Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008314.1 Hibiscus syriacus cultivar Beakdansim tig00111008_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2414839
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 10
Found at i:1362124 original size:21 final size:21
Alignment explanation
Indices: 1362100--1362146 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
1362090 CCACGTAAGC
1362100 ACCATAGACCGCCACATTAGT
1 ACCATAGACCGCCACATTAGT
1362121 ACCATAGACCGCCACATTAGT
1 ACCATAGACCGCCACATTAGT
1362142 ACCAT
1 ACCAT
1362147 GAAGTGTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.34, C:0.34, G:0.13, T:0.19
Consensus pattern (21 bp):
ACCATAGACCGCCACATTAGT
Found at i:1380922 original size:2 final size:2
Alignment explanation
Indices: 1380915--1380939 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1380905 CCTATCCCTG
1380915 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1380940 GGCATAAATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1384909 original size:20 final size:20
Alignment explanation
Indices: 1384884--1384925 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1384874 TATGGACTCA
1384884 GGCTAAAAATGAACTCTAGG
1 GGCTAAAAATGAACTCTAGG
1384904 GGCTAAAAATGAACTCTAGG
1 GGCTAAAAATGAACTCTAGG
1384924 GG
1 GG
1384926 TTGTAAGTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.14, G:0.29, T:0.19
Consensus pattern (20 bp):
GGCTAAAAATGAACTCTAGG
Found at i:1394466 original size:24 final size:24
Alignment explanation
Indices: 1394414--1394483 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
1394404 ATGAGAACTG
*
1394414 AATAAACGAACTTATAAACGAGTT
1 AATAAACGAACTTATAAACGAGTC
* * * *
1394438 GATAAACGATCTTATAAATGTGTC
1 AATAAACGAACTTATAAACGAGTC
* * *
1394462 AATAAGCGAGCTAATAAACGAG
1 AATAAACGAACTTATAAACGAG
1394484 CTTGTTCGTG
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.46, C:0.13, G:0.17, T:0.24
Consensus pattern (24 bp):
AATAAACGAACTTATAAACGAGTC
Found at i:1396460 original size:7 final size:7
Alignment explanation
Indices: 1396448--1396488 Score: 73
Period size: 7 Copynumber: 5.9 Consensus size: 7
1396438 CCACCCTGCC
*
1396448 TCTCCAG
1 TCTCCAA
1396455 TCTCCAA
1 TCTCCAA
1396462 TCTCCAA
1 TCTCCAA
1396469 TCTCCAA
1 TCTCCAA
1396476 TCTCCAA
1 TCTCCAA
1396483 TCTCCA
1 TCTCCA
1396489 TTCCCACTGC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.24, C:0.44, G:0.02, T:0.29
Consensus pattern (7 bp):
TCTCCAA
Found at i:1401290 original size:16 final size:16
Alignment explanation
Indices: 1401269--1401304 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1401259 GTATTGTATA
*
1401269 GAACTGGATCAATGGT
1 GAACTGGATCAATGAT
1401285 GAACTGGATCAATGAT
1 GAACTGGATCAATGAT
1401301 GAAC
1 GAAC
1401305 AGGTAAGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.28, T:0.22
Consensus pattern (16 bp):
GAACTGGATCAATGAT
Found at i:1409719 original size:16 final size:15
Alignment explanation
Indices: 1409694--1409731 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
1409684 ATTATTTTTT
*
1409694 ATTATATTATATTATA
1 ATTATTTTATATT-TA
1409710 ATTATTTTATATTTA
1 ATTATTTTATATTTA
1409725 ATTATTT
1 ATTATTT
1409732 GAACAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTATTTTATATTTA
Found at i:1410953 original size:15 final size:15
Alignment explanation
Indices: 1410912--1410954 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
1410902 CAATCAGTAG
* *
1410912 TTTTGAAATATCTAT
1 TTTTTAAATATTTAT
*
1410927 TTTATAAA-ATTTAT
1 TTTTTAAATATTTAT
1410941 TTTTTAAATATTTA
1 TTTTTAAATATTTA
1410955 AAAAAGTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (15 bp):
TTTTTAAATATTTAT
Found at i:1411815 original size:17 final size:17
Alignment explanation
Indices: 1411795--1411835 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1411785 AATTTTATGT
*
1411795 TAGAATTAATAAATTTA
1 TAGAATTAACAAATTTA
*
1411812 TAGAATTAACAAGTTTA
1 TAGAATTAACAAATTTA
*
1411829 TAAAATT
1 TAGAATT
1411836 TTAGGTGAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.39
Consensus pattern (17 bp):
TAGAATTAACAAATTTA
Found at i:1416477 original size:13 final size:12
Alignment explanation
Indices: 1416459--1416489 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
1416449 TAACTAATTT
1416459 TATTTTTTTAAAA
1 TATTTTTTT-AAA
1416472 TATTTTTTTAAA
1 TATTTTTTTAAA
1416484 TATTTT
1 TATTTT
1416490 GAACTGATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATTTTTTTAAA
Found at i:1416652 original size:38 final size:38
Alignment explanation
Indices: 1416604--1416680 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
1416594 TTTTCTAAAA
* *
1416604 TTTTTACTGCAATCTAATAATAAAAATGTATAAATATT
1 TTTTTACTGCAATCTAATAATAAAAAAGAATAAATATT
* *
1416642 TTTTTCCTGCAATTTAATAATAAAAAAGAATAAATATT
1 TTTTTACTGCAATCTAATAATAAAAAAGAATAAATATT
1416680 T
1 T
1416681 ATTAATTGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (38 bp):
TTTTTACTGCAATCTAATAATAAAAAAGAATAAATATT
Found at i:1426349 original size:2 final size:2
Alignment explanation
Indices: 1426342--1426392 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1426332 TCTTCCTTCA
1426342 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1426384 AT AT AT AT A
1 AT AT AT AT A
1426393 ACTCTATTAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1433264 original size:25 final size:23
Alignment explanation
Indices: 1433211--1433264 Score: 54
Period size: 25 Copynumber: 2.3 Consensus size: 23
1433201 CCCAAAAAAT
* *
1433211 AAAAATTAAAAGATATTTTATTA
1 AAAAATTAAAAGATATTTGAATA
* *
1433234 ATAAATTAAGAGTATAATTTGAATA
1 AAAAATTAAAAG-AT-ATTTGAATA
1433259 AAAAAT
1 AAAAAT
1433265 CTGACAAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
23 10 0.42
24 2 0.08
25 12 0.50
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (23 bp):
AAAAATTAAAAGATATTTGAATA
Found at i:1433586 original size:41 final size:41
Alignment explanation
Indices: 1433496--1433575 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 41
1433486 CGTTTATACC
**
1433496 ACAAACGCCGTAATAGTGTTAATCAATAGTGGCGTTTTTTA
1 ACAAACGCCACAATAGTGTTAATCAATAGTGGCGTTTTTTA
* *
1433537 ACAAACGCCACAATAGTG-TGATCAATAGTGGCTTTTTTT
1 ACAAACGCCACAATAGTGTTAATCAATAGTGGCGTTTTTT
1433576 GTATAAACGC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
40 19 0.54
41 16 0.46
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (41 bp):
ACAAACGCCACAATAGTGTTAATCAATAGTGGCGTTTTTTA
Found at i:1434029 original size:41 final size:40
Alignment explanation
Indices: 1433984--1434093 Score: 114
Period size: 41 Copynumber: 2.6 Consensus size: 40
1433974 AAGTTGTACT
**
1433984 TTAGTGGCATTTGTTACATAAACGCCGCAATAGTGT-GTCCC
1 TTAGTGGCATTT-TTA-ATAAACGCCGCAATAGAATAGTCCC
* *
1434025 TTAGTGGCATTTTCGTAATAAACGCCGTAATAGAATAGTTCC
1 TTAGTGGCATTTT--TAATAAACGCCGCAATAGAATAGTCCC
*
1434067 TTTGTGGCATTTTTAATATAAACGCCG
1 TTAGTGGCATTTTT-A-ATAAACGCCG
1434094 TAATTGTCCT
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
40 2 0.03
41 29 0.49
42 28 0.47
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (40 bp):
TTAGTGGCATTTTTAATAAACGCCGCAATAGAATAGTCCC
Found at i:1434088 original size:42 final size:39
Alignment explanation
Indices: 1433982--1434097 Score: 115
Period size: 42 Copynumber: 2.8 Consensus size: 39
1433972 AAAAGTTGTA
* **
1433982 CTTTAGTGGCATTTGTTACATAAACGCCGCAATAGTGTGTCC
1 CTTT-GTGGCATTT-TTA-ATAAACGCCGTAATAGAATGTCC
* *
1434024 CTTAGTGGCATTTTCGTAATAAACGCCGTAATAGAATAGTTC
1 CTTTGTGGCATTTT--TAATAAACGCCGTAATAGAAT-GTCC
1434066 CTTTGTGGCATTTTTAATATAAACGCCGTAAT
1 CTTTGTGGCATTTTT-A-ATAAACGCCGTAAT
1434098 TGTCCTTTAA
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
40 2 0.03
41 26 0.41
42 35 0.56
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (39 bp):
CTTTGTGGCATTTTTAATAAACGCCGTAATAGAATGTCC
Found at i:1435217 original size:12 final size:12
Alignment explanation
Indices: 1435200--1435225 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1435190 TTTAGTTCAT
1435200 CATTTCATCACC
1 CATTTCATCACC
1435212 CATTTCATCACC
1 CATTTCATCACC
1435224 CA
1 CA
1435226 CTAAAACTCA
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:0.27, C:0.42, G:0.00, T:0.31
Consensus pattern (12 bp):
CATTTCATCACC
Found at i:1438336 original size:17 final size:17
Alignment explanation
Indices: 1438314--1438354 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
1438304 AACGGTCAAC
*
1438314 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
1438331 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
1438348 GGTCAAC
1 GGTCAAC
1438355 CCGGTTCAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.17
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:1438372 original size:19 final size:20
Alignment explanation
Indices: 1438348--1438418 Score: 92
Period size: 19 Copynumber: 3.6 Consensus size: 20
1438338 AGTCGGGTCG
* *
1438348 GGTCAACCCGGTTCAG-ATC
1 GGTCAAACCGGTTCAGAACC
1438367 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAGAACC
* *
1438386 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTCAGAACC
1438406 GGTCAAACCGGTT
1 GGTCAAACCGGTT
1438419 TTCCAGCAGC
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
18 1 0.02
19 29 0.63
20 16 0.35
ACGTcount: A:0.27, C:0.28, G:0.25, T:0.20
Consensus pattern (20 bp):
GGTCAAACCGGTTCAGAACC
Found at i:1438385 original size:10 final size:10
Alignment explanation
Indices: 1438350--1438418 Score: 63
Period size: 9 Copynumber: 7.1 Consensus size: 10
1438340 TCGGGTCGGG
*
1438350 TCAACCCGGT
1 TCAAACCGGT
* *
1438360 TCAGATCGG-
1 TCAAACCGGT
1438369 TCAAACCGGT
1 TCAAACCGGT
*
1438379 TCGAACCGG-
1 TCAAACCGGT
1438388 TCAAACCGGT
1 TCAAACCGGT
*
1438398 TCAAAACTGG-
1 TC-AAACCGGT
1438408 TCAAACCGGT
1 TCAAACCGGT
1438418 T
1 T
1438419 TTCCAGCAGC
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
9 21 0.46
10 19 0.41
11 6 0.13
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:1445602 original size:17 final size:17
Alignment explanation
Indices: 1445582--1445622 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
1445572 GAAAGTCAAC
*
1445582 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
1445599 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
1445616 GGTCAAC
1 GGTCAAC
1445623 CCGGTTCAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.17
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:1445640 original size:19 final size:20
Alignment explanation
Indices: 1445616--1445686 Score: 92
Period size: 19 Copynumber: 3.6 Consensus size: 20
1445606 AGTCGGGTCG
* *
1445616 GGTCAACCCGGTTCAG-ATC
1 GGTCAAACCGGTTCAGAACC
1445635 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAGAACC
* *
1445654 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTCAGAACC
1445674 GGTCAAACCGGTT
1 GGTCAAACCGGTT
1445687 TTCCAGCAGC
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
18 1 0.02
19 29 0.63
20 16 0.35
ACGTcount: A:0.27, C:0.28, G:0.25, T:0.20
Consensus pattern (20 bp):
GGTCAAACCGGTTCAGAACC
Found at i:1445653 original size:10 final size:10
Alignment explanation
Indices: 1445618--1445686 Score: 63
Period size: 9 Copynumber: 7.1 Consensus size: 10
1445608 TCGGGTCGGG
*
1445618 TCAACCCGGT
1 TCAAACCGGT
* *
1445628 TCAGATCGG-
1 TCAAACCGGT
1445637 TCAAACCGGT
1 TCAAACCGGT
*
1445647 TCGAACCGG-
1 TCAAACCGGT
1445656 TCAAACCGGT
1 TCAAACCGGT
*
1445666 TCAAAACTGG-
1 TC-AAACCGGT
1445676 TCAAACCGGT
1 TCAAACCGGT
1445686 T
1 T
1445687 TTCCAGCAGC
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
9 21 0.46
10 19 0.41
11 6 0.13
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:1452492 original size:21 final size:21
Alignment explanation
Indices: 1452474--1452559 Score: 102
Period size: 21 Copynumber: 4.1 Consensus size: 21
1452464 ATGAAGCAAG
*
1452474 GGAAACAGAGAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
**
1452495 GGAAGCAGCTAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
