Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 23 of 318
Found at i:8766514 original size:18 final size:17
Alignment explanation
Indices: 8766399--8766554 Score: 67
Period size: 16 Copynumber: 8.9 Consensus size: 17
8766389 GGTTTACACA
8766399 TAAAAATTATTAAAA-AT
1 TAAAAATTA-TAAAATAT
* *
8766416 AAAAAAATATAAAA-AT
1 TAAAAATTATAAAATAT
** *
8766432 TATTAA-TATAAAAAAAT
1 TAAAAATTAT-AAAATAT
*
8766449 TATAGAAAATAT-AAATAT
1 TA-A-AAATTATAAAATAT
*
8766467 TAAAAA--ATGAAAATTT
1 TAAAAATTAT-AAAATAT
*
8766483 GTATAAACTTATAAAATAT
1 -TA-AAAATTATAAAATAT
8766502 TAAAAGATTATAAAAAATAT
1 TAAAA-ATTAT--AAAATAT
8766522 TAAAAA-TATAAAAT-T
1 TAAAAATTATAAAATAT
*
8766537 CTAATATATTATAAAATA
1 -TAA-AAATTATAAAATA
8766555 ATTTATATAA
Statistics
Matches: 108, Mismatches: 13, Indels: 34
0.70 0.08 0.22
Matches are distributed among these distances:
14 2 0.02
15 4 0.04
16 30 0.28
17 19 0.18
18 27 0.25
19 9 0.08
20 17 0.16
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (17 bp):
TAAAAATTATAAAATAT
Found at i:8766616 original size:22 final size:21
Alignment explanation
Indices: 8766565--8766615 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
8766555 ATTTATATAA
8766565 TTTATAAAACATATTTAAAAT
1 TTTATAAAACATATTTAAAAT
8766586 TTTATAAAAGCATA-TTAAAAT
1 TTTATAAAA-CATATTTAAAAT
8766607 TCTT-TAAAA
1 T-TTATAAAA
8766616 ATCGTAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 22 0.79
22 6 0.21
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (21 bp):
TTTATAAAACATATTTAAAAT
Found at i:8767273 original size:6 final size:6
Alignment explanation
Indices: 8767262--8767287 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
8767252 TAATCAAACC
8767262 TAAATT TAAATT TAAATT TAAATT TA
1 TAAATT TAAATT TAAATT TAAATT TA
8767288 TGAATCTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TAAATT
Found at i:8775089 original size:25 final size:25
Alignment explanation
Indices: 8775055--8775105 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
8775045 TCCTTGAGAA
8775055 TATTGAAATTAAGTCTTCTTCATGT
1 TATTGAAATTAAGTCTTCTTCATGT
8775080 TATTGAAATTAAGTCTTCTTCATGT
1 TATTGAAATTAAGTCTTCTTCATGT
8775105 T
1 T
8775106 CACTTTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.49
Consensus pattern (25 bp):
TATTGAAATTAAGTCTTCTTCATGT
Found at i:8787918 original size:23 final size:23
Alignment explanation
Indices: 8787892--8787989 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
8787882 ATAAGTGCCA
8787892 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
8787915 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
8787938 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
8787960 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
8787983 CACTGAT
1 CACTGAT
8787990 CAATAACACT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:8787957 original size:45 final size:45
Alignment explanation
Indices: 8787899--8787987 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
8787889 CCACACTGAT
* *
8787899 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
8787944 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
8787988 ATCAATAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.19
Consensus pattern (45 bp):
ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:8790875 original size:12 final size:12
Alignment explanation
Indices: 8790833--8790876 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
8790823 CTTTTAGAAA
* *
8790833 TAATATTAATTT
1 TAATATTTATAT
* *
8790845 TAATATATATAA
1 TAATATTTATAT
8790857 TAATATTTATAT
1 TAATATTTATAT
8790869 TAATATTT
1 TAATATTT
8790877 TTCTAGCACA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TAATATTTATAT
Found at i:8803403 original size:30 final size:30
Alignment explanation
Indices: 8803367--8803429 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
8803357 TAAATATAAG
*
8803367 AAAAAATATTTTGTATACATTAGGATTTTT
1 AAAAAATATTTTGTATACATTAGAATTTTT
*
8803397 AAAAAATATTTTGTATATATTAGAATTTTT
1 AAAAAATATTTTGTATACATTAGAATTTTT
8803427 AAA
1 AAA
8803430 CTCTACACGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (30 bp):
AAAAAATATTTTGTATACATTAGAATTTTT
Found at i:8809095 original size:2 final size:2
Alignment explanation
Indices: 8809090--8809137 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
8809080 GTGTGTGTGT
8809090 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
8809132 GA GA GA
1 GA GA GA
8809138 CCTGCTCTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:8814474 original size:29 final size:29
Alignment explanation
Indices: 8814432--8814492 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
8814422 CTTACAACGG
*
8814432 TTGAAACTGTTGAGCATGTACTGCTATAT
1 TTGAAACTGTTGAGCACGTACTGCTATAT
8814461 TTGAAACTGTTGAGCACGTACTGCTATAT
1 TTGAAACTGTTGAGCACGTACTGCTATAT
8814490 TTG
1 TTG
8814493 CCCGATTGCC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (29 bp):
TTGAAACTGTTGAGCACGTACTGCTATAT
Found at i:8816405 original size:86 final size:86
Alignment explanation
Indices: 8816257--8816428 Score: 283
Period size: 86 Copynumber: 2.0 Consensus size: 86
8816247 ATTGTTCAAT
* * * *
8816257 CTGTACCAAGTTCAATGAGTTCACTAGTTATGTAGATGTCATATTGTGATATGCGGTGTGCTCAT
1 CTGTACCAAGTTCAATGAGTTCACAAGTTATGTAGATGCCATATTGTGATATGAGGTATGCTCAT
8816322 GGTATGACCCTGCATATAGCA
66 GGTATGACCCTGCATATAGCA
8816343 CTGTACCAAGTT-AAGTGAGTTCACAAGTTATGTAGATGCCATATTGTGATATGAGGTATGCTCA
1 CTGTACCAAGTTCAA-TGAGTTCACAAGTTATGTAGATGCCATATTGTGATATGAGGTATGCTCA
*
8816407 TGGTATGACGCTGCATATAGCA
65 TGGTATGACCCTGCATATAGCA
8816429 GGAACCTAGT
Statistics
Matches: 80, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
85 2 0.03
86 78 0.98
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (86 bp):
CTGTACCAAGTTCAATGAGTTCACAAGTTATGTAGATGCCATATTGTGATATGAGGTATGCTCAT
GGTATGACCCTGCATATAGCA
Found at i:8823325 original size:9 final size:9
Alignment explanation
Indices: 8823311--8823340 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
8823301 TCTCATAACA
8823311 AAAAAAAAT
1 AAAAAAAAT
8823320 AAAAAAAAT
1 AAAAAAAAT
*
8823329 AAAAACAAT
1 AAAAAAAAT
8823338 AAA
1 AAA
8823341 TTTTTCATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:8824108 original size:13 final size:14
Alignment explanation
Indices: 8824090--8824122 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
8824080 CAATATATCT
8824090 ATTATTTAA-CTAA
1 ATTATTTAAGCTAA
*
8824103 ATTATTTAAGGTAA
1 ATTATTTAAGCTAA
8824117 ATTATT
1 ATTATT
8824123 CTCTTGGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (14 bp):
ATTATTTAAGCTAA
Found at i:8830497 original size:29 final size:30
Alignment explanation
Indices: 8830464--8830529 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
8830454 TAGGGACCAG
*
8830464 ATCAAATTAATCGCTCCATTATT-AAATGA
1 ATCAAATTAATCGCTACATTATTAAAATGA
* * *
8830493 ATCAATTTAATCTCTATATTATTAAAATGA
1 ATCAAATTAATCGCTACATTATTAAAATGA
*
8830523 TTCAAAT
1 ATCAAAT
8830530 AAACCCAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 19 0.63
30 11 0.37
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.39
Consensus pattern (30 bp):
ATCAAATTAATCGCTACATTATTAAAATGA
Found at i:8832240 original size:3 final size:3
Alignment explanation
Indices: 8832232--8832262 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
8832222 ACCTCTGACC
8832232 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
8832263 CCTTAATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:8834003 original size:10 final size:10
Alignment explanation
Indices: 8833988--8834026 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
8833978 TAATATTTAT
*
8833988 TATTTTAATA
1 TATTTTAAAA
8833998 TATTTTAAAA
1 TATTTTAAAA
*
8834008 TTTTTTAAAA
1 TATTTTAAAA
8834018 TTATTTTAA
1 -TATTTTAA
8834027 TCTAAACGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
10 18 0.72
11 7 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TATTTTAAAA
Found at i:8834502 original size:40 final size:38
Alignment explanation
Indices: 8834458--8834533 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 38
8834448 TAGGGTTATT
*
8834458 AGTTT-ATTTAGTATTTAATTTTTTAAAATTTTGATATTTA
1 AGTTTGATTTAATA-TTAATTTTTT-AAA-TTTGATATTTA
*
8834498 AGTTTGATTTAATATTAATTTTTTTAATTTGATATT
1 AGTTTGATTTAATATTAATTTTTTAAATTTGATATT
