Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold23
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: 3824748
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 177433 characters in sequence are not A, C, G, or T
File 2 of 14
Found at i:328476 original size:16 final size:17
Alignment explanation
Indices: 328455--328489 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
328445 TTTTGATTTG
328455 TTTTTAAA-TATTTTAA
1 TTTTTAAAGTATTTTAA
328471 TTTTTAAATGTATTTTAA
1 TTTTTAAA-GTATTTTAA
328489 T
1 T
328490 AACGTGTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
18 9 0.53
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (17 bp):
TTTTTAAAGTATTTTAA
Found at i:331565 original size:85 final size:86
Alignment explanation
Indices: 331411--331579 Score: 241
Period size: 85 Copynumber: 2.0 Consensus size: 86
331401 AGATAAAAAC
* * * * *
331411 ATTTGCAGTTACTATCACTTTTTGTGAGTGCATAACATGGTTGCAAATTAAACAAATTGCCACTA
1 ATTTACAGTTACTACCACTTGTTGTGAGTGCATAACATAGTTACAAATTAAACAAATTGCCACTA
331476 GG-TTTGTGGACGAGCCACAT
66 GGTTTTGTGGACGAGCCACAT
* * * * *
331496 ATTTACAGTTACTGCCACTTGTTGTGAGTGCATAACATATTTACAGATTAAACAAATTGTCACTG
1 ATTTACAGTTACTACCACTTGTTGTGAGTGCATAACATAGTTACAAATTAAACAAATTGCCACTA
331561 GGTTTTGTGGACGAGCCAC
66 GGTTTTGTGGACGAGCCAC
331580 CACTTTTTTG
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
85 57 0.78
86 16 0.22
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (86 bp):
ATTTACAGTTACTACCACTTGTTGTGAGTGCATAACATAGTTACAAATTAAACAAATTGCCACTA
GGTTTTGTGGACGAGCCACAT
Found at i:332343 original size:30 final size:30
Alignment explanation
Indices: 332307--332373 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
332297 CTAAGAGGGT
332307 CGTGTGGTCCACACGAGTAGCCCACACCCC
1 CGTGTGGTCCACACGAGTAGCCCACACCCC
*
332337 CGTGTGGTCTACACGAGTAGCCCACACCCC
1 CGTGTGGTCCACACGAGTAGCCCACACCCC
332367 CGTGTGG
1 CGTGTGG
332374 CTGGTCATGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.18, C:0.39, G:0.27, T:0.16
Consensus pattern (30 bp):
CGTGTGGTCCACACGAGTAGCCCACACCCC
Found at i:337759 original size:28 final size:28
Alignment explanation
Indices: 337728--337807 Score: 79
Period size: 28 Copynumber: 2.9 Consensus size: 28
337718 ACTTATGCGG
* *
337728 ATTCATAAATGCAAATTCATACATTCGT
1 ATTCATAAATGCAAATTCATACATACGA
** *** *
337756 ATTCATATGTGTGGATTCATAGATACGA
1 ATTCATAAATGCAAATTCATACATACGA
*
337784 ATTCATAGATGCAAATTCATACAT
1 ATTCATAAATGCAAATTCATACAT
337808 GCTGATTATC
Statistics
Matches: 38, Mismatches: 14, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (28 bp):
ATTCATAAATGCAAATTCATACATACGA
Found at i:337809 original size:14 final size:14
Alignment explanation
Indices: 337722--337809 Score: 59
Period size: 14 Copynumber: 6.3 Consensus size: 14
337712 AAATAAACTT
* *
337722 ATGCGGATTCATAA
1 ATGCGAATTCATAC
*
337736 ATGCAAATTCATAC
1 ATGCGAATTCATAC
* * *
337750 ATTCGTATTCATAT
1 ATGCGAATTCATAC
* * * *
337764 GTGTGGATTCATAG
1 ATGCGAATTCATAC
* *
337778 ATACGAATTCATAG
1 ATGCGAATTCATAC
*
337792 ATGCAAATTCATAC
1 ATGCGAATTCATAC
337806 ATGC
1 ATGC
337810 TGATTATCCC
Statistics
Matches: 55, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
14 55 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (14 bp):
ATGCGAATTCATAC
Found at i:347524 original size:16 final size:14
Alignment explanation
Indices: 347505--347533 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
347495 TCAATTCAGA
347505 TCTT-TTTATTTTT
1 TCTTCTTTATTTTT
347518 TCTTCTTTATTTTT
1 TCTTCTTTATTTTT
347532 TC
1 TC
347534 CTATAAGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (14 bp):
TCTTCTTTATTTTT
Found at i:353580 original size:16 final size:16
Alignment explanation
Indices: 353568--353625 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
353558 GATTATAGTT
353568 TTATTCTATTATAATC
1 TTATTCTATTATAATC
*
353584 TTATTCTATTA-CATC
1 TTATTCTATTATAATC
*
353599 TCTATT-TCATTATAACC
1 T-TATTCT-ATTATAATC
*
353616 CTATTCTATT
1 TTATTCTATT
353626 CACCCCAACC
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 5 0.15
16 26 0.76
17 3 0.09
ACGTcount: A:0.28, C:0.19, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATTCTATTATAATC
Found at i:354072 original size:15 final size:15
Alignment explanation
Indices: 354052--354090 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
354042 GTTTAGTCCC
* *
354052 TAGGGTTTTTTGGTT
1 TAGGGTTTTTAGGGT
354067 TAGGGTTTTTAGGGT
1 TAGGGTTTTTAGGGT
354082 TA-GGTTTTT
1 TAGGGTTTTT
354091 GTTAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 7 0.32
15 15 0.68
ACGTcount: A:0.10, C:0.00, G:0.33, T:0.56
Consensus pattern (15 bp):
TAGGGTTTTTAGGGT
Found at i:354133 original size:42 final size:41
Alignment explanation
Indices: 354070--354151 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 41
354060 TTTGGTTTAG
* *
354070 GGTTTTTAGGGTTAGGTTTTTGTTAAAATAATTTAAGGTTA
1 GGTTTGTAGGGTTAGGATTTTGTTAAAATAATTTAAGGTTA
*
354111 GGTTTGTAGGGTTTAGGATTTTGTTAAAATAATTTAGGGTT
1 GGTTTGTAGGG-TTAGGATTTTGTTAAAATAATTTAAGGTT
354152 CTGGGTTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
41 10 0.27
42 27 0.73
ACGTcount: A:0.26, C:0.00, G:0.27, T:0.48
Consensus pattern (41 bp):
GGTTTGTAGGGTTAGGATTTTGTTAAAATAATTTAAGGTTA
Found at i:354702 original size:125 final size:127
Alignment explanation
Indices: 354332--354850 Score: 714
Period size: 126 Copynumber: 4.1 Consensus size: 127
354322 GGATATTGGT
* *
354332 TTTTCTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACAG-TTCTGAACAAATAGTGTCAA
1 TTTT-TCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGAC-GTTTCTAAACAAATAGTGTCAA
* * * *
354396 AAACGCTTCAAGTAGGATGCACTGTCAGTAAAACT-ACTAAAAAAAGCTCCCACGTGGACGCTC
64 AAACGCTTCAAGCAGGATGCACTGTCAGCAAAAATGACTGAAAAAAGCTCCCACGTGGACGCTC
* * * * *
354459 TTTTTCTATAGTAATTTCTGAAAAAATAATTTTTAGAAGACGGTTCTAAACAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGTTTCTAAACAAATAGTGTCAAAA
* * *
354524 ACGCTTCAAGCAGGATGCACTGTCAGCTAAATTGA-TGAAAAAAGCTCCCACGTGGATGCTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAAATGACTGAAAAAAGCTCCCACGTGGACGCTC
* * *
354585 TTTTTCTACAATAGTTCCTGAAAAAATAAATTTGAGAAGACGTTTCTGAAC-AATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGTTTCTAAACAAATAGTGTCAAAA
* * * *
354649 ATGCTTCAAGCAAGG-TGCACTATTAGCAAAAATGA-TGAAAAAAGCTCCCACGTGGACGCTT
66 ACGCTTCAAGC-AGGATGCACTGTCAGCAAAAATGACTGAAAAAAGCTCCCACGTGGACGCTC
* *
354710 TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACATTTCTAAACAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGTTTCTAAACAAATAGTGTCAAAA
* * *
354775 ACACTTCAAGCGGGATGCACTGTCAGC-AAAATTACTGAAAAAAGCTCCCA--TGGACGCTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAAATGACTGAAAAAAGCTCCCACGTGGACGCTC
354834 TTTTTCTACAGTAGTTC
1 TTTTTCTACAGTAGTTC
354851 ATGTTTGGCC
Statistics
Matches: 347, Mismatches: 39, Indels: 15
0.87 0.10 0.04
Matches are distributed among these distances:
124 25 0.07
125 118 0.34
126 199 0.57
127 5 0.01
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.29
Consensus pattern (127 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGTTTCTAAACAAATAGTGTCAAAA
ACGCTTCAAGCAGGATGCACTGTCAGCAAAAATGACTGAAAAAAGCTCCCACGTGGACGCTC
Found at i:354795 original size:251 final size:250
Alignment explanation
Indices: 354332--354850 Score: 744
Period size: 251 Copynumber: 2.1 Consensus size: 250
354322 GGATATTGGT
* *
354332 TTTTCTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACAGTTCTGAACAAATAGTGTCAAA
1 TTTT-TCTACAGTAGTTCCTGAAAAAATAAATTTGAGAAGACAGTTCTGAACAAATAGTGTCAAA
* * * *
354397 AACGCTTCAAGTAGGATGCACTGTCAGTAAAACTACTAAAAAAAGCTCCCACGTGGACGCTCTTT
65 AACGCTTCAAGAAGGATGCACTATCAGCAAAAATACTAAAAAAAGCTCCCACGTGGACGCTCTTT
* * * *
354462 TTCTATAGTAATTTCTGAAAAAATAATTTTTAGAAGACGGTTCTAAACAAATAGTGTCAAAAACG
130 TTCTACAGTAATTTCTGAAAAAATAATTTTGAGAAGACAGTTCTAAACAAATAGTGTCAAAAACA
* *
354527 CTTCAAGCAGGATGCACTGTCAGCTAAATTGA-TGAAAAAAGCTCCCACGTGGATGCTC
195 CTTCAAGCAGGATGCACTGTCAGCAAAATT-ACTGAAAAAAGCTCCCA--TGGACGCTC
*
354585 TTTTTCTACAATAGTTCCTGAAAAAATAAATTTGAGAAGAC-GTTTCTGAAC-AATAGTGTCAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAAATTTGAGAAGACAG-TTCTGAACAAATAGTGTCAAA
* * * *
354648 AATGCTTCAAGCAAGG-TGCACTATTAGCAAAAATGA-TGAAAAAAGCTCCCACGTGGACGCTTT
65 AACGCTTCAAG-AAGGATGCACTATCAGCAAAAAT-ACTAAAAAAAGCTCCCACGTGGACGCTCT
* *
354711 TTTTCTACAGT-AGTTCTTGAAAAAATAATTTTGAGAAGACATTTCTAAACAAATAGTGTCAAAA
128 TTTTCTACAGTAATTTC-TGAAAAAATAATTTTGAGAAGACAGTTCTAAACAAATAGTGTCAAAA
*
354775 ACACTTCAAGCGGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCATGGACGCTC
192 ACACTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCATGGACGCTC
354834 TTTTTCTACAGTAGTTC
1 TTTTTCTACAGTAGTTC
354851 ATGTTTGGCC
Statistics
Matches: 240, Mismatches: 21, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
249 24 0.10
250 5 0.02
251 161 0.67
252 46 0.19
253 4 0.02
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.29
Consensus pattern (250 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAAATTTGAGAAGACAGTTCTGAACAAATAGTGTCAAAA
ACGCTTCAAGAAGGATGCACTATCAGCAAAAATACTAAAAAAAGCTCCCACGTGGACGCTCTTTT
TCTACAGTAATTTCTGAAAAAATAATTTTGAGAAGACAGTTCTAAACAAATAGTGTCAAAAACAC
TTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCATGGACGCTC
Found at i:358519 original size:3 final size:3
Alignment explanation
Indices: 358511--358546 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
358501 TCCTACCTTT
358511 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
358547 AGTAAACTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:360120 original size:20 final size:21
Alignment explanation
Indices: 360097--360146 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 21
360087 TTTCAACAAT
*
360097 TATTTTTT-TTTATTTTTATA
1 TATTTTTTATTTATTATTATA
360117 TATTTTTTAGATTTATTATTATA
1 TATTTTTT--ATTTATTATTATA
360140 T-TTTTTT
1 TATTTTTT
360147 GGAAATAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 8 0.31
22 6 0.23
23 12 0.46
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (21 bp):
TATTTTTTATTTATTATTATA
Found at i:360139 original size:21 final size:20
Alignment explanation
Indices: 360095--360145 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
360085 TTTTTCAACA
**
360095 ATTAT-TTTTTTTTATTTTT
1 ATTATATTTTTTAGATTTTT
360114 A-TATATTTTTTAGATTTATT
1 ATTATATTTTTTAGATTT-TT
360134 ATTATATTTTTT
1 ATTATATTTTTT
360146 TGGAAATAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 3 0.11
19 11 0.41
20 3 0.11
21 10 0.37
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.75
Consensus pattern (20 bp):
ATTATATTTTTTAGATTTTT
Found at i:361510 original size:23 final size:21
Alignment explanation
Indices: 361468--361522 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 21
361458 TTCATTTTTT
*
361468 TTATAAAAAATACATGTAAAA
1 TTATAAAAAATACATATAAAA
*
361489 TTATTAAAAATACATAAATAAAA
1 TTATAAAAAATACAT--ATAAAA
361512 -TATAAATAAAT
1 TTATAAA-AAAT
361523 GAATACTCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 14 0.50
22 5 0.18
23 9 0.32
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.31
Consensus pattern (21 bp):
TTATAAAAAATACATATAAAA
Found at i:361591 original size:20 final size:19
Alignment explanation
Indices: 361566--361604 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
361556 ATTTATTCAT
*
361566 TAAAATAATATTTTTTTAAA
1 TAAAATAAT-TTTCTTTAAA
361586 TAAAATAATTTTCTTTAAA
1 TAAAATAATTTTCTTTAAA
361605 AAATCCGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
