Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr1
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: 35726063
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1821929 characters in sequence are not A, C, G, or T
File 2 of 109
Found at i:390111 original size:16 final size:16
Alignment explanation
Indices: 390084--390126 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
390074 ATAGTTGGTT
*
390084 TATATATGTATGTGTA
1 TATATATGTATGGGTA
* *
390100 TGTATATTTATGGGTA
1 TATATATGTATGGGTA
390116 TATATATGTAT
1 TATATATGTAT
390127 TGTAGCCAAA
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:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (16 bp):
TATATATGTATGGGTA
Found at i:390878 original size:17 final size:17
Alignment explanation
Indices: 390856--390893 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
390846 CAAAGGGATG
390856 ATGATTTATTCAATGAA
1 ATGATTTATTCAATGAA
390873 ATGATTTATTCAATGAA
1 ATGATTTATTCAATGAA
390890 ATGA
1 ATGA
390894 GTGCATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.05, G:0.13, T:0.39
Consensus pattern (17 bp):
ATGATTTATTCAATGAA
Found at i:393849 original size:12 final size:12
Alignment explanation
Indices: 393832--393857 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
393822 GCAACTCATC
393832 TTATTCAAGGAA
1 TTATTCAAGGAA
393844 TTATTCAAGGAA
1 TTATTCAAGGAA
393856 TT
1 TT
393858 TGCACTGTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (12 bp):
TTATTCAAGGAA
Found at i:393952 original size:15 final size:15
Alignment explanation
Indices: 393932--393962 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
393922 GATTTTCCTT
393932 TTTAACATCATATAA
1 TTTAACATCATATAA
*
393947 TTTAACATTATATAA
1 TTTAACATCATATAA
393962 T
1 T
393963 AGCCTCAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTAACATCATATAA
Found at i:395681 original size:27 final size:27
Alignment explanation
Indices: 395651--395706 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
395641 TATGAGGATA
395651 GACTTGGTCAATAAATGACCACGTGTT
1 GACTTGGTCAATAAATGACCACGTGTT
*
395678 GACTTGGTCAATAAATGACTACGTGTT
1 GACTTGGTCAATAAATGACCACGTGTT
395705 GA
1 GA
395707 TGTTGATATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.30
Consensus pattern (27 bp):
GACTTGGTCAATAAATGACCACGTGTT
Found at i:398526 original size:15 final size:15
Alignment explanation
Indices: 398506--398536 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
398496 TGATTTTCCT
398506 TTTAACATCATATAA
1 TTTAACATCATATAA
*
398521 TTTAACATTATATAA
1 TTTAACATCATATAA
398536 T
1 T
398537 AGCCTCAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTAACATCATATAA
Found at i:398615 original size:27 final size:27
Alignment explanation
Indices: 398585--398638 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
398575 TCGGCTTCCT
398585 ATATTTCACAACCTTATTGAATTTGAA
1 ATATTTCACAACCTTATTGAATTTGAA
398612 ATATTTCACAACCTTATTGAATTTGAA
1 ATATTTCACAACCTTATTGAATTTGAA
398639 TATGGTGGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (27 bp):
ATATTTCACAACCTTATTGAATTTGAA
Found at i:399329 original size:16 final size:16
Alignment explanation
Indices: 399302--399344 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
399292 ATAGTTGGTT
*
399302 TATATATGTATGTGTA
1 TATATATGTATGGGTA
* *
399318 TGTATATTTATGGGTA
1 TATATATGTATGGGTA
399334 TATATATGTAT
1 TATATATGTAT
399345 TGTAGCCAAA
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:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (16 bp):
TATATATGTATGGGTA
Found at i:401302 original size:46 final size:46
Alignment explanation
Indices: 401235--401331 Score: 149
Period size: 46 Copynumber: 2.1 Consensus size: 46
401225 AGAATTAATA
** * **
401235 AAGAAGTTGTCTATTTAAATATGAGAAATTAAACTGGTTCAATTCT
1 AAGAAGTTGTCTACCTAAATATGAGAAATTAAACTCGCCCAATTCT
401281 AAGAAGTTGTCTACCTAAATATGAGAAATTAAACTCGCCCAATTCT
1 AAGAAGTTGTCTACCTAAATATGAGAAATTAAACTCGCCCAATTCT
401327 AAGAA
1 AAGAA
401332 TTGATGAAGA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.31
Consensus pattern (46 bp):
AAGAAGTTGTCTACCTAAATATGAGAAATTAAACTCGCCCAATTCT
Found at i:401396 original size:56 final size:57
Alignment explanation
Indices: 401281--401429 Score: 246
Period size: 56 Copynumber: 2.6 Consensus size: 57
401271 GTTCAATTCT
* *
401281 AAGAAGTTGTCTACCTAAATATGAGAAATTAAACTCGCCCAATTCTAAGAATTGATG
1 AAGAAGTTGTCTACTTAAATATGAGAAATTAAACTGGCCCAATTCTAAGAATTGATG
***
401338 AAGAAGTTGTCTACTTAAATATGAGAAA-TAAACTGGCTTGATTCTAAGAATTGATG
1 AAGAAGTTGTCTACTTAAATATGAGAAATTAAACTGGCCCAATTCTAAGAATTGATG
401394 AAGAAGTTGTCTACTTAAATATGAGAAATTAAACTG
1 AAGAAGTTGTCTACTTAAATATGAGAAATTAAACTG
401430 ATAAGATTAT
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
56 52 0.60
57 34 0.40
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.30
Consensus pattern (57 bp):
AAGAAGTTGTCTACTTAAATATGAGAAATTAAACTGGCCCAATTCTAAGAATTGATG
Found at i:401534 original size:29 final size:29
Alignment explanation
Indices: 401501--401559 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
401491 ATGTAAATCG
401501 CTTAATTGTATATATGCTTCGATCTCATC
1 CTTAATTGTATATATGCTTCGATCTCATC
*
401530 CTTAATTGTATATATGCTTCGATTTCATC
1 CTTAATTGTATATATGCTTCGATCTCATC
401559 C
1 C
401560 ATCGATTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (29 bp):
CTTAATTGTATATATGCTTCGATCTCATC
Found at i:404218 original size:120 final size:121
Alignment explanation
Indices: 404014--404234 Score: 419
Period size: 120 Copynumber: 1.8 Consensus size: 121
404004 TTTTCTCTAT
404014 TTTTTAAATAATTTTAAATATATATAAATTAATATATATATGGAGGTACTTAAATTTGACAATTT
1 TTTTTAAATAATTTTAAATATATATAAATTAATATATATATGGAGGTACTTAAATTTGACAATTT
404079 GTATATATTTGGTAGTTAAC-TTTTTTAACCTAATTTTTATTTTTTATTTTTTGAA
66 GTATATATTTGGTAGTTAACTTTTTTTAACCTAATTTTTATTTTTTATTTTTTGAA
404134 TTTTT-AATAAATTTTAAATATATATAAATTAATATATATATGGAGGTACTTAAATTTGACAATT
1 TTTTTAAAT-AATTTTAAATATATATAAATTAATATATATATGGAGGTACTTAAATTTGACAATT
404198 TGTATATATTTGGTAGTTAACTTTTTTTAACCTAATT
65 TGTATATATTTGGTAGTTAACTTTTTTTAACCTAATT
404235 GATATCTAAA
Statistics
Matches: 99, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
119 3 0.03
120 81 0.82
121 15 0.15
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.51
Consensus pattern (121 bp):
TTTTTAAATAATTTTAAATATATATAAATTAATATATATATGGAGGTACTTAAATTTGACAATTT
GTATATATTTGGTAGTTAACTTTTTTTAACCTAATTTTTATTTTTTATTTTTTGAA
Found at i:409810 original size:16 final size:16
Alignment explanation
Indices: 409789--409819 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
409779 GAAACCCCTT
409789 CAGTGTAACATAACAC
1 CAGTGTAACATAACAC
409805 CAGTGTAACATAACA
1 CAGTGTAACATAACA
409820 TCGACAAGAG
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:0.45, C:0.23, G:0.13, T:0.19
Consensus pattern (16 bp):
CAGTGTAACATAACAC
Found at i:421663 original size:20 final size:20
Alignment explanation
Indices: 421627--421664 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
421617 TTGTGATATT
*
421627 CAAAATTATTTCATAAAAAA
1 CAAAATTAGTTCATAAAAAA
421647 CAAAATTTAGTTC-TAAAA
1 CAAAA-TTAGTTCATAAAA
421665 GAGAAGGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.32
Consensus pattern (20 bp):
CAAAATTAGTTCATAAAAAA
Found at i:427635 original size:17 final size:17
Alignment explanation
Indices: 427615--427675 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
427605 ATTTCAAGAC
427615 TTATGTAATATTTTTAA
1 TTATGTAATATTTTTAA
* ***
427632 TTATGTAGTTATTCAAAGA
1 TTATGTA-ATATTTTTA-A
*
427651 CTTATGTAATGTTTTTAA
1 -TTATGTAATATTTTTAA
427669 TTATGTA
1 TTATGTA
427676 GTGATTCAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
17 14 0.44
18 6 0.19
19 5 0.16
20 7 0.22
ACGTcount: A:0.33, C:0.03, G:0.11, T:0.52
Consensus pattern (17 bp):
TTATGTAATATTTTTAA
Found at i:427651 original size:37 final size:37
Alignment explanation
Indices: 427593--427684 Score: 134
Period size: 37 Copynumber: 2.5 Consensus size: 37
427583 CTTGCATTTC
427593 AATTATGT-GTTAATTTC-AAGACTTATGTAATATTTTT
1 AATTATGTAGTT-A-TTCAAAGACTTATGTAATATTTTT
*
427630 AATTATGTAGTTATTCAAAGACTTATGTAATGTTTTT
1 AATTATGTAGTTATTCAAAGACTTATGTAATATTTTT
*
427667 AATTATGTAGTGATTCAA
1 AATTATGTAGTTATTCAA
427685 TTTGGTTAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
36 3 0.06
37 45 0.88
38 3 0.06
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.48
Consensus pattern (37 bp):
AATTATGTAGTTATTCAAAGACTTATGTAATATTTTT
Found at i:427701 original size:9 final size:9
Alignment explanation
Indices: 427689--427794 Score: 67
Period size: 9 Copynumber: 11.8 Consensus size: 9
427679 ATTCAATTTG
427689 GTTAATTCA
1 GTTAATTCA
**
427698 GTTAATTTG
1 GTTAATTCA
*
427707 GTTAATTTGA
1 GTTAA-TTCA
*
427717 G-TAATTCG
1 GTTAATTCA
