Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 206 of 240
Found at i:62477552 original size:26 final size:25
Alignment explanation
Indices: 62477519--62477580 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 25
62477509 TTTTAAATAT
62477519 TTTATAAATTTAAAAAATAATATTTAAA
1 TTTA-AAATTT-AAAAAT-ATATTTAAA
*
62477547 TTTAAAAATTTAAAAATTTATTTAAA
1 TTT-AAAATTTAAAAATATATTTAAA
62477573 TTTTAAAA
1 -TTTAAAA
62477581 ATAATATTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
26 12 0.39
27 9 0.29
28 9 0.29
29 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
TTTAAAATTTAAAAATATATTTAAA
Found at i:62477588 original size:20 final size:20
Alignment explanation
Indices: 62477523--62477593 Score: 54
Period size: 20 Copynumber: 3.2 Consensus size: 20
62477513 AAATATTTTA
*
62477523 TAAATTTAAAAAATAATATT
1 TAAATTTTAAAAATAATATT
62477543 TAAA-TTTAAAAATTTAAAAATTTATT
1 TAAATTTTAAAAA--T---AA--TATT
62477569 TAAATTTTAAAAATAATATT
1 TAAATTTTAAAAATAATATT
62477589 ATAAA
1 -TAAA
62477594 ACATTTCAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 17
0.69 0.02 0.29
Matches are distributed among these distances:
19 7 0.17
20 8 0.20
21 5 0.12
22 2 0.05
24 2 0.05
25 1 0.02
26 8 0.20
27 8 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAATTTTAAAAATAATATT
Found at i:62479231 original size:15 final size:15
Alignment explanation
Indices: 62479211--62479242 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
62479201 ACAGAGGTGG
62479211 AGCGAAGGGACTGGC
1 AGCGAAGGGACTGGC
62479226 AGCGAAGGGACTGGC
1 AGCGAAGGGACTGGC
62479241 AG
1 AG
62479243 GAAAATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.19, G:0.47, T:0.06
Consensus pattern (15 bp):
AGCGAAGGGACTGGC
Found at i:62481616 original size:20 final size:21
Alignment explanation
Indices: 62481584--62481636 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
62481574 AGAAATTGCC
**
62481584 CAAGTATCAATACCCTC-TA-
1 CAAGTATTGATACCCTCATAG
62481603 CAAGGTATTGATA-CCTCATAG
1 CAA-GTATTGATACCCTCATAG
62481624 CAAGTATTGATAC
1 CAAGTATTGATAC
62481637 ATCCTATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 7 0.25
20 18 0.64
21 3 0.11
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (21 bp):
CAAGTATTGATACCCTCATAG
Found at i:62484944 original size:7 final size:7
Alignment explanation
Indices: 62484926--62484954 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
62484916 AAAAAGTCTT
62484926 AAAATT-
1 AAAATTA
62484932 AAAATTA
1 AAAATTA
62484939 AAAATTA
1 AAAATTA
62484946 AAAATTA
1 AAAATTA
62484953 AA
1 AA
62484955 CTAACATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AAAATTA
Found at i:62486226 original size:24 final size:24
Alignment explanation
Indices: 62486194--62486290 Score: 100
Period size: 24 Copynumber: 4.2 Consensus size: 24
62486184 AACCAAATCA
62486194 ATATTTTATATATATTTAATAATT
1 ATATTTTATATATATTTAATAATT
62486218 ATATTTTATATAT-TTT--T-A-T
1 ATATTTTATATATATTTAATAATT
62486237 ATATTTTATA-A-ATTTAAAATAATT
1 ATATTTTATATATATTT--AATAATT
*
62486261 ATATTTTATATATTTTTTAATAATTT
1 ATATTTTATATA-TATTTAATAA-TT
62486287 ATAT
1 ATAT
62486291 ATATATTCGA
Statistics
Matches: 61, Mismatches: 1, Indels: 20
0.74 0.01 0.24
Matches are distributed among these distances:
18 4 0.07
19 11 0.18
20 1 0.02
21 1 0.02
22 1 0.02
23 4 0.07
24 24 0.39
25 6 0.10
26 6 0.10
27 3 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
ATATTTTATATATATTTAATAATT
Found at i:62486231 original size:9 final size:9
Alignment explanation
Indices: 62486217--62486292 Score: 59
Period size: 9 Copynumber: 8.6 Consensus size: 9
62486207 ATTTAATAAT
62486217 TATATTTTA
1 TATATTTTA
62486226 TATATTTTTA
1 TATA-TTTTA
62486236 TATATTTTA
1 TATATTTTA
*
62486245 TA-AATTTA
1 TATATTTTA
* **
62486253 -AAATAAT-
1 TATATTTTA
62486260 TATATTTTA
1 TATATTTTA
*
62486269 TATATTTTT
1 TATATTTTA
*
62486278 TAATAATTTA
1 T-ATATTTTA
62486288 TATAT
1 TATAT
62486293 ATATTCGAAT
Statistics
Matches: 51, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
7 1 0.02
8 11 0.22
9 23 0.45
10 16 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
TATATTTTA
Found at i:62486236 original size:10 final size:11
Alignment explanation
Indices: 62486194--62486297 Score: 69
Period size: 11 Copynumber: 9.5 Consensus size: 11
62486184 AACCAAATCA
62486194 ATATTTTATAT
1 ATATTTTATAT
*
62486205 ATATTTAATA-
1 ATATTTTATAT
62486215 ATTATATTT-TAT
1 A-TAT-TTTATAT
62486227 ATATTTT-TAT
1 ATATTTTATAT
62486237 ATATTTTATA-
1 ATATTTTATAT
*
62486247 A-ATTTAAAATAATT
1 ATATTT--TAT-A-T
62486261 ATATTTTATAT
1 ATATTTTATAT
*
62486272 ATTTTTTA-AT
1 ATATTTTATAT
62486282 A-ATTTATATAT
1 ATATTT-TATAT
62486293 ATATT
1 ATATT
62486298 CGAATATGTA
Statistics
Matches: 74, Mismatches: 6, Indels: 25
0.70 0.06 0.24
Matches are distributed among these distances:
9 7 0.09
10 20 0.27
11 32 0.43
12 8 0.11
13 2 0.03
14 1 0.01
15 4 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
ATATTTTATAT
Found at i:62486242 original size:43 final size:44
Alignment explanation
Indices: 62486193--62486294 Score: 149
Period size: 43 Copynumber: 2.4 Consensus size: 44
62486183 AAACCAAATC
62486193 AATATTTTATATATATTT-AATAATTATATTTTATATA-TTTTT
1 AATATTTTATATATATTTAAATAATTATATTTTATATATTTTTT
62486235 ATATATTTTATA-A-ATTTAAAATAATTATATTTTATATATTTTTT
1 A-ATATTTTATATATATTT-AAATAATTATATTTTATATATTTTTT
*
62486279 AATAATTTATATATAT
1 AATATTTTATATATAT
62486295 ATTCGAATAT
Statistics
Matches: 53, Mismatches: 1, Indels: 9
0.84 0.02 0.14
Matches are distributed among these distances:
41 4 0.08
42 2 0.04
43 38 0.72
44 7 0.13
45 2 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (44 bp):
AATATTTTATATATATTTAAATAATTATATTTTATATATTTTTT
Found at i:62486493 original size:4 final size:4
Alignment explanation
Indices: 62486484--62486512 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
62486474 CGTGGTCATG
62486484 TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
62486513 ACACACTCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:62491893 original size:18 final size:18
Alignment explanation
Indices: 62491857--62491896 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
62491847 GCAAATGTTC
*
62491857 TTTCATTCTTTACGTTTT
1 TTTCATTCTTTACGATTT
**
62491875 TTTCATTCTTTTGGATTT
1 TTTCATTCTTTACGATTT
62491893 TTTC
1 TTTC
62491897 TGCCAAACCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.10, C:0.15, G:0.07, T:0.68
Consensus pattern (18 bp):
TTTCATTCTTTACGATTT
Found at i:62494300 original size:132 final size:132
Alignment explanation
Indices: 62494124--62495402 Score: 1870
Period size: 132 Copynumber: 9.7 Consensus size: 132
62494114 TTGACAGCGA
* * * * *
62494124 AGCAGATCGAAGATGGTGGATTTTACCTCCCTGTGGTGATAGTGGGGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *
62494189 TCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTTAGATCTTGTCTCCCTAAGTAGTAGT
66 TCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
62494254 GG
131 GG
* * *
62494256 AGTAGATCAAATATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGAAAT
1 AGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * *
62494321 TCTACTTTCCTGGGTAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
62494386 GG
131 GG
* * *
62494388 AGCAGATCAAATATGGTGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCTAGTAAT
1 AGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
62494453 TCTA-TCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAG
66 TCTACT-TCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAG
62494517 TGG
130 TGG
* *
62494520 GGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGAAAT
1 AGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *
62494585 TCTACTTCCCTGGGTAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
62494650 GG
131 GG
* * * *
62494652 AACATATCAAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
*
62494717 TCTA-TCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTTTCTCCCTAAGCAGTAG
66 TCTACT-TCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAG
62494781 TGG
130 TGG
* * *
62494784 GGCAGATCAAAAATGGTGAATTTTACCTCTCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * * *
62494849 TCTACTTCCCTAGACAGTAGTGGAATAGATTGAAGATTTCAGATCTTGTCTTCCTAAGCAGTAGT
66 TCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
62494914 GG
131 GG
*
62494916 AGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
*
62494981 TCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCCAAGCAGTAGT
66 TCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
62495046 GG
131 GG
* * * *
62495048 AGCAGATCAAAGATGGCGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *
62495113 TCTA-TCTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCCAAGCAGTAG
