTATCGGCTATGGAGCAGATTTTAGCCACCAGTCTTATCTCTCTGAGATAGCAAGAGAGCAGGT
1 TGTATCGACTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGT
6264406 TG
66 TG
* * * *
6264408 TGTATCAAATATGGAGCAGATTTTAGCCACCAACCTTATCTCTCTAAGGTAGCAAGAGAGCAG
1 TGTATCGACTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAG
6264471 ATTGAAGATA
Statistics
Matches: 120, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 120 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (67 bp):
TGTATCGACTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGT
TG
Found at i:6266124 original size:15 final size:14
Alignment explanation
Indices: 6266104--6266155 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
6266094 TTTTGAATTG
6266104 TTGTATATTATGTTT
1 TTGTATATTAT-TTT
6266119 TTGTATATATATATTTT
1 TTG--TATAT-TATTTT
*
6266136 TTATATATTATTTT
1 TTGTATATTATTTT
*
6266150 ATGTAT
1 TTGTAT
6266156 TTTCTTTTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 10 0.32
15 8 0.26
17 10 0.32
18 3 0.10
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (14 bp):
TTGTATATTATTTT
Found at i:6266136 original size:17 final size:16
Alignment explanation
Indices: 6266107--6266155 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
6266097 TGAATTGTTG
6266107 TATATTATGTTTTTGTA
1 TATATTAT-TTTTTGTA
6266124 TATA-TATATTTTT-TA
1 TATATTAT-TTTTTGTA
*
6266139 TATATTATTTTATGTA
1 TATATTATTTTTTGTA
6266155 T
1 T
6266156 TTTCTTTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 10 0.36
16 14 0.50
17 4 0.14
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (16 bp):
TATATTATTTTTTGTA
Found at i:6266142 original size:13 final size:14
Alignment explanation
Indices: 6266116--6266149 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 14
6266106 GTATATTATG
6266116 TTTTTGTATATATATA
1 TTTTT-TATATAT-TA
6266132 TTTTTTATATATTA
1 TTTTTTATATATTA
6266146 TTTT
1 TTTT
6266150 ATGTATTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 7 0.39
16 5 0.28
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (14 bp):
TTTTTTATATATTA
Found at i:6266334 original size:26 final size:25
Alignment explanation
Indices: 6266290--6266355 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 25
6266280 GTATTTTATT
* *
6266290 TGTATAGTTTCTTTAAAATCTTTAA
1 TGTATATTTTCTTTAAAATCTGTAA
* *
6266315 TGTATATTTTCTTTCCAAATCTGTCA
1 TGTATATTTTCTTT-AAAATCTGTAA
6266341 TGTAAATATTTTCTT
1 TGT--ATATTTTCTT
6266356 CTAATTTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
25 13 0.38
26 11 0.32
28 10 0.29
ACGTcount: A:0.27, C:0.12, G:0.08, T:0.53
Consensus pattern (25 bp):
TGTATATTTTCTTTAAAATCTGTAA
Found at i:6266483 original size:13 final size:13
Alignment explanation
Indices: 6266465--6266489 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6266455 TTTGTATATA
6266465 TATTATTTTCATT
1 TATTATTTTCATT
6266478 TATTATTTTCAT
1 TATTATTTTCAT
6266490 ATAAATACGT
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:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTATTTTCATT
Found at i:6283854 original size:26 final size:27
Alignment explanation
Indices: 6283815--6283875 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
