Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1188
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1075576
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29
Warning! 121203 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:5432 original size:22 final size:22
Alignment explanation
Indices: 5407--5450 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5397 TCCATTGATT
* * *
5407 GCAACTCAATCATTACAAGAAC
1 GCAAATCAAACATAACAAGAAC
5429 GCAAATCAAACATAACAAGAAC
1 GCAAATCAAACATAACAAGAAC
5451 ATCAACAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.25, G:0.09, T:0.14
Consensus pattern (22 bp):
GCAAATCAAACATAACAAGAAC
Found at i:7510 original size:28 final size:28
Alignment explanation
Indices: 7475--7560 Score: 91
Period size: 28 Copynumber: 2.9 Consensus size: 28
7465 GATTGATAGA
*
7475 CAGACAGACGGACGGACGGACAGACAAG
1 CAGACAGACGGACGGACAGACAGACAAG
* * *
7503 CATACAGACGGACCGAAGGACTGACAGACAGG
1 CAGACAGACGGA-C---GGACAGACAGACAAG
*
7535 TAGACAGACGGACGGACAGACAGACA
1 CAGACAGACGGACGGACAGACAGACA
7561 CTGGATCAGA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
28 23 0.48
29 1 0.02
31 1 0.02
32 23 0.48
ACGTcount: A:0.40, C:0.24, G:0.33, T:0.03
Consensus pattern (28 bp):
CAGACAGACGGACGGACAGACAGACAAG
Found at i:7529 original size:32 final size:32
Alignment explanation
Indices: 7472--7547 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 32
7462 GCGGATTGAT
* * *
7472 AGACAGACAGACGGACGGACGGACAGACAAGC
1 AGACAGACGGACCGAAGGACGGACAGACAAGC
* * * *
7504 ATACAGACGGACCGAAGGACTGACAGACAGGT
1 AGACAGACGGACCGAAGGACGGACAGACAAGC
7536 AGACAGACGGAC
1 AGACAGACGGAC
7548 GGACAGACAG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.39, C:0.24, G:0.33, T:0.04
Consensus pattern (32 bp):
AGACAGACGGACCGAAGGACGGACAGACAAGC
Found at i:13169 original size:1 final size:1
Alignment explanation
Indices: 13163--13200 Score: 58
Period size: 1 Copynumber: 38.0 Consensus size: 1
13153 CATACATTTC
* *
13163 TTTTTTTTTTTTCTTCTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
13201 ACATATTTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.05, G:0.00, T:0.95
Consensus pattern (1 bp):
T
Found at i:13181 original size:16 final size:15
Alignment explanation
Indices: 13159--13200 Score: 68
Period size: 16 Copynumber: 2.8 Consensus size: 15
13149 ATAGCATACA
13159 TTTCTTTTTTTTTTT
1 TTTCTTTTTTTTTTT
13174 TCTTCTTTTTTTTTTT
1 T-TTCTTTTTTTTTTT
13190 TTT-TTTTTTTT
1 TTTCTTTTTTTT
13201 ACATATTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.31
15 3 0.12
16 15 0.58
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (15 bp):
TTTCTTTTTTTTTTT
Found at i:16958 original size:39 final size:39
Alignment explanation
Indices: 16909--17062 Score: 182
Period size: 39 Copynumber: 3.9 Consensus size: 39
16899 CACTAACATT
* * *
16909 GGTTGGGTGAATTAGCTATACCTATAACACTAATATTTT
1 GGTTGGGTGAATTAGCTATCCCTATAACACTAGTATTTA
* * * *
16948 GATTGGGTGAATTGGCTATCCCTATAACACTCGTGTTTA
1 GGTTGGGTGAATTAGCTATCCCTATAACACTAGTATTTA
* * *
16987 GGTTGGGTGAATCAGCTATCCCTATAACACTTGTGTTTA
1 GGTTGGGTGAATTAGCTATCCCTATAACACTAGTATTTA
* * * *
17026 GGTTGGGTGAATTGGCAATCCCTATATCACTATTATT
1 GGTTGGGTGAATTAGCTATCCCTATAACACTAGTATT
17063 CTGGTTAAAA
Statistics
Matches: 97, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 97 1.00
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.37
Consensus pattern (39 bp):
GGTTGGGTGAATTAGCTATCCCTATAACACTAGTATTTA
Found at i:17004 original size:78 final size:78
Alignment explanation
Indices: 16909--17056 Score: 215
Period size: 78 Copynumber: 1.9 Consensus size: 78
16899 CACTAACATT
* * *
16909 GGTTGGGTGAATTAGCTATACCTATAACACTAATATTTTGATTGGGTGAATTGGCTATCCCTATA
1 GGTTGGGTGAATCAGCTATACCTATAACACTAATATTTAGATTGGGTGAATTGGCAATCCCTATA
16974 ACACTCGTGTTTA
66 ACACTCGTGTTTA
* ** * *
16987 GGTTGGGTGAATCAGCTATCCCTATAACACTTGTGTTTAGGTTGGGTGAATTGGCAATCCCTATA
1 GGTTGGGTGAATCAGCTATACCTATAACACTAATATTTAGATTGGGTGAATTGGCAATCCCTATA
*
17052 TCACT
66 ACACT
17057 ATTATTCTGG
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
78 61 1.00
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (78 bp):
GGTTGGGTGAATCAGCTATACCTATAACACTAATATTTAGATTGGGTGAATTGGCAATCCCTATA
ACACTCGTGTTTA
Found at i:17108 original size:17 final size:17
Alignment explanation
Indices: 17086--17119 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
17076 CTGGCTATAC
17086 CTATAACA-CTAACATTT
1 CTATAACATC-AACATTT
17103 CTATAACATCAACATTT
1 CTATAACATCAACATTT
17120 TGGTTAGGCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.94
18 1 0.06
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.35
Consensus pattern (17 bp):
CTATAACATCAACATTT
Found at i:25537 original size:13 final size:13
Alignment explanation
Indices: 25519--25544 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25509 GGTCAATCCT
25519 GAAAGCTCTTTCA
1 GAAAGCTCTTTCA
