Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 39 of 344
Found at i:13042000 original size:31 final size:31
Alignment explanation
Indices: 13041962--13042023 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
13041952 ATTAACAGTA
13041962 AGCGGTACTCTTGTTATAGCAATCAAACATT
1 AGCGGTACTCTTGTTATAGCAATCAAACATT
13041993 AGCGGTACTCTTGTTATAGCAATCAAACATT
1 AGCGGTACTCTTGTTATAGCAATCAAACATT
13042024 GACAATAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (31 bp):
AGCGGTACTCTTGTTATAGCAATCAAACATT
Found at i:13042483 original size:12 final size:12
Alignment explanation
Indices: 13042466--13042490 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13042456 AATCAAGTTC
13042466 TATATATATATT
1 TATATATATATT
13042478 TATATATATATT
1 TATATATATATT
13042490 T
1 T
13042491 TTAAATGTCA
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:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATATATATATT
Found at i:13048293 original size:18 final size:18
Alignment explanation
Indices: 13048270--13048305 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
13048260 AATTTCAATG
13048270 GAAATTGATTTTTAGGAC
1 GAAATTGATTTTTAGGAC
13048288 GAAATTGATTTTTAGGAC
1 GAAATTGATTTTTAGGAC
13048306 CTAATTGTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.22, T:0.39
Consensus pattern (18 bp):
GAAATTGATTTTTAGGAC
Found at i:13048311 original size:18 final size:18
Alignment explanation
Indices: 13048271--13048312 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
13048261 ATTTCAATGG
*
13048271 AAATTGATTTTTAGGACG
1 AAATTGATTTTTAGGACC
13048289 AAATTGATTTTTAGGACC
1 AAATTGATTTTTAGGACC
*
13048307 TAATTG
1 AAATTG
13048313 TGAAAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.40
Consensus pattern (18 bp):
AAATTGATTTTTAGGACC
Found at i:13066554 original size:36 final size:36
Alignment explanation
Indices: 13066514--13066586 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
13066504 AGTATATACG
*
13066514 TATTGTATTTTATATTGCGAACAGATAGTTTGCGTT
1 TATTGTATTTTATATTGCCAACAGATAGTTTGCGTT
*
13066550 TATTGTATTTTATATTGCCAACGGATAGTTTGCGTT
1 TATTGTATTTTATATTGCCAACAGATAGTTTGCGTT
13066586 T
1 T
13066587 CTTGCATTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.23, C:0.10, G:0.19, T:0.48
Consensus pattern (36 bp):
TATTGTATTTTATATTGCCAACAGATAGTTTGCGTT
Found at i:13066601 original size:36 final size:36
Alignment explanation
Indices: 13066525--13066601 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
13066515 ATTGTATTTT
* * **
13066525 ATATTGCGAACAGATAGTTTGCGTTTATTGTATTTT
1 ATATTGCCAACAGATAGTTTGCGTTTATTGCATTCC
* *
13066561 ATATTGCCAACGGATAGTTTGCGTTTCTTGCATTCC
1 ATATTGCCAACAGATAGTTTGCGTTTATTGCATTCC
13066597 ATATT
1 ATATT
13066602 ACCACCAATG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.44
Consensus pattern (36 bp):
ATATTGCCAACAGATAGTTTGCGTTTATTGCATTCC
Found at i:13073517 original size:12 final size:13
Alignment explanation
Indices: 13073475--13073520 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 13
13073465 TATTTTTAAA
13073475 AAATATATAATACAT
1 AAATAT-TAATA-AT
*
13073490 AAATAATAATAA-
1 AAATATTAATAAT
13073502 AAATATTAA-AAT
1 AAATATTAATAAT
13073514 AAATATT
1 AAATATT
13073521 TTCTATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 2 0.07
12 15 0.54
13 1 0.04
14 5 0.18
15 5 0.18
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (13 bp):
AAATATTAATAAT
Found at i:13073671 original size:14 final size:14
Alignment explanation
Indices: 13073652--13073679 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
13073642 TACAATATTC
13073652 AAATAATAACAATA
1 AAATAATAACAATA
13073666 AAATAATAACAATA
1 AAATAATAACAATA
13073680 TAATGGTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAATAACAATA
Found at i:13076092 original size:16 final size:16
Alignment explanation
Indices: 13076066--13076135 Score: 95
Period size: 16 Copynumber: 4.4 Consensus size: 16
13076056 TTTGGTTCAT
* *
13076066 TGTAATGGAATAGGGC
1 TGTAATTGAATAGAGC
* *
13076082 TATAATTGAATAAAGC
1 TGTAATTGAATAGAGC
13076098 TGTAATTGAATAGAGC
1 TGTAATTGAATAGAGC
*
13076114 TGTAATTGAATAGAGT
1 TGTAATTGAATAGAGC
13076130 TGTAAT
1 TGTAAT
13076136 CAGTAATTCA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.33
Consensus pattern (16 bp):
TGTAATTGAATAGAGC
Found at i:13076401 original size:17 final size:17
Alignment explanation
Indices: 13076376--13076408 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
13076366 AATTATCATT
13076376 AAATATAATTTAATAAA
1 AAATATAATTTAATAAA
*
13076393 AAATTTAATTTAATAA
1 AAATATAATTTAATAA
13076409 CATTCTTAAT
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATATAATTTAATAAA
Found at i:13076879 original size:43 final size:43
Alignment explanation
Indices: 13076818--13076902 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
13076808 TACAAATACA
13076818 TAAGGCAACCAATTTGATGCCTTTTCCAACTTGATACCCAACC
1 TAAGGCAACCAATTTGATGCCTTTTCCAACTTGATACCCAACC
* *
13076861 TAAGGCAACCAATTTGATGTCTTTTCTAACTTGATACCCAAC
1 TAAGGCAACCAATTTGATGCCTTTTCCAACTTGATACCCAAC
13076903 TAATTCCTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.31
Consensus pattern (43 bp):
TAAGGCAACCAATTTGATGCCTTTTCCAACTTGATACCCAACC
Found at i:13081354 original size:68 final size:70
Alignment explanation
Indices: 13081235--13081393 Score: 214
Period size: 68 Copynumber: 2.3 Consensus size: 70
13081225 GGATAGAAGC
* *
13081235 ATGAAAAAGAGAGAGATGGTTGGAAGGAAATAGGAAGAAGAATGAAAAAAAGAAGATGATTCAGA
1 ATGAAAAAGAG-GAGAAGGTTCGAAGGAAATAGG-AGAAGAATGAAAAAAAGAAGATGATTCAGA
13081300 CGTGACA
64 CGTGACA
* * *
13081307 ATGAAAAAGAGGAGAAGTTTCGAAGGAAAT-GG-GAAGAATGAAAAAAAGAAGTTGCTTCAGACG
1 ATGAAAAAGAGGAGAAGGTTCGAAGGAAATAGGAGAAGAATGAAAAAAAGAAGATGATTCAGACG
*
13081370 TGAGA
66 TGACA
*
13081375 ACGAAAAAGAGGGAGAAGG
1 ATGAAAAAGA-GGAGAAGG
13081394 GTAAAGTTGA
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
68 42 0.54
69 7 0.09
70 2 0.03
71 16 0.21
72 11 0.14
ACGTcount: A:0.50, C:0.05, G:0.32, T:0.13
Consensus pattern (70 bp):
ATGAAAAAGAGGAGAAGGTTCGAAGGAAATAGGAGAAGAATGAAAAAAAGAAGATGATTCAGACG
TGACA
Found at i:13083482 original size:17 final size:18
Alignment explanation
Indices: 13083462--13083495 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
13083452 AAGTGAATTG
13083462 AAATTGC-GAAATTAAAT
1 AAATTGCAGAAATTAAAT
13083479 AAATTGCAGAAATTAAA
1 AAATTGCAGAAATTAAA
13083496 AAAAAGAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (18 bp):
AAATTGCAGAAATTAAAT
Found at i:13084050 original size:37 final size:37
Alignment explanation
Indices: 13083989--13084218 Score: 320
Period size: 37 Copynumber: 6.0 Consensus size: 37
13083979 TACGTATGAT
*
13083989 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
* *
13084024 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
*
13084061 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
13084098 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
13084135 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T--AGC
*
13084178 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGC
1 ---CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
13084218 C
1 C
13084219 GAAGCTATCA
Statistics
Matches: 178, Mismatches: 6, Indels: 20
0.87 0.03 0.10
Matches are distributed among these distances:
35 9 0.05
36 4 0.02
37 122 0.69
39 2 0.01
40 4 0.02
41 1 0.01
42 1 0.01
43 3 0.02
44 2 0.01
46 30 0.17
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
Found at i:13084188 original size:46 final size:46
Alignment explanation
Indices: 13084135--13084403 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
13084125 TAAGTGTAGC
* **
13084135 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
13084181 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
13084227 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
13084279 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
13084325 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
13084377 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
13084404 AGTACTCAAA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
46 112 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:13084254 original size:52 final size:52
Alignment explanation
Indices: 13084178--13084397 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
13084168 TAGCTAAAGC
* *
13084178 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
13084231 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
13084283 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
13084329 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
13084381 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