TAAAATAATTTTCTTTAAA
Found at i:373301 original size:79 final size:80
Alignment explanation
Indices: 373213--373374 Score: 317
Period size: 79 Copynumber: 2.0 Consensus size: 80
373203 TAATATAAAT
373213 ATAGATATATTATAAAAAAATCAAGGTTATTCATTCAAACAAACCATTTGTCATTATTACTATCT
1 ATAGATATATTATAAAAAAATCAAGGTTATTCATTCAAACAAACCATTTGTCATTATTACTATCT
373278 ATG-TTCATTGATAA
66 ATGTTTCATTGATAA
373292 ATAGATATATTATAAAAAAATCAAGGTTATTCATTCAAACAAACCATTTGTCATTATTACTATCT
1 ATAGATATATTATAAAAAAATCAAGGTTATTCATTCAAACAAACCATTTGTCATTATTACTATCT
373357 ATGTTTCATTGATAA
66 ATGTTTCATTGATAA
373372 ATA
1 ATA
373375 ACAAATGTTA
Statistics
Matches: 82, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
79 68 0.83
80 14 0.17
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.38
Consensus pattern (80 bp):
ATAGATATATTATAAAAAAATCAAGGTTATTCATTCAAACAAACCATTTGTCATTATTACTATCT
ATGTTTCATTGATAA
Found at i:381431 original size:43 final size:43
Alignment explanation
Indices: 381370--381543 Score: 348
Period size: 43 Copynumber: 4.0 Consensus size: 43
381360 TGAAGTAAAG
381370 TATGGACATAAGCATCTGGTGTATAACATGGCATCTCTAAATA
1 TATGGACATAAGCATCTGGTGTATAACATGGCATCTCTAAATA
381413 TATGGACATAAGCATCTGGTGTATAACATGGCATCTCTAAATA
1 TATGGACATAAGCATCTGGTGTATAACATGGCATCTCTAAATA
381456 TATGGACATAAGCATCTGGTGTATAACATGGCATCTCTAAATA
1 TATGGACATAAGCATCTGGTGTATAACATGGCATCTCTAAATA
381499 TATGGACATAAGCATCTGGTGTATAACATGGCATCTCTAAATA
1 TATGGACATAAGCATCTGGTGTATAACATGGCATCTCTAAATA
381542 TA
1 TA
381544 CAAGATAAAA
Statistics
Matches: 131, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 131 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.30
Consensus pattern (43 bp):
TATGGACATAAGCATCTGGTGTATAACATGGCATCTCTAAATA
Found at i:385119 original size:16 final size:16
Alignment explanation
Indices: 385098--385149 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
385088 TGAGTTACTG
385098 ATTACAGCTCTATTCT
1 ATTACAGCTCTATTCT
*
385114 ATTACAAC-CATATT-T
1 ATTACAGCTC-TATTCT
*
385129 AATAACAGCTCTATTCT
1 -ATTACAGCTCTATTCT
385146 ATTA
1 ATTA
385150 TAGTGAACCA
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
15 2 0.07
16 24 0.86
17 2 0.07
ACGTcount: A:0.35, C:0.21, G:0.04, T:0.40
Consensus pattern (16 bp):
ATTACAGCTCTATTCT
Found at i:386224 original size:19 final size:20
Alignment explanation
Indices: 386200--386239 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
386190 AGATACATAC
*
386200 ATACATAAT-GATAATGTGA
1 ATACATAATGGATAATATGA
*
386219 ATACATTATGGATAATATGA
1 ATACATAATGGATAATATGA
386239 A
1 A
386240 ATTTTGTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.47, C:0.05, G:0.15, T:0.33
Consensus pattern (20 bp):
ATACATAATGGATAATATGA
Found at i:389002 original size:18 final size:16
Alignment explanation
Indices: 388964--389005 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
388954 TTTTTTAAAC
*
388964 ATTATTATTATATTAT
1 ATTATTATCATATTAT
388980 A-TATTATCATCATTACT
1 ATTATTATCAT-ATTA-T
388997 ATTATTATC
1 ATTATTATC
389006 TCCATATTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 8 0.36
16 5 0.23
17 2 0.09
18 7 0.32
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTATTATCATATTAT
Found at i:391678 original size:25 final size:26
Alignment explanation
Indices: 391633--391688 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
391623 GCAATATTGA
** *
391633 TTTTTGTAGATTCATGGTGGAGTGTT
1 TTTTTGTAGATTCATCATGGAGGGTT
391659 TTTTTGTAGATTCA-CATGGAGGGTT
1 TTTTTGTAGATTCATCATGGAGGGTT
391684 TTTTT
1 TTTTT
391689 TTTTTTTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 13 0.48
26 14 0.52
ACGTcount: A:0.16, C:0.05, G:0.27, T:0.52
Consensus pattern (26 bp):
TTTTTGTAGATTCATCATGGAGGGTT
Found at i:397549 original size:4 final size:4
Alignment explanation
Indices: 397516--397584 Score: 53
Period size: 4 Copynumber: 18.5 Consensus size: 4
397506 AACTCAAAAT
*
397516 GAAA GAAA GTAAA -AAA -AAA -AAA G-AA G-AA GAAA GAAA GTAAA AAAA
1 GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA GAAA
*
397561 AAAA G-AA G-AA GAAA GAAA GAAA GA
1 GAAA GAAA GAAA GAAA GAAA GAAA GA
397585 CCCTTTTTTC
Statistics
Matches: 58, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
3 21 0.36
4 31 0.53
5 6 0.10
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (4 bp):
GAAA
Found at i:397557 original size:24 final size:23
Alignment explanation
Indices: 397529--397575 Score: 76
Period size: 25 Copynumber: 2.0 Consensus size: 23
397519 AGAAAGTAAA
397529 AAAAAAAAAGAAGAAGAAAGAAAGT
1 AAAAAAAAA-AAGAAG-AAGAAAGT
397554 AAAAAAAAAAAGAAGAAGAAAG
1 AAAAAAAAAAAGAAGAAGAAAG
397576 AAAGAAAGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 7 0.32
24 6 0.27
25 9 0.41
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (23 bp):
AAAAAAAAAAAGAAGAAGAAAGT
Found at i:397565 original size:27 final size:28
Alignment explanation
Indices: 397516--397579 Score: 121
Period size: 27 Copynumber: 2.3 Consensus size: 28
397506 AACTCAAAAT
397516 GAAAGAAAGTAAAAAAAAAAAAGAAGAA
1 GAAAGAAAGTAAAAAAAAAAAAGAAGAA
397544 GAAAGAAAGT-AAAAAAAAAAAGAAGAA
1 GAAAGAAAGTAAAAAAAAAAAAGAAGAA
397571 GAAAGAAAG
1 GAAAGAAAG
397580 AAAGACCCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 26 0.72
28 10 0.28
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (28 bp):
GAAAGAAAGTAAAAAAAAAAAAGAAGAA
Found at i:400322 original size:22 final size:23
Alignment explanation
Indices: 400303--400348 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
400293 TTTTTAATGT
*
400303 TTTAATTGT-CAAAAAATAATAA
1 TTTAATTGTAAAAAAAATAATAA
*
400325 TTTAATTTTAAAAAAAATAATAA
1 TTTAATTGTAAAAAAAATAATAA
400348 T
1 T
400349 CAAAATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (23 bp):
TTTAATTGTAAAAAAAATAATAA
Found at i:401670 original size:80 final size:81
Alignment explanation
Indices: 401582--401739 Score: 309
Period size: 80 Copynumber: 2.0 Consensus size: 81
401572 GACCTAATTA
401582 ATGATTCAAATTTATCATACTGAAGTATTTTTTTTATTTTGCTTTAAAAAAATTCAAATATATAT
1 ATGATTCAAATTTATCATACTGAAGTATTTTTTTTATTTTGCTTTAAAAAAATTCAAATATATAT
401647 GGTTT-AAATTTAAGT
66 GGTTTCAAATTTAAGT
401662 ATGATTCAAATTTATCATACTGAAGTATTTTTTTTATTTTGCTTTAAAAAAATTCAAATATATAT
1 ATGATTCAAATTTATCATACTGAAGTATTTTTTTTATTTTGCTTTAAAAAAATTCAAATATATAT
401727 GGTTTCAAATTTA
66 GGTTTCAAATTTA
401740 TGTGCTCTAA
Statistics
Matches: 77, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
80 70 0.91
81 7 0.09
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.47
Consensus pattern (81 bp):
ATGATTCAAATTTATCATACTGAAGTATTTTTTTTATTTTGCTTTAAAAAAATTCAAATATATAT
GGTTTCAAATTTAAGT
Found at i:404717 original size:18 final size:19
Alignment explanation
Indices: 404675--404716 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
404665 AATTCCTCCC
**
404675 TCTTTTCTCTTTCTCTTCA
1 TCTTTTCTCTTTCTCCCCA
404694 TCTTTTCT-TTTCTCCCCA
1 TCTTTTCTCTTTCTCCCCA
404712 T-TTTT
1 TCTTTT
404717 TTCATCATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 4 0.19
18 9 0.43
19 8 0.38
ACGTcount: A:0.05, C:0.31, G:0.00, T:0.64
Consensus pattern (19 bp):
TCTTTTCTCTTTCTCCCCA
Found at i:409517 original size:5 final size:5
Alignment explanation
Indices: 409507--409535 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
409497 AGGAAATCTG
409507 GAAAA GAAAA GAAAA GAAAA GAAAA GAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAA
409536 TGGTATAGAT
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:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:414546 original size:5 final size:5
Alignment explanation
Indices: 414536--414564 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
414526 AGGAAATCTG
414536 GAAAA GAAAA GAAAA GAAAA GAAAA GAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAA
414565 TGGTATAGAT
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:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:415085 original size:126 final size:127
Alignment explanation
Indices: 414885--415136 Score: 497
Period size: 126 Copynumber: 2.0 Consensus size: 127
414875 TTTAAATTTT
414885 AATTATAAAAAATAATATATTATTAGGTTTTAATTTTATTTATTTATTTGTAGAATTGGAAGTCA
1 AATTATAAAAAATAATATATTATTAGGTTTTAATTTTATTTATTTATTTGTAGAATTGGAAGTCA
414950 TTGTGATGTGGAAATACATTTGTGTAATTGAAATCCAAATTGTGTTT-AATTGCAAAAGAGG
66 TTGTGATGTGGAAATACATTTGTGTAATTGAAATCCAAATTGTGTTTAAATTGCAAAAGAGG
415011 AATTATAAAAAATAATATATTATTAGGTTTTAATTTTATTTATTTATTTGTAGAATTGGAAGTCA
1 AATTATAAAAAATAATATATTATTAGGTTTTAATTTTATTTATTTATTTGTAGAATTGGAAGTCA
415076 TTGTGATGTGGAAATACATTTGTGTAATTGAAATCCAAATTGTGTTTAAATTGCAAAAGAG
66 TTGTGATGTGGAAATACATTTGTGTAATTGAAATCCAAATTGTGTTTAAATTGCAAAAGAG
415137 TTAAAGAGTA
Statistics
Matches: 125, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
126 112 0.90
127 13 0.10
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.42
Consensus pattern (127 bp):
AATTATAAAAAATAATATATTATTAGGTTTTAATTTTATTTATTTATTTGTAGAATTGGAAGTCA
TTGTGATGTGGAAATACATTTGTGTAATTGAAATCCAAATTGTGTTTAAATTGCAAAAGAGG
Found at i:427543 original size:15 final size:16
Alignment explanation
Indices: 427519--427551 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
427509 ATTCAAACAA
*
427519 AACATTTTAATA-GCC
1 AACATGTTAATATGCC
427534 AACATGTTAATATGCC
1 AACATGTTAATATGCC
427550 AA
1 AA
427552 TTCCTTTGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.30
Consensus pattern (16 bp):
AACATGTTAATATGCC
Found at i:429295 original size:7 final size:7
Alignment explanation
Indices: 429283--429327 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
429273 TTGTTTTCAT
429283 TTATAAA
1 TTATAAA
429290 TTATAAA
1 TTATAAA
*
429297 TTATACA
1 TTATAAA
429304 TTATAAA
1 TTATAAA
* *
429311 TAATTTAA
1 TTA-TAAA
429319 TTATAAA
1 TTATAAA
429326 TT
1 TT
429328 TTATAACATA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
7 26 0.84
8 5 0.16
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (7 bp):
TTATAAA
Found at i:429341 original size:16 final size:16
Alignment explanation
Indices: 429320--429353 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
429310 ATAATTTAAT
429320 TATAAATTTTATAACA
1 TATAAATTTTATAACA
*
429336 TATAAATTTTATACCA
1 TATAAATTTTATAACA
429352 TA
1 TA
429354 GTTTCCTACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (16 bp):
TATAAATTTTATAACA
Found at i:431563 original size:25 final size:26
Alignment explanation
Indices: 431509--431568 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 26
431499 TTTGACTTTC
*
431509 ATGAGCTTCCCGATTAATGGCTGTCT
1 ATGAGCTTCCCGATTAATGGCTCTCT
*
431535 -TGAGTCTTCCC-ATTTATGGCTCT-T
1 ATGAG-CTTCCCGATTAATGGCTCTCT
*
431559 ATGAGATTCC
1 ATGAGCTTCC
431569 TAATATACAG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
24 5 0.17
25 18 0.62
26 6 0.21
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.38
Consensus pattern (26 bp):
ATGAGCTTCCCGATTAATGGCTCTCT
Found at i:431600 original size:25 final size:25
Alignment explanation
Indices: 431572--431669 Score: 92
Period size: 25 Copynumber: 3.9 Consensus size: 25
431562 AGATTCCTAA
* *
431572 TATACAGCTCGATTGAACTTCCCGT
1 TATACAGCTCGAATGAGCTTCCCGT
*
431597 TATATAGCTC-ACATGAGCTTCCCGT
1 TATACAGCTCGA-ATGAGCTTCCCGT
** *
431622 TATATGGCTCGAAAGAGCTTCCCGT
1 TATACAGCTCGAATGAGCTTCCCGT
*
431647 T-TACATGCTCGTATGAGCATTCC
1 TATACA-GCTCGAATGAGC-TTCC
431670 TGAATATGAA
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
24 3 0.05
25 52 0.87
26 5 0.08
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (25 bp):