25532 GAAAGCTCTTTCA
1 GAAAGCTCTTTCA
25545 AACTTGTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
GAAAGCTCTTTCA
Found at i:27540 original size:17 final size:15
Alignment explanation
Indices: 27518--27562 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 15
27508 ATTTATTTCT
27518 ATTTCAATATAAGCGG
1 ATTTCAATATAAGC-G
*
27534 AATTTCAAAATAAGCG
1 -ATTTCAATATAAGCG
*
27550 AGTTCAATATAAG
1 ATTTCAATATAAG
27563 TGGAGTAAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 11 0.44
16 1 0.04
17 13 0.52
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.29
Consensus pattern (15 bp):
ATTTCAATATAAGCG
Found at i:27561 original size:15 final size:17
Alignment explanation
Indices: 27520--27562 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
27510 TTATTTCTAT
*
27520 TTCAATATAAGCGGAAT
1 TTCAATATAAGCGGAAG
*
27537 TTCAAAATAAGC-G-AG
1 TTCAATATAAGCGGAAG
27552 TTCAATATAAG
1 TTCAATATAAG
27563 TGGAGTAAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 11 0.48
16 1 0.04
17 11 0.48
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (17 bp):
TTCAATATAAGCGGAAG
Found at i:31933 original size:2 final size:2
Alignment explanation
Indices: 31926--31972 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
31916 ACATAGACGT
31926 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
31968 TC TC T
1 TC TC T
31973 GTTATCTTAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:35617 original size:2 final size:2
Alignment explanation
Indices: 35612--35661 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
35602 ATATATATAT
35612 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
35654 AG AG AG AG
1 AG AG AG AG
35662 GTACATTTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:58265 original size:30 final size:30
Alignment explanation
Indices: 58231--58351 Score: 224
Period size: 30 Copynumber: 4.0 Consensus size: 30
58221 AATACGTTGC
58231 CGGTCCAATAGATCGCAGTCTATTGACCGG
1 CGGTCCAATAGATCGCAGTCTATTGACCGG
58261 CGGTCCAATAGATCGCAGTCTATTGACCGG
1 CGGTCCAATAGATCGCAGTCTATTGACCGG
58291 CGGTCCAATAGATCGCAGTCTATTGACCGG
1 CGGTCCAATAGATCGCAGTCTATTGACCGG
* *
58321 CGGTCTAATAGATCGTAGTCTATTGACCGG
1 CGGTCCAATAGATCGCAGTCTATTGACCGG
58351 C
1 C
58352 AGTTCAAAAT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 89 1.00
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.25
Consensus pattern (30 bp):
CGGTCCAATAGATCGCAGTCTATTGACCGG
Found at i:63194 original size:31 final size:32
Alignment explanation
Indices: 63159--63228 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
63149 TACCATTACC
* * *
63159 ATTACAA-TAGTTTTCAAATGTAATTAATTGA
1 ATTACAATTACTTTGCAAATGTAATTAATTAA
*
63190 ATTACAATTACTTTGCAGATGTAATTAATTAA
1 ATTACAATTACTTTGCAAATGTAATTAATTAA
63222 ATTACAA
1 ATTACAA
63229 ATTAAATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 7 0.21
32 27 0.79
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.40
Consensus pattern (32 bp):
ATTACAATTACTTTGCAAATGTAATTAATTAA
Found at i:64329 original size:13 final size:13
Alignment explanation
Indices: 64311--64335 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
64301 AATTACACTC
64311 AATTACCATTACA
1 AATTACCATTACA
64324 AATTACCATTAC
1 AATTACCATTAC
64336 CCCATCCCTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (13 bp):
AATTACCATTACA
Found at i:67085 original size:17 final size:17
Alignment explanation
Indices: 67063--67095 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
67053 TCGCATAGCC
67063 CCCTAACTCCGTCACTA
1 CCCTAACTCCGTCACTA
67080 CCCTAACTCCGTCACT
1 CCCTAACTCCGTCACT
67096 TTCGGGAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.48, G:0.06, T:0.24
Consensus pattern (17 bp):
CCCTAACTCCGTCACTA
Found at i:68522 original size:19 final size:18
Alignment explanation
Indices: 68486--68522 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
68476 ACGCCTGCCG
*
68486 ACGCCTGCCGGGGAAAAC
1 ACGCCTGCCGGAGAAAAC
68504 ACGCCTGCCGAGAGAAAAC
1 ACGCCTGCCG-GAGAAAAC
68523 CGCACGCCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.32, C:0.32, G:0.30, T:0.05
Consensus pattern (18 bp):
ACGCCTGCCGGAGAAAAC
Found at i:86919 original size:5 final size:5
Alignment explanation
Indices: 86911--86948 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
86901 TTAATATAAT
* *
86911 ATATC ATATC ATATC AAAAC ATATC ATATC ATATC ATA
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATA
86949 ATGAGGAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.34
Consensus pattern (5 bp):
ATATC
Found at i:105412 original size:17 final size:17
Alignment explanation
Indices: 105390--105422 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
105380 GATAGTGTCT
105390 ATTTGGTACTACCCAGC
1 ATTTGGTACTACCCAGC
105407 ATTTGGTACTACCCAG
1 ATTTGGTACTACCCAG
105423 TATATTTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.30
Consensus pattern (17 bp):