13084398 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:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:13084300 original size:98 final size:98
Alignment explanation
Indices: 13084135--13084403 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
13084125 TAAGTGTAGC
* * *
13084135 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
13084200 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
13084234 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
13084299 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
13084332 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
13084397 GATCAGA
66 GATCAGA
13084404 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 151 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:13087667 original size:57 final size:58
Alignment explanation
Indices: 13087588--13087705 Score: 213
Period size: 57 Copynumber: 2.1 Consensus size: 58
13087578 GCTACACGAA
13087588 ACACATATCACTACCGATGCCATAGCCCAGCTATGGTC-TACACGGAATCACAT-ATC
1 ACACATATCACTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATC
13087644 ACACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATC
1 ACACATATCAC-TACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATC
13087703 ACA
1 ACA
13087706 TGTTCACATG
Statistics
Matches: 59, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
56 11 0.19
57 27 0.46
58 15 0.25
59 6 0.10
ACGTcount: A:0.33, C:0.31, G:0.14, T:0.22
Consensus pattern (58 bp):
ACACATATCACTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATC
Found at i:13090731 original size:7 final size:7
Alignment explanation
Indices: 13090719--13090752 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
13090709 TTAATATCTA
13090719 AAATAAT
1 AAATAAT
13090726 AAATAAT
1 AAATAAT
13090733 AAAATAAT
1 -AAATAAT
13090741 AAA-AAT
1 AAATAAT
13090747 AAATAA
1 AAATAA
13090753 ACTAAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.24
7 12 0.48
8 7 0.28
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAATAAT
Found at i:13090749 original size:14 final size:14
Alignment explanation
Indices: 13090717--13090775 Score: 59
Period size: 15 Copynumber: 4.1 Consensus size: 14
13090707 TATTAATATC
13090717 TAAAATAATAAATAA
1 TAAAATAATAAA-AA
13090732 TAAAATAATAAAAA
1 TAAAATAATAAAAA
13090746 T-AAATAA-ACTAAAA
1 TAAAATAATA--AAAA
*
13090760 TAAAAAAAATAAAAA
1 T-AAAATAATAAAAA
13090775 T
1 T
13090776 TGGGTTGCCT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
12 1 0.03
13 6 0.16
14 8 0.21
15 17 0.45
16 5 0.13
17 1 0.03
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAAATAATAAAAA
Found at i:13090751 original size:10 final size:10
Alignment explanation
Indices: 13090719--13090775 Score: 52
Period size: 9 Copynumber: 6.0 Consensus size: 10
13090709 TTAATATCTA
13090719 AAATAATAAAT
1 AAATAA-AAAT
13090730 -AAT-AAAAT
1 AAATAAAAAT
13090738 -AATAAAAAT
1 AAATAAAAAT
*
13090747 AAAT-AAACT
1 AAATAAAAAT
13090756 AAAATAAAAA-
1 -AAATAAAAAT
13090766 AAATAAAAAT
1 AAATAAAAAT
13090776 TGGGTTGCCT
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
8 7 0.18
9 19 0.49
10 10 0.26
11 3 0.08
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:13090758 original size:23 final size:21
Alignment explanation
Indices: 13090718--13090772 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 21
13090708 ATTAATATCT
*
13090718 AAAATAATAAATAATAAAATA
1 AAAAAAATAAATAATAAAATA
*
13090739 ATAAAAATAAATAAACTAAAATA
1 AAAAAAATAAAT-AA-TAAAATA
13090762 AAAAAAATAAA
1 AAAAAAATAAA
13090773 AATTGGGTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 10 0.34
22 2 0.07
23 17 0.59
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (21 bp):
AAAAAAATAAATAATAAAATA
Found at i:13093491 original size:12 final size:12
Alignment explanation
Indices: 13093474--13093502 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
13093464 TTCCCTGTAA
13093474 AATAGTAAAAAT
1 AATAGTAAAAAT
13093486 AATAGTAAAAAT
1 AATAGTAAAAAT
13093498 AATAG
1 AATAG
13093503 GGGAAGTAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (12 bp):
AATAGTAAAAAT
Found at i:13094939 original size:19 final size:18
Alignment explanation
Indices: 13094900--13094952 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
13094890 AAAGTTATTG
*
13094900 AATAAAAAAAGATAAAAT
1 AATAAATAAAGATAAAAT
13094918 AATAAATAAA-ATAATAAGT
1 AATAAATAAAGATAA-AA-T
*
13094937 AATTAATAAAGGATAA
1 AATAAATAAA-GATAA
13094953 TTATTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 4 0.14
18 11 0.38
19 10 0.34
21 4 0.14
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.23
Consensus pattern (18 bp):
AATAAATAAAGATAAAAT
Found at i:13116611 original size:11 final size:11
Alignment explanation
Indices: 13116595--13116625 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
13116585 CTTTTCTTTT
13116595 ATATTTTTTAA
1 ATATTTTTTAA
13116606 ATA-TTTTTAA
1 ATATTTTTTAA
13116616 ATATTTTTTA
1 ATATTTTTTA
13116626 TTTTTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATATTTTTTAA
Found at i:13119549 original size:14 final size:14
Alignment explanation
Indices: 13119530--13119562 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
13119520 ATAAGATTAA
13119530 AGCACGTTACTTTT
1 AGCACGTTACTTTT
13119544 AGCACGTTACTTTT
1 AGCACGTTACTTTT
13119558 AGCAC
1 AGCAC
13119563 TAACCAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.36
Consensus pattern (14 bp):
AGCACGTTACTTTT
Found at i:13123891 original size:30 final size:31
Alignment explanation
Indices: 13123842--13123905 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
13123832 ACTTATTTTA
13123842 TTGTTAATTTTTATTATTATTTTA-AAGACAT
1 TTGTTAATTTTTATTATTATTTTAGAA-ACAT
*
13123873 TTGTTAA-TTTTGTTATTATTTTAGAAACAT
1 TTGTTAATTTTTATTATTATTTTAGAAACAT
13123903 TTG
1 TTG
13123906 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
30 22 0.71
31 9 0.29
ACGTcount: A:0.30, C:0.03, G:0.09, T:0.58
Consensus pattern (31 bp):
TTGTTAATTTTTATTATTATTTTAGAAACAT
Found at i:13124056 original size:12 final size:12
Alignment explanation
Indices: 13124026--13124059 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
13124016 TATATATTTT
13124026 AAAATT-ATATA
1 AAAATTAATATA
13124037 AAAA-TAATATA
1 AAAATTAATATA
13124048 AAAATTAATATA
1 AAAATTAATATA
13124060 GGTGGGCCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 13 0.62
12 7 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:13132233 original size:17 final size:18
Alignment explanation
Indices: 13132211--13132246 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
13132201 TTTAGAATAG
13132211 TTATAAAAA-AAATTATA
1 TTATAAAAATAAATTATA
*
13132228 TTATAAAAATAATTTATA
1 TTATAAAAATAAATTATA
13132246 T
1 T
13132247 ATTTTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TTATAAAAATAAATTATA
Found at i:13133755 original size:14 final size:15
Alignment explanation
Indices: 13133736--13133764 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
13133726 TAAGTTAAAA
13133736 ATAATATA-AATATT
1 ATAATATATAATATT
13133750 ATAATATATAATATT
1 ATAATATATAATATT
13133765 TATGGGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATATATAATATT
Found at i:13134066 original size:17 final size:16
Alignment explanation
Indices: 13134046--13134094 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
13134036 TAGGATTTAA
13134046 ATAATATAAATTTTGTT
1 ATAATATAAATTTT-TT
* **
13134063 ATAATTTTTATTTTTT
1 ATAATATAAATTTTTT
13134079 ATAATATAATATTTTT
1 ATAATATAA-ATTTTT
13134095 GCTATAACCA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
16 8 0.32
17 17 0.68
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (16 bp):
ATAATATAAATTTTTT
Found at i:13134632 original size:29 final size:27
Alignment explanation
Indices: 13134570--13134638 Score: 68
Period size: 29 Copynumber: 2.5 Consensus size: 27
13134560 GTGGCATGTG
13134570 GTAAAAAAATT-TTAAATAAATAAAAA
1 GTAAAAAAATTATTAAATAAATAAAAA
* ** *
13134596 TTTTAAAAATTATTAAATTTTAATAAAAA
1 GTAAAAAAATTATTAAA--TAAATAAAAA
*
13134625 GTAAAAAAAATATT
1 GTAAAAAAATTATT
13134639 TTAAATTTAT
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
26 8 0.25
27 5 0.16
29 19 0.59
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (27 bp):
GTAAAAAAATTATTAAATAAATAAAAA
Found at i:13134721 original size:20 final size:21
Alignment explanation
Indices: 13134696--13134737 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
13134686 TTGTGAAATT
13134696 TTATAAAGAT-CAT-AAAAAAA
1 TTATAAA-ATGCATCAAAAAAA
13134716 TTATAAAATGCATCAAAAAAA
1 TTATAAAATGCATCAAAAAAA
13134737 T
1 T
13134738 CATTTAACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 2 0.10
20 10 0.50
21 8 0.40
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.26
Consensus pattern (21 bp):
TTATAAAATGCATCAAAAAAA
