Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold140
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: 3130556
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82166 characters in sequence are not A, C, G, or T
File 15 of 20
Found at i:2388668 original size:2 final size:2
Alignment explanation
Indices: 2388663--2388692 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2388653 ACAAATAAAC
2388663 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2388693 AAAGAACAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2391309 original size:30 final size:30
Alignment explanation
Indices: 2391223--2391309 Score: 72
Period size: 30 Copynumber: 2.9 Consensus size: 30
2391213 CTTAATTAAG
* *
2391223 TTTATACTTTT-A-TTATACTCAGATAA-AT
1 TTTAT-CTTTTAATTTATATTCAAATAAGAT
** * * *
2391251 TTTAAATTTTAAATTTGTATTTATATAAGAT
1 TTTATCTTTT-AATTTATATTCAAATAAGAT
2391282 TTTATCTTTTAATTTATATTCAAATAAG
1 TTTATCTTTTAATTTATATTCAAATAAG
2391310 TTCTTAATAT
Statistics
Matches: 44, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
27 4 0.09
28 4 0.09
29 1 0.02
30 25 0.57
31 10 0.23
ACGTcount: A:0.37, C:0.06, G:0.05, T:0.53
Consensus pattern (30 bp):
TTTATCTTTTAATTTATATTCAAATAAGAT
Found at i:2396532 original size:20 final size:20
Alignment explanation
Indices: 2396509--2396551 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2396499 TAATTAAATA
*
2396509 TATATTTATTAAATATTTAT
1 TATATTTAATAAATATTTAT
**
2396529 TATATTTAATATTTATTTAT
1 TATATTTAATAAATATTTAT
2396549 TAT
1 TAT
2396552 TAAAATTACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TATATTTAATAAATATTTAT
Found at i:2397275 original size:25 final size:26
Alignment explanation
Indices: 2397247--2397306 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 26
2397237 AATTATTTTG
* *
2397247 AATATTTTAAA-TTTTTCATTAAATT
1 AATATTTTAAACTTATTCAATAAATT
* *
2397272 AATATCTTAAACTTATTCAATAATTT
1 AATATTTTAAACTTATTCAATAAATT
2397298 AAT-TTTTAA
1 AATATTTTAA
2397307 TATTATTGTG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
25 15 0.52
26 14 0.48
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.52
Consensus pattern (26 bp):
AATATTTTAAACTTATTCAATAAATT
Found at i:2397290 original size:26 final size:25
Alignment explanation
Indices: 2397247--2397313 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 25
2397237 AATTATTTTG
* * *
2397247 AATATTTTAAATTTTTCATTAAATT
1 AATATCTTAAATTATTCAATAAATT
*
2397272 AATATCTTAAACTTATTCAATAATTT
1 AATATCTTAAA-TTATTCAATAAATT
*
2397298 AAT-TTTTAATATTATT
1 AATATCTTAA-ATTATT
2397314 GTGAATATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
25 20 0.57
26 15 0.43
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (25 bp):
AATATCTTAAATTATTCAATAAATT
Found at i:2404801 original size:12 final size:13
Alignment explanation
Indices: 2404768--2404805 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
2404758 CATCCATTAT
2404768 AGATTCAAATATG
1 AGATTCAAATATG
*
2404781 AACATTCAAATATG
1 -AGATTCAAATATG
2404795 -GATTCAAATAT
1 AGATTCAAATAT
2404806 TCAAATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 10 0.45
14 12 0.55
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (13 bp):
AGATTCAAATATG
Found at i:2406489 original size:3 final size:3
Alignment explanation
Indices: 2406483--2406517 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2406473 TTATTATTTT
2406483 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2406518 CTCATTCTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2407583 original size:16 final size:16
Alignment explanation
Indices: 2407535--2407589 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
2407525 TTTAATCCAT
*
2407535 AATAACTTAAATTTTAA
1 AATAATTTAAA-TTTAA
* * * *
2407552 AATGAGTTGAACTTAA
1 AATAATTTAAATTTAA
2407568 AATAATTTAAATTTAA
1 AATAATTTAAATTTAA
2407584 AATAAT
1 AATAAT
2407590 CTAATTTATA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
16 22 0.73
17 8 0.27
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.38
Consensus pattern (16 bp):
AATAATTTAAATTTAA
Found at i:2408626 original size:22 final size:24
Alignment explanation
Indices: 2408600--2408652 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 24
2408590 ATAAGGTATA
2408600 ATAAAAAAATATTTATTAA-AAT-T
1 ATAAAAAAAT-TTTATTAATAATAT
2408623 -T--AAAAATTTTATTAATAATAT
1 ATAAAAAAATTTTATTAATAATAT
2408644 ATAAAAAAA
1 ATAAAAAAA
2408653 GGACCCATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
19 8 0.32
20 9 0.36
21 1 0.04
22 2 0.08
24 5 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
ATAAAAAAATTTTATTAATAATAT
Found at i:2409725 original size:15 final size:15
Alignment explanation
Indices: 2409688--2409734 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
2409678 ATTATGTTTT
* *
2409688 TTATATTATATAAAA
1 TTATAATATATAATA
2409703 TT-TAAATATATAATA
1 TTAT-AATATATAATA
2409718 TTATAATATA-AATA
1 TTATAATATATAATA
2409732 TTA
1 TTA
2409735 AAAAATGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 8 0.29
15 19 0.68
16 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTATAATATATAATA
Found at i:2409959 original size:3 final size:3
Alignment explanation
Indices: 2409946--2409977 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
2409936 AACTTAAATA
2409946 AAT ACAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT A
2409978 TAGGCAAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2410732 original size:11 final size:12
Alignment explanation
Indices: 2410716--2410744 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2410706 AAAATATATT
2410716 TTTAAAA-TTAA
1 TTTAAAATTTAA
2410727 TTTAAAATTTAA
1 TTTAAAATTTAA
2410739 TTTAAA
1 TTTAAA
2410745 TAATAAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TTTAAAATTTAA
Found at i:2410739 original size:43 final size:46
Alignment explanation
Indices: 2410651--2410752 Score: 124
Period size: 43 Copynumber: 2.3 Consensus size: 46
2410641 AATTATTATT
2410651 TAAATAAT-AAATATTATTTTTATTTAAATTTAATAAAAATATTAATA
1 TAAATAATAAAATATTATTTTTA--TAAATTTAATAAAAATATTAATA
* *
2410698 TAAATAATAAAATA-TATTTTTA-AAA-TTAATTTAAAAT-TTAATT
1 TAAATAATAAAATATTATTTTTATAAATTTAA-TAAAAATATTAATA
2410741 TAAATAATAAAA
1 TAAATAATAAAA
2410753 GTGAAATCTT
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
43 21 0.41
44 9 0.18
47 16 0.31
48 5 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (46 bp):
TAAATAATAAAATATTATTTTTATAAATTTAATAAAAATATTAATA
Found at i:2410791 original size:4 final size:4
Alignment explanation
Indices: 2410782--2410807 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2410772 ATGAGCGCTT
2410782 TTAA TTAA TTAA TTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TT
2410808 TGTTTGGTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (4 bp):
TTAA
Found at i:2410978 original size:12 final size:14
Alignment explanation
Indices: 2410933--2410969 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2410923 AAATTCATTA
**
2410933 TAAAATTTATATTT
1 TAAAATTTATAAGT
2410947 TAAAATTTATAAGT
1 TAAAATTTATAAGT
2410961 TAAAATTTA
1 TAAAATTTA
2410970 CATTAAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (14 bp):
TAAAATTTATAAGT
Found at i:2411262 original size:15 final size:15
Alignment explanation
Indices: 2411234--2411276 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
2411224 ATTACTTTAT
*
2411234 TAATTAAATTAAT-A
1 TAATTAATTTAATAA
2411248 TAATATAATTTAATAA
1 TAAT-TAATTTAATAA
*
2411264 TGATTAATTTAAT
1 TAATTAATTTAAT
2411277 TTTTATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 4 0.16
15 17 0.68
16 4 0.16
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (15 bp):
TAATTAATTTAATAA
Found at i:2430774 original size:33 final size:31
Alignment explanation
Indices: 2430713--2430774 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 31
2430703 TCTTTTATTT
2430713 AAAAAAAATTTAAATAAAAATATTAAACTCA
1 AAAAAAAATTTAAATAAAAATATTAAACTCA
*
2430744 AAAAATAAATTTAATTAAGTAAA-ATTAAACT
1 AAAAA-AAATTTAAATAA--AAATATTAAACT
