Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008526.1 Hibiscus syriacus cultivar Beakdansim tig00111398_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: 3043201
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 12
Found at i:2415402 original size:25 final size:25
Alignment explanation
Indices: 2415368--2415425 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
2415358 CGTGTAGCAC
2415368 AAGGCAGCTCCAATGGTGCTCTTCA
1 AAGGCAGCTCCAATGGTGCTCTTCA
2415393 AAGGCAGCTCCAATGGTGCTCTTCA
1 AAGGCAGCTCCAATGGTGCTCTTCA
*
2415418 GAGGCAGC
1 AAGGCAGC
2415426 GAATTCTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.24, C:0.28, G:0.28, T:0.21
Consensus pattern (25 bp):
AAGGCAGCTCCAATGGTGCTCTTCA
Found at i:2424991 original size:19 final size:19
Alignment explanation
Indices: 2424967--2425009 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
2424957 ATTAAAGTTT
2424967 TTCTCCCTTCATCACATTC
1 TTCTCCCTTCATCACATTC
2424986 TTCTCCCTTCATCACATTC
1 TTCTCCCTTCATCACATTC
2425005 TTCTC
1 TTCTC
2425010 TATATTTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.14, C:0.42, G:0.00, T:0.44
Consensus pattern (19 bp):
TTCTCCCTTCATCACATTC
Found at i:2425667 original size:2 final size:2
Alignment explanation
Indices: 2425660--2425694 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2425650 CATTAAAAGC
2425660 AT AT AT AT 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 AT AT AT AT A
2425695 AATACTATGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2426176 original size:50 final size:50
Alignment explanation
Indices: 2426069--2426177 Score: 130
Period size: 50 Copynumber: 2.2 Consensus size: 50
2426059 ATGTGAACAT
* * **
2426069 GATGAATTTCATAAAATATATTTTTTTATCAGAATTCATCACGTGGACTT
1 GATGAATTTCATAAAATATATTTTTTTATCAGAACTCATCACGTGCACAC
* ** *
2426119 GACGAATTTCATAAAATATA-TTTTTTATTTTGAACTCATCAGGTGCACAC
1 GATGAATTTCATAAAATATATTTTTTTA-TCAGAACTCATCACGTGCACAC
2426169 GATGAATTT
1 GATGAATTT
2426178 TAACAAAAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
49 7 0.14
50 42 0.86
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (50 bp):
GATGAATTTCATAAAATATATTTTTTTATCAGAACTCATCACGTGCACAC
Found at i:2426616 original size:17 final size:17
Alignment explanation
Indices: 2426594--2426629 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2426584 CCGTGTCCCG
2426594 ACCCGGATGTTACGGGT
1 ACCCGGATGTTACGGGT
* *
2426611 ACCCGGATTTTGCGGGT
1 ACCCGGATGTTACGGGT
2426628 AC
1 AC
2426630 TCGGGAATCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.17, C:0.25, G:0.33, T:0.25
Consensus pattern (17 bp):
ACCCGGATGTTACGGGT
Found at i:2426842 original size:10 final size:9
Alignment explanation
Indices: 2426827--2426851 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2426817 ATAATTATAT
2426827 ATAAAAAAA
1 ATAAAAAAA
2426836 ATAAAAAAA
1 ATAAAAAAA
2426845 ATAAAAA
1 ATAAAAA
2426852 CTAACCGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
ATAAAAAAA
Found at i:2429510 original size:2 final size:2
Alignment explanation
Indices: 2429503--2429538 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2429493 ACTCAGCTTT
2429503 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
2429539 CTTTTAGGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2432487 original size:20 final size:20
Alignment explanation
Indices: 2432462--2432499 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2432452 GTTAGTTCAC
*
2432462 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCAGTG
2432482 GGAATAAAAGATTACCAG
1 GGAATAAAAGATTACCAG
2432500 AGAATAGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.11, G:0.24, T:0.21
Consensus pattern (20 bp):
GGAATAAAAGATTACCAGTG
Found at i:2432504 original size:18 final size:19
Alignment explanation
Indices: 2432463--2432505 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
2432453 TTAGTTCACG
* *
2432463 GAATATAAGATTACCAGTGG
1 GAATAAAAGATTACCAG-GA
2432483 GAATAAAAGATTACCA-GA
1 GAATAAAAGATTACCAGGA
2432501 GAATA
1 GAATA
2432506 GGATTACTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
20 15 0.71
ACGTcount: A:0.49, C:0.09, G:0.21, T:0.21
Consensus pattern (19 bp):
GAATAAAAGATTACCAGGA
Found at i:2434374 original size:29 final size:28
Alignment explanation
Indices: 2434326--2434384 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
2434316 TTAAATCTTT
*
2434326 TTTTAAAAAATTTACTTTTATTT-AAAA
1 TTTTAAAAAATTTACATTTATTTGAAAA
*
2434353 TTTTAAAAAATATTAAGATTTATTTGAAAA
1 TTTTAAAAAAT-TT-ACATTTATTTGAAAA
2434383 TT
1 TT
2434385 CCAAAAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 11 0.41
28 2 0.07
29 8 0.30
30 6 0.22
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (28 bp):
TTTTAAAAAATTTACATTTATTTGAAAA
Found at i:2434556 original size:41 final size:41
Alignment explanation
Indices: 2434511--2434687 Score: 160
Period size: 41 Copynumber: 4.1 Consensus size: 41
2434501 GTTTTCTAAT
* *
2434511 TCGCAACGCGA-ACTTCGACTAGCGCAATGCGAATATGTAAA
1 TCGCAACGCGATA-GTCGACTATCGCAATGCGAATATGTAAA
* * *
2434552 TCGCAATGCGATAGTCGACTATCGCAATGCGAACT-TGGACTA
1 TCGCAACGCGATAGTCGACTATCGCAATGCGAA-TATGTA-AA
* *
2434594 TCGCAACGCGAACTTGCGAACTTGGACTATCGCAATGCGAATATGTAAA
1 TCGCAACGCG-A--T----A-GTCGACTATCGCAATGCGAATATGTAAA
* *
2434643 CCGCAATGCGATAGTCGACTATCGCAATGCGAATATGTAAA
1 TCGCAACGCGATAGTCGACTATCGCAATGCGAATATGTAAA
2434684 TCGC
1 TCGC
2434688 GTATTGCATT
Statistics
Matches: 109, Mismatches: 15, Indels: 24
0.74 0.10 0.16
Matches are distributed among these distances:
41 60 0.55
42 13 0.12
43 1 0.01
45 1 0.01
46 1 0.01
48 1 0.01
49 11 0.10
50 21 0.19
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.22
Consensus pattern (41 bp):
TCGCAACGCGATAGTCGACTATCGCAATGCGAATATGTAAA
Found at i:2434609 original size:21 final size:21
Alignment explanation
Indices: 2434511--2434609 Score: 87
Period size: 21 Copynumber: 4.8 Consensus size: 21
2434501 GTTTTCTAAT
* *
2434511 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
* * *
2434532 GCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* *
2434552 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
2434573 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
*
2434594 TCGCAACGCGAACTTG
1 TCGCAATGCGAACTTG
2434610 CGAACTTGGA
Statistics
Matches: 61, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
20 15 0.25
21 46 0.75
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:2434621 original size:29 final size:29
Alignment explanation
Indices: 2434579--2434634 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
2434569 ACTATCGCAA
2434579 TGCGAACTTGGACTATCGCAACGCGAACT
1 TGCGAACTTGGACTATCGCAACGCGAACT
*
2434608 TGCGAACTTGGACTATCGCAATGCGAA
1 TGCGAACTTGGACTATCGCAACGCGAA
2434635 TATGTAAACC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.21
Consensus pattern (29 bp):
TGCGAACTTGGACTATCGCAACGCGAACT
Found at i:2434771 original size:6 final size:6
Alignment explanation
Indices: 2434760--2434784 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2434750 GACACGTATT
2434760 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
2434785 GACGAGACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2435410 original size:21 final size:21
Alignment explanation
Indices: 2435385--2435455 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
2435375 ATTTTGGACT
2435385 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
2435406 ATCGCAACGCAAACTTCGACT--
1 ATCGCAACG--AACTTGGAATAA
*
2435427 ATCGTAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
2435448 ATCGCAAC
1 ATCGCAAC
2435456 ACGAACTTCG
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
19 8 0.20
21 24 0.60
23 8 0.20
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:2435440 original size:42 final size:42
Alignment explanation
Indices: 2435381--2435469 Score: 151
Period size: 42 Copynumber: 2.1 Consensus size: 42
2435371 TGCGATTTTG
*
2435381 GACTATCGCAACGAACTTGGAATAAATCGCAACGCAAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACACAAACTTC
* *
2435423 GACTATCGTAACGAACTTGGAATAAATCGCAACACGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACACAAACTTC
2435465 GACTA
1 GACTA
2435470 ATCATTTTGG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACACAAACTTC
Found at i:2435459 original size:23 final size:23
Alignment explanation
Indices: 2435391--2435463 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
2435381 GACTATCGCA
2435391 ACGAACTTGGAATAAATCGCAAC
1 ACGAACTTGGAATAAATCGCAAC
* * * * *
2435414 GCAAACTTCGACT--ATCG-TA-
1 ACGAACTTGGAATAAATCGCAAC
2435433 ACGAACTTGGAATAAATCGCAAC
1 ACGAACTTGGAATAAATCGCAAC
2435456 ACGAACTT
1 ACGAACTT
2435464 CGACTAATCA
Statistics
Matches: 36, Mismatches: 10, Indels: 8
0.67 0.19 0.15
Matches are distributed among these distances:
19 9 0.25
20 1 0.03
21 8 0.22
22 1 0.03
23 17 0.47
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (23 bp):
ACGAACTTGGAATAAATCGCAAC
Found at i:2441215 original size:2 final size:2
Alignment explanation
Indices: 2441208--2441237 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2441198 AATCTACAGG
2441208 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
2441238 ATTACATGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2441986 original size:2 final size:2
Alignment explanation
Indices: 2441979--2442011 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2441969 GTTTAGATGA
2441979 AT AT AT 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 AT AT AT A
2442012 CACTGTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2448599 original size:21 final size:22
Alignment explanation
Indices: 2448569--2448611 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
2448559 TTAGGATAAA
*
2448569 TGGGATTAGGAATAGGATTTGG
1 TGGGATTAGGAAGAGGATTTGG
*
2448591 TGGGA-TAGGAGGAGGATTTGG
1 TGGGATTAGGAAGAGGATTTGG
2448612 AGGAGGGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.26, C:0.00, G:0.47, T:0.28