TATACAGCTCGAATGAGCTTCCCGT
Found at i:445289 original size:24 final size:24
Alignment explanation
Indices: 445262--445313 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
445252 GCATACCGCA
445262 GCTC-TTATGAGCGTCCCGTATATT
1 GCTCTTTATGAGCGTCCCGT-TATT
* *
445286 GCTCTTTGTGAGCTTCCCGTTATT
1 GCTCTTTATGAGCGTCCCGTTATT
445310 GCTC
1 GCTC
445314 GCTTGAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.12, C:0.27, G:0.21, T:0.40
Consensus pattern (24 bp):
GCTCTTTATGAGCGTCCCGTTATT
Found at i:445328 original size:23 final size:24
Alignment explanation
Indices: 445275--445331 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
445265 CTTATGAGCG
** *
445275 TCCCGTATATTGCTCTTTGTGAGCT
1 TCCCGT-TATTGCTCGCTGTGAACT
445300 TCCCGTTATTGCTCGCT-TGAACT
1 TCCCGTTATTGCTCGCTGTGAACT
445323 TCCCGTTAT
1 TCCCGTTAT
445332 ATGGCTATCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 14 0.48
24 9 0.31
25 6 0.21
ACGTcount: A:0.12, C:0.28, G:0.18, T:0.42
Consensus pattern (24 bp):
TCCCGTTATTGCTCGCTGTGAACT
Found at i:445386 original size:24 final size:24
Alignment explanation
Indices: 445354--445411 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
445344 TGTTTCCTGA
*
445354 TTAAATGCTCTTCGGAGGTACCCG
1 TTAAATGCTCTTCGGAGCTACCCG
* * *
445378 TTAAGTGCTTTTCGGAGCTACTCG
1 TTAAATGCTCTTCGGAGCTACCCG
*
445402 TTATATGCTC
1 TTAAATGCTC
445412 ACATGAGCAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.36
Consensus pattern (24 bp):
TTAAATGCTCTTCGGAGCTACCCG
Found at i:454639 original size:30 final size:30
Alignment explanation
Indices: 454568--454642 Score: 109
Period size: 29 Copynumber: 2.5 Consensus size: 30
454558 TAGCCTCAAG
*
454568 CATCGAA-ATATGAAAAGGGATGGTGACGAC
1 CATCGAACA-ATGAAAAGAGATGGTGACGAC
*
454598 CATC-TACAATGAAAAGAGATGGTGACGAC
1 CATCGAACAATGAAAAGAGATGGTGACGAC
454627 CATCGAACAATGAAAA
1 CATCGAACAATGAAAA
454643 AGGATAGCTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
29 25 0.62
30 15 0.38
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (30 bp):
CATCGAACAATGAAAAGAGATGGTGACGAC
Found at i:454662 original size:30 final size:30
Alignment explanation
Indices: 454628--454690 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
454618 GGTGACGACC
*
454628 ATCGAACAATGAAAA-AGGATAGCTTCGGTT
1 ATCGAACAATGAAAAGA-GATAGCTTCAGTT
**
454658 ATCGAATTATGAAAAGAGATAGCTTCAGTT
1 ATCGAACAATGAAAAGAGATAGCTTCAGTT
454688 ATC
1 ATC
454691 AAATTATGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.27
Consensus pattern (30 bp):
ATCGAACAATGAAAAGAGATAGCTTCAGTT
Found at i:454696 original size:30 final size:29
Alignment explanation
Indices: 454640--454704 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 29
454630 CGAACAATGA
* *
454640 AAAAGGATAGCTTCGGTTATCGAATTATG
1 AAAAGGATAGCTTCAGTTATCAAATTATG
454669 AAAAGAGATAGCTTCAGTTATCAAATTATG
1 AAAAG-GATAGCTTCAGTTATCAAATTATG
454699 AAAAGG
1 AAAAGG
454705 GATGGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 6 0.18
30 27 0.82
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.28
Consensus pattern (29 bp):
AAAAGGATAGCTTCAGTTATCAAATTATG
Found at i:454716 original size:119 final size:120
Alignment explanation
Indices: 454515--454771 Score: 340
Period size: 119 Copynumber: 2.1 Consensus size: 120
454505 ATCATTGACT
* * * *
454515 AATGACAATGGATAGCTTTGGTTATCAAAATAATGAAAAGGGATAGCCTCAAGCATCGAAATATG
1 AATGAAAAAGGATAGCTTCGGTTATCAAAATAATGAAAAGAGATAGCCTCAAGCATCGAAATATG
* * *
454580 AAAAGGGATGGTGACGACCATCTACAATGAAAAGAGATGGTGACGACCATCGAAC
66 AAAAGGGATGGTAACGACCATCAACAATGAAAAGAGATGGTGACGACCATCAAAC
* * * *
454635 AATGAAAAAGGATAGCTTCGGTTATC-GAATTATGAAAAGAGATAGCTTC-AGTTATC-AAATTA
1 AATGAAAAAGGATAGCTTCGGTTATCAAAATAATGAAAAGAGATAGCCTCAAG-CATCGAAA-TA
* * *
454697 TGAAAAGGGATGGTAACGACCATCAATAATGAAAAGGGATGGTGACGACCATCAAAT
64 TGAAAAGGGATGGTAACGACCATCAACAATGAAAAGAGATGGTGACGACCATCAAAC
*
454754 AATGAAAAGGGATAGCTT
1 AATGAAAAAGGATAGCTT
454772 TCACTATTGA
Statistics
Matches: 120, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
118 5 0.04
119 92 0.77
120 23 0.19
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.22
Consensus pattern (120 bp):
AATGAAAAAGGATAGCTTCGGTTATCAAAATAATGAAAAGAGATAGCCTCAAGCATCGAAATATG
AAAAGGGATGGTAACGACCATCAACAATGAAAAGAGATGGTGACGACCATCAAAC
Found at i:454733 original size:29 final size:30
Alignment explanation
Indices: 454688--454766 Score: 133
Period size: 29 Copynumber: 2.7 Consensus size: 30
454678 AGCTTCAGTT
*
454688 ATCAAATTATGAAAAGGGATGGTAACGACC
1 ATCAAATAATGAAAAGGGATGGTAACGACC
*
454718 ATC-AATAATGAAAAGGGATGGTGACGACC
1 ATCAAATAATGAAAAGGGATGGTAACGACC
454747 ATCAAATAATGAAAAGGGAT
1 ATCAAATAATGAAAAGGGAT
454767 AGCTTTCACT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 27 0.59
30 19 0.41
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (30 bp):
ATCAAATAATGAAAAGGGATGGTAACGACC
Found at i:454793 original size:30 final size:30
Alignment explanation
Indices: 454755--454824 Score: 115
Period size: 30 Copynumber: 2.3 Consensus size: 30
454745 CCATCAAATA
454755 ATGAAAAGGGATAGCTTTC-ACTATTGAGCT
1 ATGAAAAGGGATAGC-TTCGACTATTGAGCT
*
454785 ATGCAAAGGGATAGCTTCGACTATTGAGCT
1 ATGAAAAGGGATAGCTTCGACTATTGAGCT
454815 ATGAAAAGGG
1 ATGAAAAGGG
454825 TTGGGACAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 3 0.08
30 34 0.92
ACGTcount: A:0.34, C:0.13, G:0.27, T:0.26
Consensus pattern (30 bp):
ATGAAAAGGGATAGCTTCGACTATTGAGCT
Found at i:454798 original size:119 final size:119
Alignment explanation
Indices: 454547--454802 Score: 320
Period size: 119 Copynumber: 2.2 Consensus size: 119
454537 TATCAAAATA
* * *
454547 ATGAAAAGGGATAGCCTCAAGCATCGAAATATGAAAAGGGATGGTGACGACCATCTACAATGAAA
1 ATGAAAAGGGATAGCTTCAAGCATCGAAATATGAAAAGGGATGGTAACGACCATCAACAATGAAA
* ** *
454612 AGAGATGGTGACGACCATCGAACAATGAAAAAGGATAGCTTCGGTTATCGAATT
66 AGAGATGGTGACGACCATCAAACAATGAAAAAGGATAGCTTCGACTATCGAACT
* * *
454666 ATGAAAAGAGATAGCTTC-AGTTATC-AAATTATGAAAAGGGATGGTAACGACCATCAATAATGA
1 ATGAAAAGGGATAGCTTCAAG-CATCGAAA-TATGAAAAGGGATGGTAACGACCATCAACAATGA
* * * * *
454729 AAAGGGATGGTGACGACCATCAAATAATGAAAAGGGATAGCTTTC-ACTATTGAGCT
64 AAAGAGATGGTGACGACCATCAAACAATGAAAAAGGATAGC-TTCGACTATCGAACT
*
454785 ATGCAAAGGGATAGCTTC
1 ATGAAAAGGGATAGCTTC
454803 GACTATTGAG
Statistics
Matches: 117, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
118 5 0.04
119 109 0.93
120 3 0.03
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.21
Consensus pattern (119 bp):
ATGAAAAGGGATAGCTTCAAGCATCGAAATATGAAAAGGGATGGTAACGACCATCAACAATGAAA
AGAGATGGTGACGACCATCAAACAATGAAAAAGGATAGCTTCGACTATCGAACT
Found at i:457003 original size:43 final size:42
Alignment explanation
Indices: 456942--457027 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 42
456932 TTAAAGAAAG
* *
456942 CATGCATGGGACGACATT-AAAGAAGCTGCTGATTTCTCCTTTT
1 CATGCAAGGGACGACATTAAAAG-AGCTGCTGATTCCT-CTTTT
*
456985 CATGCAAGGGACGACATTAAAAGAGCTGTTGATTCCTCTTTT
1 CATGCAAGGGACGACATTAAAAGAGCTGCTGATTCCTCTTTT
457027 C
1 C
457028 TAGGTGTCTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
42 6 0.15
43 29 0.74
44 4 0.10
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (42 bp):
CATGCAAGGGACGACATTAAAAGAGCTGCTGATTCCTCTTTT
Found at i:461634 original size:13 final size:13
Alignment explanation
Indices: 461616--461641 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
461606 CCTTATTCCC
461616 TTTCTCTATAATA
1 TTTCTCTATAATA
461629 TTTCTCTATAATA
1 TTTCTCTATAATA
461642 CACTTCCCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTCTCTATAATA
Found at i:463330 original size:50 final size:50
Alignment explanation
Indices: 463205--463491 Score: 245
Period size: 50 Copynumber: 5.6 Consensus size: 50
463195 AATAATAACA
* ** * * *
463205 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCCTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
** * * ** *
463254 TGCCAATGCCAAATCCCAGATATGGTTTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * ***
463304 TGCCCATGCCATGTCCCAGACTTGGTTTTATGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*** **
463354 TGCCAACATCATGTCCCAGACATGGTCTTACATGATACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * **
463404 TGCCAATGCCATGTCCCAGACATGGTCTTACATGTGACCTCTCATAATTTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC---GG
463460 TGCCAATGCCATGTCCCAGACATGGTCTTACA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACA
463492 CAGGCTCACA
Statistics
Matches: 190, Mismatches: 40, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
48 1 0.01
49 37 0.19
50 116 0.61
53 4 0.02
56 32 0.17
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:463567 original size:42 final size:41
Alignment explanation
Indices: 463503--463584 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 41
463493 AGGCTCACAT
* *
463503 ATCGATGTCGATACCGTGTCCCAGACATGGTCTTATACGAG
1 ATCGATGTCGATACCATATCCCAGACATGGTCTTATACGAG
* *
463544 ATCGTATGTCGATGCCATATCCCAGATATGGTCTTATACGA
1 ATCG-ATGTCGATACCATATCCCAGACATGGTCTTATACGA
463585 AAATCACATA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 4 0.11
42 32 0.89
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (41 bp):
ATCGATGTCGATACCATATCCCAGACATGGTCTTATACGAG
Found at i:475784 original size:25 final size:28
Alignment explanation
Indices: 475742--475796 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 28
475732 AAGATTTTTA
*
475742 AAATTCTTCTAAAAG-AAACTC-AAGAG
1 AAATTCTTCGAAAAGAAAACTCAAAGAG
475768 AAATTCTT-GAAAAGAAAACTCAAAGAG
1 AAATTCTTCGAAAAGAAAACTCAAAGAG
475795 AA
1 AA
475797 TTTATTAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 5 0.19
26 14 0.54
27 7 0.27
ACGTcount: A:0.55, C:0.13, G:0.13, T:0.20
Consensus pattern (28 bp):
AAATTCTTCGAAAAGAAAACTCAAAGAG
Found at i:481964 original size:25 final size:28
Alignment explanation
Indices: 481922--481976 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 28
481912 AAGATTTTTA
*
481922 AAATTCTTCTAAAAG-AAACTC-AAGAG
1 AAATTCTTCGAAAAGAAAACTCAAAGAG
481948 AAATTCTT-GAAAAGAAAACTCAAAGAG
1 AAATTCTTCGAAAAGAAAACTCAAAGAG
481975 AA
1 AA
481977 TTTATTAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 5 0.19
26 14 0.54
27 7 0.27
ACGTcount: A:0.55, C:0.13, G:0.13, T:0.20
Consensus pattern (28 bp):
AAATTCTTCGAAAAGAAAACTCAAAGAG
Found at i:485071 original size:24 final size:24
Alignment explanation
Indices: 485043--485091 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
485033 AAAATTTATT
485043 TCACATACTAACATATTTAACTTA
1 TCACATACTAACATATTTAACTTA
485067 TCACATACTAACATATTTAACTTA
1 TCACATACTAACATATTTAACTTA
485091 T
1 T
485092 ATACCTTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (24 bp):
TCACATACTAACATATTTAACTTA
Found at i:485923 original size:25 final size:25
Alignment explanation
Indices: 485888--485949 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 25
485878 AAACGATACA
*
485888 CTCCTCCGAGCTAAAAAATGGTAAG
1 CTCCTCCGAGCTAAAAAACGGTAAG
* * *
485913 CTCCTCTGAGCTGAATAACGGTAAG
1 CTCCTCCGAGCTAAAAAACGGTAAG
* *
485938 CTCATACGAGCT
1 CTCCTCCGAGCT
485950 GAGTGCTGGT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.23
Consensus pattern (25 bp):
CTCCTCCGAGCTAAAAAACGGTAAG
Found at i:485950 original size:25 final size:25
Alignment explanation
Indices: 485906--485974 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
485896 AGCTAAAAAA
*
485906 TGGTAAGCTCCT-CTGAGCTGAATAAC
1 TGGTAAGCTCATAC-GAGCTGAAT-AC
* *
485932 -GGTAAGCTCATACGAGCTGAGTGC
1 TGGTAAGCTCATACGAGCTGAATAC
*