Found at i:13134952 original size:19 final size:19
Alignment explanation
Indices: 13134928--13134964 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
13134918 ATATTTTCTT
13134928 TTTACAAATTTTATAATTC
1 TTTACAAATTTTATAATTC
**
13134947 TTTACATTTTTTATAATT
1 TTTACAAATTTTATAATT
13134965 TGCTTATGAC
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:0.32, C:0.08, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTACAAATTTTATAATTC
Found at i:13135070 original size:20 final size:19
Alignment explanation
Indices: 13135047--13135084 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
13135037 TAAAAAAATT
13135047 TAATTTTTAATAATTTTTAA
1 TAATTTTT-ATAATTTTTAA
*
13135067 TAATTTTTATATTTTTTA
1 TAATTTTTATAATTTTTA
13135085 TTGATTATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TAATTTTTATAATTTTTAA
Found at i:13135073 original size:9 final size:10
Alignment explanation
Indices: 13135047--13135084 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
13135037 TAAAAAAATT
13135047 TAATTTTTAA
1 TAATTTTTAA
13135057 TAATTTTTAA
1 TAATTTTTAA
13135067 TAATTTTT-A
1 TAATTTTTAA
*
13135076 TATTTTTTA
1 TAATTTTTA
13135085 TTGATTATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TAATTTTTAA
Found at i:13137104 original size:28 final size:28
Alignment explanation
Indices: 13137073--13137134 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
13137063 AACGACCATG
* *
13137073 TTATAACAGTTAAATTTCAATAATCATA
1 TTATAACAGTCAAATTCCAATAATCATA
* * * *
13137101 TTATAACGGTCATATTCCAATGATGATA
1 TTATAACAGTCAAATTCCAATAATCATA
13137129 TTATAA
1 TTATAA
13137135 TGGTTAAAAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (28 bp):
TTATAACAGTCAAATTCCAATAATCATA
Found at i:13138768 original size:15 final size:16
Alignment explanation
Indices: 13138750--13138782 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
13138740 TTTTATTACT
*
13138750 TTGCCATTT-ATTTTA
1 TTGCAATTTAATTTTA
13138765 TTGCAATTTAATTTTA
1 TTGCAATTTAATTTTA
13138781 TT
1 TT
13138783 TTAATTTTGT
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:0.24, C:0.09, G:0.06, T:0.61
Consensus pattern (16 bp):
TTGCAATTTAATTTTA
Found at i:13147015 original size:46 final size:44
Alignment explanation
Indices: 13146962--13147137 Score: 183
Period size: 46 Copynumber: 3.8 Consensus size: 44
13146952 TATTTGGGCA
*
13146962 TCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAA-G
*** * *
13147008 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GGAAG
* *
13147055 TCCGACCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGTGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAA-G
* *
13147101 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
13147138 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 66 0.62
47 31 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (44 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAAG
Found at i:13147117 original size:93 final size:93
Alignment explanation
Indices: 13146958--13147129 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
13146948 AGGATATTTG
* *
13146958 GGCATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
13147023 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * * * *
13147051 GGCATCCGACCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGTGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
13147116 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
13147130 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:13150098 original size:15 final size:15
Alignment explanation
Indices: 13150078--13150146 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
13150068 GTATCTTGGG
13150078 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
13150093 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
13150108 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
13150123 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
13150138 TTTCTTTAT
1 TTTCTTTAT
13150147 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:13150147 original size:30 final size:30
Alignment explanation
Indices: 13150069--13150156 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
13150059 CATAATATCG
* * * *
13150069 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
13150099 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
13150129 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
13150157 TATTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:13152594 original size:46 final size:46
Alignment explanation
Indices: 13152541--13152716 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
13152531 TATTTGGGCA
*
13152541 TCCGAACTCGTAGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *** * *
13152587 TCCGAACTCGTTGAGTTGAGTCTGAGTTCGAGAGATGTAACTAG-GCAT-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAATG
*
13152635 T-CGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
13152680 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
13152717 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
45 1 0.01
46 66 0.61
47 29 0.27
48 2 0.02
49 4 0.04
50 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:13152696 original size:93 final size:93
Alignment explanation
Indices: 13152537--13152708 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
13152527 AGGATATTTG
*
13152537 GGCATCCGAACTCGTAGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTAGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAG
*
13152602 TTGAGTCTGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * * *
13152630 GGCATTCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTAGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAG
13152695 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
13152709 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTAGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:13156363 original size:47 final size:47
Alignment explanation
Indices: 13156242--13156452 Score: 269
Period size: 47 Copynumber: 4.7 Consensus size: 47
13156232 CGGAATAAAA
* * * *
13156242 AACGTGGTGCTAAGTAGATATACCACGATTACACATATTGATACATGT
1 AACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCAT-T
*
13156290 AACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATT
1 AACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCATT
* *
13156337 AACGTGGTGCTAAGTGAATATACCACGGTTA-A-ACA-TG------T
1 AACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCATT
*
13156375 AACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATT
1 AACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCATT
*
13156422 AACGTGGTGCTAAGTGGATATACCATGGTTA
1 AACGTGGTGCTAAGTGGATATACCACGGTTA
13156453 AACATGTAAC
Statistics
Matches: 141, Mismatches: 13, Indels: 19
0.82 0.08 0.11
Matches are distributed among these distances:
38 30 0.21
39 1 0.01
40 2 0.01
41 2 0.01
44 2 0.01
45 2 0.01
46 1 0.01
47 60 0.43
48 41 0.29
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (47 bp):
AACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCATT
Found at i:13156387 original size:38 final size:38
Alignment explanation
Indices: 13156336--13156497 Score: 162
Period size: 38 Copynumber: 4.0 Consensus size: 38
13156326 ATTGATTCAT
*
13156336 TAACGTGGTGCTAAGTGAATATACCACGGTTAAACATG
1 TAACGTGGTGCTAAGTGGATATACCACGGTTAAACATG
* *
13156374 TAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTG
1 TAACGTGGTGCTAAGTGGATATACCACGGTTA-A-ACA-TG
*
13156415 ATTCATTAACGTGGTGCTAAGTGGATATACCATGGTTAAACATG
1 ------TAACGTGGTGCTAAGTGGATATACCACGGTTAAACATG
* * ** *
13156459 TAACGTGGTGCGACGTGGATATGTCACGGTTATACATG
1 TAACGTGGTGCTAAGTGGATATACCACGGTTAAACATG
13156497 T
1 T
13156498 TAATTTTAAA
Statistics
Matches: 103, Mismatches: 12, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
38 63 0.61
39 1 0.01
40 2 0.02
41 2 0.02
44 2 0.02
45 2 0.02
46 1 0.01
47 30 0.29
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (38 bp):
TAACGTGGTGCTAAGTGGATATACCACGGTTAAACATG
Found at i:13156427 original size:85 final size:85
Alignment explanation
Indices: 13156284--13156490 Score: 369
Period size: 85 Copynumber: 2.4 Consensus size: 85
13156274 ACATATTGAT
13156284 ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTA
1 ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTA
13156349 AGTGAATATACCACGGTTAA
66 AGTGAATATACCACGGTTAA
13156369 ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTA
1 ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTA
* *
13156434 AGTGGATATACCATGGTTAA
66 AGTGAATATACCACGGTTAA
* * *
13156454 ACATGTAACGTGGTGCGACGTGGATATGTCACGGTTA
1 ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTA
13156491 TACATGTTAA
Statistics
Matches: 117, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 117 1.00