Consensus pattern (22 bp):
TGGGATTAGGAAGAGGATTTGG
Found at i:2449315 original size:21 final size:21
Alignment explanation
Indices: 2449294--2449371 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
2449284 GAAACCCCAG
* *
2449294 GGGGTATCGATTCCCCTACAG
1 GGGGTATCGATTCCCCTTCAA
* *
2449315 GGGGAATCGGTTCCCCTTCAA
1 GGGGTATCGATTCCCCTTCAA
*
2449336 GGGGTATCGATTTCCCTTCAA
1 GGGGTATCGATTCCCCTTCAA
2449357 GGGGTATCGATTCCC
1 GGGGTATCGATTCCC
2449372 TCTGCACCAA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.27
Consensus pattern (21 bp):
GGGGTATCGATTCCCCTTCAA
Found at i:2457739 original size:2 final size:2
Alignment explanation
Indices: 2457732--2457757 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2457722 AAATAAAAAT
2457732 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
2457758 ATAATTCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2473453 original size:74 final size:75
Alignment explanation
Indices: 2473315--2473463 Score: 246
Period size: 74 Copynumber: 2.0 Consensus size: 75
2473305 TGTGTTAGTA
2473315 CACGTGGTTGAGTGTATAGCTGGCATATGCTGTTAAGAGTTGTTAGTCAAACTGTTAAGGGTTGT
1 CACGTGGTTGAGTGTATAGCTGGCATATGC---TAAGAGTTGTTAGTCAAACTGTTAAGGGTTGT
2473380 TAGGAATTCAATT
63 TAGGAATTCAATT
*
2473393 CACGTGGTTGAGTGTATAGCTGGCATATGC-AAGAGTTGTTAGTCAAATTGTTAAGGGTTGTTAG
1 CACGTGGTTGAGTGTATAGCTGGCATATGCTAAGAGTTGTTAGTCAAACTGTTAAGGGTTGTTAG
*
2473457 GCATTCA
66 GAATTCA
2473464 GTTATGGGTA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
74 39 0.57
78 30 0.43
ACGTcount: A:0.26, C:0.11, G:0.29, T:0.35
Consensus pattern (75 bp):
CACGTGGTTGAGTGTATAGCTGGCATATGCTAAGAGTTGTTAGTCAAACTGTTAAGGGTTGTTAG
GAATTCAATT
Found at i:2474636 original size:7 final size:7
Alignment explanation
Indices: 2474624--2474663 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
2474614 TTATTTATAT
2474624 TAAAATA
1 TAAAATA
2474631 TAAAATA
1 TAAAATA
*
2474638 TAAAACA
1 TAAAATA
2474645 TATAAATA
1 TA-AAATA
2474653 TAAATATA
1 TAAA-ATA
2474661 TAA
1 TAA
2474664 TATCATCTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
7 17 0.59
8 12 0.41
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (7 bp):
TAAAATA
Found at i:2479019 original size:27 final size:27
Alignment explanation
Indices: 2478966--2479031 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 27
2478956 TTAGAGTATT
* *
2478966 AAAATAAGAATAATTCAAAGTTAAATAATT
1 AAAATAA-AA-AA-TCAAAATTAAATAATC
* *
2478996 AAATTAAAAAATCAAAATTTAATAATC
1 AAAATAAAAAATCAAAATTAAATAATC
2479023 AAAATAAAA
1 AAAATAAAA
2479032 TTAAAAATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
27 21 0.68
28 2 0.06
29 2 0.06
30 6 0.19
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.27
Consensus pattern (27 bp):
AAAATAAAAAATCAAAATTAAATAATC
Found at i:2479022 original size:14 final size:14
Alignment explanation
Indices: 2478974--2479032 Score: 57
Period size: 14 Copynumber: 4.2 Consensus size: 14
2478964 TTAAAATAAG
*
2478974 AATAATTCAAAGTTA
1 AATAA-TCAAAATTA
*
2478989 AATAAT-TAAATTA
1 AATAATCAAAATTA
* *
2479002 AAAAATCAAAATTT
1 AATAATCAAAATTA
*
2479016 AATAATCAAAATAA
1 AATAATCAAAATTA
2479030 AAT
1 AAT
2479033 TAAAAATATA
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
13 10 0.29
14 20 0.57
15 5 0.14
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.31
Consensus pattern (14 bp):
AATAATCAAAATTA
Found at i:2481494 original size:23 final size:23
Alignment explanation
Indices: 2481468--2481655 Score: 150
Period size: 23 Copynumber: 8.3 Consensus size: 23
2481458 TTATGAACCA
* *
2481468 TTCTTCGTCTTCCATAAACACGT
1 TTCTTCTTCTTCCATAAACACAT
* *
2481491 TTCTTCTTCCTCCATAAACTCAT
1 TTCTTCTTCTTCCATAAACACAT
*
2481514 TGCTTCTTCTTCCATAAA-ACCACT
1 TTCTTCTTCTTCCATAAACA-CA-T
* * * ***
2481538 TTTTTCTT-ATACATAAACTTGT
1 TTCTTCTTCTTCCATAAACACAT
* *
2481560 TTCTTCTTCTTCCATAAACCCCT
1 TTCTTCTTCTTCCATAAACACAT
* *
2481583 TTATTCTTCTTCCGTAAACACAT
1 TTCTTCTTCTTCCATAAACACAT
**
2481606 TT-TT-TTCTTCCATAAACTTAT
1 TTCTTCTTCTTCCATAAACACAT
* **
2481627 TTCTTTTTCTTCCATAAATTCAT
1 TTCTTCTTCTTCCATAAACACAT
2481650 TTCTTC
1 TTCTTC
2481656 ATGGAGTTAC
Statistics
Matches: 129, Mismatches: 30, Indels: 12
0.75 0.18 0.07
Matches are distributed among these distances:
21 16 0.12
22 12 0.09
23 94 0.73
24 7 0.05
ACGTcount: A:0.22, C:0.28, G:0.03, T:0.47
Consensus pattern (23 bp):
TTCTTCTTCTTCCATAAACACAT
Found at i:2481564 original size:69 final size:67
Alignment explanation
Indices: 2481475--2481655 Score: 202
Period size: 69 Copynumber: 2.7 Consensus size: 67
2481465 CCATTCTTCG
* ** * *
2481475 TCTTCCATAAACACGTTTCTTCTTCCTCCATAAACTCATTGCTTCTTCTTCCATAAA-ACCACTT
1 TCTTACATAAACTTGTTTCTTCTTCTTCCATAAACTCATTTCTTCTTCTTCCATAAACA-CACTT
2481539 TTT
65 TTT
* * * * *
2481542 TCTTATACATAAACTTGTTTCTTCTTCTTCCATAAACCCCTTTATTCTTCTTCCGTAAACACATT
1 TC-T-TACATAAACTTGTTTCTTCTTCTTCCATAAACTCATTTCTTCTTCTTCCATAAACACACT
2481607 TTTT
64 TTTT
* * * *
2481611 TCTTCCATAAACTTATTTCTTTTTCTTCCATAAATTCATTTCTTC
1 TCTTACATAAACTTGTTTCTTCTTCTTCCATAAACTCATTTCTTC
2481656 ATGGAGTTAC
Statistics
Matches: 94, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
67 37 0.39
68 2 0.02
69 54 0.57
70 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.02, T:0.47
Consensus pattern (67 bp):
TCTTACATAAACTTGTTTCTTCTTCTTCCATAAACTCATTTCTTCTTCTTCCATAAACACACTTT
TT
Found at i:2486030 original size:2 final size:2
Alignment explanation
Indices: 2486023--2486059 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2486013 AGATACCATT
2486023 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
2486060 TAATAAGTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2487284 original size:94 final size:94
Alignment explanation
Indices: 2487142--2487327 Score: 372
Period size: 94 Copynumber: 2.0 Consensus size: 94
2487132 ATTTATCAAG
2487142 AAAGGTGTGGTTCCAAATTTGATCATCATCGTTAGGTATATACTACTAGTTTTGTTTTCAACTTT
1 AAAGGTGTGGTTCCAAATTTGATCATCATCGTTAGGTATATACTACTAGTTTTGTTTTCAACTTT
2487207 ATTCCCAAACCTTTTAAGTTGTATAAAAA
66 ATTCCCAAACCTTTTAAGTTGTATAAAAA
2487236 AAAGGTGTGGTTCCAAATTTGATCATCATCGTTAGGTATATACTACTAGTTTTGTTTTCAACTTT
1 AAAGGTGTGGTTCCAAATTTGATCATCATCGTTAGGTATATACTACTAGTTTTGTTTTCAACTTT
2487301 ATTCCCAAACCTTTTAAGTTGTATAAA
66 ATTCCCAAACCTTTTAAGTTGTATAAA
2487328 GATGAAGATT
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 92 1.00
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (94 bp):
AAAGGTGTGGTTCCAAATTTGATCATCATCGTTAGGTATATACTACTAGTTTTGTTTTCAACTTT
ATTCCCAAACCTTTTAAGTTGTATAAAAA
Found at i:2492324 original size:36 final size:36
Alignment explanation
Indices: 2492283--2492385 Score: 188
Period size: 36 Copynumber: 2.9 Consensus size: 36
2492273 AGTTGAGTAT
2492283 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
* *
2492319 TATCAGCTTTGATACATTCGTGTATCAATGTTATCC
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
2492355 TATCAGCTTTGGTACATTCGTGTATCAATGT
1 TATCAGCTTTGGTACATTCGTGTATCAATGT
2492386 CCAGCACCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 64 1.00
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.42
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:2500409 original size:36 final size:36
Alignment explanation
Indices: 2500368--2500470 Score: 188
Period size: 36 Copynumber: 2.9 Consensus size: 36
2500358 AGTTGAGTAT
2500368 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
* *
2500404 TATCAGCTTTGATACATTCGTGTATCAATGTTATCC
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
2500440 TATCAGCTTTGGTACATTCGTGTATCAATGT
1 TATCAGCTTTGGTACATTCGTGTATCAATGT
2500471 CCAGCACCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 64 1.00
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.42
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:2502056 original size:112 final size:112
Alignment explanation
Indices: 2501856--2502058 Score: 352
Period size: 112 Copynumber: 1.8 Consensus size: 112
2501846 TTTCGACCAA
* **
2501856 AAAGGGAAAATTTAGATCTAAGTCCCTGAACTTCTTAGATTTTTGAAACTAACCTAAAAGTTTCA
1 AAAGGGAAAAATTAGAGATAAGTCCCTGAACTTCTTAGATTTTTGAAACTAACCTAAAAGTTTCA
2501921 GAAACTTACAGTTTAGTCCATAAAATTAATTATCTGTATCAACCCAC
66 GAAACTTACAGTTTAGTCCATAAAATTAATTATCTGTATCAACCCAC
* *
2501968 AAAGGGAAAAATTAGAGATAAGTCCCTGAACTTCTTCGATTTTTGAAACTAGCCTAAAAGTTTCA
1 AAAGGGAAAAATTAGAGATAAGTCCCTGAACTTCTTAGATTTTTGAAACTAACCTAAAAGTTTCA
*
2502033 GAAACTTACAGTTTAGTCTATAAAAT
66 GAAACTTACAGTTTAGTCCATAAAAT
2502059 CCATTAATTA
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
112 85 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (112 bp):
AAAGGGAAAAATTAGAGATAAGTCCCTGAACTTCTTAGATTTTTGAAACTAACCTAAAAGTTTCA
GAAACTTACAGTTTAGTCCATAAAATTAATTATCTGTATCAACCCAC
Found at i:2506651 original size:16 final size:18
Alignment explanation
Indices: 2506630--2506665 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2506620 AGGAATATAA
2506630 TTAAATT-A-TAATTTTT
1 TTAAATTAATTAATTTTT
2506646 TTAAATTAATTAATTTTT
1 TTAAATTAATTAATTTTT
2506664 TT
1 TT
2506666 TTAAAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 1 0.06
18 10 0.56
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTAAATTAATTAATTTTT
Found at i:2508745 original size:64 final size:62
Alignment explanation
Indices: 2508674--2508830 Score: 170
Period size: 64 Copynumber: 2.5 Consensus size: 62
2508664 TTCAGTGTGT
* * *
2508674 ATCGATGCACAGGAAGTGCATCGATGCACCCATTAAAAATGGAAACATCGAATGCAATTAGTGC
1 ATCGATGCAAAGG-AGTGCATCGATGCACCCATT-AAAATGAAAACATCGAAGGCAATTAGTGC
* ** * *
2508738 ATCGATGCATAAGGAGTGCATCGATGCACCCCCTTAAAATGAAAACATCGAAGGTGATTTGTGT
1 ATCGATGCA-AAGGAGTGCATCGATGCA-CCCATTAAAATGAAAACATCGAAGGCAATTAGTGC
* **
2508802 ATCGATACATGGGTAGTGCATCGATGCAC
1 ATCGATGCAAAGG-AGTGCATCGATGCAC
2508831 ATGTTAAAGA
Statistics
Matches: 79, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
63 3 0.04
64 68 0.86
65 8 0.10
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.23