485956 TGGTAAGCTCATAGGAGCT
1 TGGTAAGCTCATACGAGCT
485975 AAAATTGTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 1 0.03
25 35 0.95
26 1 0.03
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (25 bp):
TGGTAAGCTCATACGAGCTGAATAC
Found at i:491463 original size:23 final size:24
Alignment explanation
Indices: 491424--491471 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 24
491414 TTTATTTGAT
491424 AATATTTTTTGATATAACAAATTAA
1 AATATTTTTTGATATAA-AAATTAA
*
491449 AATA-TTTTTGA-ATAAAAGTTAA
1 AATATTTTTTGATATAAAAATTAA
491471 A
1 A
491472 GGTGAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 4 0.18
24 7 0.32
25 4 0.18
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (24 bp):
AATATTTTTTGATATAAAAATTAA
Found at i:492087 original size:16 final size:16
Alignment explanation
Indices: 492056--492106 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
492046 ATTAATAATT
*
492056 CACAATAGTATCAGATA
1 CACAGTAGT-TCAGATA
492073 C-CGAGTAGTTCAGATA
1 CAC-AGTAGTTCAGATA
*
492089 CACAGTAGATCAGATA
1 CACAGTAGTTCAGATA
492105 CA
1 CA
492107 AAAATAGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
16 23 0.77
17 7 0.23
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.22
Consensus pattern (16 bp):
CACAGTAGTTCAGATA
Found at i:492813 original size:22 final size:22
Alignment explanation
Indices: 492785--492832 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
492775 AAGTTAATCA
492785 GTGTAGCTCATGTAGCTCGTCC
1 GTGTAGCTCATGTAGCTCGTCC
*
492807 GTGTAGCTCGTGTAGCTCGTCC
1 GTGTAGCTCATGTAGCTCGTCC
492829 GTGT
1 GTGT
492833 GTCTCAAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.10, C:0.25, G:0.31, T:0.33
Consensus pattern (22 bp):
GTGTAGCTCATGTAGCTCGTCC
Found at i:495178 original size:24 final size:24
Alignment explanation
Indices: 495117--495184 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
495107 ATGCAAAGGA
495117 GTTAGATGCTAAACCATTTTGTGG
1 GTTAGATGCTAAACCATTTTGTGG
* * * *
495141 GATTTTGAAG--AAACGATTTTGTGT
1 G--TTAGATGCTAAACCATTTTGTGG
495165 GTTAGATGCTAAACCATTTT
1 GTTAGATGCTAAACCATTTT
495185 AGAATTTCCA
Statistics
Matches: 33, Mismatches: 7, Indels: 8
0.69 0.15 0.17
Matches are distributed among these distances:
22 5 0.15
24 23 0.70
26 5 0.15
ACGTcount: A:0.28, C:0.10, G:0.22, T:0.40
Consensus pattern (24 bp):
GTTAGATGCTAAACCATTTTGTGG
Found at i:499665 original size:68 final size:66
Alignment explanation
Indices: 499590--499786 Score: 239
Period size: 68 Copynumber: 3.0 Consensus size: 66
499580 ATTTTAATAG
* *
499590 ATTTAATATTAAATTTAATTTAATACTTATCTTGAT-AGTATTTTATTAATTTAATATTAAAGTG
1 ATTTAATATTAAATTTAATTTAATATTTATCTTGATAAGTATTATATTAATTTAATATTAAAGTG
499654 A
66 A
* *
499655 TTATCTTAATATTAAATTTAATTTAATATTTATCTGTAGATAAATATTCTATTAATTT-A-A-T-
1 --AT-TTAATATTAAATTTAATTTAATATTTATCT-T-GATAAGTATTATATTAATTTAATATTA
499716 AA--G-
61 AAGTGA
* *
499719 ATTTAATATTAAATGTAATCTAATATTTATCTTGATAAGTATTATATTAATTTAATATTAAAGTG
1 ATTTAATATTAAATTTAATTTAATATTTATCTTGATAAGTATTATATTAATTTAATATTAAAGTG
499784 A
66 A
499785 AT
1 AT
499787 AAGTTTAATC
Statistics
Matches: 112, Mismatches: 7, Indels: 23
0.79 0.05 0.16
Matches are distributed among these distances:
59 18 0.16
60 2 0.02
61 29 0.26
62 3 0.03
63 2 0.02
65 2 0.02
66 2 0.02
67 4 0.04
68 30 0.27
69 2 0.02
70 4 0.04
71 14 0.12
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (66 bp):
ATTTAATATTAAATTTAATTTAATATTTATCTTGATAAGTATTATATTAATTTAATATTAAAGTG
A
Found at i:503566 original size:12 final size:12
Alignment explanation
Indices: 503549--503582 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
503539 TTCGTCATCA
503549 TCATCATCACCG
1 TCATCATCACCG
**
503561 TCATCATCGTCG
1 TCATCATCACCG
503573 TCATCATCAC
1 TCATCATCAC
503583 TTTTTTCATC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.24, C:0.38, G:0.09, T:0.29
Consensus pattern (12 bp):
TCATCATCACCG
Found at i:508433 original size:14 final size:14
Alignment explanation
Indices: 508411--508446 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
508401 CATAGGTATC
508411 TAAAAAAATGGAAA
1 TAAAAAAATGGAAA
* *
508425 TAAATAAATGTAAA
1 TAAAAAAATGGAAA
508439 TAAAAAAA
1 TAAAAAAA
508447 GTAAATACAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.19
Consensus pattern (14 bp):
TAAAAAAATGGAAA
Found at i:508452 original size:13 final size:13
Alignment explanation
Indices: 508411--508453 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
508401 CATAGGTATC
*
508411 TAAAAAAATGGAAA
1 TAAAAAAA-GTAAA
*
508425 TAAATAAATGTAAA
1 TAAA-AAAAGTAAA
508439 TAAAAAAAGTAAA
1 TAAAAAAAGTAAA
508452 TA
1 TA
508454 CATATTAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 10 0.40
14 12 0.48
15 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (13 bp):
TAAAAAAAGTAAA
Found at i:508614 original size:23 final size:23
Alignment explanation
Indices: 508586--508630 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
508576 ATATATTTGG
508586 ACTATA-AAATATACATAAAACAA
1 ACTATACAAATAT-CATAAAACAA
*
508609 ACTATACAAATATTATAAAACA
1 ACTATACAAATATCATAAAACA
508631 GAAATATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.24
Consensus pattern (23 bp):
ACTATACAAATATCATAAAACAA
Found at i:510847 original size:3 final size:3
Alignment explanation
Indices: 510839--510865 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
510829 CGGATATAAC
510839 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG
510866 GTAAAAGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:511109 original size:74 final size:74
Alignment explanation
Indices: 510988--511208 Score: 327
Period size: 74 Copynumber: 3.0 Consensus size: 74
510978 AAAGTTGAAG
* * * *
510988 AACCAGAGAAAATAAAAGAAGGGAAATTAGTATAAAAGTTTAGAACTAGAGAAAATGAAAGGGAA
1 AACCAGAGGAAATAAAAGAAGGGAAACTACTACAAAAGTTTAGAACTAGAGAAAATGAAAGGGAA
511053 AGTAGGAAA
66 AGTAGGAAA
* * *
511062 AACCAGAGGAAATTAAAGAAGGGAAACTACTACAAAAGTTTAGAACTAGAGAGAATGAAAAGGAA
1 AACCAGAGGAAATAAAAGAAGGGAAACTACTACAAAAGTTTAGAACTAGAGAAAATGAAAGGGAA
*
511127 AGTAGGAAG
66 AGTAGGAAA
* * *
511136 AACCAGA-GAAGACAAAAGAAGGGAAACTGCTGCAAAAGTTTAGAACTAGAGAAAATGAAAGGGA
1 AACCAGAGGAA-ATAAAAGAAGGGAAACTACTACAAAAGTTTAGAACTAGAGAAAATGAAAGGGA
511200 AAGTAGGAA
65 AAGTAGGAA
511209 CTGCTGCAAT
Statistics
Matches: 132, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
73 3 0.02
74 129 0.98
ACGTcount: A:0.54, C:0.07, G:0.26, T:0.13
Consensus pattern (74 bp):
AACCAGAGGAAATAAAAGAAGGGAAACTACTACAAAAGTTTAGAACTAGAGAAAATGAAAGGGAA
AGTAGGAAA
Found at i:511959 original size:52 final size:51
Alignment explanation
Indices: 511902--512003 Score: 136
Period size: 52 Copynumber: 2.0 Consensus size: 51
511892 CTTCTCCTTA
* * *
511902 CTTATCTTACATCACTTC-TTTTGAAACACACAACATT-TTGCAAAGCTAAAGC
1 CTTATCCTACATCAC-TCGTTTTGAAACA-A-AAAATTGCTGCAAAGCTAAAGC
511954 CTTATCCTACATCACTCGTTTTGAAACAAAAAATTGCTGCAAAGCTAAAG
1 CTTATCCTACATCACTCGTTTTGAAACAAAAAATTGCTGCAAAGCTAAAG
512004 TATGCAATAG
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
50 5 0.11
51 16 0.36
52 24 0.53
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.30
Consensus pattern (51 bp):
CTTATCCTACATCACTCGTTTTGAAACAAAAAATTGCTGCAAAGCTAAAGC
Found at i:512887 original size:205 final size:206
Alignment explanation
Indices: 512231--513093 Score: 1218
Period size: 205 Copynumber: 4.2 Consensus size: 206
512221 TTTCGAGCAT
*
512231 GATGGAAACACTATATCATGCATCCATATTATGGCATTCAACTTACAGCTTATATGGTACAATTA
1 GATGGAAACACTATATCATGCATCCATATTAAGGCATTCAACTTACAGCTTATATGGTACAATTA
** *
512296 TCCAATTGAAAACAAGGGAGAGCAGTAGAAC-ATGAAAATTAGCAATT-AATGACAGAAATATT-
66 TCCAAAAGAAAACAAGGCAGAGCAGTAGAACAAT-AAAATTAGCAATTCAATGACAGAAATATTA
512358 GCTAATTTTGGTACACAAAACACAAGATGCAATAATAC-TTCAATCCACTCTGGTTTATACAGTT
130 G-TAATTTTGGTACACAAAACACAAGATGCAATAATACTTTC-ATCCACTCTGGTTTATACAGTT
512422 TTCAAGCATTACAA
193 TTCAAGCATTACAA
* * **
512436 GATGGAAACACTATATCATGCATCCATCTTAAGGCATTCAACTTGCATTTTATATGGTACAATTA
1 GATGGAAACACTATATCATGCATCCATATTAAGGCATTCAACTTACAGCTTATATGGTACAATTA
* * * *
512501 TCCAAAAGAAATCAAGGCAGAGCAGTGGAACAATAAAATTAGCAGTTCAATGATAGAAATATTAG
66 TCCAAAAGAAAACAAGGCAGAGCAGTAGAACAATAAAATTAGCAATTCAATGACAGAAATATTAG
** *
512566 TAATTTTTGAAACACAAAACACAA-ATGCAATTATACTTTCATCCACTCTGGTTTATATACAGTT
131 TAA-TTTTGGTACACAAAACACAAGATGCAATAATACTTTCATCCACTCTGG-TT-TATACAGTT
512630 TTCAAGCATTACAA
193 TTCAAGCATTACAA
*
512644 GATGGAAACACTATATCATGCATCCATATTATGGCATTCAACTTACAGCTTATATGGTACAATTA
1 GATGGAAACACTATATCATGCATCCATATTAAGGCATTCAACTTACAGCTTATATGGTACAATTA
** *
512709 TCCAATTGAAAACAAGGGAGAGCAGTAGAAC-ATGAAAATTAGCAATT-AATGACAGAAATATT-
66 TCCAAAAGAAAACAAGGCAGAGCAGTAGAACAAT-AAAATTAGCAATTCAATGACAGAAATATTA
512771 GCTAATTTTGGTACACAAAACACAAGATGCAATAATAC-TTCAATCCACTCTGGTTTATACAGTT
130 G-TAATTTTGGTACACAAAACACAAGATGCAATAATACTTTC-ATCCACTCTGGTTTATACAGTT
512835 TTCAAGCATTACAA
193 TTCAAGCATTACAA
* * **
512849 GATGGAAACACTATATCATGCATCCATCTTAAGGCATTCAACTTGCATTTTATATGGTACAATTA
1 GATGGAAACACTATATCATGCATCCATATTAAGGCATTCAACTTACAGCTTATATGGTACAATTA
* * *
512914 TCCAAAAGAAATCAAGGCAGAGCAGTAGAACAATAAAATTAGCAGTTCAATGATAGAAATATTAG
66 TCCAAAAGAAAACAAGGCAGAGCAGTAGAACAATAAAATTAGCAATTCAATGACAGAAATATTAG
* *
512979 TAA-TTT--T----AAAACACAAGATGCAATTATACTTTCATCCATTCTGGTTTATACACAGTTT
131 TAATTTTGGTACACAAAACACAAGATGCAATAATACTTTCATCCACTCTGGTTTAT--ACAGTTT
513037 TCAAGCATTACAA
194 TCAAGCATTACAA
* * * * *
513050 GATAGAAACACCATACCATACATCCTTATTAAGGCATTCAACTT
1 GATGGAAACACTATATCATGCATCCATATTAAGGCATTCAACTT
513094 TCTAATTTCT
Statistics
Matches: 592, Mismatches: 49, Indels: 38
0.87 0.07 0.06
Matches are distributed among these distances:
199 36 0.06
200 3 0.01
201 58 0.10
203 1 0.00
205 223 0.38
206 84 0.14
207 66 0.11
208 121 0.20
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (206 bp):
GATGGAAACACTATATCATGCATCCATATTAAGGCATTCAACTTACAGCTTATATGGTACAATTA
TCCAAAAGAAAACAAGGCAGAGCAGTAGAACAATAAAATTAGCAATTCAATGACAGAAATATTAG
TAATTTTGGTACACAAAACACAAGATGCAATAATACTTTCATCCACTCTGGTTTATACAGTTTTC
AAGCATTACAA
Found at i:516363 original size:19 final size:20
Alignment explanation
Indices: 516339--516382 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
516329 TTTCTGCTTC
516339 TTCTTCTC-TTAGGTTTCTT
1 TTCTTCTCTTTAGGTTTCTT
*
516358 TTCTTCTCTTTATGTTTCTT
1 TTCTTCTCTTTAGGTTTCTT
516378 TTCTT
1 TTCTT
516383 TTCACCATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.05, C:0.20, G:0.07, T:0.68
Consensus pattern (20 bp):
TTCTTCTCTTTAGGTTTCTT
Found at i:516483 original size:16 final size:16
Alignment explanation
Indices: 516462--516492 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
516452 CGATTTCATT
516462 TTTCTTGAAATTTGTA
1 TTTCTTGAAATTTGTA
516478 TTTCTTGAAATTTGT
1 TTTCTTGAAATTTGT
516493 TGGAGTTCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.23, C:0.06, G:0.13, T:0.58
Consensus pattern (16 bp):
TTTCTTGAAATTTGTA
Found at i:525019 original size:29 final size:29
Alignment explanation
Indices: 524935--525043 Score: 98
Period size: 29 Copynumber: 3.7 Consensus size: 29
524925 ATGACATGTC
524935 AATTTTTAATTATTTTTTAAAAAT-TTTTAA-
1 AATTTTTAA-TA--TTTTAAAAATATTTTAAT
* * **
524965 AATTTTTTTATACTTTTTAGTA-ATTTTAAT
1 AA-TTTTTAATA-TTTTAAAAATATTTTAAT
* *
524995 GATTTTTAATATTTTAAAAATATTTTTAT
1 AATTTTTAATATTTTAAAAATATTTTAAT
525024 AATTTTTAATATTTTAAAAA
1 AATTTTTAATATTTTAAAAA
525044 AGTAATTAAA
Statistics
Matches: 63, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
28 6 0.10
29 46 0.73
30 5 0.08
31 6 0.10