*
1452516 GGAAGCAGAGAGAGAAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* *
1452537 GGCAGCACAGAGAG-AGACAGC
1 GGAAGCAGAGAGAGCAG-CAGC
1452558 GG
1 GG
1452560 CAGAACAGAG
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 2 0.04
21 54 0.96
ACGTcount: A:0.38, C:0.20, G:0.41, T:0.01
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAGC
Found at i:1452560 original size:21 final size:22
Alignment explanation
Indices: 1452478--1452572 Score: 90
Period size: 21 Copynumber: 4.4 Consensus size: 22
1452468 AGCAAGGGAA
1452478 ACAGAGAGAGCAGCAGCGGAAGC
1 ACAGAGAGAG-AGCAGCGGAAGC
* *
1452501 AGC-TAGAG-CAGCAGCGGAAGC
1 A-CAGAGAGAGAGCAGCGGAAGC
* *
1452522 AGAGAGAGA-AGCAGCGGCAGC
1 ACAGAGAGAGAGCAGCGGAAGC
* *
1452543 ACAGAGAGAGA-CAGCGGCAGA
1 ACAGAGAGAGAGCAGCGGAAGC
1452564 ACAGAGAGA
1 ACAGAGAGA
1452573 AGTAATATAT
Statistics
Matches: 61, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
21 54 0.89
22 1 0.02
23 5 0.08
24 1 0.02
ACGTcount: A:0.40, C:0.20, G:0.39, T:0.01
Consensus pattern (22 bp):
ACAGAGAGAGAGCAGCGGAAGC
Found at i:1453082 original size:43 final size:44
Alignment explanation
Indices: 1453021--1453130 Score: 120
Period size: 43 Copynumber: 2.5 Consensus size: 44
1453011 AAGAAAACGC
* * *
1453021 ATCAACGA-CTATTGCGGCGTTTGT-CTG-TCAAATGCCGTTAAAT
1 ATCAAC-ACCTATTGCGGCGTTTGTAATGCT-AAACGCCGCTAAAT
1453064 ATCAACACCTATTGCGGCGTTT-TAATGCTAAACGCCGCTAAAT
1 ATCAACACCTATTGCGGCGTTTGTAATGCTAAACGCCGCTAAAT
* * *
1453107 ATCAATACCTTTTGCGACGTTTGT
1 ATCAACACCTATTGCGGCGTTTGT
1453131 TGAACAATCG
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
42 2 0.04
43 53 0.93
44 2 0.04
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (44 bp):
ATCAACACCTATTGCGGCGTTTGTAATGCTAAACGCCGCTAAAT
Found at i:1454577 original size:26 final size:26
Alignment explanation
Indices: 1454520--1454570 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
1454510 ATTGCAGCGT
* *
1454520 TATAAAGACTAAAACCATAATTAGAT
1 TATAAAGACTAAAACCATAATCAGAC
1454546 TATAAAGACTAAAACCATAATCAGA
1 TATAAAGACTAAAACCATAATCAGA
1454571 GCTTAAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.55, C:0.14, G:0.08, T:0.24
Consensus pattern (26 bp):
TATAAAGACTAAAACCATAATCAGAC
Found at i:1464521 original size:12 final size:12
Alignment explanation
Indices: 1464504--1464530 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1464494 AATGGAACTA
1464504 AAATATAATTTT
1 AAATATAATTTT
1464516 AAATATAATTTT
1 AAATATAATTTT
1464528 AAA
1 AAA
1464531 AAAAATGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AAATATAATTTT
Found at i:1465514 original size:15 final size:16
Alignment explanation
Indices: 1465484--1465518 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
1465474 GATTGTCTAA
1465484 TTTTAGTGGGTAAATTT
1 TTTTAGTGGG-AAATTT
1465501 TTTTAGTGGG-AATTT
1 TTTTAGTGGGAAATTT
1465516 TTT
1 TTT
1465519 GCATATACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.44
17 10 0.56
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (16 bp):
TTTTAGTGGGAAATTT
Found at i:1466308 original size:6 final size:6
Alignment explanation
Indices: 1466297--1466690 Score: 378
Period size: 6 Copynumber: 65.8 Consensus size: 6
1466287 TACAACGATG
* * *
1466297 ATAATA ATAATA ATAATA ACAATA ATAATA ATAATA ATAACA ATAGTA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
* * * *
1466345 ATAGTA ATCATA ATAATA ATAATA ATAATA ATAGTA ATAGTA ATAATA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
* * * * * * * *
1466393 ATAGTA ATAGTA ATAGTA ATAGTA ATAGTA ATAGTA ATAGTA ATAGTA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
* * * * * * * *
1466441 ATAGTA ATAGTA ATAGTA ATAGTA ATAGTA ATAGTA ATAGTA ATAGTA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
* * * * * * *
1466489 ATAGTA ATAGTA ATAGTA ATAGTA ATAGTA ATAAT- ATAATA CTTATA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
* * * * * *
1466536 ATAGTA ATAATA ATAACA ACAAAA ATAATA ATAGTA ATCATA ATAATA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
* * *
1466584 ATAATA ATAATA ATAATA ATAGTA ATAGTA ATAGTA ATAATAA ATAATA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAAT-A ATAATA
* * *
1466633 ATAATA ATAATA ATAATA ATAAT- ATAATA ATAATA ACAACA CTAATA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
*
1466680 ATGATA ATAAT
1 ATAATA ATAAT
1466691 GATGATGATG
Statistics
Matches: 348, Mismatches: 37, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
5 10 0.03
6 332 0.95
7 6 0.02
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.32
Consensus pattern (6 bp):
ATAATA
Found at i:1466693 original size:9 final size:9
Alignment explanation
Indices: 1466297--1466690 Score: 378
Period size: 9 Copynumber: 43.9 Consensus size: 9
1466287 TACAACGATG
1466297 ATAATAATA
1 ATAATAATA
1466306 ATAATAATA
1 ATAATAATA
*
1466315 ACAATAATA
1 ATAATAATA
1466324 ATAATAATA
1 ATAATAATA
*
1466333 ATAACAATA
1 ATAATAATA
* *
1466342 GTAATAGTA
1 ATAATAATA
*
1466351 ATCATAATA
1 ATAATAATA
1466360 ATAATAATA
1 ATAATAATA
1466369 ATAATAATA
1 ATAATAATA
* *
1466378 GTAATAGTA
1 ATAATAATA
1466387 ATAATAATA
1 ATAATAATA
* *
1466396 GTAATAGTA
1 ATAATAATA
*
1466405 ATAGTAATA
1 ATAATAATA
* *
1466414 GTAATAGTA
1 ATAATAATA
*
1466423 ATAGTAATA
1 ATAATAATA
* *
1466432 GTAATAGTA
1 ATAATAATA
*
1466441 ATAGTAATA
1 ATAATAATA
* *
1466450 GTAATAGTA
1 ATAATAATA
*
1466459 ATAGTAATA
1 ATAATAATA
* *
1466468 GTAATAGTA
1 ATAATAATA
*
1466477 ATAGTAATA
1 ATAATAATA
* *
1466486 GTAATAGTA
1 ATAATAATA
*
1466495 ATAGTAATA
1 ATAATAATA
* *
1466504 GTAATAGTA
1 ATAATAATA
*
1466513 ATAGTAATA
1 ATAATAATA
1466522 AT-ATAATA
1 ATAATAATA
* *
1466530 CTTATAATA
1 ATAATAATA
*
1466539 GTAATAATA
1 ATAATAATA
* *
1466548 ATAACAACA
1 ATAATAATA
*
1466557 AAAATAATA
1 ATAATAATA
* *
1466566 ATAGTAATC
1 ATAATAATA
1466575 ATAATAATA
1 ATAATAATA
1466584 ATAATAATA
1 ATAATAATA
1466593 ATAATAATA
1 ATAATAATA
*
1466602 ATAGTAATA
1 ATAATAATA
* *
1466611 GTAATAGTA
1 ATAATAATA
1466620 ATAATAAATA
1 ATAAT-AATA
1466630 ATAATAATA
1 ATAATAATA
1466639 ATAATAATA
1 ATAATAATA
1466648 ATAATAAT-
1 ATAATAATA
1466656 ATAATAATA
1 ATAATAATA
* *
1466665 ATAACAACA
1 ATAATAATA
* *
1466674 CTAATAATG
1 ATAATAATA
1466683 ATAATAAT
1 ATAATAAT
1466691 GATGATGATG
Statistics
Matches: 299, Mismatches: 83, Indels: 6
0.77 0.21 0.02
Matches are distributed among these distances:
8 14 0.05
9 277 0.93
10 8 0.03
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.32
Consensus pattern (9 bp):
ATAATAATA
Found at i:1472614 original size:13 final size:13
Alignment explanation
Indices: 1472581--1472606 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1472571 TCACTAATAC
1472581 AGAACTACCAGAT
1 AGAACTACCAGAT
1472594 AGAACTACCAGAT
1 AGAACTACCAGAT
1472607 GATGCTACAT
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:0.46, C:0.23, G:0.15, T:0.15
Consensus pattern (13 bp):
AGAACTACCAGAT
Found at i:1479486 original size:60 final size:61
Alignment explanation
Indices: 1479399--1479522 Score: 144
Period size: 60 Copynumber: 2.0 Consensus size: 61
1479389 ATTTCATAAC
* * ** **
1479399 TTTTAATAGTCAGGGGATTCAACAAAGCTATGCCCTATAGTCGAATTACTATTT-TGTAAT
1 TTTTAATAGTCAAGGGATTCAACAAAGCAACACCCTATAGTCGAAGGACTATTTGTGTAAT
* * *
1479459 TTTTAATAGTCAAGGGACTT-AATAAAGCAACACCTTATAGTCGAGGGACTATTTGTGTAAT
1 TTTTAATAGTCAAGGGA-TTCAACAAAGCAACACCCTATAGTCGAAGGACTATTTGTGTAAT
1479520 TTT
1 TTT
1479523 CCCTAAACAT
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
60 42 0.79
61 11 0.21
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (61 bp):
TTTTAATAGTCAAGGGATTCAACAAAGCAACACCCTATAGTCGAAGGACTATTTGTGTAAT
Found at i:1482107 original size:23 final size:23
Alignment explanation
Indices: 1482072--1482115 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1482062 TGAAAAATAT
*
1482072 ATATTAATATATTTATAAATAAA
1 ATATTAATATATTTAGAAATAAA
* *
1482095 ATATTTATTTATTTAGAAATA
1 ATATTAATATATTTAGAAATA
1482116 TCAGAAAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
ATATTAATATATTTAGAAATAAA
Found at i:1482288 original size:119 final size:117
Alignment explanation
Indices: 1482078--1482298 Score: 286
Period size: 119 Copynumber: 1.9 Consensus size: 117
1482068 ATATATATTA
* * *
1482078 ATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAAGACTTCTAGGTGCCTTAA
1 ATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAAGACATCCAGGTGCCTTAA
* *
1482143 GACAGCTCTTTTCTTTGATATTAAAAATAAATAAATAATTAAAACAATTAAT
66 GACAGCTCCTTTCTTTAATATTAAAAATAAATAAATAATTAAAACAATTAAT
* * * **
1482195 ATATAATTTATAAAATAAGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAGTTGTTT
1 ATAT-ATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAA-AGACATCCAGGTGCCT
1482260 TAAGA-ATGC-CCTTTC-TTAATATTAAAAAATAAATAAATA
63 TAAGACA-GCTCCTTTCTTTAATATT-AAAAATAAATAAATA
1482299 TATATTAAAA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
117 4 0.04
118 13 0.15
119 55 0.62
120 17 0.19
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.38
Consensus pattern (117 bp):
ATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAAGACATCCAGGTGCCTTAA
GACAGCTCCTTTCTTTAATATTAAAAATAAATAAATAATTAAAACAATTAAT
Found at i:1482449 original size:3 final size:3
Alignment explanation
Indices: 1482393--1482435 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
1482383 TATTTATATA
* *
1482393 AAT AAT AAT AAG AAT AAT AAA AAGT AAT AAT AAT AA- AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT A
1482436 TTGCAAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.88
4 2 0.06
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:1482455 original size:12 final size:12
Alignment explanation
Indices: 1482392--1482457 Score: 50
Period size: 12 Copynumber: 5.5 Consensus size: 12
1482382 TTATTTATAT
1482392 AAATAATAA-TA
1 AAATAATAATTA
1482403 AGAATAATAA--A
1 A-AATAATAATTA
*
1482414 AAGTAATAATAATA
1 AAATAATAAT--TA
*
1482428 AAATAAT-ATTGC
1 AAATAATAATT-A
1482440 AAATAATAATTA
1 AAATAATAATTA
1482452 AAATAA
1 AAATAA
1482458 AAGGAATTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
10 7 0.16
11 4 0.09
12 21 0.48
13 5 0.11
14 7 0.16
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.27
Consensus pattern (12 bp):
AAATAATAATTA
Found at i:1483794 original size:3 final size:3
Alignment explanation
Indices: 1483788--1483849 Score: 78
Period size: 3 Copynumber: 22.0 Consensus size: 3
1483778 ATTATTTATT
*
1483788 TAA TAA TAA TAA T-A TAA T-A TAA TAA TAA TAA TAA TAA TAT TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1483833 CAA -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
1483850 ATAAAACAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
2 8 0.15
3 45 0.85
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1483816 original size:22 final size:23
Alignment explanation
Indices: 1483788--1483853 Score: 84
Period size: 22 Copynumber: 3.0 Consensus size: 23
1483778 ATTATTTATT
1483788 TAATAATAATAAT-ATAATATAA
1 TAATAATAATAATAATAATATAA
* *
1483810 TAATAATAATAATAATATTAAAA
1 TAATAATAATAATAATAATATAA
*
1483833 CAA-AATAATAATAATAA-ATAA
1 TAATAATAATAATAATAATATAA
1483854 AACAAATGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
21 3 0.08
22 26 0.68
23 9 0.24
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (23 bp):
TAATAATAATAATAATAATATAA
Found at i:1483822 original size:25 final size:24
Alignment explanation
Indices: 1483788--1483859 Score: 101
Period size: 25 Copynumber: 3.0 Consensus size: 24
1483778 ATTATTTATT
* *
1483788 TAATAATAATAATATAATATAATAA
1 TAATAATAATAATATAAAACAA-AA
1483813 TAATAATAATAATATTAAAACAAAA
1 TAATAATAATAATA-TAAAACAAAA
1483838 TAATAATAATAA-ATAAAACAAA
1 TAATAATAATAATATAAAACAAA
1483860 TGAAATAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.20
24 1 0.02
25 28 0.64
26 6 0.14
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (24 bp):
TAATAATAATAATATAAAACAAAA
Found at i:1484371 original size:113 final size:113
Alignment explanation