8834534 GAGGTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 9 0.27
39 2 0.06
40 15 0.45
41 7 0.21
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.61
Consensus pattern (38 bp):
AGTTTGATTTAATATTAATTTTTTAAATTTGATATTTA
Found at i:8834750 original size:23 final size:23
Alignment explanation
Indices: 8834706--8834762 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
8834696 TAAAGTTATT
8834706 TAATAC-AAATTGAAACAAAAAA
1 TAATACTAAATTGAAACAAAAAA
*
8834728 TAATACTAAATT-AAACATTAAAA
1 TAATACTAAATTGAAACA-AAAAA
*
8834751 TAAAACTCAAAT
1 TAATACT-AAAT
8834763 AACAAATAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 11 0.37
23 15 0.50
24 4 0.13
ACGTcount: A:0.63, C:0.11, G:0.02, T:0.25
Consensus pattern (23 bp):
TAATACTAAATTGAAACAAAAAA
Found at i:8842314 original size:51 final size:52
Alignment explanation
Indices: 8842222--8842384 Score: 198
Period size: 51 Copynumber: 3.2 Consensus size: 52
8842212 TACTTCTGAT
* *
8842222 CAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGA
1 CAAGTGA-AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGA
* *
8842275 CAAGTGAAAAGTGATAA-TGATAGCTTCGGCTATACTTATCTGATCAAGAGA
1 CAAGTGAAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGA
*
8842326 C------AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGA-A
1 CAAGTGAAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGA
*
8842371 CAAAGTGATAAGTG
1 C-AAGTGAAAAGTG
8842385 GCTACACTTA
Statistics
Matches: 94, Mismatches: 8, Indels: 17
0.79 0.07 0.14
Matches are distributed among these distances:
45 12 0.13
46 29 0.31
51 31 0.33
52 15 0.16
53 7 0.07
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (52 bp):
CAAGTGAAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGA
Found at i:8842374 original size:45 final size:46
Alignment explanation
Indices: 8842282--8842384 Score: 165
Period size: 46 Copynumber: 2.3 Consensus size: 46
8842272 TGACAAGTGA
* *
8842282 AAAGTGATAA-TGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGAC
*
8842327 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGA-AC
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGAC
8842372 AAAGTGATAAGTG
1 AAAGTGATAAGTG
8842385 GCTACACTTA
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
45 25 0.46
46 29 0.54
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (46 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGAC
Found at i:8842423 original size:37 final size:36
Alignment explanation
Indices: 8842349--8842456 Score: 173
Period size: 37 Copynumber: 3.0 Consensus size: 36
8842339 GATAGCTTTA
8842349 GCTACACTTATCTGATCAAGAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAACAAAGTGATAAGTG
*
8842385 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAG-AACAAAGTGATAAGTG
* *
8842422 GCTACACTTATCTGATCAGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAACAAAGTGATAAGTG
8842457 ATCATACGTA
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
35 11 0.16
36 22 0.33
37 34 0.51
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGAACAAAGTGATAAGTG
Found at i:8843830 original size:49 final size:49
Alignment explanation
Indices: 8843710--8843901 Score: 305
Period size: 49 Copynumber: 3.9 Consensus size: 49
8843700 ATGTGAACAT
8843710 GTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGT-A
1 GTGA-TATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
8843759 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* * *
8843808 GTGATATGTGATTTCGTGTAAGACCATAGTTGGGCTATGGCATCGGTAT
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* * * *
8843857 GTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCG
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCG
8843902 AGAAAACGAA
Statistics
Matches: 136, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
48 43 0.32
49 93 0.68
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.32
Consensus pattern (49 bp):
GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
Found at i:8847114 original size:52 final size:52
Alignment explanation
Indices: 8847035--8847199 Score: 207
Period size: 46 Copynumber: 3.2 Consensus size: 52
8847025 TACTTCTGAT
* *
8847035 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGCGA
1 CAAGTGA-AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGA
* ** *
8847088 CAAGTGAAAAGTGATAATTGATAGCTTCGGCTATACTTATCTGATCAAGAGA
1 CAAGTGAAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGA
8847140 C------AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGA
1 CAAGTGAAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGA
*
8847186 CAAAGTGATAAGTG
1 C-AAGTGAAAAGTG
8847200 GCTACACTTA
Statistics
Matches: 94, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
46 42 0.45
52 40 0.43
53 12 0.13
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (52 bp):
CAAGTGAAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGA
Found at i:8847207 original size:37 final size:37
Alignment explanation
Indices: 8847163--8847254 Score: 166
Period size: 37 Copynumber: 2.5 Consensus size: 37
8847153 GATAGCTTTA
*
8847163 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
8847200 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
8847237 GCTACACTTATCTGATCA
1 GCTACACTTATCTGATCA
8847255 GGGACAAGTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:8861563 original size:29 final size:30
Alignment explanation
Indices: 8861530--8861595 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
8861520 TAGGGACCAG
*
8861530 ATCAAATTAATCGCTCCATTATT-AAATGA
1 ATCAAATTAATCGCTACATTATTAAAATGA
* * *
8861559 ATCAATTTAATCTCTATATTATTAAAATGA
1 ATCAAATTAATCGCTACATTATTAAAATGA
*
8861589 TTCAAAT
1 ATCAAAT
8861596 AAACCCAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 19 0.63
30 11 0.37
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.39
Consensus pattern (30 bp):
ATCAAATTAATCGCTACATTATTAAAATGA
Found at i:8863350 original size:3 final size:3
Alignment explanation
Indices: 8863342--8863369 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
8863332 TGACCCTTTC
8863342 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
8863370 CCTTAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:8865887 original size:24 final size:25
Alignment explanation
Indices: 8865835--8865887 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
8865825 ATTTAATTAC
*
8865835 CAAATTGAAACAAAAAATTAATACT
1 CAAATTGAAACAAAAAATTAAAACT
*
8865860 -AAATT-AAACATTAAAA-TAAAACT
1 CAAATTGAAACA-AAAAATTAAAACT
8865883 CAAAT
1 CAAAT
8865888 AACAAATAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.62, C:0.11, G:0.02, T:0.25
Consensus pattern (25 bp):
CAAATTGAAACAAAAAATTAAAACT
Found at i:8869277 original size:15 final size:15
Alignment explanation
Indices: 8869259--8869289 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
8869249 CAATAATATG
8869259 TAAAGTTCTAATCAT
1 TAAAGTTCTAATCAT
8869274 TAAAGTTCTAATCAT
1 TAAAGTTCTAATCAT
8869289 T
1 T
8869290 GGGCCTATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (15 bp):
TAAAGTTCTAATCAT
Found at i:8873468 original size:3 final size:3
Alignment explanation
Indices: 8873460--8873486 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
8873450 CAACGCTTAG
8873460 CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT
8873487 TTTATTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:8889593 original size:8 final size:9
Alignment explanation
Indices: 8889580--8889723 Score: 71
Period size: 9 Copynumber: 15.6 Consensus size: 9
8889570 CGAAAAATGA
8889580 TAAAAATAT
1 TAAAAATAT
8889589 TAAAAATAT
1 TAAAAATAT
8889598 TAAAAATA-
1 TAAAAATAT
* * *
8889606 TAATATTTT
1 TAAAAATAT
8889615 CTAATAAAT-T
1 -TAA-AAATAT
* *
8889625 ATAAAATTAA
1 -TAAAAATAT
*
8889635 TAAACATAT
1 TAAAAATAT
* *
8889644 TTAAAATTT
1 TAAAAATAT
8889653 TATAAAATCAT
1 TA-AAAAT-AT
*
8889664 ATTAAAAT-T
1 -TAAAAATAT
*
8889673 CTATAAA-AT
1 -TAAAAATAT
*
8889682 GAAAAATAT
1 TAAAAATAT
*
8889691 TAAAAAATGT
1 T-AAAAATAT
*
8889701 TAAAAATGT
1 TAAAAATAT
8889710 TAAAAATAT
1 TAAAAATAT
8889719 TAAAA
1 TAAAA
8889724 TTGCTATAAA
Statistics
Matches: 100, Mismatches: 25, Indels: 20
0.69 0.17 0.14
Matches are distributed among these distances:
8 9 0.09
9 62 0.62
10 20 0.20
11 8 0.08
12 1 0.01
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (9 bp):