2430775 TAAATTTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 5 0.19
32 11 0.41
33 8 0.30
34 3 0.11
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.29
Consensus pattern (31 bp):
AAAAAAAATTTAAATAAAAATATTAAACTCA
Found at i:2430853 original size:22 final size:22
Alignment explanation
Indices: 2430842--2430892 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
2430832 ATATATATTT
2430842 TTTATATTTATATATTATATAA
1 TTTATATTTATATATTATATAA
* *
2430864 TTTATA-TCAAATGATTATATAA
1 TTTATATTTATAT-ATTATATAA
2430886 TATTATA
1 T-TTATA
2430893 GCATAAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.16
22 16 0.64
23 5 0.20
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTATATTTATATATTATATAA
Found at i:2430904 original size:24 final size:23
Alignment explanation
Indices: 2430855--2430918 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 23
2430845 ATATTTATAT
* **
2430855 ATTATATAAT-TTATATCAAATG
1 ATTATATAATATTATAGCAAAAC
2430877 ATTATATAATATTATAGCATAAAC
1 ATTATATAATATTATAGCA-AAAC
*
2430901 ATTAAATATATATATATA
1 ATTATATA-ATAT-TATA
2430919 TATGTTAACT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
22 10 0.29
23 7 0.21
24 9 0.26
25 4 0.12
26 4 0.12
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (23 bp):
ATTATATAATATTATAGCAAAAC
Found at i:2431797 original size:21 final size:20
Alignment explanation
Indices: 2431760--2431799 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
2431750 AAATCTATTC
2431760 ATTTTTTCAAATAAATATGA
1 ATTTTTTCAAATAAATATGA
2431780 ATTTTATTCCAAA-AAATATG
1 ATTTT-TT-CAAATAAATATG
2431800 TTATATATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (20 bp):
ATTTTTTCAAATAAATATGA
Found at i:2432609 original size:13 final size:13
Alignment explanation
Indices: 2432572--2432616 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
2432562 TAAAAAAAAC
*
2432572 TATTTT-TTCTCT
1 TATTTTCTTTTCT
2432584 TATTTTACTTTTCT
1 TATTTT-CTTTTCT
2432598 TATTTTCTTTTCT
1 TATTTTCTTTTCT
*
2432611 TCTTTT
1 TATTTT
2432617 TAGTAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 6 0.21
13 12 0.41
14 11 0.38
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.76
Consensus pattern (13 bp):
TATTTTCTTTTCT
Found at i:2433455 original size:82 final size:81
Alignment explanation
Indices: 2433364--2433520 Score: 183
Period size: 81 Copynumber: 1.9 Consensus size: 81
2433354 GCTATCTCTC
* * * * *
2433364 TTTCCCTTGAATTAAAA-AAGAAATTTATCAAAATAAG-GAAAATAATCCCTTTTCCTTAGTTTT
1 TTTCCCTTG-AGTAAAACAA-AAAATTATCAAAACAAGAGAAAAGAATCCCTTTTCATTAG-TTT
* *
2433427 TCTTTTTTTATTCCTTTCT
63 ACTTTTCTTATTCCTTTCT
* * *
2433446 TTTCTCTTGAGTAAAACAAAAAATTATCTAAACAAGAGAAAAGAATCCGTTTTCATTAGTTTACT
1 TTTCCCTTGAGTAAAACAAAAAATTATCAAAACAAGAGAAAAGAATCCCTTTTCATTAGTTTACT
2433511 TTTCTTATTC
66 TTTCTTATTC
2433521 TTTTTTCTTC
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
81 34 0.54
82 29 0.46
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.43
Consensus pattern (81 bp):
TTTCCCTTGAGTAAAACAAAAAATTATCAAAACAAGAGAAAAGAATCCCTTTTCATTAGTTTACT
TTTCTTATTCCTTTCT
Found at i:2438041 original size:12 final size:13
Alignment explanation
Indices: 2438012--2438049 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
2438002 TGAGTGTAAG
*
2438012 ATTTTTTTTTTTCA
1 ATTTTTATTTTT-A
2438026 ATTTTTATTTTT-
1 ATTTTTATTTTTA
2438038 ATTTTTATTTTT
1 ATTTTTATTTTT
2438050 TGTAATTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 12 0.52
14 11 0.48
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.82
Consensus pattern (13 bp):
ATTTTTATTTTTA
Found at i:2438475 original size:22 final size:22
Alignment explanation
Indices: 2438431--2438475 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
2438421 TTTTATGTGA
* *
2438431 TAAAATTTTAAAATCTTTCATT
1 TAAAATTTTAAAATCTGTAATT
2438453 TAAAATTTTAAAATAC-GTAATT
1 TAAAATTTTAAAAT-CTGTAATT
2438475 T
1 T
2438476 CATAACTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (22 bp):
TAAAATTTTAAAATCTGTAATT
Found at i:2447929 original size:6 final size:6
Alignment explanation
Indices: 2447918--2447945 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2447908 AGAGGGAAAG
2447918 AGACAC AGACAC AGACAC AGACAC AGAC
1 AGACAC AGACAC AGACAC AGACAC AGAC
2447946 TACACACTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.32, G:0.18, T:0.00
Consensus pattern (6 bp):
AGACAC
Found at i:2448504 original size:30 final size:30
Alignment explanation
Indices: 2448469--2448527 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
2448459 TTAAAATTTC
2448469 AATTATCTCAAATTGTGAAATAAAATAATT
1 AATTATCTCAAATTGTGAAATAAAATAATT
2448499 AATTATCTCAAATTGTGAAATAAAATAAT
1 AATTATCTCAAATTGTGAAATAAAATAAT
2448528 GACATTCAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.36
Consensus pattern (30 bp):
AATTATCTCAAATTGTGAAATAAAATAATT
Found at i:2451173 original size:15 final size:16
Alignment explanation
Indices: 2451115--2451170 Score: 51
Period size: 17 Copynumber: 3.5 Consensus size: 16
2451105 AACTATTTTT
*
2451115 ATTTTTATATCTTAAA
1 ATTTTTATATTTTAAA
* *
2451131 ATTTTTACTATATTAAT
1 ATTTTTA-TATTTTAAA
**
2451148 ATTTCAAT-TTTTAAA
1 ATTTTTATATTTTAAA
2451163 ATTTTTAT
1 ATTTTTAT
2451171 TTTATATTAT
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
15 11 0.35
16 8 0.26
17 12 0.39
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTTTATATTTTAAA
Found at i:2451192 original size:31 final size:29
Alignment explanation
Indices: 2451113--2451192 Score: 70
Period size: 32 Copynumber: 2.6 Consensus size: 29
2451103 AAAACTATTT
*
2451113 TTATTTTTATATCTTAAAATTTTTACTATA
1 TTATTTTTAAAT-TTAAAATTTTTACTATA
* * *
2451143 TTAATATTTCAATTTTTAAAATTTTTATTTTATA
1 TT-AT-TTTTAA-ATTTAAAATTTTTA--CTATA
2451177 TTATTTTTAAATTTAA
1 TTATTTTTAAATTTAA
2451193 TTAATATTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
30 2 0.05
31 7 0.18
32 21 0.54
33 3 0.08
34 6 0.15
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (29 bp):
TTATTTTTAAATTTAAAATTTTTACTATA
Found at i:2451456 original size:18 final size:16
Alignment explanation
Indices: 2451422--2451461 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
2451412 ATAAATTAAA
2451422 TTTTTTAAAAAAATAT
1 TTTTTTAAAAAAATAT
*
2451438 TTTTTTAATAATAATTAT
1 TTTTTTAA-AA-AAATAT
2451456 TTTTTT
1 TTTTTT
2451462 CAAATACACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 2 0.10
18 11 0.52
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTTTAAAAAAATAT
Found at i:2451753 original size:10 final size:11
Alignment explanation
Indices: 2451738--2451852 Score: 70
Period size: 10 Copynumber: 11.1 Consensus size: 11
2451728 TATATACAGT
2451738 ATTAAAA-ATA
1 ATTAAAATATA
2451748 ATTAAAATATA
1 ATTAAAATATA
*
2451759 A-TATTAA-A-A
1 ATTA-AAATATA
*
2451768 ATTATAATATA
1 ATTAAAATATA
2451779 A-TAAAATAT-
1 ATTAAAATATA
*
2451788 ATTAAAAAAT-
1 ATTAAAATATA
2451798 A-TATAAATATAA
1 ATTA-AAATAT-A
* *
2451810 AATAAAATAAA
1 ATTAAAATATA
*
2451821 ATTATAATATA
1 ATTAAAATATA
2451832 A-TAAAATAT-
1 ATTAAAATATA
*
2451841 ATAAAAATATA
1 ATTAAAATATA
2451852 A
1 A
2451853 ATTTAATATT
Statistics
Matches: 83, Mismatches: 10, Indels: 23
0.72 0.09 0.20
Matches are distributed among these distances:
9 9 0.11
10 47 0.57
11 19 0.23
12 6 0.07
13 2 0.02
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
ATTAAAATATA
Found at i:2453778 original size:20 final size:19
Alignment explanation
Indices: 2453749--2453786 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2453739 TATTAAATTT
*
2453749 ATATTTAATAAATTAATAG
1 ATATTTAATAAAATAATAG
2453768 ATATTTGAATAAAATAATA
1 ATATTT-AATAAAATAATA
2453787 ATTATGTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (19 bp):
ATATTTAATAAAATAATAG
Found at i:2453957 original size:16 final size:15
Alignment explanation
Indices: 2453934--2453962 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2453924 TACATTTTTA
2453934 AAAATTTTTAATACT
1 AAAATTTTTAATACT
2453949 AAAATTTTTAATAC
1 AAAATTTTTAATAC
2453963 AATAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (15 bp):