Indices: 1484231--1484973 Score: 1252
Period size: 113 Copynumber: 6.6 Consensus size: 113
1484221 GAATTCGAGC
* * *
1484231 AACAAGTTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGAGTTCTTCTTATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* * *
1484296 GCCCTGGCAATGTTGGTCCATCGAATGATAAATTCAAGCGAAAAGTTG
66 GACCTGGCAATGCTGATCCATCGAATGATAAATTCAAGCGAAAAGTTG
* * *
1484344 AACAAGTTCTTCTCATTAAGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATAAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* *
1484409 GCCCTGGCAATGCTGGTCCATCGAATGATAAATTCAAGCGAAAAGTTG
66 GACCTGGCAATGCTGATCCATCGAATGATAAATTCAAGCGAAAAGTTG
*
1484457 AACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
*
1484522 GACCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTG
66 GACCTGGCAATGCTGATCCATCGAATGATAAATTCAAGCGAAAAGTTG
* *
1484570 AACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTT
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* *
1484635 GACCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTG
66 GACCTGGCAATGCTGATCCATCGAATGATAAATTCAAGCGAAAAGTTG
* * *
1484683 AACAAGATCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTTTTAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
*
1484748 GACCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTG
66 GACCTGGCAATGCTGATCCATCGAATGATAAATTCAAGCGAAAAGTTG
1484796 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* * *
1484861 GACCTGGTAATGCTGATCTATCGAATGATAAATTCAAGCGAAAAGTTA
66 GACCTGGCAATGCTGATCCATCGAATGATAAATTCAAGCGAAAAGTTG
* *
1484909 AACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCACTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1484974 TTCTAGAAAT
Statistics
Matches: 601, Mismatches: 29, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
113 601 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (113 bp):
AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
GACCTGGCAATGCTGATCCATCGAATGATAAATTCAAGCGAAAAGTTG
Found at i:1484509 original size:226 final size:226
Alignment explanation
Indices: 1484119--1484973 Score: 1309
Period size: 226 Copynumber: 3.8 Consensus size: 226
1484109 AGAATCATGC
* *
1484119 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCC-TCTTCAGATGAATTCTTCTCAT
1 AAAAG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * * * *
1484183 TATGAACTC-TCTCTGGAAAAGTTGATCCATCGAGTGATGAATT----CG---AG--CAACAAGT
65 TATGAACTCGAC-CTGGCAATGCTGATCCATCGAATGATAAATTCAAGCGAAAAGTTGAACAAGT
* * * *
1484238 TCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGAGTTCTTCTTATTATGAACTCGCCCTGG
129 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGG
* * *
1484303 CAATGTTGGTCCATCGAATGATAAATTCAAGCG
194 CAATGCTGATCCATCGAATGATGAATTCAAGCG
* *
1484336 AAAAGTTGAACAAGTTCTTCTCATTAAGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
1484401 ATAAACTCGCCCTGGCAATGCTGGTCCATCGAATGATAAATTCAAGCGAAAAGTTGAACAAGTTC
66 ATGAACTCGACCTGGCAATGCTGATCCATCGAATGATAAATTCAAGCGAAAAGTTGAACAAGTTC
*
1484466 TTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCA
131 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCA
1484531 ATGCTGATCCATCGAATGATGAATTCAAGCG
196 ATGCTGATCCATCGAATGATGAATTCAAGCG
*
1484562 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * *
1484627 ATGAACTTGACCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAGATC
66 ATGAACTCGACCTGGCAATGCTGATCCATCGAATGATAAATTCAAGCGAAAAGTTGAACAAGTTC
* *
1484692 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTTTTAACTCGACCTGGCA
131 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCA
1484757 ATGCTGATCCATCGAATGATGAATTCAAGCG
196 ATGCTGATCCATCGAATGATGAATTCAAGCG
1484788 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
1484853 ATGAACTCGACCTGGTAATGCTGATCTATCGAATGATAAATTCAAGCGAAAAGTTAAACAAGTTC
66 ATGAACTCGACCTGGCAATGCTGATCCATCGAATGATAAATTCAAGCGAAAAGTTGAACAAGTTC
* *
1484918 TTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCACTATGAACTC
131 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1484974 TTCTAGAAAT
Statistics
Matches: 583, Mismatches: 44, Indels: 13
0.91 0.07 0.02
Matches are distributed among these distances:
216 34 0.06
217 58 0.10
218 1 0.00
221 2 0.00
224 2 0.00
226 486 0.83
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (226 bp):
AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTCGACCTGGCAATGCTGATCCATCGAATGATAAATTCAAGCGAAAAGTTGAACAAGTTC
TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCA
ATGCTGATCCATCGAATGATGAATTCAAGCG
Found at i:1484772 original size:339 final size:338
Alignment explanation
Indices: 1484119--1484973 Score: 1316
Period size: 339 Copynumber: 2.5 Consensus size: 338
1484109 AGAATCATGC
* * *
1484119 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTCTTCAGATGAATTCTTCTCATT
1 AAAAG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATT
* * * * *
1484184 ATGAACTC-TCTCTGGAAAAGTTGATCCATCGAGTGATGAATT----CG---AG--CAACAAGTT
65 ATGAACTCGAC-CTGGAAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTAAACAAGTT
* * *
1484239 CTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGAGTTCTTCTTATTATGAACTCGCCCTGGC
129 CTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGC
* * * *
1484304 AATGTTGGTCCATCGAATGATAAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTAAGAACTT
194 AATGCTGATCCATCGAATGATAAATTCAAGCAAAAAGTTGAACAAGATCTTCTCATTAAGAACTT
* * *
1484369 CTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATAAACTCGCCCTGGCAATGCTGGTCCATCGAA
259 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATAAACTCGACCTGGCAATGCTGATCCATCGAA
1484434 TGATAAATTCAAGCG
324 TGATAAATTCAAGCG
1484449 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-TTCTTCAGATGAGTTCTTCTCATT
* *
1484514 ATGAACTCGACCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTC
65 ATGAACTCGACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTAAACAAGTTC
*
1484579 TTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTGACCTGGCA
130 TTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCA
* *
1484644 ATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAGATCTTCTCATTATGAACTTC
195 ATGCTGATCCATCGAATGATAAATTCAAGCAAAAAGTTGAACAAGATCTTCTCATTAAGAACTTC
* *
1484709 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTTTTAACTCGACCTGGCAATGCTGATCCATCGAAT
260 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATAAACTCGACCTGGCAATGCTGATCCATCGAAT
*
1484774 GATGAATTCAAGCG
325 GATAAATTCAAGCG
1484788 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATT
* * *
1484853 ATGAACTCGACCTGGTAATGCTGATCTATCGAATGATAAATTCAAGCGAAAAGTTAAACAAGTTC
65 ATGAACTCGACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTAAACAAGTTC
* * *
1484918 TTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCACTATGAACTC
130 TTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1484974 TTCTAGAAAT
Statistics
Matches: 480, Mismatches: 33, Indels: 15
0.91 0.06 0.03
Matches are distributed among these distances:
329 34 0.07
330 62 0.13
331 1 0.00
334 2 0.00
337 2 0.00
339 378 0.79
340 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (338 bp):
AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTCGACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTAAACAAGTTCT
TCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCAA
TGCTGATCCATCGAATGATAAATTCAAGCAAAAAGTTGAACAAGATCTTCTCATTAAGAACTTCT
TCTTCCTTCTTCAGATGAGTTCTTCTCATTATAAACTCGACCTGGCAATGCTGATCCATCGAATG
ATAAATTCAAGCG
Found at i:1485434 original size:22 final size:22
Alignment explanation
Indices: 1485409--1485464 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
1485399 GATAAAGCTT
* *
1485409 TCATCTTTGAAAAGAGAATTTG
1 TCATCTTTGAAAAGAGAATCTA
* *
1485431 TCATCTTTTAAAAAGGGAATCTA
1 TCATC-TTTGAAAAGAGAATCTA
1485454 TCATCTTTGAA
1 TCATCTTTGAA
1485465 GAGTGTAGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1492020 original size:128 final size:128
Alignment explanation
Indices: 1491827--1492084 Score: 507
Period size: 128 Copynumber: 2.0 Consensus size: 128
1491817 ATATACTCCC
1491827 AAGTGAAAATTACAGAAGCTATTTTGATCATAGCAATGGGCATAAGGCTTTGGTGACACCTTCAC
1 AAGTGAAAATTACAGAAGCTATTTTGATCATAGCAATGGGCATAAGGCTTTGGTGACACCTTCAC
*
1491892 CAATCTTGGTGTAATGTATTGACCTTTAACCAAATGAGGGTACAAGTCTGAGATAGATTCTTG
66 CAATCTTGGTGTAATGTATGGACCTTTAACCAAATGAGGGTACAAGTCTGAGATAGATTCTTG
1491955 AAGTGAAAATTACAGAAGCTATTTTGATCATAGCAATGGGCATAAGGCTTTGGTGACACCTTCAC
1 AAGTGAAAATTACAGAAGCTATTTTGATCATAGCAATGGGCATAAGGCTTTGGTGACACCTTCAC
1492020 CAATCTTGGTGTAATGTATGGACCTTTAACCAAATGAGGGTACAAGTCTGAGATAGATTCTTG
66 CAATCTTGGTGTAATGTATGGACCTTTAACCAAATGAGGGTACAAGTCTGAGATAGATTCTTG
1492083 AA
1 AA
1492085 ACACCTTCAG
Statistics
Matches: 129, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
128 129 1.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.30
Consensus pattern (128 bp):
AAGTGAAAATTACAGAAGCTATTTTGATCATAGCAATGGGCATAAGGCTTTGGTGACACCTTCAC
CAATCTTGGTGTAATGTATGGACCTTTAACCAAATGAGGGTACAAGTCTGAGATAGATTCTTG
Found at i:1494060 original size:14 final size:15
Alignment explanation
Indices: 1494026--1494064 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1494016 CATAAAAATA
*
1494026 CAAATGCAAAGATGC
1 CAAATGTAAAGATGC
*
1494041 CAAATGTAAATATG-
1 CAAATGTAAAGATGC
1494055 CAAATGTAAA
1 CAAATGTAAA
1494065 AATGTAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.51, C:0.13, G:0.15, T:0.21
Consensus pattern (15 bp):
CAAATGTAAAGATGC
Found at i:1494073 original size:14 final size:14
Alignment explanation
Indices: 1494018--1494073 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
1494008 AAAGTAAACA
*
1494018 TAAAAATACAAATG
1 TAAAAATGCAAATG
* *
1494032 CAAAGATGCCAAATG
1 TAAAAATG-CAAATG
*
1494047 TAAATATGCAAATG
1 TAAAAATGCAAATG
*
1494061 TAAAAATGTAAAT
1 TAAAAATGCAAAT
1494074 TATTTAAAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.55, C:0.09, G:0.12, T:0.23
Consensus pattern (14 bp):
TAAAAATGCAAATG
Found at i:1496278 original size:23 final size:23
Alignment explanation
Indices: 1496243--1496286 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1496233 TGAAAAATAT
*
1496243 ATATTAATATATTTATAAATAAA
1 ATATTAATATATTTAGAAATAAA
* *
1496266 ATATTTATTTATTTAGAAATA
1 ATATTAATATATTTAGAAATA
1496287 TCAGAAAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
ATATTAATATATTTAGAAATAAA
Found at i:1496497 original size:122 final size:122
Alignment explanation
Indices: 1496248--1496517 Score: 293
Period size: 122 Copynumber: 2.2 Consensus size: 122
1496238 AATATATATT
* * * *
1496248 AATATATTTAT-AAATAAAATATTTATTTATTTAGAAATATCAGAAAAAGACTTCTAGGTGCCTT
1 AATA-ATTTATAAAATAAGATATTTATTTATTTAAAAATATCAGAAAAAGACATCCAGGTGCCTT
* * *
1496312 AAGACAGCTCTTTTCTTTGATATTAAAAAATAAATAAATAATTAAAACAATTAATATA
65 AAGACAGCTCCTTTCTTTAATATTAAAAAATAAATAAATAATTAAAACAATTAATAAA
* * * **
1496370 TATAATTTATAAAATAAGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAGTTGTTTT
1 AATAATTTATAAAATAAGATATTTATTTATTTAAAAATATCAGAAAA-AGACATCCAGGTGCCTT
* *
1496435 AAGA-ATGC-CCTTTC-TTAATATT-AAAAA-AAATAAATATATTAAAATATGATTATTAAA
65 AAGACA-GCTCCTTTCTTTAATATTAAAAAATAAATAAATA-ATTAAAACA--ATTAATAAA
1496492 AATAATTTATGAAATATAAGAT-TTTA
1 AATAATTTAT-AAA-ATAAGATATTTA
1496518 ACGAATAAAC
Statistics
Matches: 125, Mismatches: 15, Indels: 15
0.81 0.10 0.10
Matches are distributed among these distances:
119 9 0.07
120 13 0.10
121 13 0.10
122 59 0.47
123 24 0.19
124 7 0.06
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (122 bp):
AATAATTTATAAAATAAGATATTTATTTATTTAAAAATATCAGAAAAAGACATCCAGGTGCCTTA
AGACAGCTCCTTTCTTTAATATTAAAAAATAAATAAATAATTAAAACAATTAATAAA
Found at i:1496514 original size:29 final size:28
Alignment explanation
Indices: 1496460--1496518 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
1496450 TAATATTAAA
* *
1496460 AAAAATAAATATATTAAAATATGATTATT
1 AAAAATAAATATATGAAAATAAGATT-TT
*
1496489 AAAAAT-AATTTATGAAATATAAGATTTT
1 AAAAATAAATATATGAAA-ATAAGATTTT
1496517 AA
1 AA