TAAAAATAT
Found at i:8889670 original size:21 final size:22
Alignment explanation
Indices: 8889639--8889681 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
8889629 AATTAATAAA
*
8889639 CATATTTAAAATTTTATAAAAT
1 CATATTTAAAATTCTATAAAAT
8889661 CATA-TTAAAATTCTATAAAAT
1 CATATTTAAAATTCTATAAAAT
8889682 GAAAAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (22 bp):
CATATTTAAAATTCTATAAAAT
Found at i:8889741 original size:28 final size:27
Alignment explanation
Indices: 8889652--8889741 Score: 71
Period size: 27 Copynumber: 3.3 Consensus size: 27
8889642 ATTTAAAATT
8889652 TTATAAAATCATATTAAAATT-CTATAAA
1 TTATAAAA--ATATTAAAATTGCTATAAA
* * *
8889680 --ATGAAAAATATTAAAAAATGTTAAAAA
1 TTAT-AAAAATATT-AAAATTGCTATAAA
8889707 TGT-TAAAAATATTAAAATTGCTATAAA
1 T-TATAAAAATATTAAAATTGCTATAAA
8889734 CTTATAAA
1 -TTATAAA
8889742 GATTATAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 16
0.69 0.09 0.23
Matches are distributed among these distances:
25 5 0.10
26 7 0.15
27 21 0.44
28 14 0.29
29 1 0.02
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.34
Consensus pattern (27 bp):
TTATAAAAATATTAAAATTGCTATAAA
Found at i:8890251 original size:10 final size:9
Alignment explanation
Indices: 8890187--8890385 Score: 90
Period size: 9 Copynumber: 21.7 Consensus size: 9
8890177 AGCTTTTATG
8890187 ATAATTTTT
1 ATAATTTTT
8890196 ATAATTTTT
1 ATAATTTTT
*
8890205 AT-TTTTTT
1 ATAATTTTT
*
8890213 ATGATTTTT
1 ATAATTTTT
* **
8890222 AAAAAAATTT
1 -ATAATTTTT
8890232 ATACATTTTT
1 ATA-ATTTTT
8890242 ATAATATTTT
1 ATAAT-TTTT
*
8890252 TTATATATTTT
1 ATA-AT-TTTT
8890263 ATTAA-TTTT
1 A-TAATTTTT
****
8890272 ATAAAAAAT
1 ATAATTTTT
8890281 ATAATTTTTT
1 ATAA-TTTTT
*
8890291 ATAATTTAT
1 ATAATTTTT
8890300 -TAATTTTT
1 ATAATTTTT
8890308 ATAACTTTTT
1 ATAA-TTTTT
*
8890318 ATAATATTT
1 ATAATTTTT
*
8890327 ATAAGTTTAT
1 ATAA-TTTTT
* *
8890337 ATCTATTTTA
1 AT-AATTTTT
8890347 ATAATTCTTT
1 ATAATT-TTT
*
8890357 -TATAGTTTT
1 ATA-ATTTTT
8890366 AT-A-TTTT
1 ATAATTTTT
8890373 AT-ATTTTT
1 ATAATTTTT
8890381 A-AATT
1 ATAATT
8890386 ATTTTATGGA
Statistics
Matches: 144, Mismatches: 29, Indels: 35
0.69 0.14 0.17
Matches are distributed among these distances:
7 7 0.05
8 26 0.18
9 53 0.37
10 47 0.33
11 9 0.06
12 2 0.01
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (9 bp):
ATAATTTTT
Found at i:8890273 original size:18 final size:18
Alignment explanation
Indices: 8890250--8890311 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 18
8890240 TTATAATATT
*
8890250 TTTTATATATTTTATTAA
1 TTTTATATAATTTATTAA
* **
8890268 TTTTATAAAAAATA-TAA
1 TTTTATATAATTTATTAA
*
8890285 TTTTTTATAATTTATTAA
1 TTTTATATAATTTATTAA
8890303 TTTT-TATAA
1 TTTTATATAA
8890312 CTTTTTATAA
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
17 18 0.51
18 17 0.49
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTATATAATTTATTAA
Found at i:8890322 original size:19 final size:18
Alignment explanation
Indices: 8890181--8890352 Score: 73
Period size: 19 Copynumber: 9.1 Consensus size: 18
8890171 AGTTCTAGCT
8890181 TTTATGATAATTTTTATAA
1 TTTAT-ATAATTTTTATAA
* * *
8890200 TTTTTAT-TTTTTTATGA
1 TTTATATAATTTTTATAA
* * **
8890217 TTTTTAAAAAAATTTATACA
1 TTTAT-ATAATTTTTATA-A
*
8890237 TTTTTATAATATTTTTTATATA
1 --TTTAT-ATAATTTTTATA-A
8890259 TTT-TATTAA-TTTTATAA
1 TTTATA-TAATTTTTATAA
***
8890276 AAAATATAATTTTTTATAA
1 TTTATATAA-TTTTTATAA
8890295 TTTAT-TAATTTTTATAA
1 TTTATATAATTTTTATAA
* *
8890312 CTTTTTATAATATTTATAA
1 -TTTATATAATTTTTATAA
* *
8890331 GTTTATATCTATTTTAATAA
1 -TTTATAT-AATTTTTATAA
8890351 TT
1 TT
8890353 CTTTTATAGT
Statistics
Matches: 113, Mismatches: 28, Indels: 24
0.68 0.17 0.15
Matches are distributed among these distances:
17 26 0.23
18 20 0.18
19 41 0.36
20 12 0.11
22 14 0.12
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTATATAATTTTTATAA
Found at i:8890979 original size:23 final size:22
Alignment explanation
Indices: 8890944--8890986 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
8890934 GACATGAGCG
8890944 AATTAGAGCTGAAACAAAAAAAC
1 AATTAGAGCTG-AACAAAAAAAC
* *
8890967 AATTGGAGTTGAACAAAAAA
1 AATTAGAGCTGAACAAAAAA
8890987 GGCCTACTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.58, C:0.09, G:0.16, T:0.16
Consensus pattern (22 bp):
AATTAGAGCTGAACAAAAAAAC
Found at i:8900077 original size:22 final size:22
Alignment explanation
Indices: 8900052--8900093 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
8900042 AGTCAGGGCC
*
8900052 AAATTGATAAAAAAAATTATAA
1 AAATTAATAAAAAAAATTATAA
**
8900074 AAATTAATAACTAAAATTAT
1 AAATTAATAAAAAAAATTAT
8900094 TATTATATCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (22 bp):
AAATTAATAAAAAAAATTATAA
Found at i:8907162 original size:14 final size:14
Alignment explanation
Indices: 8907139--8907168 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
8907129 CCCCCCCCCC
8907139 AAAAAAAAAAAAAG
1 AAAAAAAAAAAAAG
*
8907153 AAAAAGAAAAAAAG
1 AAAAAAAAAAAAAG
8907167 AA
1 AA
8907169 CTCTGGCTTA
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:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAAG
Found at i:8909336 original size:122 final size:122
Alignment explanation
Indices: 8909195--8909443 Score: 408
Period size: 122 Copynumber: 2.0 Consensus size: 122
8909185 AAAAATACAA
* * *
8909195 AAAAAAAACTAACACAAATATTAGTAGTCATATATTAGATACTCTAGACTACAGTGGTATTTCAG
1 AAAAAAAACTAACAAAAATATTAGTAGTCATATATTAGATACTCTAGACCACAGTGGTATCTCAG
* *
8909260 TTCCTGGAAGTAGTGAAACTTACCTGTACCTAGCAACAGTACTACCTTTTGCATATT
66 TTCCTGGAAGTAGTGAAACTTACCTGTACCTAGCAACAGTACTACCTTCTACATATT
* *
8909317 AAAAAAAACTAACAAAAATATTATTAGTCATATATTAGATACTCTAGACCATAGTGGTATCTCAG
1 AAAAAAAACTAACAAAAATATTAGTAGTCATATATTAGATACTCTAGACCACAGTGGTATCTCAG
* *
8909382 TTCCTGGAAGTAGTGAAACTTACCTGTACCTAGCAATAGTACTGCCTTCTACATATT
66 TTCCTGGAAGTAGTGAAACTTACCTGTACCTAGCAACAGTACTACCTTCTACATATT
*
8909439 CAAAA
1 AAAAA
8909444 GCAAAACACA
Statistics
Matches: 117, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
122 117 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (122 bp):
AAAAAAAACTAACAAAAATATTAGTAGTCATATATTAGATACTCTAGACCACAGTGGTATCTCAG
TTCCTGGAAGTAGTGAAACTTACCTGTACCTAGCAACAGTACTACCTTCTACATATT
Found at i:8911901 original size:22 final size:22
Alignment explanation
Indices: 8911875--8911920 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
8911865 GTGTTGGATT
*
8911875 TATAATATGGATAAATTGCAAC
1 TATAATATGGAGAAATTGCAAC
8911897 TATAATATGGAGAAATTGCAAC
1 TATAATATGGAGAAATTGCAAC
8911919 TA
1 TA
8911921 ACTTGAGGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.46, C:0.09, G:0.15, T:0.30
Consensus pattern (22 bp):
TATAATATGGAGAAATTGCAAC
Found at i:8913723 original size:12 final size:12
Alignment explanation
Indices: 8913690--8913725 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
8913680 TTAAAACATT
*
8913690 AAAAATAAATTA
1 AAAAATATATTA
8913702 AAAAATTATATTA
1 AAAAA-TATATTA
8913715 AAAAATATATT
1 AAAAATATATT
8913726 TTATAGTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAAATATATTA
Found at i:8914944 original size:13 final size:14
Alignment explanation
Indices: 8914928--8914963 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
8914918 CAATCTCATA
8914928 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
8914941 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
8914954 TCTC-ATTTCA
1 TCTCAATTTCA
8914964 TTCCAATAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:8914953 original size:18 final size:19
Alignment explanation
Indices: 8914915--8914955 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
8914905 TGGTTCATGT
8914915 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
8914934 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
8914952 TTTC
1 TTTC
8914956 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:8915185 original size:23 final size:23
Alignment explanation
Indices: 8915117--8915201 Score: 106
Period size: 21 Copynumber: 3.9 Consensus size: 23
8915107 CCTGATCAGT
8915117 ATACGACACATAAAGTGCCT-AA
1 ATACGACACATAAAGTGCCTGAA
* *
8915139 A-ACGACACATGAGGTGCCTG--
1 ATACGACACATAAAGTGCCTGAA
* *
8915159 ATACGACACACAAGGTGCCTGAA
1 ATACGACACATAAAGTGCCTGAA
8915182 ATACGACACATAAAGTGCCT
1 ATACGACACATAAAGTGCCT