ATTTGGTACTACCCAGC
Found at i:105435 original size:19 final size:17
Alignment explanation
Indices: 105389--105425 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
105379 TGATAGTGTC
105389 TATTTGGTACTACCCAG
1 TATTTGGTACTACCCAG
*
105406 CATTTGGTACTACCCAG
1 TATTTGGTACTACCCAG
105423 TAT
1 TAT
105426 ATTTGATACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.35
Consensus pattern (17 bp):
TATTTGGTACTACCCAG
Found at i:105706 original size:23 final size:23
Alignment explanation
Indices: 105672--105728 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
105662 CAGCATATTT
*
105672 GATAGTTTCTAT-TTGGTACATTG
1 GATAGTTTCTATCCTGG-ACATTG
* *
105695 GATTGTTTCTATCCTGGACATTT
1 GATAGTTTCTATCCTGGACATTG
105718 GATAGTTTCTA
1 GATAGTTTCTA
105729 CCCAGTGCAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 26 0.90
24 3 0.10
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.47
Consensus pattern (23 bp):
GATAGTTTCTATCCTGGACATTG
Found at i:105852 original size:23 final size:24
Alignment explanation
Indices: 105802--105854 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
105792 TGAGTAGGAA
*
105802 CTATCCAATGTACAGTATATAAAT
1 CTATCCAATGCACAGTATATAAAT
105826 -TATCCAATGCACAG-A-ATAGAAT
1 CTATCCAATGCACAGTATATA-AAT
105848 CTATCCA
1 CTATCCA
105855 TTATCCAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 3 0.12
22 4 0.15
23 19 0.73
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (24 bp):
CTATCCAATGCACAGTATATAAAT
Found at i:105901 original size:22 final size:23
Alignment explanation
Indices: 105856--105906 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
105846 ATCTATCCAT
* *
105856 TATCCAATATACTGGGTAGGAAC
1 TATCCAATATACTGGATAGAAAC
*
105879 TATCCAAT-TACTGTATAGAAAC
1 TATCCAATATACTGGATAGAAAC
105901 TATCCA
1 TATCCA
105907 TTGTATATAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 17 0.68
23 8 0.32
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (23 bp):
TATCCAATATACTGGATAGAAAC
Found at i:106110 original size:23 final size:23
Alignment explanation
Indices: 106070--106127 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
106060 TTAATACTAG
* **
106070 GTAGAAACCATCCCATGTACAGA
1 GTAGAAACTATCAAATGTACAGA
* * *
106093 GTAGAAATTATCAAATGTACTGG
1 GTAGAAACTATCAAATGTACAGA
106116 GTAGAAACTATC
1 GTAGAAACTATC
106128 GAATAATTTA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (23 bp):
GTAGAAACTATCAAATGTACAGA
Found at i:107324 original size:23 final size:23
Alignment explanation
Indices: 107292--107387 Score: 86
Period size: 23 Copynumber: 4.2 Consensus size: 23
107282 GCAGTATTTT
* *
107292 GATAGTTTCTACCTAGTAAATTG
1 GATAGATTCTACCCAGTAAATTG
* *
107315 GGTAGATTCTACCCAGTCAATTG
1 GATAGATTCTACCCAGTAAATTG
* * * *
107338 GATAGCTTCTAGCAAGTACATTG
1 GATAGATTCTACCCAGTAAATTG
* * *
107361 GATAG-GTCTACCCAGTATATTT
1 GATAGATTCTACCCAGTAAATTG
107383 GATAG
1 GATAG
107388 TGTCTAGCCT
Statistics
Matches: 58, Mismatches: 15, Indels: 1
0.78 0.20 0.01
Matches are distributed among these distances:
22 17 0.29
23 41 0.71
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (23 bp):
GATAGATTCTACCCAGTAAATTG
Found at i:107387 original size:45 final size:45
Alignment explanation
Indices: 107283--107395 Score: 115
Period size: 45 Copynumber: 2.5 Consensus size: 45
107273 AGCTTCTATG
* * * *
107283 CAGTAT-TTTGATAGTTTCTACCTAGTAAATTGGGTAGATTCTACC
1 CAGTATATTTGATAG-TTCTAGCAAGTAAATTGGATAGAGTCTACC
* *
107328 CAGTCA-ATTGGATAGCTTCTAGCAAGTACATTGGATAG-GTCTACC
1 CAGT-ATATTTGATAG-TTCTAGCAAGTAAATTGGATAGAGTCTACC
107373 CAGTATATTTGATAGTGTCTAGC
1 CAGTATATTTGATAGT-TCTAGC
107396 CTTCACAATG
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
44 2 0.04
45 28 0.50
46 26 0.46
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.35
Consensus pattern (45 bp):
CAGTATATTTGATAGTTCTAGCAAGTAAATTGGATAGAGTCTACC
Found at i:107469 original size:23 final size:23
Alignment explanation
Indices: 107439--107482 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
107429 GAGAGATTCT
*
107439 ACCCAGAATATTTGATAGTTTTA
1 ACCCAGAACATTTGATAGTTTTA
*
107462 ACCCAGAACATTTTATAGTTT
1 ACCCAGAACATTTGATAGTTT
107483 CTACTCAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (23 bp):
ACCCAGAACATTTGATAGTTTTA
Found at i:110327 original size:17 final size:17
Alignment explanation
Indices: 110305--110337 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
110295 TTTGACTGTT
110305 ATATTCAAAATTGTGAA
1 ATATTCAAAATTGTGAA
110322 ATATTCAAAATTGTGA
1 ATATTCAAAATTGTGA
110338 TAAAAAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.36
Consensus pattern (17 bp):
ATATTCAAAATTGTGAA
Found at i:111381 original size:17 final size:17
Alignment explanation
Indices: 111361--111393 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
111351 AACTCTCAGT
111361 TTAGCCGATAACTGGTC
1 TTAGCCGATAACTGGTC
111378 TTAGCCGATAACTGGT
1 TTAGCCGATAACTGGT