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (85 bp):
ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTA
AGTGAATATACCACGGTTAA
Found at i:13162615 original size:14 final size:14
Alignment explanation
Indices: 13162596--13162622 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13162586 AGTATGAAGG
13162596 AGTAAATTGAGATA
1 AGTAAATTGAGATA
13162610 AGTAAATTGAGAT
1 AGTAAATTGAGAT
13162623 GATCTTTTCG
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:0.00, G:0.22, T:0.30
Consensus pattern (14 bp):
AGTAAATTGAGATA
Found at i:13164333 original size:23 final size:23
Alignment explanation
Indices: 13164307--13164384 Score: 57
Period size: 23 Copynumber: 3.2 Consensus size: 23
13164297 TAATTTAAGT
13164307 TAACCTATCATGATAGTAAATAA
1 TAACCTATCATGATAGTAAATAA
* * * ** *
13164330 TAACATATAATTATCCTTTAATTTAA
1 TAACCTATCATGAT--AGTAA-ATAA
13164356 GTTAACCTATCATGATAGTAAATAA
1 --TAACCTATCATGATAGTAAATAA
13164381 TAAC
1 TAAC
13164385 ATGTAATTAT
Statistics
Matches: 38, Mismatches: 12, Indels: 10
0.63 0.20 0.17
Matches are distributed among these distances:
23 15 0.39
25 6 0.16
26 6 0.16
28 11 0.29
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.36
Consensus pattern (23 bp):
TAACCTATCATGATAGTAAATAA
Found at i:13164351 original size:51 final size:51
Alignment explanation
Indices: 13164295--13164398 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
13164285 TTAGATCACT
13164295 TTTAATTTAAGTTAACCTATCATGATAGTAAATAATAACATATAATTATCC
1 TTTAATTTAAGTTAACCTATCATGATAGTAAATAATAACATATAATTATCC
*
13164346 TTTAATTTAAGTTAACCTATCATGATAGTAAATAATAACATGTAATTATCC
1 TTTAATTTAAGTTAACCTATCATGATAGTAAATAATAACATATAATTATCC
13164397 TT
1 TT
13164399 ATTATATATG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.40
Consensus pattern (51 bp):
TTTAATTTAAGTTAACCTATCATGATAGTAAATAATAACATATAATTATCC
Found at i:13174653 original size:36 final size:37
Alignment explanation
Indices: 13174607--13174677 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 37
13174597 ACTCAAAATA
* *
13174607 ATCATTTTTTGCTTAATTGTTCC-ATCAAAACAAACT
1 ATCATCTTTTGCTTAATTCTTCCGATCAAAACAAACT
* * *
13174643 ATCATCTTTTGTTTAGTTCTTCCGATTAAAACAAA
1 ATCATCTTTTGCTTAATTCTTCCGATCAAAACAAA
13174678 AAATCAAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
36 19 0.66
37 10 0.34
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.42
Consensus pattern (37 bp):
ATCATCTTTTGCTTAATTCTTCCGATCAAAACAAACT
Found at i:13187788 original size:20 final size:20
Alignment explanation
Indices: 13187763--13187801 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
13187753 ACGTAACCCC
*
13187763 CAATAGTTAACGGTTGCAAT
1 CAATAGTTAAAGGTTGCAAT
13187783 CAATAGTTAAAGGTTGCAA
1 CAATAGTTAAAGGTTGCAA
13187802 ATTGGAGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (20 bp):
CAATAGTTAAAGGTTGCAAT
Found at i:13193675 original size:14 final size:14
Alignment explanation
Indices: 13193656--13193685 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
13193646 GTAGATTAGC
*
13193656 TCCCTCTTAAGCAG
1 TCCCTCTTAAGAAG
13193670 TCCCTCTTAAGAAG
1 TCCCTCTTAAGAAG
13193684 TC
1 TC
13193686 TTAAACAGTA
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:0.23, C:0.33, G:0.13, T:0.30
Consensus pattern (14 bp):
TCCCTCTTAAGAAG
Found at i:13199924 original size:20 final size:20
Alignment explanation
Indices: 13199891--13199929 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
13199881 TAAAAACTAG
13199891 CATCTATTGATTTTATGGATT
1 CATCTATTGATTTT-TGGATT
*
13199912 CATC-ATTGGTTTTTGGAT
1 CATCTATTGATTTTTGGAT
13199930 CCTCAACTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 8 0.47
21 4 0.24
ACGTcount: A:0.21, C:0.10, G:0.18, T:0.51
Consensus pattern (20 bp):
CATCTATTGATTTTTGGATT
Found at i:13201075 original size:49 final size:49
Alignment explanation
Indices: 13201017--13201120 Score: 199
Period size: 49 Copynumber: 2.1 Consensus size: 49
13201007 GATTTAATCA
*
13201017 TTTCCTTAAATCTATTTTTGTAGGGACCCAGTGAATTGAAAACAAACAT
1 TTTCTTTAAATCTATTTTTGTAGGGACCCAGTGAATTGAAAACAAACAT
13201066 TTTCTTTAAATCTATTTTTGTAGGGACCCAGTGAATTGAAAACAAACAT
1 TTTCTTTAAATCTATTTTTGTAGGGACCCAGTGAATTGAAAACAAACAT
13201115 TTTCTT
1 TTTCTT
13201121 GTTTGTTTTC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 54 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (49 bp):
TTTCTTTAAATCTATTTTTGTAGGGACCCAGTGAATTGAAAACAAACAT
Found at i:13203968 original size:12 final size:12
Alignment explanation
Indices: 13203951--13203975 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13203941 CCATTTACTT
13203951 TAAAGGCAAAAC
1 TAAAGGCAAAAC
13203963 TAAAGGCAAAAC
1 TAAAGGCAAAAC
13203975 T
1 T
13203976 TGGCCAAACC
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:0.56, C:0.16, G:0.16, T:0.12
Consensus pattern (12 bp):
TAAAGGCAAAAC
Found at i:13209219 original size:41 final size:43
Alignment explanation
Indices: 13209108--13209235 Score: 147
Period size: 43 Copynumber: 3.0 Consensus size: 43
13209098 AGCTCGTATA
* * *
13209108 ATGCCAACTTCCCAGACGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAACATCCCAGACGTGGTCTTACACGAAATCAAATATCG
* *
13209151 ATGTC-ACTGTCCCAGACAG-GGTCTTACACGAAATCAAATA-CG
1 ATGCCAAC-ATCCCAGAC-GTGGTCTTACACGAAATCAAATATCG
* *
13209193 ATGCCAACAT-CCAGACGTGGTCTTACACGATATCACATATCG
1 ATGCCAACATCCCAGACGTGGTCTTACACGAAATCAAATATCG
13209235 A
1 A
13209236 AAATCCTATG
Statistics
Matches: 72, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
40 1 0.01
41 25 0.35
42 12 0.17
43 33 0.46
44 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (43 bp):
ATGCCAACATCCCAGACGTGGTCTTACACGAAATCAAATATCG
Found at i:13211948 original size:15 final size:14
Alignment explanation
Indices: 13211930--13211979 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
13211920 TAGATTTATG
13211930 TTTAATTAATCAAAT
1 TTTAATTAAT-AAAT
13211945 TTTAATTAAATAAAT
1 TTTAATT-AATAAAT
*
13211960 TATAATTAATTAAAT
1 TTTAATTAA-TAAAT
*
13211975 GTTAA
1 TTTAA
13211980 CTGAAGTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 2 0.07
15 25 0.83
16 3 0.10
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (14 bp):
TTTAATTAATAAAT
Found at i:13216120 original size:45 final size:45
Alignment explanation
Indices: 13216056--13216229 Score: 230
Period size: 45 Copynumber: 3.9 Consensus size: 45
13216046 TATTGTACGG
* *
13216056 TACTATTTGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
1 TACTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGA
*
13216101 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
1 TACTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGA
* * * *
13216146 TACTATTCAGGCCTTCGAGCCTAGCAAGCTATAATGCCAGTGAAA
1 TACTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGA
* *
13216191 TGA-TA-TCGGG-CTTCGAACCTAGCAGGCGA-AATGCCGGTG
1 T-ACTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTG
13216230 GATGAATTCG
Statistics
Matches: 117, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
42 9 0.08
43 16 0.14
44 4 0.03
45 87 0.74
46 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (45 bp):
TACTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGA
Found at i:13218212 original size:42 final size:42
Alignment explanation
Indices: 13218153--13218237 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
13218143 TTCATGATTC
*
13218153 ATAGTGATAGAGAGAGTTTAAGCAAGACAATTGGTGATGCAT
1 ATAGTGACAGAGAGAGTTTAAGCAAGACAATTGGTGATGCAT
13218195 ATAGTGACAGAGAGAGTTTAAGCAAGACAATTGGTGATGCAT
1 ATAGTGACAGAGAGAGTTTAAGCAAGACAATTGGTGATGCAT
13218237 A
1 A
13218238 CTCTTAGATG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.39, C:0.08, G:0.28, T:0.25
Consensus pattern (42 bp):
ATAGTGACAGAGAGAGTTTAAGCAAGACAATTGGTGATGCAT
Found at i:13222169 original size:31 final size:31
Alignment explanation
Indices: 13222123--13222181 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
13222113 TAGGTATCTA
* *
13222123 AACTTGGCTTCTTGGTTCAAATTGGTACCTG
1 AACTTGGCTTCTTGGTCCAAATTAGTACCTG
* *
13222154 AACTTGGTTTTTTGGTCCAAATTAGTAC
1 AACTTGGCTTCTTGGTCCAAATTAGTAC
13222182 TTATGGTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (31 bp):
AACTTGGCTTCTTGGTCCAAATTAGTACCTG
Found at i:13223241 original size:23 final size:23
Alignment explanation
Indices: 13223197--13223241 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
13223187 TTATTCTACT
* ** *
13223197 TTAATTAAATAAAGTAATATTGC
1 TTAATAAAATAAAAAAAAATTGC
13223220 TTAATAAAATAAAAAAAAATTG
1 TTAATAAAATAAAAAAAAATTG
13223242 TATTTAAATC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.33
Consensus pattern (23 bp):
TTAATAAAATAAAAAAAAATTGC
Found at i:13225650 original size:3 final size:3
Alignment explanation
Indices: 13225642--13225756 Score: 58