8915202 AATCGGTAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
20 1 0.02
21 33 0.62
22 1 0.02
23 18 0.34
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAA
Found at i:8915957 original size:39 final size:39
Alignment explanation
Indices: 8915913--8916036 Score: 221
Period size: 39 Copynumber: 3.2 Consensus size: 39
8915903 CGAAATCTAG
* *
8915913 CTGAAGCACATAAGTGCTAAACGGCAGCCCGAAGGCTAA
1 CTGAAGCACATAAGTGCTAAACGGAAGCCCGGAGGCTAA
*
8915952 TTGAAGCACATAAGTGCTAAACGGAAGCCCGGAGGCTAA
1 CTGAAGCACATAAGTGCTAAACGGAAGCCCGGAGGCTAA
8915991 CTGAAGCACATAAGTGCTAAACGGAAGCCCGGAGGCTAA
1 CTGAAGCACATAAGTGCTAAACGGAAGCCCGGAGGCTAA
8916030 CTGAAGC
1 CTGAAGC
8916037 TCATCAGAGT
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 81 1.00
ACGTcount: A:0.35, C:0.23, G:0.27, T:0.14
Consensus pattern (39 bp):
CTGAAGCACATAAGTGCTAAACGGAAGCCCGGAGGCTAA
Found at i:8916092 original size:20 final size:19
Alignment explanation
Indices: 8916027--8916111 Score: 53
Period size: 20 Copynumber: 4.2 Consensus size: 19
8916017 GCCCGGAGGC
*
8916027 TAACTGAAGCTCATCAGAGT
1 TAACTGAAACTCAT-AGAGT
* * *
8916047 TGAACTGAAACCCCAAAAGGGT
1 T-AACTGAAA-CTC-ATAGAGT
8916069 TAACTGAAACTCATATGAGT
1 TAACTGAAACTCATA-GAGT
* * *
8916089 TAACGGAAGCTCGTACGAGT
1 TAACTGAAACTCATA-GAGT
8916109 TAA
1 TAA
8916112 ACGGAAAGCA
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
19 2 0.04
20 25 0.50
21 15 0.30
22 7 0.14
23 1 0.02
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (19 bp):
TAACTGAAACTCATAGAGT
Found at i:8918515 original size:15 final size:15
Alignment explanation
Indices: 8918490--8918545 Score: 85
Period size: 15 Copynumber: 3.7 Consensus size: 15
8918480 TCATATATAT
8918490 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
8918506 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
8918521 AATAATTTCAATCAA
1 TATAAATTCAATCAA
8918536 TATAAATTCA
1 TATAAATTCA
8918546 GTAAAACAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
15 32 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:8919093 original size:13 final size:13
Alignment explanation
Indices: 8919075--8919102 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
8919065 CCTCTTTTTA
8919075 TTCTTTTGTTTCT
1 TTCTTTTGTTTCT
8919088 TTCTTTTGTTTCT
1 TTCTTTTGTTTCT
8919101 TT
1 TT
8919103 TATATATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (13 bp):
TTCTTTTGTTTCT
Found at i:8919151 original size:18 final size:18
Alignment explanation
Indices: 8919130--8919166 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
8919120 AATAACAACT
*
8919130 ATAATAAAAATTTATTTA
1 ATAACAAAAATTTATTTA
*
8919148 ATAACAAATATTTATTTA
1 ATAACAAAAATTTATTTA
8919166 A
1 A
8919167 CACTTGTGCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
ATAACAAAAATTTATTTA
Found at i:8919610 original size:30 final size:30
Alignment explanation
Indices: 8919556--8919612 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
8919546 GGGTCGTTAC
8919556 AATTATATAATATTATTATTTAACATATAT
1 AATTATATAATATTATTATTTAACATATAT
8919586 AATTAATATAATATT-TT-TTATAACATA
1 AATT-ATATAATATTATTATT-TAACATA
8919613 AGATATTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
29 2 0.08
30 13 0.52
31 10 0.40
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (30 bp):
AATTATATAATATTATTATTTAACATATAT
Found at i:8936486 original size:12 final size:12
Alignment explanation
Indices: 8936469--8936493 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8936459 CTGACTACCT
8936469 GACTAAATTGTA
1 GACTAAATTGTA
8936481 GACTAAATTGTA
1 GACTAAATTGTA
8936493 G
1 G
8936494 GTATTTTTAT
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:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (12 bp):
GACTAAATTGTA
Found at i:8937977 original size:19 final size:20
Alignment explanation
Indices: 8937955--8938008 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
8937945 AATTGTAATA
*
8937955 TATTTATTTAATTA-ATTTT
1 TATTTATTTAAATAGATTTT
**
8937974 TATTTAAGTAAATAGATTTT
1 TATTTATTTAAATAGATTTT
*
8937994 TATTATATTAAAATA
1 TATT-TATTTAAATA
8938009 TTAAATTATA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
19 11 0.41
20 9 0.33
21 7 0.26
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.56
Consensus pattern (20 bp):
TATTTATTTAAATAGATTTT
Found at i:8942206 original size:23 final size:21
Alignment explanation
Indices: 8942139--8942212 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
8942129 CCTGATCAAT
* * *
8942139 ATACGGCACATAA-GTGCCTG
1 ATACGACACACAAGGTGCTTG
* *
8942159 AAACGACACACGAGGTGCTTG
1 ATACGACACACAAGGTGCTTG
8942180 ATACGACACACAAGGTGCTTG
1 ATACGACACACAAGGTGCTTG
8942201 AAATACGACACA
1 --ATACGACACA
8942213 TAAAGTGCCT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 9 0.20
21 25 0.57
23 10 0.23
ACGTcount: A:0.36, C:0.24, G:0.23, T:0.16
Consensus pattern (21 bp):
ATACGACACACAAGGTGCTTG
Found at i:8942220 original size:23 final size:22
Alignment explanation
Indices: 8942145--8942220 Score: 75
Period size: 21 Copynumber: 3.5 Consensus size: 22
8942135 CAATATACGG
*
8942145 CACATAAGTGCCTGAA-ACGACA
1 CACA-AAGTGCTTGAATACGACA
* *
8942167 CACGAGGTGCTTG-ATACGACA
1 CACAAAGTGCTTGAATACGACA
*
8942188 CACAAGGTGCTTGAAATACGACA
1 CACAAAGTGCTTG-AATACGACA
*
8942211 CATAAAGTGC
1 CACAAAGTGC
8942221 CTGATCAGTA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
20 1 0.02
21 25 0.56
22 3 0.07
23 16 0.36
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (22 bp):
CACAAAGTGCTTGAATACGACA
Found at i:8942441 original size:23 final size:24
Alignment explanation
Indices: 8942415--8942509 Score: 93
Period size: 28 Copynumber: 3.6 Consensus size: 24
8942405 AAATGTCCAA
8942415 CCAAAACACACCAG-TATAATCCT
1 CCAAAACACACCAGATATAATCCT
8942438 CCAAAACACACCAGTATCATATAATCCT
1 CCAAAACACACCAG----ATATAATCCT
*
8942466 CCCAAACACACCAGAATAATATAATCCAT
1 CCAAAACACACCAG----ATATAATCC-T
8942495 CCAAAACACACCAGA
1 CCAAAACACACCAGA
8942510 ATAGCACAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
23 14 0.23
25 1 0.02
28 33 0.53
29 14 0.23
ACGTcount: A:0.46, C:0.34, G:0.04, T:0.16
Consensus pattern (24 bp):
CCAAAACACACCAGATATAATCCT
Found at i:8942511 original size:29 final size:28
Alignment explanation
Indices: 8942429--8942512 Score: 132
Period size: 28 Copynumber: 3.0 Consensus size: 28
8942419 AACACACCAG
* *
8942429 TATAATCCTCCAAAACACACCAGTATCA
1 TATAATCCTCCAAAACACACCAGAATAA
*
8942457 TATAATCCTCCCAAACACACCAGAATAA
1 TATAATCCTCCAAAACACACCAGAATAA
8942485 TATAATCCATCCAAAACACACCAGAATA
1 TATAATCC-TCCAAAACACACCAGAATA
8942513 GCACAAAGTG
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 33 0.65
29 18 0.35
ACGTcount: A:0.46, C:0.31, G:0.04, T:0.19
Consensus pattern (28 bp):
TATAATCCTCCAAAACACACCAGAATAA
Found at i:8945009 original size:12 final size:12
Alignment explanation
Indices: 8944992--8945037 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
8944982 ATAACACTCC
8944992 ATAAATATTTAT
1 ATAAATATTTAT
8945004 ATAAATA-TT-T
1 ATAAATATTTAT
8945014 ATAAATATTTAT
1 ATAAATATTTAT
*
8945026 AAAAATATTTAT
1 ATAAATATTTAT
8945038 GGCTCGTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
10 8 0.26
11 4 0.13
12 19 0.61
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATAAATATTTAT
Found at i:8945017 original size:22 final size:22
Alignment explanation
Indices: 8944992--8945037 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
8944982 ATAACACTCC
*
8944992 ATAAATATTTATATAAATATTT
1 ATAAATATTTATAAAAATATTT
8945014 ATAAATATTTATAAAAATATTT
1 ATAAATATTTATAAAAATATTT
8945036 AT
1 AT
8945038 GGCTCGTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAATATTTATAAAAATATTT
Found at i:8945018 original size:10 final size:10
Alignment explanation
Indices: 8944992--8945028 Score: 56
Period size: 10 Copynumber: 3.5 Consensus size: 10
8944982 ATAACACTCC
8944992 ATAAATATTTAT
1 ATAAATA-TT-T
8945004 ATAAATATTT
1 ATAAATATTT
8945014 ATAAATATTT
1 ATAAATATTT
8945024 ATAAA
1 ATAAA
8945029 AATATTTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 16 0.64
11 2 0.08
12 7 0.28
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
ATAAATATTT
Found at i:8946199 original size:19 final size:21
Alignment explanation
Indices: 8946143--8946204 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
8946133 ATTGGGTAGA
*