6283805 TAAACCAAAC
6283815 TTTTCAAAAGCACTTCTCAAAAATACT
1 TTTTCAAAAGCACTTCTCAAAAATACT
* * *
6283842 TTTTCACAA-CACTTTTCAAAAGTAC-
1 TTTTCAAAAGCACTTCTCAAAAATACT
6283867 TTTTCAAAA
1 TTTTCAAAA
6283876 ACATTCCCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 8 0.27
26 14 0.47
27 8 0.27
ACGTcount: A:0.39, C:0.21, G:0.03, T:0.36
Consensus pattern (27 bp):
TTTTCAAAAGCACTTCTCAAAAATACT
Found at i:6283868 original size:13 final size:13
Alignment explanation
Indices: 6283813--6283875 Score: 65
Period size: 13 Copynumber: 4.8 Consensus size: 13
6283803 TTTAAACCAA
6283813 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* **
6283826 ACTTCTCAAAAAT
1 ACTTTTCAAAAGC
*
6283839 ACTTTTTCACAA-C
1 AC-TTTTCAAAAGC
*
6283852 ACTTTTCAAAAGT
1 ACTTTTCAAAAGC
6283865 ACTTTTCAAAA
1 ACTTTTCAAAA
6283876 ACATTCCCAA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
12 8 0.20
13 25 0.62
14 7 0.17
ACGTcount: A:0.40, C:0.22, G:0.03, T:0.35
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:6283878 original size:26 final size:26
Alignment explanation
Indices: 6283813--6283886 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 26
6283803 TTTAAACCAA
*
6283813 ACTTTTCAAAAGCACTTCTCAAAAAT
1 ACTTTTCAAAAACACTTCTCAAAAAT
* * *
6283839 ACTTTTTC-ACAACACTTTTCAAAAGT
1 AC-TTTTCAAAAACACTTCTCAAAAAT
*
6283865 ACTTTTCAAAAACA-TTCCCAAA
1 ACTTTTCAAAAACACTTCTCAAA
6283887 CTAGTTCTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
25 11 0.28
26 23 0.59
27 5 0.13
ACGTcount: A:0.41, C:0.24, G:0.03, T:0.32
Consensus pattern (26 bp):
ACTTTTCAAAAACACTTCTCAAAAAT
Found at i:6288425 original size:19 final size:19
Alignment explanation
Indices: 6288401--6288497 Score: 90
Period size: 19 Copynumber: 5.1 Consensus size: 19
6288391 TACAAGCTTA
*
6288401 TGTGCCAGGATGCACTTTG
1 TGTGCCAAGATGCACTTTG
* **
6288420 TGTGCC-AGATACGCGCTCCG
1 TGTGCCAAGAT--GCACTTTG
6288440 TGTGCCAAGATGCACTTTG
1 TGTGCCAAGATGCACTTTG
**
6288459 TGTGCC-AGCATGCACTTCC
1 TGTGCCAAG-ATGCACTTTG
*
6288478 TGTGCCAAGATGCATTTTG
1 TGTGCCAAGATGCACTTTG
6288497 T
1 T
6288498 ACGCCAGTAT
Statistics
Matches: 61, Mismatches: 12, Indels: 10
0.73 0.14 0.12
Matches are distributed among these distances:
18 5 0.08
19 39 0.64
20 13 0.21
21 4 0.07
ACGTcount: A:0.18, C:0.26, G:0.27, T:0.30
Consensus pattern (19 bp):
TGTGCCAAGATGCACTTTG
Found at i:6288924 original size:27 final size:27
Alignment explanation
Indices: 6288886--6288940 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
6288876 TTATAAAGAA
6288886 TTTGATTCATGGTTAATATTGAATTGG
1 TTTGATTCATGGTTAATATTGAATTGG
6288913 TTTGATTCATGGTTAATATTGAATTGG
1 TTTGATTCATGGTTAATATTGAATTGG
6288940 T
1 T
6288941 ATGTAAGGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.04, G:0.22, T:0.49
Consensus pattern (27 bp):
TTTGATTCATGGTTAATATTGAATTGG
Found at i:6290663 original size:62 final size:61
Alignment explanation
Indices: 6290548--6290663 Score: 133
Period size: 62 Copynumber: 1.9 Consensus size: 61
6290538 CTGACTATCA
* * * * * * * *
6290548 TGGTAAACCATCGTTGTTGTGCATTTGAGGTGGTAAGTTATCGTTGTCAGGCAATTCGGGG
1 TGGTAAACCATCATTGTCGGGCATCTGAAGTGGTAACTCATCATTGTCAGGCAATTCGGGG
* *