1496519 CGAATAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (28 bp):
AAAAATAAATATATGAAAATAAGATTTT
Found at i:1496571 original size:13 final size:12
Alignment explanation
Indices: 1496558--1496622 Score: 58
Period size: 12 Copynumber: 5.2 Consensus size: 12
1496548 TTATTATATA
*
1496558 AATAATAAGAAT
1 AATAATAAAAAT
1496570 AATAATAAAAAGT
1 AATAATAAAAA-T
1496583 AATAATAATAAAAT
1 AATAAT-A-AAAAT
* **
1496597 AATATTGCAAAT
1 AATAATAAAAAT
*
1496609 AATAATTAAAAT
1 AATAATAAAAAT
1496621 AA
1 AA
1496623 AAGGAATTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
12 25 0.58
13 7 0.16
14 7 0.16
15 4 0.09
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.28
Consensus pattern (12 bp):
AATAATAAAAAT
Found at i:1496586 original size:16 final size:15
Alignment explanation
Indices: 1496558--1496595 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
1496548 TTATTATATA
*
1496558 AATAATAAGAATAAT
1 AATAAAAAGAATAAT
1496573 AATAAAAAGTAATAAT
1 AATAAAAAG-AATAAT
1496589 AATAAAA
1 AATAAAA
1496596 TAATATTGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (15 bp):
AATAAAAAGAATAAT
Found at i:1496614 original size:3 final size:3
Alignment explanation
Indices: 1496558--1496600 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
1496548 TTATTATATA
* *
1496558 AAT AAT AAG AAT AAT AAT AAA AAGT AAT AAT AAT AA- AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT A
1496601 TTGCAAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.88
4 2 0.06
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:1496661 original size:15 final size:14
Alignment explanation
Indices: 1496628--1496669 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
1496618 AATAAAAGGA
* *
1496628 ATTAAAAATATAGT
1 ATTAAAAATAAAAT
1496642 ATTAAAATATAAAAT
1 ATTAAAA-ATAAAAT
1496657 ATTAAAAA-AAAAT
1 ATTAAAAATAAAAT
1496670 CAAAAATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 5 0.20
14 8 0.32
15 12 0.48
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (14 bp):
ATTAAAAATAAAAT
Found at i:1497941 original size:3 final size:3
Alignment explanation
Indices: 1497933--1498015 Score: 68
Period size: 3 Copynumber: 29.0 Consensus size: 3
1497923 GGCCTGTTTG
* * *
1497933 TAA TAA TAA TAA TTA T-T TAT TTAA TAA TAA TAA T-A TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
* * *
1497976 TAA TTA TAA TAA TAA TAT TAA -AA CAA -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1498016 ATAAAACAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
2 9 0.13
3 56 0.84
4 2 0.03
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:1497990 original size:25 final size:24
Alignment explanation
Indices: 1497954--1498025 Score: 92
Period size: 25 Copynumber: 3.0 Consensus size: 24
1497944 ATTATTTATT
* *
1497954 TAATAATAATAATATAATATAATAA
1 TAATAATAATAATATAAAACAA-AA
*
1497979 TTATAATAATAATATTAAAACAAAA
1 TAATAATAATAATA-TAAAACAAAA
1498004 TAATAATAATAA-ATAAAACAAA
1 TAATAATAATAATATAAAACAAA
1498026 TGAAATAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
23 9 0.21
24 1 0.02
25 26 0.62
26 6 0.14
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (24 bp):
TAATAATAATAATATAAAACAAAA
Found at i:1498005 original size:28 final size:28
Alignment explanation
Indices: 1497954--1498015 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
1497944 ATTATTTATT
* * * *
1497954 TAATAATAATAATATAATATAATAATTA
1 TAATAATAATAATAAAACAAAATAATAA
*
1497982 TAATAATAATATTAAAACAAAATAATAA
1 TAATAATAATAATAAAACAAAATAATAA
1498010 TAATAA
1 TAATAA
1498016 ATAAAACAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (28 bp):
TAATAATAATAATAAAACAAAATAATAA
Found at i:1498006 original size:22 final size:23
Alignment explanation
Indices: 1497955--1498025 Score: 81
Period size: 23 Copynumber: 3.0 Consensus size: 23
1497945 TTATTTATTT
* *
1497955 AATAATAATAATATAATATAATAA
1 AATAATAATAATA-AATAAAACAA
* *
1497979 TTATAATAATAAT-ATTAAAACAA
1 -AATAATAATAATAAATAAAACAA
1498002 AATAATAATAATAAATAAAACAA
1 AATAATAATAATAAATAAAACAA
1498025 A
1 A
1498026 TGAAATAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
22 11 0.28
23 17 0.44
25 11 0.28
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (23 bp):
AATAATAATAATAAATAAAACAA
Found at i:1498026 original size:22 final size:22
Alignment explanation
Indices: 1497955--1498026 Score: 74
Period size: 22 Copynumber: 3.1 Consensus size: 22
1497945 TTATTTATTT
* *
1497955 AATAATAATAATATAATATAATA
1 AATAATAATAATA-AATAAAACA
*
1497978 ATTATAATAATAAT-ATTAAAACAA
1 A--ATAATAATAATAAATAAAAC-A
1498002 AATAATAATAATAAATAAAACA
1 AATAATAATAATAAATAAAACA
1498024 AAT
1 AAT
1498027 GAAATAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
22 15 0.37
23 13 0.32
24 2 0.05
25 11 0.27
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (22 bp):
AATAATAATAATAAATAAAACA
Found at i:1502650 original size:3 final size:3
Alignment explanation
Indices: 1502642--1502760 Score: 161
Period size: 3 Copynumber: 39.0 Consensus size: 3
1502632 TATAGGTATA
1502642 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
1502690 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAGT GAT GT-T CAT ATGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT -TAT TAT -TAT
1502737 TA- TAT TAT TAT TAT TAT TAAT TAT
1 TAT TAT TAT TAT TAT TAT T-AT TAT
1502761 ATGAGTTAAT
Statistics
Matches: 104, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.02
3 96 0.92
4 6 0.06
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1503622 original size:42 final size:42
Alignment explanation
Indices: 1503553--1503664 Score: 188
Period size: 42 Copynumber: 2.7 Consensus size: 42
1503543 AATTCTCGTG
* *
1503553 TTTGTTTCATGTAATTCGTTTTTCGGAAAATGTTTTCCCGTA
1 TTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCCCGTA
*
1503595 TTTGTTTCACGTAATTCATTTTCCGGAAAATGTTTTCCCGTA
1 TTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCCCGTA
*
1503637 TTTGTTTCACGTAATTGGTTTTCCGGAA
1 TTTGTTTCACGTAATTCGTTTTCCGGAA
1503665 TGTAATTCAT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.20, C:0.16, G:0.17, T:0.47
Consensus pattern (42 bp):
TTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCCCGTA
Found at i:1503876 original size:34 final size:31
Alignment explanation
Indices: 1503836--1503956 Score: 89
Period size: 31 Copynumber: 4.1 Consensus size: 31
1503826 CATTTTCATC
1503836 AAAATAT--TATT-TATTTATTAATATT-TAT
1 AAAATATAATATTATATTT-TTAATATTATAT
1503864 AATAATATAATATTATATTTTTAATATTATAT
1 AA-AATATAATATTATATTTTTAATATTATAT
* *
1503896 AAAATAATCA-ATTATA-TTATAATA--ATAT
1 AAAAT-ATAATATTATATTTTTAATATTATAT
* * * *
1503924 AAGATATTATATT-TTTATTTTAATAATATAT
1 AAAATATAATATTATAT-TTTTAATATTATAT
1503955 AA
1 AA
1503957 TAATTTTTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 19
0.75 0.06 0.19
Matches are distributed among these distances:
27 4 0.05
28 13 0.17
29 12 0.16
30 7 0.09
31 27 0.36
32 13 0.17
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (31 bp):
AAAATATAATATTATATTTTTAATATTATAT
Found at i:1503882 original size:22 final size:23
Alignment explanation
Indices: 1503851--1503894 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1503841 ATTATTTATT
1503851 TATTAATATTTATAATAATATAA
1 TATTAATATTTATAATAATATAA
* *
1503874 TATT-ATATTTTTAATATTATA
1 TATTAATATTTATAATAATATA
1503895 TAAAATAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTAATATTTATAATAATATAA
Found at i:1503947 original size:29 final size:28
Alignment explanation
Indices: 1503910--1504010 Score: 93
Period size: 29 Copynumber: 3.5 Consensus size: 28
1503900 TAATCAATTA
*
1503910 TATTATAATAATATA-AGAT-ATTATATTTT
1 TATTTTAATAATATATA-ATAATT-T-TTTT
1503939 TATTTTAATAATATATAATAATTTTTTT
1 TATTTTAATAATATATAATAATTTTTTT
*
1503967 TATATTTAATAATGA-ATAGT-ATTTTTTAT
1 TAT-TTTAATAAT-ATATAATAATTTTTT-T
1503996 ATATTTTAATAATAT
1 -TATTTTAATAATAT
1504011 TTTAATAAAG
Statistics
Matches: 63, Mismatches: 2, Indels: 14
0.80 0.03 0.18
Matches are distributed among these distances:
28 15 0.24
29 40 0.63
30 8 0.13
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (28 bp):
TATTTTAATAATATATAATAATTTTTTT
Found at i:1503954 original size:24 final size:23
Alignment explanation
Indices: 1503922--1503968 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
1503912 TTATAATAAT
* *
1503922 ATAAGATATTATATTTTTATTTTA
1 ATAAGATATAATAATTTT-TTTTA
*
1503946 ATAATATATAATAATTTTTTTTA
1 ATAAGATATAATAATTTTTTTTA
1503969 TATTTAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
ATAAGATATAATAATTTTTTTTA
Found at i:1504039 original size:23 final size:23
Alignment explanation
Indices: 1504013--1504057 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1504003 AATAATATTT
1504013 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
1504036 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
1504058 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:1508316 original size:149 final size:141
Alignment explanation
Indices: 1508034--1508848 Score: 776
Period size: 149 Copynumber: 5.8 Consensus size: 141
1508024 TGTGCCTAGA
* *
1508034 TCATCTTATTTCACTCGGCCTACTCCACACGTTA-AGGTGCTCGGCGTAAGATCAGGTCATCCTG
1 TCAT-TTATTTCACCCGGCCTACTCCACACGTTAGA-GCGCTCGGCGTAAGATCAGGTCATCCTG
* * *
1508098 CCTACTCCCATCTGGAAGCACTCGGCATGAACTCTGTCTACCCTGCCTACCCCACACGTTGAAGC
64 CCTACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCT-CCCTGCCTACCCTACACGTTGAAGC
*
1508163 GCTCGACGTGATAT
128 GCTCGGCGTGATAT
*
1508177 TAAAGCACATTTTATTTCACCCGGCCTACTCCACACGTTAGGGCGCTCGGCGTAAGATCAGGTCA
1 T------CA-TTTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCA
* *
1508242 TCTTGCCTACTCCCCTCTAGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTACCCTACACGTT
59 TCCTGCCTACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCT-CCCTGCCTACCCTACACGTT
*
1508307 G-AGATGCTCGGCGTGA-A-
123 GAAG-CGCTCGGCGTGATAT
** ** ** *
1508324 TC-TGGGA---CACCTTGCCTACTCCACACGTTAGAGCGCTCAACGTAAGATCAGGACATCCTGC
1 TCAT-TTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCTGC
* * * * *
1508385 CTACTCCCCTCTGGAAGCGCTCGACATGCACTCTATCTCCTCTGCCTACTCTAAACGTTGAAGCG
65 CTACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTCC-CTGCCTACCCTACACGTTGAAGCG
1508450 CTCGGCGTGATAT
129 CTCGGCGTGATAT
* *
1508463 TAAAGCACATATTATTTCACCTGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCA
1 T------CAT-TTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCA
* * * * *
1508528 TCCTGTCTACTCCCCTCTGGAAGCGCTTGGCAT-ATACTCTGACTCCCATGTCTACTCT-CAACG
59 TCCTGCCTACTCCCCTCTGGAAGCGCTCGGCATGA-ACTCTGTCTCCC-TGCCTACCCTAC-ACG
*
1508591 TTGAAGTGCTCGGCGTGATAT
121 TTGAAGCGCTCGGCGTGATAT
* * * * *
1508612 T-A--TA--GCACCCTGCCTACTCCACACGTTAGAGCGCCCGACGTAAGATCAGGTCATCCTGCT
1 TCATTTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCTGCC
* * * * * * * *
1508672 TACTCCCCACTGGAAGCGCTCGGTATGAACTCTGTCCCCCTTCCAACTCTTA-ACGGTGAAGTGC
66 TACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTCCCTGCCTAC-CCTACACGTTGAAGCGC
1508736 TCGGCGTGA-A-
130 TCGGCGTGATAT
* * * * *
1508746 --ATTGGA-AT-ACCCTGCCTACTCCACACGTTAGAGCGCCCGACGTAAGATCAGGTCATCC-GT
1 TCATT-TATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCTG-
* *
1508806 CCTACTCCCCACTGGAAGCGCTCGGCATGAACTCTGTCCCCCT
64 CCTACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTCCCT
1508849 TCCAACTCTT
Statistics
Matches: 571, Mismatches: 66, Indels: 77
0.80 0.09 0.11
Matches are distributed among these distances:
133 1 0.00
135 2 0.00
136 118 0.21
137 191 0.33
138 4 0.01
139 4 0.01
140 1 0.00
141 1 0.00
142 1 0.00
143 1 0.00
145 1 0.00
146 2 0.00
147 1 0.00
148 4 0.01
149 238 0.42
150 1 0.00
ACGTcount: A:0.21, C:0.33, G:0.20, T:0.25
Consensus pattern (141 bp):
TCATTTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCTGCC
TACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTCCCTGCCTACCCTACACGTTGAAGCGCT
CGGCGTGATAT
Found at i:1508453 original size:137 final size:137