Period size: 3 Copynumber: 39.3 Consensus size: 3
13225632 TAACGAAAAC
* * * **
13225642 AAT AAT AAT AGT AAT -AT AAAT AAT GAT AAT AGT GGT AA- AAT -AT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * *
13225685 GAT AAT ACT AAT GAT AAT AAT AAT AAT AGT CAT -AT AAT AAT ATT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
13225732 ATT AGT AAT AAT AAG AAT GAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
13225757 CAAATAATGC
Statistics
Matches: 82, Mismatches: 25, Indels: 10
0.70 0.21 0.09
Matches are distributed among these distances:
2 8 0.10
3 72 0.88
4 2 0.02
ACGTcount: A:0.55, C:0.02, G:0.10, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:13226135 original size:19 final size:19
Alignment explanation
Indices: 13226107--13226162 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 19
13226097 ACATAATATG
*
13226107 TACATGATATATAAAAATA
1 TACATAATATATAAAAATA
*
13226126 TACATAATATATTAAAGTATA
1 TACATAATATA-TAAA-AATA
* *
13226147 GACATAATATACAAAA
1 TACATAATATATAAAA
13226163 TAAAAAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
19 10 0.33
20 7 0.23
21 13 0.43
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.30
Consensus pattern (19 bp):
TACATAATATATAAAAATA
Found at i:13226137 original size:21 final size:21
Alignment explanation
Indices: 13226108--13226157 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
13226098 CATAATATGT
* *
13226108 ACATGATATA-TAAA-AATAT
1 ACATAATATATTAAAGAATAG
*
13226127 ACATAATATATTAAAGTATAG
1 ACATAATATATTAAAGAATAG
13226148 ACATAATATA
1 ACATAATATA
13226158 CAAAATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 9 0.35
20 4 0.15
21 13 0.50
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.32
Consensus pattern (21 bp):
ACATAATATATTAAAGAATAG
Found at i:13226235 original size:13 final size:13
Alignment explanation
Indices: 13226208--13226244 Score: 51
Period size: 11 Copynumber: 3.0 Consensus size: 13
13226198 AAAAGAACGA
*
13226208 ATATACATAATAT
1 ATATACGTAATAT
13226221 AT-TAC-TAATAT
1 ATATACGTAATAT
13226232 ATATACGTAATAT
1 ATATACGTAATAT
13226245 GGAGTATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 8 0.36
12 6 0.27
13 8 0.36
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.41
Consensus pattern (13 bp):
ATATACGTAATAT
Found at i:13229327 original size:23 final size:23
Alignment explanation
Indices: 13229297--13229343 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
13229287 TATTACTAAC
13229297 TCAGCATTTAGAAAGTCACATAG
1 TCAGCATTTAGAAAGTCACATAG
13229320 TCAGCATTTAGAAAGTCACATAG
1 TCAGCATTTAGAAAGTCACATAG
13229343 T
1 T
13229344 AAATGGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (23 bp):
TCAGCATTTAGAAAGTCACATAG
Found at i:13229844 original size:14 final size:14
Alignment explanation
Indices: 13229803--13229840 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
13229793 AATAAAAAAT
13229803 ATATAAAATCATTAA
1 ATATAAAAT-ATTAA
*
13229818 ATATTAAATATTAA
1 ATATAAAATATTAA
13229832 A-ATAAAATA
1 ATATAAAATA
13229841 ATTATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 7 0.33
14 6 0.29
15 8 0.38
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (14 bp):
ATATAAAATATTAA
Found at i:13231466 original size:23 final size:22
Alignment explanation
Indices: 13231440--13231506 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
13231430 TTGATTTTGT
13231440 TTTTATAGAAGTATTTAAATTTA
1 TTTTATA-AAGTATTTAAATTTA
* * *
13231463 TTTTCAAAAATTATTTAAATCTA
1 TTTT-ATAAAGTATTTAAATTTA
* *
13231486 TTTT-TAACGTATTAAAATTTA
1 TTTTATAAAGTATTTAAATTTA
13231507 AATTTTTTTA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
21 12 0.34
23 21 0.60
24 2 0.06
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (22 bp):
TTTTATAAAGTATTTAAATTTA
Found at i:13237305 original size:12 final size:12
Alignment explanation
Indices: 13237288--13237326 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
13237278 CAAAACAAAA
13237288 TAAATAAAAAGG
1 TAAATAAAAAGG
*
13237300 TAAATAAATA-G
1 TAAATAAAAAGG
*
13237311 AAAATAAAAAGG
1 TAAATAAAAAGG
13237323 TAAA
1 TAAA
13237327 AGGGGTGAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.69, C:0.00, G:0.13, T:0.18
Consensus pattern (12 bp):
TAAATAAAAAGG
Found at i:13247607 original size:41 final size:41
Alignment explanation
Indices: 13247562--13247690 Score: 143
Period size: 41 Copynumber: 3.1 Consensus size: 41
13247552 TTTATGAGGG
* * *
13247562 AAACGCCACAAAAGGTCTAACATTAGCGGCATTTATGATAA
1 AAACGCCACAAAAGGTCCAGCATTAGCGGCGTTTATGATAA
** * * *
13247603 AAACGCTGCAAAAAGTCCAGCATTAGCGACGTTTATGAGAA
1 AAACGCCACAAAAGGTCCAGCATTAGCGGCGTTTATGATAA
* * *
13247644 AAATG-CAGTAAAAGGTCCAGCATTAGCGGCGTTTATGCTAA
1 AAACGCCA-CAAAAGGTCCAGCATTAGCGGCGTTTATGATAA
13247685 AAACGC
1 AAACGC
13247691 TGCAAAAAAC
Statistics
Matches: 69, Mismatches: 17, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
41 69 1.00
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (41 bp):
AAACGCCACAAAAGGTCCAGCATTAGCGGCGTTTATGATAA
Found at i:13251924 original size:25 final size:25
Alignment explanation
Indices: 13251896--13251944 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
13251886 TTGAAGTATA
*
13251896 ATTTGTATTTGTTATTTTTGGTTGG
1 ATTTGTATTTATTATTTTTGGTTGG
*
13251921 ATTTGTATTTATTGTTTTTGGTTG
1 ATTTGTATTTATTATTTTTGGTTG
13251945 TTACAAGAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.12, C:0.00, G:0.22, T:0.65
Consensus pattern (25 bp):
ATTTGTATTTATTATTTTTGGTTGG
Found at i:13253496 original size:20 final size:20
Alignment explanation
Indices: 13253446--13253488 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
13253436 ATTAGTTTGT
13253446 TATGAAATTGTCATTAACAC
1 TATGAAATTGTCATTAACAC
*
13253466 TATGAAATTGTCATTAACGC
1 TATGAAATTGTCATTAACAC
13253486 TAT
1 TAT
13253489 CGATTTGTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (20 bp):
TATGAAATTGTCATTAACAC
Found at i:13254051 original size:26 final size:28
Alignment explanation
Indices: 13254002--13254053 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
13253992 TATTAGAATG
*
13254002 TTTATAAATTTTTATGAAATTTGTTACT
1 TTTATAAATTTATATGAAATTTGTTACT
*
13254030 TTTATAAGTTTATAT-AAA-TTGTTA
1 TTTATAAATTTATATGAAATTTGTTA
13254054 AATGTTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 6 0.27
27 3 0.14
28 13 0.59
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.56
Consensus pattern (28 bp):
TTTATAAATTTATATGAAATTTGTTACT
Found at i:13254317 original size:11 final size:11
Alignment explanation
Indices: 13254301--13254331 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
13254291 ATACCCATAC
13254301 CCCATACCTTG
1 CCCATACCTTG
*
13254312 CCCATACCTTT
1 CCCATACCTTG
13254323 CCCATACCT
1 CCCATACCT
13254332 ACCCATACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.48, G:0.03, T:0.29
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:13254902 original size:18 final size:18
Alignment explanation
Indices: 13254875--13254967 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
13254865 TACGACCGTT
13254875 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
13254893 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
13254911 TACAGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
13254929 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
13254947 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
13254965 TAC
1 TAC
13254968 AGTAATTGGG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:13259037 original size:11 final size:11
Alignment explanation
Indices: 13259021--13259051 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
13259011 ATACCCATAC
13259021 CCCATACCTTG
1 CCCATACCTTG
*
13259032 CCCATACCTTT
1 CCCATACCTTG
13259043 CCCATACCT
1 CCCATACCT
13259052 ACCCATACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.48, G:0.03, T:0.29
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:13262274 original size:4 final size:4
Alignment explanation
Indices: 13262265--13262299 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
13262255 TAGACAACTA
13262265 TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
13262300 CATATTTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:13263161 original size:21 final size:20
Alignment explanation
Indices: 13263132--13263179 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
13263122 GAATATTTTT
13263132 AAATT-TTTAACTTTCTTTA
1 AAATTATTTAACTTTCTTTA
* * *
13263151 TATATTATTTAATTTTTTTTA
1 -AAATTATTTAACTTTCTTTA
13263172 AAATTATT
1 AAATTATT
13263180 AAATATTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (20 bp):
AAATTATTTAACTTTCTTTA
Found at i:13263179 original size:20 final size:20
Alignment explanation