111394 ACAGTACCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (17 bp):
TTAGCCGATAACTGGTC
Found at i:112891 original size:22 final size:22
Alignment explanation
Indices: 112828--114204 Score: 985
Period size: 22 Copynumber: 62.5 Consensus size: 22
112818 CTATACATGT
112828 ACTACAAGTGA-TGCTTCTCTAC
1 ACTACAAGT-ATTGCTTCTCTAC
* *
112850 ACTACATGTATATTGC--CTCTAT
1 ACTACAAG--TATTGCTTCTCTAC
112872 ACTACAAGTATTGCTTCTCTAC
1 ACTACAAGTATTGCTTCTCTAC
* * * * * *
112894 AATGCATGAATTGCCTCTCTAT
1 ACTACAAGTATTGCTTCTCTAC
* **
112916 ACTACAAGTATTGCCTCTAAAC
1 ACTACAAGTATTGCTTCTCTAC
* * *
112938 ACCACATGTATTGCTGCTCTAC
1 ACTACAAGTATTGCTTCTCTAC
* * *
112960 AGTACAAGTACTGCTGCTCTAC
1 ACTACAAGTATTGCTTCTCTAC
* * *
112982 -TTACATGTATTGCCTCTCTAC
1 ACTACAAGTATTGCTTCTCTAC
*
113003 ACTACATGTATTG-TCTCTCTAC
1 ACTACAAGTATTGCT-TCTCTAC
* *
113025 ACTACAAGTATTGCCTCTCTAT
1 ACTACAAGTATTGCTTCTCTAC
* *
113047 ACTACATGTATTGC--CTCTAT
1 ACTACAAGTATTGCTTCTCTAC
* *
113067 ACAACAAGTATTGCTTCTTTAC
1 ACTACAAGTATTGCTTCTCTAC
* * * *
113089 AATGCAAGTATTGCCTCTCTAT
1 ACTACAAGTATTGCTTCTCTAC
* *
113111 ACTACAAGTATTGCCTCCCTATAC
1 ACTACAAGTATTG-CT-TCTCTAC
* *
113135 ACTACATGTATT-ATCTCTCTAC
1 ACTACAAGTATTGCT-TCTCTAC
*
113157 ACTACATGTATTG-TCTCTCTAC
1 ACTACAAGTATTGCT-TCTCTAC
*
113179 ACTACAAGCATTGC--CTCTAC
1 ACTACAAGTATTGCTTCTCTAC
* * * *
113199 ACCACATGTATTGCCTCTCTAT
1 ACTACAAGTATTGCTTCTCTAC
* * * * *
113221 ACCACATGTATTGCCTCTCAAT
1 ACTACAAGTATTGCTTCTCTAC
* *
113243 ATTACATGTATTGCGGCTATTGCCTCT-C
1 ACTACAAGTATT---GC--TT--CTCTAC
113271 TAC-ACTACACGTATTG-TCTCTCTAC
1 -ACTAC-A-A-GTATTGCT-TCTCTAC
* *
113296 ACTACATGTATTG-TCTCTCTTC
1 ACTACAAGTATTGCT-TCTCTAC
*
113318 ACTACATGTATTG-TCTCTCTAC
1 ACTACAAGTATTGCT-TCTCTAC
* *
113340 ACTACATGTATAG-TCTCTCTAC
1 ACTACAAGTATTGCT-TCTCTAC
*
113362 ACTACAAGTATTGC--CTCTAT
1 ACTACAAGTATTGCTTCTCTAC
* *
113382 ACAACAAGTATTGCTTCTTTAC
1 ACTACAAGTATTGCTTCTCTAC
* * * *
113404 AATGCAAGTATTGCCTCTCTAT
1 ACTACAAGTATTGCTTCTCTAC
* *
113426 ACTACAAGTATTGCCTCCCTATAC
1 ACTACAAGTATTG-CT-TCTCTAC
* * * *
113450 ACTACATGTATTACCTCTCTTC
1 ACTACAAGTATTGCTTCTCTAC
113472 ACTACAAGTATTG-TCTCTCTAC
1 ACTACAAGTATTGCT-TCTCTAC
*
113494 ACTACATGTATTG-TCTCTCTAC
1 ACTACAAGTATTGCT-TCTCTAC
* *
113516 ACCACATGTATTG-TCTCTCTAC
1 ACTACAAGTATTGCT-TCTCTAC
* *
113538 ACTACATGTACTG-TCTCTCTAC
1 ACTACAAGTATTGCT-TCTCTAC
*
113560 ACTACATGTATTG-TCTCTCTAC
1 ACTACAAGTATTGCT-TCTCTAC
*
113582 ACTACATGTATTG-TCTCTCTAC
1 ACTACAAGTATTGCT-TCTCTAC
*
113604 A--ACAAGTATTGCTTCTTTAC
1 ACTACAAGTATTGCTTCTCTAC
* * *
113624 AATGCAAGTATTGCCTCTCTAC
1 ACTACAAGTATTGCTTCTCTAC
* *
113646 ACTACAAGTATTGCCTCTCTAT
1 ACTACAAGTATTGCTTCTCTAC
113668 ACTACAAGTATTG-TCTCTCTAC
1 ACTACAAGTATTGCT-TCTCTAC
* *
113690 ACTACAAGTATTGCCTCTCTAT
1 ACTACAAGTATTGCTTCTCTAC
*
113712 ACTACATGTATTG-TCTCTCTAC
1 ACTACAAGTATTGCT-TCTCTAC
* *
113734 ACTACAAGTATTGCCTCTCTAT
1 ACTACAAGTATTGCTTCTCTAC
*
113756 ACTACAAGTATTG-TCTCTCTAT
1 ACTACAAGTATTGCT-TCTCTAC
113778 ACTACAAGTATTG-TCTCTCTAC
1 ACTACAAGTATTGCT-TCTCTAC
* *
113800 ACTACATGTACTG-TCTCTCTAC
1 ACTACAAGTATTGCT-TCTCTAC
*
113822 ACTACAAGTATTGC--CTCTAT
1 ACTACAAGTATTGCTTCTCTAC
113842 ACTACAAGTATTGCTTCTCTAC
1 ACTACAAGTATTGCTTCTCTAC
* *
113864 AATGCAAGTATTGCTTCTCTAC
1 ACTACAAGTATTGCTTCTCTAC
* *
113886 ACTACATGTATTG-TCTCTCTAT
1 ACTACAAGTATTGCT-TCTCTAC
113908 ACTACAAGTATTG-TCTCTCTAC
1 ACTACAAGTATTGCT-TCTCTAC
*
113930 ACTACATGTATTG-TCTCTCTAC
1 ACTACAAGTATTGCT-TCTCTAC
* *
113952 ACTACACGTATTG-TCTCCCTAC
1 ACTACAAGTATTGCT-TCTCTAC
* *
113974 ACTACATGTACTG-TCTCTCTAC
1 ACTACAAGTATTGCT-TCTCTAC
* *
113996 ACTACATGTACTG-TCTCTCTAC
1 ACTACAAGTATTGCT-TCTCTAC
* *
114018 ACTACATGTATTG-TCTCCCTAC
1 ACTACAAGTATTGCT-TCTCTAC
* * *
114040 ACTACATGTACTG-TCTCTTTAC
1 ACTACAAGTATTGCT-TCTCTAC
* *
114062 ACTACATGTACTG-TCTCTCTAC
1 ACTACAAGTATTGCT-TCTCTAC
*
114084 ACTACAAGTATTG-TCTCTCTAT
1 ACTACAAGTATTGCT-TCTCTAC
114106 ACTACAAGTATTG-TCTCTCTAC
1 ACTACAAGTATTGCT-TCTCTAC
*
114128 ACTACAAGTATTGCCTCTCTAC
1 ACTACAAGTATTGCTTCTCTAC
*
114150 ACTACATGTATTGGC-TCTCTAC
1 ACTACAAGTATT-GCTTCTCTAC
*
114172 ACTACATGTATTG-TCTCTCTAC
1 ACTACAAGTATTGCT-TCTCTAC
*
114194 ACTACATGTAT
1 ACTACAAGTAT
114205 GATTTAGGTC
Statistics
Matches: 1142, Mismatches: 161, Indels: 104
0.81 0.11 0.07
Matches are distributed among these distances:
20 94 0.08
21 19 0.02
22 961 0.84
23 6 0.01
24 41 0.04
25 6 0.01
26 1 0.00
27 1 0.00
28 3 0.00
29 5 0.00
31 5 0.00
ACGTcount: A:0.26, C:0.28, G:0.10, T:0.37
Consensus pattern (22 bp):
ACTACAAGTATTGCTTCTCTAC
Found at i:112949 original size:66 final size:66
Alignment explanation
Indices: 112866--114204 Score: 1384
Period size: 66 Copynumber: 20.3 Consensus size: 66
112856 TGTATATTGC
* * * * * * *
112866 CTCTATACTACAAGTATTG-CTTCTCTACAATGCATGAATTGCCTCTCTATACTACAAGTATTGC
1 CTCTACACTACATGTATTGTC-TCTCTACACTACAAGTATTGTCTCTCTATACTACAAGTATTGC
112930 CT