*
427725 GTTAATTCT
1 GTTAATTCA
427734 GTTAATTC-
1 GTTAATTCA
*
427742 GATTAATTCG
1 G-TTAATTCA
*
427752 GTTAATTCG
1 GTTAATTCA
*
427761 GGTAATT-A
1 GTTAATTCA
*
427769 GTGTAATT-T
1 GT-TAATTCA
427778 GATTAATTCA
1 G-TTAATTCA
427788 GTTAATT
1 GTTAATT
427795 TTTAACCAAA
Statistics
Matches: 78, Mismatches: 12, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
8 5 0.06
9 67 0.86
10 6 0.08
ACGTcount: A:0.28, C:0.07, G:0.18, T:0.47
Consensus pattern (9 bp):
GTTAATTCA
Found at i:427706 original size:18 final size:18
Alignment explanation
Indices: 427683--427795 Score: 113
Period size: 18 Copynumber: 6.3 Consensus size: 18
427673 GTAGTGATTC
427683 AATTTGGTTAATTCAGTT
1 AATTTGGTTAATTCAGTT
*
427701 AATTTGGTTAATTTGAG-T
1 AATTTGGTTAA-TTCAGTT
* *
427719 AATTCGGTTAATTCTGTT
1 AATTTGGTTAATTCAGTT
* * *
427737 AATTCGATTAATTCGGTT
1 AATTTGGTTAATTCAGTT
* *
427755 AATTCGGGTAATT-AGTGT
1 AATTTGGTTAATTCAGT-T
*
427773 AATTTGATTAATTCAGTT
1 AATTTGGTTAATTCAGTT
427791 AATTT
1 AATTT
427796 TTAACCAAAA
Statistics
Matches: 79, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
17 5 0.06
18 67 0.85
19 7 0.09
ACGTcount: A:0.28, C:0.06, G:0.18, T:0.48
Consensus pattern (18 bp):
AATTTGGTTAATTCAGTT
Found at i:427775 original size:27 final size:27
Alignment explanation
Indices: 427691--427794 Score: 102
Period size: 27 Copynumber: 3.9 Consensus size: 27
427681 TCAATTTGGT
* * * *
427691 TAATTCAGTTAATTTGGTTAATTTGAG
1 TAATTCGGTTAATTCGGTTAATTAGTG
* *
427718 TAATTCGGTTAATTCTGTTAATTCGAT-
1 TAATTCGGTTAATTCGGTTAATTAG-TG
*
427745 TAATTCGGTTAATTCGGGTAATTAGTG
1 TAATTCGGTTAATTCGGTTAATTAGTG
* * *
427772 TAATTTGATTAATTCAGTTAATT
1 TAATTCGGTTAATTCGGTTAATT
427795 TTTAACCAAA
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
26 1 0.02
27 62 0.98
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.47
Consensus pattern (27 bp):
TAATTCGGTTAATTCGGTTAATTAGTG
Found at i:428756 original size:4 final size:4
Alignment explanation
Indices: 428747--428792 Score: 92
Period size: 4 Copynumber: 11.5 Consensus size: 4
428737 TACTCAATAC
428747 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC
428793 CATTAAGTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:436533 original size:32 final size:32
Alignment explanation
Indices: 436496--436563 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
436486 TTGAACAAGT
436496 TGAACCGATTTAATATTTTTTTTAAAAGTTTA
1 TGAACCGATTTAATATTTTTTTTAAAAGTTTA
436528 TGAACCGATTTAATATTTTTTTTAAAAGTTTA
1 TGAACCGATTTAATATTTTTTTTAAAAGTTTA
436560 TGAA
1 TGAA
436564 TTTTTAATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.49
Consensus pattern (32 bp):
TGAACCGATTTAATATTTTTTTTAAAAGTTTA
Found at i:451594 original size:30 final size:30
Alignment explanation
Indices: 451549--451606 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
451539 CACGGATTGG
* *
451549 CACATGGGCGTGTGGCTAGCCCGTGTGGCT
1 CACAAGGGCGTGTGGCCAGCCCGTGTGGCT
*
451579 CACAAGGGTGTGTGGCCAGCCCGTGTGG
1 CACAAGGGCGTGTGGCCAGCCCGTGTGG
451607 AAATGCCCAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.12, C:0.26, G:0.41, T:0.21
Consensus pattern (30 bp):
CACAAGGGCGTGTGGCCAGCCCGTGTGGCT
Found at i:456069 original size:8 final size:8
Alignment explanation
Indices: 456058--456084 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
456048 TGATTACAAT
456058 ATTATAAA
1 ATTATAAA
456066 ATTATAAA
1 ATTATAAA
456074 ATTATAAA
1 ATTATAAA
456082 ATT
1 ATT
456085 TGATTTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
ATTATAAA
Found at i:456420 original size:22 final size:20
Alignment explanation
Indices: 456392--456442 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
456382 CATCAGTAAA
*
456392 TAAATATAAATTAATTAATTAT
1 TAAATATAAA-T-ATTAAATAT
456414 TAAATATCAAATATTAAATAT
1 TAAATAT-AAATATTAAATAT
456435 TAAA-ATAA
1 TAAATATAA
456443 TATAGTACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 2 0.07
20 2 0.07
21 12 0.44
22 8 0.30
23 3 0.11
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
TAAATATAAATATTAAATAT
Found at i:456435 original size:7 final size:7
Alignment explanation
Indices: 456392--456438 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
456382 CATCAGTAAA
456392 TAAATA-
1 TAAATAT
456398 TAAATTAAT
1 TAAA-T-AT
*
456407 TAATTAT
1 TAAATAT
456414 TAAATAT
1 TAAATAT
*
456421 CAAATAT
1 TAAATAT
456428 TAAATAT
1 TAAATAT
456435 TAAA
1 TAAA
456439 ATAATATAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
6 4 0.12
7 25 0.74
8 2 0.06
9 3 0.09
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (7 bp):
TAAATAT
Found at i:456743 original size:107 final size:107
Alignment explanation
Indices: 456611--456818 Score: 344
Period size: 107 Copynumber: 1.9 Consensus size: 107
456601 AAAAATAGGG
*
456611 AAAATAATACAAGCAAAGGGCAGGGATAAGGGTTTTTTTCTTACACCAAATTAATTTTAAAAACA
1 AAAATAATACAAGCAAAGGGCAGGGATAAGGGTTTTTTTCTTACACCAAATTAATTTAAAAAACA
* * *
456676 CATTAAATTAATAAATTTCAAACATTATGCATTGAATTCGGA
66 CACTAAATTAATAAATTTCAAACATAATGCACTGAATTCGGA
* ***
456718 AAAATAATACGAGCAAAGGGCAGGGATAATTTTTTTTTTCTTACACCAAATTAATTTAAAAAACA
1 AAAATAATACAAGCAAAGGGCAGGGATAAGGGTTTTTTTCTTACACCAAATTAATTTAAAAAACA
456783 CACTAAATTAATAAATTTCAAACATAATGCACTGAA
66 CACTAAATTAATAAATTTCAAACATAATGCACTGAA
456819 ATAATGTAAA
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
107 93 1.00
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.30
Consensus pattern (107 bp):
AAAATAATACAAGCAAAGGGCAGGGATAAGGGTTTTTTTCTTACACCAAATTAATTTAAAAAACA
CACTAAATTAATAAATTTCAAACATAATGCACTGAATTCGGA
Found at i:457607 original size:38 final size:38
Alignment explanation
Indices: 457565--457720 Score: 312
Period size: 38 Copynumber: 4.1 Consensus size: 38
457555 TTTTTGACAC
457565 AATACCTAGAACTACCCATAACCCCTCTCCAACCCATA
1 AATACCTAGAACTACCCATAACCCCTCTCCAACCCATA
457603 AATACCTAGAACTACCCATAACCCCTCTCCAACCCATA
1 AATACCTAGAACTACCCATAACCCCTCTCCAACCCATA
457641 AATACCTAGAACTACCCATAACCCCTCTCCAACCCATA
1 AATACCTAGAACTACCCATAACCCCTCTCCAACCCATA
457679 AATACCTAGAACTACCCATAACCCCTCTCCAACCCATA
1 AATACCTAGAACTACCCATAACCCCTCTCCAACCCATA
457717 AATA
1 AATA
457721 AGAGGATAAT
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 118 1.00
ACGTcount: A:0.38, C:0.41, G:0.03, T:0.19
Consensus pattern (38 bp):
AATACCTAGAACTACCCATAACCCCTCTCCAACCCATA
Found at i:492280 original size:21 final size:21
Alignment explanation
Indices: 492256--492297 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
492246 GTAGGAACAT
*
492256 TTTCTGAAAATTTTGCATTGA
1 TTTCTGAAAACTTTGCATTGA
492277 TTTCTGAAAACTTTGCATTGA
1 TTTCTGAAAACTTTGCATTGA
492298 AATAATCATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (21 bp):
TTTCTGAAAACTTTGCATTGA
Found at i:494277 original size:20 final size:20
Alignment explanation
Indices: 494238--494277 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
494228 TTTAGCATCC
494238 AAATGGTTAATGTCTTAGTTG
1 AAATGGTTAATG-CTTAGTTG
494259 AAATGGTATAATG-TTAGTT
1 AAATGGT-TAATGCTTAGTT
494278 ATGCTAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 7 0.39
22 5 0.28
ACGTcount: A:0.33, C:0.03, G:0.23, T:0.42
Consensus pattern (20 bp):
AAATGGTTAATGCTTAGTTG
Found at i:498931 original size:21 final size:21
Alignment explanation
Indices: 498907--498949 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
498897 CCCATTATCC
498907 AATAAAAACATAAAAATT-CCT
1 AATAAAAA-ATAAAAATTGCCT
* *
498928 AATAATAAATCAAAATTGCCT
1 AATAAAAAATAAAAATTGCCT
498949 A
1 A
498950 TTCGATTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (21 bp):
AATAAAAAATAAAAATTGCCT
Found at i:499708 original size:16 final size:16
Alignment explanation
Indices: 499687--499722 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
499677 AATTCAGAGG
499687 ATGAAAACTCTTAATA
1 ATGAAAACTCTTAATA
499703 ATGAAAACTCTTAATA
1 ATGAAAACTCTTAATA
499719 ATGA
1 ATGA
499723 TTGAGAATTT
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:0.50, C:0.11, G:0.08, T:0.31
Consensus pattern (16 bp):
ATGAAAACTCTTAATA
Found at i:501270 original size:13 final size:13
Alignment explanation
Indices: 501252--501277 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
501242 AAAGTGCGAG
501252 CCTGTTGAAGACA
1 CCTGTTGAAGACA
501265 CCTGTTGAAGACA
1 CCTGTTGAAGACA
501278 ATATGCAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (13 bp):
CCTGTTGAAGACA
Found at i:502096 original size:28 final size:29
Alignment explanation
Indices: 501997--502096 Score: 154
Period size: 28 Copynumber: 3.6 Consensus size: 29
501987 AAAAATAAAA
501997 ATTTA-CAAAA-ATAGTACAACTTTTTTTT
1 ATTTACCAAAATATA-TACAACTTTTTTTT
*
502025 ATTTACGAAAATAT-TACAACTTTTTTTT
1 ATTTACCAAAATATATACAACTTTTTTTT
502053 ATTTACCAAAATATATA-AACTTTTTTTT