6290609 TGGTAAACCATCATTGTCGGGCAATCTGAAGTGGTAACTCATCATTTTCGGGCAA
1 TGGTAAACCATCATTGTCGGGC-ATCTGAAGTGGTAACTCATCATTGTCAGGCAA
6290664 CCCAAGATGA
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
61 19 0.43
62 25 0.57
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.32
Consensus pattern (61 bp):
TGGTAAACCATCATTGTCGGGCATCTGAAGTGGTAACTCATCATTGTCAGGCAATTCGGGG
Found at i:6292616 original size:32 final size:32
Alignment explanation
Indices: 6292573--6292639 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
6292563 AGATCATGCC
* *
6292573 TCCACTTGCTAATCCCCTATAGAAGGATTAGT
1 TCCACTCGCTAATCCCCCATAGAAGGATTAGT
6292605 TCCACTCGCTAATCCCCCATAGAAGGATTAGT
1 TCCACTCGCTAATCCCCCATAGAAGGATTAGT
6292637 TCC
1 TCC
6292640 TCATGGCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.28
Consensus pattern (32 bp):
TCCACTCGCTAATCCCCCATAGAAGGATTAGT
Found at i:6306759 original size:25 final size:25
Alignment explanation
Indices: 6306730--6306779 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
6306720 TATCTAAATT
6306730 ATCGAGCAAAAAAGAGTAAAAATAA
1 ATCGAGCAAAAAAGAGTAAAAATAA
*
6306755 ATCGAGCAAAAGAGAGTAAAAATAA
1 ATCGAGCAAAAAAGAGTAAAAATAA
6306780 GTAATCTTAT
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:0.62, C:0.08, G:0.18, T:0.12
Consensus pattern (25 bp):
ATCGAGCAAAAAAGAGTAAAAATAA
Found at i:6310175 original size:19 final size:19
Alignment explanation
Indices: 6310151--6310188 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
6310141 AGAACAAGAA
6310151 GAAGGAAATAAGGTTTCTG
1 GAAGGAAATAAGGTTTCTG
6310170 GAAGGAAATAAGGTTTCTG
1 GAAGGAAATAAGGTTTCTG
6310189 AAGTTGCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.05, G:0.32, T:0.26
Consensus pattern (19 bp):
GAAGGAAATAAGGTTTCTG
Found at i:6313065 original size:16 final size:16
Alignment explanation
Indices: 6313044--6313075 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
6313034 CATAAGTCAC
6313044 AAAACTTGCCTTATTT
1 AAAACTTGCCTTATTT
6313060 AAAACTTGCCTTATTT
1 AAAACTTGCCTTATTT
6313076 GTACTTGGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
AAAACTTGCCTTATTT
Found at i:6315218 original size:2 final size:2
Alignment explanation
Indices: 6315211--6315264 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
6315201 ATGATAAGAC
6315211 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
6315253 CA CA CA CA CA CA
1 CA CA CA CA CA CA
6315265 TATATATATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:6315947 original size:25 final size:25
Alignment explanation
Indices: 6315883--6315988 Score: 76
Period size: 25 Copynumber: 4.2 Consensus size: 25
6315873 ATATTTGCTT
* *
6315883 ATACGAGCT-ATGAAACGATATGCTC
1 ATACGAGCTGA-GAATCGATAAGCTC
* *
6315908 -TCACGAGTTGTGAATCGATAAGCTC
1 AT-ACGAGCTGAGAATCGATAAGCTC
* *
6315933 ATACGAGCTGAGAATCGGTAAACTC
1 ATACGAGCTGAGAATCGATAAGCTC
* *
6315958 -TCACGAGCTGAAAATTGGA-AAGCTC
1 AT-ACGAGCTGAGAA-TCGATAAGCTC
6315983 ATACGA
1 ATACGA
6315989 TCTGTGGTGT
Statistics
Matches: 63, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
24 2 0.03
25 57 0.90
26 4 0.06
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.23
Consensus pattern (25 bp):