8946143 TCAGCTCTTACGAGCTTTTAT
1 TCAGCTCTTACGAGCTTTTGT
* *
8946164 TCAGCTCTTATGAGCTTCTGT
1 TCAGCTCTTACGAGCTTTTGT
8946185 TCAGCT-TT-CGAGCTTTTGT
1 TCAGCTCTTACGAGCTTTTGT
8946204 T
1 T
8946205 GGTGTATTCA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
19 10 0.28
20 2 0.06
21 24 0.67
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.45
Consensus pattern (21 bp):
TCAGCTCTTACGAGCTTTTGT
Found at i:8948747 original size:21 final size:21
Alignment explanation
Indices: 8948705--8948747 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
8948695 TGTTTATGTC
*
8948705 TTTTATCAATTTAATTTTTAT
1 TTTTATCAATTTAATTTATAT
*
8948726 TTTTAT-AGTTTAATTTGATAT
1 TTTTATCAATTTAATTT-ATAT
8948747 T
1 T
8948748 AAATATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (21 bp):
TTTTATCAATTTAATTTATAT
Found at i:8949429 original size:26 final size:26
Alignment explanation
Indices: 8949377--8949429 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
8949367 TTTGCATGTG
* *
8949377 AATAATTGTATTAATTTTTGTAAAAA
1 AATAATTGTATTAATATTTATAAAAA
*
8949403 AATAATTGTATTAATAATTTATGAAAA
1 AATAATTGTATTAAT-ATTTATAAAAA
8949430 TTAAATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (26 bp):
AATAATTGTATTAATATTTATAAAAA
Found at i:8949475 original size:18 final size:18
Alignment explanation
Indices: 8949437--8949474 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
8949427 AAATTAAATT
8949437 AAATTAAAATTTTATATA
1 AAATTAAAATTTTATATA
8949455 AAATTAAAATTTT-TATA
1 AAATTAAAATTTTATATA
8949472 AAA
1 AAA
8949475 AAATTATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATTAAAATTTTATATA
Found at i:8949476 original size:19 final size:18
Alignment explanation
Indices: 8949437--8949476 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
8949427 AAATTAAATT
*
8949437 AAATTAAAATTTTATATA
1 AAATTAAAATTTTATAAA
8949455 AAATTAAAATTTTTATAAA
1 AAATTAAAA-TTTTATAAA
8949474 AAA
1 AAA
8949477 ATTATATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATTAAAATTTTATAAA
Found at i:8949496 original size:32 final size:32
Alignment explanation
Indices: 8949442--8949507 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 32
8949432 AAATTAAATT
* ** *
8949442 AAAATTTTATATAAAATTAAAATTTTTATAAA
1 AAAATTATATATAAAACCAAAATTGTTATAAA
* *
8949474 AAAATTATATATTAAACCAAAATTGTTATGAA
1 AAAATTATATATAAAACCAAAATTGTTATAAA
8949506 AA
1 AA
8949508 TTTGAGATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (32 bp):
AAAATTATATATAAAACCAAAATTGTTATAAA
Found at i:8956465 original size:16 final size:17
Alignment explanation
Indices: 8956444--8956476 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
8956434 CACATTGAAG
8956444 TGTTTT-TTGAAAACCA
1 TGTTTTATTGAAAACCA
8956460 TGTTTTCATTGAAAACC
1 TGTTTT-ATTGAAAACC
8956477 CTTCTTGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (17 bp):
TGTTTTATTGAAAACCA
Found at i:8957270 original size:59 final size:59
Alignment explanation
Indices: 8957135--8957273 Score: 158
Period size: 60 Copynumber: 2.3 Consensus size: 59
8957125 CAGTGTTAAC
* *
8957135 TGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGTCTCTTACAGTAACAGAGTATAT
1 TGGGCCTT-GCCCATATCAATATCAATCTGGGCCATAGTCCCTTACAGT-ACAGAGTATAT
* * * *
8957196 TGGGCCTAGCCCATATTAGTATCAATCTGGGCCGTAG-CCCTATACAAGT-C-GAGATATAT
1 TGGGCCTTGCCCATATCAATATCAATCTGGGCCATAGTCCCT-TAC-AGTACAGAG-TATAT
8957255 TGGGCCTTGCCCATATCAA
1 TGGGCCTTGCCCATATCAA
8957274 CACAGTTGGG
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
58 3 0.05
59 25 0.38
60 28 0.42
61 10 0.15
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (59 bp):
TGGGCCTTGCCCATATCAATATCAATCTGGGCCATAGTCCCTTACAGTACAGAGTATAT
Found at i:8958602 original size:18 final size:18
Alignment explanation
Indices: 8958572--8958627 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 18
8958562 GAAAATCGGC
8958572 AAGAGGAGAAAGAAAAGAG
1 AAGAGG-GAAAGAAAAGAG
* *
8958591 AAGAGGGAAAGAGATGAG
1 AAGAGGGAAAGAAAAGAG
* *
8958609 -AGAAGGAAAGAAAATAG
1 AAGAGGGAAAGAAAAGAG
8958626 AA
1 AA
8958628 AATAGAATTG
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
17 13 0.43
18 11 0.37
19 6 0.20
ACGTcount: A:0.61, C:0.00, G:0.36, T:0.04
Consensus pattern (18 bp):
AAGAGGGAAAGAAAAGAG
Found at i:8961657 original size:53 final size:53
Alignment explanation
Indices: 8961576--8961726 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
8961566 CTTACATGGT
* *
8961576 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
8961631 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
8961684 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
8961727 GCACACTTAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:8967086 original size:61 final size:62
Alignment explanation
Indices: 8967002--8967131 Score: 253
Period size: 61 Copynumber: 2.1 Consensus size: 62
8966992 TTTGTTTTCA
8967002 ATAATATACCATCACATTTTATCTTAAAGGTTACCTGCTAAAGTCCCGTTCATTTTAAAAAT
1 ATAATATACCATCACATTTTATCTTAAAGGTTACCTGCTAAAGTCCCGTTCATTTTAAAAAT
8967064 ATAATA-ACCATCACATTTTATCTTAAAGGTTACCTGCTAAAGTCCCGTTCATTTTAAAAAT
1 ATAATATACCATCACATTTTATCTTAAAGGTTACCTGCTAAAGTCCCGTTCATTTTAAAAAT
8967125 ATAATAT
1 ATAATAT
8967132 TAAAACATAC
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
61 61 0.91
62 6 0.09
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (62 bp):
ATAATATACCATCACATTTTATCTTAAAGGTTACCTGCTAAAGTCCCGTTCATTTTAAAAAT
Found at i:8968317 original size:39 final size:39
Alignment explanation
Indices: 8968259--8968482 Score: 394
Period size: 39 Copynumber: 5.7 Consensus size: 39
8968249 TTCCAACACA
* *
8968259 AATGCCTTCGGGTCTTAGCCCGGATATAGCACCAGCACG
1 AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG
*
8968298 AATACCTTCGGGACTTAGCCCGGATATAACACCAGCACG
1 AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG
8968337 AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG
1 AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG
* *
8968376 AATGCCTTCGAGACTTAGCCCGGACATAACACCAGCACG
1 AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG
8968415 AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG
1 AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG
*
8968454 AATGCCTTTGGGACTTAGCCCGGATATAA
1 AATGCCTTCGGGACTTAGCCCGGATATAA
8968483 ATCTCACACA
Statistics
Matches: 176, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 176 1.00
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG
Found at i:8977594 original size:14 final size:14
Alignment explanation
Indices: 8977575--8977601 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
8977565 ATACTTTATT
8977575 TATATACACATATA
1 TATATACACATATA
8977589 TATATACACATAT
1 TATATACACATAT
8977602 GGATGTCACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (14 bp):
TATATACACATATA
Found at i:8980449 original size:5 final size:5
Alignment explanation
Indices: 8980428--8980480 Score: 61
Period size: 5 Copynumber: 10.0 Consensus size: 5
8980418 TTAAAAAATA
* *
8980428 TATAT TAAAT TATTAT TATAT TATAG TATAT TATATT ATATAT TATAT
1 TATAT TATAT TA-TAT TATAT TATAT TATAT TATA-T -TATAT TATAT
8980476 TATAT
1 TATAT
8980481 AAATAAGTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 31 0.76
6 6 0.15
7 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:8980459 original size:10 final size:9
Alignment explanation
Indices: 8980425--8980481 Score: 59
Period size: 8 Copynumber: 6.6 Consensus size: 9
8980415 GTGTTAAAAA
8980425 ATATATATT
1 ATATATATT
*
8980434 AAAT-TATT
1 ATATATATT
8980442 AT-TATATT
1 ATATATATT
8980450 ATAGTATATT
1 ATA-TATATT
8980460 ATAT-TA-T
1 ATATATATT
8980467 ATATTATATT
1 ATA-TATATT
8980477 ATATA
1 ATATA
8980482 AATAAGTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
7 5 0.12
8 14 0.35
9 8 0.20
10 13 0.32
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (9 bp):
ATATATATT
Found at i:8980471 original size:12 final size:12
Alignment explanation
Indices: 8980426--8980481 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
8980416 TGTTAAAAAA
*
8980426 TATATATTAAAT
1 TATATATTATAT
8980438 TAT-TATTATATT
1 TATATATTATA-T
8980450 ATAGTATATTATAT
1 -TA-TATATTATAT
8980464 TATATATTATAT
1 TATATATTATAT
8980476 TATATA
1 TATATA
8980482 AATAAGTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 6 0.15
12 20 0.51
13 4 0.10
14 2 0.05