Consensus pattern (62 bp):
ATCGATGCAAAGGAGTGCATCGATGCACCCATTAAAATGAAAACATCGAAGGCAATTAGTGC
Found at i:2509676 original size:2 final size:2
Alignment explanation
Indices: 2509669--2509718 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2509659 AATAGAAGTA
2509669 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
2509711 AT AT AT AT
1 AT AT AT AT
2509719 GTTTATAAGT
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:2510903 original size:2 final size:2
Alignment explanation
Indices: 2510896--2510932 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2510886 AATATGTATG
2510896 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
2510933 CGTATACATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2512959 original size:24 final size:24
Alignment explanation
Indices: 2512932--2513047 Score: 153
Period size: 24 Copynumber: 4.8 Consensus size: 24
2512922 TTCGATTTGA
2512932 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
* *
2512956 ATTCTAATATGATA-TCTGACATGG
1 ATTCTGATCTGATACT-TGACATGG
*
2512980 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
*
2513004 ATTCTGATCTGATACTTGACCTGG
1 ATTCTGATCTGATACTTGACATGG
* **
2513028 ATTTTGATAAGATACTTGAC
1 ATTCTGATCTGATACTTGAC
2513048 CTAATTTTTG
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
23 1 0.01
24 79 0.98
25 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.39
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:2513266 original size:2 final size:2
Alignment explanation
Indices: 2513259--2513327 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
2513249 CGGATGGGGG
2513259 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
2513301 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 T
2513328 GTTTTAAAAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2515094 original size:2 final size:2
Alignment explanation
Indices: 2515087--2515111 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2515077 TATTTTCATG
2515087 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
2515112 TGAATGGAAA
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:2515930 original size:11 final size:10
Alignment explanation
Indices: 2515916--2515959 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
2515906 TAAGTTACGT
2515916 ATATATGAAAA
1 ATATAT-AAAA
2515927 ATATATAAAA
1 ATATATAAAA
* *
2515937 ACACGATAAAA
1 ATA-TATAAAA
2515948 ATATATAAAA
1 ATATATAAAA
2515958 AT
1 AT
2515960 TAGCAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
10 14 0.50
11 14 0.50
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.25
Consensus pattern (10 bp):
ATATATAAAA
Found at i:2517552 original size:2 final size:2
Alignment explanation
Indices: 2517545--2517582 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2517535 AATATGGGTA
2517545 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
2517583 GTTAGAATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2528588 original size:110 final size:110
Alignment explanation
Indices: 2528395--2528593 Score: 335
Period size: 110 Copynumber: 1.8 Consensus size: 110
2528385 TGAATTAGGA
* * *
2528395 TGTGGCCTACATGTAGCCAGAAAAACTTTCACATTAAGTTATAACTTCATAACCCCATGTCCTTG
1 TGTGGCCTACACGTAGCCAGAAAAACTTGCACATTAAGTTATAACTTCACAACCCCATGTCCTTG
*
2528460 TATGATTGGCACATCACTTTTGTTTGAATTGGGATGTCATAAGGC
66 TATGATTGACACATCACTTTTGTTTGAATTGGGATGTCATAAGGC
* * *
2528505 TGTGGCCTACACGTAGCCAGCAAAACTTGCACATTAAGTTATAACTTCACAACTCTATGTCCTTG
1 TGTGGCCTACACGTAGCCAGAAAAACTTGCACATTAAGTTATAACTTCACAACCCCATGTCCTTG
2528570 TATGATTGACACATCACTTTTGTT
66 TATGATTGACACATCACTTTTGTT
2528594 CAGGATGAGC
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
110 82 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.34
Consensus pattern (110 bp):
TGTGGCCTACACGTAGCCAGAAAAACTTGCACATTAAGTTATAACTTCACAACCCCATGTCCTTG
TATGATTGACACATCACTTTTGTTTGAATTGGGATGTCATAAGGC
Found at i:2534465 original size:51 final size:51
Alignment explanation
Indices: 2534389--2534489 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 51
2534379 TAAGGAAAGG
*
2534389 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGTTGAAATTCCTTGTAACTA
1 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACTA
*
2534440 ATAGGCTGTAAAGAAATATCGGTTTGAACTGGCTGAAATTCCTTGTAACT
1 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACT
2534490 CTCCCCCTGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.32
Consensus pattern (51 bp):
ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACTA
Found at i:2548367 original size:15 final size:15
Alignment explanation
Indices: 2548342--2548383 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
2548332 AGTTTAGTCG
2548342 TTATGTTTTAATTTAA
1 TTAT-TTTTAATTTAA
*
2548358 TTATTTTTAATTTTA
1 TTATTTTTAATTTAA
2548373 TATATTTTTAA
1 T-TATTTTTAA
2548384 AATTTAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
TTATTTTTAATTTAA
Found at i:2549327 original size:13 final size:14
Alignment explanation
Indices: 2549294--2549320 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2549284 GTTTTTTTTT
2549294 TAATTTTTAAAAAC
1 TAATTTTTAAAAAC
2549308 TAATTTTTAAAAA
1 TAATTTTTAAAAA
2549321 TTATTTTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (14 bp):
TAATTTTTAAAAAC
Found at i:2551153 original size:17 final size:18
Alignment explanation
Indices: 2551131--2551164 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2551121 TTAACGTGAA
2551131 TAAAAAAT-AAAATAATT
1 TAAAAAATAAAAATAATT
2551148 TAAAAAATAAAAATAAT
1 TAAAAAATAAAAATAAT
2551165 ATAATTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
TAAAAAATAAAAATAATT
Found at i:2551172 original size:22 final size:22
Alignment explanation
Indices: 2551133--2551195 Score: 90
Period size: 22 Copynumber: 2.8 Consensus size: 22
2551123 AACGTGAATA
2551133 AAAAATAAAATAATTTAAAAAAT
1 AAAAATAAAATAA-TTAAAAAAT
*
2551156 AAAAATAATATAATTAAAAAAT
1 AAAAATAAAATAATTAAAAAAT
* *
2551178 AAGAATAAAATTATTAAA
1 AAAAATAAAATAATTAAA
2551196 GTAAATCCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 24 0.67
23 12 0.33
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (22 bp):
AAAAATAAAATAATTAAAAAAT
Found at i:2552335 original size:16 final size:15
Alignment explanation
Indices: 2552297--2552335 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
2552287 TTGGTTGATG
*
2552297 TAAGTTTT-CTTCTT
1 TAAGTTTTGTTTCTT
2552311 TAAGTTTTGTTTCTT
1 TAAGTTTTGTTTCTT
2552326 TAATGTTTTG
1 TAA-GTTTTG
2552336 AATAAGTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.36
15 8 0.36
16 6 0.27
ACGTcount: A:0.15, C:0.08, G:0.13, T:0.64
Consensus pattern (15 bp):
TAAGTTTTGTTTCTT
Found at i:2556589 original size:15 final size:15
Alignment explanation
Indices: 2556569--2556598 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2556559 TCCAGATTAC
2556569 AAATATTAAATAATA
1 AAATATTAAATAATA
2556584 AAATATTAAATAATA
1 AAATATTAAATAATA
2556599 CAAGCATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATATTAAATAATA
Found at i:2558428 original size:40 final size:41
Alignment explanation
Indices: 2558325--2558436 Score: 120
Period size: 43 Copynumber: 2.7 Consensus size: 41
2558315 TTGGTTGTTG
**
2558325 GGGATGACACTGCTCATACGTGATGAAGAGTTCGGGTCGTCTAA
1 GGGATGACACTGCTCATACGTGATGAAGAAATCGGGTCG--T-A
* * * * *
2558369 GGG-TGACACGGATCCTACGTGATGAGGAAATCTGGTCG-A
1 GGGATGACACTGCTCATACGTGATGAAGAAATCGGGTCGTA
2558408 GGGATGACACTGCTCATACGTGATGAAGA
1 GGGATGACACTGCTCATACGTGATGAAGA
2558437 GTTCTGGTCA
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
39 4 0.07
40 21 0.38
43 28 0.50
44 3 0.05
ACGTcount: A:0.27, C:0.18, G:0.33, T:0.22
Consensus pattern (41 bp):
GGGATGACACTGCTCATACGTGATGAAGAAATCGGGTCGTA
Found at i:2558521 original size:41 final size:42
Alignment explanation
Indices: 2558464--2558751 Score: 255
Period size: 41 Copynumber: 6.7 Consensus size: 42
2558454 TAAGGTGATA
**
2558464 ACACGGCTAATACGTGATGAAGAGTTCTGGTTATC-AGGTTG
1 ACACGGCTCCTACGTGATGAAGAGTTCTGGTTATCTAGGTTG
2558505 ACACGGCTCCTACGTGATGAAGAGTTCTGGTTATC-AGGTTG
1 ACACGGCTCCTACGTGATGAAGAGTTCTGGTTATCTAGGTTG
* *
2558546 ACACGGCTCCTACGTGATGAAGAGTTCTGGTCATCTATAGGATGATA
1 ACACGGCTCCTACGTGATGAAGAGTTCTGGTTATC--TAGG-T--TG
* * * ** *
2558593 ATACGGTTCCTACGTGATGAAGAGTTCTAGCCATCTAAAGGTGATA
1 ACACGGCTCCTACGTGATGAAGAGTTCTGGTTATCT--AGGT--TG
* * *
2558639 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGTTG
1 ACACGGCTCCTACGTGATGAAGA-GTTCTGGTTATCTA-GGTTG
* * * * *
2558682 ACACGGCTCATACGTGATGAGGAGATCTGG---TCTGGGGATG
1 ACACGGCTCCTACGTGATGAAGAGTTCTGGTTATCT-AGGTTG
*
2558722 ACACGGCTCATACGTGATGAAGAGTTCTGG
1 ACACGGCTCCTACGTGATGAAGAGTTCTGG
2558752 CCATCTAAAG
Statistics
Matches: 213, Mismatches: 22, Indels: 25
0.82 0.08 0.10
Matches are distributed among these distances:
40 35 0.16
41 73 0.34
42 1 0.00
43 26 0.12
44 4 0.02
45 5 0.02
46 33 0.15
47 36 0.17
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (42 bp):
ACACGGCTCCTACGTGATGAAGAGTTCTGGTTATCTAGGTTG
Found at i:2558530 original size:91 final size:90
Alignment explanation
Indices: 2558329--2558713 Score: 295
Period size: 91 Copynumber: 4.4 Consensus size: 90
2558319 TTGTTGGGGA
* * * * *
2558329 TGACACTGCTCATACGTGATGAAGAGTTCGGGTCGTC---TAAGG-G-TGACACGGATCCTACGT
1 TGACACGGCTCATACGTGATGAAGAGTTCTGGTCATCTTATAAGGTGATAACACGGCTCCTACGT
* ** * *
2558389 GATGAGGAAATCTGG---TCGAGGGA
66 GATGAAGAGTTCTGGTTATCTA-GGT
* **
2558412 TGACACTGCTCATACGTGATGAAGAGTTCTGGTCATCTTTAGTAAGGTGATAACACGGCTAATAC
1 TGACACGGCTCATACGTGATGAAGAGTTCTGGTCATC-TTA-TAAGGTGATAACACGGCTCCTAC
2558477 GTGATGAAGAGTTCTGGTTATC-AGGT
64 GTGATGAAGAGTTCTGGTTATCTAGGT
* * *
2558503 TGACACGGCTCCTACGTGATGAAGAGTTCTGG-----TTATCAGGT--TGACACGGCTCCTACGT
1 TGACACGGCTCATACGTGATGAAGAGTTCTGGTCATCTTATAAGGTGATAACACGGCTCCTACGT
*
2558561 GATGAAGAGTTCTGGTCATCTATAGGAT
66 GATGAAGAGTTCTGGTTATC--TAGG-T
* * * * * * *