Indices: 13263113--13263194 Score: 62
Period size: 19 Copynumber: 4.1 Consensus size: 20
13263103 CCTCAACATT
*
13263113 ATTATGTTAGAATATTTTT-AA
1 ATTAT-TTA-AATTTTTTTAAA
* * *
13263134 ATT-TTTAACTTTCTTTATAT
1 ATTATTTAAATTTTTTTA-AA
*
13263154 ATTATTTAATTTTTTTTAAA
1 ATTATTTAAATTTTTTTAAA
*
13263174 ATTA-TTAAATATTTTTAAA
1 ATTATTTAAATTTTTTTAAA
13263193 AT
1 AT
13263195 ATAATTTTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
18 6 0.12
19 18 0.37
20 10 0.20
21 15 0.31
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (20 bp):
ATTATTTAAATTTTTTTAAA
Found at i:13266370 original size:24 final size:25
Alignment explanation
Indices: 13266320--13266370 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
13266310 GTGCTTTAAT
*
13266320 AAAAAAATTATATAGTTAATTGAGAC
1 AAAAAAATTATATACTTAATT-AGAC
*
13266346 AAAAAATTTATATACTTAATT-GAC
1 AAAAAAATTATATACTTAATTAGAC
13266370 A
1 A
13266371 TTGAAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 4 0.17
26 19 0.83
ACGTcount: A:0.53, C:0.06, G:0.08, T:0.33
Consensus pattern (25 bp):
AAAAAAATTATATACTTAATTAGAC
Found at i:13266503 original size:20 final size:20
Alignment explanation
Indices: 13266478--13266515 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
13266468 CAAATTGGGA
13266478 TAAAATAAA-ACTTAAAATAC
1 TAAAATAAACA-TTAAAATAC
13266498 TAAAATAAACATTAAAAT
1 TAAAATAAACATTAAAAT
13266516 TAAATACAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (20 bp):
TAAAATAAACATTAAAATAC
Found at i:13285307 original size:56 final size:56
Alignment explanation
Indices: 13285221--13285333 Score: 199
Period size: 56 Copynumber: 2.0 Consensus size: 56
13285211 TCGTTTGGTA
*
13285221 TGTATTATTCTTTGAGCTCCTGAATTCAAATATAACTGTGATTCCTTGATTACATG
1 TGTATTATTCTTTGAGCTCCTGAATCCAAATATAACTGTGATTCCTTGATTACATG
* *
13285277 TGTATTATTCTTTGAGCTTCTGAATCCAAATATAACTGTGATTCCTTGATTTCATG
1 TGTATTATTCTTTGAGCTCCTGAATCCAAATATAACTGTGATTCCTTGATTACATG
13285333 T
1 T
13285334 ATAAACTGTG
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (56 bp):
TGTATTATTCTTTGAGCTCCTGAATCCAAATATAACTGTGATTCCTTGATTACATG
Found at i:13290571 original size:18 final size:18
Alignment explanation
Indices: 13290550--13290648 Score: 94
Period size: 18 Copynumber: 5.5 Consensus size: 18
13290540 TAATAATCAG
* *
13290550 TTATTCAGTAACGGTCGT
1 TTATTCAGTAACAGTCGA
* * *
13290568 TTATTCATTATCAGTCAA
1 TTATTCAGTAACAGTCGA
** *
13290586 TTATTCAGTAGTAGT-TA
1 TTATTCAGTAACAGTCGA
13290603 GTTATTCAGTAACAGTC-A
1 -TTATTCAGTAACAGTCGA
13290621 TTGATTCAGTAACAGTCGA
1 TT-ATTCAGTAACAGTCGA
13290640 TTATTCAGT
1 TTATTCAGT
13290649 GGCAGTTAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
17 3 0.05
18 60 0.91
19 3 0.05
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.40
Consensus pattern (18 bp):
TTATTCAGTAACAGTCGA
Found at i:13290608 original size:54 final size:54
Alignment explanation
Indices: 13290548--13290666 Score: 150
Period size: 54 Copynumber: 2.2 Consensus size: 54
13290538 AGTAATAATC
* * * * * *
13290548 AGTTATTCAGTAACGGTCGTTTATTCATTATCAGTCAATTATTCAGTAGTAGTT
1 AGTTATTCAGTAACAGTCATTGATTCAGTAACAGTCAATTATTCAGTAGCAGTT
* *
13290602 AGTTATTCAGTAACAGTCATTGATTCAGTAACAGTCGATTATTCAGTGGCAGTT
1 AGTTATTCAGTAACAGTCATTGATTCAGTAACAGTCAATTATTCAGTAGCAGTT
*
13290656 AATT-TTCAGTA
1 AGTTATTCAGTA
13290667 TCTTTATTTA
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
53 7 0.12
54 49 0.88
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.39
Consensus pattern (54 bp):
AGTTATTCAGTAACAGTCATTGATTCAGTAACAGTCAATTATTCAGTAGCAGTT
Found at i:13298302 original size:25 final size:25
Alignment explanation
Indices: 13298273--13298326 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
13298263 TTAATCCTTA
*
13298273 TTAAATCTAATCCTAAGTTCTAAAC
1 TTAAATCTAATCCGAAGTTCTAAAC
* *
13298298 TTAAATCTAATTCGAAGTTTTAAAC
1 TTAAATCTAATCCGAAGTTCTAAAC
13298323 TTAA
1 TTAA
13298327 GTTCTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.39
Consensus pattern (25 bp):
TTAAATCTAATCCGAAGTTCTAAAC
Found at i:13299601 original size:20 final size:20
Alignment explanation
Indices: 13299576--13299620 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
13299566 ACTCACAAGA
*
13299576 TGTATGGATAGAAA-TGGACT
1 TGTATGGATA-AAAGTGAACT
13299596 TGTATGGATAAAAGTGAACT
1 TGTATGGATAAAAGTGAACT
13299616 TGTAT
1 TGTAT
13299621 CAATATAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (20 bp):
TGTATGGATAAAAGTGAACT
Found at i:13307237 original size:10 final size:10
Alignment explanation
Indices: 13307202--13307240 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
13307192 TTAGGGTTTA
*
13307202 ATATTTATTT
1 ATATTTAATT
*
13307212 ATAATTAATT
1 ATATTTAATT
13307222 ATTATTTAATT
1 A-TATTTAATT
13307233 ATATTTAA
1 ATATTTAA
13307241 ATAAAGTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
ATATTTAATT
Found at i:13317614 original size:31 final size:31
Alignment explanation
Indices: 13317579--13317647 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
13317569 CTATTTTTTT
*
13317579 ATTTAATTGTGATATATTAACTAATATGGTA
1 ATTTAATTGGGATATATTAACTAATATGGTA
* * *
13317610 ATTTAATTGGGATGTATTAACTATTGTGGTA
1 ATTTAATTGGGATATATTAACTAATATGGTA
13317641 ATTTAAT
1 ATTTAAT
13317648 ATGGTTAAGG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.35, C:0.03, G:0.16, T:0.46
Consensus pattern (31 bp):
ATTTAATTGGGATATATTAACTAATATGGTA
Found at i:13320189 original size:46 final size:46
Alignment explanation
Indices: 13320108--13320287 Score: 154
Period size: 46 Copynumber: 3.8 Consensus size: 46
13320098 TCGGCATTTT
* * * * *
13320108 GACGAGAGCTAGTGTAAGATATGTTTGGGACATGCATTGGCCT-CGA
1 GACGATAGCCAGTGTAAGACATGTCTGGGACATGCATCGG-CTACGA
* *
13320154 GACG-TAAGCCAGTGTAGGACATGTCTGGAACATGCATCGGCTACGA
1 GACGAT-AGCCAGTGTAAGACATGTCTGGGACATGCATCGGCTACGA
* * *
13320200 GATGATAGTCAGTGTAAGACCATGTCTGGGACATGGCATCGACTTA--A
1 GACGATAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-TACGA
*
13320247 GATG-TGAGCCAGTGTAAGACTATGTCTGGGACATGGCATCG
1 GACGAT-AGCCAGTGTAAGAC-ATGTCTGGGACAT-GCATCG
13320288 ACACTTTACC
Statistics
Matches: 113, Mismatches: 13, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
45 2 0.02
46 51 0.45
47 51 0.45
48 7 0.06
49 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (46 bp):
GACGATAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCTACGA
Found at i:13320236 original size:140 final size:140
Alignment explanation
Indices: 13320024--13320281 Score: 313
Period size: 140 Copynumber: 1.8 Consensus size: 140
13320014 TTATTTGGCT
* **
13320024 AGTGTAAGACATGTCTGAAACATGCATCGACCACATTATGAGAGCCAGTGAAAGATTATGCCTGG
1 AGTGTAAGACATGTCTGAAACATGCATCGACCACATGATGAGAGCCAGTGAAAGACCATGCCTGG
* * ** * *
13320089 GTCATGGCATCGGCATTTTGACGAGAGCTAGTGTAAGA-TATGTTTGGGACATGCATTGGCCTCG
66 GACATGGCATCGAC-TTAAGACGAGAGCCAGTGTAAGACTATGTCTGGGACATGCATTGGCCTCG
13320153 AGACGTAAGCC
130 AGACGTAAGCC
* * * * * * * *
13320164 AGTGTAGGACATGTCTGGAACATGCATCGGCTACGA-GATGATAGTCAGTGTAAGACCATGTCTG
1 AGTGTAAGACATGTCTGAAACATGCATCGACCAC-ATGATGAGAGCCAGTGAAAGACCATGCCTG
* *
13320228 GGACATGGCATCGACTTAAGATGTGAGCCAGTGTAAGACTATGTCTGGGACATG
65 GGACATGGCATCGACTTAAGACGAGAGCCAGTGTAAGACTATGTCTGGGACATG
13320282 GCATCGACAC
Statistics
Matches: 97, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
139 18 0.19
140 78 0.80
141 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (140 bp):
AGTGTAAGACATGTCTGAAACATGCATCGACCACATGATGAGAGCCAGTGAAAGACCATGCCTGG
GACATGGCATCGACTTAAGACGAGAGCCAGTGTAAGACTATGTCTGGGACATGCATTGGCCTCGA
GACGTAAGCC
Found at i:13320250 original size:47 final size:47
Alignment explanation
Indices: 13320160--13320289 Score: 160
Period size: 47 Copynumber: 2.8 Consensus size: 47
13320150 TCGAGACGTA
* * *
13320160 AGCCAGTGTAGGA-CATGTCTGGAACAT-GCATCGGCTACGAGATGAT-
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACTAC-AGATG-TG
*
13320206 AGTCAGTGTAAGACCATGTCTGGGACATGGCATCGACTTA-AGATGTG
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGAC-TACAGATGTG
*
13320253 AGCCAGTGTAAGACTATGTCTGGGACATGGCATCGAC
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGAC
13320290 ACTTTACCCA
Statistics
Matches: 74, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
46 12 0.16
47 53 0.72
48 7 0.09
49 2 0.03
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (47 bp):
AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACTACAGATGTG
Found at i:13320553 original size:37 final size:37
Alignment explanation
Indices: 13320503--13320577 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
13320493 TTTGGTATCA
* * *
13320503 TGAGCATATAGATCATTGATAAAATGTTATTGTTGTG
1 TGAGCATACAGATCATTGATAAAATGTTACTATTGTG
*
13320540 TGAGCATGCAGATCATTGATAAAATGTTACTATTGTG
1 TGAGCATACAGATCATTGATAAAATGTTACTATTGTG