15 7 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:8981825 original size:18 final size:19
Alignment explanation
Indices: 8981802--8981840 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
8981792 ATATATAGAT
8981802 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
8981820 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
8981839 AT
1 AT
8981841 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:8982126 original size:41 final size:41
Alignment explanation
Indices: 8982078--8982178 Score: 104
Period size: 38 Copynumber: 2.5 Consensus size: 41
8982068 TCGACCTCGA
*
8982078 GTCGATGAGACACTGGGTGTCACTATA-TTT-CTTCGGATAG
1 GTCGATGAGACACTGGGTGTCACCA-ACTTTACTTCGGATAG
* **
8982118 ATTCGATGAGGTACT-GG-GT-ACCAACTTTACTTCGGATAG
1 -GTCGATGAGACACTGGGTGTCACCAACTTTACTTCGGATAG
*
8982157 GCCGATGAGACACTGGGTGTCA
1 GTCGATGAGACACTGGGTGTCA
8982179 AATATTGCTT
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
37 1 0.02
38 16 0.34
39 14 0.30
40 4 0.09
41 12 0.26
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (41 bp):
GTCGATGAGACACTGGGTGTCACCAACTTTACTTCGGATAG
Found at i:8982190 original size:39 final size:39
Alignment explanation
Indices: 8982080--8982214 Score: 121
Period size: 39 Copynumber: 3.4 Consensus size: 39
8982070 GACCTCGAGT
* * *
8982080 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA-AATATTACTTCGGATAG-TC
** ** * *
8982121 CGATGAGGTACTGGGTACCAACT-TTACTTCGGATAGGC
1 CGATGAGACACTGGGTGTCAAATATTACTTCGGATAGTC
* *
8982159 CGATGAGACACTGGGTGTCAAATATTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAAATATTACTTCGGA-TAGTC
*
8982198 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
8982215 CCATATTGGT
Statistics
Matches: 74, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
38 18 0.24
39 37 0.50
40 3 0.04
41 16 0.22
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAAATATTACTTCGGATAGTC
Found at i:8982358 original size:18 final size:19
Alignment explanation
Indices: 8982337--8982377 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
8982327 AATGAAATGA
8982337 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
8982355 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
8982374 GAAA
1 GAAA
8982378 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:8986900 original size:5 final size:5
Alignment explanation
Indices: 8986874--8986931 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
8986864 ATGTGTTAAA
* * *
8986874 ATATAT ATATT AAATT ATTATT ATATT ATAGT ATAGT ATATTAT ATATT
1 ATAT-T ATATT ATATT A-TATT ATATT ATATT ATATT ATA-T-T ATATT
8986923 ATATT ATAT
1 ATATT ATAT
8986932 AAATAAGTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
5 32 0.71
6 9 0.20
7 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (5 bp):
ATATT
Found at i:8986925 original size:12 final size:12
Alignment explanation
Indices: 8986877--8986932 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
8986867 TGTTAAAATA
*
8986877 TATATATTAAAT
1 TATATATTATAT
8986889 TAT-TATTATAT
1 TATATATTATAT
8986900 TATAGTATAGTATAT
1 TATA-TAT--TATAT
8986915 TATATATTATAT
1 TATATATTATAT
8986927 TATATA
1 TATATA
8986933 AATAAGTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 14 0.36
13 3 0.08
14 3 0.08
15 9 0.23
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (12 bp):
TATATATTATAT
Found at i:8988270 original size:18 final size:19
Alignment explanation
Indices: 8988247--8988285 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
8988237 ATATATAGAT
8988247 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
8988265 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
8988284 AT
1 AT
8988286 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:8988571 original size:41 final size:41
Alignment explanation
Indices: 8988523--8988623 Score: 104
Period size: 38 Copynumber: 2.5 Consensus size: 41
8988513 TCGACCTCGA
*
8988523 GTCGATGAGACACTGGGTGTCACTATA-TTT-CTTCGGATAG
1 GTCGATGAGACACTGGGTGTCACCA-ACTTTACTTCGGATAG
* **
8988563 ATTCGATGAGGTACT-GG-GT-ACCAACTTTACTTCGGATAG
1 -GTCGATGAGACACTGGGTGTCACCAACTTTACTTCGGATAG
*
8988602 GCCGATGAGACACTGGGTGTCA
1 GTCGATGAGACACTGGGTGTCA
8988624 AATATTGCTT
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
37 1 0.02
38 16 0.34
39 14 0.30
40 4 0.09
41 12 0.26
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (41 bp):
GTCGATGAGACACTGGGTGTCACCAACTTTACTTCGGATAG
Found at i:8988635 original size:39 final size:40
Alignment explanation
Indices: 8988525--8988635 Score: 109
Period size: 39 Copynumber: 2.8 Consensus size: 40
8988515 GACCTCGAGT
* * **
8988525 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA-AATATTACTTCGGATAGAGC
** ** *
8988566 CGATGAGGTACTGGGTACCAACT-TTACTTCGGATAG-GC
1 CGATGAGACACTGGGTGTCAAATATTACTTCGGATAGAGC
*
8988604 CGATGAGACACTGGGTGTCAAATATTGCTTCG
1 CGATGAGACACTGGGTGTCAAATATTACTTCG
8988636 AACTATCCGA
Statistics
Matches: 54, Mismatches: 15, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
38 18 0.33
39 19 0.35
40 1 0.02
41 16 0.30
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAAATATTACTTCGGATAGAGC
Found at i:8988790 original size:17 final size:19
Alignment explanation
Indices: 8988768--8988807 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
8988758 GAATGAATGA
8988768 GAAATTGA-AT-TGAGATT
1 GAAATTGAGATATGAGATT
8988785 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
8988804 GAAA
1 GAAA
8988808 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 8 0.38
18 2 0.10
19 11 0.52
ACGTcount: A:0.45, C:0.00, G:0.25, T:0.30
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:8995731 original size:15 final size:15
Alignment explanation
Indices: 8995695--8995724 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
8995685 CAATCAATAA
*
8995695 TCATAAATTTGAAAT
1 TCATAATTTTGAAAT
8995710 TCATAATTTTGAAAT
1 TCATAATTTTGAAAT
8995725 ATATAATCTT
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:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (15 bp):
TCATAATTTTGAAAT
Found at i:8996275 original size:15 final size:15
Alignment explanation
Indices: 8996255--8996284 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
8996245 GTTTAATTAT
*
8996255 TTATGAGATGTTGGA
1 TTATGACATGTTGGA
8996270 TTATGACATGTTGGA
1 TTATGACATGTTGGA
8996285 AAAACGGCTT
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:0.27, C:0.03, G:0.30, T:0.40
Consensus pattern (15 bp):
TTATGACATGTTGGA
Found at i:8996578 original size:20 final size:19
Alignment explanation
Indices: 8996528--8996589 Score: 76
Period size: 20 Copynumber: 3.3 Consensus size: 19
8996518 ATAATCAAAT
8996528 TTAATTAGTTTAATATTAAA
1 TTAATTA-TTTAATATTAAA
8996548 TTAA--ATTTAATATTAAGA
1 TTAATTATTTAATATTAA-A
8996566 -TAATTATTTTAATATTAAA
1 TTAATTA-TTTAATATTAAA
8996585 TTAAT
1 TTAAT
8996590 AAAATACTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
17 14 0.38
18 2 0.05
19 2 0.05
20 19 0.51
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
TTAATTATTTAATATTAAA
Found at i:9010782 original size:18 final size:19
Alignment explanation
Indices: 9010761--9010801 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
9010751 AATGAAATGA
9010761 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
9010779 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
9010798 GAAA
1 GAAA
9010802 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:9011948 original size:7 final size:7
Alignment explanation
Indices: 9011934--9011976 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
9011924 AGGGATGAGG
9011934 AGGGTTT
1 AGGGTTT
*
9011941 AAGGTTT
1 AGGGTTT
* *
9011948 AAGATTT
1 AGGGTTT
9011955 AGGGTTT
1 AGGGTTT
9011962 AGGGTTT
1 AGGGTTT
9011969 AGGGTTT
1 AGGGTTT
9011976 A
1 A
9011977 TGGCAACATG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.23, C:0.00, G:0.35, T:0.42
Consensus pattern (7 bp):
AGGGTTT
Found at i:9015761 original size:23 final size:22
Alignment explanation
Indices: 9015730--9015779 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
9015720 TTACGGAATT
*
9015730 AAAACAATTAAAATTCATTAGTA
1 AAAATAATTAAAATTCA-TAGTA
* * *
9015753 AAAATAATTTAATTTCATATTA
1 AAAATAATTAAAATTCATAGTA
9015775 AAAAT
1 AAAAT
9015780 TTCAATTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.36
Consensus pattern (22 bp):