ATACGAGCTGAGAATCGATAAGCTC
Found at i:6333803 original size:39 final size:39
Alignment explanation
Indices: 6333753--6333833 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
6333743 AATTATCTTA
6333753 AATCATTTGCTTCCTAAACATCACATTTTGCAATGAATC
1 AATCATTTGCTTCCTAAACATCACATTTTGCAATGAATC
6333792 AATCATTTGCTTCCTAAACATCACATTTTGCAATGAATC
1 AATCATTTGCTTCCTAAACATCACATTTTGCAATGAATC
6333831 AAT
1 AAT
6333834 TAGATGAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.35, C:0.22, G:0.07, T:0.36
Consensus pattern (39 bp):
AATCATTTGCTTCCTAAACATCACATTTTGCAATGAATC
Found at i:6338345 original size:17 final size:17
Alignment explanation
Indices: 6338320--6338353 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6338310 CAGATGGAGT
*
6338320 ACATTGATACCATCATC
1 ACATCGATACCATCATC
*
6338337 ACATCGATACCCTCATC
1 ACATCGATACCATCATC
6338354 TTCATCATCA
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:0.32, C:0.35, G:0.06, T:0.26
Consensus pattern (17 bp):
ACATCGATACCATCATC
Found at i:6343596 original size:14 final size:15
Alignment explanation
Indices: 6343562--6343593 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
6343552 GTTTAATAGT
6343562 AAACTAACAAGATAA
1 AAACTAACAAGATAA
6343577 AAACTAACAAGATAA
1 AAACTAACAAGATAA
6343592 AA
1 AA
6343594 CTACAAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.69, C:0.12, G:0.06, T:0.12
Consensus pattern (15 bp):
AAACTAACAAGATAA
Found at i:6347978 original size:13 final size:13
Alignment explanation
Indices: 6347960--6348002 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
6347950 AGATTTTTTT
6347960 CTAAATATTATCA
1 CTAAATATTATCA
*
6347973 CTAAATA--AT-T
1 CTAAATATTATCA
6347983 CTAAATATTATCA
1 CTAAATATTATCA
6347996 CTAAATA
1 CTAAATA
6348003 ATTTAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 7 0.28
11 2 0.08
12 2 0.08
13 14 0.56
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:6348011 original size:23 final size:23
Alignment explanation
Indices: 6347958--6348009 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
6347948 TTAGATTTTT
6347958 TTCTAAATATTATCACTAAATAA
1 TTCTAAATATTATCACTAAATAA
6347981 TTCTAAATATTATCACTAAATAA
1 TTCTAAATATTATCACTAAATAA
6348004 TT-TAAA
1 TTCTAAA
6348010 ATTTAAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 4 0.14
23 25 0.86
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (23 bp):
TTCTAAATATTATCACTAAATAA
Found at i:6348459 original size:14 final size:14
Alignment explanation
Indices: 6348442--6348472 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
6348432 TAAGGCATAG
6348442 ATATCAAAGCTAGT
1 ATATCAAAGCTAGT
*
6348456 ATATCAAAGTTAGT
1 ATATCAAAGCTAGT
6348470 ATA
1 ATA
6348473 GTACTAAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (14 bp):
ATATCAAAGCTAGT
Found at i:6356504 original size:22 final size:22
Alignment explanation
Indices: 6356478--6356522 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
6356468 AAATTGTGTT
6356478 AAAATAAATAAAACAAAATGAA
1 AAAATAAATAAAACAAAATGAA
6356500 AAAATAAATAAAACAAAATGAA
1 AAAATAAATAAAACAAAATGAA
6356522 A
1 A
6356523 TTATCTCCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.13
Consensus pattern (22 bp):