1 ATTTACCAAAATATATACAACTTTTTTTT
502081 ATTTACCAAAATATAT
1 ATTTACCAAAATATAT
502097 CAAAAACAAA
Statistics
Matches: 67, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
28 59 0.88
29 6 0.09
30 2 0.03
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (29 bp):
ATTTACCAAAATATATACAACTTTTTTTT
Found at i:502211 original size:18 final size:18
Alignment explanation
Indices: 502174--502249 Score: 80
Period size: 19 Copynumber: 4.1 Consensus size: 18
502164 TGAACTCATT
* *
502174 TTTTTATTTAATAATTCTA
1 TTTTAATTTAATAA-ACTA
*
502193 TTTTAATTTTATAAACTA
1 TTTTAATTTAATAAACTA
* * *
502211 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAA-ACTA
502230 TTTTAATTTAATAAACTA
1 TTTTAATTTAATAAACTA
502248 TT
1 TT
502250 AAGTAATACT
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
18 19 0.41
19 27 0.59
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTTAATTTAATAAACTA
Found at i:502224 original size:37 final size:37
Alignment explanation
Indices: 502179--502249 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
502169 TCATTTTTTT
* *
502179 ATTTAATAATTCTATTTTAATTTTATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
502216 ATTTAATAACTCTATTTTAATTTAATAAACTATT
1 ATTTAATAACTCTATTTTAATTTAATAAACTATT
502250 AAGTAATACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
Found at i:502591 original size:37 final size:37
Alignment explanation
Indices: 502548--502621 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
502538 ATTAAGTATT
* *
502548 ACTTAATAGTTTATTAAATTAAAATATATTTATTAAA
1 ACTTAATAGTTTATTAAATTAAAATAGAGTTATTAAA
502585 ACTTAATAGTTTATTAAATTAAAATAGAGTTATTAAA
1 ACTTAATAGTTTATTAAATTAAAATAGAGTTATTAAA
502622 TAAAAAAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (37 bp):
ACTTAATAGTTTATTAAATTAAAATAGAGTTATTAAA
Found at i:502610 original size:18 final size:18
Alignment explanation
Indices: 502552--502626 Score: 75
Period size: 18 Copynumber: 4.1 Consensus size: 18
502542 AGTATTACTT
502552 AATAGTTTATTAAATTAA
1 AATAGTTTATTAAATTAA
*
502570 AATATATTTATTAAAACTT--
1 AATA-GTTTATT-AAA-TTAA
502589 AATAGTTTATTAAATTAA
1 AATAGTTTATTAAATTAA
*
502607 AATAGAGTTATTAAA-TAA
1 AATAG-TTTATTAAATTAA
502625 AA
1 AA
502627 AAATGAGTTG
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
16 2 0.04
17 3 0.06
18 20 0.42
19 18 0.38
20 3 0.06
21 2 0.04
ACGTcount: A:0.52, C:0.01, G:0.05, T:0.41
Consensus pattern (18 bp):
AATAGTTTATTAAATTAA
Found at i:502634 original size:20 final size:19
Alignment explanation
Indices: 502595--502635 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
502585 ACTTAATAGT
* *
502595 TTATTAAATTAAAATAGAG
1 TTATTAAATAAAAAAAGAG
502614 TTATTAAATAAAAAAATGAG
1 TTATTAAATAAAAAAA-GAG
502634 TT
1 TT
502636 GAAGGGGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.37
Consensus pattern (19 bp):
TTATTAAATAAAAAAAGAG
Found at i:502887 original size:37 final size:37
Alignment explanation
Indices: 502845--502915 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
502835 AGTATTACTT
* *
502845 AATAGTTTATTAAATTAAAATATATTTATTAAATGAG
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
502882 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
502916 AAAAAAATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.42
Consensus pattern (37 bp):
AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
Found at i:502920 original size:19 final size:19
Alignment explanation
Indices: 502845--502919 Score: 93
Period size: 18 Copynumber: 4.1 Consensus size: 19
502835 AGTATTACTT
502845 AATAG-TTTATTAAATTAA
1 AATAGATTTATTAAATTAA
* * *
502863 AATATATTTATTAAATGAG
1 AATAGATTTATTAAATTAA
502882 AATAG-TTTATTAAATTAA
1 AATAGATTTATTAAATTAA
*
502900 AATAGAGTTATTAAA-TAA
1 AATAGATTTATTAAATTAA
502918 AA
1 AA
502920 AAATGAGTTG
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
18 25 0.52
19 23 0.48
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (19 bp):
AATAGATTTATTAAATTAA
Found at i:502927 original size:20 final size:19
Alignment explanation
Indices: 502888--502928 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
502878 TGAGAATAGT
* *
502888 TTATTAAATTAAAATAGAG
1 TTATTAAATAAAAAAAGAG
502907 TTATTAAATAAAAAAATGAG
1 TTATTAAATAAAAAAA-GAG
502927 TT
1 TT
502929 GAAGGGGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.37
Consensus pattern (19 bp):
TTATTAAATAAAAAAAGAG
Found at i:503063 original size:27 final size:26
Alignment explanation
Indices: 502992--503042 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
502982 CATTTTTTCC
*
502992 CTTTGGCACCATGGTGCCGCCAATGA
1 CTTTGGCACCATGGTGCCACCAATGA
503018 CTTTGGCACCAATGGTGCCACCAAT
1 CTTTGGCACC-ATGGTGCCACCAAT
503043 TTATTTGGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.22, C:0.31, G:0.24, T:0.24
Consensus pattern (26 bp):
CTTTGGCACCATGGTGCCACCAATGA
Found at i:503167 original size:28 final size:28
Alignment explanation
Indices: 503132--503229 Score: 162
Period size: 28 Copynumber: 3.5 Consensus size: 28
503122 TTTTTTATAT
503132 ATATTTTGGTAAATAAAAAAAAGTT-TA
1 ATATTTTGGTAAATAAAAAAAAGTTGTA
*
503159 TATATTTTGGAAAATAAAAAAAAGTTGTA
1 -ATATTTTGGTAAATAAAAAAAAGTTGTA
*
503188 ATATTTTCGTAAATAAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAAGTTGTA
503216 ATATTTTGGTAAAT
1 ATATTTTGGTAAAT
503230 TTTTATTTTT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
28 63 0.97
29 2 0.03
ACGTcount: A:0.49, C:0.01, G:0.12, T:0.38
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTGTA
Found at i:520507 original size:15 final size:15
Alignment explanation
Indices: 520487--520547 Score: 113
Period size: 15 Copynumber: 4.1 Consensus size: 15
520477 TAGCAAAGAA
520487 GAACCCCTCACCTCT
1 GAACCCCTCACCTCT
520502 GAACCCCTCACCTCT
1 GAACCCCTCACCTCT
520517 GAACCCCTCACCTCT
1 GAACCCCTCACCTCT
*
520532 GAACCCCCCACCTCT
1 GAACCCCTCACCTCT
520547 G
1 G
520548 GAAATCAGAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.20, C:0.54, G:0.08, T:0.18
Consensus pattern (15 bp):
GAACCCCTCACCTCT
Found at i:530784 original size:68 final size:68
Alignment explanation
Indices: 530675--530876 Score: 395
Period size: 68 Copynumber: 3.0 Consensus size: 68
530665 TGTTCAATTA
530675 AGCTAAATAAATTTGTGTTTCCTTTTGTCGAAGCACTCTCTGTTTTCTTATTAGTAACTACGTCA
1 AGCTAAATAAATTTGTGTTTCCTTTTGTCGAAGCACTCTCTGTTTTCTTATTAGTAACTACGTCA
530740 TTT
66 TTT
530743 AGCTAAATAAATTTGTGTTTCCTTTTGTCGAAGCACTCTCTGTTTTCTTATTAGTAACTACGTCA
1 AGCTAAATAAATTTGTGTTTCCTTTTGTCGAAGCACTCTCTGTTTTCTTATTAGTAACTACGTCA
530808 TTT
66 TTT
*
530811 AGCTAAATAAATTTGTGTTTCCTTTTGTCGAAGCACTCTCTGTTTTCTTATTAGTAACTATGTCA
1 AGCTAAATAAATTTGTGTTTCCTTTTGTCGAAGCACTCTCTGTTTTCTTATTAGTAACTACGTCA
530876 T
66 T
530877 GCACTCTTTA
Statistics
Matches: 133, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 133 1.00
ACGTcount: A:0.24, C:0.17, G:0.13, T:0.46
Consensus pattern (68 bp):
AGCTAAATAAATTTGTGTTTCCTTTTGTCGAAGCACTCTCTGTTTTCTTATTAGTAACTACGTCA
TTT
Found at i:531790 original size:12 final size:13
Alignment explanation
Indices: 531773--531805 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
531763 AATACGCATG
531773 TACATTTAC-ATT
1 TACATTTACAATT
531785 TACATTTACAATT
1 TACATTTACAATT
*
531798 TATATTTA
1 TACATTTA
531806 GTTAGATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (13 bp):
TACATTTACAATT
Found at i:538799 original size:20 final size:21
Alignment explanation
Indices: 538774--538823 Score: 77
Period size: 19 Copynumber: 2.4 Consensus size: 21
538764 TTTAAAATAC
538774 TTTAAAAATATTTTTT-TATT
1 TTTAAAAATATTTTTTGTATT
538794 TTT-AAAATATTTTTTGTATT
1 TTTAAAAATATTTTTTGTATT
538814 TATTAAAAAT
1 T-TTAAAAAT
538824 CGGGCCGGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 12 0.44
20 8 0.30
21 2 0.07
22 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TTTAAAAATATTTTTTGTATT
Found at i:541521 original size:3 final size:3
Alignment explanation
Indices: 541513--541553 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
541503 AAAATGTTTG
541513 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
541554 GGAACATGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:545687 original size:6 final size:6
Alignment explanation
Indices: 545676--545715 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
545666 TAATGACCCT
545676 CCATAG CCATAG CCATAG CCATAG CCATAG CCATAG CCAT
1 CCATAG CCATAG CCATAG CCATAG CCATAG CCATAG CCAT
545716 GGCCTGCTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.33, C:0.35, G:0.15, T:0.17
Consensus pattern (6 bp):
CCATAG
Found at i:546658 original size:19 final size:19
Alignment explanation
Indices: 546627--546663 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
546617 TTGTTCAAAT
546627 AATAATAATTTATTTATAG