2558589 GATAATACGGTTCCTACGTGATGAAGAGTTCTAGCCATC-TA-AAGGTGATAACACGGTTCCTAC
1 --TGACACGGCTCATACGTGATGAAGAGTTCTGGTCATCTTATAAGGTGATAACACGGCTCCTAC
* *
2558652 GTGATGAGGACG-GCTGGTTATCTATGGT
64 GTGATGAAGA-GTTCTGGTTATCTA-GGT
* *
2558680 TGACACGGCTCATACGTGATGAGGAGATCTGGTC
1 TGACACGGCTCATACGTGATGAAGAGTTCTGGTC
2558714 TGGGGATGAC
Statistics
Matches: 242, Mismatches: 35, Indels: 44
0.75 0.11 0.14
Matches are distributed among these distances:
82 33 0.14
83 35 0.14
84 5 0.02
85 6 0.02
86 1 0.00
88 33 0.14
89 27 0.11
90 25 0.10
91 39 0.16
92 5 0.02
93 32 0.13
94 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (90 bp):
TGACACGGCTCATACGTGATGAAGAGTTCTGGTCATCTTATAAGGTGATAACACGGCTCCTACGT
GATGAAGAGTTCTGGTTATCTAGGT
Found at i:2558628 original size:47 final size:46
Alignment explanation
Indices: 2558424--2558787 Score: 201
Period size: 41 Copynumber: 8.2 Consensus size: 46
2558414 ACACTGCTCA
* * * **
2558424 TACGTGATGAAGAGTTCTGGTCATCTTTAGTAAGGTGATAACACGGCTAA
1 TACGTGATGAAGAGTTCTAGCCATC--TA--AAGGTGATAACACGGTTCC
* ** * *
2558474 TACGTGATGAAGAGTTCTGGTTATC---AGGT--TGACACGGCTCC
1 TACGTGATGAAGAGTTCTAGCCATCTAAAGGTGATAACACGGTTCC
* ** * *
2558515 TACGTGATGAAGAGTTCTGGTTATC---AGGT--TGACACGGCTCC
1 TACGTGATGAAGAGTTCTAGCCATCTAAAGGTGATAACACGGTTCC
* * * *
2558556 TACGTGATGAAGAGTTCTGGTCATCTATAGGATGATAATACGGTTCC
1 TACGTGATGAAGAGTTCTAGCCATCTAAAGG-TGATAACACGGTTCC
2558603 TACGTGATGAAGAGTTCTAGCCATCTAAAGGTGATAACACGGTTCC
1 TACGTGATGAAGAGTTCTAGCCATCTAAAGGTGATAACACGGTTCC
* * * ** * * * *
2558649 TACGTGATGAGGACG-GCTGGTTATCT-ATGGT--TGACACGGCTCA
1 TACGTGATGAAGA-GTTCTAGCCATCTAAAGGTGATAACACGGTTCC
* * * * * * *
2558692 TACGTGATGAGGAGATCT-G--GTCT---GGGGATGACACGGCTCA
1 TACGTGATGAAGAGTTCTAGCCATCTAAAGGTGATAACACGGTTCC
* *
2558732 TACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACATGGTTCC
1 TACGTGATGAAGAGTTCTAGCCATCTAAAGGTGATAACACGGTTCC
2558778 TACGTGATGA
1 TACGTGATGA
2558788 GGACGGCTGG
Statistics
Matches: 266, Mismatches: 32, Indels: 36
0.80 0.10 0.11
Matches are distributed among these distances:
38 2 0.01
40 31 0.12
41 75 0.28
42 2 0.01
43 31 0.12
44 3 0.01
45 5 0.02
46 55 0.21
47 38 0.14
50 24 0.09
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (46 bp):
TACGTGATGAAGAGTTCTAGCCATCTAAAGGTGATAACACGGTTCC
Found at i:2558671 original size:175 final size:177
Alignment explanation
Indices: 2558424--2558787 Score: 477
Period size: 175 Copynumber: 2.1 Consensus size: 177
2558414 ACACTGCTCA
* *
2558424 TACGTGATGAAGAGTTCTGGTCATCTTTAGTAAGGTGATAACACGGCTAATACGTGATGAAGAGT
1 TACGTGATGAAGAGTTCTAGCCATC-TTAG-AAGGTGATAACACGGCTAATACGTGATGAAGAGT
* * * *
2558489 TCTGGTTATC-A-GGTTGACACGGCTCCTACGTGATGAAGAGTTCTGGTTATCAGGTTGACACGG
64 GCTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGG-TATCAGGATGACACGG
* * * *
2558552 CTCCTACGTGATGAAGAGTTCTGGTCATCTATAGGATGATAATACGGTTCC
128 CTCATACGTGATGAAGAGTTCTGGCCATCTAAAGG-TGATAACACGGTTCC
* ** *
2558603 TACGTGATGAAGAGTTCTAGCCATC-TA-AAGGTGATAACACGGTTCCTACGTGATGAGGACG-G
1 TACGTGATGAAGAGTTCTAGCCATCTTAGAAGGTGATAACACGGCTAATACGTGATGAAGA-GTG
* * **
2558665 CTGGTTATCTATGGTTGACACGGCTCATACGTGATGAGGAGATCTGGTCTGGGGATGACACGGCT
65 CTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTATCAGGATGACACGGCT
*
2558730 CATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACATGGTTCC
130 CATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCC
2558778 TACGTGATGA
1 TACGTGATGA
2558788 GGACGGCTGG
Statistics
Matches: 163, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
175 60 0.37
176 46 0.28
177 34 0.21
179 23 0.14
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (177 bp):
TACGTGATGAAGAGTTCTAGCCATCTTAGAAGGTGATAACACGGCTAATACGTGATGAAGAGTGC
TGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTATCAGGATGACACGGCTC
ATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCC
Found at i:2558744 original size:129 final size:132
Alignment explanation
Indices: 2558326--2558803 Score: 432
Period size: 129 Copynumber: 3.7 Consensus size: 132
2558316 TGGTTGTTGG
* * * * * * *
2558326 GGATGACACTGCTCATACGTGATGAAGAGTTCGGGTCGTCT-AAGG-G-TGACACGGATCCTACG
1 GGATAACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACG
*** * * * *
2558388 TGATGAGGAAATCTGG---TCGAGGGATGACACTGCTCATACGTGATGAAGAGTTCTGGTCATCT
66 TGATGAGGACGGCTGGTTATCTA-GGTTGACACGGCTCATACGTGATGAAGAGATCTGG--ATC-
* *
2558450 TTAGTAA
127 ATAG-GA
* ** * *
2558457 GGTGATAACACGGCTAATACGTGATGAAGAGTTCTGGTTATC---AGGT--TGACACGGCTCCTA
1 -G-GATAACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTA
* * * *
2558517 CGTGATGAAGA-GTTCTGGTTATC-AGGTTGACACGGCTCCTACGTGATGAAGAGTTCTGGTCAT
64 CGTGATGAGGACG-GCTGGTTATCTAGGTTGACACGGCTCATACGTGATGAAGAGATCTGG--AT
2558580 CTATAGGA
126 C-ATAGGA
* * * * *
2558588 TGATAATACGGTTCCTACGTGATGAAGAGTTCTAGCCATCTAAAGGTGATAACACGGTTCCTACG
1 GGATAACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACG
*
2558653 TGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGTGATGAGGAGATCTGG-TC-T-
66 TGATGAGGACGGCTGGTTATCTA-GGTTGACACGGCTCATACGTGATGAAGAGATCTGGATCATA
2558715 GG-
130 GGA
* *
2558717 GGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACATGGTTCCTACG
1 GGATAACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACG
2558782 TGATGAGGACGGCTGGTTATCT
66 TGATGAGGACGGCTGGTTATCT
2558804 CTAGGATAAT
Statistics
Matches: 296, Mismatches: 36, Indels: 31
0.82 0.10 0.09
Matches are distributed among these distances:
129 112 0.38
130 2 0.01
131 33 0.11
132 46 0.16
133 36 0.12
134 33 0.11
135 2 0.01
136 32 0.11
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (132 bp):
GGATAACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACG
TGATGAGGACGGCTGGTTATCTAGGTTGACACGGCTCATACGTGATGAAGAGATCTGGATCATAG
GA
Found at i:2559184 original size:35 final size:36
Alignment explanation
Indices: 2559143--2559217 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 36
2559133 ACGAAATTCA
* **
2559143 TTTCAAGGTAAAC-GATCTCAAAGAT-GTTTATTTTG
1 TTTCAAGGGAAACAGAT-TCAAAGATGGTAAATTTTG
2559178 TTTCAAGGGAAACAGATTCAAAGATGGTAAATTTTG
1 TTTCAAGGGAAACAGATTCAAAGATGGTAAATTTTG
2559214 TTTC
1 TTTC
2559218 CAAAGAAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 20 0.57
36 15 0.43
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (36 bp):
TTTCAAGGGAAACAGATTCAAAGATGGTAAATTTTG
Found at i:2559677 original size:63 final size:64
Alignment explanation
Indices: 2559371--2559730 Score: 209
Period size: 64 Copynumber: 5.6 Consensus size: 64
2559361 GTATCTTAGT
* * *
2559371 GAGACAAAATTTTGTTTTC-AAAGAAACAGACTC--AGATTTTTCTTCAAAAGAAACTGT-TTTA
1 GAGACAAAATTTTG-TTTCAAAAGAAACAAACTCAAAGATTTTT-TTCAAAAGAAATTGTCTTCA
2559432 A
64 A
* * ** * * * * *
2559433 GGGATAAAACCTTGTTTCCAGAGAAACAAACTCAAAGATGATCTTATTTTAAGAGAAAATGT-TT
1 GAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT--T-TT-TTTCAAAAGAAATTGTCTT
2559497 CAA
62 CAA
* * ** * * ** * * **
2559500 GAGACAAAA-TTCGTTTGAAGGGAAAC-GACTCAAAGATGTCATTGAAAGGAAACGGTC-TCATG
1 GAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTTTCAAAAGAAATTGTCTTCA--
*
2559562 C
64 A
* * * * * * *
2559563 GAGACAAAA-TTAGTTTTAATAGAAACAATCTCAAAGGTGGGTATTTTCAAAAGAAGTTGTC-TC
1 GAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT---TTTTTTCAAAAGAAATTGTCTTC
*
2559626 GA
63 AA
* *
2559628 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTCAAAAGAAATTGTCTTTAA
1 GAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTTTCAAAAGAAATTGTCTTCAA
* **
2559692 GAGATAAAATTTTGTTTCAAAAGAAACTGACTCAAAGAT
1 GAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT
2559731 GGATCTCATC
Statistics
Matches: 223, Mismatches: 59, Indels: 30
0.71 0.19 0.10
Matches are distributed among these distances:
61 17 0.08
62 23 0.10
63 40 0.18
64 49 0.22
65 19 0.09
66 36 0.16
67 38 0.17
68 1 0.00
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.29
Consensus pattern (64 bp):
GAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTTTCAAAAGAAATTGTCTTCAA
Found at i:2559726 original size:130 final size:128
Alignment explanation
Indices: 2559371--2559731 Score: 304
Period size: 129 Copynumber: 2.8 Consensus size: 128
2559361 GTATCTTAGT
2559371 GAGACAAAATTTTGTTTTCAAA-GAAACAGACTC--AGATTTTTCTTCAAAAGAAACTGT-TTTA
1 GAGACAAAATTTTG-TTTCAAAGGAAACAGACTCAAAGATTTTT-TTCAAAAGAAACTGTCTTTA
* * * * * * *
2559432 AGGGATAAAACCTTGTTTCCAGAGAAACAAACTCAAAGATGATCTTATTTTAAGAGAAAATGTTT
64 AGAGATAAAA-TTTGTTTCAAAAGAAAC-AACTCAAAGATGA-CGTATTTTAAAAGAAAATGTCT
2559497 CAA
126 CAA
* * * * ** * * * * **
2559500 GAGACAAAA-TTCGTTTGAAGGGAAAC-GACTCAAAGATGTCATTGAAAGGAAACGGTCTCATGC
1 GAGACAAAATTTTGTTTCAAAGGAAACAGACTCAAAGATTTTTTTCAAAAGAAACTGTCT-TTAA
* * * * * * ** *
2559563 GAGACAAAATTAGTTTTAATAGAAACAATCTCAAAGGTG-GGTATTTTCAAAAGAAGTTGTCTCG
65 GAGATAAAATTTGTTTCAAAAGAAACAA-CTCAAAGATGACGTATTTT-AAAAGAAAATGTCTCA
2559627 A
128 A
* *
2559628 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTCAAAAGAAATTGTCTTTAAG
1 GAGACAAAATTTTGTTTCAAAGGAAACAGACTCAAAGATTTTTTTCAAAAGAAACTGTCTTTAAG
*
2559693 AGATAAAATTTTGTTTCAAAAGAAACTGACTCAAAGATG
66 AGATAAAA-TTTGTTTCAAAAGAAAC-AACTCAAAGATG
2559732 GATCTCATCT
Statistics
Matches: 174, Mismatches: 47, Indels: 21
0.72 0.19 0.09
Matches are distributed among these distances:
127 16 0.09
128 43 0.25
129 59 0.34
130 55 0.32
131 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.29
Consensus pattern (128 bp):
GAGACAAAATTTTGTTTCAAAGGAAACAGACTCAAAGATTTTTTTCAAAAGAAACTGTCTTTAAG
AGATAAAATTTGTTTCAAAAGAAACAACTCAAAGATGACGTATTTTAAAAGAAAATGTCTCAA
Found at i:2559999 original size:66 final size:66
Alignment explanation
Indices: 2559911--2560126 Score: 276
Period size: 67 Copynumber: 3.3 Consensus size: 66
2559901 AAAGATTTAC
** * * * * *
2559911 TTCAAAAGAAACGGTCTCAAGAGATACAAAATTCAT-TTT-AAGAGAAACAGATTCAAAGATTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATT-TTGTTTCAA-AGAAACAAACTCAAAGATTTT
2559974 TGT
64 TGT
*
2559977 TTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTC-AAAGAAACAAACTCAAAGATTTTT