65 CT
** * * * *
112932 CTAAACACCACATGTATTG-CTGCTCTACAGTACAAGTACTG-CTGCTC--TACTTACATGTATT
1 CTCTACACTACATGTATTGTCT-CTCTACACTACAAGTATTGTCT-CTCTATAC-TACAAGTATT
112993 GCCT
63 GCCT
* *
112997 CTCTACACTACATGTATTGTCTCTCTACACTACAAGTATTGCCTCTCTATACTACATGTATTGCC
1 CTCTACACTACATGTATTGTCTCTCTACACTACAAGTATTGTCTCTCTATACTACAAGTATTGCC
113062 T
66 T
* * * * * *
113063 CTATACA--ACAAGTATTG-CTTCTTTACAATGCAAGTATTGCCTCTCTATACTACAAGTATTGC
1 CTCTACACTACATGTATTGTC-TCTCTACACTACAAGTATTGTCTCTCTATACTACAAGTATTGC
113125 CT
65 CT
* * * * *
113127 CCCTATACACTACATGTATTATCTCTCTACACTACATGTATTGTCTCTCTACACTACAAGCATTG
1 --CTCTACACTACATGTATTGTCTCTCTACACTACAAGTATTGTCTCTCTATACTACAAGTATTG
113192 -C-
64 CCT
* * * * * * * *
113193 CTCTACACCACATGTATTGCCTCTCTATACCACATGTATTGCCTCTCAATATTACATGTATTGCG
1 CTCTACACTACATGTATTGTCTCTCTACACTACAAGTATTGTCTCTCTATACTACA---A-----
113258 GCTATTGCCT
58 G-TATTGCCT
* * * *
113268 CTCTACACTACACGTATTGTCTCTCTACACTACATGTATTGTCTCTCT-TCACTACATGTATTGT
1 CTCTACACTACATGTATTGTCTCTCTACACTACAAGTATTGTCTCTCTAT-ACTACAAGTATTGC
113332 CT
65 CT
* * *
113334 CTCTACACTACATGTATAGTCTCTCTACACTACAAGTATTG-C-CTCTATACAACAAGTATTGCT
1 CTCTACACTACATGTATTGTCTCTCTACACTACAAGTATTGTCTCTCTATACTACAAGTATTGCC
113397 T
66 T
* * * * * * * * * *
113398 CTTTACAATGCAAGTATTGCCTCTCTATACTACAAGTATTGCCTCCCTATACACTACATGTATTA
1 CTCTACACTACATGTATTGTCTCTCTACACTACAAGTATTGTCTCTCTAT--ACTACAAGTATTG
113463 CCT
64 CCT
* * * * * * *
113466 CTCTTCACTACAAGTATTGTCTCTCTACACTACATGTATTGTCTCTCTACACCACATGTATTGTC
1 CTCTACACTACATGTATTGTCTCTCTACACTACAAGTATTGTCTCTCTATACTACAAGTATTGCC
113531 T
66 T
* * * * *
113532 CTCTACACTACATGTACTGTCTCTCTACACTACATGTATTGTCTCTCTACACTACATGTATTGTC
1 CTCTACACTACATGTATTGTCTCTCTACACTACAAGTATTGTCTCTCTATACTACAAGTATTGCC
113597 T
66 T
* * * * * *
113598 CTCTACA--ACAAGTATTG-CTTCTTTACAATGCAAGTATTGCCTCTCTACACTACAAGTATTGC
1 CTCTACACTACATGTATTGTC-TCTCTACACTACAAGTATTGTCTCTCTATACTACAAGTATTGC
113660 CT
65 CT
* * * * *
113662 CTCTATACTACAAGTATTGTCTCTCTACACTACAAGTATTGCCTCTCTATACTACATGTATTGTC
1 CTCTACACTACATGTATTGTCTCTCTACACTACAAGTATTGTCTCTCTATACTACAAGTATTGCC
113727 T
66 T
* * * *
113728 CTCTACACTACAAGTATTGCCTCTCTATACTACAAGTATTGTCTCTCTATACTACAAGTATTGTC
1 CTCTACACTACATGTATTGTCTCTCTACACTACAAGTATTGTCTCTCTATACTACAAGTATTGCC
113793 T
66 T
* *
113794 CTCTACACTACATGTACTGTCTCTCTACACTACAAGTATTG-C-CTCTATACTACAAGTATTGCT
1 CTCTACACTACATGTATTGTCTCTCTACACTACAAGTATTGTCTCTCTATACTACAAGTATTGCC
113857 T
66 T
* * * * *
113858 CTCTACAATGCAAGTATTG-CTTCTCTACACTACATGTATTGTCTCTCTATACTACAAGTATTGT
1 CTCTACACTACATGTATTGTC-TCTCTACACTACAAGTATTGTCTCTCTATACTACAAGTATTGC
113922 CT
65 CT
* * * * * *
113924 CTCTACACTACATGTATTGTCTCTCTACACTACACGTATTGTCTCCCTACACTACATGTACTGTC
1 CTCTACACTACATGTATTGTCTCTCTACACTACAAGTATTGTCTCTCTATACTACAAGTATTGCC
113989 T
66 T
* * * * * * *
113990 CTCTACACTACATGTACTGTCTCTCTACACTACATGTATTGTCTCCCTACACTACATGTACTGTC
1 CTCTACACTACATGTATTGTCTCTCTACACTACAAGTATTGTCTCTCTATACTACAAGTATTGCC
114055 T
66 T
* * *
114056 CTTTACACTACATGTACTGTCTCTCTACACTACAAGTATTGTCTCTCTATACTACAAGTATTGTC
1 CTCTACACTACATGTATTGTCTCTCTACACTACAAGTATTGTCTCTCTATACTACAAGTATTGCC
114121 T
66 T
* * * * * * *
114122 CTCTACACTACAAGTATTGCCTCTCTACACTACATGTATTGGCTCTCTACACTACATGTATTGTC
1 CTCTACACTACATGTATTGTCTCTCTACACTACAAGTATTGTCTCTCTATACTACAAGTATTGCC
114187 T
66 T
114188 CTCTACACTACATGTAT
1 CTCTACACTACATGTAT
114205 GATTTAGGTC
Statistics
Matches: 1088, Mismatches: 147, Indels: 76
0.83 0.11 0.06
Matches are distributed among these distances:
63 3 0.00
64 255 0.23
65 57 0.05
66 616 0.57
67 8 0.01
68 95 0.09
69 1 0.00
72 1 0.00
73 4 0.00
74 2 0.00
75 46 0.04
ACGTcount: A:0.26, C:0.28, G:0.10, T:0.37
Consensus pattern (66 bp):
CTCTACACTACATGTATTGTCTCTCTACACTACAAGTATTGTCTCTCTATACTACAAGTATTGCC
T
Found at i:113292 original size:53 final size:53
Alignment explanation
Indices: 113207--113308 Score: 141
Period size: 53 Copynumber: 1.9 Consensus size: 53
113197 ACACCACATG
* * * *
113207 TATTGCCTCTCTATACCACATGTATTGCCTCTCAATATTACATGTATTGCGGC
1 TATTGCCTCTCTACACCACACGTATTGCCTCTCAACACTACATGTATTGCGGC
* * *
113260 TATTGCCTCTCTACACTACACGTATTGTCTCTCTACACTACATGTATTG
1 TATTGCCTCTCTACACCACACGTATTGCCTCTCAACACTACATGTATTG
113309 TCTCTCTTCA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 42 1.00
ACGTcount: A:0.23, C:0.27, G:0.12, T:0.38
Consensus pattern (53 bp):
TATTGCCTCTCTACACCACACGTATTGCCTCTCAACACTACATGTATTGCGGC
Found at i:140330 original size:19 final size:20
Alignment explanation
Indices: 140291--140335 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
140281 ATGTCAAAAT
*
140291 TTGA-AAGCCAAATATCAAG
1 TTGATAAGCAAAATATCAAG
140310 TT-ATAAGCAAAATA-CAGAG
1 TTGATAAGCAAAATATCA-AG
140329 TTGATAA
1 TTGATAA
140336 TTCTTTGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 3 0.14
19 15 0.68
20 4 0.18
ACGTcount: A:0.49, C:0.11, G:0.16, T:0.24
Consensus pattern (20 bp):
TTGATAAGCAAAATATCAAG