1 AATAATAATTTATTTATAG
546646 AATATATAA-TTATTTATA
1 AATA-ATAATTTATTTATA
546664 TAAACTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
AATAATAATTTATTTATAG
Found at i:548695 original size:9 final size:10
Alignment explanation
Indices: 548682--548707 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
548672 AAACATTCAA
548682 AAAAAATCAT
1 AAAAAATCAT
548692 AAAAAATCAT
1 AAAAAATCAT
548702 AAAAAA
1 AAAAAA
548708 ATTTAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAATCAT
Found at i:548695 original size:11 final size:11
Alignment explanation
Indices: 548681--548709 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
548671 AAAACATTCA
548681 AAAAAAATCAT
1 AAAAAAATCAT
548692 -AAAAAATCAT
1 AAAAAAATCAT
548702 AAAAAAAT
1 AAAAAAAT
548710 TTAAAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAAAAATCAT
Found at i:561093 original size:2 final size:2
Alignment explanation
Indices: 561086--561114 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
561076 TGTACGTTGC
561086 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 A
561115 CTATGGCAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:562454 original size:17 final size:17
Alignment explanation
Indices: 562427--562464 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
562417 GAATTAAGCA
562427 TTTAAAAAATAT-ATTT
1 TTTAAAAAATATAATTT
562443 TTTAATAAAATATAATTT
1 TTTAA-AAAATATAATTT
562461 TTTA
1 TTTA
562465 TTTAAGACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 5 0.25
17 7 0.35
18 8 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTAAAAAATATAATTT
Found at i:568161 original size:16 final size:15
Alignment explanation
Indices: 568140--568169 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
568130 ACGATGGGGC
568140 TATTATTTGTATTATT
1 TATTATTTG-ATTATT
568156 TATTATTTGATTAT
1 TATTATTTGATTAT
568170 GTGCATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (15 bp):
TATTATTTGATTATT
Found at i:569245 original size:29 final size:28
Alignment explanation
Indices: 569193--569248 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
569183 AATTGTAGAA
*
569193 TAAATTGTAAAATTTGAGTATTAGGGAC
1 TAAATTGTAAAATTTGAATATTAGGGAC
569221 TAAATTGTGAAAATTTGAA-ATTTAGGGA
1 TAAATTGT-AAAATTTGAATA-TTAGGGA
569249 TTTAAGTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.41, C:0.02, G:0.21, T:0.36
Consensus pattern (28 bp):
TAAATTGTAAAATTTGAATATTAGGGAC
Found at i:569265 original size:18 final size:19
Alignment explanation
Indices: 569236--569271 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
569226 TGTGAAAATT
*
569236 TGAAATTTAGGGATTTAAG
1 TGAAATTTAGGGAGTTAAG
569255 TGAAA-TTAGGGAGTTAA
1 TGAAATTTAGGGAGTTAA
569272 ATCTAATCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.39, C:0.00, G:0.28, T:0.33
Consensus pattern (19 bp):
TGAAATTTAGGGAGTTAAG
Found at i:570164 original size:14 final size:14
Alignment explanation
Indices: 570145--570184 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
570135 TTGATTAGCA
570145 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
570159 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
570173 GGAAAATGTTTT
1 GTAAAATGTTTT
570185 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:570197 original size:34 final size:35
Alignment explanation
Indices: 570153--570219 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
570143 CAGTAAAATG
* *
570153 TTTTCCGTAAAATGA-TTTCTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
*
570187 TTTTCTGTAAAATGACTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTT
570220 CTTGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 14 0.48
35 15 0.52
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
Found at i:570206 original size:20 final size:20
Alignment explanation
Indices: 570168--570207 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
570158 CGTAAAATGA
**
570168 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGACTTACT
*
570188 TTTCTGTAAAATGACTTACT
1 TTTCTGGAAAATGACTTACT
570208 GGAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTCTGGAAAATGACTTACT
Found at i:574193 original size:23 final size:23
Alignment explanation
Indices: 574163--574207 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
574153 NNNNNNNNGA
*
574163 TAGCTTCGGCTACATTTCAGTGG
1 TAGCTTCGGCTACATATCAGTGG
574186 TAGCTTCGGCTACATATCAGTG
1 TAGCTTCGGCTACATATCAGTG
574208 TGGCACTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.33
Consensus pattern (23 bp):
TAGCTTCGGCTACATATCAGTGG
Found at i:574648 original size:77 final size:78
Alignment explanation
Indices: 574519--574673 Score: 276
Period size: 77 Copynumber: 2.0 Consensus size: 78
574509 TCTTCTTTTC
*
574519 TTGTTTTATAGTGTGATTTGAACTTGAGCGAATTGGGGATCGTCGGAGCTCGTATCACACTATCA
1 TTGTTTTATAG-GTGATTTGAACTTGAGCGAAGTGGGGATCGTCGGAGCTCGTATCACACTATCA
574584 TAATCATCTCGGTT
65 TAATCATCTCGGTT
*
574598 TTGTTTTATA-GTGATTTGAACTTGATCGAAGTGGGGATCGTCGGAGCTCGTATCACACTATCAT
1 TTGTTTTATAGGTGATTTGAACTTGAGCGAAGTGGGGATCGTCGGAGCTCGTATCACACTATCAT
574662 AATCATCTCGGT
66 AATCATCTCGGT
574674 ATTATGTGCT
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
77 64 0.86
79 10 0.14
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (78 bp):
TTGTTTTATAGGTGATTTGAACTTGAGCGAAGTGGGGATCGTCGGAGCTCGTATCACACTATCAT
AATCATCTCGGTT
Found at i:575629 original size:37 final size:39
Alignment explanation
Indices: 575582--575678 Score: 108
Period size: 40 Copynumber: 2.5 Consensus size: 39
575572 GGATTAATTT
**
575582 GATGAGGCACTGGGTGCCAA-T-TTACTTCGGTTTAGCC
1 GATGAGGCACTGGGTGCCAATTATTACTTCGAATTAGCC
* ** **
575619 GATGAGGCACTGAGTGTTAAATTATTACTTCGAATTATTC
1 GATGAGGCACTGGGTG-CCAATTATTACTTCGAATTAGCC
575659 GATGAGGCACTGGGTGCCAA
1 GATGAGGCACTGGGTGCCAA
575679 ACTGGTGTGT
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
37 15 0.32
38 2 0.04
39 3 0.06
40 27 0.57
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.30
Consensus pattern (39 bp):
GATGAGGCACTGGGTGCCAATTATTACTTCGAATTAGCC
Found at i:604288 original size:29 final size:29
Alignment explanation
Indices: 604248--604309 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
604238 TTTATTTTTT
604248 ATTT-TTTAATAATAAAAAGATTAATTTA
1 ATTTATTTAATAATAAAAAGATTAATTTA
*
604276 ATTTATTTAATAATAAAGAGATTAATTTA
1 ATTTATTTAATAATAAAAAGATTAATTTA
604305 ATTTA
1 ATTTA
604310 GTCTTTATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 4 0.12
29 28 0.88
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (29 bp):
ATTTATTTAATAATAAAAAGATTAATTTA
Found at i:605381 original size:19 final size:19
Alignment explanation
Indices: 605349--605385 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
605339 ACTAATAACT
* *
605349 TAAAATTTAGAATTAAAAA
1 TAAAAATTAAAATTAAAAA
605368 TAAAAATTAAAATTAAAA
1 TAAAAATTAAAATTAAAA
605386 TACAAATATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (19 bp):
TAAAAATTAAAATTAAAAA
Found at i:605801 original size:31 final size:30
Alignment explanation
Indices: 605733--605801 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 30
605723 GATGATGGTC
*
605733 GGACTATAATTTTTAAATTGAAAAAGTATAT
1 GGACTA-AATTTTTAAATTGAAAAAGTATAG
* *
605764 GAACTAAA-TTTTAAATTTTAAATAAGTATAG
1 GGACTAAATTTTTAAA-TTGAAA-AAGTATAG
605795 GGACTAA
1 GGACTAA
605802 CAACATAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 7 0.22
30 7 0.22
31 18 0.56
ACGTcount: A:0.46, C:0.04, G:0.13, T:0.36
Consensus pattern (30 bp):
GGACTAAATTTTTAAATTGAAAAAGTATAG
Found at i:617971 original size:16 final size:16
Alignment explanation
Indices: 617944--617989 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 16
617934 AAAAAGTATT
617944 TTAAAAATATTTTAAAA
1 TTAAAAA-ATTTTAAAA
617961 TTAAAAAA-TTTAAAA
1 TTAAAAAATTTTAAAA
*
617976 TTTAAAAATATTTA
1 TTAAAAAAT-TTTA
617990 TTATATCGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 14 0.54
16 1 0.04
17 11 0.42
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TTAAAAAATTTTAAAA
Found at i:617989 original size:17 final size:17
Alignment explanation
Indices: 617943--617989 Score: 71
Period size: 17 Copynumber: 2.8 Consensus size: 17
617933 AAAAAAGTAT
617943 TTTAAAAATATTTTAAAA
1 TTTAAAAATA-TTTAAAA
617961 -TTAAAAA-ATTTAAAA
1 TTTAAAAATATTTAAAA
617976 TTTAAAAATATTTA
1 TTTAAAAATATTTA
617990 TTATATCGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 7 0.26
16 8 0.30
17 12 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTTAAAAATATTTAAAA
Found at i:620653 original size:44 final size:44
Alignment explanation
Indices: 620570--620653 Score: 105
Period size: 44 Copynumber: 1.9 Consensus size: 44
620560 TTAGGGTTTT
* * *
620570 TCTGCTTAACTTTGTAGTGTTGGGCCAGGAACCGTTTTGGGCCG