66 TCTACT-TCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAG
62495177 TGG
130 TGG
* * ** * * *
62495180 AGCAAATCAAAGATGG-CAGATTTTACCTCATTGAGGTTGCAATGGAGTACATTGAAGCCAGTAA
1 AGCAGATCAAAGATGGTGA-ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA
* * * * * * *
62495244 TTCTATTTCCCTGGGTAGCAGTGGAATATATTGAATATTACAGATCTTATCTACCT-AGACAGTA
65 TTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAG-CAGTA
62495308 GTGG
129 GTGG
* ** * * * *
62495312 AGTAGATTGAAGTTGGT-AGATTTTACCTCTCTGAGGTTACAGTGGAGTATATTGAAGCCAGTAA
1 AGCAGATCAAAGATGGTGA-ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA
* * *
62495376 TTCTAAC-TCACTGGTCGGCAGTGGAAT
65 TTCT-ACTTCCCTGGGCAGCAGTGGAAT
62495403 CGATCAAAGA
Statistics
Matches: 1046, Mismatches: 91, Indels: 20
0.90 0.08 0.02
Matches are distributed among these distances:
131 5 0.00
132 1037 0.99
133 4 0.00
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.30
Consensus pattern (132 bp):
AGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
TCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
GG
Found at i:62494651 original size:44 final size:44
Alignment explanation
Indices: 62494603--62494783 Score: 104
Period size: 44 Copynumber: 4.1 Consensus size: 44
62494593 CCTGGGTAGC
62494603 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
* * ** ** * * * **
62494647 AGTGGAACATATCAAAGATGGCGGATTTTACCTCCCT--GTGGTT
1 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAG-T
* * * ** *
62494690 ACAGTGGAGTACATTGAAG---CCAGTAAT-TCTATCTCCCTGGGCAGC
1 --AGTGGAATAGATTGAAGATTTCAG--ATCT-TATCTCCCTAAGCAGT
*
62494735 AGTGGAATAGATTGAAGATTTCAGATCTTTTCTCCCTAAGCAGT
1 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
62494779 AGTGG
1 AGTGG
62494784 GGCAGATCAA
Statistics
Matches: 96, Mismatches: 29, Indels: 24
0.64 0.19 0.16
Matches are distributed among these distances:
42 4 0.04
43 17 0.18
44 57 0.59
45 13 0.14
46 5 0.05
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (44 bp):
AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
Found at i:62498383 original size:16 final size:17
Alignment explanation
Indices: 62498350--62498384 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
62498340 ATTATTTTTA
*
62498350 TATTTTTTAAAAATAAT
1 TATTTATTAAAAATAAT
62498367 TATTTATTAAAAA-AAT
1 TATTTATTAAAAATAAT
62498383 TA
1 TA
62498385 AAATTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TATTTATTAAAAATAAT
Found at i:62506848 original size:17 final size:17
Alignment explanation
Indices: 62506822--62506854 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
62506812 ATTAACTCTG
62506822 TTAAACAGTAAATATTT
1 TTAAACAGTAAATATTT
*
62506839 TTAAATAGTAAATATT
1 TTAAACAGTAAATATT
62506855 ATCTCGATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (17 bp):
TTAAACAGTAAATATTT
Found at i:62515148 original size:22 final size:21
Alignment explanation
Indices: 62515105--62515146 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
62515095 CCTGACCCGT
62515105 TGAGGTGCATAAAAACGCAAA
1 TGAGGTGCATAAAAACGCAAA
*
62515126 TGAGGTGCATGAAAACGCAAA
1 TGAGGTGCATAAAAACGCAAA
62515147 ATTGAAACCC
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:0.45, C:0.14, G:0.26, T:0.14
Consensus pattern (21 bp):
TGAGGTGCATAAAAACGCAAA
Found at i:62529412 original size:22 final size:20
Alignment explanation
Indices: 62529380--62529420 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
62529370 TTCAATAAGA
*
62529380 TATTTTTATATAATAATATTTT
1 TATTTTAATAT-AT-ATATTTT
62529402 TATTTTAATATATATATTT
1 TATTTTAATATATATATTT
62529421 AAAATATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 2 0.11
22 10 0.56
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTTTAATATATATATTTT
Found at i:62529920 original size:22 final size:21
Alignment explanation
Indices: 62529889--62529932 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
62529879 ATAATTTAGC
* *
62529889 ATTTTTATTTATTTTTTTATA
1 ATTTTTATTTATATATTTATA
62529910 ATTTTTAATTTATATATTTATA
1 ATTTTT-ATTTATATATTTATA
62529932 A
1 A
62529933 GATTTTAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
ATTTTTATTTATATATTTATA
Found at i:62531002 original size:17 final size:16
Alignment explanation
Indices: 62530989--62531021 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
62530979 TATTTTTATT
62530989 AATTTAAAATTTTTAA
1 AATTTAAAATTTTTAA
*
62531005 AATTTTAAA-TTTTAA
1 AATTTAAAATTTTTAA
62531020 AA
1 AA
62531022 AAAATTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTTAAAATTTTTAA
Found at i:62531022 original size:16 final size:16
Alignment explanation
Indices: 62530989--62531022 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
62530979 TATTTTTATT
*
62530989 AATTTAAAATTTTTAA
1 AATTTAAAATTTTAAA
*
62531005 AATTTTAAATTTTAAA
1 AATTTAAAATTTTAAA
62531021 AA
1 AA
62531023 AAATTAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTTAAAATTTTAAA
Found at i:62531790 original size:22 final size:22
Alignment explanation
Indices: 62531760--62531801 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
62531750 AAATGATATT
*
62531760 AAAATAGTAGAAAAACAACAAC
1 AAAACAGTAGAAAAACAACAAC
62531782 AAAACAGTAGAAAAACAACA
1 AAAACAGTAGAAAAACAACA
62531802 GTAAACTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.69, C:0.14, G:0.10, T:0.07
Consensus pattern (22 bp):
AAAACAGTAGAAAAACAACAAC
Found at i:62531812 original size:22 final size:23
Alignment explanation
Indices: 62531759--62531813 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
62531749 GAAATGATAT
*
62531759 TAAAATAGTAGAAAAACAACAAC
1 TAAACTAGTAGAAAAACAACAAC
* *
62531782 AAAAC-AGTAGAAAAACAAC-AG
1 TAAACTAGTAGAAAAACAACAAC
62531803 TAAACTAGTAG
1 TAAACTAGTAG
62531814 TTTTTTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 5 0.19
22 19 0.70
23 3 0.11
ACGTcount: A:0.62, C:0.13, G:0.13, T:0.13
Consensus pattern (23 bp):
TAAACTAGTAGAAAAACAACAAC
Found at i:62540027 original size:12 final size:11
Alignment explanation
Indices: 62540000--62540024 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
62539990 ATATTTTATG
62540000 TTTAAAATTTT
1 TTTAAAATTTT
62540011 TTTAAAATTTT
1 TTTAAAATTTT
62540022 TTT
1 TTT
62540025 TAATAATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTAAAATTTT
Found at i:62545118 original size:30 final size:31
Alignment explanation
Indices: 62545084--62545143 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
62545074 AAACCTTTTA
*
62545084 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
62545114 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
62545144 TCTCACCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:62545901 original size:5 final size:5
Alignment explanation
Indices: 62545891--62545917 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
62545881 GAAAATTTTT
62545891 GATTC GATTC GATTC GATTC GATTC GA
1 GATTC GATTC GATTC GATTC GATTC GA
62545918 CCGAATGCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (5 bp):
GATTC
Found at i:62556274 original size:25 final size:25
Alignment explanation
Indices: 62556205--62556284 Score: 85
Period size: 25 Copynumber: 3.2 Consensus size: 25
62556195 TACCCGTTAT
*
62556205 TGGCTCACATGAGCTTCCCGATT--A
1 TGGCTCACATGAGCTTCCTG-TTACA
*
62556229 TGACTC-CTATGAGCTTCCTGTTACA
1 TGGCTCAC-ATGAGCTTCCTGTTACA
* *
62556254 TGGCTCACATGAGCTTTCTGTTATA
1 TGGCTCACATGAGCTTCCTGTTACA
62556279 TGGCTC
1 TGGCTC
62556285 GAGAGACGGT
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
23 3 0.06
24 16 0.34
25 27 0.57
26 1 0.02
ACGTcount: A:0.19, C:0.26, G:0.20, T:0.35
Consensus pattern (25 bp):
TGGCTCACATGAGCTTCCTGTTACA
Found at i:62557274 original size:7 final size:7
Alignment explanation
Indices: 62557262--62557291 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
62557252 ACATTCCAAT
62557262 TATACCA
1 TATACCA
62557269 TATACCA
1 TATACCA
62557276 TATACCA
1 TATACCA
62557283 TATACCA
1 TATACCA
62557290 TA
1 TA
62557292 ATCCTCTCGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.30
Consensus pattern (7 bp):
TATACCA
Found at i:62559586 original size:22 final size:22
Alignment explanation
Indices: 62559557--62559673 Score: 92
Period size: 22 Copynumber: 5.0 Consensus size: 22
62559547 TGCACTAATG
*
62559557 AACAGAGAGCATTGAAGTGCTA
1 AACAGAGAGCACTGAAGTGCTA
* * *
62559579 TACAGAGAGCACAGATGTGCTA
1 AACAGAGAGCACTGAAGTGCTA
*
62559601 AACAGAGAGCACTGACGTGCTA
1 AACAGAGAGCACTGAAGTGCTA
*
62559623 GTAATCAGATAGCACTGACA-TGCTAA
1 --AA-CAGAGAGCACTGA-AGTGCT-A
* *
62559649 TAATCAGATAGCACTGATGTGCTA
1 -AA-CAGAGAGCACTGAAGTGCTA
62559673 A
1 A
62559674 TAATCAGATA
Statistics
Matches: 79, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
22 37 0.47
23 1 0.01
24 3 0.04
25 37 0.47