AAAATAATTAAAATTCATAGTA
Found at i:9016676 original size:20 final size:20
Alignment explanation
Indices: 9016651--9016693 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
9016641 CCTAAATTGC
* *
9016651 TTATTTATAAGATTATTATT
1 TTATTTATAAAACTATTATT
9016671 TTATTTATAAAACTATTATT
1 TTATTTATAAAACTATTATT
9016691 TTA
1 TTA
9016694 ATAAATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (20 bp):
TTATTTATAAAACTATTATT
Found at i:9016936 original size:62 final size:59
Alignment explanation
Indices: 9016807--9016943 Score: 147
Period size: 62 Copynumber: 2.3 Consensus size: 59
9016797 TTTAAAGTTT
* * *
9016807 TTAAATTT-TAATT-TTTTAAGAATTTAAGACTAAATTGATAGAATGTATAAAGTTGAAGA
1 TTAAATTTATTATTATTTT-AG-ATTTAAGACTAAATTGATAGAATGTATAAAATAGAAGA
*
9016866 TTAAATTTATTGATTATTTTAGATTTATGACTAAATTGATAGAATATGTA-AACAATAG-AGAA
1 TTAAATTTATT-ATTATTTTAGATTTAAGACTAAATTGATAG-A-ATGTATAA-AATAGAAG-A
9016928 TTAAATTTATTATTAT
1 TTAAATTTATTATTAT
9016944 GCTAATAAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
59 8 0.12
60 20 0.30
61 15 0.22
62 24 0.36
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.43
Consensus pattern (59 bp):
TTAAATTTATTATTATTTTAGATTTAAGACTAAATTGATAGAATGTATAAAATAGAAGA
Found at i:9017486 original size:5 final size:5
Alignment explanation
Indices: 9017476--9017504 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
9017466 AAAAATAAAG
9017476 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
9017505 ATAGTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:9017512 original size:24 final size:24
Alignment explanation
Indices: 9017485--9017530 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
9017475 GTTTATTTTA
*
9017485 TTTT-ATTTTATTTTATTTTAATAG
1 TTTTAATTTT-TTTTAATTTAATAG
9017509 TTTTAATTTTTTTTAATTTAAT
1 TTTTAATTTTTTTTAATTTAAT
9017531 CACTTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (24 bp):
TTTTAATTTTTTTTAATTTAATAG
Found at i:9017522 original size:10 final size:11
Alignment explanation
Indices: 9017476--9017527 Score: 53
Period size: 10 Copynumber: 5.2 Consensus size: 11
9017466 AAAAATAAAG
9017476 TTTATTTT-AT
1 TTTATTTTAAT
9017486 TTTATTTT-AT
1 TTTATTTTAAT
9017496 TTTATTTTAA-
1 TTTATTTTAAT
9017506 --TAGTTTTAAT
1 TTTA-TTTTAAT
9017516 TTT-TTTTAAT
1 TTTATTTTAAT
9017526 TT
1 TT
9017528 AATCACTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
8 2 0.05
9 6 0.16
10 27 0.73
11 1 0.03
12 1 0.03
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (11 bp):
TTTATTTTAAT
Found at i:9028964 original size:13 final size:13
Alignment explanation
Indices: 9028946--9028977 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
9028936 ATAGTTTAAT
9028946 AATAAAATAAAGA
1 AATAAAATAAAGA
9028959 AATAAAATAAAGA
1 AATAAAATAAAGA
9028972 AATAAA
1 AATAAA
9028978 TGAAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (13 bp):
AATAAAATAAAGA
Found at i:9028994 original size:14 final size:14
Alignment explanation
Indices: 9028975--9029010 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
9028965 ATAAAGAAAT
9028975 AAATGAAATAAAAG
1 AAATGAAATAAAAG
*
9028989 AAATGAAATATAAG
1 AAATGAAATAAAAG
9029003 AAATGAAA
1 AAATGAAA
9029011 AAGAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (14 bp):
AAATGAAATAAAAG
Found at i:9029342 original size:15 final size:15
Alignment explanation
Indices: 9029319--9029366 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
9029309 TATCAAATTT
9029319 ATATTGATTGAAATC
1 ATATTGATTGAAATC
* * *
9029334 ATTTTGATTGAATTT
1 ATATTGATTGAAATC
9029349 ATATTGATTGAAAT-
1 ATATTGATTGAAATC
9029363 ATAT
1 ATAT
9029367 ATTATATATA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (15 bp):
ATATTGATTGAAATC
Found at i:9032053 original size:21 final size:21
Alignment explanation
Indices: 9031989--9032057 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
9031979 AATAATGCTA
*
9031989 ATAATAATCTAATATAAAACC
1 ATAATAATTTAATATAAAACC
* **
9032010 ATAAT--GTTAAT-TAATAATT
1 ATAATAATTTAATATAA-AACC
9032029 ATAATAATTTAATATAAAACC
1 ATAATAATTTAATATAAAACC
9032050 ATAATAAT
1 ATAATAAT
9032058 AATCATTATA
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
18 3 0.08
19 11 0.30
21 20 0.54
22 3 0.08
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.36
Consensus pattern (21 bp):
ATAATAATTTAATATAAAACC
Found at i:9032790 original size:18 final size:19
Alignment explanation
Indices: 9032769--9032809 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
9032759 AATGAAATGA
9032769 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
9032787 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
9032806 GAAA
1 GAAA
9032810 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:9035516 original size:136 final size:136
Alignment explanation
Indices: 9035272--9035535 Score: 501
Period size: 136 Copynumber: 1.9 Consensus size: 136
9035262 TTTCTATTGA
* * *
9035272 AAAAGAGTACATGATTGTGATGTGTATTGATCCCACTGCAAAGTAGAGTAGATAGTGGACTAGTA
1 AAAAGAGTACATGATTGTGATGTGTACTAATCCCAATGCAAAGTAGAGTAGATAGTGGACTAGTA
9035337 TTACAACCTTCTTGAACTTGCCATATTTTTTTATCACTTTCAAGAAGATACAAATTGCATGTAGA
66 TTACAACCTTCTTGAACTTGCCATATTTTTTTATCACTTTCAAGAAGATACAAATTGCATGTAGA
9035402 GTTTTC
131 GTTTTC
9035408 AAAAGAGTACATGATTGTGATGTGTACTAATCCCAATGCAAAGTAGAGTAGATAGTGGACTAGTA
1 AAAAGAGTACATGATTGTGATGTGTACTAATCCCAATGCAAAGTAGAGTAGATAGTGGACTAGTA
9035473 TTACAACCTTCTTGAACTTGCCATATTTTTTTATCACTTTCAAGAAGATACAAATTGCATGTA
66 TTACAACCTTCTTGAACTTGCCATATTTTTTTATCACTTTCAAGAAGATACAAATTGCATGTA
9035536 TAACAGAGTT
Statistics
Matches: 125, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
136 125 1.00
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Consensus pattern (136 bp):
AAAAGAGTACATGATTGTGATGTGTACTAATCCCAATGCAAAGTAGAGTAGATAGTGGACTAGTA
TTACAACCTTCTTGAACTTGCCATATTTTTTTATCACTTTCAAGAAGATACAAATTGCATGTAGA
GTTTTC
Found at i:9042056 original size:19 final size:17
Alignment explanation
Indices: 9042033--9042076 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
9042023 TTATATTTTA
*
9042033 AAAAATATTAATTATTAT
1 AAAAATATTAA-TATGAT
9042051 ATAAAATTATTAATATGAT
1 A-AAAA-TATTAATATGAT
9042070 AAAAATA
1 AAAAATA
9042077 ATTTCTAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 2 0.09
18 5 0.22
19 10 0.43
20 6 0.26
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
AAAAATATTAATATGAT
Found at i:9042802 original size:16 final size:16
Alignment explanation
Indices: 9042781--9042811 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9042771 TAAAAATATA
*
9042781 ATATAATATTTATAAT
1 ATATAACATTTATAAT
9042797 ATATAACATTTATAA
1 ATATAACATTTATAA
9042812 AAAATTTTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATAACATTTATAAT
Found at i:9043233 original size:24 final size:23
Alignment explanation
Indices: 9043205--9043265 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
9043195 GCTTATAATA
* *
9043205 TAATTTTTATAAATTGTATAAAAG
1 TAATTTTTTTAAA-TATATAAAAG
*
9043229 TAATTTTTTTGACATATATAAAAG
1 TAATTTTTTT-AAATATATAAAAG
9043253 TAATTTTTTTAAA
1 TAATTTTTTTAAA
9043266 ATTAGATTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 2 0.06
24 28 0.88
25 2 0.06
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (23 bp):
TAATTTTTTTAAATATATAAAAG
Found at i:9044945 original size:16 final size:16
Alignment explanation
Indices: 9044909--9044943 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
9044899 AAATATCATT
9044909 ATTTATATTAGAAATA
1 ATTTATATTAGAAATA
9044925 ATTTATATTAG-AATA
1 ATTTATATTAGAAATA
9044940 ATTT
1 ATTT
9044944 TAAAAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (16 bp):
ATTTATATTAGAAATA
Found at i:9045413 original size:31 final size:31
Alignment explanation
Indices: 9045232--9045445 Score: 74
Period size: 31 Copynumber: 6.9 Consensus size: 31
9045222 TTTAAAAAGA
* *
9045232 ATATAAATA-ATTAGATTAATTTATATTTTAT
1 ATATAATTATATTAAATT-ATTTATATTTTAT
* * * * *
9045263 TTATCATTATATTAAATTATTTAAATATCAT
1 ATATAATTATATTAAATTATTTATATTTTAT
* *
9045294 TTATCATTATATTAAATTTTATTTAGTA--TTAT
1 ATATAATTATATTAAA--TTATTTA-TATTTTAT
* * * * *
9045326 GT-TTATTTTTTTAAAAATATTTTATATATTATCAAT
1 ATATAATTATATT-AAATTA-TTTATAT-TT-T--AT
* *
9045362 TTATAAATA-ATTTAAA--ATTTATATTTTAT
1 ATATAATTATA-TTAAATTATTTATATTTTAT
* * *
9045391 ATATAATTATATTAAATTATTTAAATATCAT