2560042 GT
65 GT
*
2560044 TTCAAAAGAAACTATCTTAAGAGAGAAAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTT-CAAAGAAACAAACTCAAAGATTTTT
2560109 -T
65 GT
* *
2560110 TTTAAAAGAAACAATCT
1 TTCAAAAGAAACTATCT
2560127 CAAAGATTTT
Statistics
Matches: 134, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
65 1 0.01
66 47 0.35
67 83 0.62
68 3 0.02
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.30
Consensus pattern (66 bp):
TTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCAAAGAAACAAACTCAAAGATTTTTG
T
Found at i:2560020 original size:37 final size:36
Alignment explanation
Indices: 2559971--2560092 Score: 130
Period size: 37 Copynumber: 3.5 Consensus size: 36
2559961 ATTCAAAGAT
*
2559971 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
1 TTTTGTTTCAAAAGAAACTATCTTAAGAGAGA-AAAA
* * * *
2560008 TTTTGTTTCAAAAGAAACAAAC-TCA-A-AG---AT
1 TTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAA
2560038 TTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAAA
1 TTTTGTTTCAAAAGAAACTATCTTAAGAGAG-AAAAA
*
2560075 TTTTGTTTCCAAAGAAAC
1 TTTTGTTTCAAAAGAAAC
2560093 AAACTCAAAG
Statistics
Matches: 68, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
30 21 0.31
31 2 0.03
32 1 0.01
33 2 0.03
34 2 0.03
35 1 0.01
36 2 0.03
37 37 0.54
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (36 bp):
TTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAA
Found at i:2560047 original size:67 final size:67
Alignment explanation
Indices: 2559953--2560126 Score: 278
Period size: 67 Copynumber: 2.6 Consensus size: 67
2559943 TCATTTTAAG
* * * *
2559953 AGAAACAGATTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCA
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAAATTTTGTTTCA
2560018 AA
66 AA
*
2560020 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAAATTTTGTTTCC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAAATTTTGTTTCA
2560085 AA
66 AA
* *
2560087 AGAAACAAACTCAAAGATTTTT-TTTTAAAAGAAACAATCT
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCT
2560127 CAAAGATTTT
Statistics
Matches: 100, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
66 16 0.16
67 84 0.84
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.31
Consensus pattern (67 bp):
AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAAATTTTGTTTCA
AA
Found at i:2560065 original size:29 final size:30
Alignment explanation
Indices: 2560008--2560137 Score: 127
Period size: 29 Copynumber: 4.1 Consensus size: 30
2559998 AGAGACAAAA
2560008 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
* * * *
2560038 TTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAAA
1 TTTTGTTTCAAAAGAAACAAAC-TCA-A-AG----AT
*
2560075 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
* *
2560105 TTTT-TTTTAAAAGAAACAATCTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
2560134 TTTT
1 TTTT
2560138 TTCACAAAAT
Statistics
Matches: 81, Mismatches: 12, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
29 26 0.32
30 25 0.31
31 2 0.02
32 1 0.01
33 2 0.02
34 2 0.02
35 1 0.01
36 2 0.02
37 20 0.25
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.34
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAACAAACTCAAAGAT
Found at i:2560200 original size:52 final size:53
Alignment explanation
Indices: 2560125--2560228 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 53
2560115 AAGAAACAAT
2560125 CTCAAAGATTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
1 CTCAAAGA-TTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
*
2560179 CTCAAAGA-TTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
2560229 AAATAAATAG
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
52 41 0.84
54 8 0.16
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (53 bp):
CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
Found at i:2560253 original size:26 final size:25
Alignment explanation
Indices: 2560224--2560345 Score: 86
Period size: 29 Copynumber: 4.5 Consensus size: 25
2560214 CAAAACTTTG
*
2560224 TTTCAAAATAAATAGACTCAAAGATT
1 TTTCAAAAGAAA-AGACTCAAAGATT
*
2560250 TTTCAAAAGAAACGACTCAAAGATATT
1 TTTCAAAAGAAAAGACTCAAAG--ATT
*
2560277 TATTCAAAAGGAACAA-ACTCCAAGATTTT
1 T-TTCAAAA-GAA-AAGACTCAAAGA--TT
2560306 TATTCAAAAGGAACAA-ACTCAAAGATTT
1 T-TTCAAAA-GAA-AAGACTCAAAGA-TT
*
2560334 TTTCAAGAGAAA
1 TTTCAAAAGAAA
2560346 CTGTCTCAAG
Statistics
Matches: 83, Mismatches: 6, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
25 10 0.12
26 14 0.17
27 11 0.13
28 11 0.13
29 36 0.43
30 1 0.01
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.27
Consensus pattern (25 bp):
TTTCAAAAGAAAAGACTCAAAGATT
Found at i:2560301 original size:29 final size:28
Alignment explanation
Indices: 2560239--2560339 Score: 120
Period size: 29 Copynumber: 3.7 Consensus size: 28
2560229 AAATAAATAG
* *
2560239 ACTCAAAG--ATTTTTCAAAAGAAAC-G
1 ACTCAAAGATATTTTTCAAAAGGAACAA
2560264 ACTCAAAGATATTTATTCAAAAGGAACAA
1 ACTCAAAGATATTT-TTCAAAAGGAACAA
* *
2560293 ACTCCAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGATATTT-TTCAAAAGGAACAA
2560322 ACTCAAAGAT-TTTTTCAA
1 ACTCAAAGATATTTTTCAA
2560340 GAGAAACTGT
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
25 8 0.12
27 9 0.13
28 14 0.21
29 36 0.54
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.28
Consensus pattern (28 bp):
ACTCAAAGATATTTTTCAAAAGGAACAA
Found at i:2560695 original size:36 final size:36
Alignment explanation
Indices: 2560584--2560702 Score: 102
Period size: 36 Copynumber: 3.4 Consensus size: 36
2560574 AGAAAATGAT
** * *
2560584 GTCTCAAGCGAGATGAAATTTG-CTTTA-AGATATA-
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGAGA-AAAC
** **
2560618 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAAC
*
2560654 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAAC
*
2560689 GATCTCAAGTGAGA
1 G-TCTCAAGCGAGA
2560703 TCAACTTTGT
Statistics
Matches: 68, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
34 18 0.26
35 12 0.18
36 38 0.56
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (36 bp):
GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAAC
Found at i:2560714 original size:36 final size:36
Alignment explanation
Indices: 2560618--2560702 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 36
2560608 TTAAGATATA
* **
2560618 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
* *
2560654 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
2560689 GATCTCAAGTGAGA
1 G-TCTCAAGTGAGA
2560703 TCAACTTTGT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
35 7 0.17
36 35 0.83
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (36 bp):
GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
Found at i:2560833 original size:105 final size:104
Alignment explanation
Indices: 2560654--2560893 Score: 310
Period size: 105 Copynumber: 2.3 Consensus size: 104
2560644 TAGAGAAATT
* *
2560654 GTCTCAAGCGAGAC-AAAGTTTGTTTT-TGAG-AAAACGATCTCAAGTGAGATCAACTTTGTTTA
1 GTCTCAAGCGAGACGAAA-TTTGTTTTAAGAGAAAAACAATCTCAAGTGAGATCAACTTTGTTTA
* *
2560716 ATGTGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAG
65 ATGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
* * *
2560756 GTCTCAAGCGAGACGAAATTTGTTTTAAAAGAAACAACAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACGAAATTTGTTTTAAGAGAAA-AACAATCTCAA-GTGAGATCAACTTTG-TT
* * *
2560820 TAA-GTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
63 TAATGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
*
2560861 GTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAA
1 GTCTCAAGCGAGACGAAATTTGTTTTAAGAGAA
2560894 TTTGTCTCAA
Statistics
Matches: 120, Mismatches: 12, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
102 22 0.18
103 5 0.04
104 4 0.03
105 84 0.70
106 5 0.04
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.30
Consensus pattern (104 bp):
GTCTCAAGCGAGACGAAATTTGTTTTAAGAGAAAAACAATCTCAAGTGAGATCAACTTTGTTTAA
TGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:2560900 original size:36 final size:36
Alignment explanation
Indices: 2560860--2560996 Score: 170
Period size: 36 Copynumber: 3.8 Consensus size: 36
2560850 AAAGGAAAAA
* * *
2560860 TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAATT
1 TGTCTCAAGCGAGACAAAATTTGTTTTAAGAGAAAT
* * **
2560896 TGTCTCAAACGAGACAAAATTTGTTTTTAGA-AAGC
1 TGTCTCAAGCGAGACAAAATTTGTTTTAAGAGAAAT
*
2560931 TGTCTCAAGCGAGACAAAATTTGCTTTGAA-AGAAAT
1 TGTCTCAAGCGAGACAAAATTTG-TTTTAAGAGAAAT
2560967 TGTCTCAAGCGAGACAAAAATTTGTTTTAA
1 TGTCTCAAGCGAGAC-AAAATTTGTTTTAA
2560997 AATTCTCAAA
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
35 25 0.29
36 53 0.62
37 8 0.09
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTAAGAGAAAT
Found at i:2560970 original size:71 final size:72
Alignment explanation
Indices: 2560860--2560994 Score: 202
Period size: 71 Copynumber: 1.9 Consensus size: 72
2560850 AAAGGAAAAA
* * * *
2560860 TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAATTTGTCTCAAACGAGAC-AAAATTTGTTTTT
1 TGTCTCAAGCGAGACAAAATTTGTTTGAAGAGAAATTGTCTCAAACGAGACAAAAATTTGTTTTT
2560924 AGAAAGC
66 AGAAAGC
*
2560931 TGTCTCAAGCGAGACAAAATTTGCTTTGAA-AGAAATTGTCTCAAGCGAGACAAAAATTTGTTTT
1 TGTCTCAAGCGAGACAAAATTTG-TTTGAAGAGAAATTGTCTCAAACGAGACAAAAATTTGTTTT
2560995 AAAATTCTCA
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
71 40 0.70
72 17 0.30
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (72 bp):
TGTCTCAAGCGAGACAAAATTTGTTTGAAGAGAAATTGTCTCAAACGAGACAAAAATTTGTTTTT
AGAAAGC
Found at i:2561374 original size:16 final size:16
Alignment explanation
Indices: 2561353--2561428 Score: 60
Period size: 16 Copynumber: 5.2 Consensus size: 16
2561343 TGTAACATGC
2561353 ATGTATGTGTTGATGT
1 ATGTATGTGTTGATGT
*
2561369 ATGTA--T-AT-ATGT
1 ATGTATGTGTTGATGT
*
2561381 ATGTATGAGTTGATGT
1 ATGTATGTGTTGATGT
*
2561397 ATGTA--T-AT-ATGT
1 ATGTATGTGTTGATGT
*
2561409 ATGTATGAGTTGATGT