26 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.21
Consensus pattern (22 bp):
AACAGAGAGCACTGAAGTGCTA
Found at i:62559636 original size:25 final size:25
Alignment explanation
Indices: 62559603--62559685 Score: 130
Period size: 25 Copynumber: 3.3 Consensus size: 25
62559593 ATGTGCTAAA
* *
62559603 CAGAGAGCACTGACGTGCTAGTAAT
1 CAGATAGCACTGACGTGCTAATAAT
*
62559628 CAGATAGCACTGACATGCTAATAAT
1 CAGATAGCACTGACGTGCTAATAAT
*
62559653 CAGATAGCACTGATGTGCTAATAAT
1 CAGATAGCACTGACGTGCTAATAAT
62559678 CAGATAGC
1 CAGATAGC
62559686 GCACTAAGGT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 53 1.00
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (25 bp):
CAGATAGCACTGACGTGCTAATAAT
Found at i:62560565 original size:13 final size:13
Alignment explanation
Indices: 62560547--62560586 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
62560537 TTAATTTTCC
62560547 CTTTTCTTTCTTT
1 CTTTTCTTTCTTT
62560560 CTTTTCTTTCTTT
1 CTTTTCTTTCTTT
* *
62560573 C-CTTCTTTCCTT
1 CTTTTCTTTCTTT
62560585 CT
1 CT
62560587 CTGTTTCGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (13 bp):
CTTTTCTTTCTTT
Found at i:62560727 original size:23 final size:23
Alignment explanation
Indices: 62560697--62560743 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
62560687 AATAAGTATG
62560697 TACATATATTAATTACAAATGTA
1 TACATATATTAATTACAAATGTA
* *
62560720 TACATATATTTATTACACATGTA
1 TACATATATTAATTACAAATGTA
62560743 T
1 T
62560744 TTATAATTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.43
Consensus pattern (23 bp):
TACATATATTAATTACAAATGTA
Found at i:62563873 original size:31 final size:31
Alignment explanation
Indices: 62563829--62563899 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
62563819 AATGTTAATG
*
62563829 AGTGACTAATTTG-TAACTTTTTGATAACGTT-
1 AGTGACTGATTTGTTAACTTTTTGA-AA-GTTA
* **
62563860 AGTGACTGTTTTGTTATTTTTTTGAAAGTTA
1 AGTGACTGATTTGTTAACTTTTTGAAAGTTA
62563891 AGTGACTGA
1 AGTGACTGA
62563900 ATTAAAACTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
30 3 0.09
31 21 0.64
32 9 0.27
ACGTcount: A:0.27, C:0.07, G:0.20, T:0.46
Consensus pattern (31 bp):
AGTGACTGATTTGTTAACTTTTTGAAAGTTA
Found at i:62564549 original size:39 final size:38
Alignment explanation
Indices: 62564466--62564551 Score: 104
Period size: 38 Copynumber: 2.3 Consensus size: 38
62564456 GGCATAAGTG
*
62564466 TATT-TTATTATAAAACTTAAAGTTAAAATATATAATA
1 TATTATTATAATAAAACTTAAAGTTAAAATATATAATA
* * *
62564503 TAATATTATAATAAAACTTAAATGTT-AAGTGTATATATA
1 TATTATTATAATAAAACTTAAA-GTTAAAATATATA-ATA
62564542 TATTATTATA
1 TATTATTATA
62564552 TTATATTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
37 3 0.07
38 23 0.56
39 15 0.37
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (38 bp):
TATTATTATAATAAAACTTAAAGTTAAAATATATAATA
Found at i:62564645 original size:25 final size:23
Alignment explanation
Indices: 62564578--62564653 Score: 71
Period size: 25 Copynumber: 3.1 Consensus size: 23
62564568 AGTAAAAGAA
*
62564578 AAAGAAATAGAAAAAGAAGGAGAG
1 AAAGAAATA-AAAAAGAAGGAAAG
* *
62564602 AAAGAAACGAAATATAGAAGGAAAG
1 AAAGAAA-TAAA-AAAGAAGGAAAG
*
62564627 AAAGGAAATAAAAAGAGAAAGAAAG
1 AAA-GAAATAAAAA-AGAAGGAAAG
62564652 AA
1 AA
62564654 GGAGAAAAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
24 10 0.24
25 28 0.67
26 4 0.10
ACGTcount: A:0.68, C:0.01, G:0.25, T:0.05
Consensus pattern (23 bp):
AAAGAAATAAAAAAGAAGGAAAG
Found at i:62564651 original size:21 final size:22
Alignment explanation
Indices: 62564598--62564651 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
62564588 AAAAAGAAGG
* *
62564598 AGAGAAAGAAACGAAATATAGA
1 AGAGAAAGAAAGGAAATATAAA
62564620 AG-GAAAGAAAGGAAATA-AAA
1 AGAGAAAGAAAGGAAATATAAA
62564640 AGAGAAAGAAAG
1 AGAGAAAGAAAG
62564652 AAGGAGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 4 0.14
21 23 0.79
22 2 0.07
ACGTcount: A:0.67, C:0.02, G:0.26, T:0.06
Consensus pattern (22 bp):
AGAGAAAGAAAGGAAATATAAA
Found at i:62564957 original size:18 final size:19
Alignment explanation
Indices: 62564928--62564963 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
62564918 GTAAAAATTT
*
62564928 TGAAATTTAGAGATTTAAG
1 TGAAATTTAGAGAGTTAAG
62564947 TGAAA-TTAGAGAGTTAA
1 TGAAATTTAGAGAGTTAA
62564964 ATCTAGTTTA
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:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (19 bp):
TGAAATTTAGAGAGTTAAG
Found at i:62565659 original size:40 final size:40
Alignment explanation
Indices: 62565540--62565662 Score: 117
Period size: 40 Copynumber: 3.1 Consensus size: 40
62565530 GATGAGACGT
* *
62565540 TGGGTGTCAATTTATTACTTCGGATTAATTCGATGAGGCAC
1 TGGGTGTCAATTTATTACTTCGGATT-ATCCGATGAGGTAC
* * * * * **
62565581 TGGGTGCCAA--T-TTACTTCGGTTTAGCCAATAAAATAC
1 TGGGTGTCAATTTATTACTTCGGATTATCCGATGAGGTAC
**
62565618 TGGGTGTCAATTTATTACTTCAAATTATCCGATGAGGTAC
1 TGGGTGTCAATTTATTACTTCGGATTATCCGATGAGGTAC
62565658 TGGGT
1 TGGGT
62565663 ACCAAACTGG
Statistics
Matches: 61, Mismatches: 18, Indels: 7
0.71 0.21 0.08
Matches are distributed among these distances:
37 16 0.26
38 11 0.18
39 2 0.03
40 23 0.38
41 9 0.15
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (40 bp):
TGGGTGTCAATTTATTACTTCGGATTATCCGATGAGGTAC
Found at i:62565854 original size:21 final size:22
Alignment explanation
Indices: 62565829--62565870 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
62565819 GCTATTTGTC
*
62565829 TAGCAAG-AATGAGATTTGAAG
1 TAGCAAGTAATGAGAATTGAAG
*
62565850 TAGCAAGTGATGAGAATTGAA
1 TAGCAAGTAATGAGAATTGAA
62565871 TATGTTATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.43, C:0.05, G:0.29, T:0.24
Consensus pattern (22 bp):
TAGCAAGTAATGAGAATTGAAG
Found at i:62574102 original size:7 final size:7
Alignment explanation
Indices: 62574090--62574115 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
62574080 TCGATTATTG
62574090 GGGCAAT
1 GGGCAAT
62574097 GGGCAAT
1 GGGCAAT
62574104 GGGCAAT
1 GGGCAAT
62574111 GGGCA
1 GGGCA
62574116 GTTTATTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.15, G:0.46, T:0.12
Consensus pattern (7 bp):
GGGCAAT
Found at i:62582269 original size:15 final size:15
Alignment explanation
Indices: 62582249--62582277 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
62582239 CATAACTTTA
62582249 AAAATATTTGAATTT
1 AAAATATTTGAATTT
62582264 AAAATATTTGAATT
1 AAAATATTTGAATT
62582278 CATAATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (15 bp):
AAAATATTTGAATTT
Found at i:62582284 original size:15 final size:15
Alignment explanation
Indices: 62582249--62582298 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
62582239 CATAACTTTA
*
62582249 AAAATATTTGAATTT
1 AAAATATTTGAATTC
62582264 AAAATATTTGAATTC
1 AAAATATTTGAATTC
* *
62582279 ATAATAATTTCAAATTC
1 AAAAT-ATTT-GAATTC
62582296 AAA
1 AAA
62582299 CTTAAAAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 18 0.62
16 4 0.14
17 7 0.24
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (15 bp):
AAAATATTTGAATTC
Found at i:62583052 original size:20 final size:20
Alignment explanation
Indices: 62583006--62583052 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
62582996 CAGTTTGTTA
62583006 AAAAATATTTATTTTAATAT
1 AAAAATATTTATTTTAATAT
*** *
62583026 TTTAATATTTATTTTTATAT
1 AAAAATATTTATTTTAATAT
62583046 AAAAATA
1 AAAAATA
62583053 ATCTAAAGAG
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AAAAATATTTATTTTAATAT
Found at i:62598617 original size:19 final size:19
Alignment explanation
Indices: 62598589--62598626 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
62598579 GCAACTAAAA
*
62598589 ATTTCGAAGCTTAACATGT
1 ATTTCAAAGCTTAACATGT
62598608 ATTTCAAAGCTTAACATGT
1 ATTTCAAAGCTTAACATGT
62598627 TTACATTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (19 bp):
ATTTCAAAGCTTAACATGT
Found at i:62601955 original size:27 final size:27
Alignment explanation
Indices: 62601925--62601994 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
62601915 TCTATTAAGA
**
62601925 ATGTTATAATTTGGACAGCAACAATGC
1 ATGTTATAATTCAGACAGCAACAATGC
* *
62601952 ATGTTTTAATTCAGACAGCATCAATGC
1 ATGTTATAATTCAGACAGCAACAATGC
* *
62601979 ATGTTTTAAGTCAGAC
1 ATGTTATAATTCAGAC
62601995 CTATTAACTA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (27 bp):
ATGTTATAATTCAGACAGCAACAATGC
Found at i:62610414 original size:19 final size:18
Alignment explanation
Indices: 62610377--62610411 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
62610367 AAATTTTGGA
*
62610377 ATTTTTATAAATAATTTG
1 ATTTTTAAAAATAATTTG
*
62610395 ATTTTTAAAAATCATTT
1 ATTTTTAAAAATAATTT
62610412 TGAAAATTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (18 bp):
ATTTTTAAAAATAATTTG
Found at i:62616814 original size:16 final size:16
Alignment explanation