1 TCTGCTTAACTTTGTAATGTTGGACCAGGAACCGCTTTGGGCCG
* * * *
620614 TCTGTTTAATTTTGTAATGTTGGACTAGGAACTGCTTTGG
1 TCTGCTTAACTTTGTAATGTTGGACCAGGAACCGCTTTGG
620654 ACCGATTGGG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
44 33 1.00
ACGTcount: A:0.17, C:0.15, G:0.29, T:0.39
Consensus pattern (44 bp):
TCTGCTTAACTTTGTAATGTTGGACCAGGAACCGCTTTGGGCCG
Found at i:623694 original size:236 final size:236
Alignment explanation
Indices: 623262--623961 Score: 1039
Period size: 236 Copynumber: 3.0 Consensus size: 236
623252 TGGTGACTAA
* * * * * *
623262 TTAAAATACTACACATCGAGTTTACGTTTTATGCATATTTCAAGTTCGAGCAGAACTTGGTCCGG
1 TTAAAATACTACACATCGAGTTTATGTTTTATGTATATTTCAAGTTCGAGTAGAACTCGGTTCAG
* *
623327 AGCCATTAGTTGAAACGGAAGTAACTAATGAGTACGATGAGTGGACTCAAAGTGAACAAACTAAT
66 AGCCATTAGTTGAAACCGAAGTAACTAATGAGT---ATGGGTGGACTCAAAGTGAACAAACTAAT
* * * * * *
623392 GAATTTATAACACCCTATCCAGTTTTCGACAATGAGAACTTTATTGCTAACGGGAATGAAGTGAT
128 GAATTTATAACTCCCTGTCCGGTTTTCGACAATGAGAACTTTATTGATGATGGGAATGAAGTGAT
* * *
623457 CTCCTATCACCAGTCGCAAGTAATAACACTTTTCTCGGAAATTT
193 CTCCAATCACCAGTCACAAGTAAGAACACTTTTCTCGGAAATTT
623501 TTAAAATACTACACATCGAGTTTATGTTTTATGTATATTTCAAGTTCGAGTAGAACTCGGTTCAG
1 TTAAAATACTACACATCGAGTTTATGTTTTATGTATATTTCAAGTTCGAGTAGAACTCGGTTCAG
*
623566 AGCCATTAGTTGAAACCGAAGTTACTAATGAGTATGGGTGGACTCAAAGTGAACAAACTAATGAA
66 AGCCATTAGTTGAAACCGAAGTAACTAATGAGTATGGGTGGACTCAAAGTGAACAAACTAATGAA
*
623631 TTTATAACTCCCTGTCCGGTTTTCGACAATGAGAACTTTATTGATGATTGGAATGAAGTGATCTC
131 TTTATAACTCCCTGTCCGGTTTTCGACAATGAGAACTTTATTGATGATGGGAATGAAGTGATCTC
623696 CAATCACCAAG-CACAAGTAAGAACACTTTTCTCGGAAATTT
196 CAATCACC-AGTCACAAGTAAGAACACTTTTCTCGGAAATTT
* * *
623737 TTAAAATACTACACATTGAGTTTATGTTTTATGTATATTTCAGGTTCAAGTAGAACTCGGTTCAG
1 TTAAAATACTACACATCGAGTTTATGTTTTATGTATATTTCAAGTTCGAGTAGAACTCGGTTCAG
* * *
623802 AGCCATTAGTTGAAAACGAAGTAACTAATGAGTACGGGTGGACTCAAAGTGAACAAACTTATGAA
66 AGCCATTAGTTGAAACCGAAGTAACTAATGAGTATGGGTGGACTCAAAGTGAACAAACTAATGAA
623867 TTTATAACTCCCTGTCCGGTTTTCGAC-------A--TTA---ATGATGGGAATGAAGTGATCTC
131 TTTATAACTCCCTGTCCGGTTTTCGACAATGAGAACTTTATTGATGATGGGAATGAAGTGATCTC
*
623920 CAATCACCAGTCACAAGTAAGAACAATTTTCTCGGAAATTT
196 CAATCACCAGTCACAAGTAAGAACACTTTTCTCGGAAATTT
623961 T
1 T
623962 GAAGTTTAGT
Statistics
Matches: 431, Mismatches: 28, Indels: 19
0.90 0.06 0.04
Matches are distributed among these distances:
223 2 0.00
224 59 0.14
227 3 0.01
229 1 0.00
236 274 0.64
237 2 0.00
239 90 0.21
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (236 bp):
TTAAAATACTACACATCGAGTTTATGTTTTATGTATATTTCAAGTTCGAGTAGAACTCGGTTCAG
AGCCATTAGTTGAAACCGAAGTAACTAATGAGTATGGGTGGACTCAAAGTGAACAAACTAATGAA
TTTATAACTCCCTGTCCGGTTTTCGACAATGAGAACTTTATTGATGATGGGAATGAAGTGATCTC
CAATCACCAGTCACAAGTAAGAACACTTTTCTCGGAAATTT
Found at i:628348 original size:18 final size:20
Alignment explanation
Indices: 628311--628349 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
628301 TAAAAAAATT
*
628311 TATTATTTAAATTATTTAAA
1 TATTATTTAAAATATTTAAA
628331 TATT-TTTAAAAT-TTTAAA
1 TATTATTTAAAATATTTAAA
628349 T
1 T
628350 TAATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 7 0.39
20 4 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTATTTAAAATATTTAAA
Found at i:628409 original size:29 final size:32
Alignment explanation
Indices: 628349--628413 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 32
628339 AAATTTTAAA
* **
628349 TTAATATATATATATAATTTTATCTTTTTCTT
1 TTAATATATATATATAATTTAATCTTAATCTT
628381 TTAATAT-TATATAT-ATTTAAT-TTAATCTT
1 TTAATATATATATATAATTTAATCTTAATCTT
628410 TTAA
1 TTAA
628414 AAATTATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 10 0.33
30 6 0.20
31 7 0.23
32 7 0.23
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (32 bp):
TTAATATATATATATAATTTAATCTTAATCTT
Found at i:630863 original size:32 final size:34
Alignment explanation
Indices: 630800--630875 Score: 111
Period size: 32 Copynumber: 2.3 Consensus size: 34
630790 GATAATTTAT
630800 AACAGTATATTACAAATTTTATAACAATATATTAA
1 AACAGTATATTAC-AATTTTATAACAATATATTAA
* *
630835 ACCAGTATATTAC-A-TTTATAACAGTATATTAA
1 AACAGTATATTACAATTTTATAACAATATATTAA
630867 AACAGTATA
1 AACAGTATA
630876 CTAAAACAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
32 25 0.66
33 1 0.03
35 12 0.32
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.36
Consensus pattern (34 bp):
AACAGTATATTACAATTTTATAACAATATATTAA
Found at i:630872 original size:13 final size:13
Alignment explanation
Indices: 630854--630892 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
630844 TTACATTTAT
630854 AACAGTATATTAA
1 AACAGTATATTAA
*
630867 AACAGTATACTAA
1 AACAGTATATTAA
630880 AACAGTATATTAA
1 AACAGTATATTAA
630893 CTACAATAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (13 bp):
AACAGTATATTAA
Found at i:630937 original size:67 final size:67
Alignment explanation
Indices: 630866--631002 Score: 233
Period size: 67 Copynumber: 2.0 Consensus size: 67
630856 CAGTATATTA
*
630866 AAACAGTATACTAAAAC-AG-TATATTAACTACAATAGATCAAACTTATATTTACAGTAAAGATC
1 AAACAGTATAAT-AAACTAGTTAT-TTAACTACAATAGATCAAACTTATATTTACAGTAAAGATC
630929 AGAG
64 AGAG
630933 AAACAGTATAATAAACTAGTTATTTAACTACAATAGATCAAACTTATATTTACAGTAAAGATCAG
1 AAACAGTATAATAAACTAGTTATTTAACTACAATAGATCAAACTTATATTTACAGTAAAGATCAG
630998 AG
66 AG
631000 AAA
1 AAA
631003 GAAAGAAAAA
Statistics
Matches: 67, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
66 4 0.06
67 60 0.90
68 3 0.04
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (67 bp):
AAACAGTATAATAAACTAGTTATTTAACTACAATAGATCAAACTTATATTTACAGTAAAGATCAG
AG
Found at i:632714 original size:49 final size:51
Alignment explanation
Indices: 632647--632783 Score: 190
Period size: 49 Copynumber: 2.7 Consensus size: 51
632637 AGTGTGGTAA
* * * **
632647 TATGTGAAGGCCACTTTGTAAAGAAAGATAGTTTTGGTCACAA-T-TGTGG
1 TATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCACAAGTCAGTAC
632696 TATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCACAAGTGCAGTAC
1 TATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCACAAGT-CAGTAC
*
632748 TATGTGAAGGCCACTTTGTGAAG-AAGGTAGCTTTGG
1 TATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGG
632784 CTACAAGGGT
Statistics
Matches: 79, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
49 41 0.52
50 1 0.01
51 12 0.15
52 25 0.32
ACGTcount: A:0.29, C:0.12, G:0.28, T:0.30
Consensus pattern (51 bp):
TATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCACAAGTCAGTAC
Found at i:634213 original size:41 final size:41
Alignment explanation
Indices: 634168--634275 Score: 155
Period size: 41 Copynumber: 2.6 Consensus size: 41
634158 TTTTAAAAAT
*
634168 AAAAAAATAAAAAAAGTATTTTAAAAATATTTT-AAGATTTA
1 AAAAAAATTAAAAAAGTATTTTAAAAATATTTTCAA-ATTTA
** *
634209 AAAAATTTTAAAAAAGTATTTTAAAAATATTTTCAATTTTA
1 AAAAAAATTAAAAAAGTATTTTAAAAATATTTTCAAATTTA
*
634250 AAAAAAATTTAAAAAGTATTTTAAAA
1 AAAAAAATTAAAAAAGTATTTTAAAA
634276 TTAAAAAATA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
41 57 0.97
42 2 0.03
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (41 bp):
AAAAAAATTAAAAAAGTATTTTAAAAATATTTTCAAATTTA
Found at i:634253 original size:30 final size:31
Alignment explanation
Indices: 634212--634271 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
634202 AGATTTAAAA
* *
634212 AATTTTAAAAAAGTATTTTAAAAA-TATTTTC
1 AATTTTAAAAAA-AAATTTAAAAAGTATTTTC
634243 AATTTT-AAAAAAAATTTAAAAAGTATTTT
1 AATTTTAAAAAAAAATTTAAAAAGTATTTT
634272 AAAATTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 9 0.35
30 11 0.42
31 6 0.23
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (31 bp):
AATTTTAAAAAAAAATTTAAAAAGTATTTTC
Found at i:634279 original size:29 final size:29
Alignment explanation
Indices: 634228--634283 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
634218 AAAAAAGTAT
**
634228 TTTAAAAATATTTTCAATTTTAAAAAAAA
1 TTTAAAAATATTTTCAAAATTAAAAAAAA
634257 TTTAAAAAGTATTTT-AAAATTAAAAAA
1 TTTAAAAA-TATTTTCAAAATTAAAAAA
634284 TAAAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (29 bp):
TTTAAAAATATTTTCAAAATTAAAAAAAA
Found at i:635168 original size:36 final size:36
Alignment explanation
Indices: 635127--635197 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
635117 GATTATTTAA
*
635127 TCTTAGAGTTTTAATTGTATACAGCTTCTAATTATG
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTATG
*
635163 TCTTAGAGTTCTAATTGTATACAGCTTTTAATTAT
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTAT
635198 AGCCTTTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.48
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAGCTTCTAATTATG
Found at i:638793 original size:236 final size:236
Alignment explanation
Indices: 638370--638841 Score: 653