AAAATTTTTAATACT
Found at i:2453992 original size:12 final size:12
Alignment explanation
Indices: 2453975--2454021 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 12
2453965 TAAAAAAACC
*
2453975 TATTTTTTAATT
1 TATTTTTTAATA
2453987 TA-TTTTTAA-A
1 TATTTTTTAATA
2453997 TATTTTTTAATA
1 TATTTTTTAATA
* *
2454009 TATATTATAATA
1 TATTTTTTAATA
2454021 T
1 T
2454022 TAATCCCATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 2 0.07
11 14 0.47
12 14 0.47
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TATTTTTTAATA
Found at i:2454020 original size:22 final size:22
Alignment explanation
Indices: 2453975--2454022 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2453965 TAAAAAAACC
* *
2453975 TATTTTTTAATTTATTTTTAAA
1 TATTTTTTAATATATTTATAAA
2453997 TATTTTTTAATATATATTAT-AA
1 TATTTTTTAATATAT-TTATAAA
2454019 TATT
1 TATT
2454023 AATCCCATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TATTTTTTAATATATTTATAAA
Found at i:2454579 original size:21 final size:21
Alignment explanation
Indices: 2454529--2454579 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 21
2454519 AGATTTTTAC
2454529 TTTTTAAAATTTAAAAATTAA
1 TTTTTAAAATTTAAAAATTAA
* *
2454550 -TTTAAAAAATT-AAAATTAA
1 TTTTTAAAATTTAAAAATTAA
2454569 GGTTTTTAAAA
1 --TTTTTAAAA
2454580 GTATTTATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
19 8 0.33
20 9 0.38
22 7 0.29
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (21 bp):
TTTTTAAAATTTAAAAATTAA
Found at i:2457744 original size:2 final size:2
Alignment explanation
Indices: 2457737--2457779 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2457727 CTGCCTGTAA
2457737 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
2457779 A
1 A
2457780 AACATAAGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2463326 original size:2 final size:2
Alignment explanation
Indices: 2463255--2463315 Score: 70
Period size: 2 Copynumber: 30.5 Consensus size: 2
2463245 GAAAATAACA
* ** *
2463255 AT AT AT AT AT AT AT AT AT AT AA AGT GC A- AA AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
2463297 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
2463316 AACAATATAT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (2 bp):
AT
Found at i:2463928 original size:26 final size:26
Alignment explanation
Indices: 2463899--2463954 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
2463889 ATATTAAATA
*
2463899 ATTTTTGTATTATAATTTGATTTATG
1 ATTTTTGTATTATAATTCGATTTATG
*
2463925 ATTTTTGTATTTTAATTCGATTTATG
1 ATTTTTGTATTATAATTCGATTTATG
2463951 ATTT
1 ATTT
2463955 GATATTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.25, C:0.02, G:0.11, T:0.62
Consensus pattern (26 bp):
ATTTTTGTATTATAATTCGATTTATG
Found at i:2464662 original size:27 final size:30
Alignment explanation
Indices: 2464632--2464688 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
2464622 TATAAAAGTT
2464632 TAAATGT-ATTTTTTATG-TAT-ATTTATA
1 TAAATGTAATTTTTTATGATATAATTTATA
*
2464659 TAAATTTAAATTTTTTATGATATAATTTAT
1 TAAATGT-AATTTTTTATGATATAATTTAT
2464689 TTTTATTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 6 0.24
29 10 0.40
30 3 0.12
31 6 0.24
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (30 bp):
TAAATGTAATTTTTTATGATATAATTTATA
Found at i:2464709 original size:74 final size:72
Alignment explanation
Indices: 2464608--2464856 Score: 249
Period size: 73 Copynumber: 3.4 Consensus size: 72
2464598 TTTTTTTTAC
* * *
2464608 AATTTATCTTTATTTATAAAAGTTTAAATGTATTTTTTATGTAT-ATTTATATAAATTTAAATTT
1 AATTTATTTTTATTTGTAAAAATTTAAATGTATTTTTTA-GTATGA-TTA-ATAAATTTAAATTT
2464672 TTTATGATAT
63 TTTATGATAT
* * * * * *
2464682 AATTTATTTTTATTTGTCAAAGTTTAAATTTATTTTTTGAGTATGATTAACAAGTTTATATTTTT
1 AATTTATTTTTATTTGTAAAAATTTAAATGTATTTTTT-AGTATGATTAATAAATTTAAATTTTT
* *
2464747 GATCATAT
65 TATGATAT
* * *
2464755 AATTCATTTGTATTTGTAAAAATTTAAAT-T-TGTTTTTAGGT-TGATTACATCAATTTAAA-TT
1 AATTTATTTTTATTTGTAAAAATTTAAATGTAT-TTTTTA-GTATGATTA-ATAAATTTAAATTT
2464816 TTTAGTG-TAT
63 TTTA-TGATAT
*
2464826 TATTTATTTTTATTTGTAAAAATTTAAATGT
1 AATTTATTTTTATTTGTAAAAATTTAAATGT
2464857 TTATTTAAAT
Statistics
Matches: 146, Mismatches: 22, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
71 42 0.29
72 17 0.12
73 44 0.30
74 41 0.28
75 2 0.01
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (72 bp):
AATTTATTTTTATTTGTAAAAATTTAAATGTATTTTTTAGTATGATTAATAAATTTAAATTTTTT
ATGATAT
Found at i:2465039 original size:23 final size:22
Alignment explanation
Indices: 2465009--2465052 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
2464999 GAGGTATTAT
*
2465009 AATTTTATTAATCATATATTTA
1 AATTTTATTAATCATAAATTTA
*
2465031 AATTATTATTAATTATAAATTT
1 AATT-TTATTAATCATAAATTT
2465053 TGTAAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
AATTTTATTAATCATAAATTTA
Found at i:2466078 original size:14 final size:15
Alignment explanation
Indices: 2466061--2466093 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
2466051 AATTAATAAT
2466061 ATTA-AATATAAAAA
1 ATTACAATATAAAAA
2466075 ATTACTAATATAAAAA
1 ATTAC-AATATAAAAA
2466091 ATT
1 ATT
2466094 TCAAACAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
16 13 0.76
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (15 bp):
ATTACAATATAAAAA
Found at i:2466446 original size:15 final size:15
Alignment explanation
Indices: 2466426--2466455 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2466416 TCTTACTTTT
2466426 AAATTTTTTAATTTA
1 AAATTTTTTAATTTA
*
2466441 AAATTTTTTATTTTA
1 AAATTTTTTAATTTA
2466456 TTAAAAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
AAATTTTTTAATTTA
Found at i:2466578 original size:74 final size:75
Alignment explanation
Indices: 2466443--2466592 Score: 171
Period size: 74 Copynumber: 2.0 Consensus size: 75
2466433 TTAATTTAAA
** * *** *
2466443 ATTTTTTATTTTATTAAAAATAATAATTAATATTTTAAATTTTTAATATAAATTTTCAAATTTAA
1 ATTTTTTATTTTATTAAAAATAATAATTAATAAGTTAAATTTTTAACATAAATTAAAAAATTAAA
2466508 -TTAATTTTT
66 TTTAATTTTT
* *
2466517 ATTTTTTATTTTATTAAAATTTAATAATTAATACAGTT-GA-TTTTAACATAAATTAAAAAATTA
1 ATTTTTTATTTTATTAAAA-ATAATAATTAATA-AGTTAAATTTTTAACATAAATTAAAAAATTA
*
2466580 AATTTTATTTTT
64 AATTTAATTTTT
2466592 A
1 A
2466593 AAATTTTTAT
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
74 39 0.62
75 22 0.35
76 2 0.03
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (75 bp):
ATTTTTTATTTTATTAAAAATAATAATTAATAAGTTAAATTTTTAACATAAATTAAAAAATTAAA
TTTAATTTTT
Found at i:2466994 original size:22 final size:22
Alignment explanation
Indices: 2466966--2467016 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
2466956 TAAAAAATAA
* *
2466966 AAAATAATTATTTTCTAA-AAAT
1 AAAATAATAATTTT-GAAGAAAT
2466988 AAAATAATAATTTTGAAGAAAT
1 AAAATAATAATTTTGAAGAAAT
2467010 AAAATAA
1 AAAATAA
2467017 AAGAATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 2 0.08
22 24 0.92
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (22 bp):
AAAATAATAATTTTGAAGAAAT
Found at i:2467749 original size:21 final size:21
Alignment explanation
Indices: 2467711--2467776 Score: 75
Period size: 21 Copynumber: 3.1 Consensus size: 21
2467701 AATTGTATGA
2467711 AATTGAAAATTTTA-TTATTCA-
1 AATT-AAAATTTTATTTATT-AT
2467732 AA-TAAAATTTTTATTTATTAT
1 AATTAAAA-TTTTATTTATTAT
*
2467753 AATTAAAAATTTATTTATTAT
1 AATTAAAATTTTATTTATTAT
2467774 AAT
1 AAT
2467777 CAATATAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
19 4 0.10
20 7 0.17
21 24 0.60
22 5 0.12
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
AATTAAAATTTTATTTATTAT
Found at i:2467842 original size:12 final size:13
Alignment explanation
Indices: 2467819--2467847 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2467809 TAATTTTATT
2467819 ATTAAAATTTAAA
1 ATTAAAATTTAAA
2467832 ATTAAAA-TTAAA
1 ATTAAAATTTAAA
2467844 ATTA
1 ATTA
2467848 TTTACTTGCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATTAAAATTTAAA
Found at i:2468083 original size:5 final size:5
Alignment explanation