Found at i:156202 original size:64 final size:64
Alignment explanation
Indices: 156101--156223 Score: 228
Period size: 64 Copynumber: 1.9 Consensus size: 64
156091 CTACCTAGCC
*
156101 GGGGGAAGGCCTAGGTTTAATTCAAAAATCCCTTTTAATAAGAACCTTACACTTAACTTAGCTG
1 GGGGGAAGGCCTAGGTTTAATACAAAAATCCCTTTTAATAAGAACCTTACACTTAACTTAGCTG
*
156165 GGGGGAAGGCCTAGGTTTAATACATAAATCCCTTTTAATAAGAACCTTACACTTAACTT
1 GGGGGAAGGCCTAGGTTTAATACAAAAATCCCTTTTAATAAGAACCTTACACTTAACTT
156224 TTAGTCTAAG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (64 bp):
GGGGGAAGGCCTAGGTTTAATACAAAAATCCCTTTTAATAAGAACCTTACACTTAACTTAGCTG
Found at i:159273 original size:51 final size:51
Alignment explanation
Indices: 159155--159273 Score: 166
Period size: 51 Copynumber: 2.3 Consensus size: 51
159145 ATCGTTCTCC
* * *
159155 GGCTCCTCCAGGCTGAAGGTCTCTGGCGGGGTCTGGACTACATCTTCCTCA
1 GGCTCCTCCAGGCTGATGCTCTCTGGCGGCGTCTGGACTACATCTTCCTCA
* * * *
159206 GGCTCATCCAGGCTGATGCTCTCTGGCGTCGTCTGGTCTACATCTTTCTCA
1 GGCTCCTCCAGGCTGATGCTCTCTGGCGGCGTCTGGACTACATCTTCCTCA
*
159257 TGCTCCTCCAGGCTGAT
1 GGCTCCTCCAGGCTGAT
159274 CCTCCCCAGG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.13, C:0.32, G:0.26, T:0.29
Consensus pattern (51 bp):
GGCTCCTCCAGGCTGATGCTCTCTGGCGGCGTCTGGACTACATCTTCCTCA
Found at i:162477 original size:38 final size:38
Alignment explanation
Indices: 162435--162553 Score: 100
Period size: 38 Copynumber: 3.2 Consensus size: 38
162425 TACAATAGGG
162435 GTACCAAAATAAATACTGTAACTTTGGTCAATTGTGCT
1 GTACCAAAATAAATACTGTAACTTTGGTCAATTGTGCT
* * *** * * ** * *
162473 GTACCACATTCCCT-CAGGAGTTATTGGTACAATAG-G-G
1 GTACCAAAATAAATACTGTAACT-TTGGT-CAATTGTGCT
162510 GTACCAAAATAAATACTGTAACTTTGGTCAATTGTGCT
1 GTACCAAAATAAATACTGTAACTTTGGTCAATTGTGCT
162548 GTACCA
1 GTACCA
162554 CATTCTGGAC
Statistics
Matches: 54, Mismatches: 22, Indels: 10
0.63 0.26 0.12
Matches are distributed among these distances:
36 5 0.09
37 19 0.35
38 25 0.46
39 5 0.09
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Consensus pattern (38 bp):
GTACCAAAATAAATACTGTAACTTTGGTCAATTGTGCT
Found at i:162502 original size:75 final size:75
Alignment explanation
Indices: 162413--162558 Score: 292
Period size: 75 Copynumber: 1.9 Consensus size: 75
162403 TTCCTCTAGG
162413 AGGAGTTATTGGTACAATAGGGGTACCAAAATAAATACTGTAACTTTGGTCAATTGTGCTGTACC
1 AGGAGTTATTGGTACAATAGGGGTACCAAAATAAATACTGTAACTTTGGTCAATTGTGCTGTACC
162478 ACATTCCCTC
66 ACATTCCCTC
162488 AGGAGTTATTGGTACAATAGGGGTACCAAAATAAATACTGTAACTTTGGTCAATTGTGCTGTACC
1 AGGAGTTATTGGTACAATAGGGGTACCAAAATAAATACTGTAACTTTGGTCAATTGTGCTGTACC
162553 ACATTC
66 ACATTC
162559 TGGACATCCT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.31
Consensus pattern (75 bp):
AGGAGTTATTGGTACAATAGGGGTACCAAAATAAATACTGTAACTTTGGTCAATTGTGCTGTACC
ACATTCCCTC
Found at i:164518 original size:14 final size:15
Alignment explanation
Indices: 164496--164524 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
164486 AGATATAAAT
164496 AAATGAAAGAAATTA
1 AAATGAAAGAAATTA
164511 AAAT-AAAGAAATTA
1 AAATGAAAGAAATTA
164525 TAAAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (15 bp):
AAATGAAAGAAATTA
Found at i:167811 original size:11 final size:11
Alignment explanation
Indices: 167783--167812 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
167773 CCCCCCCCCC
167783 AAAAAAA-AAA
1 AAAAAAACAAA
167793 AAAAAAACAAA
1 AAAAAAACAAA
167804 AAAAAAACA
1 AAAAAAACA
167813 GACGCTAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.37
11 12 0.63
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:177088 original size:40 final size:40
Alignment explanation
Indices: 177033--177142 Score: 202
Period size: 40 Copynumber: 2.8 Consensus size: 40
177023 CTGTAGGCAG
* *
177033 AGACCGTTTACACCAAGTGTACACAATGTACAAAGCGTAT
1 AGACCGTTTACACCAAGTATACACAATGTACAAAGCGAAT
177073 AGACCGTTTACACCAAGTATACACAATGTACAAAGCGAAT
1 AGACCGTTTACACCAAGTATACACAATGTACAAAGCGAAT
177113 AGACCGTTTACACCAAGTATACACAATGTA
1 AGACCGTTTACACCAAGTATACACAATGTA
177143 TCATCGGTTA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 68 1.00
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.22
Consensus pattern (40 bp):
AGACCGTTTACACCAAGTATACACAATGTACAAAGCGAAT
Found at i:177092 original size:20 final size:20
Alignment explanation
Indices: 177069--177133 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
177059 TGTACAAAGC
177069 GTATAGACCGTTTACACCAA
1 GTATAGACCGTTTACACCAA
* ** *
177089 GTATACACAATGTACA--AA
1 GTATAGACCGTTTACACCAA
*
177107 GCGAATAGACCGTTTACACCAA
1 --GTATAGACCGTTTACACCAA
177129 GTATA
1 GTATA
177134 CACAATGTAT
Statistics
Matches: 31, Mismatches: 10, Indels: 8
0.63 0.20 0.16
Matches are distributed among these distances:
18 2 0.06
20 27 0.87
22 2 0.06
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.23
Consensus pattern (20 bp):
GTATAGACCGTTTACACCAA
Found at i:177912 original size:15 final size:15