Indices: 62616793--62616841 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 16
62616783 ATATATATCT
62616793 TATATATTCAAGTTAA
1 TATATATTCAAGTTAA
*
62616809 TATATATT-ATGTT-A
1 TATATATTCAAGTTAA
*
62616823 TAT-T-TACAAGTTAA
1 TATATATTCAAGTTAA
62616837 TATAT
1 TATAT
62616842 TAAATATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
12 1 0.04
13 5 0.19
14 8 0.30
15 5 0.19
16 8 0.30
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (16 bp):
TATATATTCAAGTTAA
Found at i:62616832 original size:28 final size:27
Alignment explanation
Indices: 62616781--62616841 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 27
62616771 ATAATATATG
62616781 ATATATATATCTTATATATTCAAGTTA
1 ATATATATATCTTATATATTCAAGTTA
*
62616808 ATATATATTATGTTATAT-TTACAAGTTA
1 ATATATA-TATCTTATATATT-CAAGTTA
62616836 ATATAT
1 ATATAT
62616842 TAAATATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
27 9 0.29
28 22 0.71
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (27 bp):
ATATATATATCTTATATATTCAAGTTA
Found at i:62626804 original size:37 final size:37
Alignment explanation
Indices: 62626760--62626851 Score: 175
Period size: 37 Copynumber: 2.5 Consensus size: 37
62626750 CACTTGTCCC
62626760 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
1 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
*
62626797 TGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCT
1 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
62626834 TGATCAGATAAGTGTAGC
1 TGATCAGATAAGTGTAGC
62626852 TAAAGCTATC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.37
Consensus pattern (37 bp):
TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
Found at i:62626882 original size:46 final size:46
Alignment explanation
Indices: 62626815--62627083 Score: 349
Period size: 46 Copynumber: 5.6 Consensus size: 46
62626805 TAAGTGTAGC
**
62626815 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
* * **
62626861 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
62626907 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
* *
62626959 CAGTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
*
62627005 CACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
62627057 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
62627084 AGTACTCAAA
Statistics
Matches: 198, Mismatches: 13, Indels: 24
0.84 0.06 0.10
Matches are distributed among these distances:
46 111 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.36
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
Found at i:62626934 original size:52 final size:52
Alignment explanation
Indices: 62626858--62627077 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
62626848 TAGCTAAAGC
* * * **
62626858 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACT
*
62626911 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCAGT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACT
*
62626963 TATCAC---T---TTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACT
* *
62627009 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACT
62627061 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
62627078 ATCAGAAGTA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 86 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACT
Found at i:62626978 original size:98 final size:98
Alignment explanation
Indices: 62626832--62627083 Score: 441
Period size: 98 Copynumber: 2.6 Consensus size: 98
62626822 CACTTTGTTT
62626832 CTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAG
1 CTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAG
* *
62626897 CCGAAGCTATCACTTATCACTTTTCACTTGTCA
66 CCAAAGCTATCACTTATCACTTTCCACTTGTCA
* *
62626930 CTTGATCAGATAAGTGTAGCTAAAGCTATCAGTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
1 CTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAG
*
62626995 CTAAAGCTATCACTTATCACTTTCCACTTGTCA
66 CCAAAGCTATCACTTATCACTTTCCACTTGTCA
* *
62627028 CTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGA
1 CTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCTTGATCAGA
62627084 AGTACTCAAA
Statistics
Matches: 146, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 146 1.00
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (98 bp):
CTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAG
CCAAAGCTATCACTTATCACTTTCCACTTGTCA
Found at i:62630750 original size:34 final size:35
Alignment explanation
Indices: 62630707--62630783 Score: 111
Period size: 36 Copynumber: 2.2 Consensus size: 35
62630697 TTACTGGTGT
* * *
62630707 CAGGTGTCAAG-TTGAGAGGATAGATATCTTGTTA
1 CAGGTGTCAAGTTTAAGAGGATAGATATATTATTA
62630741 CAGGTGTCAAGTTTTAAGAGGATAGATATATTATTA
1 CAGGTGTCAAG-TTTAAGAGGATAGATATATTATTA
62630777 CAGGTGT
1 CAGGTGT
62630784 AGGCGTATGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 11 0.29
36 27 0.71
ACGTcount: A:0.31, C:0.08, G:0.27, T:0.34
Consensus pattern (35 bp):
CAGGTGTCAAGTTTAAGAGGATAGATATATTATTA
Found at i:62634831 original size:11 final size:12
Alignment explanation
Indices: 62634807--62634831 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
62634797 CTCTCTAAAC
62634807 AAAAATTTCAAA
1 AAAAATTTCAAA
62634819 AAAAATTTCAAA
1 AAAAATTTCAAA
62634831 A
1 A
62634832 TGATTTTTAA
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:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAAATTTCAAA
Found at i:62636850 original size:4 final size:4
Alignment explanation
Indices: 62636843--62636919 Score: 127
Period size: 4 Copynumber: 19.2 Consensus size: 4
62636833 CAATAAACAA
* *
62636843 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAC ACAT ACAT ACAC
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
62636891 ACAT ACAT ACAT ACAT ACAT ACAC ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
62636920 ATAATAGTTT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 67 1.00
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.21
Consensus pattern (4 bp):
ACAT
Found at i:62642029 original size:20 final size:21
Alignment explanation
Indices: 62641999--62642037 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
62641989 TAATGTCATA
*
62641999 TCAGCATTTTCATTCTAAATT
1 TCAGCATTTTCATCCTAAATT
62642020 TCAG-ATTTTCATCCTAAA
1 TCAGCATTTTCATCCTAAA
62642038 AGAAAAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.31, C:0.21, G:0.05, T:0.44
Consensus pattern (21 bp):
TCAGCATTTTCATCCTAAATT
Found at i:62642964 original size:16 final size:17
Alignment explanation
Indices: 62642940--62642980 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
62642930 ATTATTTAGT
*
62642940 AATACTTTTATTTTAAA
1 AATACTTTTATTTAAAA
*
62642957 AATATTTTTATTTAAAA
1 AATACTTTTATTTAAAA
62642974 AATACTT
1 AATACTT
62642981 CTGAAAAGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (17 bp):
AATACTTTTATTTAAAA
Found at i:62651933 original size:21 final size:21
Alignment explanation
Indices: 62651907--62651947 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
62651897 ATCTGCTCAA
* *
62651907 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
62651928 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
62651948 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:62658325 original size:134 final size:129
Alignment explanation
Indices: 62658012--62658404 Score: 394
Period size: 133 Copynumber: 3.0 Consensus size: 129
62658002 ACCAAAAGGG
62658012 AATTGTTTGATGCACTTAGGCAGGAACTTGAGTGAGTCTTGTGGATCCTTCATTGTTGTTAACAG
1 AATTGTTTGATGCACTTAGGCAGGAACTTGAGTGAGTCTTGT-GATCCTTCATTGTT-TTAACAG
** ** * * *
62658077 CTAACGCTTGATGTTTCTTAGACTGTTTCATGTATTTCTTTCAT-TTTTTATCCTCCCAGCCTGA
64 CTAA-GCTCAATAATGCTTAGA-TGTTTCATGTACTTCTTTCATGTTTTTA-CCTCCCAGCCTAA
* *
62658141 GGAG
126 AGAA
* * * * *
62658145 AATTTTTTGATGCACTTAGGCGGGAACTTGAGTGGGTCTTGTTGATCCTTCATTGATTTCAATAG
1 AATTGTTTGATGCACTTAGGCAGGAACTTGAGTGAGTCTTG-TGATCCTTCATTG-TTTTAACAG
* * * *
62658210 CTGAAGCTCAAAAATGCTTAGATGGTTTCGTGTCCTTCTTTCATGTTCTTACCTTCCCAGCCTAA
64 CT-AAGCTCAATAATGCTTAGAT-GTTTCATGTACTTCTTTCATGTTTTTACC-TCCCAGCCTAA
62658275 AGAA
126 AGAA
* * * **
62658279 AATTGTTTGATGCACTTAAGCAGGAACTTGAGTGACTGTTGCTGAT-CTTTGTTGTTTTTAACAG
1 AATTGTTTGATGCACTTAGGCAGGAACTTGAGTGAGTCTTG-TGATCCTTCATTG-TTTTAACAG
* * * * *
62658343 CTAAAGTTCAATAATGCTTTAGATATTTCATGTGCTTCTTTCATGTTTTTACGTCCCGGCCT
64 CT-AAGCTCAATAATGC-TTAGATGTTTCATGTACTTCTTTCATGTTTTTACCTCCCAGCCT
62658405 GTAGTTTATC
Statistics
Matches: 214, Mismatches: 39, Indels: 15
0.80 0.15 0.06
Matches are distributed among these distances:
132 9 0.04
133 138 0.64
134 67 0.31
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (129 bp):
AATTGTTTGATGCACTTAGGCAGGAACTTGAGTGAGTCTTGTGATCCTTCATTGTTTTAACAGCT
AAGCTCAATAATGCTTAGATGTTTCATGTACTTCTTTCATGTTTTTACCTCCCAGCCTAAAGAA