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.59
Consensus pattern (29 bp):
AATTTTTAATATTTTAAAAATATTTTAAT
Found at i:528639 original size:52 final size:52
Alignment explanation
Indices: 528579--528679 Score: 148
Period size: 52 Copynumber: 1.9 Consensus size: 52
528569 AAATGGTAAA
** * * *
528579 AAAATATTATTTAATTATTTAATTTTAATTTGTTAATTATTATGATGTTAAG
1 AAAATATTATCAAATTATTAAATTTTAAATAGTTAATTATTATGATGTTAAG
*
528631 AAAATATTATCAAATTATTAAATTTTAAATAGTTAATTATTATGTTGTT
1 AAAATATTATCAAATTATTAAATTTTAAATAGTTAATTATTATGATGTT
528680 TAGATTAATA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.41, C:0.01, G:0.07, T:0.51
Consensus pattern (52 bp):
AAAATATTATCAAATTATTAAATTTTAAATAGTTAATTATTATGATGTTAAG
Found at i:530270 original size:12 final size:12
Alignment explanation
Indices: 530253--530278 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
530243 TTTACACCAC
530253 CATGTACCACAA
1 CATGTACCACAA
530265 CATGTACCACAA
1 CATGTACCACAA
530277 CA
1 CA
530279 CACGCAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.35, G:0.08, T:0.15
Consensus pattern (12 bp):
CATGTACCACAA
Found at i:530367 original size:63 final size:63
Alignment explanation
Indices: 530268--530416 Score: 190
Period size: 63 Copynumber: 2.4 Consensus size: 63
530258 ACCACAACAT
* * ** * * *
530268 GTACCACAACACACGCAATCATTCTTTGCTCCAACACAATCATCACTAGTTTATTTTACACAA
1 GTACCATAACACGCGCAATCATTCCCTGCACCAACACAATCATCACCAATTTATTTTACACAA
* * *
530331 GTACCATAACACGTGCAATCATTCCCTGCACCAACACAGTCATCGCCAATTTATTTTACACAA
1 GTACCATAACACGCGCAATCATTCCCTGCACCAACACAATCATCACCAATTTATTTTACACAA
* *
530394 GCACCATAACACGCACAATCATT
1 GTACCATAACACGCGCAATCATT
530417 TCTTAGACCG
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
63 73 1.00
ACGTcount: A:0.35, C:0.32, G:0.08, T:0.26
Consensus pattern (63 bp):
GTACCATAACACGCGCAATCATTCCCTGCACCAACACAATCATCACCAATTTATTTTACACAA
Found at i:540413 original size:9 final size:9
Alignment explanation
Indices: 540367--540397 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
540357 CAGTGGAGGT
540367 AAAAAAACA
1 AAAAAAACA
*
540376 AAAAAAACC
1 AAAAAAACA
540385 AAAAAAACA
1 AAAAAAACA
540394 AAAA
1 AAAA
540398 CATAAAAAAA
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:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAACA
Found at i:541971 original size:131 final size:131
Alignment explanation
Indices: 541730--542668 Score: 1392
Period size: 131 Copynumber: 7.1 Consensus size: 131
541720 GATCGGTGAA
* *
541730 ACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTCAAGATTGTAGATCTTATCTCCCTAAGT
1 ACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGC
* * * *
541795 AGTAGTGGAGCAGATCGAACACGGTGAATCTTATCTTACCGAGGTAATAGGAAGCAGATTTAAGC
66 AGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCGAGGTAGTAGGAAGCAGATTTAAGC
541860 C
131 C
* * * *
541861 ACCAGTCCTATTTCTCTGAGCAACAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGA
1 ACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGC
* **
541926 AGTAATGGAGCAGATCGAAGACGGCGAATCTTATCTTCCAAAGGTAGTAGGAAGCAGATTTAAGC
66 AGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCGAGGTAGTAGGAAGCAGATTTAAGC
541991 C
131 C
* * *
541992 ACCAGTCCTATCTCCCTGAGCAGTAGTGGAGTGGGTTGAAGATTGTAGATCTTATCTCCTTAAGC
1 ACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGC
*
542057 AGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCTGAGGTAGTAGGAAGCAGATTTAAGC
66 AGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCGAGGTAGTAGGAAGCAGATTTAAGC
542122 C
131 C
* * *
542123 ACCAGTCCTATCTCCTTGAGCAGCAGTGGAGTAGGTTTAAGATTGTAGATCTTATCTCCCTAAAC
1 ACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGC
** * *
542188 AGTAGCAGAGTAGATCGAAGACGGCGAATCTTATTTTCCCGAGGTAGTAGGAAGCAGCAGATTTA
66 AGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCGAGGTAGTAGG-A--AGCAGATTTA
542253 AGCC
128 AGCC
*
542257 ACCAGTCCTATCTCTCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGC
1 ACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGC
* * * *
542322 AGTAGTGGAGTAGATCGAAGATGGCGAATCTTATTTTCCCAAGGTAGTAGGAAGCAGATTTAAGC
66 AGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCGAGGTAGTAGGAAGCAGATTTAAGC
542387 C
131 C
* * *
542388 ATCAGTCCTATCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATTGTAGATCTTATCTCCCTAAGC
1 ACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGC
* * ** * * *
542453 AGTAGTGGAGCAAATTGAAGACGGTAAATCTTATCTTCCCGACGTAGTGGGAATCAGATTTAAGC
66 AGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCGAGGTAGTAGGAAGCAGATTTAAGC
542518 C
131 C
* * * *
542519 ACCAGTTCTATCTCCTTGAGTAGCAGTAGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGC
1 ACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGC
* * *** *
542584 AGTAGTGGAGCAGATCGAAGACGACGAATCTTATCTTCTCGAGGTAGTAGGAAGCAGACAAAAGA
66 AGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCGAGGTAGTAGGAAGCAGATTTAAGC
*
542649 A
131 C
*
542650 ACCAATCCTATCTCCCTGA
1 ACCAGTCCTATCTCCCTGA
542669 AGTTGCAGTG
Statistics
Matches: 725, Mismatches: 80, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
131 601 0.83
132 1 0.00
133 1 0.00
134 122 0.17
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (131 bp):
ACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGC
AGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCGAGGTAGTAGGAAGCAGATTTAAGC
C
Found at i:542329 original size:44 final size:44
Alignment explanation
Indices: 541885--542604 Score: 224
Period size: 44 Copynumber: 16.4 Consensus size: 44
541875 TCTGAGCAAC
* *
541885 AGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGAAGT
1 AGTGGAGTAGATTGAAGATTGTAGATCTTATCTCCCTAAGCAGT
* * * * ** * *
541929 AATGGAGCAGATCGAAGA-CGGCGAATCTTATCTTCCAAAG--GT
1 AGTGGAGTAGATTGAAGATTGTAG-ATCTTATCTCCCTAAGCAGT
* * ***** * *
541971 AGTAGGAAGCAGATTTAAGCCACCAG-TCCTATCTCCCTGAGCAGT
1 AGT-GG-AGTAGATTGAAGATTGTAGATCTTATCTCCCTAAGCAGT
* * *
542016 AGTGGAGTGGGTTGAAGATTGTAGATCTTATCTCCTTAAGCAGT
1 AGTGGAGTAGATTGAAGATTGTAGATCTTATCTCCCTAAGCAGT
* * * ** * *
542060 AGTGGAGCAGATCGAAGA-CGGCGAATCTTATCTTCCTGAG--GT
1 AGTGGAGTAGATTGAAGATTGTAG-ATCTTATCTCCCTAAGCAGT
* * ***** * * * *
542102 AGTAGGAAGCAGATTTAAGCCACCAG-TCCTATCTCCTTGAGCAGC
1 AGT-GG-AGTAGATTGAAGATTGTAGATCTTATCTCCCTAAGCAGT
* * *
542147 AGTGGAGTAGGTTTAAGATTGTAGATCTTATCTCCCTAAACAGT
1 AGTGGAGTAGATTGAAGATTGTAGATCTTATCTCCCTAAGCAGT
** * * ** * * * *
542191 AGCAGAGTAGATCGAAGA-CGGCGAATCTTATTTTCCCGAGGTAGT
1 AGTGGAGTAGATTGAAGATTGTAG-ATCTTA-TCTCCCTAAGCAGT
* * ***** * * * *
542236 AG-GAAGCAGCAGATTTAAGCCACCAG-TCCTATCTCTCTGAGCAGC
1 AGTG--G-AGTAGATTGAAGATTGTAGATCTTATCTCCCTAAGCAGT
*
542281 AGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGT
1 AGTGGAGTAGATTGAAGATTGTAGATCTTATCTCCCTAAGCAGT
* ** *
542325 AGTGGAGTAGATCGAAGA-TGGCGAATCTTATTTTCCC-AAG--GT
1 AGTGGAGTAGATTGAAGATTGTAG-ATCTTA-TCTCCCTAAGCAGT
* * * * *
542367 AGTAGGAAGCAGATTTAAGCCA-T-CAG-TCCTATCTCCCTGAGCAGT
1 AGT-GG-AGTAGATTGAAG--ATTGTAGATCTTATCTCCCTAAGCAGT
* *
542412 AGTGGAGTAGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGT
1 AGTGGAGTAGATTGAAGATTGTAGATCTTATCTCCCTAAGCAGT
* * ** * *
542456 AGTGGAGCAAATTGAAGACGGTAAATCTTATCTTCCC-GA-C-GT
1 AGTGGAGTAGATTGAAGATTGTAGATCTTATC-TCCCTAAGCAGT
* * ***** * * * * *
542498 AGTGGGAATCAGATTTAAGCCACCAGTTC-TATCTCCTTGAGTAGC
1 AGT-GGAGT-AGATTGAAGATTGTAGATCTTATCTCCCTAAGCAGT
* *
542543 AGTAGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGT
1 AGTGGAGTAGATTGAAGATTGTAGATCTTATCTCCCTAAGCAGT
* *
542587 AGTGGAGCAGATCGAAGA
1 AGTGGAGTAGATTGAAGA
542605 CGACGAATCT
Statistics
Matches: 468, Mismatches: 167, Indels: 82
0.65 0.23 0.11
Matches are distributed among these distances:
41 1 0.00
42 28 0.06
43 108 0.23
44 263 0.56
45 50 0.11
46 8 0.02
47 9 0.02
48 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (44 bp):
AGTGGAGTAGATTGAAGATTGTAGATCTTATCTCCCTAAGCAGT
Found at i:542459 original size:396 final size:396
Alignment explanation
Indices: 541730--542640 Score: 1459
Period size: 396 Copynumber: 2.3 Consensus size: 396
541720 GATCGGTGAA
* *
541730 ACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTCAAGATTGTAGATCTTATCTCCCTAAGT
1 ACCAGTCCTATCTCCTTGAGCAGCAGTGGAGTAGGTTCAAGATTGTAGATCTTATCTCCCTAAGC
* * * *
541795 AGTAGTGGAGCAGATCGAACACGGTGAATCTTATCTTACCGAGGTAATAGG-A--AGCAGATTTA
66 AGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCGAGGTAGTAGGAAGCAGCAGATTTA
*
541857 AGCCACCAGTCCTATTTCTCTGAGCAACAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCT
131 AGCCACCAGTCCTATCTCTCTGAGCAACAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCT
541922 AAGAAGTAATGGAGCAGATCGAAGACGGCGAATCTTATCTTCCAAAGGTAGTAGGAAGCAGATTT
196 AAGAAGTAATGGAGCAGATCGAAGACGGCGAATCTTATCTTCCAAAGGTAGTAGGAAGCAGATTT
* * *
541987 AAGCCACCAGTCCTATCTCCCTGAGCAGTAGTGGAGTGGGTTGAAGATTGTAGATCTTATCTCCT
261 AAGCCACCAGTCCTATCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATTGTAGATCTTATCTCCC
* * * *
542052 TAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCTGAGGTAGTAGGAAGCAGATT
326 TAAGCAGTAGTGGAGCAAATCGAAGACGGCAAATCTTATCTTCCCGACGTAGTAGGAAGCAGATT
542117 TAAGCC
391 TAAGCC
* *
542123 ACCAGTCCTATCTCCTTGAGCAGCAGTGGAGTAGGTTTAAGATTGTAGATCTTATCTCCCTAAAC
1 ACCAGTCCTATCTCCTTGAGCAGCAGTGGAGTAGGTTCAAGATTGTAGATCTTATCTCCCTAAGC
** * *
542188 AGTAGCAGAGTAGATCGAAGACGGCGAATCTTATTTTCCCGAGGTAGTAGGAAGCAGCAGATTTA
66 AGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCGAGGTAGTAGGAAGCAGCAGATTTA
*
542253 AGCCACCAGTCCTATCTCTCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCT
131 AGCCACCAGTCCTATCTCTCTGAGCAACAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCT
* * * * * *
542318 AAGCAGTAGTGGAGTAGATCGAAGATGGCGAATCTTATTTTCCCAAGGTAGTAGGAAGCAGATTT
196 AAGAAGTAATGGAGCAGATCGAAGACGGCGAATCTTATCTTCCAAAGGTAGTAGGAAGCAGATTT
*
542383 AAGCCATCAGTCCTATCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATTGTAGATCTTATCTCCC
261 AAGCCACCAGTCCTATCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATTGTAGATCTTATCTCCC
* * * *
542448 TAAGCAGTAGTGGAGCAAATTGAAGACGGTAAATCTTATCTTCCCGACGTAGTGGGAATCAGATT
326 TAAGCAGTAGTGGAGCAAATCGAAGACGGCAAATCTTATCTTCCCGACGTAGTAGGAAGCAGATT
542513 TAAGCC
391 TAAGCC
* * * *
542519 ACCAGTTCTATCTCCTTGAGTAGCAGTAGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGC
1 ACCAGTCCTATCTCCTTGAGCAGCAGTGGAGTAGGTTCAAGATTGTAGATCTTATCTCCCTAAGC
* *
542584 AGTAGTGGAGCAGATCGAAGACGACGAATCTTATCTTCTCGAGGTAGTAGGAAGCAG
66 AGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCGAGGTAGTAGGAAGCAG
542641 ACAAAAGAAA
Statistics
Matches: 472, Mismatches: 43, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
393 104 0.22
394 1 0.00
396 367 0.78
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (396 bp):
ACCAGTCCTATCTCCTTGAGCAGCAGTGGAGTAGGTTCAAGATTGTAGATCTTATCTCCCTAAGC
AGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCGAGGTAGTAGGAAGCAGCAGATTTA
AGCCACCAGTCCTATCTCTCTGAGCAACAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCT
AAGAAGTAATGGAGCAGATCGAAGACGGCGAATCTTATCTTCCAAAGGTAGTAGGAAGCAGATTT
AAGCCACCAGTCCTATCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATTGTAGATCTTATCTCCC
TAAGCAGTAGTGGAGCAAATCGAAGACGGCAAATCTTATCTTCCCGACGTAGTAGGAAGCAGATT
TAAGCC
Found at i:542721 original size:44 final size:43
Alignment explanation
Indices: 542666--542899 Score: 194
Period size: 44 Copynumber: 5.5 Consensus size: 43
542656 CCTATCTCCC
*
542666 TGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCT
1 TGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCTCT
***
542709 TCGAAGTTGCAGTGGAGCAGA-TCGTATC-CAG-TCTTATCTCT
1 T-GAAGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCTCT
** * *
542750 ATGAAGTTGCAGTGGAGCAGACGAAAGA-AACAAATCTTATCTCCT
1 -TGAAGTTGCAGTGGAGCAGATTAAA-ATCACAGATCTTATCT-CT
** *
542795 TGAAGTTGCAGTGGAGTGGATTAAAACCACAGATCTTATCTCT
1 TGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCTCT
* * * *** *
542838 CTGAAGTTACAGTAGAACAGA-TCGCATC-CAG-TCTTATCTCCC
1 -TGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCT-CT
*
542880 TAAAGTTGCAGTGGAGCAGA
1 TGAAGTTGCAGTGGAGCAGA
542900 CAAAAGAAAC
Statistics
Matches: 151, Mismatches: 30, Indels: 22
0.74 0.15 0.11
Matches are distributed among these distances:
41 53 0.35
42 8 0.05
43 14 0.09
44 74 0.49
45 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.27
Consensus pattern (43 bp):
TGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCTCT
Found at i:542791 original size:129 final size:129
Alignment explanation
Indices: 542636--542909 Score: 415
Period size: 129 Copynumber: 2.1 Consensus size: 129
542626 GGTAGTAGGA
* *
542636 AGCAGACAAAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATC
1 AGCAGACAAAAGAAACAAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATC
* * * * * *
542701 TTATCTCT-TCGAAGTTGCAGTGGAGCAGATCGTATCCAGTCTTATCTCTATGAAGTTGCAGTGG
66 TTATCTCTCT-GAAGTTACAGTAGAACAGATCGCATCCAGTCTTATCTCCATAAAGTTGCAGTGG
* * * *
542765 AGCAGACGAAAGAAACAAATCTTATCTCCTTGAAGTTGCAGTGGAGTGGATTAAAACCACAGATC
1 AGCAGACAAAAGAAACAAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATC
*
542830 TTATCTCTCTGAAGTTACAGTAGAACAGATCGCATCCAGTCTTATCTCCCTAAAGTTGCAGTGG
66 TTATCTCTCTGAAGTTACAGTAGAACAGATCGCATCCAGTCTTATCTCCATAAAGTTGCAGTGG
542894 AGCAGACAAAAGAAAC
1 AGCAGACAAAAGAAAC
542910 CAATTTCGTC
Statistics
Matches: 130, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
129 129 0.99
130 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (129 bp):
AGCAGACAAAAGAAACAAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATC
TTATCTCTCTGAAGTTACAGTAGAACAGATCGCATCCAGTCTTATCTCCATAAAGTTGCAGTGG
Found at i:542941 original size:129 final size:129
Alignment explanation
Indices: 542636--542981 Score: 376
Period size: 129 Copynumber: 2.7 Consensus size: 129
542626 GGTAGTAGGA
* * * * ** * *
542636 AGCAGACAAAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATC
1 AGCAGACAAAAGAAACAAATCTTATCACCTTGAAGTTGCAGCAGAGTGGATTAAAACCACAGATC
* * * * *
542701 TTATCTCT-TCGAAGTTGCAGTGGAGCAGATCGTATCCAGTCTTATCTCTATGAAGTTGCAGTGG
66 TTATCTCTCT-GAAGTTGCAGTAGAACAGATCGCATCCAGTCTTATCTCCATAAAGTTGCAGTGG
* * **
542765 AGCAGACGAAAGAAACAAATCTTATCTCCTTGAAGTTGCAGTGGAGTGGATTAAAACCACAGATC
1 AGCAGACAAAAGAAACAAATCTTATCACCTTGAAGTTGCAGCAGAGTGGATTAAAACCACAGATC
* *
542830 TTATCTCTCTGAAGTTACAGTAGAACAGATCGCATCCAGTCTTATCTCCCTAAAGTTGCAGTGG
66 TTATCTCTCTGAAGTTGCAGTAGAACAGATCGCATCCAGTCTTATCTCCATAAAGTTGCAGTGG
* * * * * * * * *
542894 AGCAGACAAAAGAAACCAAT-TTCGTCACTTTGAATTTGTAGCAGAGTGGGTTGAAGCTACATG-
1 AGCAGACAAAAGAAACAAATCTT-ATCACCTTGAAGTTGCAGCAGAGTGGATTAAAACCACA-GA
*
542957 TCGTATCTCTCTGAAG-TGCAGTAGA
64 TCTTATCTCTCTGAAGTTGCAGTAGA
542982 GTGGATCGAA
Statistics
Matches: 186, Mismatches: 28, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
128 10 0.05
129 174 0.94
130 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (129 bp):
AGCAGACAAAAGAAACAAATCTTATCACCTTGAAGTTGCAGCAGAGTGGATTAAAACCACAGATC
TTATCTCTCTGAAGTTGCAGTAGAACAGATCGCATCCAGTCTTATCTCCATAAAGTTGCAGTGG
Found at i:547254 original size:24 final size:24
Alignment explanation
Indices: 547207--547255 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
547197 GAGCTATATT
*
547207 TCGCATTCCCATGCTCTTCACGTG
1 TCGCATTCCCATGCTCTCCACGTG
*
547231 TCGCATTCCCATGCTCTCCGCGTG
1 TCGCATTCCCATGCTCTCCACGTG
547255 T
1 T
547256 TTCTCAAAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.10, C:0.39, G:0.18, T:0.33
Consensus pattern (24 bp):
TCGCATTCCCATGCTCTCCACGTG
Found at i:549071 original size:36 final size:36
Alignment explanation
Indices: 549024--549097 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
549014 TAATGCAAGC
549024 AAAGTAATGTCAACATATTGTTTATCTCAAAAAACT
1 AAAGTAATGTCAACATATTGTTTATCTCAAAAAACT
549060 AAAGTAATGTCAACATATTGTTTATCTCAAAAAACT
1 AAAGTAATGTCAACATATTGTTTATCTCAAAAAACT
549096 AA
1 AA
549098 CTTGAACCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (36 bp):
AAAGTAATGTCAACATATTGTTTATCTCAAAAAACT
Found at i:550872 original size:31 final size:31
Alignment explanation
Indices: 550837--550896 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
550827 GTGTGCAATC
550837 ATATACACAAATTTTAATTTT-ATACAATTAT
1 ATATACA-AAATTTTAATTTTGATACAATTAT
* *
550868 ATATATAAAATTTTAATTTTGATTCAATT
1 ATATACAAAATTTTAATTTTGATACAATT
550897 TTCCCCGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (31 bp):
ATATACAAAATTTTAATTTTGATACAATTAT
Found at i:557258 original size:13 final size:13
Alignment explanation
Indices: 557237--557269 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
557227 AAAAATGATG
557237 AAATGAAAATGAA
1 AAATGAAAATGAA
*
557250 AAGTGAAAATGAA
1 AAATGAAAATGAA
557263 AAATGAA
1 AAATGAA
557270 GAACGGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.15
Consensus pattern (13 bp):
AAATGAAAATGAA
Found at i:558719 original size:44 final size:44
Alignment explanation
Indices: 558574--559782 Score: 1544
Period size: 44 Copynumber: 27.4 Consensus size: 44
558564 GTTGAAAAGT
* * * * *
558574 AGCAAATCTTGTCTTTATGTATTGACATGAAGTAGATCAAAGAA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
* *
558618 AGCAGATCTTGTCTTCCCATACTAGTGGC--GAAGTAGATCAGAA-AA
1 AGCAGATCTTGTCTT--CAT-GTATTGGCGTGAAGTAGATC-GAAGAA
* * *
558663 AGTAGATATTGTCTTCATGTATTGGCATGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
*
558707 AACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCG-AGTACA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAG-A-A
558752 A-CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCG-AGTACA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAG-A-A
*** * * * * **
558796 A-CAGATCTTGTCTTCCCATACTGGTGGCGAAGTATATATAAGAA
1 AGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGAA
*
558840 AGCAGATCTTGTCTTCATGTATTGGTGTGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
*
558884 AGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
* *
558928 AACAGATCTTGTCTTCATGTGTTGGCGTGAAGTAGATCG-AGTACA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAG-A-A
*
558973 A-CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATC-AGAGAT
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGA-AGAA
* *** * * * *
559016 AGTAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAA
1 AGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGAA
*
559061 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATC-AGAGAT
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGA-AGAA
* *** * * * *
559105 AGTAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGAATGGAA-AA
1 AGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAG-ATCGAAGAA
*
559150 AGCAGATATTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
* *
559194 AGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCCAAGAA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
559238 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
*
559282 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
* *
559326 AGAAGATCTTATCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
* * *
559370 AGCAGATCTTGTCTTCATGTATTGGCCTGAAGTAGATCAAAGAT
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
*** * *
559414 AGCAGATCTTGTCTTCCCATACTGGCGGCGAAGTAGATCGGAA-AA
1 AGCAGATCTTGTCTTCATGTATTGGC-GTGAAGTAGATC-GAAGAA
*
559459 AGCAGATATTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
559503 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
*
559547 AGCAGATCTTGTCTTTATGTATTGGCGTGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
* * *
559591 GGCAGATCTTATCTTCATGTATTGGCGAGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
* *
559635 AGCAGATCTTGTCTTTATGTATTGGCGTGAAGAAGATCGAAGAA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
* *
559679 AACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGAA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
* * *
559723 AGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGAG
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
*
559767 AGCATATCTTGTCTTC
1 AGCAGATCTTGTCTTC
559783 CCATCCTGGT
Statistics
Matches: 1018, Mismatches: 120, Indels: 54
0.85 0.10 0.05
Matches are distributed among these distances:
42 6 0.01
43 20 0.02
44 820 0.81
45 154 0.15
46 12 0.01
47 6 0.01
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (44 bp):
AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
Found at i:559810 original size:221 final size:219
Alignment explanation
Indices: 558574--559782 Score: 1528
Period size: 221 Copynumber: 5.5 Consensus size: 219
558564 GTTGAAAAGT
* * * *
558574 AGCAAATCTTGTCTTTATGTATTGACATGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCCCATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTT--CAT-
* * * *
558639 CTAGTGGC--GAAGTAGATCAGAA-AAAGTAGATATTGTCTTCATGTATTGGCATGAAGTAGATC
63 GTATTGGCGTGAAGTAGATCA-AAGAAAGCAGATCTTGTCTTCATGTATTGGC-TGAAGTAGATC
*
558701 GAAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCG-AGTACAA-CAGATCTTGTC
126 GAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAG-A-AAGCAGATCTTGTC
558764 TTCATGTATTGGCGTGAAGTAGATCG-AGTACA
189 TTCATGTATTGGCGTGAAGTAGATCGAAG-A-A
*** * * * *
558796 A-CAGATCTTGTCTTCCCATACTGGTGGCGAAGTATAT-ATAAGAAAGCAGATCTTGTCTTCATG
1 AGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCA-AAGAAAGCAGATCTTGTCTTCATG
* *
558859 TATTGGTGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGA
64 TATTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGGC-TGAAGTAGATCGA
* *
558924 AGAAAACAGATCTTGTCTTCATGTGTTGGCGTGAAGTAGATCG-AGTACAA-CAGATCTTGTCTT
128 AGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAG-A-AAGCAGATCTTGTCTT
*
558987 CATGTATTGGCGTGAAGTAGATC-AGAGAT
191 CATGTATTGGCGTGAAGTAGATCGA-AGAA
* *** * * *
559016 AGTAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGT
1 AGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGT
* * * * ** *
559081 ATTGGCGTGAAGTAGATCAGAGATAGTAGATCTTGTCTTCCCATACTGGTGGC-GAAGTAGAATG
65 ATTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTT--CAT-GTATTGGCTGAAGTAG-ATC
*
559145 GAA-AAAGCAGATATTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTT
126 GAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTT
* *
559209 CATGTATTGGCATGAAGTAGATCCAAGAA
191 CATGTATTGGCGTGAAGTAGATCGAAGAA
*
559238 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTA
* * * *
559303 TTGGCGTGAAGTAGATCGAAGATAGAAGATCTTATCTTCATGTATTGGCGTGAAGTAGATCGAAG
66 TTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGGC-TGAAGTAGATCGAAG
* * * ***
559368 AAAGCAGATCTTGTCTTCATGTATTGGCCTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCCA
130 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATG
* *
559433 TACTGGCGGCGAAGTAGATCGGAA-AA
195 TATTGGC-GTGAAGTAGATC-GAAGAA
* *
559459 AGCAGATATTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTA
* *
559524 TTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTTATGTATTGGCGTGAAGTAGATCGAAG
66 TTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGGC-TGAAGTAGATCGAAG
* * * *