Period size: 236 Copynumber: 2.0 Consensus size: 236
638360 TGGTGACTAA
* * * * * *
638370 TTAAAATATTACACATCGAGTTTATGTTTTATGTATATTTCAGGTTCGAGTAGAACTTGGTCCGG
1 TTAAAATACTACACATCGAGTTTACGTTTTATGTATATTTCAGATTAGAGTAGAACTCGGTCCAG
*
638435 AGCCATTAGTTGAAACAGAAGTCACTAATGAGTACGAGTGGACTCAAAGTGAACAAACTAATGAA
66 AGCCATTAGTTGAAACAGAAGTCACTAAAGAGTACGAGTGGACTCAAAGTGAACAAACTAATGAA
* * * * *
638500 TTTATAACACCATATCTGGTTTTCGACAATGAGAACTCTATTGATGACGGGAATGAAGTGATCTC
131 TTTAGAACACCATATCCGGTTTTCAACAACGAGAACTCTATTGATGACGGGAATGAAGTGAGCTC
*
638565 CAATTACCAGTCACAAGTAAGAACGCTTTTCTCGGAAATTT
196 CAATCACCAGTCACAAGTAAGAACGCTTTTCTCGGAAATTT
**
638606 TTAAAATACTACACATCGAGTTTACGTTTTATGTATATTTCAGATTAGAGTAGAACTCGGTTTAG
1 TTAAAATACTACACATCGAGTTTACGTTTTATGTATATTTCAGATTAGAGTAGAACTCGGTCCAG
* *
638671 AGCCATTAGTTGAAATC-GAAGT-AGCTAAAGAGTACG-GATGGACTCGAGGTGAACAAACTAAT
66 AGCCATTAGTTGAAA-CAGAAGTCA-CTAAAGAGTACGAG-TGGACTCAAAGTGAACAAACTAAT
* * * * * *
638733 GAATTTAGAACTCCCTGTCCGGTTTTCAACAACGAGAACTTTATTGATGATGGTAATGAAGTGAG
128 GAATTTAGAACACCATATCCGGTTTTCAACAACGAGAACTCTATTGATGACGGGAATGAAGTGAG
* * * *
638798 CTCTAATCACCAGTCACAAGTAAGAACTCTTTTCTTGTAAATTT
193 CTCCAATCACCAGTCACAAGTAAGAACGCTTTTCTCGGAAATTT
638842 CGAAGTTCAG
Statistics
Matches: 206, Mismatches: 27, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
235 2 0.01
236 203 0.99
237 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (236 bp):
TTAAAATACTACACATCGAGTTTACGTTTTATGTATATTTCAGATTAGAGTAGAACTCGGTCCAG
AGCCATTAGTTGAAACAGAAGTCACTAAAGAGTACGAGTGGACTCAAAGTGAACAAACTAATGAA
TTTAGAACACCATATCCGGTTTTCAACAACGAGAACTCTATTGATGACGGGAATGAAGTGAGCTC
CAATCACCAGTCACAAGTAAGAACGCTTTTCTCGGAAATTT
Found at i:643550 original size:236 final size:233
Alignment explanation
Indices: 643129--643825 Score: 1052
Period size: 236 Copynumber: 3.0 Consensus size: 233
643119 TGGTGACTAA
* ** * *
643129 TTAAAATACTACACATCAAGTTTATGTTTTATGTATATTTCAGGTTCAAGTAGAACTTGGTCCGG
1 TTAAAATACTACACATCGAGTTTATGTTTTATGTATATTTCAGGTTCAAGTAGAACTCAGTTCAG
* * * *
643194 AGCCATTAGTTGAAACGGAAGTAACTAATGAGTACGAGTGGACTCAAAGTGAACAAATTAATGAA
66 AGCCATTAGTTGAAACCGAAGTAACTAATGAGTATGGGTGGACTCAAAGTGAACAAACTAATGAA
* * *
643259 TTTATAACACCCTATCCAGTTTTCAACAATGAGAACTTTATTGATGACGGGAATGAAGTGATCTC
131 TTTATAACTCCCTGTCCAGTTTTC-ACAA-GA-AACTTTATTGATGATGGGAATGAAGTGATCTC
*
643324 CCATCACCAGTCACAAGTAAGAACACTTTTCTCGGAAATTT
193 CAATCACCAGTCACAAGTAAGAACACTTTTCTCGGAAATTT
643365 TTAAAATACTACACATCGAGTTTATGTTTTATGTATATTTCAGGTTCAAGTAGAACTCAGTTCAG
1 TTAAAATACTACACATCGAGTTTATGTTTTATGTATATTTCAGGTTCAAGTAGAACTCAGTTCAG
* *
643430 AGTCATTAGTTGAAACCGAAGTAACTAATGAGTATGGGTTGACTCAAAGTGAACAAACTAATGAA
66 AGCCATTAGTTGAAACCGAAGTAACTAATGAGTATGGGTGGACTCAAAGTGAACAAACTAATGAA
* *
643495 TTTATAACTCCCTGTCCGGTTTTCGACAACGAAAACTTTATTGATGATTGGAATGAAGTGATCTC
131 TTTATAACTCCCTGTCCAGTTTTC-ACAA-G-AAACTTTATTGATGATGGGAATGAAGTGATCTC
*
643560 CAATCACCAGTCACAAGTAAGAACACTTTTCTCGAAAATTT
193 CAATCACCAGTCACAAGTAAGAACACTTTTCTCGGAAATTT
*
643601 TTAAAATACTACACATTGAGTTTATGTTTTATGTATATTTCAGGTTCAAGTAGAACTCAGTTCAG
1 TTAAAATACTACACATCGAGTTTATGTTTTATGTATATTTCAGGTTCAAGTAGAACTCAGTTCAG
* *
643666 AGCCATTAGTTGAAATCGAAGTAACTAATGAGTATAGGTGGACTCAAAGTGAACAAACTAATGAA
66 AGCCATTAGTTGAAACCGAAGTAACTAATGAGTATGGGTGGACTCAAAGTGAACAAACTAATGAA
*
643731 TTTATAACTCCCTGTCCAGTTTT----AG--AC---ATAGATGATGGGAATGAAGTGATCTCCAA
131 TTTATAACTCCCTGTCCAGTTTTCACAAGAAACTTTATTGATGATGGGAATGAAGTGATCTCCAA
* * *
643787 TAACCAGTCACAAGTAAGATCACTTTTCTCAGAAATTT
196 TCACCAGTCACAAGTAAGAACACTTTTCTCGGAAATTT
643825 T
1 T
643826 GAAGTTTAGT
Statistics
Matches: 428, Mismatches: 32, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
224 62 0.14
227 2 0.00
230 1 0.00
231 1 0.00
236 361 0.84
237 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.31
Consensus pattern (233 bp):
TTAAAATACTACACATCGAGTTTATGTTTTATGTATATTTCAGGTTCAAGTAGAACTCAGTTCAG
AGCCATTAGTTGAAACCGAAGTAACTAATGAGTATGGGTGGACTCAAAGTGAACAAACTAATGAA
TTTATAACTCCCTGTCCAGTTTTCACAAGAAACTTTATTGATGATGGGAATGAAGTGATCTCCAA
TCACCAGTCACAAGTAAGAACACTTTTCTCGGAAATTT
Found at i:646270 original size:51 final size:51
Alignment explanation
Indices: 646215--646318 Score: 174
Period size: 51 Copynumber: 2.0 Consensus size: 51
646205 TCAATAACGG
* *
646215 AACAGTAACAGTATTCGACACACAAAGTGCTGAATCGGTAAC-GATAACAGT
1 AACAGTAACAATATTCGACACACAAAGTGCCGAATCGGTAACAG-TAACAGT
646266 AACAGTAACAATATTCGACACACAAAGTGCCGAATCGGTAACAGTAACAGT
1 AACAGTAACAATATTCGACACACAAAGTGCCGAATCGGTAACAGTAACAGT
646317 AA
1 AA
646319 TCAGCACATA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
51 49 0.98
52 1 0.02
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.18
Consensus pattern (51 bp):
AACAGTAACAATATTCGACACACAAAGTGCCGAATCGGTAACAGTAACAGT
Found at i:647536 original size:9 final size:9
Alignment explanation
Indices: 647522--647571 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
647512 CATTTGAATA
647522 AATAATTAT
1 AATAATTAT
647531 AATAATTAT
1 AATAATTAT
*
647540 AATATTTAT
1 AATAATTAT
647549 -ATACA-TAT
1 AATA-ATTAT
*
647557 AATATTTAT
1 AATAATTAT
647566 ATATAA
1 A-ATAA
647572 CTTAAACAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
8 6 0.18
9 24 0.73
10 3 0.09
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (9 bp):
AATAATTAT
Found at i:651644 original size:18 final size:18
Alignment explanation
Indices: 651616--651660 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
651606 TGCAATATGA
* *
651616 ACACACGCACGCACGCAC
1 ACACACACACGCACACAC
*
651634 GCACACACACGCACACAC
1 ACACACACACGCACACAC
651652 ACACACACA
1 ACACACACA
651661 AAATTTTTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.40, C:0.49, G:0.11, T:0.00
Consensus pattern (18 bp):
ACACACACACGCACACAC
Found at i:651646 original size:14 final size:14
Alignment explanation
Indices: 651617--651657 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
651607 GCAATATGAA
* *
651617 CACACGCACGCACG
1 CACACACACACACG
*
651631 CACGCACACACACG
1 CACACACACACACG
651645 CACACACACACAC
1 CACACACACACAC
651658 ACAAAATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.37, C:0.51, G:0.12, T:0.00
Consensus pattern (14 bp):
CACACACACACACG
Found at i:653590 original size:23 final size:25
Alignment explanation
Indices: 653559--653606 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
653549 TTCTGTTATT
653559 AACAGAGA-TTCCCGATCTTTGCCA
1 AACAGAGATTTCCCGATCTTTGCCA
653583 AACA-AGATTTCCCGATCTTTGCCA
1 AACAGAGATTTCCCGATCTTTGCCA
653607 CATCAAAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (25 bp):
AACAGAGATTTCCCGATCTTTGCCA
Found at i:658166 original size:6 final size:6
Alignment explanation
Indices: 658155--658192 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
658145 AGGTGACATG
658155 CATATA CATATA CATATA CATATA CATATA CATATA CA
1 CATATA CATATA CATATA CATATA CATATA CATATA CA
658193 GGTATTAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (6 bp):
CATATA
Found at i:677382 original size:89 final size:91
Alignment explanation
Indices: 677213--677408 Score: 254
Period size: 89 Copynumber: 2.2 Consensus size: 91
677203 AGGCTACTTG
* * *** * *
677213 CAAAAAG-CCCTCAAACTTTTTCAAAAAAAGCAATTAAGACCTTGTTTTTCTTTTTGCACTCATT
1 CAAAAAGACCCTCAAACCTTTTCAAAAAAAGCAATTAAGACCCTGACCTTCTTTTTGCACCCAAT
*
677277 TGGGTACTTGAACTTTCAAAATGCAT
66 TAGGTACTTGAACTTTCAAAATGCAT
* *
677303 CAAAAAGATCCTCAAACCTTTTCAAAAAAAGCAATTAAGCCCCT-ACCTT-TTTTTGCACCCAAT
1 CAAAAAGACCCTCAAACCTTTTCAAAAAAAGCAATTAAGACCCTGACCTTCTTTTTGCACCCAAT
*
677366 TAGGTACTTGAACTTTCAAAATGTAT
66 TAGGTACTTGAACTTTCAAAATGCAT
* *
677392 TAAAAAAACCCTCAAAC
1 CAAAAAGACCCTCAAAC
677409 TTAAAAAAAA
Statistics
Matches: 91, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
89 50 0.55
90 9 0.10
91 32 0.35
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.31
Consensus pattern (91 bp):
CAAAAAGACCCTCAAACCTTTTCAAAAAAAGCAATTAAGACCCTGACCTTCTTTTTGCACCCAAT
TAGGTACTTGAACTTTCAAAATGCAT
Found at i:677502 original size:19 final size:19
Alignment explanation
Indices: 677454--677503 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
677444 AAAAAAAATT
*
677454 AAAAATAATAAATTTTAGA
1 AAAAATATTAAATTTTAGA
* *
677473 AAAATTATTAAATTTTAATA
1 AAAAATATTAAATTTT-AGA
677493 AAAAAT-TTAAA
1 AAAAATATTAAA
677504 AAATTAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
AAAAATATTAAATTTTAGA
Found at i:677514 original size:38 final size:38
Alignment explanation
Indices: 677472--677584 Score: 104
Period size: 38 Copynumber: 3.0 Consensus size: 38
677462 TAAATTTTAG
* *
677472 AAAAATTATTAAATTTTAATAAAAAAT-TTAAAAAATTA
1 AAAAATTATTAAATTTT-ATAAAAAATCGTAAAAAAATA
* ***
677510 AAAAATAGATTTTTTTTTATAAAAAATCGTAAAAAAATA
1 AAAAAT-TATTAAATTTTATAAAAAATCGTAAAAAAATA
* * * *