1 ATGTATGTGTTGATGT
2561425 ATGT
1 ATGT
2561429 TTCTCAATCT
Statistics
Matches: 45, Mismatches: 7, Indels: 16
0.66 0.10 0.24
Matches are distributed among these distances:
12 18 0.40
13 2 0.04
14 1 0.02
15 2 0.04
16 22 0.49
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.47
Consensus pattern (16 bp):
ATGTATGTGTTGATGT
Found at i:2561385 original size:28 final size:28
Alignment explanation
Indices: 2561353--2561428 Score: 143
Period size: 28 Copynumber: 2.7 Consensus size: 28
2561343 TGTAACATGC
*
2561353 ATGTATGTGTTGATGTATGTATATATGT
1 ATGTATGAGTTGATGTATGTATATATGT
2561381 ATGTATGAGTTGATGTATGTATATATGT
1 ATGTATGAGTTGATGTATGTATATATGT
2561409 ATGTATGAGTTGATGTATGT
1 ATGTATGAGTTGATGTATGT
2561429 TTCTCAATCT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.47
Consensus pattern (28 bp):
ATGTATGAGTTGATGTATGTATATATGT
Found at i:2561428 original size:4 final size:4
Alignment explanation
Indices: 2561365--2561415 Score: 56
Period size: 4 Copynumber: 13.8 Consensus size: 4
2561355 GTATGTGTTG
* *
2561365 ATGT ATGT ATAT ATGT ATGT ATG- A-GT -TG- ATGT ATGT ATAT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2561409 ATGT ATG
1 ATGT ATG
2561416 AGTTGATGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
2 1 0.03
3 4 0.10
4 34 0.87
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (4 bp):
ATGT
Found at i:2562646 original size:13 final size:13
Alignment explanation
Indices: 2562613--2562647 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
2562603 TGTTCTTTGC
2562613 TTTCTCTTTGATT
1 TTTCTCTTTGATT
*
2562626 TTT-GCTTTGATT
1 TTTCTCTTTGATT
2562638 TTTCTCTTTG
1 TTTCTCTTTG
2562648 CTCTTTGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.06, C:0.14, G:0.11, T:0.69
Consensus pattern (13 bp):
TTTCTCTTTGATT
Found at i:2563344 original size:26 final size:26
Alignment explanation
Indices: 2563266--2563345 Score: 73
Period size: 26 Copynumber: 3.3 Consensus size: 26
2563256 TTTCAAGGTG
*
2563266 GAAAGAATATTTCAAAGTCTCAAAGA
1 GAAAGAATATTTCAAGGTCTCAAAGA
** *
2563292 GAGGGAATGTTTCAAGG--TC---GA
1 GAAAGAATATTTCAAGGTCTCAAAGA
2563313 -AAAGAATATTTCAAGGTCTCAAAGA
1 GAAAGAATATTTCAAGGTCTCAAAGA
*
2563338 GATAGAAT
1 GAAAGAAT
2563346 GTCAAAAATT
Statistics
Matches: 40, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
20 13 0.32
21 2 0.05
22 2 0.05
24 2 0.05
25 2 0.05
26 19 0.47
ACGTcount: A:0.44, C:0.10, G:0.23, T:0.24
Consensus pattern (26 bp):
GAAAGAATATTTCAAGGTCTCAAAGA
Found at i:2563346 original size:46 final size:45
Alignment explanation
Indices: 2563254--2563347 Score: 143
Period size: 46 Copynumber: 2.1 Consensus size: 45
2563244 ATAAATACAG
* *
2563254 TGTTTCAAGGTGGAAAGAATATTTCAAAGTCTCAAAGAGAGGGAA
1 TGTTTCAAGGTGAAAAGAATATTTCAAAGTCTCAAAGAGAGAGAA
* *
2563299 TGTTTCAAGGTCGAAAAGAATATTTCAAGGTCTCAAAGAGATAGAA
1 TGTTTCAAGGT-GAAAAGAATATTTCAAAGTCTCAAAGAGAGAGAA
2563345 TGT
1 TGT
2563348 CAAAAATTGG
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 11 0.25
46 33 0.75
ACGTcount: A:0.39, C:0.10, G:0.24, T:0.27
Consensus pattern (45 bp):
TGTTTCAAGGTGAAAAGAATATTTCAAAGTCTCAAAGAGAGAGAA
Found at i:2565623 original size:31 final size:32
Alignment explanation
Indices: 2565567--2565628 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2565557 TGACAAAATG
2565567 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
2565599 ACACAAACAAAAGAGAA-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
2565629 CATGTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:2567593 original size:16 final size:16
Alignment explanation
Indices: 2567572--2567602 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2567562 TCCAGATTAC
2567572 AAATATTAAATAATAA
1 AAATATTAAATAATAA
2567588 AAATATTAAATAATA
1 AAATATTAAATAATA
2567603 CAAGCATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATATTAAATAATAA
Found at i:2573100 original size:16 final size:16
Alignment explanation
Indices: 2573079--2573111 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2573069 TAATAAATAA
2573079 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
2573095 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
2573111 A
1 A
2573112 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:2573192 original size:10 final size:10
Alignment explanation
Indices: 2573177--2573229 Score: 50
Period size: 10 Copynumber: 6.1 Consensus size: 10
2573167 CATTTAATAA
2573177 ATAAACGAAC
1 ATAAACGAAC
2573187 ATAAACGAAC
1 ATAAACGAAC
2573197 ----ACGAAC
1 ATAAACGAAC
2573203 ATAAACGAAC
1 ATAAACGAAC
2573213 ----ACGAAC
1 ATAAACGAAC
2573219 ATAAACGAAC
1 ATAAACGAAC
2573229 A
1 A
2573230 CGAACATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 16
0.69 0.00 0.31
Matches are distributed among these distances:
6 12 0.34
10 23 0.66
ACGTcount: A:0.58, C:0.23, G:0.11, T:0.08
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:2573202 original size:16 final size:16
Alignment explanation
Indices: 2573181--2573257 Score: 145
Period size: 16 Copynumber: 4.8 Consensus size: 16
2573171 TAATAAATAA
2573181 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
2573197 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
2573213 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
2573229 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
2573245 ACGAACATAAACG
1 ACGAACATAAACG
2573258 TTGGAGACCA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 59 1.00
ACGTcount: A:0.56, C:0.23, G:0.13, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:2573438 original size:16 final size:16
Alignment explanation
Indices: 2573417--2573452 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
2573407 TAAATGATTC
2573417 ACACGACTTTAATTTA
1 ACACGACTTTAATTTA
2573433 ACACGACTTTAATTTA
1 ACACGACTTTAATTTA
2573449 ACAC
1 ACAC
2573453 TATAACATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (16 bp):
ACACGACTTTAATTTA
Found at i:2574034 original size:14 final size:14
Alignment explanation
Indices: 2574017--2574072 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
2574007 AATGAACATA
*
2574017 AACGAACATAATCG
1 AACGAACATAACCG
2574031 AACGAACAT-A---
1 AACGAACATAACCG
*
2574041 AACGAACATAACCA
1 AACGAACATAACCG
2574055 AACGAACATAACCG
1 AACGAACATAACCG
2574069 AACG
1 AACG
2574073 TTCATGAACG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 26 0.70
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:2574037 original size:24 final size:24
Alignment explanation
Indices: 2573997--2574071 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
2573987 GATTGGGTTA
*
2573997 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
2574021 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
* * *
2574045 AACATAACCAAACGAACATAACCG
1 AACATAATCGAACGAACATAAACG
2574069 AAC
1 AAC
2574072 GTTCATGAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 3 0.07
24 43 0.93
ACGTcount: A:0.56, C:0.21, G:0.11, T:0.12
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:2578504 original size:421 final size:416
Alignment explanation
Indices: 2577941--2578769 Score: 1281
Period size: 421 Copynumber: 2.0 Consensus size: 416
2577931 AAATTTGTAC
* *
2577941 AGGGCCCCTAATAACCTAGCCACGGCCCTATATAATATTGTAAGGCGAAACTCCATTAGAAAAGG
1 AGGGCCCCTAATAACCTAGCCACAGCCCTATATAATACTGTAAGGCGAAACTCCATTAGAAAAGG
* * *
2578006 TGGGGAACACGAAAACAGTTGTAATACAACTAAGCATTGCCCTTGCCTTTGAGGAACACGAAAAT
66 CGGGGAACACGAAAACAATTGTAATACAACTAAGCATTGCCCTTGCCTTTGAGGAACACGAAAAC
* * *
2578071 TGGAACACATCACTCATTTGGTGTAATACACCTGTATTAATACTGCTTATTAATATAATATTGTT
131 TGGAAAACATCACCCATTTGGTGTAATACACCTGTATTAATACTGCTCATTAATATAATATTGTT
* *
2578136 TATTAATAGTCAATGAGGAACCACAACATTAATTTGGTGTAATACAACTTTTGTTTGGATGCATA
196 CATTAATAGTCAATGAGGAACCACAACATTAATTTGGTGTAATAAAAC---T-TTTGGATGCATA
* *
2578201 AAAA-GGTCCCTTGATATATAAAAAGGGGAATATAAAAAATATATCGTGTGGTCAAATACTTGGG
257 AAAAGGGCCCCTTGATATATAAAAA-GGGAATAT-AAAAATATATCATGTGGTCAAATACTTGGG
*
2578265 AGAAAGCAAAGGGAAACTTGGATGCATAAAAAGAGCCCCTTTAAGAATCATAAAAATAAG-GGT-
320 AGAAAGCAAAGGGAAACTTAGATGCATAAAAAGAGCCCCTTTAAGAATCATAAAAAT-AGTGGTC
2578328 TCGAAATCGAATAGATCTAGAAAATAGGGGCCTT
384 T-GAAATCGAATAGATCTAGAAAATAGGGGCCTT
* * *
2578362 AGGGCCCCTGATAACCTAGCCACAGCCTTGTATAATACTGTAAGGCGAAACTCCATTAGAAAAGG
1 AGGGCCCCTAATAACCTAGCCACAGCCCTATATAATACTGTAAGGCGAAACTCCATTAGAAAAGG
*
2578427 CGGGGAACACGAAAACAATTGTAATACAGCTAAGCATTGCCAC-TGCCTTTG-GAGAACACGAAA
66 CGGGGAACACGAAAACAATTGTAATACAACTAAGCATTGCC-CTTGCCTTTGAG-GAACACGAAA
2578490 ACTGGAAAACATCACCCATTTGGTGTAATACACCTGTATTAATACTGCTCATTAATATAATATTG
129 ACTGGAAAACATCACCCATTTGGTGTAATACACCTGTATTAATACTGCTCATTAATATAATATTG
* * * ** *
2578555 TTCATTAATGGTCAGTGGGGAACCACGCCATTTATTTGGTGTAATAAAACTTTTGGATGCATAAA
194 TTCATTAATAGTCAATGAGGAACCACAACATTAATTTGGTGTAATAAAACTTTTGGATGCATAAA
*
2578620 AAGGGCCCCTTGATATATAAAAAGGGTATATAAAAATATATCATGTGGTCAAATACTTGGGAGAA
259 AAGGGCCCCTTGATATATAAAAAGGGAATATAAAAATATATCATGTGGTCAAATACTTGGGAGAA
* * *
2578685 AGCAAAGGGGAACTTAGATGTATAAAAAGGGCCCCTTTAAGAATCATAAAAATAGTGGTCTGAAA
324 AGCAAAGGGAAACTTAGATGCATAAAAAGAGCCCCTTTAAGAATCATAAAAATAGTGGTCTGAAA
*
2578750 TCGAATATATCTAGAAAATA
389 TCGAATAGATCTAGAAAATA
2578770 AGAGCCCCTT
Statistics
Matches: 375, Mismatches: 28, Indels: 15
0.90 0.07 0.04
Matches are distributed among these distances:
415 2 0.01
416 108 0.29
417 24 0.06
418 20 0.05
420 1 0.00
421 219 0.58
422 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (416 bp):
AGGGCCCCTAATAACCTAGCCACAGCCCTATATAATACTGTAAGGCGAAACTCCATTAGAAAAGG
CGGGGAACACGAAAACAATTGTAATACAACTAAGCATTGCCCTTGCCTTTGAGGAACACGAAAAC
TGGAAAACATCACCCATTTGGTGTAATACACCTGTATTAATACTGCTCATTAATATAATATTGTT
CATTAATAGTCAATGAGGAACCACAACATTAATTTGGTGTAATAAAACTTTTGGATGCATAAAAA
GGGCCCCTTGATATATAAAAAGGGAATATAAAAATATATCATGTGGTCAAATACTTGGGAGAAAG
CAAAGGGAAACTTAGATGCATAAAAAGAGCCCCTTTAAGAATCATAAAAATAGTGGTCTGAAATC
GAATAGATCTAGAAAATAGGGGCCTT
Found at i:2586400 original size:16 final size:17