559589 AAGGCAGATCTTATCTTCATGTATTGGCGAGAAGTAGATCGAAGAAAGCAGATCTTGTCTTTATG
130 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATG
*
559654 TATTGGCGTGAAGAAGATCGAAGAA
195 TATTGGCGTGAAGTAGATCGAAGAA
*
559679 AACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTA
* * *
559744 TTGGCATGAAGTAGATCAAAGAGAGCATATCTTGTCTTC
66 TTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTC
559783 CCATCCTGGT
Statistics
Matches: 877, Mismatches: 88, Indels: 46
0.87 0.09 0.05
Matches are distributed among these distances:
218 5 0.01
219 16 0.02
220 185 0.21
221 517 0.59
222 138 0.16
223 11 0.01
224 5 0.01
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (219 bp):
AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTA
TTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGGCTGAAGTAGATCGAAGA
AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGT
ATTGGCGTGAAGTAGATCGAAGAA
Found at i:566675 original size:2 final size:2
Alignment explanation
Indices: 566668--566692 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
566658 TCATCCTATA
566668 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
566693 ATTATATGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:570111 original size:16 final size:15
Alignment explanation
Indices: 570092--570141 Score: 66
Period size: 16 Copynumber: 3.3 Consensus size: 15
570082 CAAATATTGA
570092 AAAAAAATAAGAAATT
1 AAAAAAATAA-AAATT
570108 AAAAAAATAAAAA-T
1 AAAAAAATAAAAATT
*
570122 AAAAATAATAAAAATG
1 AAAAA-AATAAAAATT
570138 AAAA
1 AAAA
570142 TGACTTAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 6 0.19
15 11 0.35
16 14 0.45
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (15 bp):
AAAAAAATAAAAATT
Found at i:570122 original size:22 final size:21
Alignment explanation
Indices: 570094--570142 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
570084 AATATTGAAA
570094 AAAAATAAGAAATTAA-AAAAAT
1 AAAAATAA-AAA-TAATAAAAAT
570116 AAAAATAAAAATAATAAAAAT
1 AAAAATAAAAATAATAAAAAT
*
570137 GAAAAT
1 AAAAAT
570143 GACTTAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 3 0.12
21 14 0.56
22 8 0.32
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (21 bp):
AAAAATAAAAATAATAAAAAT
Found at i:570142 original size:15 final size:15
Alignment explanation
Indices: 570091--570141 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
570081 ACAAATATTG
570091 AAAAAAAATAAGAAAT
1 AAAAAAAATAA-AAAT
*
570107 TAAAAAAATAAAAAT
1 AAAAAAAATAAAAAT
*
570122 AAAAATAATAAAAAT
1 AAAAAAAATAAAAAT
570137 GAAAA
1 -AAAA
570142 TGACTTAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
15 17 0.55
16 14 0.45
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (15 bp):
AAAAAAAATAAAAAT
Found at i:573848 original size:56 final size:50
Alignment explanation
Indices: 573787--573960 Score: 152
Period size: 50 Copynumber: 3.4 Consensus size: 50
573777 GAGATGACAT
*
573787 GTAAGACCACGTCTGGGACATGTCATTAGCATTATTGAGGTTATGAGAGGTCCCAC
1 GTAAGACCACGTCTGGGACATGGCATTAGC---ATTGA-G--ATGAGAGGTCCCAC
* * * *
573843 GTAAGACCATGTCTGGGACATGGCGTTGGCATTGAGATGAGAGGTCCCCC
1 GTAAGACCACGTCTGGGACATGGCATTAGCATTGAGATGAGAGGTCCCAC
** * * ** *
573893 GTAAGACC-CTGTCTGGGACATGGCATGGGCATCGATATGAGAACTCCCAT
1 GTAAGACCAC-GTCTGGGACATGGCATTAGCATTGAGATGAGAGGTCCCAC
**
573943 GTAAGACCATATCTGGGA
1 GTAAGACCACGTCTGGGA
573961 AATAACATTG
Statistics
Matches: 100, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
50 68 0.68
52 1 0.01
53 5 0.05
56 26 0.26
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (50 bp):
GTAAGACCACGTCTGGGACATGGCATTAGCATTGAGATGAGAGGTCCCAC
Found at i:573889 original size:50 final size:50
Alignment explanation
Indices: 573829--573960 Score: 174
Period size: 50 Copynumber: 2.6 Consensus size: 50
573819 TATTGAGGTT
* * *
573829 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCGTTGGCATTGAG
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCATCGAG
* * *
573879 ATGAGAGGTCCCCCGTAAGACCCTGTCTGGGACATGGCATGGGCATCGAT
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCATCGAG
** * *
573929 ATGAGAACTCCCATGTAAGACCATATCTGGGA
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGA
573961 AATAACATTG
Statistics
Matches: 70, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 70 1.00
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.21
Consensus pattern (50 bp):
ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCATCGAG
Found at i:574821 original size:17 final size:19
Alignment explanation
Indices: 574799--574835 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
574789 AGGCAAAGGA
574799 ATTTT-ATATTA-TGAGAT
1 ATTTTAATATTAGTGAGAT
*
574816 ATTTTAATTTTAGTGAGAT
1 ATTTTAATATTAGTGAGAT
574835 A
1 A
574836 GGGTCAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 5 0.29
18 5 0.29
19 7 0.41
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (19 bp):
ATTTTAATATTAGTGAGAT
Found at i:588462 original size:15 final size:15
Alignment explanation
Indices: 588408--588465 Score: 52
Period size: 15 Copynumber: 3.9 Consensus size: 15
588398 TTACAATAAC
588408 ATAAAATAACCTAAG-
1 ATAAAA-AACCTAAGA
588423 -T-AAAAA-CTAAGA
1 ATAAAAAACCTAAGA
588435 ATGAAAGAAAACCTAAGA
1 AT--AA-AAAACCTAAGA
588453 ATAAAAAACCTAA
1 ATAAAAAACCTAA
588466 AATTGTGTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 14
0.72 0.00 0.28
Matches are distributed among these distances:
11 5 0.14
12 2 0.06
13 4 0.11
14 1 0.03
15 9 0.25
16 3 0.08
17 4 0.11
18 8 0.22
ACGTcount: A:0.64, C:0.12, G:0.09, T:0.16
Consensus pattern (15 bp):
ATAAAAAACCTAAGA
Found at i:588818 original size:15 final size:15
Alignment explanation
Indices: 588798--588829 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
588788 CATTTCACTA
*
588798 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
588813 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
588828 TT
1 TT
588830 TGCATGTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:595221 original size:56 final size:56
Alignment explanation
Indices: 595139--595252 Score: 201
Period size: 56 Copynumber: 2.0 Consensus size: 56
595129 GTTATTAATC
* *
595139 TATAAAGTAATTTCTTTCAATTCATTAGCCTCAATTTCATGTAATATTCAATTTAA
1 TATAAAGTAATTTATTTCAATTCATTAGCCTCAATTTCATGTAATATACAATTTAA
*
595195 TATAAAGTAATTTATTTCAATTCATTAGCCTCAATTTTATGTAATATACAATTTAA
1 TATAAAGTAATTTATTTCAATTCATTAGCCTCAATTTCATGTAATATACAATTTAA
595251 TA
1 TA
595253 ACTATATCCT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (56 bp):
TATAAAGTAATTTATTTCAATTCATTAGCCTCAATTTCATGTAATATACAATTTAA
Found at i:599576 original size:39 final size:39
Alignment explanation
Indices: 599515--599593 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
599505 CGCATACTCT
599515 TCAATCACATCTATCTCCATCTCTTTTAGTACTTTTAGC
1 TCAATCACATCTATCTCCATCTCTTTTAGTACTTTTAGC
* *
599554 TCAATCACATCTGTCTCTATCTCTTTTAGTACTTTTAGC
1 TCAATCACATCTATCTCCATCTCTTTTAGTACTTTTAGC
599593 T
1 T
599594 TAGTTCTTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.22, C:0.27, G:0.06, T:0.46
Consensus pattern (39 bp):
TCAATCACATCTATCTCCATCTCTTTTAGTACTTTTAGC
Found at i:604407 original size:99 final size:99
Alignment explanation
Indices: 604303--604506 Score: 286
Period size: 99 Copynumber: 2.1 Consensus size: 99
604293 ATTTTATGTA
* *
604303 CTTTTTAATAAAAGGA-AAATATAT-TTTTTTAATTTCTCGAAAAATTTTAAAGCTTTCCATATT
1 CTTTTTTATAAAAGCATAAATATATATTTTTTAA-TTCTCGAAAAATTTTAAAGCTTTCCATATT
604366 CTTTTGATTTGTTAGTTTTTTTGAAATTATCTTCT
65 CTTTTGATTTGTTAGTTTTTTTGAAATTATCTTCT
* **** ** * *
604401 CTTTTTTCTTTTTGCATATTTGTGTATTTTTTAATTCTCGAAAAATTTTAAAGCTTTCCATATTC
1 CTTTTTTATAAAAGCATAAATATATATTTTTTAATTCTCGAAAAATTTTAAAGCTTTCCATATTC
604466 TTTTGATTTGTTAGTTTTTTTGAAATTATCTTCT
66 TTTTGATTTGTTAGTTTTTTTGAAATTATCTTCT
604500 CTTTTTT
1 CTTTTTT
604507 CTTTTTGCAT
Statistics
Matches: 93, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
98 9 0.10
99 76 0.82
100 8 0.09
ACGTcount: A:0.25, C:0.10, G:0.08, T:0.56
Consensus pattern (99 bp):
CTTTTTTATAAAAGCATAAATATATATTTTTTAATTCTCGAAAAATTTTAAAGCTTTCCATATTC
TTTTGATTTGTTAGTTTTTTTGAAATTATCTTCT
Found at i:604507 original size:99 final size:100
Alignment explanation
Indices: 604327--604529 Score: 399
Period size: 99 Copynumber: 2.0 Consensus size: 100
604317 GAAAATATAT
604327 TTTTTTAATTTCTCGAAAAATTTTAAAGCTTTCCATATTCTTTTGATTTGTTAGTTTTTTTGAAA
1 TTTTTTAATTTCTCGAAAAATTTTAAAGCTTTCCATATTCTTTTGATTTGTTAGTTTTTTTGAAA
604392 TTATCTTCTCTTTTTTCTTTTTGCATATTTGTGTA
66 TTATCTTCTCTTTTTTCTTTTTGCATATTTGTGTA
604427 TTTTTTAA-TTCTCGAAAAATTTTAAAGCTTTCCATATTCTTTTGATTTGTTAGTTTTTTTGAAA
1 TTTTTTAATTTCTCGAAAAATTTTAAAGCTTTCCATATTCTTTTGATTTGTTAGTTTTTTTGAAA
604491 TTATCTTCTCTTTTTTCTTTTTGCATATTTGTGTA
66 TTATCTTCTCTTTTTTCTTTTTGCATATTTGTGTA
604526 TTTT
1 TTTT
604530 CACTTTTTTT
Statistics
Matches: 103, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
99 95 0.92
100 8 0.08
ACGTcount: A:0.21, C:0.11, G:0.09, T:0.60
Consensus pattern (100 bp):
TTTTTTAATTTCTCGAAAAATTTTAAAGCTTTCCATATTCTTTTGATTTGTTAGTTTTTTTGAAA
TTATCTTCTCTTTTTTCTTTTTGCATATTTGTGTA
Found at i:604521 original size:46 final size:46
Alignment explanation
Indices: 604372--604522 Score: 114
Period size: 46 Copynumber: 3.1 Consensus size: 46
604362 TATTCTTTTG
604372 ATTTGTTAGTTTTTTTGAAATTATCTTCTCTTTTTTCTTTTTGCAT
1 ATTTGTTAGTTTTTTTGAAATTATCTTCTCTTTTTTCTTTTTGCAT
* * ** *
604418 ATTTGTGTATTTTTTAATTCTCGAAAAATTTTAAAGCTT-TCCATATTC-TTTTG---
1 ATTTGT-TA-GTTTT--TT-T-G--AAA--TT--ATCTTCTCTTTTTTCTTTTTGCAT
604471 ATTTGTTAGTTTTTTTGAAATTATCTTCTCTTTTTTCTTTTTGCAT
1 ATTTGTTAGTTTTTTTGAAATTATCTTCTCTTTTTTCTTTTTGCAT
604517 ATTTGT
1 ATTTGT
604523 GTATTTTCAC
Statistics
Matches: 78, Mismatches: 10, Indels: 34
0.64 0.08 0.28
Matches are distributed among these distances:
41 4 0.05
42 6 0.08
43 7 0.09
45 3 0.04
46 12 0.15
47 3 0.04
48 5 0.06
49 2 0.03
50 2 0.03
51 5 0.06
52 3 0.04
53 6 0.08
54 3 0.04
56 7 0.09
57 6 0.08
58 4 0.05
ACGTcount: A:0.19, C:0.11, G:0.09, T:0.61
Consensus pattern (46 bp):
ATTTGTTAGTTTTTTTGAAATTATCTTCTCTTTTTTCTTTTTGCAT
Found at i:605392 original size:22 final size:21
Alignment explanation
Indices: 605358--605398 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
605348 ATATTGTTGA
**
605358 GGTTGTTGCTATTATCATTTGT
1 GGTTGTTAATATTAT-ATTTGT
605380 GGTTGTTAATATTATATTT
1 GGTTGTTAATATTATATTT
605399 ATTATTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.20, C:0.05, G:0.20, T:0.56
Consensus pattern (21 bp):
GGTTGTTAATATTATATTTGT
Found at i:610037 original size:26 final size:26
Alignment explanation
Indices: 610003--610065 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
609993 TTTACTCCAG
* *
610003 TAAATTTTTGACGATTTTATCCCCGA
1 TAAAATTTTGACGATTTTACCCCCGA
* *
610029 TAAAATTTTAATGATTTTACCCCCGA
1 TAAAATTTTGACGATTTTACCCCCGA
610055 TAAAATTTTGA
1 TAAAATTTTGA
610066 GAAAATTCTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (26 bp):
TAAAATTTTGACGATTTTACCCCCGA
Found at i:610422 original size:26 final size:26
Alignment explanation
Indices: 610386--610445 Score: 120
Period size: 26 Copynumber: 2.3 Consensus size: 26
610376 TTCAACGAGC
610386 TAGTGGAGGGGTCGATTGAACATATG
1 TAGTGGAGGGGTCGATTGAACATATG
610412 TAGTGGAGGGGTCGATTGAACATATG
1 TAGTGGAGGGGTCGATTGAACATATG
610438 TAGTGGAG
1 TAGTGGAG
610446 ACTCAAATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.27, C:0.07, G:0.40, T:0.27
Consensus pattern (26 bp):
TAGTGGAGGGGTCGATTGAACATATG
Found at i:612203 original size:41 final size:41