677549 AAAAATTGTAAAATTTTAT-AAATATCATAAAAAAAT
1 AAAAATTATTAAATTTTATAAAAAATCGTAAAAAAAT
677585 GACCCCTAGT
Statistics
Matches: 59, Mismatches: 14, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
37 15 0.25
38 22 0.37
39 22 0.37
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (38 bp):
AAAAATTATTAAATTTTATAAAAAATCGTAAAAAAATA
Found at i:678425 original size:19 final size:19
Alignment explanation
Indices: 678375--678426 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
678365 AATTAGAAAA
*
678375 AAATTACAATAAAA-TAAT
1 AAATTTCAATAAAATTAAT
*
678393 AAATTTCAGA-AAAATTATT
1 AAATTTCA-ATAAAATTAAT
*
678412 AAATTTTAATAAAAT
1 AAATTTCAATAAAAT
678427 ATAAAAATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 12 0.43
19 16 0.57
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (19 bp):
AAATTTCAATAAAATTAAT
Found at i:683742 original size:23 final size:23
Alignment explanation
Indices: 683713--683787 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
683703 GTGTTATTGA
683713 TCAGTGGTAGCTTCGGCTACAGT
1 TCAGTGGTAGCTTCGGCTACAGT
* *
683736 TCGGTGGTAGCTTCGGCTACATT
1 TCAGTGGTAGCTTCGGCTACAGT
683759 TCAGTGGTAGCTTCGGCTACA-T
1 TCAGTGGTAGCTTCGGCTACAGT
683781 ATCAGTG
1 -TCAGTG
683788 TGGCACTTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
22 1 0.02
23 47 0.98
ACGTcount: A:0.17, C:0.21, G:0.29, T:0.32
Consensus pattern (23 bp):
TCAGTGGTAGCTTCGGCTACAGT
Found at i:684813 original size:2 final size:2
Alignment explanation
Indices: 684806--684831 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
684796 TACAGAATTC
684806 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
684832 TTGATATTTT
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):
AT
Found at i:687865 original size:17 final size:17
Alignment explanation
Indices: 687826--687867 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
687816 TTTTTTTAAG
687826 TTTATA-ATTCTTTATA
1 TTTATATATTCTTTATA
687842 TTATATATATT-TTTATA
1 TT-TATATATTCTTTATA
687859 TATTATATA
1 T-TTATATA
687868 ATTTACAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 2 0.09
17 17 0.74
18 4 0.17
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTATATATTCTTTATA
Found at i:687977 original size:16 final size:16
Alignment explanation
Indices: 687948--687988 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 16
687938 TGTTAAGATG
*
687948 ATTATATAAAAAAATTC
1 ATTAAATAAAAAAA-TC
687965 ATTAAATAAAAAAATC
1 ATTAAATAAAAAAATC
687981 ATTAAATA
1 ATTAAATA
687989 TTAAATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTAAATAAAAAAATC
Found at i:688008 original size:22 final size:23
Alignment explanation
Indices: 687965--688012 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
687955 AAAAAAATTC
687965 ATTAAATAAAAAAATCATTAAAT
1 ATTAAATAAAAAAATCATTAAAT
*
687988 ATTAAATTAAAAGAA-CA-TAAAT
1 ATTAAA-TAAAAAAATCATTAAAT
688010 ATT
1 ATT
688013 TTTAAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 8 0.35
23 8 0.35
24 7 0.30
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (23 bp):
ATTAAATAAAAAAATCATTAAAT
Found at i:696805 original size:9 final size:9
Alignment explanation
Indices: 696784--696843 Score: 59
Period size: 9 Copynumber: 6.7 Consensus size: 9
696774 CAATAAGTTT
*
696784 TTTTTGTAA
1 TTTTTATAA
696793 TTTTTAT-A
1 TTTTTATAA
*
696801 TTTTTGTATA
1 TTTTTATA-A
696811 TTTTTATAA
1 TTTTTATAA
**
696820 TGATTATAA
1 TTTTTATAA
*
696829 TTTTTATTA
1 TTTTTATAA
696838 TTTTTA
1 TTTTTA
696844 ATAAAAATTA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
8 7 0.17
9 26 0.63
10 8 0.20
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (9 bp):
TTTTTATAA
Found at i:696853 original size:28 final size:27
Alignment explanation
Indices: 696796--696853 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
696786 TTTGTAATTT
* **
696796 TTATATTTTTGTATATTTTTATAATGA
1 TTATATTTTTATATATTTTTATAAAAA
696823 TTATAATTTTTAT-TATTTTTAATAAAAA
1 TTAT-ATTTTTATATATTTTT-ATAAAAA
696851 TTA
1 TTA
696854 GTTTTCACCA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 11 0.42
28 15 0.58
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.60
Consensus pattern (27 bp):
TTATATTTTTATATATTTTTATAAAAA
Found at i:708910 original size:8 final size:8
Alignment explanation
Indices: 708888--708920 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
708878 TTTTCAACAA
708888 AAAAAAAT
1 AAAAAAAT
708896 AAGAAAAAT
1 AA-AAAAAT
708905 -AAAAAAT
1 AAAAAAAT
708912 AAAAAAAT
1 AAAAAAAT
708920 A
1 A
708921 CTCCTCTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 6 0.26
8 11 0.48
9 6 0.26
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (8 bp):
AAAAAAAT
Found at i:711672 original size:3 final size:3
Alignment explanation
Indices: 711664--711695 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
711654 CTTTATGGTC
*
711664 TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
711696 TTTAACTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:714719 original size:14 final size:14
Alignment explanation
Indices: 714700--714739 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
714690 TTGATTGGCA
714700 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
714714 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
714728 GGAAAATGTTTT
1 GTAAAATGTTTT
714740 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:714752 original size:34 final size:35
Alignment explanation
Indices: 714708--714774 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
714698 CAGTAAAATG
* *
714708 TTTTCCGTAAAATGA-TTTCTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
*
714742 TTTTCTGTAAAATGACTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTT
714775 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 14 0.48
35 15 0.52
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
Found at i:714761 original size:20 final size:20
Alignment explanation
Indices: 714723--714762 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
714713 CGTAAAATGA
**
714723 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGACTTACT
*
714743 TTTCTGTAAAATGACTTACT
1 TTTCTGGAAAATGACTTACT
714763 GGAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTCTGGAAAATGACTTACT
Found at i:721039 original size:6 final size:6
Alignment explanation
Indices: 721025--721078 Score: 63
Period size: 6 Copynumber: 9.0 Consensus size: 6
721015 TATGCGAATC
* * ** *
721025 CAGAAA CAGACA CAGAAA CAAAAA CAGAAA CAGACC CAGAAA CAAAAA
1 CAGAAA CAGAAA CAGAAA CAGAAA CAGAAA CAGAAA CAGAAA CAGAAA
721073 CAGAAA
1 CAGAAA
721079 ATAAAATCCA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.65, C:0.22, G:0.13, T:0.00
Consensus pattern (6 bp):
CAGAAA
Found at i:721057 original size:24 final size:24
Alignment explanation
Indices: 721025--721078 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
721015 TATGCGAATC
721025 CAGAAACAGACACAGAAACAAAAA
1 CAGAAACAGACACAGAAACAAAAA
*
721049 CAGAAACAGACCCAGAAACAAAAA
1 CAGAAACAGACACAGAAACAAAAA
721073 CAGAAA
1 CAGAAA
721079 ATAAAATCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.65, C:0.22, G:0.13, T:0.00
Consensus pattern (24 bp):
CAGAAACAGACACAGAAACAAAAA
Found at i:723498 original size:1 final size:1
Alignment explanation
Indices: 723494--723525 Score: 55
Period size: 1 Copynumber: 32.0 Consensus size: 1
723484 TAATTTTTTT
*
723494 AAAAAACAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
723526 CAAGGCATGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.97, C:0.03, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:728863 original size:21 final size:22
Alignment explanation
Indices: 728814--728863 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
728804 ATATTATTTT
* *
728814 AAATT-TTTTAATATTTATATT
1 AAATTATTTCAATATTTATATA
*
728835 ATATTATTTCAATATTTA-ATA
1 AAATTATTTCAATATTTATATA
728856 AAATTATT
1 AAATTATT
728864 AATTTTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
AAATTATTTCAATATTTATATA
Found at i:729241 original size:11 final size:12
Alignment explanation
Indices: 729227--729255 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
729217 AAAATTTAAA
729227 TTAAAT-ATTAT
1 TTAAATAATTAT
729238 TTAAATAATTAT
1 TTAAATAATTAT
729250 TTAAAT
1 TTAAAT
729256 TAAGGAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAAATAATTAT
Found at i:733033 original size:20 final size:21
Alignment explanation
Indices: 732983--733034 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
732973 CGCTTGGAGT
*
732983 ACTCTTTTCGATATTACTCTA
1 ACTCTTTTCAATATTACTCTA
* *
733004 ACTTTTTTCAATATTATTCTA
1 ACTCTTTTCAATATTACTCTA
733025 A-TCTTTTCAA
1 ACTCTTTTCAA
733035 ATCTGGGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 8 0.30