Found at i:62659878 original size:20 final size:20
Alignment explanation
Indices: 62659849--62659888 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
62659839 ATTTTTATAG
* *
62659849 AATAATATAATATTAAAATA
1 AATAAAATAAAATTAAAATA
*
62659869 AATAAAATAAAATTGAAATA
1 AATAAAATAAAATTAAAATA
62659889 TTTTTCATTA
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:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (20 bp):
AATAAAATAAAATTAAAATA
Found at i:62662314 original size:15 final size:16
Alignment explanation
Indices: 62662286--62662315 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
62662276 TATCAATAAG
62662286 TTTAAAAATATTTATT
1 TTTAAAAATATTTATT
62662302 TTTAAAAAT-TTTAT
1 TTTAAAAATATTTAT
62662316 CACTAAAATT
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTAAAAATATTTATT
Found at i:62662498 original size:32 final size:30
Alignment explanation
Indices: 62662462--62662532 Score: 72
Period size: 32 Copynumber: 2.3 Consensus size: 30
62662452 CACATCAATT
* *
62662462 AAATTATATTTTCATCC-CTCAATCAAATAATA
1 AAATTATATTATAATCCTCTCAA--AAAT-ATA
*
62662494 AAATTTTATTATAATCCTCTCAAAAATATA
1 AAATTATATTATAATCCTCTCAAAAATATA
*
62662524 AAAATATAT
1 AAATTATAT
62662533 AATTTAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
30 10 0.30
31 4 0.12
32 14 0.42
33 5 0.15
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (30 bp):
AAATTATATTATAATCCTCTCAAAAATATA
Found at i:62663062 original size:3 final size:3
Alignment explanation
Indices: 62663047--62663093 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
62663037 AGCATTGGTG
* * * *
62663047 GCT GCT CCT GCT GCT GCT GCT CCT GCT GCT GCT GCT CCT GCT CCT GC
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GC
62663094 ATAAAGGCAA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.43, G:0.26, T:0.32
Consensus pattern (3 bp):
GCT
Found at i:62663067 original size:15 final size:15
Alignment explanation
Indices: 62663047--62663093 Score: 85
Period size: 15 Copynumber: 3.1 Consensus size: 15
62663037 AGCATTGGTG
62663047 GCTGCTCCTGCTGCT
1 GCTGCTCCTGCTGCT
62663062 GCTGCTCCTGCTGCT
1 GCTGCTCCTGCTGCT
*
62663077 GCTGCTCCTGCTCCT
1 GCTGCTCCTGCTGCT
62663092 GC
1 GC
62663094 ATAAAGGCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.00, C:0.43, G:0.26, T:0.32
Consensus pattern (15 bp):
GCTGCTCCTGCTGCT
Found at i:62665889 original size:19 final size:19
Alignment explanation
Indices: 62665862--62665908 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
62665852 TAACTTTCTC
*
62665862 TATATATATTTCAAATTTT
1 TATAAATATTTCAAATTTT
**
62665881 TATAAATATTTTGAATTTT
1 TATAAATATTTCAAATTTT
62665900 T-TAAA-ATTT
1 TATAAATATTT
62665909 TTTTTGTGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 4 0.16
18 4 0.16
19 17 0.68
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (19 bp):
TATAAATATTTCAAATTTT
Found at i:62675262 original size:28 final size:28
Alignment explanation
Indices: 62675222--62675278 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
62675212 TCATAATCAG
62675222 ACTTAACATAATTTAAGTATTAACATGT
1 ACTTAACATAATTTAAGTATTAACATGT
*
62675250 ACTTAACATAATTTAAGTCTTAACATGT
1 ACTTAACATAATTTAAGTATTAACATGT
62675278 A
1 A
62675279 TTGCAGGAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (28 bp):
ACTTAACATAATTTAAGTATTAACATGT
Found at i:62692288 original size:14 final size:14
Alignment explanation
Indices: 62692269--62692295 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
62692259 CCATAAGCCA
62692269 TAAATCTTAAACCC
1 TAAATCTTAAACCC
62692283 TAAATCTTAAACC
1 TAAATCTTAAACC
62692296 TCGAACTCTA
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:0.44, C:0.26, G:0.00, T:0.30
Consensus pattern (14 bp):
TAAATCTTAAACCC
Found at i:62694125 original size:24 final size:25
Alignment explanation
Indices: 62694080--62694126 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
62694070 AGATTTGCCT
62694080 ATTATAAAAAGATGATTGTTATACA
1 ATTATAAAAAGATGATTGTTATACA
* *
62694105 ATTATAACAATATG-TTGTTATA
1 ATTATAAAAAGATGATTGTTATA
62694127 GAGAGTTACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.40
Consensus pattern (25 bp):
ATTATAAAAAGATGATTGTTATACA
Found at i:62694611 original size:29 final size:31
Alignment explanation
Indices: 62694568--62694625 Score: 75
Period size: 29 Copynumber: 1.9 Consensus size: 31
62694558 TTAGTTTATG
** *
62694568 TACTTTGACAAAATTTGAGATTTAATCTTTA
1 TACTTTGACAAAATTAAAAATTTAATCTTTA
62694599 TACTTT-A-AAAATTAAAAATTTAATCTT
1 TACTTTGACAAAATTAAAAATTTAATCTT
62694626 CCTACCTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 17 0.71
30 1 0.04
31 6 0.25
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (31 bp):
TACTTTGACAAAATTAAAAATTTAATCTTTA
Found at i:62696127 original size:20 final size:20
Alignment explanation
Indices: 62696098--62696135 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
62696088 GAAAGCTCTT
*
62696098 CGATTAGTCTCGTCGGATCC
1 CGATTAGTCTCGACGGATCC
*
62696118 CGATTTGTCTCGACGGAT
1 CGATTAGTCTCGACGGAT
62696136 GTTCTTTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.26, G:0.26, T:0.32
Consensus pattern (20 bp):
CGATTAGTCTCGACGGATCC
Found at i:62701119 original size:15 final size:15
Alignment explanation
Indices: 62701077--62701117 Score: 59
Period size: 14 Copynumber: 2.8 Consensus size: 15
62701067 ATAAGATAAC
62701077 TAAATTATTAAATCA
1 TAAATTATTAAATCA
62701092 TAATATT-TTAAAT-A
1 TAA-ATTATTAAATCA
62701106 TAAATTATTAAA
1 TAAATTATTAAA
62701118 ATGTACATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 3 0.12
14 9 0.38
15 9 0.38
16 3 0.12
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
TAAATTATTAAATCA
Found at i:62708462 original size:26 final size:27
Alignment explanation
Indices: 62708433--62708486 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
62708423 TATTTTTATA
*
62708433 TAATTAATATAA-TTTTAAAATAATTT
1 TAATGAATATAATTTTTAAAATAATTT
* * *
62708459 TAATGATTTTAATTTTTAAAATAGTTT
1 TAATGAATATAATTTTTAAAATAATTT
62708486 T
1 T
62708487 TATATTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (27 bp):
TAATGAATATAATTTTTAAAATAATTT
Found at i:62708486 original size:27 final size:25
Alignment explanation
Indices: 62708445--62708514 Score: 79
Period size: 28 Copynumber: 2.6 Consensus size: 25
62708435 ATTAATATAA
62708445 TTTTAAAATAATTTTAATGATTTTAAT
1 TTTTAAAAT-ATTTTAAT-ATTTTAAT
*
62708472 TTTTAAAATAGTTTTTATATTTTTTAAT
1 TTTTAAAATA--TTTTA-ATATTTTAAT
62708500 TTTTAAAA-ATTTTAA
1 TTTTAAAATATTTTAA
62708515 AAATTAATTA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
24 1 0.03
25 5 0.13
26 1 0.03
27 10 0.26
28 20 0.51
29 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.59
Consensus pattern (25 bp):
TTTTAAAATATTTTAATATTTTAAT
Found at i:62708525 original size:27 final size:27
Alignment explanation
Indices: 62708434--62708530 Score: 65
Period size: 26 Copynumber: 3.6 Consensus size: 27
62708424 ATTTTTATAT
* *
62708434 AATTAATATAATTTTAAAATAATTTTAAT
1 AATTAAT-TAATTTTTAAA-AATTTTAAA
* *
62708463 GATT--TTAATTTTTAAAATAGTTTT-TA
1 AATTAATTAATTTTTAAAA-A-TTTTAAA
* **
62708489 TATTTTTTAATTTTTAAAAATTTTAAA
1 AATTAATTAATTTTTAAAAATTTTAAA
*
62708516 AATTAATTAAATTTT
1 AATTAATTAATTTTT
62708531 GACGTGTCAT
Statistics
Matches: 53, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
25 1 0.02
26 18 0.34
27 18 0.34
28 13 0.25
29 3 0.06
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (27 bp):
AATTAATTAATTTTTAAAAATTTTAAA
Found at i:62709204 original size:21 final size:21
Alignment explanation
Indices: 62709155--62709204 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
62709145 CATGTATGAA
* *
62709155 TAAATAAATAATATATAAAAT
1 TAAATTAATAAAATATAAAAT
*
62709176 TAATTTAATAAAATA-AAAAT
1 TAAATTAATAAAATATAAAAT
62709196 TATAATTAA
1 TA-AATTAA
62709205 AAAGTGCTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAATTAATAAAATATAAAAT
Found at i:62710188 original size:12 final size:12
Alignment explanation
Indices: 62710171--62710200 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
62710161 ACAATCATTA
62710171 AATTATCGCTTG
1 AATTATCGCTTG
62710183 AATTATCGCTTG
1 AATTATCGCTTG
62710195 AATTAT
1 AATTAT
62710201 TTTATTCAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (12 bp):
AATTATCGCTTG
Found at i:62711765 original size:20 final size:19
Alignment explanation
Indices: 62711737--62711795 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 19
62711727 AATTGTTAAA
*
62711737 ATTATAAAAACAATAAATTT
1 ATTA-AAAAATAATAAATTT
* *
62711757 ATTACAAAATTATAATATTT
1 ATTAAAAAATAATAA-ATTT
*
62711777 ATTAATAAATAATAAATTT
1 ATTAAAAAATAATAAATTT
62711796 CAAAAATCAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
19 12 0.38
20 20 0.62