Alignment explanation
Indices: 1508193--1508867 Score: 718
Period size: 137 Copynumber: 4.8 Consensus size: 137
1508183 ACATTTTATT
* * * *
1508193 TCACCCGGCCTACTCCACACGTTAGGGCGCTCGGCGTAAGATCAGGTCATCTTGCCTACTCCCCT
1 TCACCCTGCCTACTCCACACGTTAGAGCGCTCGACGTAAGATCAGGTCATCCTGCCTACTCCCCT
* * * *
1508258 CTAGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTACCCTACACGTTG-AGATGCTCGGCGTG
66 CTGGAAGCGCTCGGCATGAACTCTATCT-CCCTGCCTACTCTAAACGTTGAAG-TGCTCGGCGTG
*
1508322 A-ATCTGGGA
129 ATAT-TGGTA
* * *
1508331 -CACCTTGCCTACTCCACACGTTAGAGCGCTCAACGTAAGATCAGGACATCCTGCCTACTCCCCT
1 TCACCCTGCCTACTCCACACGTTAGAGCGCTCGACGTAAGATCAGGTCATCCTGCCTACTCCCCT
* * *
1508395 CTGGAAGCGCTCGACATGCACTCTATCTCCTCTGCCTACTCTAAACGTTGAAGCGCTCGGCGTGA
66 CTGGAAGCGCTCGGCATGAACTCTATCTCC-CTGCCTACTCTAAACGTTGAAGTGCTCGGCGTGA
*
1508460 TATTAAAGCACATA
130 TATT---G---GTA
* * * *
1508474 TTATTTCACCTGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGTCTACT
1 TCA---C-CCT-GCCTACTCCACACGTTAGAGCGCTCGACGTAAGATCAGGTCATCCTGCCTACT
* * *
1508539 CCCCTCTGGAAGCGCTTGGCAT-ATACTCTGA-CTCCCATGTCTACTCTCAACGTTGAAGTGCTC
61 CCCCTCTGGAAGCGCTCGGCATGA-ACTCT-ATCTCCC-TGCCTACTCTAAACGTTGAAGTGCTC
*
1508602 GGCGTGATATT-ATA
123 GGCGTGATATTGGTA
* * * *
1508616 GCACCCTGCCTACTCCACACGTTAGAGCGCCCGACGTAAGATCAGGTCATCCTGCTTACTCCCCA
1 TCACCCTGCCTACTCCACACGTTAGAGCGCTCGACGTAAGATCAGGTCATCCTGCCTACTCCCCT
* * * * * * * *
1508681 CTGGAAGCGCTCGGTATGAACTCTGTCCCCCTTCCAACTCTTAACGGTGAAGTGCTCGGCGTGAA
66 CTGGAAGCGCTCGGCATGAACTCTATCTCCCTGCCTACTCTAAACGTTGAAGTGCTCGGCGTGAT
*
1508746 ATTGGAA
131 ATTGGTA
*
1508753 T-ACCCTGCCTACTCCACACGTTAGAGCGCCCGACGTAAGATCAGGTCATCC-GTCCTACTCCCC
1 TCACCCTGCCTACTCCACACGTTAGAGCGCTCGACGTAAGATCAGGTCATCCTG-CCTACTCCCC
* * * * * * *
1508816 ACTGGAAGCGCTCGGCATGAACTCTGTCCCCCTTCCAACTCTTAACGCTGAA
65 TCTGGAAGCGCTCGGCATGAACTCTATCTCCCTGCCTACTCTAAACGTTGAA
1508868 ATGTTCGACG
Statistics
Matches: 462, Mismatches: 53, Indels: 46
0.82 0.09 0.08
Matches are distributed among these distances:
135 1 0.00
136 142 0.31
137 187 0.40
138 8 0.02
139 1 0.00
140 1 0.00
142 4 0.01
143 1 0.00
144 1 0.00
147 1 0.00
148 3 0.01
149 111 0.24
150 1 0.00
ACGTcount: A:0.21, C:0.34, G:0.21, T:0.24
Consensus pattern (137 bp):
TCACCCTGCCTACTCCACACGTTAGAGCGCTCGACGTAAGATCAGGTCATCCTGCCTACTCCCCT
CTGGAAGCGCTCGGCATGAACTCTATCTCCCTGCCTACTCTAAACGTTGAAGTGCTCGGCGTGAT
ATTGGTA
Found at i:1508594 original size:286 final size:285
Alignment explanation
Indices: 1508051--1508841 Score: 974
Period size: 286 Copynumber: 2.8 Consensus size: 285
1508041 ATTTCACTCG
* * *
1508051 GCCTACTCCACACGTTA-AGGTGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCATCTGGAA
1 GCCTACTCCACACGTTAGA-GCGCTCGACGTAAGATCAGGTCATCCTGCCTACTCCCCTCTGGAA
* * * * *
1508115 GCACTCGGCATGAACTCTGTCTACCCTGCCTACCCCACACGTTGAAGCGCTCGACGTGATATTAA
65 GCGCTCGGCATGAACTCTGTCT-CCCTGCCTACTCTAAACGTTGAAGCGCTCGGCGTGATATTAA
* * * *
1508180 AGCACATTTTATTTCACCCGGCCTACTCCACACGTTAGGGCGCTCGGCGTAAGATCAGGTCATCT
129 AGCACATATTATTTCACCTGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCC
* * *
1508245 TGCCTACTCCCCTCTAGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTACCCTACACGTTG-A
194 TGTCTACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGACTACCCTGCCTACCCTACACGTTGAA
* *
1508309 GATGCTCGGCGTGA-ATCT-GGGACACCTT
259 G-TGCTCGGCGTGATAT-TAGAG-CACCCT
* *
1508337 GCCTACTCCACACGTTAGAGCGCTCAACGTAAGATCAGGACATCCTGCCTACTCCCCTCTGGAAG
1 GCCTACTCCACACGTTAGAGCGCTCGACGTAAGATCAGGTCATCCTGCCTACTCCCCTCTGGAAG
* * *
1508402 CGCTCGACATGCACTCTATCTCCTCTGCCTACTCTAAACGTTGAAGCGCTCGGCGTGATATTAAA
66 CGCTCGGCATGAACTCTGTCTCC-CTGCCTACTCTAAACGTTGAAGCGCTCGGCGTGATATTAAA
*
1508467 GCACATATTATTTCACCTGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCT
130 GCACATATTATTTCACCTGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCT
* * *
1508532 GTCTACTCCCCTCTGGAAGCGCTTGGCAT-ATACTCTGACT-CCCATGTCTACTCT-CAACGTTG
195 GTCTACTCCCCTCTGGAAGCGCTCGGCATGA-ACTCTGACTACCC-TGCCTACCCTAC-ACGTTG
*
1508594 AAGTGCTCGGCGTGATATTATAGCACCCT
257 AAGTGCTCGGCGTGATATTAGAGCACCCT
* * *
1508623 GCCTACTCCACACGTTAGAGCGCCCGACGTAAGATCAGGTCATCCTGCTTACTCCCCACTGGAAG
1 GCCTACTCCACACGTTAGAGCGCTCGACGTAAGATCAGGTCATCCTGCCTACTCCCCTCTGGAAG
* * * * * * * *
1508688 CGCTCGGTATGAACTCTGTCCCCCTTCCAACTCTTAACGGTGAAGTGCTCGGCGTGAAATT---G
66 CGCTCGGCATGAACTCTGTCTCCCTGCCTACTCTAAACGTTGAAGCGCTCGGCGTGATATTAAAG
* * *
1508750 --GA-A-TA---C-CCT-GCCTACTCCACACGTTAGAGCGCCCGACGTAAGATCAGGTCATCC-G
131 CACATATTATTTCACCTGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCTG
*
1508805 TCCTACTCCCCACTGGAAGCGCTCGGCATGAACTCTG
196 T-CTACTCCCCTCTGGAAGCGCTCGGCATGAACTCTG
1508842 TCCCCCTTCC
Statistics
Matches: 446, Mismatches: 49, Indels: 33
0.84 0.09 0.06
Matches are distributed among these distances:
272 2 0.00
273 73 0.16
274 4 0.01
275 1 0.00
278 2 0.00
279 1 0.00
280 1 0.00
282 1 0.00
285 39 0.09
286 316 0.71
287 6 0.01
ACGTcount: A:0.22, C:0.33, G:0.21, T:0.24
Consensus pattern (285 bp):
GCCTACTCCACACGTTAGAGCGCTCGACGTAAGATCAGGTCATCCTGCCTACTCCCCTCTGGAAG
CGCTCGGCATGAACTCTGTCTCCCTGCCTACTCTAAACGTTGAAGCGCTCGGCGTGATATTAAAG
CACATATTATTTCACCTGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCTG
TCTACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGACTACCCTGCCTACCCTACACGTTGAAGT
GCTCGGCGTGATATTAGAGCACCCT
Found at i:1508782 original size:136 final size:136
Alignment explanation
Indices: 1508486--1508867 Score: 529
Period size: 136 Copynumber: 2.8 Consensus size: 136
1508476 ATTTCACCTG
* * * *
1508486 GCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTG-TCTACTCCCCTCTGGAA
1 GCCTACTCCACACGTTAGAGCGCCCGACGTAAGATCAGGTCATCCTGCT-TACTCCCCACTGGAA
* * * * * * *
1508550 GCGCTTGGCAT-ATACTCTGACTCCCATGT-CTACTCTCAACGTTGAAGTGCTCGGCGTGATATT
65 GCGCTCGGCATGA-ACTCTGTC-CCCCT-TCCAACTCTTAACGCTGAAGTGCTCGGCGTGAAATT
* *
1508613 ATAGCACCCT
127 AGAACACCCT
1508623 GCCTACTCCACACGTTAGAGCGCCCGACGTAAGATCAGGTCATCCTGCTTACTCCCCACTGGAAG
1 GCCTACTCCACACGTTAGAGCGCCCGACGTAAGATCAGGTCATCCTGCTTACTCCCCACTGGAAG
* * *
1508688 CGCTCGGTATGAACTCTGTCCCCCTTCCAACTCTTAACGGTGAAGTGCTCGGCGTGAAATTGGAA
66 CGCTCGGCATGAACTCTGTCCCCCTTCCAACTCTTAACGCTGAAGTGCTCGGCGTGAAATTAGAA
*
1508753 TACCCT
131 CACCCT
*
1508759 GCCTACTCCACACGTTAGAGCGCCCGACGTAAGATCAGGTCATCC-GTCCTACTCCCCACTGGAA
1 GCCTACTCCACACGTTAGAGCGCCCGACGTAAGATCAGGTCATCCTG-CTTACTCCCCACTGGAA
1508823 GCGCTCGGCATGAACTCTGTCCCCCTTCCAACTCTTAACGCTGAA
65 GCGCTCGGCATGAACTCTGTCCCCCTTCCAACTCTTAACGCTGAA
1508868 ATGTTCGACG
Statistics
Matches: 222, Mismatches: 19, Indels: 9
0.89 0.08 0.04
Matches are distributed among these distances:
135 2 0.01
136 144 0.65
137 74 0.33
138 2 0.01
ACGTcount: A:0.21, C:0.34, G:0.21, T:0.24
Consensus pattern (136 bp):
GCCTACTCCACACGTTAGAGCGCCCGACGTAAGATCAGGTCATCCTGCTTACTCCCCACTGGAAG
CGCTCGGCATGAACTCTGTCCCCCTTCCAACTCTTAACGCTGAAGTGCTCGGCGTGAAATTAGAA
CACCCT
Found at i:1517179 original size:59 final size:60
Alignment explanation
Indices: 1517001--1517166 Score: 248
Period size: 59 Copynumber: 2.8 Consensus size: 60
1516991 CCCTAAATTT
* * *
1517001 TAGGACATTGCTTTGTTGAGTC-CCTCGACTATTAAAAGTTATAAAATGATCCATTGAGTA
1 TAGGACATTACTTTGTTGAGTCTCC-CGACTATTAAAAGTTACAAAATGATCCATTGACTA
*
1517061 TAGGACATTACTTTGTTGAGTCT-CCTACTATTAAAAGTTACAAAATGATCCATTGACTA
1 TAGGACATTACTTTGTTGAGTCTCCCGACTATTAAAAGTTACAAAATGATCCATTGACTA
* *
1517120 TAGG-TATTACTTTGTTGAGTCTCCCGATTATTAAAAGTTACAAAATG
1 TAGGACATTACTTTGTTGAGTCTCCCGACTATTAAAAGTTACAAAATG
1517167 GTCACCCGAC
Statistics
Matches: 97, Mismatches: 7, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
58 17 0.18
59 58 0.60
60 22 0.23
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (60 bp):
TAGGACATTACTTTGTTGAGTCTCCCGACTATTAAAAGTTACAAAATGATCCATTGACTA
Found at i:1517801 original size:60 final size:60
Alignment explanation
Indices: 1517696--1517902 Score: 249
Period size: 60 Copynumber: 3.5 Consensus size: 60
1517686 AATTTTGGGT
* * * * *** *
1517696 AAAG-TATAGAAATGGTCCCTGGACTATAGGGCATTGA-TTTATTGAGTCTATCGACTTTTA
1 AAAGTTATA-AAATGATCCCTTGACTATAGGACATT-ACTTTGTTGAGTCCCCCGACTATTA
*
1517756 AAAGTTATAAAATGATCCCTTGACTATAGGACAATACTTTGTTGAGTCCCCCGACTATTA
1 AAAGTTATAAAATGATCCCTTGACTATAGGACATTACTTTGTTGAGTCCCCCGACTATTA
* *
1517816 AAAGTTAAAAAATGATCCCTTGACTATAGGATATTACTTTGTTGAGTCCCCCGACTATTA
1 AAAGTTATAAAATGATCCCTTGACTATAGGACATTACTTTGTTGAGTCCCCCGACTATTA
* *
1517876 AAAGTTACAAAATGGTCACC-TGACTAT
1 AAAGTTATAAAATGATC-CCTTGACTAT
1517903 TCATGTGTTC
Statistics
Matches: 130, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
59 1 0.01
60 123 0.95
61 6 0.05
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Consensus pattern (60 bp):
AAAGTTATAAAATGATCCCTTGACTATAGGACATTACTTTGTTGAGTCCCCCGACTATTA
Found at i:1518256 original size:723 final size:721
Alignment explanation
Indices: 1516761--1518572 Score: 2569
Period size: 723 Copynumber: 2.5 Consensus size: 721
1516751 TTTATATTTT
* *
1516761 GAATGATGGTATGAATAGCAGGAGATTTAGAGGTATCTTGTGAAGTTACTATGGTTGAAGAAGAA
1 GAATGATGGTATGAACAGCGGGAGATTTAGAGGTATCTTGTGAAGTTACTATGGTTGAAGAAGAA
* * * * * *
1516826 TGTGAAAATTTTTAAAAAAGAAGAA-AATATTAAG-TAAAAAATAT-G-TGCTCTAATATCATAA
66 TGTGAAAAATTTTAAAAAAGAAAAAGAAGA-AAAGATTAAGAATATGGTTGCTCTAATATCATAA
* * * *
1516887 AGATGTTAGAGATATTGCCTTTGACATACAAAATTTTTAACATAACTAGTAAAATTGTTTTACTA
130 AGATGTTAGAGATATTACCTTTGACATACAAAATTTTGAACATAAGTAGTAAAATTGTTTTACTT
** * * * *
1516952 TTTTTTCAAATAAAATTTTGGGTAAAGTACACAAATGGTCCCTAAATTTTAGGACATTGCTTTGT
195 TTTTTTCAAATAAAATTTTGGGTAAAGTACACAAATGGTCCCTGGACTATAGGGCATTGATTTGT
* *
1517017 TGAGTCCCTCGACTATTAAAAGTTATAAAATGATCCATTGAGTATAGGACATTACTTTGTTGAGT
260 TGAGTCCATCGACTATTAAAAGTTATAAAATGATCCATTGACTATAGGACATTACTTTGTTGAGT
* * *
1517082 -CTCCTACTATTAAAAGTTACAAAATGATCCATTGACTATAGGTATTACTTTGTTGAGTCTCCCG
325 CCCCCAACTATTAAAAGTTACAAAATGATCCATTGACTATAGGTATTACTTTGTTGAGTCCCCCG
*
1517146 ATTATTAAAAGTTACAAAATGGTCACCCGACTATTCATGTGTTACAAACTAGTCATTTTCCGTTA
390 ACTATTAAAAGTTACAAAATGGTCACCCGACTATTCATGTGTTACAAACTAGTCATTTTCCGTTA
**
1517211 GCAAACGATGACGGTCTGACCTATATGTTAATCTATTAACTGAGATATGATAGTCGTTTGAGATT
455 AAAAACGATGACGGTCTGACCTATATGTTAATCTATTAACTGAGATATGATAGTCGTTTGAGATT
* *
1517276 TTATGATCATATTTTATCACATCATAGTCAACAGGTTAACGTCCAACTCAGACTGATATCAAATT
520 TTAGGATCAGATTTTATCACATCATAGTCAACAGGTTAACGTCCAACTCAGACTGATATCAAATT
* * *
1517341 TTTAATAGAAAATGACGAGTTTGGAGCATATAAATAGTAGGGTGATCATTTTATAACTTTTAAAA
585 TTTAATAGAAAATGACGAGTTTGGAACATATAAATAGTAGGGTGACCATTTTACAACTTTTAAAA
* *
1517406 ATCGGAGAACTCAACAAAGTAATGTCTATAGTCAAGGAACCATTTCATAACTTTTATAATTTTGG
650 ATCGGAGAACTCAACAAAGTAATGCCTATAGTCAAGGAACCATTTCATAACTTTTATAATTTTAG
1517471 ATAATTG
715 ATAATTG
** * ** *
1517478 GAAAAATGGTATGAACAACGGGAGATGGAGAGGTATCTTGTGAAGTTAATATGGTTGAAGAAGAA
1 GAATGATGGTATGAACAGCGGGAGATTTAGAGGTATCTTGTGAAGTTACTATGGTTGAAGAAGAA
*
1517543 TGTGAAAAATTTTAAAAACAGAATAAGAAGAAAAGATTAAGAATATGGTTGCTCTAATATCATAA
66 TGTGAAAAATTTTAAAAA-AGAAAAAGAAGAAAAGATTAAGAATATGGTTGCTCTAATATCATAA
*
1517608 AGATGTTAGAGATATTACCTTTGACATACAAAATTTTGAACAAAAGTAGTAAAATTGTTTTACTT
130 AGATGTTAGAGATATTACCTTTGACATACAAAATTTTGAACATAAGTAGTAAAATTGTTTTACTT
* * *
1517673 TTTTTTCAAATAAAATTTTGGGTAAAGTATAGAAATGGTCCCTGGACTATAGGGCATTGATTTAT
195 TTTTTTCAAATAAAATTTTGGGTAAAGTACACAAATGGTCCCTGGACTATAGGGCATTGATTTGT
* * * *
1517738 TGAGTCTATCGACTTTTAAAAGTTATAAAATGATCCCTTGACTATAGGACAATACTTTGTTGAGT
260 TGAGTCCATCGACTATTAAAAGTTATAAAATGATCCATTGACTATAGGACATTACTTTGTTGAGT
* * *
1517803 CCCCCGACTATTAAAAGTTAAAAAATGATCCCTTGACTATAGGATATTACTTTGTTGAGTCCCCC
325 CCCCCAACTATTAAAAGTTACAAAATGATCCATTGACTATAGG-TATTACTTTGTTGAGTCCCCC
* *
1517868 GACTATTAAAAGTTACAAAATGGTCACCTGACTATTCATGTGTT-CAAAACTAGTCATTTTTCGT
389 GACTATTAAAAGTTACAAAATGGTCACCCGACTATTCATGTGTTAC-AAACTAGTCATTTTCCGT
* * *
1517932 TAAAAAATGATGATGGTCTGACCTATATGTTAATCTATTGACTGAGATATGATAGTCGTTTGAGA
453 TAAAAAACGATGACGGTCTGACCTATATGTTAATCTATTAACTGAGATATGATAGTCGTTTGAGA
* *
1517997 TTTTAGGATTAGATTTTATCACATCATAGTCAATAGGTTAACGT-CAAGCTCAGACTGATATCAA