Indices: 2468073--2468107 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
2468063 TGAAGAGAGT
*
2468073 TTTTA TTTTA TTTTA ATTTA TTTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTTT
2468108 TGCCGCCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:2468091 original size:11 final size:11
Alignment explanation
Indices: 2468072--2468108 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
2468062 TTGAAGAGAG
2468072 TTTTTATTTTA
1 TTTTTATTTTA
*
2468083 -TTTTAATTTA
1 TTTTTATTTTA
2468093 TTTTTATTTTA
1 TTTTTATTTTA
2468104 TTTTT
1 TTTTT
2468109 GCCGCCCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:2468099 original size:16 final size:15
Alignment explanation
Indices: 2468074--2468103 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2468064 GAAGAGAGTT
2468074 TTTATTTTATTTTAA
1 TTTATTTTATTTTAA
2468089 TTTATTTTTATTTTA
1 TTTA-TTTTATTTTA
2468104 TTTTTGCCGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTATTTTATTTTAA
Found at i:2472555 original size:3 final size:3
Alignment explanation
Indices: 2472542--2472583 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
2472532 TTCTTGGTTA
*
2472542 CTT CCT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
2472584 TACGTAAGTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:2473698 original size:49 final size:50
Alignment explanation
Indices: 2473626--2473727 Score: 143
Period size: 49 Copynumber: 2.1 Consensus size: 50
2473616 AACGACTTCT
*
2473626 ATATAAATAATTAAACCTAGCTTAAAGCTCAAGAACAACTAGG-GTTTAA
1 ATATAAATAATTAAACCTAGCTTAAAGCTCAAGAACAACGAGGAGTTTAA
* * * * *
2473675 ATATAAATAGTTAAACCTAGCTTAGAGTTGAAGTACAACGAGGAGTTTAA
1 ATATAAATAATTAAACCTAGCTTAAAGCTCAAGAACAACGAGGAGTTTAA
2473725 ATA
1 ATA
2473728 GCCAAAATCA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
49 37 0.80
50 9 0.20
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (50 bp):
ATATAAATAATTAAACCTAGCTTAAAGCTCAAGAACAACGAGGAGTTTAA
Found at i:2473828 original size:33 final size:34
Alignment explanation
Indices: 2473765--2473831 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 34
2473755 TGATACTACA
* * *
2473765 TAAATTATAAAATTTAATATATTATAATTATATT
1 TAAATTATAAAATATAATATAATAAAATTATATT
2473799 TAAA-TATAAAA-ATAATATAATAAATATTATATT
1 TAAATTATAAAATATAATATAATAAA-ATTATATT
2473832 ATTTTTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
32 10 0.34
33 15 0.52
34 4 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (34 bp):
TAAATTATAAAATATAATATAATAAAATTATATT
Found at i:2475234 original size:6 final size:7
Alignment explanation
Indices: 2475217--2475244 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
2475207 CTCTCTAAAC
2475217 AAAAAAT
1 AAAAAAT
2475224 AAAAAAT
1 AAAAAAT
2475231 AAAAAAT
1 AAAAAAT
2475238 AAAAAAT
1 AAAAAAT
2475245 TATAATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAAAT
Found at i:2475654 original size:60 final size:60
Alignment explanation
Indices: 2475581--2475694 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
2475571 GATTCTTGTT
* *
2475581 AGAGATGAGAGCTTTCATCAAGGTGATCAGAATCATCCCGTTTAAA-ATCGGATTCCTCCC
1 AGAGATGAGAGCTTTCATCAAGATGATCA-AATCATCACGTTTAAAGATCGGATTCCTCCC
* *
2475641 AGAGATTGA-AGCTTTCATTAAGATGATCAAATCATCAGGTTTAAAGATCGGATT
1 AGAGA-TGAGAGCTTTCATCAAGATGATCAAATCATCACGTTTAAAGATCGGATT
2475695 TTTTTCCAGA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
59 14 0.29
60 31 0.65
61 3 0.06
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (60 bp):
AGAGATGAGAGCTTTCATCAAGATGATCAAATCATCACGTTTAAAGATCGGATTCCTCCC
Found at i:2480447 original size:24 final size:23
Alignment explanation
Indices: 2480399--2480448 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
2480389 AAAATTCAAT
* *
2480399 TAATTAATTTTTTACAAATTACA
1 TAATTAATCTTTTACAAAATACA
*
2480422 TAATATAATCTTTTACAAAATGCA
1 TAAT-TAATCTTTTACAAAATACA
2480446 TAA
1 TAA
2480449 AATTTTCAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATTAATCTTTTACAAAATACA
Found at i:2480765 original size:25 final size:24
Alignment explanation
Indices: 2480724--2480771 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2480714 AAATAATAAA
* * *
2480724 TTTAATTTTTATTTTTATTTTTAT
1 TTTAAATTTAATTTTTATATTTAT
2480748 TTTAAATTTAATTATTTATATTTA
1 TTTAAATTTAATT-TTTATATTTA
2480772 AATTTTAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (24 bp):
TTTAAATTTAATTTTTATATTTAT
Found at i:2480778 original size:21 final size:19
Alignment explanation
Indices: 2480734--2480780 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 19
2480724 TTTAATTTTT
*
2480734 ATTTTTATTTTTATTTTAA
1 ATTTTAATTTTTATTTTAA
2480753 A-TTTAATTATTTATATTTAA
1 ATTTTAATT-TTTAT-TTTAA
2480773 ATTTTAAT
1 ATTTTAAT
2480781 CAAAATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 6 0.25
19 6 0.25
20 6 0.25
21 6 0.25
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
ATTTTAATTTTTATTTTAA
Found at i:2486998 original size:31 final size:29
Alignment explanation
Indices: 2486932--2486991 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
2486922 CTCTTGATTA
* *
2486932 TATTATTTTTAAATAAATTTTTATATTTT
1 TATTATATTTAAATAAATTTTTATTTTTT
2486961 TATTATATTTAAATAAATTTTTATTTTTT
1 TATTATATTTAAATAAATTTTTATTTTTT
2486990 TA
1 TA
2486992 ATTTATAGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (29 bp):
TATTATATTTAAATAAATTTTTATTTTTT
Found at i:2487008 original size:31 final size:29
Alignment explanation
Indices: 2486941--2487017 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
2486931 ATATTATTTT
* **
2486941 TAAATAAATTTTTATATTTTTATTATATT
1 TAAATAAATTTTTATTTTTTTATTATAGC
2486970 TAAATAAATTTTTATTTTTTTAATTTATAGC
1 TAAATAAATTTTTATTTTTTT-A-TTATAGC
* *
2487001 TAGATAAACTTTTATTT
1 TAAATAAATTTTTATTT
2487018 CAAACAGATT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
29 20 0.49
30 1 0.02
31 20 0.49
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (29 bp):
TAAATAAATTTTTATTTTTTTATTATAGC
Found at i:2488756 original size:2 final size:2
Alignment explanation
Indices: 2488749--2488777 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2488739 AAAGCAGAAT
2488749 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 T
2488778 CATGTTTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2490477 original size:21 final size:23
Alignment explanation
Indices: 2490438--2490484 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
2490428 TTTACATATC
*
2490438 AAATAAAAATAATATAATAAATT
1 AAATAAAAATAATAAAATAAATT
*
2490461 AAAT-AAAA-AATAAAATAATTT
1 AAATAAAAATAATAAAATAAATT
2490482 AAA
1 AAA
2490485 ATAATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 14 0.64
22 4 0.18
23 4 0.18
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (23 bp):
AAATAAAAATAATAAAATAAATT
Found at i:2490858 original size:10 final size:10
Alignment explanation
Indices: 2490843--2490880 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
2490833 AAGCTTATAT
2490843 AATTATTTAA
1 AATTATTTAA
2490853 AATTATATT-A
1 AATTAT-TTAA
*
2490863 AATAATTTAA
1 AATTATTTAA
2490873 AATTATTT
1 AATTATTT
2490881 TTATTAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
9 2 0.08
10 20 0.83
11 2 0.08
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
AATTATTTAA
Found at i:2491393 original size:42 final size:42
Alignment explanation
Indices: 2491262--2491393 Score: 142
Period size: 42 Copynumber: 3.1 Consensus size: 42
2491252 TCATATTCTA
* * *
2491262 TTTGATAATGGCAGTTAAGCCTTGGTTTTCAAGTTAAATTTTA-
1 TTTGGTAA-GGCAGTTAAGACTTGATTTT-AAGTTAAATTTTAT
* * * *
2491305 TTTGGTATGGCAGTTAAGACTTAGTTTTTAATTTAAATTTTGT
1 TTTGGTAAGGCAGTTAAGACTT-GATTTTAAGTTAAATTTTAT
*
2491348 TTTGGTAAGGTAGTTAAGACTTGATTTTAAG-TATAATTTTAT
1 TTTGGTAAGGCAGTTAAGACTTGATTTTAAGTTA-AATTTTAT
2491390 TTTG
1 TTTG
2491394 ACGGATAGAA
Statistics
Matches: 75, Mismatches: 11, Indels: 7
0.81 0.12 0.08
Matches are distributed among these distances:
41 2 0.03
42 42 0.56
43 31 0.41
ACGTcount: A:0.27, C:0.05, G:0.19, T:0.48
Consensus pattern (42 bp):
TTTGGTAAGGCAGTTAAGACTTGATTTTAAGTTAAATTTTAT