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTAAAAAATAATAAATTT
Found at i:62713721 original size:17 final size:16
Alignment explanation
Indices: 62713690--62713731 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
62713680 TTTTTGGATA
*
62713690 AAATTTACA-CAAAAT
1 AAATTTAAAGCAAAAT
62713705 AGAATTTAAAGCAAAAT
1 A-AATTTAAAGCAAAAT
62713722 AAATTTAAAG
1 AAATTTAAAG
62713732 AGAATTCATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 1 0.04
16 16 0.67
17 7 0.29
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.26
Consensus pattern (16 bp):
AAATTTAAAGCAAAAT
Found at i:62714031 original size:6 final size:6
Alignment explanation
Indices: 62714009--62714058 Score: 57
Period size: 6 Copynumber: 8.2 Consensus size: 6
62713999 TAAGGATTGC
* *
62714009 TAGGGA T-GGGTA TAGGGA TAGGGA TAGGGA TAGGGA CAGAGA TAGAGGA
1 TAGGGA TAGGG-A TAGGGA TAGGGA TAGGGA TAGGGA TAGGGA TAG-GGA
62714058 T
1 T
62714059 GAAAGTGAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
5 3 0.08
6 28 0.76
7 6 0.16
ACGTcount: A:0.34, C:0.02, G:0.46, T:0.18
Consensus pattern (6 bp):
TAGGGA
Found at i:62717394 original size:22 final size:21
Alignment explanation
Indices: 62717355--62717456 Score: 68
Period size: 22 Copynumber: 4.8 Consensus size: 21
62717345 AAAATATTCA
*
62717355 TAAAAATTAA-TAATAATTATAT
1 TAAAAA-TAATTAAAAATTA-AT
62717377 TAAAAATAATTAAAAATTAA-
1 TAAAAATAATTAAAAATTAAT
* *
62717397 -AAGAAT-ATGAAAAATTATATT
1 TAAAAATAATTAAAAATTA-A-T
* *
62717418 TAAAAATAAATAAAAATGAAT
1 TAAAAATAATTAAAAATTAAT
*
62717439 TAAAGCATAATTTAAAAA
1 TAAA-AATAA-TTAAAAA
62717457 ATATTTTTTT
Statistics
Matches: 63, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
18 10 0.16
19 6 0.10
21 9 0.14
22 24 0.38
23 14 0.22
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (21 bp):
TAAAAATAATTAAAAATTAAT
Found at i:62717491 original size:17 final size:18
Alignment explanation
Indices: 62717471--62717505 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
62717461 TTTTTTGTTA
62717471 AAAAATAAAAAAT-AATT
1 AAAAATAAAAAATCAATT
62717488 AAAAATAAAAAATCAATT
1 AAAAATAAAAAATCAATT
62717506 TTACCAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAAATAAAAAATCAATT
Found at i:62735355 original size:61 final size:61
Alignment explanation
Indices: 62735260--62735605 Score: 494
Period size: 61 Copynumber: 5.7 Consensus size: 61
62735250 GATACATGGT
* * *
62735260 TGAATTTGGCTCTAAGTAGCAGATCAGTGAGCCAATTCAGCTCCTTTCATAGTTAGATAGC
1 TGAATTTGGCTCTCAGTAGAATATCAGTGAGCCAATTCAGCTCCTTTCATAGTTAGATAGC
* * *
62735321 TGAATTTGGCTCTCAGTAGCACAACAGTGAGCCAATTCAGCTCCTTTCATAGTTAGATAGC
1 TGAATTTGGCTCTCAGTAGAATATCAGTGAGCCAATTCAGCTCCTTTCATAGTTAGATAGC
* * * *
62735382 TGAATTTCGCTATCAGTAGAATATCAGTGAGCCAATTCAGTTCCTTTCATAGTTACATAGC
1 TGAATTTGGCTCTCAGTAGAATATCAGTGAGCCAATTCAGCTCCTTTCATAGTTAGATAGC
* * * *
62735443 TGAATTCGGCTCTCAGTAGAATATCAGTGAGTCAATTAAGTTCCTTTCATAGTTAGATAGC
1 TGAATTTGGCTCTCAGTAGAATATCAGTGAGCCAATTCAGCTCCTTTCATAGTTAGATAGC
* * * * * *
62735504 TGAATTTGGCTCTAAGTAGAATATCAGTGAGTCGATTCAGCTCCTTCCATAGATACATAGC
1 TGAATTTGGCTCTCAGTAGAATATCAGTGAGCCAATTCAGCTCCTTTCATAGTTAGATAGC
* *
62735565 TGAATTTGGCTCTCAGTAGAATATTAGTGAGTCAATTCAGC
1 TGAATTTGGCTCTCAGTAGAATATCAGTGAGCCAATTCAGC
62735606 CCCTATAAAA
Statistics
Matches: 258, Mismatches: 27, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 258 1.00
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (61 bp):
TGAATTTGGCTCTCAGTAGAATATCAGTGAGCCAATTCAGCTCCTTTCATAGTTAGATAGC
Found at i:62736495 original size:20 final size:20
Alignment explanation
Indices: 62736458--62736496 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
62736448 TTGATATTTT
**
62736458 TGGAACCATTTCCCTGTTGG
1 TGGAACCATTTCAATGTTGG
*
62736478 TGGAACCTTTTCAATGTTG
1 TGGAACCATTTCAATGTTG
62736497 ATCCAAAGGC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.38
Consensus pattern (20 bp):
TGGAACCATTTCAATGTTGG
Found at i:62742722 original size:33 final size:33
Alignment explanation
Indices: 62742680--62742797 Score: 218
Period size: 33 Copynumber: 3.6 Consensus size: 33
62742670 ATGTAAAGGG
* *
62742680 GGTTGCTAAGTGTTGATTCCCTGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
62742713 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
62742746 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
62742779 GGTTGCTAAGTGCTGATTC
1 GGTTGCTAAGTGCTGATTC
62742798 TACCGTATCA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 83 1.00
ACGTcount: A:0.15, C:0.19, G:0.28, T:0.38
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:62751002 original size:19 final size:19
Alignment explanation
Indices: 62750978--62751014 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
62750968 CTCGTTCTTG
* *
62750978 CTGGTTTCTCCCTTGTTTA
1 CTGGTTTATCCCTCGTTTA
62750997 CTGGTTTATCCCTCGTTT
1 CTGGTTTATCCCTCGTTT
62751015 TTGCTAGTTT
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:0.05, C:0.27, G:0.16, T:0.51
Consensus pattern (19 bp):
CTGGTTTATCCCTCGTTTA
Found at i:62751036 original size:21 final size:21
Alignment explanation
Indices: 62750966--62751029 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
62750956 CAGAAATCTC
*
62750966 CCCTCGTTCTTGCTGGTTTCT
1 CCCTCGTTTTTGCTGGTTTCT
* * *
62750987 CCCT--TGTTTACTGGTTTAT
1 CCCTCGTTTTTGCTGGTTTCT
*
62751006 CCCTCGTTTTTGCTAGTTTCT
1 CCCTCGTTTTTGCTGGTTTCT
62751027 CCC
1 CCC
62751030 CTCTTTTATA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
19 15 0.45
21 18 0.55
ACGTcount: A:0.05, C:0.31, G:0.16, T:0.48
Consensus pattern (21 bp):
CCCTCGTTTTTGCTGGTTTCT
Found at i:62753560 original size:6 final size:6
Alignment explanation
Indices: 62753549--62753635 Score: 113
Period size: 6 Copynumber: 14.2 Consensus size: 6
62753539 TATTGTTGAT
62753549 AATGGG AATGGG AATGGG AAATGGG AATGGG AATGGG AATGGG AATGGG
1 AATGGG AATGGG AATGGG -AATGGG AATGGG AATGGG AATGGG AATGGG
* * *
62753598 AAATGGG AATGGG TAT-TG CATGGG AATGGG AAATGGG A
1 -AATGGG AATGGG AATGGG AATGGG AATGGG -AATGGG A
62753636 GGAGGGCACG
Statistics
Matches: 72, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
5 3 0.04
6 51 0.71
7 18 0.25
ACGTcount: A:0.34, C:0.01, G:0.46, T:0.18
Consensus pattern (6 bp):
AATGGG
Found at i:62753587 original size:31 final size:31
Alignment explanation
Indices: 62753549--62753635 Score: 140
Period size: 31 Copynumber: 2.8 Consensus size: 31
62753539 TATTGTTGAT
62753549 AATGGGAATGGGAATGGGAAATGGGAATGGG
1 AATGGGAATGGGAATGGGAAATGGGAATGGG
62753580 AATGGGAATGGGAATGGGAAATGGGAATGGG
1 AATGGGAATGGGAATGGGAAATGGGAATGGG
* * *
62753611 TAT-TGCATGGGAATGGGAAATGGGA
1 AATGGGAATGGGAATGGGAAATGGGA
62753636 GGAGGGCACG
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 20 0.38
31 33 0.62
ACGTcount: A:0.34, C:0.01, G:0.46, T:0.18
Consensus pattern (31 bp):
AATGGGAATGGGAATGGGAAATGGGAATGGG
Found at i:62753620 original size:24 final size:24
Alignment explanation
Indices: 62753549--62753635 Score: 113
Period size: 25 Copynumber: 3.5 Consensus size: 24
62753539 TATTGTTGAT
62753549 AATGGGAATGGGAATGGGAAATGGG
1 AATGGGAATGGGAATGGG-AATGGG
62753574 AATGGGAATGGGAATGGGAATGGG
1 AATGGGAATGGGAATGGGAATGGG
* * *
62753598 AAATGGGAATGGGTAT-TGCATGGG
1 -AATGGGAATGGGAATGGGAATGGG
62753622 AATGGGAAATGGGA
1 AATGGG-AATGGGA
62753636 GGAGGGCACG
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
23 6 0.11
24 18 0.32
25 32 0.57
ACGTcount: A:0.34, C:0.01, G:0.46, T:0.18
Consensus pattern (24 bp):
AATGGGAATGGGAATGGGAATGGG
Found at i:62753658 original size:23 final size:23
Alignment explanation
Indices: 62753632--62753702 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 23
62753622 AATGGGAAAT
62753632 GGGAGGAGGGCACGGTGGAAGAG
1 GGGAGGAGGGCACGGTGGAAGAG
** *
62753655 GGGA-GATGGG-AATG-GGAA-AT
1 GGGAGGA-GGGCACGGTGGAAGAG
62753675 GGGAGGAGGGCACGGTGGAAGAG
1 GGGAGGAGGGCACGGTGGAAGAG
62753698 GGGAG
1 GGGAG
62753703 ATGGGAATGG
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
20 8 0.22
21 8 0.22
22 8 0.22
23 13 0.35
ACGTcount: A:0.28, C:0.06, G:0.59, T:0.07
Consensus pattern (23 bp):
GGGAGGAGGGCACGGTGGAAGAG
Found at i:62753664 original size:43 final size:43
Alignment explanation
Indices: 62753617--62753737 Score: 233
Period size: 43 Copynumber: 2.8 Consensus size: 43
62753607 TGGGTATTGC
62753617 ATGGGAATGGGAAATGGGAGGAGGGCACGGTGGAAGAGGGGAG
1 ATGGGAATGGGAAATGGGAGGAGGGCACGGTGGAAGAGGGGAG
62753660 ATGGGAATGGGAAATGGGAGGAGGGCACGGTGGAAGAGGGGAG
1 ATGGGAATGGGAAATGGGAGGAGGGCACGGTGGAAGAGGGGAG
*
62753703 ATGGGAATGGGAAATGGGAGGACGGCACGGTGGAA
1 ATGGGAATGGGAAATGGGAGGAGGGCACGGTGGAA
62753738 TGGGAAATTG
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
43 77 1.00
ACGTcount: A:0.31, C:0.06, G:0.54, T:0.10
Consensus pattern (43 bp):