1 ATATAATTATATTAAATTATTTATATTTTAT
9045422 ATAT--TTA-ATTAAATT-TTTA-ATTTT
1 ATATAATTATATTAAATTATTTATATTTT
9045446 CACTATTATA
Statistics
Matches: 140, Mismatches: 26, Indels: 39
0.68 0.13 0.19
Matches are distributed among these distances:
26 3 0.02
27 4 0.03
28 8 0.06
29 17 0.12
30 5 0.04
31 58 0.41
32 16 0.11
33 15 0.11
34 3 0.02
36 6 0.04
37 5 0.04
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (31 bp):
ATATAATTATATTAAATTATTTATATTTTAT
Found at i:9045418 original size:24 final size:23
Alignment explanation
Indices: 9045386--9045432 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
9045376 AAATTTATAT
*
9045386 TTTATATATAATTATATTAAATTA
1 TTTAAATATAA-TATATTAAATTA
* *
9045410 TTTAAATATCATATATTTAATTA
1 TTTAAATATAATATATTAAATTA
9045433 AATTTTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTAAATATAATATATTAAATTA
Found at i:9045425 original size:40 final size:40
Alignment explanation
Indices: 9045342--9045427 Score: 95
Period size: 40 Copynumber: 2.1 Consensus size: 40
9045332 TTTTTTAAAA
* * *
9045342 ATATTTTATATATTATCAATTTATAAATAATTTAAAATTT
1 ATATTTTATATATAATCAATATATAAATAATTTAAAATAT
* *
9045382 ATATTTTATATATAAT-TATAT-TAAATTATTTAAATATCAT
1 ATATTTTATATATAATCAATATATAAATAATTTAAA-AT-AT
9045422 ATATTT
1 ATATTT
9045428 AATTAAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
38 12 0.31
39 5 0.13
40 22 0.56
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (40 bp):
ATATTTTATATATAATCAATATATAAATAATTTAAAATAT
Found at i:9048795 original size:20 final size:20
Alignment explanation
Indices: 9048770--9048810 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
9048760 TTAATAATTA
9048770 ATATTTAAAATATAATTTAC
1 ATATTTAAAATATAATTTAC
* *
9048790 ATATTTAAATTATATTTTAC
1 ATATTTAAAATATAATTTAC
9048810 A
1 A
9048811 AATAATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTTAAAATATAATTTAC
Found at i:9050802 original size:22 final size:23
Alignment explanation
Indices: 9050774--9050834 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
9050764 AAATCGAAGA
* *
9050774 ATATATATAATTTTATATA-AAT
1 ATATATATATTTTTATATATAAC
*
9050796 ATATATA-ATTTTTATCTATAAC
1 ATATATATATTTTTATATATAAC
*
9050818 ATGTATATATTTTTATA
1 ATATATATATTTTTATA
9050835 CATTCTATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
21 9 0.28
22 15 0.47
23 8 0.25
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (23 bp):
ATATATATATTTTTATATATAAC
Found at i:9050829 original size:23 final size:21
Alignment explanation
Indices: 9050773--9050833 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 21
9050763 AAAATCGAAG
*
9050773 AATATATATAATTTTA-TATA
1 AATATATATATTTTTATTATA
9050793 AATATATATAATTTTTATCTATA
1 AATATATAT-ATTTTTAT-TATA
*
9050816 ACATGTATATATTTTTAT
1 A-ATATATATATTTTTAT
9050834 ACATTCTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 9 0.26
21 6 0.17
23 13 0.37
24 7 0.20
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (21 bp):
AATATATATATTTTTATTATA
Found at i:9064517 original size:55 final size:55
Alignment explanation
Indices: 9064433--9064552 Score: 231
Period size: 55 Copynumber: 2.2 Consensus size: 55
9064423 TCTGGGGCAC
9064433 CTATTCCCTTTTTATTCATTTTGTATTCCAGCAATGTTTGTTGACTGTGATTAAT
1 CTATTCCCTTTTTATTCATTTTGTATTCCAGCAATGTTTGTTGACTGTGATTAAT
*
9064488 CTATTCCCTTTTTATTCATTTTGTATTCCAGTAATGTTTGTTGACTGTGATTAAT
1 CTATTCCCTTTTTATTCATTTTGTATTCCAGCAATGTTTGTTGACTGTGATTAAT
9064543 CTATTCCCTT
1 CTATTCCCTT
9064553 CAAATTTTGT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 64 1.00
ACGTcount: A:0.19, C:0.17, G:0.12, T:0.52
Consensus pattern (55 bp):
CTATTCCCTTTTTATTCATTTTGTATTCCAGCAATGTTTGTTGACTGTGATTAAT
Found at i:9065195 original size:44 final size:43
Alignment explanation
Indices: 9065061--9065205 Score: 141
Period size: 44 Copynumber: 3.3 Consensus size: 43
9065051 ACTTTAACCA
*
9065061 CCTAAGCAGTAGGGTAACAGGCTGAAGATATAGATCTTATCAC
1 CCTAAGCAGTAGGGTAACAAGCTGAAGATATAGATCTTATCAC
* * * * ** * * *
9065104 CCTAAGCATTAGGGAAAC-AGATCAAAGGCA-ACGAGCTTTAACCC
1 CCTAAGCAGTAGGGTAACAAGCT-GAAGATATA-GATC-TTATCAC
*
9065148 CCTAAGCAGTAGGGTAACAAGCTGAAGTTTATAGATCTTATCAC
1 CCTAAGCAGTAGGGTAACAAGCTGAAG-ATATAGATCTTATCAC
9065192 CCTAAGCAGTAGGG
1 CCTAAGCAGTAGGG
9065206 AAGCAGATCA
Statistics
Matches: 77, Mismatches: 19, Indels: 11
0.72 0.18 0.10
Matches are distributed among these distances:
42 3 0.04
43 23 0.30
44 43 0.56
45 7 0.09
46 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (43 bp):
CCTAAGCAGTAGGGTAACAAGCTGAAGATATAGATCTTATCAC
Found at i:9065213 original size:88 final size:87
Alignment explanation
Indices: 9065052--9065217 Score: 278
Period size: 88 Copynumber: 1.9 Consensus size: 87
9065042 ATTCACCAGA
* *
9065052 CTTTAACCACCTAAGCAGTAGGGTAACAGGCTGAAGATATAGATCTTATCACCCTAAGCATTAGG
1 CTTTAACCACCTAAGCAGTAGGGTAACAAGCTGAAGATATAGATCTTATCACCCTAAGCAGTAGG
9065117 GAAACAGATCAAAGGCAACGAG
66 GAAACAGATCAAAGGCAACGAG
* *
9065139 CTTTAACCCCCTAAGCAGTAGGGTAACAAGCTGAAGTTTATAGATCTTATCACCCTAAGCAGTAG
1 CTTTAACCACCTAAGCAGTAGGGTAACAAGCTGAAG-ATATAGATCTTATCACCCTAAGCAGTAG
*
9065204 GGAAGCAGATCAAA
65 GGAAACAGATCAAA
9065218 AGACGGCGAA
Statistics
Matches: 73, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
87 34 0.47
88 39 0.53
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (87 bp):
CTTTAACCACCTAAGCAGTAGGGTAACAAGCTGAAGATATAGATCTTATCACCCTAAGCAGTAGG
GAAACAGATCAAAGGCAACGAG
Found at i:9065649 original size:43 final size:42
Alignment explanation
Indices: 9065590--9065739 Score: 142
Period size: 43 Copynumber: 3.5 Consensus size: 42
9065580 GAGCTTCAAC
* * *
9065590 CCCCTAAGCAATAGGGTAACAAGCCAAATTTTCAAACCTTAAA
1 CCCCTAAGCAGTAGGGTAACAAGTC-AATTTACAAACCTTAAA
* * * *
9065633 CCCCTAAGCAGTAGGGTAACAGGTTGAATTTACAGATC-TAAA
1 CCCCTAAGCAGTAGGGTAACAAG-TCAATTTACAAACCTTAAA
* * * *
9065675 CCCCTAAGCAGTAGGGAAAC-AGATCAATGATGACAAGCCTTAAC
1 CCCCTAAGCAGTAGGGTAACAAG-TCAAT--TTACAAACCTTAAA
9065719 CCCCTAAGCAGTAGGGTAACA
1 CCCCTAAGCAGTAGGGTAACA
9065740 GGCTGAAAAT
Statistics
Matches: 85, Mismatches: 17, Indels: 8
0.77 0.15 0.07
Matches are distributed among these distances:
41 5 0.06
42 23 0.27
43 35 0.41
44 22 0.26
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (42 bp):
CCCCTAAGCAGTAGGGTAACAAGTCAATTTACAAACCTTAAA
Found at i:9066691 original size:23 final size:25
Alignment explanation
Indices: 9066665--9066711 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
9066655 TATCATTCAT
*
9066665 TTCATTATAT-CA-ATATTTTATGC
1 TTCATCATATCCATATATTTTATGC
*
9066688 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
9066712 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGC
Found at i:9067032 original size:46 final size:47
Alignment explanation
Indices: 9066972--9067107 Score: 188
Period size: 46 Copynumber: 3.0 Consensus size: 47
9066962 TTTGACGTGA
* * * * * *
9066972 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
*
9067018 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
9067064 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAG
9067108 AGAGCATACT
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
45 3 0.04
46 78 0.96
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (47 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
Found at i:9069285 original size:31 final size:30
Alignment explanation
Indices: 9069241--9069305 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
9069231 CTAATAAAAT
*
9069241 AATAATAAATATCTTATTAAAGT-ATTAATAA
1 AATAATAAATATCTAATTAAA-TAATT-ATAA
**
9069272 AATAATATTTATCTAATTAAATAATTATAA
1 AATAATAAATATCTAATTAAATAATTATAA
9069302 AATA
1 AATA
9069306 TCAAAATATC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 9 0.30
31 21 0.70
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (30 bp):
AATAATAAATATCTAATTAAATAATTATAA
Found at i:9071158 original size:15 final size:15
Alignment explanation
Indices: 9071138--9071181 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
9071128 ATATTGTAAA
9071138 TATCATATTATGTTT
1 TATCATATTATGTTT
*
9071153 TATCATGTATATGTTT
1 TATCATAT-TATGTTT
9071169 TAAT-ATATTATGT
1 T-ATCATATTATGT
9071182 GTATATTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 12 0.48
16 11 0.44
17 2 0.08
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.57
Consensus pattern (15 bp):
TATCATATTATGTTT
Done.