Alignment explanation
Indices: 2586370--2586402 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2586360 ATTTAATTTT
2586370 ATAAAATATAATTTTTAC
1 ATAAAATAT-ATTTTTAC
2586388 ATAAAATAT-TTTTTA
1 ATAAAATATATTTTTA
2586403 TTGTTATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
ATAAAATATATTTTTAC
Found at i:2588612 original size:29 final size:29
Alignment explanation
Indices: 2588579--2588864 Score: 132
Period size: 29 Copynumber: 9.9 Consensus size: 29
2588569 ACAGTCAACT
2588579 ATTACGAAAATAACACATTTTTTTAAATA
1 ATTACGAAAATAACACATTTTTTTAAATA
* *
2588608 ATTACGAAAATATCAC-TTTTTTCAAAATA
1 ATTACGAAAATAACACATTTTTT-TAAATA
* **
2588637 ATTACCAAAATATTAC-TTTTTTTCAAAATA
1 ATTACGAAAATAACACATTTTTTT--AAATA
* * **
2588667 ATTACCAAAATATCAC-TTTTTCGAAATA
1 ATTACGAAAATAACACATTTTTTTAAATA
* **
2588695 ATTATC-AAAATATCATTTTTTTTTCCGAAATA
1 ATTA-CGAAAATAACACATTTTTTT---AAATA
* * **
2588727 ATTACCAAAATATCAC--TTTTCGAAATA
1 ATTACGAAAATAACACATTTTTTTAAATA
* *
2588754 ATTACCAAAAT-A-TCATTTTTTTCGAAATA
1 ATTACGAAAATAACACATTTTTTT--AAATA
* * *
2588783 TTTACGAAACTAACACA--TTCTTAACAGTA
1 ATTACGAAAATAACACATTTTTTTAA-A-TA
* *
2588812 TTTACGAAACT-A-ACATTTTTTTAATAATA
1 ATTACGAAAATAACACATTTTTTT-A-AATA
* *
2588841 TTTACGAAACT-A-ACATTTTTTTAA
1 ATTACGAAAATAACACATTTTTTTAA
2588865 CAATATTTAC
Statistics
Matches: 212, Mismatches: 24, Indels: 44
0.76 0.09 0.16
Matches are distributed among these distances:
25 1 0.00
27 26 0.12
28 27 0.13
29 104 0.49
30 32 0.15
31 4 0.02
32 18 0.08
ACGTcount: A:0.42, C:0.14, G:0.03, T:0.40
Consensus pattern (29 bp):
ATTACGAAAATAACACATTTTTTTAAATA
Found at i:2588677 original size:59 final size:57
Alignment explanation
Indices: 2588594--2588787 Score: 268
Period size: 59 Copynumber: 3.4 Consensus size: 57
2588584 GAAAATAACA
* *
2588594 CATTTTTTT--AAATAATTACGAAAATATCACTTTTTTCAAAATAATTACCAAAATAT
1 CATTTTTTTCGAAATAATTACCAAAATATCAC-TTTTTCGAAATAATTACCAAAATAT
* * *
2588650 TACTTTTTTTCAAAATAATTACCAAAATATCACTTTTTCGAAATAATTATCAAAATAT
1 CA-TTTTTTTCGAAATAATTACCAAAATATCACTTTTTCGAAATAATTACCAAAATAT
2588708 CATTTTTTTTTCCGAAATAATTACCAAAATATCAC-TTTTCGAAATAATTACCAAAATAT
1 CA--TTTTTTT-CGAAATAATTACCAAAATATCACTTTTTCGAAATAATTACCAAAATAT
*
2588767 CATTTTTTTCGAAATATTTAC
1 CATTTTTTTCGAAATAATTAC
2588788 GAAACTAACA
Statistics
Matches: 124, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
56 12 0.10
57 14 0.11
58 24 0.19
59 52 0.42
60 22 0.18
ACGTcount: A:0.41, C:0.14, G:0.03, T:0.42
Consensus pattern (57 bp):
CATTTTTTTCGAAATAATTACCAAAATATCACTTTTTCGAAATAATTACCAAAATAT
Found at i:2588747 original size:87 final size:85
Alignment explanation
Indices: 2588579--2588791 Score: 250
Period size: 87 Copynumber: 2.4 Consensus size: 85
2588569 ACAGTCAACT
* * **
2588579 ATTACGAAAATAACACATTTTTTTAAATAATTACGAAAATATCACTTTTTTCAAAATAATTACCA
1 ATTACCAAAATATCAC-TTTTTCGAAATAATTACGAAAATATCACTTTTTTCAAAATAATTACCA
*
2588644 AAATATTACTTTTTTTCAAAATA
65 AAATATCAC--TTTTTCAAAATA
* *
2588667 ATTACCAAAATATCACTTTTTCGAAATAATTATC-AAAATATCATTTTTTTTTCCGAAATAATTA
1 ATTACCAAAATATCACTTTTTCGAAATAATTA-CGAAAATATCA--CTTTTTT-CAAAATAATTA
*
2588731 CCAAAATATCAC-TTTTCGAAATA
62 CCAAAATATCACTTTTTCAAAATA
* *
2588754 ATTACCAAAATATCATTTTTTTCGAAATATTTACGAAA
1 ATTACCAAAATATCA-CTTTTTCGAAATAATTACGAAA
2588792 CTAACACATT
Statistics
Matches: 109, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
87 49 0.45
88 33 0.30
89 6 0.06
90 21 0.19
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.39
Consensus pattern (85 bp):
ATTACCAAAATATCACTTTTTCGAAATAATTACGAAAATATCACTTTTTTCAAAATAATTACCAA
AATATCACTTTTTCAAAATA
Found at i:2588869 original size:29 final size:29
Alignment explanation
Indices: 2588779--2588874 Score: 147
Period size: 29 Copynumber: 3.3 Consensus size: 29
2588769 TTTTTTTCGA
** *
2588779 AATATTTACGAAACTAACACATTCTTAAC
1 AATATTTACGAAACTAACATTTTTTTAAC
* *
2588808 AGTATTTACGAAACTAACATTTTTTTAAT
1 AATATTTACGAAACTAACATTTTTTTAAC
2588837 AATATTTACGAAACTAACATTTTTTTAAC
1 AATATTTACGAAACTAACATTTTTTTAAC
2588866 AATATTTAC
1 AATATTTAC
2588875 AAAAATACTA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.42, C:0.15, G:0.04, T:0.40
Consensus pattern (29 bp):
AATATTTACGAAACTAACATTTTTTTAAC
Found at i:2589430 original size:20 final size:20
Alignment explanation
Indices: 2589405--2589443 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
2589395 TACTTCATTT
2589405 TATTTTATTCT-TAGTGCTAA
1 TATTTTATT-TATAGTGCTAA
2589425 TATTTTATTTATAGTGCTA
1 TATTTTATTTATAGTGCTA
2589444 TAGGATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (20 bp):
TATTTTATTTATAGTGCTAA
Found at i:2594758 original size:12 final size:12
Alignment explanation
Indices: 2594738--2594775 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
2594728 TTACATAATT
2594738 ATATAATATAAA
1 ATATAATATAAA
*
2594750 ATATGATATAAA
1 ATATAATATAAA
2594762 A-ATAAT-TAAA
1 ATATAATATAAA
2594772 ATAT
1 ATAT
2594776 TAATTTCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 5 0.22
11 6 0.26
12 12 0.52
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (12 bp):
ATATAATATAAA
Found at i:2597180 original size:169 final size:170
Alignment explanation
Indices: 2596901--2597240 Score: 673
Period size: 169 Copynumber: 2.0 Consensus size: 170
2596891 AATACATTTC
2596901 AGAAATGCATAGGACTCTAACTCAATCTTAAATTGGTGAAGTTACCGTAATTATTTTTTTTAAGA
1 AGAAATGCATAGGACTCTAACTCAATCTTAAATTGGTGAAGTTACCGTAATTATTTTTTTTAAGA
2596966 ACAAGTAGTACATTAGAATTTCTTGAATTGAAGAATCTTATGGTTC-TTAATAGATGACTATGTT
66 ACAAGTAGTACATTAGAATTTCTTGAATTGAAGAATCTTATGGTTCTTTAATAGATGACTATGTT
2597030 AATTCTTAATATTTTTTCGCATCATAGATGACTTGGGATA
131 AATTCTTAATATTTTTTCGCATCATAGATGACTTGGGATA
2597070 AGAAATGCATAGGACTCTAACTCAATCTTAAATTGGTGAAGTTACCGTAATTATTTTTTTTAAGA
1 AGAAATGCATAGGACTCTAACTCAATCTTAAATTGGTGAAGTTACCGTAATTATTTTTTTTAAGA
2597135 ACAAGTAGTACATTAGAATTTCTTGAATTGAAGAATCTTATGGTTCTTTAATAGATGACTATGTT
66 ACAAGTAGTACATTAGAATTTCTTGAATTGAAGAATCTTATGGTTCTTTAATAGATGACTATGTT
2597200 AATTCTTAATATTTTTTCGCATCATAGATGACTTGGGATA
131 AATTCTTAATATTTTTTCGCATCATAGATGACTTGGGATA
2597240 A
1 A
2597241 CCTAATCGGA
Statistics
Matches: 170, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
169 111 0.65
170 59 0.35
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (170 bp):
AGAAATGCATAGGACTCTAACTCAATCTTAAATTGGTGAAGTTACCGTAATTATTTTTTTTAAGA
ACAAGTAGTACATTAGAATTTCTTGAATTGAAGAATCTTATGGTTCTTTAATAGATGACTATGTT
AATTCTTAATATTTTTTCGCATCATAGATGACTTGGGATA
Found at i:2597998 original size:59 final size:59
Alignment explanation
Indices: 2597887--2597998 Score: 145
Period size: 59 Copynumber: 1.9 Consensus size: 59
2597877 ATATACAAGT
* * * **
2597887 GATCATTTTGTAACTTTTAATAGTTAAGAGACTCAATAAAACAACATTTTATAGTTGGG
1 GATCATTTTATAACTTTTAATAGTCAAGAGACTCAACAAAACAACACATTATAGTTGGG
* *
2597946 GATCATTTTATAACTTTTAATAGTC-AGAGAACTTAACAAAACAATACATTATA
1 GATCATTTTATAACTTTTAATAGTCAAGAG-ACTCAACAAAACAACACATTATA
2597999 ATCAGGAGAC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
58 4 0.09
59 41 0.91
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.36
Consensus pattern (59 bp):
GATCATTTTATAACTTTTAATAGTCAAGAGACTCAACAAAACAACACATTATAGTTGGG
Found at i:2599569 original size:3 final size:3
Alignment explanation
Indices: 2599561--2599623 Score: 119
Period size: 3 Copynumber: 21.3 Consensus size: 3
2599551 TATACATCCA
2599561 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
2599609 TAT TAT TA- TAT TAT T
1 TAT TAT TAT TAT TAT T
2599624 GTTCAGTAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 57 0.97
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2602667 original size:16 final size:17
Alignment explanation
Indices: 2602636--2602670 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2602626 CGTATCGCCG
*
2602636 ACAAAATTTTACTATTC
1 ACAAAATTTCACTATTC
2602653 ACAAAA-TTCACTATTC
1 ACAAAATTTCACTATTC
2602669 AC
1 AC
2602671 GTAAATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.43, C:0.23, G:0.00, T:0.34
Consensus pattern (17 bp):
ACAAAATTTCACTATTC
Found at i:2611792 original size:33 final size:32
Alignment explanation
Indices: 2611745--2611833 Score: 88
Period size: 33 Copynumber: 2.7 Consensus size: 32
2611735 TTGGTGAAAG
** *
2611745 CAAATCTGTCATAGGTGATGAAGGAGGGGAAGA
1 CAAATCTG-CATAGGTGATGAAACAGAGGAAGA
* *
2611778 CAAATCTGCAATAGGTGACGAAACAGAGGAAGC
1 CAAATCTGC-ATAGGTGATGAAACAGAGGAAGA
*
2611811 CAAATATGCTATAGGTGACTGAA
1 CAAATCTGC-ATAGGTGA-TGAA
2611834 TAGAAAAACC
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
32 1 0.02
33 42 0.91
34 3 0.07
ACGTcount: A:0.39, C:0.13, G:0.29, T:0.18
Consensus pattern (32 bp):
CAAATCTGCATAGGTGATGAAACAGAGGAAGA
Found at i:2621709 original size:18 final size:17
Alignment explanation
Indices: 2621686--2621720 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2621676 GGAACAACCG
2621686 TATCATAAAATTTTAAAT
1 TATCAT-AAATTTTAAAT
*
2621704 TATCATATATTTTAAAT
1 TATCATAAATTTTAAAT
2621721 ATTTTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (17 bp):
TATCATAAATTTTAAAT
Found at i:2629231 original size:21 final size:21
Alignment explanation
Indices: 2629202--2629241 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2629192 ATATATAATT
* *
2629202 TAAAGTTTAAAGTTTAGAACA
1 TAAACTTTAAAATTTAGAACA
2629223 TAAACTTTAAAATTTAGAA
1 TAAACTTTAAAATTTAGAA
2629242 TTTTAAGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (21 bp):
TAAACTTTAAAATTTAGAACA
Found at i:2629544 original size:20 final size:20
Alignment explanation
Indices: 2629519--2629575 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
2629509 ATTTACAGTT
2629519 TAAAATTTAAGATTTAGGTC
1 TAAAATTTAAGATTTAGGTC
* *
2629539 TAAAATTTAAGATTTAAGTT
1 TAAAATTTAAGATTTAGGTC
* *
2629559 TAGAATTTAGGATTTAG
1 TAAAATTTAAGATTTAG
2629576 ATTTTAAGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.40, C:0.02, G:0.16, T:0.42
Consensus pattern (20 bp):
TAAAATTTAAGATTTAGGTC