ATGGGAATGGGAAATGGGAGGAGGGCACGGTGGAAGAGGGGAG
Found at i:62753911 original size:31 final size:30
Alignment explanation
Indices: 62753851--62754075 Score: 293
Period size: 29 Copynumber: 7.6 Consensus size: 30
62753841 TGTATTTAAA
* **
62753851 ATTTTAAAAATTAAAAAATACGTGTAGTGT
1 ATTTTAAAAATAAAAAAATATATGTAGTGT
62753881 ATTTTAAAAATAAAAAATATATATGTAGTGT
1 ATTTTAAAAATAAAAAA-ATATATGTAGTGT
* *
62753912 ATTTTAAAAAT-AAAAAATATATGTACTAT
1 ATTTTAAAAATAAAAAAATATATGTAGTGT
62753941 ATTTTAAAAATAAAAAATATATATGTAGTGT
1 ATTTTAAAAATAAAAAA-ATATATGTAGTGT
*
62753972 ATTTT-AAAAT----ATATATATGTAGTGT
1 ATTTTAAAAATAAAAAAATATATGTAGTGT
*
62753997 ATTTTAAAAGTAAAAAAAAATATATGTAGTGT
1 ATTTTAAAA--ATAAAAAAATATATGTAGTGT
*
62754029 ATTTTAAAAGT-AAAAAATATATGTAGTGT
1 ATTTTAAAAATAAAAAAATATATGTAGTGT
62754058 ATTTTAAAAATAAAAAAA
1 ATTTTAAAAATAAAAAAA
62754076 AAATATAAAG
Statistics
Matches: 171, Mismatches: 13, Indels: 22
0.83 0.06 0.11
Matches are distributed among these distances:
25 18 0.11
26 4 0.02
28 1 0.01
29 50 0.29
30 37 0.22
31 38 0.22
32 23 0.13
ACGTcount: A:0.52, C:0.01, G:0.10, T:0.38
Consensus pattern (30 bp):
ATTTTAAAAATAAAAAAATATATGTAGTGT
Found at i:62753946 original size:60 final size:60
Alignment explanation
Indices: 62753851--62754074 Score: 330
Period size: 60 Copynumber: 3.8 Consensus size: 60
62753841 TGTATTTAAA
**
62753851 ATTTTAAAAATTAAAAAATACGTGTAGTGTATTTTAAAAATAAAAAATATATATGTAGTGT
1 ATTTTAAAAA-TAAAAAATATATGTAGTGTATTTTAAAAATAAAAAATATATATGTAGTGT
* *
62753912 ATTTTAAAAATAAAAAATATATGTACTATATTTTAAAAATAAAAAATATATATGTAGTGT
1 ATTTTAAAAATAAAAAATATATGTAGTGTATTTTAAAAATAAAAAATATATATGTAGTGT
* * *
62753972 ATTTT-AAAAT---ATATATATGTAGTGTATTTTAAAAGTAAAAAAAAATATATGTAGTGT
1 ATTTTAAAAATAAAAAATATATGTAGTGTATTTTAAAAAT-AAAAAATATATATGTAGTGT
*
62754029 ATTTTAAAAGTAAAAAATATATGTAGTGTATTTTAAAAATAAAAAA
1 ATTTTAAAAATAAAAAATATATGTAGTGTATTTTAAAAATAAAAAA
62754075 AAAATATAAA
Statistics
Matches: 146, Mismatches: 12, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
56 22 0.15
57 24 0.16
58 4 0.03
59 5 0.03
60 57 0.39
61 34 0.23
ACGTcount: A:0.51, C:0.01, G:0.10, T:0.38
Consensus pattern (60 bp):
ATTTTAAAAATAAAAAATATATGTAGTGTATTTTAAAAATAAAAAATATATATGTAGTGT
Found at i:62753981 original size:23 final size:24
Alignment explanation
Indices: 62753953--62754005 Score: 97
Period size: 25 Copynumber: 2.2 Consensus size: 24
62753943 TTTAAAAATA
62753953 AAAAATATATATGTAGTGTATTTT
1 AAAAATATATATGTAGTGTATTTT
62753977 AAAATATATATATGTAGTGTATTTT
1 AAAA-ATATATATGTAGTGTATTTT
62754002 AAAA
1 AAAA
62754006 GTAAAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 4 0.14
25 24 0.86
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.43
Consensus pattern (24 bp):
AAAAATATATATGTAGTGTATTTT
Found at i:62757954 original size:21 final size:21
Alignment explanation
Indices: 62757930--62757982 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
62757920 CATTATTTCT
* *
62757930 AATCTCACCGCTATAGTACCC
1 AATCTCACCGCTACAGTAACC
*
62757951 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
62757972 AATCTCACCGC
1 AATCTCACCGC
62757983 CACCGCTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.38, G:0.09, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:62758504 original size:21 final size:21
Alignment explanation
Indices: 62758478--62758526 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
62758468 GTCATAGTCT
*
62758478 AACGACTGAATTTAATTTCCC
1 AACGACCGAATTTAATTTCCC
62758499 AACGACCGAATTTAATTTCCC
1 AACGACCGAATTTAATTTCCC
62758520 AACGACC
1 AACGACC
62758527 CTTATCCTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.29, G:0.10, T:0.27
Consensus pattern (21 bp):
AACGACCGAATTTAATTTCCC
Found at i:62766418 original size:42 final size:39
Alignment explanation
Indices: 62766342--62766416 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
62766332 TTATATATGA
*
62766342 AAAATAATTATTAGAAATAAAGAAATGAATAAAAAACTT
1 AAAAGAATTATTAGAAATAAAGAAATGAATAAAAAACTT
**
62766381 AAAAGAATTATTATTAATAAAGAAATGAATAAAAAA
1 AAAAGAATTATTAGAAATAAAGAAATGAATAAAAAA
62766417 AACTTTCTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.65, C:0.01, G:0.08, T:0.25
Consensus pattern (39 bp):
AAAAGAATTATTAGAAATAAAGAAATGAATAAAAAACTT
Found at i:62769238 original size:12 final size:13
Alignment explanation
Indices: 62769223--62769251 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
62769213 TTAAATTTTA
62769223 TTAGGATTATT-T
1 TTAGGATTATTAT
62769235 TTAGGATTATTAT
1 TTAGGATTATTAT
62769248 TTAG
1 TTAG
62769252 ATTTAATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.55
Consensus pattern (13 bp):
TTAGGATTATTAT
Found at i:62770580 original size:115 final size:115
Alignment explanation
Indices: 62770378--62770604 Score: 391
Period size: 115 Copynumber: 2.0 Consensus size: 115
62770368 AAAAAAACAG
**
62770378 TCAGAGGTGGTAGGGACTCAGAGTAACCCATTGCCAGAAATAGAAGCAGGCAACGAAGTTGAGTC
1 TCAGAGGTGGTAGGGACTCAGAGTAACCCATCACCAGAAATAGAAGCAGGCAACGAAGTTGAGTC
*
62770443 TAGGGTTAATGAAAACCCTACTCAAAAACTAGAAAACGAAAGAGTAGGAC
66 TAGGGTTAATGAAAACCCTACTCAAAAACTAAAAAACGAAAGAGTAGGAC
* *
62770493 TCAGAGGTGGTAGGGACTCAGAGTAACCCATCACCGGAAATAGAAGCAGGCGACGAAGTTGAGTC
1 TCAGAGGTGGTAGGGACTCAGAGTAACCCATCACCAGAAATAGAAGCAGGCAACGAAGTTGAGTC
* *
62770558 TAGGGTTAATGAAAACCCTACTCAAACACTAAAAAACGAAAGTGTAG
66 TAGGGTTAATGAAAACCCTACTCAAAAACTAAAAAACGAAAGAGTAG
62770605 AAGTCAATCC
Statistics
Matches: 105, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
115 105 1.00
ACGTcount: A:0.39, C:0.18, G:0.26, T:0.17
Consensus pattern (115 bp):
TCAGAGGTGGTAGGGACTCAGAGTAACCCATCACCAGAAATAGAAGCAGGCAACGAAGTTGAGTC
TAGGGTTAATGAAAACCCTACTCAAAAACTAAAAAACGAAAGAGTAGGAC
Found at i:62771560 original size:46 final size:46
Alignment explanation
Indices: 62771456--62771795 Score: 614
Period size: 46 Copynumber: 7.5 Consensus size: 46
62771446 TACGTATGAT
* *
62771456 CACTTATCA-TTTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
62771499 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
62771545 CACTTATCTCTTTGTCACTTAATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
62771591 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
62771637 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
62771683 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
62771729 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
62771775 CACTTATCACTTTGTCACTTG
1 CACTTATCACTTTGTCACTTG
62771796 TCACTGATCA
Statistics
Matches: 287, Mismatches: 7, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
43 9 0.03
44 6 0.02
45 20 0.07
46 252 0.88
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:62774897 original size:26 final size:27
Alignment explanation
Indices: 62774863--62774926 Score: 112
Period size: 28 Copynumber: 2.4 Consensus size: 27
62774853 AATAAAAATA
62774863 ACCAAAATATTATAAA-TTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTATTT
62774889 ACCAAAATATTATAAATTTTTTTTATTT
1 ACCAAAATATTATAAA-TTTTTTTATTT
62774917 ACCAAAATAT
1 ACCAAAATAT
62774927 ACCAAAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 16 0.44
28 20 0.56
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (27 bp):
ACCAAAATATTATAAATTTTTTTATTT
Found at i:62775070 original size:37 final size:37
Alignment explanation
Indices: 62775020--62775106 Score: 165
Period size: 37 Copynumber: 2.4 Consensus size: 37
62775010 TCAGCCTGAT
*
62775020 AATAGAGTTATTAAATGAGAATAGTTTATTAAATTAA
1 AATAGAGTTATTAAATGAGAATAATTTATTAAATTAA
62775057 AATAGAGTTATTAAATGAGAATAATTTATTAAATTAA
1 AATAGAGTTATTAAATGAGAATAATTTATTAAATTAA
62775094 AATAGAGTTATTA
1 AATAGAGTTATTA
62775107 CTTAATTAGA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (37 bp):
AATAGAGTTATTAAATGAGAATAATTTATTAAATTAA
Found at i:62775111 original size:18 final size:19
Alignment explanation
Indices: 62775020--62775106 Score: 106
Period size: 18 Copynumber: 4.7 Consensus size: 19
62775010 TCAGCCTGAT
* *
62775020 AATAGAGTTATTAAATGAG
1 AATAGAGTTATTAAATTAA
*
62775039 AATAG-TTTATTAAATTAA
1 AATAGAGTTATTAAATTAA
* *
62775057 AATAGAGTTATTAAATGAG
1 AATAGAGTTATTAAATTAA
*
62775076 AATA-ATTTATTAAATTAA
1 AATAGAGTTATTAAATTAA
62775094 AATAGAGTTATTA
1 AATAGAGTTATTA
62775107 CTTAATTAGA
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
18 30 0.54
19 26 0.46
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (19 bp):
AATAGAGTTATTAAATTAA
Found at i:62775715 original size:27 final size:27
Alignment explanation
Indices: 62775674--62775725 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
62775664 CATTTTAGTC
62775674 CTTTGGCACCATTGGTGCCGCCAATCT
1 CTTTGGCACCATTGGTGCCGCCAATCT
*
62775701 CTTTGGCACCTTTGGTGCCGCCAAT
1 CTTTGGCACCATTGGTGCCGCCAAT