Alignment explanation
Indices: 177850--177904 Score: 101
Period size: 15 Copynumber: 3.7 Consensus size: 15
177840 GGAGTCAGTC
177850 GATTTCTCTGGAGAG
1 GATTTCTCTGGAGAG
177865 GATTTCTCTGGAGAG
1 GATTTCTCTGGAGAG
*
177880 GATTTCTCTGGCGAG
1 GATTTCTCTGGAGAG
177895 GATTTCTCTG
1 GATTTCTCTG
177905 ACAAGGATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.16, C:0.16, G:0.31, T:0.36
Consensus pattern (15 bp):
GATTTCTCTGGAGAG
Found at i:177912 original size:30 final size:30
Alignment explanation
Indices: 177850--177912 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
177840 GGAGTCAGTC
*
177850 GATTTCTCTGGAGAGGATTTCTCTGGAGAG
1 GATTTCTCTGGAGAGGATTTCTCTGGAAAG
*
177880 GATTTCTCTGGCGAGGATTTCTCT-GACAAG
1 GATTTCTCTGGAGAGGATTTCTCTGGA-AAG
177910 GAT
1 GAT
177913 AAGGATTTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 2 0.07
30 28 0.93
ACGTcount: A:0.21, C:0.16, G:0.30, T:0.33
Consensus pattern (30 bp):
GATTTCTCTGGAGAGGATTTCTCTGGAAAG
Found at i:177947 original size:21 final size:21
Alignment explanation
Indices: 177893--177954 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
177883 TTCTCTGGCG
* *
177893 AGGATTTCTCTGACAAGGATA
1 AGGATTTCTCTGGCGAGGATA
177914 AGGATTTCTCTGGCGAGGATA
1 AGGATTTCTCTGGCGAGGATA
177935 AGGATTTCTCTGGCGAGGAT
1 AGGATTTCTCTGGCGAGGAT
177955 TCCGATGTAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.29
Consensus pattern (21 bp):
AGGATTTCTCTGGCGAGGATA
Found at i:178109 original size:12 final size:13
Alignment explanation
Indices: 178087--178115 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
178077 TATTGTTAAG
178087 GCAGAAGATGTCA
1 GCAGAAGATGTCA
178100 GCAG-AGATGTCA
1 GCAGAAGATGTCA
178112 GCAG
1 GCAG
178116 GGCATGAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.34, C:0.17, G:0.34, T:0.14
Consensus pattern (13 bp):
GCAGAAGATGTCA
Found at i:207387 original size:33 final size:33
Alignment explanation
Indices: 207270--207377 Score: 155
Period size: 33 Copynumber: 3.3 Consensus size: 33
207260 TTGTGTCGAT
* *
207270 CTCTGGAATCATCTCGGTACTGTTCATGTCGAC
1 CTCTGGAATCATCTCGGTACCGTTCATGTTGAC
*
207303 CTCTGGAATCATCTCGGTACCGTTCGTGTTGAC
1 CTCTGGAATCATCTCGGTACCGTTCATGTTGAC
* *
207336 CTCTGTAAGT-GTCTCGGTACCGTTCATGTTGAC
1 CTCTGGAA-TCATCTCGGTACCGTTCATGTTGAC
207369 CTCTGGAAT
1 CTCTGGAAT
207378 TGTCGCGGTA
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
32 1 0.01
33 65 0.97
34 1 0.01
ACGTcount: A:0.17, C:0.26, G:0.23, T:0.34
Consensus pattern (33 bp):
CTCTGGAATCATCTCGGTACCGTTCATGTTGAC
Found at i:215452 original size:16 final size:16
Alignment explanation
Indices: 215427--215458 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
215417 CATAAAGACA
*
215427 ATGTGTAAAGCTATGT
1 ATGTGCAAAGCTATGT
215443 ATGTGCAAAGCTATGT
1 ATGTGCAAAGCTATGT
215459 TGTTGTAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.09, G:0.25, T:0.34
Consensus pattern (16 bp):
ATGTGCAAAGCTATGT
Found at i:216998 original size:41 final size:40
Alignment explanation
Indices: 216941--217021 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 40
216931 AATGCATTTT
* * * *
216941 AATTATGAATGTTTGAATATATTTTATGTTTTTCTTGTAC
1 AATTATGAATATTTGAATATAGTATATGTTTTTCCTGTAC
216981 AATTATAGAATATTTGAATATAGTATATGTTTTTCCTGTAC
1 AATTAT-GAATATTTGAATATAGTATATGTTTTTCCTGTAC
217022 TATTTCAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 6 0.17
41 30 0.83
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.51
Consensus pattern (40 bp):
AATTATGAATATTTGAATATAGTATATGTTTTTCCTGTAC
Found at i:218757 original size:21 final size:22
Alignment explanation
Indices: 218726--218774 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
218716 AAGTTGTTCC
*
218726 TGAAAATTCATGCACCAATATG
1 TGAAAAGTCATGCACCAATATG
* *
218748 -GAAAAGTCATGCATCAATGTG
1 TGAAAAGTCATGCACCAATATG
218769 TGAAAA
1 TGAAAA
218775 TGACTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.24
Consensus pattern (22 bp):
TGAAAAGTCATGCACCAATATG
Found at i:229302 original size:2 final size:2
Alignment explanation
Indices: 229295--229339 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
229285 CTTTATTGAG
* * *
229295 TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC TC -C CC CC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
229336 TC TC
1 TC TC
229340 AGGTCTTAGG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:254411 original size:6 final size:6
Alignment explanation
Indices: 254402--254426 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
254392 CACCCCCCAA
254402 AAAAAC AAAAAC AAAAAC AAAAAC A
1 AAAAAC AAAAAC AAAAAC AAAAAC A
254427 CACATACAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:256369 original size:21 final size:21
Alignment explanation
Indices: 256335--256414 Score: 90
Period size: 21 Copynumber: 3.8 Consensus size: 21
256325 AAATTCATGC
* * *
256335 TATGCTATGGTATGTGATTT-