21 19 0.70
ACGTcount: A:0.27, C:0.19, G:0.02, T:0.52
Consensus pattern (21 bp):
ACTCTTTTCAATATTACTCTA
Found at i:746779 original size:518 final size:517
Alignment explanation
Indices: 745803--746826 Score: 1829
Period size: 518 Copynumber: 2.0 Consensus size: 517
745793 AGAATCTTTA
*
745803 ATTCCGCGTGGAGTTTCTCCATCAATCAATGACTCGCGCTTGCTTTTACTTTGGGATAAACTAAC
1 ATTCCGCGTGGAGTTTCTCCATCAAGCAATGACTCGCGCTTGCTTTTACTTTGGGATAAACTAAC
*
745868 TTTTAATCTTTGATTTTGATATTTTTTTAATTTAGTCCTTAATTTTTTTGGTTTACTTTAGTTTT
66 TTTTAATCATTGATTTTGATATTTTTTTAATTTAGTCCTTAATTTTTTTGGTTTACTTTAGTTTT
745933 AGAATTTGATAAATTTCTTTTTTTAGTTTTAGGTCAGGTGATGACATGATAATATGATATTGTAC
131 AGAATTTGATAAATTTCTTTTTTTAGTTTTAGGTCAGGTGATGACATGATAATATGATATTGTAC
*
745998 TATGTTATCACTTAAAAAATATATTTTTCTTTTCGTTTTAGGAATTTTTATTTGTTCTCGTAGTA
196 TATGTTATCACTTAAAAAATATATTTTTCTTTTCGTTTTAGGAATTTTTATCTGTTCTCGTAGTA
*
746063 TATTTTTTTAGTCTTGTTTATACAAATAACCTTAGTCTTACAAGTGGTTTTATGGATAGTTTTGT
261 TATTTTTTTAGTCTTGTTTATACAAATAACCTTAGTCTTACAAGTAGTTTTATGGATAGTTTTGT
*
746128 TGCCGTTCTCTCTAGTTTGATGAATGCTCTAATATTTTTTCGATTTTTACCTACCGCTTTGGATC
326 TGCCGTTCTCTCTAGTTTGATGAATACTCTAATATTTTTTCGATTTTTACCTACCGCTTTGGATC
746193 ATCCATGGTTGATTATCTTATCGCATTAAGTGCTTGCAATCACTCTATATATATCGTGCTTGAAT
391 ATCCATGGTTGATTATCTTATCGCATTAAGTGCTTGCAATCACTCTATATATATCGTGCTTGAAT
746258 TGTGATAATGCCAATTGTCAACAGGTCGGGTCATGATACTGAAGCTAAAGTTGAAACAGTGT
456 TGTGATAATGCCAATTGTCAACAGGTCGGGTCATGATACTGAAGCTAAAGTTGAAACAGTGT
*
746320 ATTCCGCGTGGGGTTTCTCCATCAAGCAATGACTCGC-CATTGCTTTTACTTTGGGATAAACTAA
1 ATTCCGCGTGGAGTTTCTCCATCAAGCAATGACTCGCGC-TTGCTTTTACTTTGGGATAAACTAA
746384 CTTTTAATCATTGATTTTGATATTTTTTTTAATTTAGTCCTTAATTTTTTTGGTTTACTTTAGTT
65 CTTTTAATCATTGATTTTGATA-TTTTTTTAATTTAGTCCTTAATTTTTTTGGTTTACTTTAGTT
* * *
746449 TTAGAATTTGATAATTTTTTTTTTTTAGTTTTAGGTCAGGTGGTGACATGATAATATGATATTGT
129 TTAGAATTTGATAAATTTCTTTTTTTAGTTTTAGGTCAGGTGATGACATGATAATATGATATTGT
* *
746514 ACTATGTTATCACTTTAAAAATATATTTTTC-TTTCTGTTTTAGGAATTTTTATCTGTTCTTGTA
194 ACTATGTTATCACTTAAAAAATATATTTTTCTTTTC-GTTTTAGGAATTTTTATCTGTTCTCGTA
* *
746578 GTA-AGTTTTTTTAGTCTTGTTTATACAAATAACTTTAGTTTTACAAGTAGTTTTATGGATAGTT
258 GTATA-TTTTTTTAGTCTTGTTTATACAAATAACCTTAGTCTTACAAGTAGTTTTATGGATAGTT
*
746642 TTGTTGTCGTTCTCTCTAGTTTGATGAATACTCTAATATTTTTTCGATTTTTACCTACCGCTTTG
322 TTGTTGCCGTTCTCTCTAGTTTGATGAATACTCTAATATTTTTTCGATTTTTACCTACCGCTTTG
746707 GATCATCCATGGTTGATTATCTTATCGCATTAAGTGCTTGCAATCACTCTATATATATCGTGCTT
387 GATCATCCATGGTTGATTATCTTATCGCATTAAGTGCTTGCAATCACTCTATATATATCGTGCTT
* * * *
746772 GAATTGTGATAATGCCATTTGTTAACGGGTCGGGTCATGATATTGAAGCTAAAGT
452 GAATTGTGATAATGCCAATTGTCAACAGGTCGGGTCATGATACTGAAGCTAAAGT
746827 CTTTGTTGTG
Statistics
Matches: 485, Mismatches: 18, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
516 1 0.00
517 86 0.18
518 398 0.82
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.46
Consensus pattern (517 bp):
ATTCCGCGTGGAGTTTCTCCATCAAGCAATGACTCGCGCTTGCTTTTACTTTGGGATAAACTAAC
TTTTAATCATTGATTTTGATATTTTTTTAATTTAGTCCTTAATTTTTTTGGTTTACTTTAGTTTT
AGAATTTGATAAATTTCTTTTTTTAGTTTTAGGTCAGGTGATGACATGATAATATGATATTGTAC
TATGTTATCACTTAAAAAATATATTTTTCTTTTCGTTTTAGGAATTTTTATCTGTTCTCGTAGTA
TATTTTTTTAGTCTTGTTTATACAAATAACCTTAGTCTTACAAGTAGTTTTATGGATAGTTTTGT
TGCCGTTCTCTCTAGTTTGATGAATACTCTAATATTTTTTCGATTTTTACCTACCGCTTTGGATC
ATCCATGGTTGATTATCTTATCGCATTAAGTGCTTGCAATCACTCTATATATATCGTGCTTGAAT
TGTGATAATGCCAATTGTCAACAGGTCGGGTCATGATACTGAAGCTAAAGTTGAAACAGTGT
Found at i:751388 original size:179 final size:180
Alignment explanation
Indices: 751088--751446 Score: 711
Period size: 179 Copynumber: 2.0 Consensus size: 180
751078 TTTCATGGAT
751088 TATTTTCAATGATGACTCTCAGATTGTGGAAACAAAACGAAACAAACAGAGAAAGTCGTGGTCAA
1 TATTTTCAATGATGACTCTCAGATTGTGGAAACAAAACGAAACAAACAGAGAAAGTCGTGGTCAA
751153 AGGTTTGGGTGGACTTTGATAAGTTTGAAGAACATGGAAAACAAGTAGCCAAATGTAAACACTGC
66 AGGTTTGGGTGGACTTTGATAAGTTTGAAGAACATGGAAAACAAGTAGCCAAATGTAAACACTGC
751218 CCCAAGGTGTTTACAGGGTCAAGTAAGAGTGGAACCACA-ACTTGAATAA
131 CCCAAGGTGTTTACAGGGTCAAGTAAGAGTGGAACCACACACTTGAATAA
751267 TATTTTCAATGATGACTCTCAGATTGTGGAAACAAAACGAAACAAACAGAGAAAGTCGTGGTCAA
1 TATTTTCAATGATGACTCTCAGATTGTGGAAACAAAACGAAACAAACAGAGAAAGTCGTGGTCAA
751332 AGGTTTGGGTGGACTTTGATAAGTTTGAAGAACATGGAAAACAAGTAGCCAAATGTAAACACTGC
66 AGGTTTGGGTGGACTTTGATAAGTTTGAAGAACATGGAAAACAAGTAGCCAAATGTAAACACTGC
751397 CCCAAGGTGTTTACAGGGTCAAGTAAGAGTGGAACCACACACTTGAATAA
131 CCCAAGGTGTTTACAGGGTCAAGTAAGAGTGGAACCACACACTTGAATAA
751447 CCACTCGAAA
Statistics
Matches: 179, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
179 169 0.94
180 10 0.06
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (180 bp):
TATTTTCAATGATGACTCTCAGATTGTGGAAACAAAACGAAACAAACAGAGAAAGTCGTGGTCAA
AGGTTTGGGTGGACTTTGATAAGTTTGAAGAACATGGAAAACAAGTAGCCAAATGTAAACACTGC
CCCAAGGTGTTTACAGGGTCAAGTAAGAGTGGAACCACACACTTGAATAA
Found at i:763695 original size:18 final size:18
Alignment explanation
Indices: 763672--763713 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
763662 CCACAGGAAA
*
763672 GATAATCTTAGCTTTGAG
1 GATAATCCTAGCTTTGAG
*
763690 GATAATCCTAGCTTTGCG
1 GATAATCCTAGCTTTGAG
763708 GATAAT
1 GATAAT
763714 AGTTTGTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (18 bp):
GATAATCCTAGCTTTGAG
Found at i:763990 original size:31 final size:31
Alignment explanation
Indices: 763955--764020 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
763945 TAATTCCATC
763955 TATCTGCTTTTGATTCTATCCAATTAAAATA
1 TATCTGCTTTTGATTCTATCCAATTAAAATA
763986 TATCTGCTTTTGATTCTATCCAATTAAAATA
1 TATCTGCTTTTGATTCTATCCAATTAAAATA
764017 -ATCT
1 TATCT
764021 TAAATTATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 4 0.11
31 31 0.89
ACGTcount: A:0.32, C:0.17, G:0.06, T:0.45
Consensus pattern (31 bp):
TATCTGCTTTTGATTCTATCCAATTAAAATA
Found at i:764145 original size:24 final size:24
Alignment explanation
Indices: 764101--764148 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
764091 GATACATCCA
* *
764101 TACTAAAATAAATTATTTTAAAAT
1 TACTAAAATAAATGATGTTAAAAT
764125 TACTAAAAATAAATGA-GTTAAAAT
1 TACT-AAAATAAATGATGTTAAAAT
764149 AAATTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.35
Consensus pattern (24 bp):
TACTAAAATAAATGATGTTAAAAT
Found at i:768458 original size:32 final size:32
Alignment explanation
Indices: 768414--768478 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
768404 TAATAAGGTA
768414 AGATTTCGATCCTTAATTATAAGGATTCCAAC
1 AGATTTCGATCCTTAATTATAAGGATTCCAAC
* *
768446 AGATTTCTATCCTTAATTATAGGGATTCCAAC
1 AGATTTCGATCCTTAATTATAAGGATTCCAAC
768478 A
1 A
768479 ATAGAAGCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.35
Consensus pattern (32 bp):
AGATTTCGATCCTTAATTATAAGGATTCCAAC
Found at i:769553 original size:21 final size:22
Alignment explanation
Indices: 769504--769554 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
769494 TATCCTGCCA
* *
769504 AAAATTATTGGTATTTTTAAAT
1 AAAATTATTAGTATTATTAAAT
* *
769526 GAAATTATTAGTA-TATTATAT
1 AAAATTATTAGTATTATTAAAT
769547 AAAATTAT
1 AAAATTAT
769555 ATAAAGAGAG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (22 bp):
AAAATTATTAGTATTATTAAAT
Found at i:775126 original size:18 final size:18
Alignment explanation
Indices: 775103--775139 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
775093 TGACAATGAT
775103 GGCCAAATGGAGGATAGC
1 GGCCAAATGGAGGATAGC
775121 GGCCAAATGGAGGATAGC
1 GGCCAAATGGAGGATAGC
775139 G
1 G
775140 ATGAAGATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.41, T:0.11
Consensus pattern (18 bp):
GGCCAAATGGAGGATAGC
Found at i:776071 original size:44 final size:46
Alignment explanation
Indices: 776016--776104 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
776006 CATCTTATTA
*
776016 CATTCAACCAAACACAAGA-ATACC-ATTACGCCTCTATTCCATTC
1 CATTCAACCAAACAAAAGATATACCTATTACGCCTCTATTCCATTC
* * * *
776060 CATTTAACCAAACAAAATATTTACCTATTACGTCTCTATTCCATT
1 CATTCAACCAAACAAAAGATATACCTATTACGCCTCTATTCCATT
776105 ACGCATCTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
44 16 0.42
45 4 0.11
46 18 0.47
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.31
Consensus pattern (46 bp):
CATTCAACCAAACAAAAGATATACCTATTACGCCTCTATTCCATTC
Found at i:776107 original size:16 final size:15
Alignment explanation
Indices: 776086--776138 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
776076 ATATTTACCT
776086 ATTACGTCTCTATTCC
1 ATTACG-CTCTATTCC
*
776102 ATTACGCATCTATTTC
1 ATTACGC-TCTATTCC
*
776118 ATTACACCTCTATTCC
1 ATTAC-GCTCTATTCC
776134 ATTAC
1 ATTAC
776139 AACGAACCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 1 0.03
16 30 0.94
17 1 0.03
ACGTcount: A:0.25, C:0.30, G:0.04, T:0.42
Consensus pattern (15 bp):
ATTACGCTCTATTCC
Done.