518 TTTTAGGATCAGATTTTATCACATCATAGTCAACAGGTTAACGTCCAA-CTCAGACTGATATCAA
1518061 ATTTTTAATAGAAAATGACGAGTTTGGAACATATAAATAGTAGGGTGACCATTTTACAACTTTTA
582 ATTTTTAATAGAAAATGACGAGTTTGGAACATATAAATAGTAGGGTGACCATTTTACAACTTTTA
* * * * *
1518126 AAAGTCGGAGGACTCGACAAAGTAATGCCTATAGTCAATGAACCATTTTATAACTTTTATAATTT
647 AAAATCGGAGAACTCAACAAAGTAATGCCTATAGTCAAGGAACCATTTCATAACTTTTATAATTT
1518191 TAGATAATTG
712 TAGATAATTG
* ** * *
1518201 GAATGATTGTATGAGGAGCGGGAGATTTAAAGGTATCTTGTGAAGTTACTATGGTTGGAGAAGAA
1 GAATGATGGTATGAACAGCGGGAGATTTAGAGGTATCTTGTGAAGTTACTATGGTTGAAGAAGAA
**
1518266 TGTGAAAAAATTAAAAAAAGAAAAGAAAGAAAGAAAGAAAGAAAGAAAAGATTAAAGTAAAAAAT
66 TGTG-AAAAATT-----------TTAAA-AAAG-AA-AAAG-AAGAAAAGATT-AAG-----AAT
* * *
1518331 ATGTTTGCTCTAATATCATAAAGATGTTAGAGATATAACCTTTGACAGACAAAATTTTGAACATA
109 ATGGTTGCTCTAATATCATAAAGATGTTAGAGATATTACCTTTGACATACAAAATTTTGAACATA
* *
1518396 AGTAGTAAAATTGTTTTA-TTTTTTTTCAAATAAAATTTTGGGTAAAGTACACAAATGATACCTG
174 AGTAGTAAAATTGTTTTACTTTTTTTTCAAATAAAATTTTGGGTAAAGTACACAAATGGTCCCTG
* * * * * *
1518460 GACTATAGGGCATTGTTTTGTTGAGTCCATCAACTCTTAAACGTTATAAAATGATTCATTCACTA
239 GACTATAGGGCATTGATTTGTTGAGTCCATCGACTATTAAAAGTTATAAAATGATCCATTGACTA
* * *
1518525 TAAGACATTACTTTGTTGACTCCCTCAACTATTAAAAGTTACAAAATG
304 TAGGACATTACTTTGTTGAGTCCCCCAACTATTAAAAGTTACAAAATG
1518573 GTCACCGAAC
Statistics
Matches: 966, Mismatches: 98, Indels: 36
0.88 0.09 0.03
Matches are distributed among these distances:
717 74 0.08
718 9 0.01
719 11 0.01
720 1 0.00
721 191 0.20
722 42 0.04
723 383 0.40
724 7 0.01
735 5 0.01
736 4 0.00
737 3 0.00
738 11 0.01
739 3 0.00
743 140 0.14
744 82 0.08
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.33
Consensus pattern (721 bp):
GAATGATGGTATGAACAGCGGGAGATTTAGAGGTATCTTGTGAAGTTACTATGGTTGAAGAAGAA
TGTGAAAAATTTTAAAAAAGAAAAAGAAGAAAAGATTAAGAATATGGTTGCTCTAATATCATAAA
GATGTTAGAGATATTACCTTTGACATACAAAATTTTGAACATAAGTAGTAAAATTGTTTTACTTT
TTTTTCAAATAAAATTTTGGGTAAAGTACACAAATGGTCCCTGGACTATAGGGCATTGATTTGTT
GAGTCCATCGACTATTAAAAGTTATAAAATGATCCATTGACTATAGGACATTACTTTGTTGAGTC
CCCCAACTATTAAAAGTTACAAAATGATCCATTGACTATAGGTATTACTTTGTTGAGTCCCCCGA
CTATTAAAAGTTACAAAATGGTCACCCGACTATTCATGTGTTACAAACTAGTCATTTTCCGTTAA
AAAACGATGACGGTCTGACCTATATGTTAATCTATTAACTGAGATATGATAGTCGTTTGAGATTT
TAGGATCAGATTTTATCACATCATAGTCAACAGGTTAACGTCCAACTCAGACTGATATCAAATTT
TTAATAGAAAATGACGAGTTTGGAACATATAAATAGTAGGGTGACCATTTTACAACTTTTAAAAA
TCGGAGAACTCAACAAAGTAATGCCTATAGTCAAGGAACCATTTCATAACTTTTATAATTTTAGA
TAATTG
Found at i:1518296 original size:4 final size:4
Alignment explanation
Indices: 1518282--1518313 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
1518272 AAAATTAAAA
1518282 AAAG AAAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG -AAAG AAAG AAAG AAAG AAAG AAAG AAA
1518314 AGATTAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:1519610 original size:13 final size:13
Alignment explanation
Indices: 1519580--1519621 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
1519570 ACGAATTAAG
*
1519580 TATTTTGATTTT-
1 TATTTTTATTTTA
1519592 T-TTTTTATATTTA
1 TATTTTTAT-TTTA
1519605 TATTTTTATTTTA
1 TATTTTTATTTTA
1519618 TATT
1 TATT
1519622 AAATTTGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 6 0.23
12 4 0.15
13 9 0.35
14 7 0.27
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (13 bp):
TATTTTTATTTTA
Found at i:1519632 original size:19 final size:19
Alignment explanation
Indices: 1519587--1519633 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1519577 AAGTATTTTG
* *
1519587 ATTTTTTTTTTATATTTAT
1 ATTTTTATTTTATATTTAA
1519606 ATTTTTATTTTATA-TTAA
1 ATTTTTATTTTATATTTAA
1519624 ATTTGTTATT
1 ATTT-TTATT
1519634 ATTAAATCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (19 bp):
ATTTTTATTTTATATTTAA
Found at i:1519748 original size:39 final size:39
Alignment explanation
Indices: 1519644--1519749 Score: 124
Period size: 39 Copynumber: 2.7 Consensus size: 39
1519634 ATTAAATCTC
1519644 AAATAATTTCACTCTT-ACATTCTAAATTCCTAACTTCTT
1 AAATAATTTCACT-TTAACATTCTAAATTCCTAACTTCTT
* ** * *
1519683 AAATCATTTCACCGTAACATTCTAAATTCTTAATTTCTT
1 AAATAATTTCACTTTAACATTCTAAATTCCTAACTTCTT
* * *
1519722 AAATTATTTCACTTTAATATTTTAAATT
1 AAATAATTTCACTTTAACATTCTAAATT
1519750 ATTTTTAACT
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
38 1 0.02
39 55 0.98
ACGTcount: A:0.35, C:0.18, G:0.01, T:0.46
Consensus pattern (39 bp):
AAATAATTTCACTTTAACATTCTAAATTCCTAACTTCTT
Found at i:1522025 original size:15 final size:15
Alignment explanation
Indices: 1522007--1522079 Score: 64
Period size: 15 Copynumber: 5.1 Consensus size: 15
1521997 AAATTCTAAA
1522007 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
1522022 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
** *
1522037 TCA--TCGAT-AATA-
1 T-ATTTAAATAAAAAT
1522049 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
1522064 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
1522079 T
1 T
1522080 CATCGATAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
11 1 0.02
12 1 0.02
13 6 0.13
14 6 0.13
15 30 0.67
16 1 0.02
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.42
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:1522052 original size:42 final size:42
Alignment explanation
Indices: 1522006--1522094 Score: 178
Period size: 42 Copynumber: 2.1 Consensus size: 42
1521996 GAAATTCTAA
1522006 ATATTTAAATAAAAATTATTTATATAAAAATTCATCGATAAT
1 ATATTTAAATAAAAATTATTTATATAAAAATTCATCGATAAT
1522048 ATATTTAAATAAAAATTATTTATATAAAAATTCATCGATAAT
1 ATATTTAAATAAAAATTATTTATATAAAAATTCATCGATAAT
1522090 ATATT
1 ATATT
1522095 ATTTTATTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (42 bp):
ATATTTAAATAAAAATTATTTATATAAAAATTCATCGATAAT
Found at i:1534843 original size:57 final size:58
Alignment explanation
Indices: 1534782--1534916 Score: 157
Period size: 60 Copynumber: 2.3 Consensus size: 58
1534772 CATCTTTAAT
* * * *
1534782 TTTTAAAATATTCTATATCAAT-TCTTAAATTAT-CCTCATTCTGAACTGGTTTTTAGA
1 TTTTAAAATATTCTATATCAATGTC-TAAATTATACCTCATTCTAAACTGATTTCTAAA
* * * *
1534839 TTTTAAAGTATTCTATATCAATGTCTAAATTATGACCCTCGTTTTAAATTGATTTCTAAA
1 TTTTAAAATATTCTATATCAATGTCTAAATTAT-A-CCTCATTCTAAACTGATTTCTAAA
1534899 TTTTAAAATATTCTATAT
1 TTTTAAAATATTCTATAT
1534917 TAGTCCAAGA
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
57 29 0.45
58 2 0.03
60 34 0.52
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.47
Consensus pattern (58 bp):
TTTTAAAATATTCTATATCAATGTCTAAATTATACCTCATTCTAAACTGATTTCTAAA
Found at i:1534933 original size:60 final size:59
Alignment explanation
Indices: 1534869--1534981 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 59
1534859 ATGTCTAAAT
* * *
1534869 TATGACCCTCGTTTTAAATTGATTTCTAAAT-TTTAAAATATTCTATATTAGTCCAAGAAC
1 TATGACCCTCATTTTAAATTG-GTTC-AAATCTTTAAAACATTCTATATTAGTCCAAGAAC
* *
1534929 TATGACCCTCATTTTAATTTGGTTCATATGCTTTAAAACATTCTATATTAGTC
1 TATGACCCTCATTTTAAATTGGTTCAAAT-CTTTAAAACATTCTATATTAGTC
1534982 TTCATACTCT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
58 3 0.07
59 3 0.07
60 40 0.87
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (59 bp):
TATGACCCTCATTTTAAATTGGTTCAAATCTTTAAAACATTCTATATTAGTCCAAGAAC
Found at i:1539047 original size:30 final size:31
Alignment explanation
Indices: 1539011--1539090 Score: 108
Period size: 32 Copynumber: 2.6 Consensus size: 31
1539001 CTTATCTAAC
*
1539011 TTAAAAATATATTTTA-TCTCATCTTAACTT
1 TTAAAAATATATTTTATTATCATCTTAACTT
*
1539041 TTAAAAATATAATTTTATTATCATTTTAACTT
1 TTAAAAATAT-ATTTTATTATCATCTTAACTT
* *
1539073 TTAAAAATGTATTGTATT
1 TTAAAAATATATTTTATT
1539091 CTTACTTTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
30 10 0.23
31 13 0.30
32 21 0.48
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.51
Consensus pattern (31 bp):
TTAAAAATATATTTTATTATCATCTTAACTT
Found at i:1539173 original size:30 final size:30
Alignment explanation
Indices: 1538880--1539285 Score: 219
Period size: 30 Copynumber: 13.5 Consensus size: 30
1538870 ATAATTTATG
* *
1538880 TATTTTAACTTTAAAAAATATATTTTATTTT
1 TATTTTAAC-TTAAAATATATATTTTATTCT
* * *
1538911 TATCTT-ACATTATTAA-ATATATTTTATTAT
1 TATTTTAAC-TTA-AAATATATATTTTATTCT
* ** ** * *
1538941 AAAATTAAAATAAAATATATATTTAACTCT
1 TATTTTAACTTAAAATATATATTTTATTCT
** * *
1538971 TATTTTATTTTAAAATTTTATTTTTTTATTCT
1 TATTTTAACTTAAAA-TATA-TATTTTATTCT
*
1539003 TA-TCTAACTTAAAA-ATATATTTTA-TCT
1 TATTTTAACTTAAAATATATATTTTATTCT
* * *
1539030 CATCTTAACTTTTAAAA-ATATAATTTTATTAT
1 TATTTTAAC--TTAAAATATAT-ATTTTATTCT
* * *
1539062 CATTTTAACTTTTAAAA-ATGTATTGTATTCT
1 TATTTTAAC--TTAAAATATATATTTTATTCT
* * * *
1539093 TACTTTAAATTATTAA-ATATGTTTTATT-T
1 TATTTTAACTTA-AAATATATATTTTATTCT
* * *
1539122 ATATATTAACAT-AAA-A-ATATTTTAATCT
1 -TATTTTAACTTAAAATATATATTTTATTCT
*
1539150 TATTTTAGCTTAAACA-ATATATTTTATTCT
1 TATTTTAACTTAAA-ATATATATTTTATTCT
* ** *
1539180 TGTCATAACTTAAAATATATATTTTATTCG
1 TATTTTAACTTAAAATATATATTTTATTCT
*
1539210 TATTTTAACTTAAAATGTATATTTTATTCT
1 TATTTTAACTTAAAATATATATTTTATTCT
* * *
1539240 TATATTGA-TATAAAATATATATTTTATTTT
1 TATTTTAACT-TAAAATATATATTTTATTCT
* *
1539270 TATCTTAATTTAAAAT
1 TATTTTAACTTAAAAT
1539286 TATTATTAAC
Statistics
Matches: 286, Mismatches: 70, Indels: 39
0.72 0.18 0.10
Matches are distributed among these distances:
27 20 0.07
28 16 0.06
29 12 0.04
30 166 0.58
31 41 0.14
32 31 0.11
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (30 bp):
TATTTTAACTTAAAATATATATTTTATTCT
Found at i:1539425 original size:31 final size:29
Alignment explanation
Indices: 1539364--1539515 Score: 105
Period size: 31 Copynumber: 5.2 Consensus size: 29
1539354 TATTTTTGGA
* * * *
1539364 ATATATTTAAATTAAGA-CAAAATAAAAT
1 ATATTTTTAAATTAAAATAAAAACAAAAT
*
1539392 ATATTTTTGAAATTAAAGATAATAACAAAAT
1 ATATTTTT-AAATTAAA-ATAAAAACAAAAT
* * *
1539423 ATATTTTTTAGTTAAAATAAAAATAAAAT
1 ATATTTTTAAATTAAAATAAAAACAAAAT
* * *
1539452 ATATTTTT-AAGTAAAATAAGAATAAAAT
1 ATATTTTTAAATTAAAATAAAAACAAAAT
* * * *
1539480 AAACACTTTTAAATAAAAATAATAA-AAAAT
1 --ATATTTTTAAATTAAAATAAAAACAAAAT
1539510 AT-TTTT
1 ATATTTT
1539516 AAAAAATAAG
Statistics
Matches: 99, Mismatches: 19, Indels: 13
0.76 0.15 0.10
Matches are distributed among these distances:
27 3 0.03
28 25 0.25
29 26 0.26
30 18 0.18
31 27 0.27
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.36
Consensus pattern (29 bp):
ATATTTTTAAATTAAAATAAAAACAAAAT
Found at i:1539450 original size:29 final size:29
Alignment explanation
Indices: 1539382--1539480 Score: 128
Period size: 29 Copynumber: 3.4 Consensus size: 29
1539372 AAATTAAGAC
*
1539382 AAAATAAAATATATTTTTGAAATTAAAGATA
1 AAAATAAAATATATTTTT-AAGTTAAA-ATA
* * *
1539413 ATAACAAAATATATTTTTTAGTTAAAATA
1 AAAATAAAATATATTTTTAAGTTAAAATA
1539442 AAAATAAAATATATTTTTAAG-TAAAATA
1 AAAATAAAATATATTTTTAAGTTAAAATA
*
1539470 AGAATAAAATA
1 AAAATAAAATA
1539481 AACACTTTTA
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
28 17 0.28
29 21 0.35
30 6 0.10
31 16 0.27
ACGTcount: A:0.59, C:0.01, G:0.05, T:0.35
Consensus pattern (29 bp):
AAAATAAAATATATTTTTAAGTTAAAATA
Found at i:1539553 original size:24 final size:24
Alignment explanation
Indices: 1539520--1539568 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
1539510 ATTTTTAAAA
1539520 AATAAGTTT-AGAATAAAATATATTT
1 AATAAGTTTAAG-ATAAAA-ATATTT
1539545 AATAA-TTTAAGATAAAAATATTT
1 AATAAGTTTAAGATAAAAATATTT
1539568 A
1 A
1539569 TTTTTTAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 7 0.30
24 9 0.39
25 7 0.30
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (24 bp):
AATAAGTTTAAGATAAAAATATTT
Found at i:1539762 original size:20 final size:19
Alignment explanation
Indices: 1539726--1539766 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
1539716 CTTGGAAAAG
*
1539726 AAAATAAATATATTAATTT
1 AAAATAAATAAATTAATTT
1539745 AAAATAAATTAAATTAATTT
1 AAAATAAA-TAAATTAATTT
1539765 AA
1 AA
1539767 TCCTTACACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATAAATAAATTAATTT
Found at i:1555746 original size:11 final size:12
Alignment explanation
Indices: 1555725--1555778 Score: 56
Period size: 12 Copynumber: 4.3 Consensus size: 12
1555715 CTTAATTTAA
1555725 AAAATCATTTTT
1 AAAATCATTTTT
1555737 AAAA-CATTTTTT
1 AAAATCA-TTTTT
* *
1555749 AACATTATTTTT
1 AAAATCATTTTT
1555761 AAAGATCACTTTTT
1 AAA-ATCA-TTTTT
1555775 AAAA
1 AAAA
1555779 GCAATATCGA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
11 2 0.06
12 19 0.56
13 5 0.15
14 8 0.24
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.46
Consensus pattern (12 bp):
AAAATCATTTTT
Found at i:1563538 original size:144 final size:142
Alignment explanation
Indices: 1563280--1563565 Score: 457
Period size: 144 Copynumber: 2.0 Consensus size: 142
1563270 AGTTTCGTTT
* * * *
1563280 CGATCATCTAACTATGGTTTTTTTCTTCAAAATTATACTTTTTTATTAAGCTAGAGTAATTACAA
1 CGATCACCTAACTATGATATTTTTCTTCAAAATTATACTTTTTTATTAAGCTAGAGTAACTACAA
* *
1563345 AGTAATATATGTACTAAATACTCTCAACCATTTAATAATGAACGTTCAATCACCCTTGTAGTTGC
66 AGTAATATATGTACTAAATACTCTCAACCATTTAATAATGAACGTTCAATCACCCTTGCAGTTAC
1563410 TGGTGCTTGAAC
131 TGGTGCTTGAAC
* *
1563422 CGATCACCTAACTATGATATTTTT-TTCAAAATTATACATTTTTTTTATTAAGTTAGAGTGACTA
1 CGATCACCTAACTATGATATTTTTCTTCAAAATTATAC---TTTTTTATTAAGCTAGAGTAACTA
1563486 CAAAGTAATATATGTACTAAATACTCTCAACCATTTAATAATGAACGTTCAATCACCCTTGCAGT
63 CAAAGTAATATATGTACTAAATACTCTCAACCATTTAATAATGAACGTTCAATCACCCTTGCAGT
*
1563551 TATTGGTGCTTGAAC
128 TACTGGTGCTTGAAC
1563566 TCATGATCTC
Statistics
Matches: 132, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
141 13 0.10
142 21 0.16
144 98 0.74
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (142 bp):
CGATCACCTAACTATGATATTTTTCTTCAAAATTATACTTTTTTATTAAGCTAGAGTAACTACAA
AGTAATATATGTACTAAATACTCTCAACCATTTAATAATGAACGTTCAATCACCCTTGCAGTTAC
TGGTGCTTGAAC
Found at i:1564218 original size:11 final size:11
Alignment explanation
Indices: 1564204--1564228 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1564194 TATTTCACTT
1564204 TTAAATATTAA
1 TTAAATATTAA
1564215 TTAAATATTAA
1 TTAAATATTAA
1564226 TTA
1 TTA
1564229 TTTAGTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TTAAATATTAA
Found at i:1565368 original size:15 final size:14
Alignment explanation
Indices: 1565323--1565380 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 14
1565313 AAAGAAGAAG
1565323 ATAATAATA-ATA-
1 ATAATAATATATAT
*
1565335 GTAATAAT-TATAT
1 ATAATAATATATAT
1565348 -TAAT-ATATATAT
1 ATAATAATATATAT
1565360 A-AATAATATATAT
1 ATAATAATATATAT
1565373 ATAATAAT
1 ATAATAAT
1565381 TTGTAAACAA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
11 2 0.05
12 22 0.56
13 9 0.23
14 6 0.15
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (14 bp):
ATAATAATATATAT
Found at i:1565423 original size:18 final size:18
Alignment explanation
Indices: 1565389--1565423 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1565379 ATTTGTAAAC
1565389 AAAAAAAAGTAATAATAT
1 AAAAAAAAGTAATAATAT
1565407 AAAAATAAAGTAA-AATA
1 AAAAA-AAAGTAATAATA
1565424 AGAAATATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (18 bp):
AAAAAAAAGTAATAATAT
Found at i:1567185 original size:105 final size:106
Alignment explanation
Indices: 1566979--1568037 Score: 1653
Period size: 106 Copynumber: 10.0 Consensus size: 106
1566969 ATATTGTTCT
* * * *
1566979 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGTCAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1567044 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCAT-
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * *
1567085 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTTTAAAATTGGGAGGTTG-TTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
1567149 CCAGCAGTCCCTTCGCCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1567190 GAGTCCAATATCCTTCGCCGTGAAGTTAAAATTGGCTCTGAAATTGGGAGGTTG-TTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1567254 CCAGCGGTCCCTTCGTCGTGAA-TTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1567294 GAGTCCAATATCATTCGCTGTGATGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
1567359 TCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1567400 TAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
1567465 CCAGCGGTCTCTTCGTCGTGAAGTTGAACTTGCGTTGTCCG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1567506 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1567571 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1567612 GAGTCCAATATCCATCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAGGTTG-TTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1567676 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
1567717 GAGTCCAATATCCTTCGTTGTGAAGTTGAATTTGACTCTAAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1567782 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1567823 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGGGAGGTTG-TTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1567887 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1567928 GAGTCCAATATCCTTCGCCGTGAAGTTAAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
1567993 CCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1568034 GAGT
1 GAGT
1568038 GGCACGATAT
Statistics
Matches: 877, Mismatches: 71, Indels: 10
0.92 0.07 0.01
Matches are distributed among these distances:
104 68 0.08
105 349 0.40
106 460 0.52
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1567777 original size:211 final size:211
Alignment explanation
Indices: 1566979--1568037 Score: 1676
Period size: 211 Copynumber: 5.0 Consensus size: 211
1566969 ATATTGTTCT
* * * *
1566979 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGTCAA
1 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAGGTTG-TTGTTGACAA
1567044 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCAT-GAGTCCAATATCCTTCGCTGTGA
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TGGAGTCCAATATCCTTCGCTGTGA
* * * * *
1567108 AGTTGAAATTGGCTTTAAAATTGGGAGGTTG-TTGTTGACAACCAGCAGTCCCTTCGCCGTGAAG
129 AGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
1567172 TTGAACTTGCGTTGTCTG
194 TTGAACTTGCGTTGTCTG
* * *
1567190 GAGTCCAATATCCTTCGCCGTGAAGTTAAAATTGGCTCTGAAATTGGGAGGTTGTTGTTGACAAC
1 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAGGTTGTTGTTGACAAC
* *
1567255 CAGCGGTCCCTTCGTCGTGAA-TTGAACTTGCGTTGTCTGGAGTCCAATATCATTCGCTGTGATG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAG
* * *
1567319 TTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAATCAACGGTCCCTTCGTCGTGAAGTT
131 TTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
*
1567384 GAACTTGCGTTGTCTA
196 GAACTTGCGTTGTCTG
* ** *
1567400 TAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAGGTTG-TTGTTGACAA
* * *
1567465 CCAGCGGTCTCTTCGTCGTGAAGTTGAACTTGCGTTGTCCGGAGTCCAATATCCTTCGTTGTGAA
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
*
1567530 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
130 GTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
1567595 TGAACTTGCGTTGTCTG
195 TGAACTTGCGTTGTCTG
*
1567612 GAGTCCAATATCCA-TCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAGGTTGTTGTTGACAA
1 GAGTCCAATAT-CATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAGGTTGTTGTTGACAA
* *
1567676 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAA
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
* * * * *
1567741 GTTGAATTTGACTCTAAAATTGAGAAGTTATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
130 GTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
1567806 TGAACTTGCGTTGTCTG
195 TGAACTTGCGTTGTCTG
* *
1567823 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGGGAGGTTGTTGTTGACAAC
1 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAGGTTGTTGTTGACAAC
* *
1567888 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGCCGTGAAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAG
* *
1567953 TTAAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTCGTGAAGTT
131 TTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* *
1568018 GAACTTGTGTTGTCTC
196 GAACTTGCGTTGTCTG
1568034 GAGT
1 GAGT
1568038 GGCACGATAT
Statistics
Matches: 780, Mismatches: 62, Indels: 12
0.91 0.07 0.01
Matches are distributed among these distances:
208 1 0.00
209 65 0.08
210 126 0.16
211 424 0.54
212 162 0.21
213 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (211 bp):
GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAGGTTGTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAG
TTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
GAACTTGCGTTGTCTG
Found at i:1570850 original size:22 final size:21
Alignment explanation
Indices: 1570820--1570862 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
1570810 TTCATGTTAG
1570820 TGAAAATGCTTAAAAATG-AAGA
1 TGAAAATGC--AAAAATGCAAGA
*
1570842 TGAATATGCAAAAATGCAAGA
1 TGAAAATGCAAAAATGCAAGA
1570863 ATGCATGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 7 0.37
21 4 0.21
22 8 0.42
ACGTcount: A:0.53, C:0.07, G:0.19, T:0.21
Consensus pattern (21 bp):
TGAAAATGCAAAAATGCAAGA
Found at i:1576427 original size:18 final size:19
Alignment explanation
Indices: 1576404--1576440 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
1576394 TGTGAAAATA
1576404 AAATAATTT-TCTTTAAAC
1 AAATAATTTATCTTTAAAC
1576422 AAATAATTTACTCTTTAAA
1 AAATAATTTA-TCTTTAAA
1576441 TTTATTGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
20 8 0.47
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (19 bp):
AAATAATTTATCTTTAAAC
Found at i:1582656 original size:26 final size:25
Alignment explanation
Indices: 1582604--1582656 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 25
1582594 CCTCTCAAAA
*
1582604 TTTTTAATATAATTCTATTTTAGAT
1 TTTTTAATATAATTCTATTTTACAT
* * *
1582629 TTTTTAGTTTAATATCTATTTTTCAT
1 TTTTTAATATAAT-TCTATTTTACAT
1582655 TT
1 TT
1582657 ATGCAAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.64
Consensus pattern (25 bp):
TTTTTAATATAATTCTATTTTACAT
Found at i:1586029 original size:28 final size:28
Alignment explanation
Indices: 1585997--1586056 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
1585987 TACAGATAGA
* *
1585997 TGATTTGGATTCATGGTATTTAAATAAG
1 TGATTTAGATTCATGGTATTAAAATAAG
*
1586025 TGATTTAGATTCATGGTATTAAAATAGG
1 TGATTTAGATTCATGGTATTAAAATAAG
1586053 TGAT
1 TGAT
1586057 CTAAATTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.03, G:0.22, T:0.42
Consensus pattern (28 bp):
TGATTTAGATTCATGGTATTAAAATAAG
Found at i:1591077 original size:24 final size:24
Alignment explanation
Indices: 1591045--1591126 Score: 155
Period size: 24 Copynumber: 3.4 Consensus size: 24
1591035 GGTTGTAATA
1591045 TGTTAGTTTGATGTATTTATAGAT
1 TGTTAGTTTGATGTATTTATAGAT
1591069 TGTTAGTTTGATGTATTTATAGAT
1 TGTTAGTTTGATGTATTTATAGAT
1591093 TGTTAGTTTGATGTATTTATAGAT
1 TGTTAGTTTGATGTATTTATAGAT
*
1591117 TGTTATTTTG
1 TGTTAGTTTG
1591127 GTGGTAATAT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.23, C:0.00, G:0.21, T:0.56
Consensus pattern (24 bp):
TGTTAGTTTGATGTATTTATAGAT
Found at i:1591887 original size:39 final size:38
Alignment explanation
Indices: 1591834--1591914 Score: 110
Period size: 39 Copynumber: 2.1 Consensus size: 38
1591824 CATTAAACCT
*
1591834 TTTTATATTTTAAATTTTGTAAAAAAAATATATATAA-A
1 TTTTATAATTTAAATTTTGTAAAAAAAATATATA-AATA
* *
1591872 TTTTATGAATTTAAATTTTTTAAAGAAAATATATAAATA
1 TTTTAT-AATTTAAATTTTGTAAAAAAAATATATAAATA
1591911 TTTT
1 TTTT
1591915 CCAACTCGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
38 8 0.21
39 30 0.79
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (38 bp):
TTTTATAATTTAAATTTTGTAAAAAAAATATATAAATA
Found at i:1592091 original size:20 final size:19
Alignment explanation
Indices: 1592062--1592101 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
1592052 AGTAATCCTA
1592062 TTCCCTGGTAATATTACAT