Found at i:2495835 original size:43 final size:42
Alignment explanation
Indices: 2495689--2495832 Score: 189
Period size: 43 Copynumber: 3.4 Consensus size: 42
2495679 AAAAGGGGAG
* * *
2495689 AAGTCAAATTCTATTTGGTAATGGCAACTAAAACTTGGTTTCC
1 AAGTCAAATTCTATTTGGT-ATGGTAGCTAAAACTTGGTTTTC
* *
2495732 AAATCAAATTCTATTTGGTATGGTAGCTAAAACTTTGTTTTC
1 AAGTCAAATTCTATTTGGTATGGTAGCTAAAACTTGGTTTTC
* *
2495774 AACTCAAATTCTATTTTGGTATGGTAGCTAAGACTTGGTTTTC
1 AAGTCAAATTCTA-TTTGGTATGGTAGCTAAAACTTGGTTTTC
* *
2495817 AAGTCTAATTCAATTT
1 AAGTCAAATTCTATTT
2495833 TGGCTGGATA
Statistics
Matches: 89, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
42 34 0.38
43 55 0.62
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (42 bp):
AAGTCAAATTCTATTTGGTATGGTAGCTAAAACTTGGTTTTC
Found at i:2497332 original size:74 final size:74
Alignment explanation
Indices: 2497206--2497355 Score: 230
Period size: 74 Copynumber: 2.0 Consensus size: 74
2497196 AAACCAAAGC
*
2497206 GTAACATGATTGGAAAGTCCAACAACATCACTTTAATTTATTCCTTCGCCAAAGCAAA-GGTTGA
1 GTAACATGATTGGAAAGTCCAACAACATCACTTTAATTTATTACTTCGCCAAAG-AAATGGTTGA
*
2497270 TGAAGGCGAG
65 CGAAGGCGAG
* ** *
2497280 GTAAGATGATTGGAAAGTCCGCCAACATCGCTTTAATTTATTACTTCGCCAAAGAAATGGTTGAC
1 GTAACATGATTGGAAAGTCCAACAACATCACTTTAATTTATTACTTCGCCAAAGAAATGGTTGAC
2497345 GAAGGCGAG
66 GAAGGCGAG
2497354 GT
1 GT
2497356 GGCATGCAAG
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
73 3 0.04
74 66 0.96
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (74 bp):
GTAACATGATTGGAAAGTCCAACAACATCACTTTAATTTATTACTTCGCCAAAGAAATGGTTGAC
GAAGGCGAG
Found at i:2500401 original size:20 final size:20
Alignment explanation
Indices: 2500373--2500410 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2500363 TAATAAGGGA
*
2500373 AATGGTGAGCTCGAAAAGCT
1 AATGATGAGCTCGAAAAGCT
*
2500393 AATGATGAGCTTGAAAAG
1 AATGATGAGCTCGAAAAG
2500411 GCAAAAAAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.11, G:0.29, T:0.21
Consensus pattern (20 bp):
AATGATGAGCTCGAAAAGCT
Found at i:2501467 original size:13 final size:13
Alignment explanation
Indices: 2501451--2501475 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2501441 ATGAAAAGAT
2501451 AAAAAGTGACAAA
1 AAAAAGTGACAAA
2501464 AAAAAGTGACAA
1 AAAAAGTGACAA
2501476 TATGAAAACT
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:0.68, C:0.08, G:0.16, T:0.08
Consensus pattern (13 bp):
AAAAAGTGACAAA
Found at i:2501860 original size:11 final size:10
Alignment explanation
Indices: 2501844--2501881 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
2501834 AAAATATTTT
2501844 AAATATAATTA
1 AAATATAA-TA
2501855 AAATATAATA
1 AAATATAATA
2501865 AAATAT-A-A
1 AAATATAATA
2501873 AAATATAAT
1 AAATATAAT
2501882 TACCATTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
8 7 0.28
9 2 0.08
10 8 0.32
11 8 0.32
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
AAATATAATA
Found at i:2501866 original size:20 final size:18
Alignment explanation
Indices: 2501812--2501881 Score: 63
Period size: 18 Copynumber: 3.8 Consensus size: 18
2501802 AATTATTAAC
*
2501812 ATATTAAAAT-TTATATAA
1 ATATTAAAATATAATA-AA
**
2501830 ATA-TAAAATATTTTAAA
1 ATATTAAAATATAATAAA
2501847 TATAATTAAAATATAATAAA
1 -AT-ATTAAAATATAATAAA
*
2501867 ATATAAAAATATAAT
1 ATATTAAAATATAAT
2501882 TACCATTTCT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
17 8 0.18
18 21 0.48
19 3 0.07
20 12 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATTAAAATATAATAAA
Found at i:2501877 original size:45 final size:44
Alignment explanation
Indices: 2501762--2501880 Score: 113
Period size: 43 Copynumber: 2.7 Consensus size: 44
2501752 TAACATAAAA
* *
2501762 AATTAAAATATGATACGAA-ATAAATATA-AAAATATCTTTAAATT
1 AATTAAAATAT-ATA-AAATATAAAAATATAAAATATCTTTAAATT
* *
2501806 -ATTAACATAT-TAAAATTTATATAAATATAAAATAT-TTTAAATAT
1 AATTAAAATATATAAAA--TATAAAAATATAAAATATCTTTAAAT-T
2501850 AATTAAAATATAATAAAATATAAAAATATAA
1 AATTAAAATAT-ATAAAATATAAAAATATAA
2501881 TTACCATTTC
Statistics
Matches: 61, Mismatches: 6, Indels: 15
0.74 0.07 0.18
Matches are distributed among these distances:
40 2 0.03
41 2 0.03
43 23 0.38
44 8 0.13
45 21 0.34
47 5 0.08
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.36
Consensus pattern (44 bp):
AATTAAAATATATAAAATATAAAAATATAAAATATCTTTAAATT
Found at i:2502387 original size:19 final size:19
Alignment explanation
Indices: 2502360--2502400 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2502350 TTTCATGACA
2502360 TAATATATAAT-TATTAATT
1 TAATATATAATATA-TAATT
*
2502379 TAATTTATAATATATAATT
1 TAATATATAATATATAATT
2502398 TAA
1 TAA
2502401 AAATTAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATATATAATATATAATT
Found at i:2502407 original size:26 final size:26
Alignment explanation
Indices: 2502359--2502409 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
2502349 ATTTCATGAC
* *
2502359 ATAATATATAATTATTAATTTAATTT
1 ATAATATATAATTATAAAATTAATTT
2502385 ATAATATATAATT-TAAAAATTAATT
1 ATAATATATAATTAT-AAAATTAATT
2502410 AATTAACTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
ATAATATATAATTATAAAATTAATTT
Found at i:2503408 original size:23 final size:23
Alignment explanation
Indices: 2503377--2503424 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
2503367 GTAATGCAGT
* *
2503377 AAATCAAAATTATATATTTAAAA
1 AAATAAAAAATATATATTTAAAA
*
2503400 AAATAAAAAATATATATTTTAAA
1 AAATAAAAAATATATATTTAAAA
2503423 AA
1 AA
2503425 GTAGGATTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
AAATAAAAAATATATATTTAAAA
Found at i:2503705 original size:17 final size:17
Alignment explanation
Indices: 2503683--2503716 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2503673 AATAAAAAAT
*
2503683 AAAATTTTTATGATTTA
1 AAAATTGTTATGATTTA
*
2503700 AAAATTGTTATTATTTA
1 AAAATTGTTATGATTTA
2503717 TTTTAGCTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
AAAATTGTTATGATTTA
Found at i:2504791 original size:22 final size:22
Alignment explanation
Indices: 2504749--2504807 Score: 75
Period size: 22 Copynumber: 2.5 Consensus size: 22
2504739 TACTTTAAAC
2504749 TTAAAAGAATAAACTTTTT-AAATA
1 TTAAAA-AAT-AA-TTTTTAAAATA
2504773 TTAAATAAATAATTTTTAAAATA
1 TTAAA-AAATAATTTTTAAAATA
2504796 TTAAAAAATAAT
1 TTAAAAAATAAT
2504808 ATAAATTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
22 12 0.36
23 12 0.36
24 8 0.24
25 1 0.03
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
TTAAAAAATAATTTTTAAAATA
Found at i:2504823 original size:19 final size:19
Alignment explanation
Indices: 2504801--2504843 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2504791 AAATATTAAA
2504801 AAATAATATAAATTA-TTTT
1 AAATAA-ATAAATTATTTTT
* *
2504820 AAATAAATTACTTATTTTT
1 AAATAAATAAATTATTTTT
2504839 AAATA
1 AAATA
2504844 TAAATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
AAATAAATAAATTATTTTT
Found at i:2505494 original size:16 final size:16
Alignment explanation
Indices: 2505482--2505530 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
2505472 AAAAATATAT
2505482 ATTTAAAATAATAAAA
1 ATTTAAAATAATAAAA
2505498 ATTTAAAAT-ATAAAA
1 ATTTAAAATAATAAAA
* *
2505513 ATAATAAAATCATAAAA
1 AT-TTAAAATAATAAAA
2505530 A
1 A
2505531 ACTTTTTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 8 0.27
16 15 0.50
17 7 0.23
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (16 bp):
ATTTAAAATAATAAAA
Found at i:2505576 original size:4 final size:4
Alignment explanation
Indices: 2505563--2505609 Score: 53
Period size: 4 Copynumber: 12.0 Consensus size: 4
2505553 ACACATTTTA
* *
2505563 AAAT -AAT AAAT AAAT AAAT AAAT AATTT AAA- AAAT AAAT ATAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT
2505610 GGCTCGCTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
3 6 0.17
4 27 0.75
5 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (4 bp):
AAAT
Found at i:2505968 original size:3 final size:3
Alignment explanation
Indices: 2505949--2505981 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