13320577 T
1 T
13320578 ACTTACTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.39
Consensus pattern (37 bp):
TGAGCATACAGATCATTGATAAAATGTTACTATTGTG
Found at i:13327103 original size:15 final size:15
Alignment explanation
Indices: 13327065--13327108 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
13327055 CATAGTATCG
* *
13327065 TATCTTGGGTTTCTT
1 TATCTTGGATTTCTC
13327080 TAT-TCTGGATTTCTC
1 TATCT-TGGATTTCTC
13327095 TATCTTGGATTTCT
1 TATCTTGGATTTCT
13327109 TTATTCGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 1 0.04
15 23 0.92
16 1 0.04
ACGTcount: A:0.11, C:0.16, G:0.16, T:0.57
Consensus pattern (15 bp):
TATCTTGGATTTCTC
Found at i:13329092 original size:46 final size:46
Alignment explanation
Indices: 13329042--13329217 Score: 183
Period size: 46 Copynumber: 3.8 Consensus size: 46
13329032 TGGTTGAGCA
* *
13329042 TCCGAACTCGTTGAGTTAAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAATG
*** * * * *
13329088 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAGTCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATACGAAT-G
* * * *
13329135 TCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATTCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAATG
* * *
13329181 CCCGAGCTCGTTGAGTTGAGTCCAAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
13329218 GCGGTTACAT
Statistics
Matches: 104, Mismatches: 23, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
46 70 0.67
47 34 0.33
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAATG
Found at i:13330922 original size:3 final size:3
Alignment explanation
Indices: 13330916--13330954 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
13330906 GTCACATTGC
13330916 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
13330955 GTCTTGTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:13341937 original size:46 final size:49
Alignment explanation
Indices: 13341873--13342038 Score: 190
Period size: 49 Copynumber: 3.6 Consensus size: 49
13341863 ATATGCTTCT
* * * *
13341873 GTGTAAGACCATATCTGGGATATGGCATC-A-GTGAGATATGTGA-TCC
1 GTGTAAGACCATAGCTGGGCTATGGCATCGATATGAGATATGTGATTAC
* *
13341919 GTGTAAGACTATAGCTGGGCTATGGCATCGATATGTGATATGTGATTAC
1 GTGTAAGACCATAGCTGGGCTATGGCATCGATATGAGATATGTGATTAC
*
13341968 GTGTAAGACCATAGCTGGGCTATGGCATCGATATGTGA-A--T-A-T--
1 GTGTAAGACCATAGCTGGGCTATGGCATCGATATGAGATATGTGATTAC
*
13342010 GTGTAAGACCATAGCTGGGCTATGACATC
1 GTGTAAGACCATAGCTGGGCTATGGCATC
13342039 ATTATGTGAA
Statistics
Matches: 109, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
42 28 0.26
44 1 0.01
45 1 0.01
46 27 0.25
47 1 0.01
48 12 0.11
49 39 0.36
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (49 bp):
GTGTAAGACCATAGCTGGGCTATGGCATCGATATGAGATATGTGATTAC
Found at i:13342014 original size:42 final size:42
Alignment explanation
Indices: 13341955--13342080 Score: 173
Period size: 42 Copynumber: 3.0 Consensus size: 42
13341945 ATCGATATGT
* *
13341955 GATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATC
1 GATATGTGAATATGTGTAAGACCATAGCTGGGCTATGGCATC
*
13341997 GATATGTGAATATGTGTAAGACCATAGCTGGGCTATGACATC
1 GATATGTGAATATGTGTAAGACCATAGCTGGGCTATGGCATC
* * **
13342039 -ATTATGTGAAGATGTGTAAGACCATAGTTGAACTATGGCATC
1 GA-TATGTGAATATGTGTAAGACCATAGCTGGGCTATGGCATC
13342081 AAGAAAACGA
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
41 1 0.01
42 74 0.99
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.29
Consensus pattern (42 bp):
GATATGTGAATATGTGTAAGACCATAGCTGGGCTATGGCATC
Found at i:13342045 original size:91 final size:91
Alignment explanation
Indices: 13341873--13342047 Score: 228
Period size: 91 Copynumber: 1.9 Consensus size: 91
13341863 ATATGCTTCT
* * *
13341873 GTGTAAGACCATATCTGGGATATGGCATCAGTGAGATATGTGATCCGTGTAAGACTATAGCTGGG
1 GTGTAAGACCATAGCTGGGATATGGCATC----AGATATGTGATACGTGTAAGACCATAGCTGGG
*
13341938 CTATGGCATCGATATGTGATATGTGATTAC
62 CTATGACATCGATATGTGATATGTGATTAC
* *
13341968 GTGTAAGACCATAGCTGGGCTATGGCATC-GATATGTGAATATGTGTAAGACCATAGCTGGGCTA
1 GTGTAAGACCATAGCTGGGATATGGCATCAGATATGTG-ATACGTGTAAGACCATAGCTGGGCTA
13342032 TGACATC-ATTATGTGA
65 TGACATCGA-TATGTGA
13342048 AGATGTGTAA
Statistics
Matches: 72, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
90 9 0.12
91 36 0.50
95 27 0.38
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (91 bp):
GTGTAAGACCATAGCTGGGATATGGCATCAGATATGTGATACGTGTAAGACCATAGCTGGGCTAT
GACATCGATATGTGATATGTGATTAC
Found at i:13358579 original size:15 final size:15
Alignment explanation
Indices: 13358559--13358588 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13358549 CATTTTATTT
*
13358559 ATATTAGGATAATTA
1 ATATTAAGATAATTA
13358574 ATATTAAGATAATTA
1 ATATTAAGATAATTA
13358589 TTAGGATTAT
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:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATATTAAGATAATTA
Found at i:13361995 original size:5 final size:5
Alignment explanation
Indices: 13361981--13362037 Score: 57
Period size: 5 Copynumber: 11.4 Consensus size: 5
13361971 GTAACCTAAT
*
13361981 TTTTA TTTTTA TTTTA TTTTA TTTTTA TTTT- TATTTA TTTTA TCTTA
1 TTTTA -TTTTA TTTTA TTTTA -TTTTA TTTTA T-TTTA TTTTA TTTTA
13362028 --TTA TTTTA TT
1 TTTTA TTTTA TT
13362038 ATTTATTATT
Statistics
Matches: 45, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
3 3 0.07
4 1 0.02
5 30 0.67
6 11 0.24
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:13362002 original size:16 final size:16
Alignment explanation
Indices: 13361981--13362044 Score: 76
Period size: 16 Copynumber: 3.8 Consensus size: 16
13361971 GTAACCTAAT
13361981 TTTTATTTTTATTTTA
1 TTTTATTTTTATTTTA
13361997 TTTTATTTTTATTTT-
1 TTTTATTTTTATTTTA
*
13362012 TATTTATTTTATCTTATTA
1 T-TTTATTTT-TATT-TTA
13362031 TTTTATTATTTATT
1 TTTTATT-TTTATT
13362045 ATTTTCAGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
15 1 0.02
16 23 0.56
17 3 0.07
18 11 0.27
19 3 0.07
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTATTTTTATTTTA
Found at i:13362034 original size:28 final size:26
Alignment explanation
Indices: 13361979--13362049 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 26
13361969 AGGTAACCTA
*
13361979 ATTTTTATTTTTATTTTATTTTATTTTT
1 ATTTTTA--TTTATTTTATCTTATTTTT
13362007 ATTTTTATTTATTTTATCTTATTATTTT
1 ATTTTTATTTATTTTATCTTA-T-TTTT
13362035 ATTATTTA-TTATTTT
1 ATT-TTTATTTATTTT
13362050 CAGATATTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
26 13 0.33
27 1 0.03
28 21 0.54
29 4 0.10
ACGTcount: A:0.21, C:0.01, G:0.00, T:0.77
Consensus pattern (26 bp):
ATTTTTATTTATTTTATCTTATTTTT
Found at i:13362039 original size:21 final size:21
Alignment explanation
Indices: 13361979--13362044 Score: 87
Period size: 22 Copynumber: 2.9 Consensus size: 21
13361969 AGGTAACCTA
13361979 ATTTTTATTTTTATTTTATTTT
1 ATTTTTATTTTTA-TTTATTTT
13362001 ATTTTTATTTTTATTTATTTT
1 ATTTTTATTTTTATTTATTTT
13362022 ATCTTATTATTTTATTATTTATT
1 AT-TT-TTA-TTT-TTATTTATT
13362045 ATTTTCAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
21 10 0.25
22 15 0.38
23 3 0.08
24 3 0.08
25 9 0.22
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (21 bp):
ATTTTTATTTTTATTTATTTT
Found at i:13366314 original size:26 final size:26
Alignment explanation
Indices: 13366284--13366388 Score: 183
Period size: 26 Copynumber: 4.0 Consensus size: 26
13366274 AATTCCCATA
13366284 ATGGAACATTTACCTAACCCATTATC
1 ATGGAACATTTACCTAACCCATTATC
13366310 ATGGAACATTTACCTAACCCATTATC
1 ATGGAACATTTACCTAACCCATTATC
*
13366336 ATGAAACATTTACCTAACCCATTATC
1 ATGGAACATTTACCTAACCCATTATC
* *
13366362 ATGGAACATTTACTTAACTCATTATC
1 ATGGAACATTTACCTAACCCATTATC
13366388 A
1 A
13366389 ATTTGTATCA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.32
Consensus pattern (26 bp):
ATGGAACATTTACCTAACCCATTATC
Found at i:13367690 original size:12 final size:12
Alignment explanation
Indices: 13367673--13367705 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
13367663 CTACTTCCCA
13367673 TTTACTATTATT
1 TTTACTATTATT
13367685 TTTACTATTATT
1 TTTACTATTATT
*
13367697 TTAACTATT
1 TTTACTATT
13367706 TTACAGGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTACTATTATT
Found at i:13369306 original size:59 final size:60
Alignment explanation
Indices: 13369214--13369329 Score: 189
Period size: 59 Copynumber: 1.9 Consensus size: 60
13369204 CTAATTCTTC
*
13369214 GTATAGAAATGCACTCTTTCCATCAAATTTCCATAGTTTCCAACC-TTCAAAGTAGCTTT
1 GTATAGAAATACACTCTTTCCATCAAATTTCCATAGTTTCCAACCTTTCAAAGTAGCTTT
* * *
13369273 GTATAGAAATATATTCTTTCCATCAAGTTTCCATAGTTTCCAACCTTTCAAAGTAGC
1 GTATAGAAATACACTCTTTCCATCAAATTTCCATAGTTTCCAACCTTTCAAAGTAGC
13369330 AAGCGAAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
59 41 0.79
60 11 0.21