1 TTCCCTGGTAATATTACAT
*
1592081 TTCCACTGGTAATCTTACAT
1 TTCC-CTGGTAATATTACAT
1592101 T
1 T
1592102 CTGTGAACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.42
Consensus pattern (19 bp):
TTCCCTGGTAATATTACAT
Found at i:1595583 original size:19 final size:18
Alignment explanation
Indices: 1595541--1595583 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
1595531 CAATAATCCT
**
1595541 ATTCCCTGATAATCTTTT
1 ATTCCCTGATAATCTTAC
1595559 ATTTCCACTGATAATCTTAC
1 A-TTCC-CTGATAATCTTAC
1595579 ATTCC
1 ATTCC
1595584 GTGAACCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 8 0.38
20 12 0.57
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.44
Consensus pattern (18 bp):
ATTCCCTGATAATCTTAC
Found at i:1601822 original size:2 final size:2
Alignment explanation
Indices: 1601815--1601855 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1601805 TAACTAACTT
1601815 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1601856 CTTCGTATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1606598 original size:2 final size:2
Alignment explanation
Indices: 1606591--1606617 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1606581 ATTCATTTCA
1606591 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1606618 ATTTTTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1607980 original size:29 final size:30
Alignment explanation
Indices: 1607947--1608027 Score: 80
Period size: 29 Copynumber: 2.8 Consensus size: 30
1607937 AAAAAATAAG
1607947 TAATTAATAAATTAATAT-AATATTT-AAAA
1 TAATTAATAAATTAATATAAAT-TTTAAAAA
* * *
1607976 TAATTATTAAAATAATGTAAATTTTAAAAA
1 TAATTAATAAATTAATATAAATTTTAAAAA
* *
1608006 TCATTAA-AAATTACTA-AAATTT
1 TAATTAATAAATTAATATAAATTT
1608028 CATAAAGACG
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
28 6 0.14
29 24 0.57
30 12 0.29
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (30 bp):
TAATTAATAAATTAATATAAATTTTAAAAA
Found at i:1615031 original size:23 final size:23
Alignment explanation
Indices: 1615004--1615054 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
1614994 ATCATTTATT
* *
1615004 TTATTTTTGTTTTTTTATTAC-TA
1 TTATTTTT-TTATTTTAATACTTA
1615027 TTATTTTTTTATTTTAATACTTA
1 TTATTTTTTTATTTTAATACTTA
1615050 TTATT
1 TTATT
1615055 ACTATTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 10 0.40
23 15 0.60
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.73
Consensus pattern (23 bp):
TTATTTTTTTATTTTAATACTTA
Found at i:1625866 original size:16 final size:17
Alignment explanation
Indices: 1625831--1625868 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1625821 GAAAAAATTG
*
1625831 AAAAAGAGAACAAAAGA
1 AAAAAGAGAACAAAACA
*
1625848 AAAAAGAGAA-AGAACA
1 AAAAAGAGAACAAAACA
1625864 AAAAA
1 AAAAA
1625869 TAAGGTGGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.79, C:0.05, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAAGAGAACAAAACA
Found at i:1627127 original size:99 final size:99
Alignment explanation
Indices: 1626948--1627132 Score: 246
Period size: 99 Copynumber: 1.9 Consensus size: 99
1626938 GATATCATGC
* * * *
1626948 CAATTTCAACTTCACAGCGAAGGATACTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
1 CAATTTCAACTTCACAACGAAGGATACTAGACTCAAGACAACACAAGCTCAACTTCACAACGAAG
* *
1627013 GGACGATTGATTGTCAACAAACAAATTTCATAGT
66 GGACGACTGACTGTCAACAAACAAATTTCATAGT
* * ***
1627047 CAATTTCAACTTCACAATGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCACGGTGAAG
1 CAATTTCAACTTCACAACGAAGGATACTAGACTCAAGACAACACAAGCTCAACTTCACAACGAAG
*
1627112 GGGCTG-CTGACTGTCAACAAA
66 GGAC-GACTGACTGTCAACAAA
1627133 GAATTTCCCA
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
99 72 0.99
100 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.22
Consensus pattern (99 bp):
CAATTTCAACTTCACAACGAAGGATACTAGACTCAAGACAACACAAGCTCAACTTCACAACGAAG
GGACGACTGACTGTCAACAAACAAATTTCATAGT
Found at i:1627376 original size:280 final size:273
Alignment explanation
Indices: 1626978--1627530 Score: 847
Period size: 280 Copynumber: 2.0 Consensus size: 273
1626968 AGGATACTGG
* *
1626978 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGATTGATTGTCAACAAACAAATTTCA
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGATTGTCAACAAACAAATTTCA
* * * *
1627043 TAGTCAATTTCAACTTCACAATGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCACGGT
66 GAGTCAATTTCAACTTCACAACGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCACAGC
* * *
1627108 GAAGGGGCTG-CTGACTGTCAACAAAGAATTTCCCAGTTCCAGAGCTAATTTCAACTTTACGACG
131 GAAGGGGC-GACTGACTGTCAACAAACAATTTCCCAGTTCCAGAGCCAATTTCAACTTCACGACG
* *
1627172 GATGATATTGGACTCGGAGCAATACAACTTACTTGGATTTCAACTTCACGACGAAGGATATTCAA
195 GAGGATATTGGACTCGGAGCAATACAACTTACTTGGATTTCAACTTCACGACGAAGGATATCCAA
1627237 TTACCAGGCTCAAC
260 TTACCAGGCTCAAC
* * *
1627251 ACTCAAGACAACACAAGTTCAACTTCACAACGAATGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGATTGTCAACAAAC-A------
* * *
1627316 AATTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAGCACAAGCTCAACT
59 AATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTAGACTCAAGACAACACAAGCTCAACT
1627381 TCACAGCGAAGGGGCGACTGACTGTCAACAAACAATTTCCCAGTTCCAGAGCCAATTTCAACTTC
124 TCACAGCGAAGGGGCGACTGACTGTCAACAAACAATTTCCCAGTTCCAGAGCCAATTTCAACTTC
* * *
1627446 ACGATGGAGGATATTGGACTCTGAGCAATACAACTTACTTGGATTTCAACTTCACGACGAATGAT
189 ACGACGGAGGATATTGGACTCGGAGCAATACAACTTACTTGGATTTCAACTTCACGACGAAGGAT
1627511 ATCCAATTACCAGGCTCAAC
254 ATCCAATTACCAGGCTCAAC
1627531 TTCACGACGA
Statistics
Matches: 252, Mismatches: 20, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
273 52 0.21
274 1 0.00
279 1 0.00
280 198 0.79
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (273 bp):
ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGATTGTCAACAAACAAATTTCA
GAGTCAATTTCAACTTCACAACGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCACAGC
GAAGGGGCGACTGACTGTCAACAAACAATTTCCCAGTTCCAGAGCCAATTTCAACTTCACGACGG
AGGATATTGGACTCGGAGCAATACAACTTACTTGGATTTCAACTTCACGACGAAGGATATCCAAT
TACCAGGCTCAAC
Found at i:1627466 original size:106 final size:106
Alignment explanation
Indices: 1627251--1627447 Score: 277
Period size: 106 Copynumber: 1.9 Consensus size: 106
1627241 CAGGCTCAAC
* * * **
1627251 ACTCAAGACAACACAAGTTCAACTTCACAACGAATGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCAAGACAACACAAGCTCAACTTCACAACGAAGGGACGACTGACTGTCAACAAACAACTTCCC
* *
1627316 AATTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAG
66 AATTCCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAG
* * * * *
1627357 ACTCGAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAATTTCCC
1 ACTCAAGACAACACAAGCTCAACTTCACAACGAAGGGACGACTGACTGTCAACAAACAACTTCCC
*
1627422 AGTTCCAGAGCCAATTTCAACTTCAC
66 AATTCCAGAGCCAATTTCAACTTCAC
1627448 GATGGAGGAT
Statistics
Matches: 78, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
106 78 1.00
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (106 bp):
ACTCAAGACAACACAAGCTCAACTTCACAACGAAGGGACGACTGACTGTCAACAAACAACTTCCC
AATTCCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAG
Found at i:1628556 original size:2 final size:2
Alignment explanation
Indices: 1628549--1628627 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
1628539 TTTATACTTT
1628549 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1628591 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1628628 TACTTAATTT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1628698 original size:19 final size:18
Alignment explanation
Indices: 1628668--1628703 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1628658 TTTATTTTTG
*
1628668 TTTTTTTATTTATTACTA
1 TTTTTTTATTTAATACTA
1628686 TTTTTTTATTTTAATACT
1 TTTTTTTA-TTTAATACT
1628704 TATTATTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTTTATTTAATACTA
Found at i:1632484 original size:24 final size:22
Alignment explanation
Indices: 1632449--1632492 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 22
1632439 TATCATTTAT
1632449 ATTATATAATTATTAATTTTATCA
1 ATTATATAATTA--AATTTTATCA
1632473 ATTATAGT-ATTAAATTTTAT
1 ATTATA-TAATTAAATTTTAT
1632493 TTTTTGTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 8 0.42
24 10 0.53
25 1 0.05
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
ATTATATAATTAAATTTTATCA
Found at i:1632488 original size:29 final size:28
Alignment explanation
Indices: 1632439--1632496 Score: 64
Period size: 29 Copynumber: 2.0 Consensus size: 28
1632429 TTAGACGTTA
* *
1632439 TATCATTTATATTATATAATTATTAATTT
1 TATCAATTATAGTATATAATT-TTAATTT
*
1632468 TATCAATTATAGTAT-TAAATTTTATTTT
1 TATCAATTATAGTATAT-AATTTTAATTT
1632496 T
1 T
1632497 TGTTTCAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (28 bp):
TATCAATTATAGTATATAATTTTAATTT
Found at i:1633803 original size:2 final size:2
Alignment explanation
Indices: 1633796--1633845 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1633786 GATAGAGGTC
1633796 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1633838 AT AT AT AT
1 AT AT AT AT
1633846 TTGACTCTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1634286 original size:50 final size:51
Alignment explanation
Indices: 1634232--1634334 Score: 122
Period size: 51 Copynumber: 2.0 Consensus size: 51
1634222 GATAATTAGT
* * *
1634232 TATTGTATATATTA-AATTCGTCA-TGAGGACATGAA-GAATTTTATAAAATA
1 TATTGAATA-ATTAGAATTCGTCATTGAGAACA-CAACGAATTTTATAAAATA
* *
1634282 TATTGAATAATTAGAATTTGTCATTGAGAACACAACGAGTTTTATAAAATA
1 TATTGAATAATTAGAATTCGTCATTGAGAACACAACGAATTTTATAAAATA
1634333 TA
1 TA
1634335 ATAAATTGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
49 4 0.09
50 18 0.40
51 23 0.51
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.37
Consensus pattern (51 bp):
TATTGAATAATTAGAATTCGTCATTGAGAACACAACGAATTTTATAAAATA
Found at i:1636495 original size:35 final size:35
Alignment explanation
Indices: 1636449--1636625 Score: 354
Period size: 35 Copynumber: 5.1 Consensus size: 35
1636439 TTAATCATGA
1636449 TAGTTTAATTAATGAAAATAGAATAAAAGTGTAAT
1 TAGTTTAATTAATGAAAATAGAATAAAAGTGTAAT
1636484 TAGTTTAATTAATGAAAATAGAATAAAAGTGTAAT
1 TAGTTTAATTAATGAAAATAGAATAAAAGTGTAAT
1636519 TAGTTTAATTAATGAAAATAGAATAAAAGTGTAAT
1 TAGTTTAATTAATGAAAATAGAATAAAAGTGTAAT
1636554 TAGTTTAATTAATGAAAATAGAATAAAAGTGTAAT
1 TAGTTTAATTAATGAAAATAGAATAAAAGTGTAAT
1636589 TAGTTTAATTAATGAAAATAGAATAAAAGTGTAAT
1 TAGTTTAATTAATGAAAATAGAATAAAAGTGTAAT
1636624 TA
1 TA
1636626 ATTGGACAAT
Statistics
Matches: 142, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 142 1.00
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.34
Consensus pattern (35 bp):
TAGTTTAATTAATGAAAATAGAATAAAAGTGTAAT
Found at i:1637432 original size:14 final size:14
Alignment explanation
Indices: 1637413--1637443 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1637403 ATTTTTAACA
1637413 AAAAAAATTATTTT
1 AAAAAAATTATTTT
1637427 AAAAAAATTATTTT
1 AAAAAAATTATTTT
1637441 AAA
1 AAA
1637444 CATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AAAAAAATTATTTT
Found at i:1646377 original size:13 final size:13
Alignment explanation
Indices: 1646359--1646383 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1646349 TTTAATTATC
1646359 CACAATAAAATGT
1 CACAATAAAATGT
1646372 CACAATAAAATG
1 CACAATAAAATG
1646384 ATATCATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.16, G:0.08, T:0.20
Consensus pattern (13 bp):
CACAATAAAATGT
Found at i:1651821 original size:29 final size:29
Alignment explanation
Indices: 1651784--1651848 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
1651774 TGAGATATGC
*
1651784 GGCCCTAGTTGTAAAGATTAAA-AGAGTGG
1 GGCCTTAGTTGTAAAGATTAAAGA-AGTGG
*
1651813 GGCCTTAGTTGTACAGATTAAAGAAGTGG
1 GGCCTTAGTTGTAAAGATTAAAGAAGTGG
*
1651842 GGTCTTA
1 GGCCTTA
1651849 ACTTAGGTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 31 0.97
30 1 0.03
ACGTcount: A:0.31, C:0.11, G:0.31, T:0.28
Consensus pattern (29 bp):
GGCCTTAGTTGTAAAGATTAAAGAAGTGG
Done.