Found at i:2634655 original size:35 final size:35
Alignment explanation
Indices: 2634609--2634684 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
2634599 AAAACAATCA
* *
2634609 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
2634644 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
2634679 TCAATT
1 TCAATT
2634685 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:2635222 original size:130 final size:130
Alignment explanation
Indices: 2635076--2635323 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
2635066 TATTTATATA
** *
2635076 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGCG
* *
2635141 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGTT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGTT
2635206 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGCG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGCG
* * * *
2635271 TTAACACATGATCATGATATATGTTATTGGTGACACGTGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
2635324 GAAGAAAATT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGCG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGTT
Found at i:2635354 original size:130 final size:129
Alignment explanation
Indices: 2635090--2635354 Score: 309
Period size: 130 Copynumber: 2.0 Consensus size: 129
2635080 ATTTGGTCCT
** * *
2635090 AAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGCGTTAACACATGATCA
* *** * * **** *
2635155 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGTTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGTTATCAAAGAAGT-CA
2635220 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGCGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGCGTTAACACATGATCA
* * * *
2635285 TGATATATGTTATTGGTGACACGTGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGTTATCAAAGAAGT
2635349 -A
128 CA
2635350 AAATT
1 AAATT
2635355 TGGGTCTTGG
Statistics
Matches: 113, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
130 99 0.88
132 8 0.07
133 6 0.05
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGCGTTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGTTATCAAAGAAGTCA
Found at i:2635682 original size:28 final size:27
Alignment explanation
Indices: 2635651--2635713 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
2635641 AGTTGATACA
*
2635651 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
2635679 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
2635707 ATATTTT
1 ATATTTT
2635714 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:2635814 original size:16 final size:18
Alignment explanation
Indices: 2635793--2635826 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
2635783 ATTTCTTATT
2635793 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
2635809 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
2635827 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:2647362 original size:21 final size:21
Alignment explanation
Indices: 2647320--2647362 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2647310 TTTTTGGGCT
* *
2647320 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
2647341 AGGGGAATCGATCCCCCCTCA
1 AGGGGAATCGATACCCACTCA
2647362 A
1 A
2647363 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:2648058 original size:103 final size:103
Alignment explanation
Indices: 2647879--2648096 Score: 418
Period size: 103 Copynumber: 2.1 Consensus size: 103
2647869 GTAGAGGGTT
* *
2647879 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
2647944 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
2647982 TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
2648047 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
2648085 TATGTGGTCCTT
1 TATGTGGTCCTT
2648097 ATGGACATTA
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 113 1.00
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:2648146 original size:23 final size:23
Alignment explanation
Indices: 2648113--2648175 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
2648103 ATTATTATAT
2648113 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * *
2648136 GGCACTCCGGTGTAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
2648159 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
2648176 ATATGAGTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 33 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:2649963 original size:23 final size:23
Alignment explanation
Indices: 2649930--2650020 Score: 128
Period size: 23 Copynumber: 4.0 Consensus size: 23
2649920 CATTTTATAT
* * *
2649930 GGCACTTCGGTGCAATTCTACGT
1 GGCACTACGGTGCATTTCTACGC
2649953 GGCACTACGGTGCATTTCTACGC
1 GGCACTACGGTGCATTTCTACGC
*
2649976 GGCACTACGGTGCATTTTTACGC
1 GGCACTACGGTGCATTTCTACGC
* *
2649999 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCATTTCTACG
2650021 AGCTATGGTG
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 62 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.30
Consensus pattern (23 bp):
GGCACTACGGTGCATTTCTACGC
Found at i:2650523 original size:12 final size:12
Alignment explanation
Indices: 2650506--2650544 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
2650496 CGTAGGTTAC
2650506 AGAAGCGAGAAG
1 AGAAGCGAGAAG
2650518 AGAAGCGAGAAG
1 AGAAGCGAGAAG
*
2650530 AGAAGGGAAGAAG
1 AGAAGCG-AGAAG
2650543 AG
1 AG
2650545 CAAGACAGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 18 0.72
13 7 0.28
ACGTcount: A:0.51, C:0.05, G:0.44, T:0.00
Consensus pattern (12 bp):
AGAAGCGAGAAG
Found at i:2652915 original size:27 final size:27
Alignment explanation
Indices: 2652862--2652916 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
2652852 GTTATTCTTA
**
2652862 TTATAAATAAAAGTTTTAATTTCATTT
1 TTATAAATAAAAGTTTTAATGACATTT
* *
2652889 TTATAAATAAAAGTTTTTATGAGATTT
1 TTATAAATAAAAGTTTTAATGACATTT
2652916 T
1 T
2652917 AAAGTTTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (27 bp):
TTATAAATAAAAGTTTTAATGACATTT
Found at i:2656760 original size:73 final size:73
Alignment explanation
Indices: 2656641--2656789 Score: 298
Period size: 73 Copynumber: 2.0 Consensus size: 73
2656631 CTTTGCCCTC
2656641 TATTCACTTCTTTTAGAGTATTTTAGCTTTAAATGTTTTAATTTTTGGTCAAAATAGCATTTGTT
1 TATTCACTTCTTTTAGAGTATTTTAGCTTTAAATGTTTTAATTTTTGGTCAAAATAGCATTTGTT
2656706 GGATGAAA
66 GGATGAAA
2656714 TATTCACTTCTTTTAGAGTATTTTAGCTTTAAATGTTTTAATTTTTGGTCAAAATAGCATTTGTT
1 TATTCACTTCTTTTAGAGTATTTTAGCTTTAAATGTTTTAATTTTTGGTCAAAATAGCATTTGTT
2656779 GGATGAAA
66 GGATGAAA
2656787 TAT
1 TAT
2656790 ATAAGTTGAC
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 76 1.00
ACGTcount: A:0.29, C:0.08, G:0.15, T:0.48
Consensus pattern (73 bp):
TATTCACTTCTTTTAGAGTATTTTAGCTTTAAATGTTTTAATTTTTGGTCAAAATAGCATTTGTT
GGATGAAA
Found at i:2656987 original size:32 final size:32
Alignment explanation
Indices: 2656948--2657023 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
2656938 CTAAAGTAAG
2656948 GTGATGATGTGA-CATGTGTC-TCATAATTCAAA
1 GTGATGATGTGATCATGTGTCAT-ATAA-TCAAA
*
2656980 GTGATGATAT-ATCATGTGTCATATAATCAAA
1 GTGATGATGTGATCATGTGTCATATAATCAAA
* *
2657011 TTGTTGATGTGAT
1 GTGATGATGTGAT
2657024 GTATATATCA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
31 13 0.35
32 23 0.62
33 1 0.03
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (32 bp):
GTGATGATGTGATCATGTGTCATATAATCAAA
Found at i:2666884 original size:7 final size:7
Alignment explanation
Indices: 2666872--2666917 Score: 74
Period size: 7 Copynumber: 6.6 Consensus size: 7
2666862 CCCTATGCTA
2666872 CCTAAAC
1 CCTAAAC
2666879 CCTAAAC
1 CCTAAAC
* *
2666886 TCTAAAT
1 CCTAAAC
2666893 CCTAAAC
1 CCTAAAC
2666900 CCTAAAC
1 CCTAAAC
2666907 CCTAAAC
1 CCTAAAC
2666914 CCTA
1 CCTA
2666918 CTTCCAACTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.41, C:0.39, G:0.00, T:0.20
Consensus pattern (7 bp):
CCTAAAC
Found at i:2670408 original size:15 final size:16
Alignment explanation
Indices: 2670388--2670423 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
2670378 AATTAGGGTA
*
2670388 ATTTTTTATC-CTTTT
1 ATTTTTTATCTATTTT
2670403 ATTTTTTATCTATTTT
1 ATTTTTTATCTATTTT
2670419 ATTTT
1 ATTTT
2670424 GATTTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (16 bp):
ATTTTTTATCTATTTT
Found at i:2673215 original size:13 final size:13
Alignment explanation
Indices: 2673197--2673235 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
2673187 CAACGGTCAA
*
2673197 CGGTCGGGTCGGT
1 CGGTCGGGTCAGT
2673210 CGGTCGGGTCAGT
1 CGGTCGGGTCAGT
2673223 CGGGTCGGGTCAG
1 C-GGTCGGGTCAG
2673236 ACCGGTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.05, C:0.23, G:0.51, T:0.21
Consensus pattern (13 bp):
CGGTCGGGTCAGT
Found at i:2673279 original size:20 final size:21
Alignment explanation
Indices: 2673243--2673281 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2673233 CAGACCGGTC
*
2673243 AAACCGGTTCGAACCGGTTGA
1 AAACCGGTTCAAACCGGTTGA
2673264 AAACCGG-TCAAACCGGTT
1 AAACCGGTTCAAACCGGTT
2673282 TCCAGCCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.31, C:0.26, G:0.26, T:0.18
Consensus pattern (21 bp):
AAACCGGTTCAAACCGGTTGA
Found at i:2674061 original size:14 final size:13
Alignment explanation
Indices: 2674038--2674069 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
2674028 GTCCAGTGAC
2674038 CAAAATAACTTTT
1 CAAAATAACTTTT
2674051 CAAACATAACTTTT
1 CAAA-ATAACTTTT
2674065 CAAAA
1 CAAAA
2674070 CTAGTGACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (13 bp):
CAAAATAACTTTT
Found at i:2682792 original size:6 final size:6
Alignment explanation
Indices: 2682781--2682823 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
2682771 TAGCCGTGTC
2682781 CTCAAT CTCAAT CTCAAT CTCAAT CTCAAT CTCAAT CTCAAT C
1 CTCAAT CTCAAT CTCAAT CTCAAT CTCAAT CTCAAT CTCAAT C
2682824 ACTTGCACTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.33
Consensus pattern (6 bp):
CTCAAT
Done.