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.36
Consensus pattern (60 bp):
GTATAGAAATACACTCTTTCCATCAAATTTCCATAGTTTCCAACCTTTCAAAGTAGCTTT
Found at i:13371059 original size:8 final size:8
Alignment explanation
Indices: 13371046--13371073 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
13371036 GATTTTTAAA
13371046 TATTATTT
1 TATTATTT
13371054 TATTATTT
1 TATTATTT
13371062 TATTATTT
1 TATTATTT
13371070 TATT
1 TATT
13371074 TAGTATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TATTATTT
Found at i:13376378 original size:22 final size:21
Alignment explanation
Indices: 13376352--13376421 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 21
13376342 AATAAAATTT
13376352 ATTTTTTTCTACAAATTTTATA
1 ATTTTTTT-TACAAATTTTATA
* **
13376374 TTTTTTTTTACATTTTTTATA
1 ATTTTTTTTACAAATTTTATA
*
13376395 ATTTTCTTATGA-AAATTTTATA
1 ATTTT-TT-TTACAAATTTTATA
13376417 ATTTT
1 ATTTT
13376422 CTTATGACTT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
21 15 0.38
22 22 0.56
23 2 0.05
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.64
Consensus pattern (21 bp):
ATTTTTTTTACAAATTTTATA
Found at i:13376388 original size:19 final size:20
Alignment explanation
Indices: 13376351--13376389 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
13376341 CAATAAAATT
13376351 TATTTTTTTCTACAAATTTTA
1 TATTTTTTTCTAC-AATTTTA
*
13376372 TATTTTTTTTTAC-ATTTT
1 TATTTTTTTCTACAATTTT
13376390 TTATAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
21 12 0.71
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (20 bp):
TATTTTTTTCTACAATTTTA
Found at i:13376398 original size:10 final size:10
Alignment explanation
Indices: 13376367--13376510 Score: 66
Period size: 10 Copynumber: 14.3 Consensus size: 10
13376357 TTTCTACAAA
*
13376367 TTTTATATTT
1 TTTTATAATT
*
13376377 TTTTTTACATT
1 TTTTATA-ATT
13376388 TTTTATAATT
1 TTTTATAATT
**
13376398 TTCTTATGAAAA
1 TT-TTAT-AATT
13376410 TTTTATAATT
1 TTTTATAATT
*
13376420 TTCTTATGA--
1 TT-TTATAATT
* *
13376429 CTTTATAAAT
1 TTTTATAATT
13376439 TTTTATAATT
1 TTTTATAATT
* *
13376449 ATTTTCTAATC
1 -TTTTATAATT
*
13376460 TTTAAT-ATT
1 TTTTATAATT
13376469 TTTT-TACA-T
1 TTTTATA-ATT
**
13376478 TTTTATTAAAA
1 TTTTA-TAATT
*
13376489 TTTAATAA-T
1 TTTTATAATT
13376498 TTTTATAATT
1 TTTTATAATT
13376508 TTT
1 TTT
13376511 ATTGATTTTT
Statistics
Matches: 99, Mismatches: 22, Indels: 26
0.67 0.15 0.18
Matches are distributed among these distances:
8 6 0.06
9 18 0.18
10 36 0.36
11 35 0.35
12 4 0.04
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.63
Consensus pattern (10 bp):
TTTTATAATT
Found at i:13376399 original size:9 final size:9
Alignment explanation
Indices: 13376387--13376536 Score: 56
Period size: 9 Copynumber: 15.6 Consensus size: 9
13376377 TTTTTTACAT
13376387 TTTTTATAA
1 TTTTTATAA
13376396 TTTTCTTATGAAA
1 -TTT-TTAT--AA
*
13376409 ATTTTATAA
1 TTTTTATAA
*
13376418 TTTTCTTATGA
1 -TTT-TTATAA
*
13376429 CTT-TATAAA
1 TTTTTAT-AA
13376438 TTTTTATAA
1 TTTTTATAA
*
13376447 TTATTTTCTAA
1 -T-TTTTATAA
*
13376458 TCTTTA-ATA
1 TTTTTATA-A
*
13376467 TTTTTTTACA
1 TTTTTATA-A
13376477 TTTTTATTAAA
1 TTTTTA-T-AA
* *
13376488 ATTTAATAA
1 TTTTTATAA
13376497 TTTTTATAA
1 TTTTTATAA
*
13376506 TTTTTATTGA
1 TTTTTA-TAA
13376516 TTTTTAT--
1 TTTTTATAA
*
13376523 TTTTTATCA
1 TTTTTATAA
13376532 TTTTT
1 TTTTT
13376537 TACAACATGT
Statistics
Matches: 106, Mismatches: 18, Indels: 33
0.68 0.11 0.21
Matches are distributed among these distances:
7 7 0.07
8 4 0.04
9 36 0.34
10 28 0.26
11 26 0.25
12 3 0.03
13 2 0.02
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:13376518 original size:10 final size:10
Alignment explanation
Indices: 13376430--13376523 Score: 63
Period size: 10 Copynumber: 9.6 Consensus size: 10
13376420 TTCTTATGAC
*
13376430 TTTATAAATT
1 TTTATTAATT
13376440 TTTA-TAATT
1 TTTATTAATT
*
13376449 ATTT-TCTAATC
1 -TTTAT-TAATT
*
13376460 TTTAAT-ATT
1 TTTATTAATT
13376469 TTT-TTACATT
1 TTTATTA-ATT
**
13376479 TTTATTAAAA
1 TTTATTAATT
*
13376489 TTTAATAATT
1 TTTATTAATT
13376499 TTTA-TAATT
1 TTTATTAATT
*
13376508 TTTATTGATT
1 TTTATTAATT
13376518 TTTATT
1 TTTATT
13376524 TTTTATCATT
Statistics
Matches: 65, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
8 1 0.02
9 18 0.28
10 39 0.60
11 7 0.11
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (10 bp):
TTTATTAATT
Found at i:13376521 original size:29 final size:28
Alignment explanation
Indices: 13376437--13376536 Score: 89
Period size: 29 Copynumber: 3.5 Consensus size: 28
13376427 GACTTTATAA
*
13376437 ATTTTTATAATTATTT-TCTAATCTTTAAT
1 ATTTTTATAATT-TTTAT-TAATATTTAAT
* *
13376466 ATTTTTTTACATTTTTATTAAAATTTAAT
1 ATTTTTATA-ATTTTTATTAATATTTAAT
* *
13376495 AATTTTTATAATTTTTATTGAT-TTTTAT
1 -ATTTTTATAATTTTTATTAATATTTAAT
*
13376523 -TTTTTATCATTTTT
1 ATTTTTATAATTTTT
13376537 TACAACATGT
Statistics
Matches: 60, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
26 13 0.22
28 5 0.08
29 30 0.50
30 12 0.20
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (28 bp):
ATTTTTATAATTTTTATTAATATTTAAT
Found at i:13376808 original size:85 final size:85
Alignment explanation
Indices: 13376640--13376853 Score: 270
Period size: 85 Copynumber: 2.5 Consensus size: 85
13376630 ATTTTGGCAG
* *
13376640 TTCAAGTACCCAATCGAGTGTAAAAAAAAATAGGGGCTTAAATGCTTTTATTGAAAAAGTTTGAG
1 TTCAAGTACCCAATTGAGTG----AAAAAATAGGGGCTTAATTGCTTTTATTGAAAAAGTTTGAG
*
13376705 GGTCTTTTTGATGTATTTTGAAAA
62 GGTCTTTTTGATGCATTTTGAAAA
* *
13376729 TTCAAGTACCCAATTGAGTGCAAAAAACAGGAGCTTAATTGCTTATT-TTG-AAAAGTTTGAGGG
1 TTCAAGTACCCAATTGAGTG-AAAAAATAGGGGCTTAATTGCTT-TTATTGAAAAAGTTTGAGGG
*
13376792 TCTTTTTGATGCATTTTGAAAG
64 TCTTTTTGATGCATTTTGAAAA
* * *
13376814 TTTAAGTACCAAATTAAGTGAAAAAATTAGGGGCTTAATT
1 TTCAAGTACCCAATTGAGTGAAAAAA-TAGGGGCTTAATT
13376854 TATTTTTTAT
Statistics
Matches: 111, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
84 6 0.05
85 61 0.55
86 23 0.21
87 2 0.02
89 19 0.17
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.35
Consensus pattern (85 bp):
TTCAAGTACCCAATTGAGTGAAAAAATAGGGGCTTAATTGCTTTTATTGAAAAAGTTTGAGGGTC
TTTTTGATGCATTTTGAAAA
Found at i:13380228 original size:22 final size:22
Alignment explanation
Indices: 13380184--13380243 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
13380174 TTAAAATAAA
**
13380184 ATTAAAATTTTAAA-TA-ATTT
1 ATTAAAATAATAAATTATATTT
13380204 ATTAAAATAATAAATTATATTT
1 ATTAAAATAATAAATTATATTT
* * *
13380226 ATTATATTAATAATTTAT
1 ATTAAAATAATAAATTAT
13380244 TATATCACTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
20 12 0.36
21 2 0.06
22 19 0.58
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTAAAATAATAAATTATATTT
Found at i:13382394 original size:31 final size:30
Alignment explanation
Indices: 13382351--13382410 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
13382341 AAAGGTCAGT
*
13382351 TAATTTTGAAAAATAATTAAGAA-AATAAAA
1 TAATATTGAAAAATAATTAA-AATAATAAAA
13382381 TAATATTGTAAAAATAATTAAAATAATAAA
1 TAATATTG-AAAAATAATTAAAATAATAAA
13382411 TAAAAATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 9 0.33
31 18 0.67
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (30 bp):
TAATATTGAAAAATAATTAAAATAATAAAA
Found at i:13382421 original size:21 final size:22
Alignment explanation
Indices: 13382389--13382434 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
13382379 AATAATATTG
13382389 TAAAAATAATTAAAATAATAAA
1 TAAAAATAATTAAAATAATAAA
*
13382411 TAAAAAT-ATTAAAATAATATA
1 TAAAAATAATTAAAATAATAAA
13382432 TAA
1 TAA
13382435 TTTTGGAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAAAATAATTAAAATAATAAA
Found at i:13382424 original size:31 final size:31
Alignment explanation
Indices: 13382359--13382420 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 31
13382349 GTTAATTTTG
*
13382359 AAAAATAATTAAGAAAATAAAATAATATTGT
1 AAAAATAATTAAGAAAATAAAAAAATATTGT
13382390 AAAAATAATTAA-AATAATAAATAAAAATATT
1 AAAAATAATTAAGAA-AAT-AA-AAAAATATT
13382421 AAAATAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 2 0.07
31 15 0.56
32 2 0.07
33 8 0.30
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (31 bp):
AAAAATAATTAAGAAAATAAAAAAATATTGT
Found at i:13382560 original size:44 final size:44
Alignment explanation
Indices: 13382510--13382609 Score: 173
Period size: 44 Copynumber: 2.3 Consensus size: 44
13382500 TCATACAACC
*
13382510 CATTTAATAATATTGAAAAGATATTTACACTAAATTAATTATCT
1 CATTTAATAATATTGAAAAGATATTTACACTAAACTAATTATCT
* *
13382554 CATTTAATAATTTTGAAAAGATATTTACGCTAAACTAATTATCT
1 CATTTAATAATATTGAAAAGATATTTACACTAAACTAATTATCT
13382598 CATTTAATAATA
1 CATTTAATAATA
13382610 ACAATTAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (44 bp):
CATTTAATAATATTGAAAAGATATTTACACTAAACTAATTATCT
Done.