2505939 TTTTGATTGT
*
2505949 TTA TCA TTA TT- TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2505982 AGTTTAATGC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2506964 original size:13 final size:13
Alignment explanation
Indices: 2506946--2506986 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
2506936 AATAGTATTT
2506946 ATATTTTAATTAA
1 ATATTTTAATTAA
*
2506959 ATA-TTTAAAT-A
1 ATATTTTAATTAA
2506970 ATATTTTAATTTAA
1 ATATTTTAA-TTAA
2506984 ATA
1 ATA
2506987 GATATATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
11 4 0.17
12 11 0.48
13 4 0.17
14 4 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
ATATTTTAATTAA
Found at i:2507182 original size:22 final size:20
Alignment explanation
Indices: 2507151--2507192 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2507141 ATTAAATTAA
2507151 TTATTAAATATTATATTAATAT
1 TTATTAAATA--ATATTAATAT
*
2507173 TTATTTAATAATATTAATAT
1 TTATTAAATAATATTAATAT
2507193 AAAATATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTATTAAATAATATTAATAT
Found at i:2507186 original size:14 final size:14
Alignment explanation
Indices: 2507162--2507206 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
2507152 TATTAAATAT
*
2507162 TATATTAATATTTA
1 TATAATAATATTTA
* *
2507176 TTTAATAATATTAA
1 TATAATAATATTTA
2507190 TATAA-AATATTTA
1 TATAATAATATTTA
2507203 TATA
1 TATA
2507207 TTTGACTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TATAATAATATTTA
Found at i:2515061 original size:22 final size:23
Alignment explanation
Indices: 2515036--2515099 Score: 58
Period size: 27 Copynumber: 2.6 Consensus size: 23
2515026 AATGAATCTG
2515036 AATTTAAAAATTTATTTGA-AAA
1 AATTTAAAAATTTATTTGATAAA
*
2515058 AATTTGAATTCGAATTTGATTTGATAAA
1 AATTT-AA---AAATTT-ATTTGATAAA
*
2515086 AAGTTAAAAATTTA
1 AATTTAAAAATTTA
2515100 AATCTTAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 11
0.70 0.06 0.23
Matches are distributed among these distances:
22 5 0.15
23 3 0.09
24 5 0.15
26 5 0.15
27 8 0.24
28 7 0.21
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (23 bp):
AATTTAAAAATTTATTTGATAAA
Found at i:2515690 original size:16 final size:15
Alignment explanation
Indices: 2515669--2515698 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2515659 ATGTTACATT
2515669 TAGAATAGCAATATAG
1 TAGAATAG-AATATAG
2515685 TAGAATAGAATATA
1 TAGAATAGAATATA
2515699 AAGTTAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.03, G:0.17, T:0.27
Consensus pattern (15 bp):
TAGAATAGAATATAG
Found at i:2516381 original size:16 final size:16
Alignment explanation
Indices: 2516340--2516382 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
2516330 TGTAATAATA
*
2516340 AATTATTTAAAAAATT
1 AATTATATAAAAAATT
*
2516356 AATTTTATATAACAAATT
1 AA--TTATATAAAAAATT
2516374 AATTATATA
1 AATTATATA
2516383 TATAAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 9 0.39
18 14 0.61
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTATATAAAAAATT
Found at i:2516598 original size:16 final size:16
Alignment explanation
Indices: 2516579--2516621 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
2516569 CCTGAACTCG
* *
2516579 AACCTGAAAAAGTTCA
1 AACCCGAAAAAGTCCA
*
2516595 AACCCGAATAAGTCCA
1 AACCCGAAAAAGTCCA
*
2516611 AACTCGAAAAA
1 AACCCGAAAAA
2516622 ATTCGAACTC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.51, C:0.23, G:0.12, T:0.14
Consensus pattern (16 bp):
AACCCGAAAAAGTCCA
Found at i:2519313 original size:14 final size:14
Alignment explanation
Indices: 2519294--2519323 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2519284 CATGATTTTG
2519294 GAAGAAAAAAAAAA
1 GAAGAAAAAAAAAA
*
2519308 GAAGAAGAAAAAAA
1 GAAGAAAAAAAAAA
2519322 GA
1 GA
2519324 CAGCTTTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (14 bp):
GAAGAAAAAAAAAA
Found at i:2521175 original size:3 final size:3
Alignment explanation
Indices: 2521169--2521198 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2521159 TTAGTAGTAT
2521169 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2521199 TGGGCAATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2521317 original size:26 final size:25
Alignment explanation
Indices: 2521253--2521315 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 25
2521243 TTTATATTTT
*
2521253 TTATATAATAAATATATTTTAAATA
1 TTATATAATAAATAAATTTTAAATA
* *
2521278 TTATCTATTTAAATAAATTTTAATATA
1 TTATATA-ATAAATAAATTTTAA-ATA
2521305 TTA-ATAATAAA
1 TTATATAATAAA
2521316 ATTACATAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
25 10 0.32
26 15 0.48
27 6 0.19
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (25 bp):
TTATATAATAAATAAATTTTAAATA
Found at i:2522488 original size:21 final size:20
Alignment explanation
Indices: 2522435--2522489 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
2522425 AAATTTTATA
*
2522435 AAAAATTATTAAAATTATTT
1 AAAAATTATTAAAATTAATT
*
2522455 AATAGATTATTAAAATTGAATT
1 AA-AAATTATTAAAATT-AATT
*
2522477 AAAAATTGTTAAA
1 AAAAATTATTAAA
2522490 TTTATGTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 2 0.07
21 22 0.76
22 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (20 bp):
AAAAATTATTAAAATTAATT
Found at i:2523869 original size:19 final size:19
Alignment explanation
Indices: 2523834--2523870 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2523824 TTAATTTTAT
2523834 TTATTTTTAAAATATAAAA
1 TTATTTTTAAAATATAAAA
2523853 TTATTATTTAAAA-ATAAA
1 TTATT-TTTAAAATATAAA
2523871 TAAAATAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TTATTTTTAAAATATAAAA
Found at i:2524165 original size:61 final size:60
Alignment explanation
Indices: 2524083--2524208 Score: 198
Period size: 61 Copynumber: 2.1 Consensus size: 60
2524073 TAAATTGAAT
* * *
2524083 ACTATTAAGATAAGTGAACTTGATTAACGGATGAAGAGACTGTCTCGAGAATTGTTTAATA
1 ACTAATAAGACAAGTGAACTTGATTAACAGATGAAGAGACTGTCTCGAG-ATTGTTTAATA
* *
2524144 ACTAATAAGACAAGTGAACTTGATTAACAGATGAAGAGACTGTCTCGAGTTTGTTTACTA
1 ACTAATAAGACAAGTGAACTTGATTAACAGATGAAGAGACTGTCTCGAGATTGTTTAATA
2524204 ACTAA
1 ACTAA
2524209 ATGTTTGTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
60 14 0.23
61 46 0.77
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (60 bp):
ACTAATAAGACAAGTGAACTTGATTAACAGATGAAGAGACTGTCTCGAGATTGTTTAATA
Found at i:2524397 original size:14 final size:14
Alignment explanation
Indices: 2524378--2524425 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
2524368 TTATTTTGTG
2524378 AAAAATAAATTTTT
1 AAAAATAAATTTTT
* *
2524392 AAAAATAACTTTTA
1 AAAAATAAATTTTT
*
2524406 AAAAATAATTTTTTT
1 AAAAATAA-ATTTTT
2524421 AAAAA
1 AAAAA
2524426 AGTGATTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 20 0.69
15 9 0.31
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (14 bp):
AAAAATAAATTTTT
Found at i:2524422 original size:16 final size:17
Alignment explanation
Indices: 2524401--2524437 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
2524391 TAAAAATAAC
2524401 TTTTAAAAAA-TAATTT
1 TTTTAAAAAAGTAATTT
*
2524417 TTTTAAAAAAGTGATTT
1 TTTTAAAAAAGTAATTT
2524434 TTTT
1 TTTT
2524438 TATTGTTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (17 bp):
TTTTAAAAAAGTAATTT
Found at i:2524610 original size:63 final size:61
Alignment explanation
Indices: 2524543--2524693 Score: 169
Period size: 62 Copynumber: 2.4 Consensus size: 61
2524533 ATATTTAAAT
*
2524543 GATCAATCTTTTCTTTATTTGCTTTAACTTTTATTCTTAGAGAATCAATCCCTATAAGTAAGA
1 GATCAAT-TTTT-TTTATTTGCTTTAACTTTTAATCTTAGAGAATCAATCCCTATAAGTAAGA
* ** ** * * *
2524606 GATCAATTTTTTTAATTTTTTATTAACTTTTAATCTTAGATTATTAATCCGTATAAGTAGGA
1 GATCAATTTTTTTTATTTGCT-TTAACTTTTAATCTTAGAGAATCAATCCCTATAAGTAAGA
2524668 GATCAATATTTTTTGT-TTTGCTTTAA
1 GATCAAT-TTTTTT-TATTTGCTTTAA
2524694 TAAGAGATTG
Statistics
Matches: 73, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
61 7 0.10
62 49 0.67
63 17 0.23
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.49
Consensus pattern (61 bp):
GATCAATTTTTTTTATTTGCTTTAACTTTTAATCTTAGAGAATCAATCCCTATAAGTAAGA