Alignment explanation
Indices: 612166--612300 Score: 227
Period size: 41 Copynumber: 3.3 Consensus size: 41
612156 ATCGGCACTT
*
612166 AGCCTGCTAGACAG-AAAGTCTGATATGTTTCACCGGCATCA
1 AGCCTGCTAGAC-GTAAAGTCTGGTATGTTTCACCGGCATCA
*
612207 AGCCTGCTAGACGTAAAGTCTGGTATGTTTCACCGACATCA
1 AGCCTGCTAGACGTAAAGTCTGGTATGTTTCACCGGCATCA
*
612248 AGCCTGCTAGACGTAATGTCTGGTATGTTTCACCGGCATCA
1 AGCCTGCTAGACGTAAAGTCTGGTATGTTTCACCGGCATCA
612289 AGCCTGCTAGAC
1 AGCCTGCTAGAC
612301 ATAATGTTTG
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
40 1 0.01
41 88 0.99
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (41 bp):
AGCCTGCTAGACGTAAAGTCTGGTATGTTTCACCGGCATCA
Found at i:621848 original size:114 final size:114
Alignment explanation
Indices: 621648--621879 Score: 383
Period size: 114 Copynumber: 2.0 Consensus size: 114
621638 AAAGTAGATG
* * *
621648 AACCTTCTGTTTACAAATGTTTAGGGGATGAAAAGATGGTCTTTCTCGTTCTATATGTTGAAGAC
1 AACCTTCTGTTTACAAATGCTTAGGGGATGAAAAGATGGTCTTTCTCGTTCGATATGTCGAAGAC
* *
621713 ATTCTACTAATTGGGAATGATGTAGGGACCTTTTGATTAAATTGTGGTT
66 ATTCTACTAATTGGAAATGATGTAGGGACCTTTTGATTAAATTATGGTT
* * *
621762 AACCTTGTGTTTACAAATGCTTAGGGGATGGAAAGATGGTCTTTCTCGTTCGATATGTCGATGAC
1 AACCTTCTGTTTACAAATGCTTAGGGGATGAAAAGATGGTCTTTCTCGTTCGATATGTCGAAGAC
*
621827 ATTCTACTAATTGGAAATGATGTAGGGACCTTTTGATTACATTATGGTT
66 ATTCTACTAATTGGAAATGATGTAGGGACCTTTTGATTAAATTATGGTT
621876 AACC
1 AACC
621880 CAAGAGTTTA
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 109 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (114 bp):
AACCTTCTGTTTACAAATGCTTAGGGGATGAAAAGATGGTCTTTCTCGTTCGATATGTCGAAGAC
ATTCTACTAATTGGAAATGATGTAGGGACCTTTTGATTAAATTATGGTT
Found at i:624671 original size:106 final size:102
Alignment explanation
Indices: 624496--624698 Score: 282
Period size: 106 Copynumber: 2.0 Consensus size: 102
624486 TGCAGTAATT
* *
624496 CTTTATAGAACAATCTAGGAATATAAAATGAGAATAAAAAAAAAAAAACTTTTTATGTGTTTTTG
1 CTTTATAGAACAATCTAGGAATATAAAATGAGAATAAAAAAAAAAAAACTTTTGATGTGTTTTTC
* *
624561 TAGTGTGCCAGGTAAATGAAATTTGGCTCCTATAAAA
66 TAGTGTACCAGGCAAATGAAATTTGGCTCCTATAAAA
** *
624598 CTTTATAGAACAATCTAGGAATATAAAA-GATTGTGTGAGAATAGAAAAAAAACTTTTGATGTGT
1 CTTTATAGAACAATCTAGGAATATAAAATGA--GAAT-A-AA-AAAAAAAAAACTTTTGATGTGT
*
624662 TTTTCTAGTGTATCAGGCAAATGAAATTTGGCTCCTA
61 TTTTCTAGTGTACCAGGCAAATGAAATTTGGCTCCTA
624699 GTTATAAAAA
Statistics
Matches: 88, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
101 2 0.02
102 28 0.32
103 2 0.02
104 1 0.01
105 2 0.02
106 53 0.60
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.33
Consensus pattern (102 bp):
CTTTATAGAACAATCTAGGAATATAAAATGAGAATAAAAAAAAAAAAACTTTTGATGTGTTTTTC
TAGTGTACCAGGCAAATGAAATTTGGCTCCTATAAAA
Found at i:626273 original size:3 final size:3
Alignment explanation
Indices: 626265--626299 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
626255 AGGACCTTAC
626265 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
626300 GGCCCTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:633303 original size:66 final size:66
Alignment explanation
Indices: 633197--633328 Score: 237
Period size: 66 Copynumber: 2.0 Consensus size: 66
633187 AATTCAATTC
*
633197 GATCCTGATTGAACGACGCCGTTTAGGGAAGTAGGGAAAATTTCCCTTCCGGTCCCTCCATGTAA
1 GATCCTGATTGAACGACGCCGTTTAGGGAAGTAGGGAAAATTTCCCTTCCGGTCCCTCAATGTAA
633262 T
66 T
* *
633263 GATCCTGATTGAACGACGCTGTTTAGGGAAGTAGGGAAAATTTCCCTTCTGGTCCCTCAATGTAA
1 GATCCTGATTGAACGACGCCGTTTAGGGAAGTAGGGAAAATTTCCCTTCCGGTCCCTCAATGTAA
633328 T
66 T
633329 ACACGCGTTC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (66 bp):
GATCCTGATTGAACGACGCCGTTTAGGGAAGTAGGGAAAATTTCCCTTCCGGTCCCTCAATGTAA
T
Found at i:633618 original size:4 final size:4
Alignment explanation
Indices: 633611--633653 Score: 52
Period size: 4 Copynumber: 10.5 Consensus size: 4
633601 AAAAAACAAA
*
633611 TATT TATT TATT TATAT ATATG TATT TATT TATT TA-T TATT TA
1 TATT TATT TATT TAT-T -TATT TATT TATT TATT TATT TATT TA
633654 GTTTTTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
3 3 0.09
4 27 0.79
5 1 0.03
6 3 0.09
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (4 bp):
TATT
Found at i:639792 original size:18 final size:18
Alignment explanation
Indices: 639765--639804 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
639755 AGATTCAATC
639765 AAAAAAAAAAGAA-AACAG
1 AAAAAAAAAAGAAGAA-AG
*
639783 AAAAAGAAAAGAAGAAAG
1 AAAAAAAAAAGAAGAAAG
639801 AAAA
1 AAAA
639805 TGGAGAGGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAGAAGAAAG
Found at i:642650 original size:15 final size:14
Alignment explanation
Indices: 642632--642661 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
642622 TCTCTTGTTC
642632 TTCTTCTTTTCTTTT
1 TTCTTCTTTT-TTTT
642647 TTCTTCTTTTTTTT
1 TTCTTCTTTTTTTT
642661 T
1 T
642662 CTTTTTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTCTTCTTTTTTTT
Found at i:642666 original size:18 final size:19
Alignment explanation
Indices: 642620--642666 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
642610 AATTCTCTTA
642620 TTTC-TCTTGTTCTTCTTCT
1 TTTCTTCTT-TTCTTCTTCT
642639 TTTCTT-TTTTCTTCTT-T
1 TTTCTTCTTTTCTTCTTCT
*
642656 TTTTTTCTTTT
1 TTTCTTCTTTT
642667 TCAAACAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 6 0.24
18 12 0.48
19 6 0.24
20 1 0.04
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTCTTCTTTTCTTCTTCT
Found at i:647341 original size:25 final size:25
Alignment explanation
Indices: 647313--647364 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
647303 TTTTAAAACC
647313 TTAGCATATCTAGATACTTGTTTAA
1 TTAGCATATCTAGATACTTGTTTAA
*
647338 TTAGCATATCTAGGTACTTGTTTAA
1 TTAGCATATCTAGATACTTGTTTAA
647363 TT
1 TT
647365 GCGTCAATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.46
Consensus pattern (25 bp):
TTAGCATATCTAGATACTTGTTTAA
Found at i:651288 original size:44 final size:44
Alignment explanation
Indices: 651195--651316 Score: 140
Period size: 44 Copynumber: 2.8 Consensus size: 44
651185 AAAGATGGCA
* * * *
651195 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGAT
1 AATCCTATCTCCCTGAAGTTGCAGAGGAGCAGATCAAAGACGAT
* **
651239 AATCCTATCTCCCTGAAGTTGCAGAGGAGCGGATCAAA-ACTTT
1 AATCCTATCTCCCTGAAGTTGCAGAGGAGCAGATCAAAGACGAT
* *
651282 GGATCCTATCTCTCTGAAGTTGCAGA-GAGCAGATC
1 -AATCCTATCTCCCTGAAGTTGCAGAGGAGCAGATC
651317 GCATCTGGTC
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
43 10 0.15
44 57 0.85
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (44 bp):
AATCCTATCTCCCTGAAGTTGCAGAGGAGCAGATCAAAGACGAT
Found at i:651383 original size:44 final size:45
Alignment explanation
Indices: 651324--651603 Score: 143
Period size: 44 Copynumber: 6.4 Consensus size: 45
651314 ATCGCATCTG
* * *
651324 GTCTTGTCTCCCTGAAGTTGCAGTGGAGAAGACTGAGT-AAGAAA
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGAAGACTGAATGAACAAA
* * ** * *
651368 GTCTTATCCCCCTGAAATTATAGTGGGGCAGACTGAATGAACAAA
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGAAGACTGAATGAACAAA
* * ** * **
651413 -TCCTATCTCCCTGAAGTTGCAGAGGAGCGGA-TTAA--AACATTG
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGAAGACTGAATGAACA-AA
* * * * * **
651455 GATCTTATCTCTCTGAAGTTACAG-GGAGCAGATTGCAT---C-TG
1 G-TCTTATCTCCCTGAAGTTGCAGTGGAGAAGACTGAATGAACAAA
* * * * * *
651496 GTCTTCTCTCCCTAAAGTTGCAATGGAGCAGACTGAGT-AAGAAA
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGAAGACTGAATGAACAAA
* * * *
651540 GTCTTATCCCCCTGAAATTGCAGTGGGGCAGACTGAATGAACAAA
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGAAGACTGAATGAACAAA
* *
651585 -TCCTATCTCCCTAAAGTTG
1 GTCTTATCTCCCTGAAGTTG
651604 AGGAGGAGTG
Statistics
Matches: 176, Mismatches: 49, Indels: 22
0.71 0.20 0.09
Matches are distributed among these distances:
40 17 0.10
41 18 0.10
43 11 0.06
44 120 0.68
45 10 0.06
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (45 bp):
GTCTTATCTCCCTGAAGTTGCAGTGGAGAAGACTGAATGAACAAA
Found at i:651486 original size:172 final size:172
Alignment explanation
Indices: 651239--651618 Score: 618
Period size: 172 Copynumber: 2.2 Consensus size: 172
651229 TAAAGCCGAT
* * *
651239 AATCCTATCTCCCTGAAGTTGCAGAGGAGCGGATCAAAACTTTGGATCCTATCTCTCTGAAGTTG
1 AATCCTATCTCCCTGAAGTTGCAGAGGAGCGGATTAAAACATTGGATCCTATCTCTCTGAAGTTA
* * *
651304 CAGAGAGCAGATCGCATCTGGTCTTGTCTCCCTGAAGTTGCAGTGGAGAAGACTGAGTAAGAAAG
66 CAGAGAGCAGATCGCATCTGGTCTTCTCTCCCTAAAGTTGCAATGGAGAAGACTGAGTAAGAAAG
*
651369 TCTTATCCCCCTGAAATTATAGTGGGGCAGACTGAATGAACA
131 TCTTATCCCCCTGAAATTACAGTGGGGCAGACTGAATGAACA
*
651411 AATCCTATCTCCCTGAAGTTGCAGAGGAGCGGATTAAAACATTGGATCTTATCTCTCTGAAGTTA
1 AATCCTATCTCCCTGAAGTTGCAGAGGAGCGGATTAAAACATTGGATCCTATCTCTCTGAAGTTA
* * *
651476 CAGGGAGCAGATTGCATCTGGTCTTCTCTCCCTAAAGTTGCAATGGAGCAGACTGAGTAAGAAAG
66 CAGAGAGCAGATCGCATCTGGTCTTCTCTCCCTAAAGTTGCAATGGAGAAGACTGAGTAAGAAAG
*
651541 TCTTATCCCCCTGAAATTGCAGTGGGGCAGACTGAATGAACA
131 TCTTATCCCCCTGAAATTACAGTGGGGCAGACTGAATGAACA
* *
651583 AATCCTATCTCCCTAAAGTTG-AGGAGGAGTGGATTA
1 AATCCTATCTCCCTGAAGTTGCA-GAGGAGCGGATTA
651619 GAATGATCGG
Statistics
Matches: 193, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
171 1 0.01
172 192 0.99
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (172 bp):
AATCCTATCTCCCTGAAGTTGCAGAGGAGCGGATTAAAACATTGGATCCTATCTCTCTGAAGTTA
CAGAGAGCAGATCGCATCTGGTCTTCTCTCCCTAAAGTTGCAATGGAGAAGACTGAGTAAGAAAG
TCTTATCCCCCTGAAATTACAGTGGGGCAGACTGAATGAACA
Found at i:652981 original size:22 final size:22
Alignment explanation
Indices: 652935--652981 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
652925 AATTGAGTAT
* *
652935 TTTTATTCTTTTAAATTTACCA
1 TTTTATTCTTTTAAAATTACAA
652957 TTTTATTCATTTTAAAATT-CAA
1 TTTTATTC-TTTTAAAATTACAA
652979 TTT
1 TTT
652982 GATCCTGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTATTCTTTTAAAATTACAA
Found at i:659938 original size:14 final size:14
Alignment explanation
Indices: 659919--659947 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
659909 TACAAAAAGA
659919 TTGTACAGGGAAGT
1 TTGTACAGGGAAGT
659933 TTGTACAGGGAAGT
1 TTGTACAGGGAAGT
659947 T
1 T
659948 CAAGCTCAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.34, T:0.31
Consensus pattern (14 bp):
TTGTACAGGGAAGT
Found at i:661108 original size:84 final size:84
Alignment explanation
Indices: 660995--661281 Score: 256
Period size: 84 Copynumber: 3.4 Consensus size: 84
660985 AAGCCGATAA
* *
660995 TCCTATCTCCCTGAAGTTGCAAAGGAGCAGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCA
1 TCCTATCTCCCTGAAGTTGCAGAGGAGCAGATTAAAACCTTGGATCTTATCTCTCTGAAATTGCA
661060 GAGAGCAGATCGCATCTGG
66 GAGAGCAGATCGCATCTGG
* * * * * **** * * * *
661079 TCTTATCTCCCTGAAGTTCCAGTGGAGCAGACTGAGTAA-GAAAG-TCTCATCCCCCTAAAATTG
1 TCCTATCTCCCTGAAGTTGCAGAGGAGCAGA-TTA-AAACCTTGGATCTTATCTCTCTGAAATTG
* * * ***
661142 CAGTGGGGCAGA-CTGAATGAACAAA
64 CAG-AGAGCAGATC-GCAT---CTGG
* * *
661167 TCCTATCTCCCTGAAGTTGCAGACGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAATTACA
1 TCCTATCTCCCTGAAGTTGCAGAGGAGCAGATTAAAACCTTGGATCTTATCTCTCTGAAATTGCA
*
661232 GAGAGCAGATTGCATCTGG
66 GAGAGCAGATCGCATCTGG
*
661251 TCCTATCTCCCTGAAGTTGCAGTGGAGCAGA
1 TCCTATCTCCCTGAAGTTGCAGAGGAGCAGA
661282 CTGAGTAAGA
Statistics
Matches: 146, Mismatches: 47, Indels: 20
0.69 0.22 0.09
Matches are distributed among these distances:
84 74 0.51
85 12 0.08
86 4 0.03
87 12 0.08
88 44 0.30
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (84 bp):
TCCTATCTCCCTGAAGTTGCAGAGGAGCAGATTAAAACCTTGGATCTTATCTCTCTGAAATTGCA
GAGAGCAGATCGCATCTGG
Done.