62775726 GTGATTGGCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.13, C:0.33, G:0.23, T:0.31
Consensus pattern (27 bp):
CTTTGGCACCATTGGTGCCGCCAATCT
Found at i:62775733 original size:27 final size:27
Alignment explanation
Indices: 62775676--62775734 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
62775666 TTTTAGTCCT
*
62775676 TTGGCACCATTGGTGCCGCCAATCTCT
1 TTGGCACCATTGGTGCCGCCAATCTCA
* * *
62775703 TTGGCACCTTTGGTGCCGCCAATGTGA
1 TTGGCACCATTGGTGCCGCCAATCTCA
62775730 TTGGC
1 TTGGC
62775735 CTGATCAGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.14, C:0.29, G:0.27, T:0.31
Consensus pattern (27 bp):
TTGGCACCATTGGTGCCGCCAATCTCA
Found at i:62775815 original size:27 final size:28
Alignment explanation
Indices: 62775785--62775849 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
62775775 TTTTTTTGGT
*
62775785 ATATTTTGGTAAAT-AAAAAAATTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
62775812 ATATTTTGGTAAATAAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
62775840 ATATTTTGGT
1 ATATTTTGGT
62775850 TTTTTATAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 14 0.39
28 22 0.61
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.42
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTATA
Found at i:62781569 original size:45 final size:45
Alignment explanation
Indices: 62781503--62781594 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
62781493 TCCATCACCA
62781503 CACCTCAACCTTTGACATCTTCACACTCACCTAACCTACCAAGTT
1 CACCTCAACCTTTGACATCTTCACACTCACCTAACCTACCAAGTT
*
62781548 CACCTCAACCTTTGACCTCTTCACACTCACCTAACCTACCAAGTT
1 CACCTCAACCTTTGACATCTTCACACTCACCTAACCTACCAAGTT
62781593 CA
1 CA
62781595 ACACAGGCAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.28, C:0.41, G:0.04, T:0.26
Consensus pattern (45 bp):
CACCTCAACCTTTGACATCTTCACACTCACCTAACCTACCAAGTT
Found at i:62792627 original size:25 final size:24
Alignment explanation
Indices: 62792598--62792645 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
62792588 ATCATGGGAA
62792598 AAATGTG-AAGACATTGAAATGTATT
1 AAATGTGAAAGA-ATTGAAA-GTATT
62792623 AAATGTGAAAGAATTGAAAGTAT
1 AAATGTGAAAGAATTGAAAGTAT
62792646 AATATATGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.18
25 14 0.64
26 4 0.18
ACGTcount: A:0.48, C:0.02, G:0.21, T:0.29
Consensus pattern (24 bp):
AAATGTGAAAGAATTGAAAGTATT
Found at i:62812378 original size:2 final size:2
Alignment explanation
Indices: 62812371--62812411 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
62812361 ACTATAGGAT
*
62812371 TG TG TG TG TG TG TG TG TG TG TG TG TG TA TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
62812412 ACTATAGAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.02, C:0.00, G:0.46, T:0.51
Consensus pattern (2 bp):
TG
Found at i:62823580 original size:30 final size:31
Alignment explanation
Indices: 62823537--62823595 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
62823527 TTAGGGCCGG
*
62823537 AATTAAATTTTAAATTTTTATAATTTTTAAAA
1 AATTAAA-TTTAAATTATTATAATTTTTAAAA
*
62823569 AATTAAA-TTAAATTATTATTATTTTTA
1 AATTAAATTTAAATTATTATAATTTTTA
62823596 TAAATGTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 18 0.72
32 7 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (31 bp):
AATTAAATTTAAATTATTATAATTTTTAAAA
Found at i:62828439 original size:20 final size:19
Alignment explanation
Indices: 62828416--62828454 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
62828406 TCTATATTAT
62828416 TATATTATTAATATTATTTA
1 TATATTATTAATA-TATTTA
62828436 TATATTATTAATATATTTA
1 TATATTATTAATATATTTA
62828455 ATTTATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TATATTATTAATATATTTA
Found at i:62828440 original size:11 final size:11
Alignment explanation
Indices: 62828416--62828465 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
62828406 TCTATATTAT
62828416 TATATTA-TTA
1 TATATTATTTA
62828426 -ATATTATTTA
1 TATATTATTTA
*
62828436 TATATTATTAA
1 TATATTATTTA
62828447 TATATTTAATTTA
1 TATA-TT-ATTTA
62828460 TATATT
1 TATATT
62828466 TAAATGATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 6 0.18
10 3 0.09
11 13 0.38
12 4 0.12
13 8 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATATTATTTA
Found at i:62828465 original size:13 final size:13
Alignment explanation
Indices: 62828431--62828468 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
62828421 TATTAATATT
62828431 ATTTATATA-TT-
1 ATTTATATATTTA
*
62828442 ATTAATATATTTA
1 ATTTATATATTTA
62828455 ATTTATATATTTA
1 ATTTATATATTTA
62828468 A
1 A
62828469 ATGATAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 8 0.35
12 2 0.09
13 13 0.57
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
ATTTATATATTTA
Found at i:62828480 original size:24 final size:24
Alignment explanation
Indices: 62828431--62828480 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
62828421 TATTAATATT
* **
62828431 ATTTATATATTATTAATATATTTA
1 ATTTATATATTATAAATATAAATA
62828455 ATTTATATATT-TAAATGATAAATA
1 ATTTATATATTATAAAT-ATAAATA
62828479 AT
1 AT
62828481 AAAATAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
ATTTATATATTATAAATATAAATA
Found at i:62828492 original size:15 final size:15
Alignment explanation
Indices: 62828474--62828506 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
62828464 TTTAAATGAT
62828474 AAATAATAAAATAAA
1 AAATAATAAAATAAA
62828489 AAATAATAAAATAAA
1 AAATAATAAAATAAA
62828504 AAA
1 AAA
62828507 CTAAATCCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (15 bp):
AAATAATAAAATAAA
Found at i:62828883 original size:10 final size:10
Alignment explanation
Indices: 62828868--62828901 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
62828858 GGCCCTTGCC
62828868 CTGCCCTGCA
1 CTGCCCTGCA
62828878 CTGCCCTGCA
1 CTGCCCTGCA
* *
62828888 CTGCACAGCA
1 CTGCCCTGCA
62828898 CTGC
1 CTGC
62828902 GTGACGGGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.15, C:0.47, G:0.21, T:0.18
Consensus pattern (10 bp):
CTGCCCTGCA
Found at i:62828884 original size:15 final size:15
Alignment explanation
Indices: 62828864--62828893 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
62828854 GGCGGGCCCT
*
62828864 TGCCCTGCCCTGCAC
1 TGCCCTGCACTGCAC
62828879 TGCCCTGCACTGCAC
1 TGCCCTGCACTGCAC
62828894 AGCACTGCGT
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:0.10, C:0.50, G:0.20, T:0.20
Consensus pattern (15 bp):
TGCCCTGCACTGCAC
Found at i:62830901 original size:22 final size:22
Alignment explanation
Indices: 62830873--62830934 Score: 99
Period size: 22 Copynumber: 2.8 Consensus size: 22
62830863 CCTTTGTTGG
62830873 CCACCCACCTTAGCCACCAACT
1 CCACCCACCTTAGCCACCAACT
62830895 CCACCCACCTTAGCCACCAACT
1 CCACCCACCTTAGCCACCAACT
*
62830917 CCA-CCACCCTTGGCCACC
1 CCACCCA-CCTTAGCCACC
62830935 TAAACCACCC
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
21 3 0.08
22 35 0.92
ACGTcount: A:0.24, C:0.56, G:0.06, T:0.13
Consensus pattern (22 bp):
CCACCCACCTTAGCCACCAACT
Found at i:62831043 original size:23 final size:21
Alignment explanation
Indices: 62831017--62831064 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
62831007 GTTTTTGGTT
62831017 TTTTGGAGAAGGATTGTTCTTTG
1 TTTTGGAGAAGG-TT-TTCTTTG
* *
62831040 TTTTGGAGGAGGTTTTTTTTG
1 TTTTGGAGAAGGTTTTCTTTG
62831061 TTTT
1 TTTT
62831065 TCGGAGGTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 10 0.43
22 2 0.09
23 11 0.48
ACGTcount: A:0.12, C:0.02, G:0.29, T:0.56
Consensus pattern (21 bp):
TTTTGGAGAAGGTTTTCTTTG
Found at i:62831062 original size:21 final size:21
Alignment explanation
Indices: 62831017--62831082 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
62831007 GTTTTTGGTT
* *
62831017 TTTTGGAGAAGGATTGTTCTTTG
1 TTTTGGAGGAGG-TT-TTTTTTG
62831040 TTTTGGAGGAGGTTTTTTTTG
1 TTTTGGAGGAGGTTTTTTTTG
**
62831061 TTTT-TCGGAGGTGTTTTTTTG
1 TTTTGGAGGAGGT-TTTTTTTG
62831082 T
1 T
62831083 AAAAAAGGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.16
21 19 0.50
22 2 0.05
23 11 0.29
ACGTcount: A:0.11, C:0.03, G:0.30, T:0.56
Consensus pattern (21 bp):
TTTTGGAGGAGGTTTTTTTTG
Found at i:62831424 original size:3 final size:3
Alignment explanation
Indices: 62831410--62831494 Score: 56
Period size: 3 Copynumber: 28.3 Consensus size: 3
62831400 GAGCTTTGTT
*
62831410 TTA TTA TT- TTA TTA TT- TTAA CTA TTA TT- TATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA T-TA TTA TTA TTA TTA
*
62831454 TT- TCTCA TGTA TATA TTA TTT TTA -TA TTA TTA TTA -TA TTA T
1 TTA T-T-A T-TA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
62831495 ATATGCCCTC
Statistics
Matches: 66, Mismatches: 6, Indels: 20
0.72 0.07 0.22
Matches are distributed among these distances:
2 10 0.15
3 47 0.71
4 7 0.11
5 2 0.03
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Done.