Found at i:2524809 original size:20 final size:20
Alignment explanation
Indices: 2524772--2524810 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2524762 GTCTTAACAC
*
2524772 TTTTCAAAAGTATAAGATAG
1 TTTTCAAAAGAATAAGATAG
*
2524792 TTTTCAAAAGAATGAGATA
1 TTTTCAAAAGAATAAGATA
2524811 ACTTTCAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.33
Consensus pattern (20 bp):
TTTTCAAAAGAATAAGATAG
Found at i:2524816 original size:20 final size:20
Alignment explanation
Indices: 2524773--2524818 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2524763 TCTTAACACT
* **
2524773 TTTCAAAAGTATAAGATAGT
1 TTTCAAAAGAATAAGATAAC
*
2524793 TTTCAAAAGAATGAGATAAC
1 TTTCAAAAGAATAAGATAAC
2524813 TTTCAA
1 TTTCAA
2524819 TTGATTCAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.33
Consensus pattern (20 bp):
TTTCAAAAGAATAAGATAAC
Found at i:2525403 original size:72 final size:71
Alignment explanation
Indices: 2525327--2525715 Score: 265
Period size: 72 Copynumber: 5.4 Consensus size: 71
2525317 AGGGTTACGA
*
2525327 GTATTATTTATCTTTATTTGTAGAAGTTTAATTATTGTTTTTAGTTTGATTATAAAAGTTTAAAT
1 GTATTATTTATCTTTATTTGTAGAAGTTTAATTATT-TTTTTAGTATGATTATAAAAGTTTAAAT
*
2525392 TTTAAAG
65 TTTTAAG
* * *
2525399 GTATTATTTATCTTTATTTGTAGAAGTTTAAATT-TATTTTTGAGTATGATTATACATG-TTAAG
1 GTATTATTTATCTTTATTTGTAGAAGTTT-AATTAT-TTTTTTAGTATGATTATAAAAGTTTAA-
*
2525462 A-TCTTAAG
63 ATTTTTAAG
* * * * * * * **
2525470 GATATAATTTATTTTTATTTATAAAAATTTAA--ATTTTTTTGGTATGCTTAT-ACGGCTTTAAA
1 G-TATTATTTATCTTTATTTGTAGAAGTTTAATTATTTTTTTAGTATGATTATAAAAG-TTTAAA
*
2525532 TTTTTTA-
64 TTTTTAAG
* * * * * * ** * **
2525539 TTATATAATTAATTTTTATTTTTAAAAGTTTAAACGTATTTTTTGGGTATAATTATACTAGTTTA
1 GTAT-T-ATTTATCTTTATTTGTAGAAGTTT-AA-TTATTTTTTTAGTATGATTATAAAAGTTTA
* **
2525604 TATTTTTATT
62 AATTTTTAAG
* * * * * * **
2525614 GTGTAATTCATTTTTATTTGTAGAAATTTAAATTA-TTTTTTAGGT-TGATTACATGAGTTTAAA
1 GTATTATTTATCTTTATTTGTAGAAGTTT-AATTATTTTTTTA-GTATGATTATAAAAGTTTAAA
2525677 TTTTTAAG
64 TTTTTAAG
2525685 GTATTATTTATCTTTATTTGTAGAAGTTTAA
1 GTATTATTTATCTTTATTTGTAGAAGTTTAA
2525716 ACTATTATTA
Statistics
Matches: 245, Mismatches: 55, Indels: 36
0.73 0.16 0.11
Matches are distributed among these distances:
68 4 0.02
69 15 0.06
70 32 0.13
71 62 0.25
72 75 0.31
73 28 0.11
74 26 0.11
75 3 0.01
ACGTcount: A:0.31, C:0.03, G:0.12, T:0.54
Consensus pattern (71 bp):
GTATTATTTATCTTTATTTGTAGAAGTTTAATTATTTTTTTAGTATGATTATAAAAGTTTAAATT
TTTAAG
Found at i:2525627 original size:73 final size:70
Alignment explanation
Indices: 2525471--2525654 Score: 185
Period size: 73 Copynumber: 2.6 Consensus size: 70
2525461 GATCTTAAGG
* ** *
2525471 ATATAATTTATTTTTATTTATAAAAATTTAAAT-TTTTTTGGTATGCTTATACGGCTTTAAATTT
1 ATATAATTAATTTTTATTTAT-AAAATTTAAATATTTTTTGGTATAATTATACAGCTTTAAATTT
2525535 TTTATT
65 TTTATT
* *
2525541 ATATAATTAATTTTTATTTTTAAAAGTTTAAACGTATTTTTTGGGTATAATTATACTAG-TTTAT
1 ATATAATTAATTTTTATTTATAAAA-TTTAAA--TATTTTTT-GGTATAATTATAC-AGCTTTAA
2525605 A-TTTTTATT
61 ATTTTTTATT
* * * *
2525614 GTGTAATTCATTTTTATTTGTAGAAATTTAAATTATTTTTT
1 ATATAATTAATTTTTATTTATA-AAATTTAAA-TATTTTTT
2525655 AGGTTGATTA
Statistics
Matches: 96, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
69 4 0.04
70 25 0.26
72 9 0.09
73 38 0.40
74 19 0.20
75 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.08, T:0.57
Consensus pattern (70 bp):
ATATAATTAATTTTTATTTATAAAATTTAAATATTTTTTGGTATAATTATACAGCTTTAAATTTT
TTATT
Found at i:2526599 original size:24 final size:23
Alignment explanation
Indices: 2526571--2526617 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
2526561 TTCAATTGTG
2526571 TATTATGTT-CAAAAGTTAATAATT
1 TATTAT-TTACAAAA-TTAATAATT
*
2526595 TATTATTTACAAAATTTATAATT
1 TATTATTTACAAAATTAATAATT
2526618 ATAATACCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (23 bp):
TATTATTTACAAAATTAATAATT
Found at i:2527262 original size:158 final size:157
Alignment explanation
Indices: 2526846--2527281 Score: 502
Period size: 159 Copynumber: 2.7 Consensus size: 157
2526836 TAATATTAAA
* * *
2526846 CATAAAAAATTAATAATATTAAAAATTTCAAACAACATCAAGAGACATCTAAATGAGCATTTCAT
1 CATAAAAAATTAATAATATTAAAAATTTCAAATAACATCAAGAGATAT-TTAATGAGCATTTCAT
* *** * *
2526911 ATTACTTAAAAAAAATATAACGT-AAAACTACGTTAAACTAAGCCATTTTATTTTTTATTTCTTA
65 ATTAATT--AAAAAATATAAC-TAAAAACTACGTTAAACTAAGTTTTTTTATTTTTGATATCTTA
*
2526975 AACATAATTTTGATATATTAAATAAGAATAT
127 AACATAATTTTGATATATTAAATAAGAATAC
* * * *
2527006 CA-AAAAAATTAAAAATATAAAAAATCTT-AAATAACACCAAGAGCTATTTAAATGAGCATTTCA
1 CATAAAAAATTAATAATATTAAAAAT-TTCAAATAACATCAAGAGATATTT-AATGAGCATTTCA
* * * * *
2527069 TATTAATTAAAAAATAAAACAAAAAACCATGTTAAACTATGTTTTTTTATTTTTGATATCTTAAA
64 TATTAATTAAAAAATATAACTAAAAACTACGTTAAACTAAGTTTTTTTATTTTTGATATCTT--A
*
2527134 AACAT-ATTTTGATATATTAAATAAGCATAC
127 AACATAATTTTGATATATTAAATAAGAATAC
* * * * *
2527164 CATAAAAAATTAATAATATTAAAAATTTCAAATAACATCAAAAGGTATTTAACGAGTATTTTATA
1 CATAAAAAATTAATAATATTAAAAATTTCAAATAACATCAAGAGATATTTAATGAGCATTTCATA
* * * *
2527229 TTAATTAAAAAATATAATTAAAAACTACATTAAATTAAGTCTTTTTAATTTTT
66 TTAATTAAAAAATATAACTAAAAACTACGTTAAACTAAGT-TTTTTTATTTTT
2527282 TGGCTTAATT
Statistics
Matches: 231, Mismatches: 37, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
157 43 0.19
158 72 0.31
159 112 0.48
160 4 0.02
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.36
Consensus pattern (157 bp):
CATAAAAAATTAATAATATTAAAAATTTCAAATAACATCAAGAGATATTTAATGAGCATTTCATA
TTAATTAAAAAATATAACTAAAAACTACGTTAAACTAAGTTTTTTTATTTTTGATATCTTAAACA
TAATTTTGATATATTAAATAAGAATAC
Found at i:2527397 original size:18 final size:19
Alignment explanation
Indices: 2527374--2527423 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
2527364 CTTTGGTTTT
*
2527374 TTTTTTTCTT-TTTATTTC
1 TTTTTTTCTTCTCTATTTC
*
2527392 -TTTTTTCTTCTCTCTTTC
1 TTTTTTTCTTCTCTATTTC
*
2527410 TTTTTTTTTTCTCT
1 TTTTTTTCTTCTCT
2527424 TCTTTTTCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 9 0.33
18 6 0.22
19 12 0.44
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTTTTCTTCTCTATTTC
Found at i:2527420 original size:11 final size:11
Alignment explanation
Indices: 2527371--2527432 Score: 54
Period size: 11 Copynumber: 5.6 Consensus size: 11
2527361 TTTCTTTGGT
*
2527371 TTTTTTTTTTC
1 TTTTTCTTTTC
*
2527382 TTTTT-ATTTC
1 TTTTTCTTTTC
*
2527392 TTTTTTCTTCTC
1 -TTTTTCTTTTC
* *
2527404 TCTTTCTTTTT
1 TTTTTCTTTTC
*
2527415 TTTTTCTCTTC
1 TTTTTCTTTTC
2527426 TTTTTCT
1 TTTTTCT
2527433 AATTCAAAGT
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
10 4 0.10
11 33 0.82
12 3 0.08
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:2527422 original size:17 final size:17
Alignment explanation
Indices: 2527374--2527430 Score: 62
Period size: 18 Copynumber: 3.3 Consensus size: 17
2527364 CTTTGGTTTT
* *
2527374 TTTTTTTCTTTTTATTTC
1 TTTTTTT-TTTCTCTTTC
*
2527392 TTTTTTCTTCTCTCTTTC
1 TTTTTT-TTTTCTCTTTC
2527410 TTTTTTTTTTCTC-TTC
1 TTTTTTTTTTCTCTTTC
2527426 TTTTT
1 TTTTT
2527431 CTAATTCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
16 8 0.24
17 6 0.18
18 19 0.56
19 1 0.03
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTTTTTTCTCTTTC
Found at i:2527431 original size:22 final size:21
Alignment explanation
Indices: 2527370--2527432 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 21
2527360 GTTTCTTTGG
*
2527370 TTTTTTTT-TTTCTTTTTATT
1 TTTTTTTTCTTTCTTTTTCTT
* *
2527390 TCTTTTTTCTTCTCTCTTTCTT
1 TTTTTTTTCTT-TCTTTTTCTT
2527412 TTTTTTTTCTCTTCTTTTTCT
1 TTTTTTTTCT-TTCTTTTTCT
2527433 AATTCAAAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 7 0.20
21 2 0.06
22 25 0.71
23 1 0.03
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTTTTTTCTTTCTTTTTCTT
Found at i:2527565 original size:73 final size:72
Alignment explanation
Indices: 2527469--2527681 Score: 245
Period size: 73 Copynumber: 3.0 Consensus size: 72
2527459 CTGATCACGG
* * *
2527469 CATC-TAAAAATTTAAATTTATATAATCAAACTAAAAAATAAATTTTAAATTTTTACAAATAAAA
1 CATCATAAAAATTTAAACTCATATAATCAAA-TAAAAAATAAA-TTTAAATTTCTACAAATAAAA