AAAATAAATAAAACAAAATGAA
Found at i:6356772 original size:27 final size:28
Alignment explanation
Indices: 6356729--6356783 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
6356719 GAATGTTTCC
* *
6356729 ATTGATGAATATGTATG-ATTTTTGATG
1 ATTGATGAAGATGTATGAATATTTGATG
6356756 ATTGATGATAGAT-TATGAATATTTGATG
1 ATTGATGA-AGATGTATGAATATTTGATG
6356784 TTAGTTAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.45
Consensus pattern (28 bp):
ATTGATGAAGATGTATGAATATTTGATG
Found at i:6357335 original size:40 final size:40
Alignment explanation
Indices: 6357280--6357382 Score: 116
Period size: 40 Copynumber: 2.6 Consensus size: 40
6357270 ACATATCGGT
* *
6357280 TAAATGTGGCACTTAGTGTGCGGTTCAATATAGCTTCAGC
1 TAAATATGGCACTTAGTGTGCGATTCAATATAGCTTCAGC
* * ** *
6357320 TAAATTTGGCACTTAGTGTGTGATTTGATATAGCTTCGGC
1 TAAATATGGCACTTAGTGTGCGATTCAATATAGCTTCAGC
* * *
6357360 TATATATAGTACTTAGTGTGCGA
1 TAAATATGGCACTTAGTGTGCGA
6357383 GACATTAATT
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (40 bp):
TAAATATGGCACTTAGTGTGCGATTCAATATAGCTTCAGC
Found at i:6357410 original size:28 final size:28
Alignment explanation
Indices: 6357370--6357471 Score: 186
Period size: 28 Copynumber: 3.6 Consensus size: 28
6357360 TATATATAGT
*
6357370 ACTTAGTGTGCGAGACATTAATTATGGC
1 ACTTAGTGTGCGAGACATTGATTATGGC
6357398 ACTTAGTGTGCGAGACATTGATTATGGC
1 ACTTAGTGTGCGAGACATTGATTATGGC
*
6357426 ACTTAGTGTGCGAGACATTGATTGTGGC
1 ACTTAGTGTGCGAGACATTGATTATGGC
6357454 ACTTAGTGTGCGAGACAT
1 ACTTAGTGTGCGAGACAT
6357472 CGAGTATGCG
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 72 1.00
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.31
Consensus pattern (28 bp):
ACTTAGTGTGCGAGACATTGATTATGGC
Found at i:6359511 original size:18 final size:19
Alignment explanation
Indices: 6359488--6359524 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
6359478 TCAAATACAT
*
6359488 TTAAAACATAAAA-AAATA
1 TTAAAACAAAAAACAAATA
6359506 TTAAAACAAAAAACAAATA
1 TTAAAACAAAAAACAAATA
6359525 AAAAATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.19
Consensus pattern (19 bp):
TTAAAACAAAAAACAAATA
Found at i:6359540 original size:11 final size:12
Alignment explanation
Indices: 6359526--6359578 Score: 56
Period size: 11 Copynumber: 4.6 Consensus size: 12
6359516 AAACAAATAA
6359526 AAAATAATAC-T
1 AAAATAATACAT
* *
6359537 AAAATAATTCTT
1 AAAATAATACAT
6359549 AAAATAATACAT
1 AAAATAATACAT
* *
6359561 AAATTAA-AAAT
1 AAAATAATACAT
6359572 AAAATAA
1 AAAATAA
6359579 AAAGTAATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
11 18 0.51
12 17 0.49
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (12 bp):
AAAATAATACAT
Found at i:6359637 original size:17 final size:17
Alignment explanation
Indices: 6359617--6359654 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
6359607 GAAACAAATT
6359617 AAAATTAAATTAAGAAC
1 AAAATTAAATTAAGAAC
* *
6359634 AAAATTATATTAATAAC
1 AAAATTAAATTAAGAAC
6359651 AAAA
1 AAAA
6359655 GTTTTACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (17 bp):
AAAATTAAATTAAGAAC
Found at i:6361731 original size:18 final size:18
Alignment explanation
Indices: 6361708--6361743 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
6361698 AAATGGTATG
6361708 CTCGTGGCTCAAGAAAGC
1 CTCGTGGCTCAAGAAAGC
6361726 CTCGTGGCTCAAGAAAGC
1 CTCGTGGCTCAAGAAAGC
6361744 ATTTTTGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.17
Consensus pattern (18 bp):
CTCGTGGCTCAAGAAAGC
Found at i:6372393 original size:50 final size:51
Alignment explanation
Indices: 6372303--6372404 Score: 188
Period size: 50 Copynumber: 2.0 Consensus size: 51
6372293 AGAAGATGAA
6372303 TTAGCTGAATATAGAACAAAAAATAAATAAGCTCACATCAATATTCATAAG
1 TTAGCTGAATATAGAACAAAAAATAAATAAGCTCACATCAATATTCATAAG
*
6372354 TTAGCTGAATATAGAAC-AAAAATAAATAAGTTCACATCAATATTCATAAG
1 TTAGCTGAATATAGAACAAAAAATAAATAAGCTCACATCAATATTCATAAG
6372404 T
1 T
6372405 AAACAATAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 33 0.66
51 17 0.34
ACGTcount: A:0.50, C:0.13, G:0.10, T:0.27
Consensus pattern (51 bp):
TTAGCTGAATATAGAACAAAAAATAAATAAGCTCACATCAATATTCATAAG
Found at i:6374933 original size:23 final size:22
Alignment explanation
Indices: 6374907--6374955 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
6374897 AAATCCATAA
6374907 AATTAAAAAAGAAAAAATGAATC
1 AATTAAAAAAGAAAAAA-GAATC
* *
6374930 AATTAAAAAATAATAAAGAATC
1 AATTAAAAAAGAAAAAAGAATC
6374952 AATT
1 AATT
6374956 CATTCTCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.67, C:0.04, G:0.06, T:0.22
Consensus pattern (22 bp):
AATTAAAAAAGAAAAAAGAATC
Found at i:6384652 original size:27 final size:27
Alignment explanation
Indices: 6384622--6384684 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
6384612 AATTTTCATA
6384622 CAATGAACATTCAAATCATATTCACAT
1 CAATGAACATTCAAATCATATTCACAT
6384649 CAATGAACATTCAAATCATATTCACAT
1 CAATGAACATTCAAATCATATTCACAT
6384676 CAAT-AACAT
1 CAATGAACAT
6384685 ACAATCTCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 5 0.14
27 31 0.86
ACGTcount: A:0.46, C:0.22, G:0.03, T:0.29
Consensus pattern (27 bp):
CAATGAACATTCAAATCATATTCACAT
Found at i:6387834 original size:19 final size:19
Alignment explanation
Indices: 6387801--6387852 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
6387791 TGCTTTTGAT
*
6387801 GTTAAAAGTATTTTTA-AA
1 GTTAGAAGTATTTTTAGAA
6387819 GTTAGAAGTAATTTTTAGAA
1 GTTAGAAGT-ATTTTTAGAA
*
6387839 -TTAGAAGTGTTTTT
1 GTTAGAAGTATTTTT
6387853 CAACTCGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 13 0.43
19 15 0.50
20 2 0.07
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (19 bp):
GTTAGAAGTATTTTTAGAA
Found at i:6390170 original size:60 final size:60
Alignment explanation
Indices: 6390057--6390170 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 60
6390047 CTATGATTTT
* * *
6390057 TTTCCTTTTCGGTCACTCAACTATGAAAAGTTACAAAATGGCCATCCAGCTATTAGTAAA
1 TTTCCTTTTCGGTCACCCAACTATGAAAAGTTACAAAATAGCCATCCAACTATTAGTAAA
* *
6390117 TTTCCTTTTTGGTCACCCAACTATGAAAAGTTACAAAATAGTCA-CTCAACTATT
1 TTTCCTTTTCGGTCACCCAACTATGAAAAGTTACAAAATAGCCATC-CAACTATT
6390171 CAATTTTCTC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
59 1 0.02
60 47 0.98
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.33
Consensus pattern (60 bp):
TTTCCTTTTCGGTCACCCAACTATGAAAAGTTACAAAATAGCCATCCAACTATTAGTAAA
Done.