2527533 ATAAATT-T
64 ATAAATTAT
* * * *
2527541 CATCATAAAAATTTAAACTCATATAATCATATTTAAAAAACACATTTAAATTTCTACAAATCAAA
1 CATCATAAAAATTTAAACTCATATAATCA-A-ATAAAAAATAAATTTAAATTTCTACAAATAAAA
2527606 ATAAATTAT
64 ATAAATTAT
* * * ** *
2527615 -AACAAAAAAATTTAAAC-CTTATAATCAAATAAAAAATAAATTTAAACATCTATAAATAAAAAT
1 CATCATAAAAATTTAAACTCATATAATCAAATAAAAAATAAATTTAAATTTCTACAAATAAAAAT
2527678 AAAT
66 AAAT
2527682 AATACATTTA
Statistics
Matches: 120, Mismatches: 17, Indels: 10
0.82 0.12 0.07
Matches are distributed among these distances:
70 32 0.27
71 1 0.01
72 13 0.11
73 63 0.52
74 11 0.09
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (72 bp):
CATCATAAAAATTTAAACTCATATAATCAAATAAAAAATAAATTTAAATTTCTACAAATAAAAAT
AAATTAT
Found at i:2527698 original size:27 final size:26
Alignment explanation
Indices: 2527638--2527701 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 26
2527628 AAACCTTATA
2527638 ATCAAATAAAAAATAAATTTAAACATCT
1 ATCAAAT-AAAAATAAA-TTAAACATCT
*
2527666 AT-AAATAAAAATAAA-TAATACATTT
1 ATCAAATAAAAATAAATTAA-ACATCT
2527691 ATTCAAATAAA
1 A-TCAAATAAA
2527702 TCTTATAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
24 3 0.09
25 6 0.19
26 10 0.31
27 11 0.34
28 2 0.06
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.30
Consensus pattern (26 bp):
ATCAAATAAAAATAAATTAAACATCT
Found at i:2528175 original size:21 final size:21
Alignment explanation
Indices: 2528108--2528177 Score: 58
Period size: 21 Copynumber: 3.4 Consensus size: 21
2528098 TAAATTTTTT
2528108 AATTTAAT-TT-TTTTTATAAA
1 AATTTAATATTATTTTT-TAAA
*
2528128 AA--TAATAATTAATATTTTAAA
1 AATTTAAT-ATT-ATTTTTTAAA
**
2528149 TTTTTAATATTATTTTTTAAA
1 AATTTAATATTATTTTTTAAA
2528170 AATTTAAT
1 AATTTAAT
2528178 TAAAATTTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 11
0.69 0.11 0.20
Matches are distributed among these distances:
18 4 0.11
20 4 0.11
21 19 0.50
22 7 0.18
23 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
AATTTAATATTATTTTTTAAA
Found at i:2528178 original size:41 final size:46
Alignment explanation
Indices: 2528094--2528185 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 46
2528084 TGATATTTTG
* *
2528094 ATTTTAAATTTTTTAATTTAATTTTTTTTATAAAAATAATAATTAAT
1 ATTTTAAATTTTTTAA-TTAATTATTTTTATAAAAATAATAATTAAA
*
2528141 ATTTTAAA-TTTTTAA-T-ATTATTTTT-TAAAAAT-TTAATTAAA
1 ATTTTAAATTTTTTAATTAATTATTTTTATAAAAATAATAATTAAA
2528182 ATTT
1 ATTT
2528186 ATTTTTATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
41 11 0.26
42 7 0.17
43 8 0.19
44 1 0.02
46 7 0.17
47 8 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (46 bp):
ATTTTAAATTTTTTAATTAATTATTTTTATAAAAATAATAATTAAA
Found at i:2528240 original size:76 final size:68
Alignment explanation
Indices: 2528108--2528263 Score: 154
Period size: 72 Copynumber: 2.2 Consensus size: 68
2528098 TAAATTTTTT
* * *
2528108 AATTTAATTTTTTTTATAAAAATAATAATTAATATTTTAAATTTTTAATATTATTTTTTAAAAAT
1 AATTTATTTTTTTTTATAAAAATAATAATTAATATATTAAATTTTTAATA-TAATTTTT---AAT
2528173 TTAATTAA
62 TTAATT-A
* *
2528181 AATTTATTTTTATTTTATTAAAATTTAATAATTAATATATT-GA-TTTTAATATGAAATTTTTAA
1 AATTTATTTTT-TTTTA-TAAAA-ATAATAATTAATATATTAAATTTTTAATAT--AATTTTTAA
2528244 TTTAATTA
61 TTTAATTA
2528252 AATTATATTTTT
1 AATT-TATTTTT
2528264 CAATTTTCAT
Statistics
Matches: 72, Mismatches: 5, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
71 5 0.07
72 16 0.22
73 11 0.15
74 13 0.18
75 12 0.17
76 15 0.21
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (68 bp):
AATTTATTTTTTTTTATAAAAATAATAATTAATATATTAAATTTTTAATATAATTTTTAATTTAA
TTA
Found at i:2528252 original size:23 final size:23
Alignment explanation
Indices: 2528226--2528269 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
2528216 TATATTGATT
2528226 TTAATATGAAATTTTT-AATTTAA
1 TTAA-ATGAAATTTTTCAATTTAA
* *
2528249 TTAAATTATATTTTTCAATTT
1 TTAAATGAAATTTTTCAATTT
2528270 TCATGATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (23 bp):
TTAAATGAAATTTTTCAATTTAA
Found at i:2528395 original size:23 final size:23
Alignment explanation
Indices: 2528364--2528442 Score: 65
Period size: 23 Copynumber: 3.3 Consensus size: 23
2528354 ATTTTTAAAA
*
2528364 ATATAATTTAAAATTAAAAAATT
1 ATATTATTTAAAATTAAAAAATT
*
2528387 ATATTATTTAAATATTTTTAAAAA-T
1 ATATTATTTAAA-A--TTAAAAAATT
2528412 ATA--ATTTAAAAATTAACAAAATT
1 ATATTATTT-AAAATTAA-AAAATT
*
2528435 TTATTATT
1 ATATTATT
2528443 ATTATCATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
21 3 0.07
22 4 0.09
23 19 0.43
24 4 0.09
25 7 0.16
26 7 0.16
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (23 bp):
ATATTATTTAAAATTAAAAAATT
Found at i:2528400 original size:46 final size:48
Alignment explanation
Indices: 2528350--2528442 Score: 163
Period size: 46 Copynumber: 2.0 Consensus size: 48
2528340 ATATCTTCAA
2528350 AAATATTTTTAAAAATATAATTT-AAAATTAA-AAAATTATATTATTT
1 AAATATTTTTAAAAATATAATTTAAAAATTAACAAAATTATATTATTT
*
2528396 AAATATTTTTAAAAATATAATTTAAAAATTAACAAAATTTTATTATT
1 AAATATTTTTAAAAATATAATTTAAAAATTAACAAAATTATATTATT
2528443 ATTATCATAA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 23 0.52
47 8 0.18
48 13 0.30
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (48 bp):
AAATATTTTTAAAAATATAATTTAAAAATTAACAAAATTATATTATTT
Found at i:2528456 original size:46 final size:46
Alignment explanation
Indices: 2528360--2528456 Score: 117
Period size: 46 Copynumber: 2.1 Consensus size: 46
2528350 AAATATTTTT
** *
2528360 AAAAATATAATTTAAAATTAAAAAATTATATTATTTAAATATTTTT
1 AAAAATATAATTTAAAATTAAAAAATTATATTATTTAAATATCATA
* *
2528406 AAAAATATAATTTAAAAATTAACAAAATTTTATTA-TT-ATTATCATA
1 AAAAATATAATTT-AAAATTAA-AAAATTATATTATTTAAATATCATA
2528452 AAAAA
1 AAAAA
2528457 GGCCGTAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
46 23 0.52
47 10 0.23
48 11 0.25
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (46 bp):
AAAAATATAATTTAAAATTAAAAAATTATATTATTTAAATATCATA
Found at i:2529695 original size:52 final size:54
Alignment explanation
Indices: 2529639--2529748 Score: 145
Period size: 52 Copynumber: 2.1 Consensus size: 54
2529629 TATGTATAAA
* * *
2529639 AAATG-GAGTTATTTAAATAATAAATTAAATTTTTTATTTAAT-AT-TTTTATAC
1 AAATGAGA-TTATTTAAATAATAAATTAAAATTTTAATATAATAATATTTTATAC
* *
2529691 AAATGAGATTATTTAAATAATGAATTAAAATTTTAATATAATAATATTTTATTC
1 AAATGAGATTATTTAAATAATAAATTAAAATTTTAATATAATAATATTTTATAC
2529745 AAAT
1 AAAT
2529749 TCAATTAATC
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
52 35 0.70
53 4 0.08
54 11 0.22
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (54 bp):
AAATGAGATTATTTAAATAATAAATTAAAATTTTAATATAATAATATTTTATAC
Found at i:2534654 original size:3 final size:3
Alignment explanation
Indices: 2534646--2534696 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
2534636 CCCAGATTCA
2534646 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2534694 AAT
1 AAT
2534697 GAGAAGTTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2537154 original size:6 final size:6
Alignment explanation
Indices: 2537140--2537191 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
2537130 TTAGTATTTA
* * ** * *
2537140 TTATTT TTATAT TTATAT TTATAT TCATAT TCGTAT TCATAT TTATTT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
2537188 TTAT
1 TTAT
2537192 TACCATCATC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (6 bp):
TTATAT
Found at i:2538619 original size:12 final size:12
Alignment explanation
Indices: 2538602--2538626 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2538592 TGAAAATTTC
2538602 AAAAATAAATAA
1 AAAAATAAATAA
2538614 AAAAATAAATAA
1 AAAAATAAATAA
2538626 A
1 A
2538627 TAACTGGTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAATAAATAA
Found at i:2539207 original size:2 final size:2
Alignment explanation
Indices: 2539200--2539224 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2539190 TGATTCGACT
2539200 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
2539225 TAGAAATCGT
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
Done.