1 TATGATATGCTATGAGATTTG
256355 TAATGATATGCTATGAGATTTG
1 T-ATGATATGCTATGAGATTTG
*
256377 TATGCTATGCTATGAGATTTG
1 TATGATATGCTATGAGATTTG
**
256398 TATGCCATGCTATGAGA
1 TATGATATGCTATGAGA
256415 AATTGAAATG
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
20 1 0.02
21 51 0.96
22 1 0.02
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.41
Consensus pattern (21 bp):
TATGATATGCTATGAGATTTG
Found at i:256383 original size:42 final size:42
Alignment explanation
Indices: 256335--256414 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
256325 AAATTCATGC
* * *
256335 TATGCTATGGTATGTGATTT-TAATGATATGCTATGAGATTTG
1 TATGCTATGCTATGAGATTTGT-ATGACATGCTATGAGATTTG
*
256377 TATGCTATGCTATGAGATTTGTATGCCATGCTATGAGA
1 TATGCTATGCTATGAGATTTGTATGACATGCTATGAGA
256415 AATTGAAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 32 0.97
43 1 0.03
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.41
Consensus pattern (42 bp):
TATGCTATGCTATGAGATTTGTATGACATGCTATGAGATTTG
Found at i:256458 original size:15 final size:15
Alignment explanation
Indices: 256438--256471 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
256428 GGCTTAATGA
256438 TATGGTATGCTATAC
1 TATGGTATGCTATAC
* *
256453 TATGGTATGGTATGC
1 TATGGTATGCTATAC
256468 TATG
1 TATG
256472 AGATTTGAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.09, G:0.26, T:0.41
Consensus pattern (15 bp):
TATGGTATGCTATAC
Found at i:256744 original size:21 final size:21
Alignment explanation
Indices: 256669--256744 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
256659 TGAGATTGAT
* *
256669 TGCTATGGTATGAGG-TTCCAA
1 TGCTATGCTATG-GGATTTCAA
** *
256690 TGCTATGCTATGAAATTTAAA
1 TGCTATGCTATGGGATTTCAA
*
256711 TGATATGCTATGGGATTTCAA
1 TGCTATGCTATGGGATTTCAA
256732 TGCTATGCTATGG
1 TGCTATGCTATGG
256745 TGTATGTTGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.37
Consensus pattern (21 bp):
TGCTATGCTATGGGATTTCAA
Found at i:263575 original size:20 final size:20
Alignment explanation
Indices: 263550--263590 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
263540 ACGAGGTAAG
263550 TTCTTATATG-CATTCATATT
1 TTCTTA-ATGACATTCATATT
263570 TTCTTAATGACATTCATATT
1 TTCTTAATGACATTCATATT
263590 T
1 T
263591 AAATACATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.27, C:0.15, G:0.05, T:0.54
Consensus pattern (20 bp):
TTCTTAATGACATTCATATT
Found at i:269159 original size:4 final size:4
Alignment explanation
Indices: 269150--269209 Score: 65
Period size: 4 Copynumber: 15.8 Consensus size: 4
269140 TAATTTTGTT
* *
269150 TTTG TTTG TTTG TTTG -GTG TTTT TTTG TTT- TTT- TTT- TTTGG TTTG
1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTT-G TTTG
269195 TTTG TTTG TTTG TTT
1 TTTG TTTG TTTG TTT
269210 TTGTCGTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
3 11 0.22
4 35 0.71
5 3 0.06
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (4 bp):
TTTG
Found at i:269175 original size:37 final size:38
Alignment explanation
Indices: 269143--269228 Score: 122
Period size: 39 Copynumber: 2.3 Consensus size: 38
269133 CTTTTTTTAA
269143 TTTTGTTTTT-GTTTGTTTGTTTG-GTGTTTTTTTGTT
1 TTTTGTTTTTGGTTTGTTTGTTTGTGTGTTTTTTTGTT
* * *
269179 TTTTTTTTTTGGTTTGTTTGTTTGTTTGTTTTTGTCGTT
1 TTTTGTTTTTGGTTTGTTTGTTTGTGTGTTTTT-TTGTT
269218 TTTTGTTTTTG
1 TTTTGTTTTTG
269229 TAAAGGTGGG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 9 0.21
37 13 0.30
38 7 0.16
39 14 0.33
ACGTcount: A:0.00, C:0.01, G:0.21, T:0.78
Consensus pattern (38 bp):
TTTTGTTTTTGGTTTGTTTGTTTGTGTGTTTTTTTGTT
Found at i:269227 original size:8 final size:8
Alignment explanation
Indices: 269148--269227 Score: 60
Period size: 8 Copynumber: 10.4 Consensus size: 8
269138 TTTAATTTTG
269148 TTTTTGTT
1 TTTTTGTT
*
269156 TGTTTG-T
1 TTTTTGTT
**
269163 TTGGTGTT
1 TTTTTGTT
269171 TTTTTG-T
1 TTTTTGTT
269178 TTTTT-TT
1 TTTTTGTT
*
269185 TTTTGGTT
1 TTTTTGTT
*
269193 TGTTTGTT
1 TTTTTGTT
*
269201 TGTTTGTT
1 TTTTTGTT
*
269209 TTTGTCG-T
1 TTT-TTGTT
269217 TTTTTGTT
1 TTTTTGTT
269225 TTT
1 TTT
269228 GTAAAGGTGG
Statistics
Matches: 55, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
7 17 0.31
8 36 0.65
9 2 0.04
ACGTcount: A:0.00, C:0.01, G:0.20, T:0.79
Consensus pattern (8 bp):
TTTTTGTT
Found at i:279981 original size:4 final size:4
Alignment explanation
Indices: 279964--280011 Score: 78
Period size: 4 Copynumber: 12.0 Consensus size: 4
279954 TTCTACTTAC
* *
279964 ATAA ATAC ATAA ATAA ATAA ATAA ATAA ATAA ATAA AAAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
280012 CAAATCTAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (4 bp):
ATAA
Found at i:288685 original size:21 final size:21
Alignment explanation
Indices: 288651--288728 Score: 113
Period size: 21 Copynumber: 3.7 Consensus size: 21
288641 GGCAAGTCTT
*
288651 ACCACAGTCAAGACAAT-TTTC
1 ACCACAGTCAAGAC-ATGTTAC
* *
288672 ACCTCAGCCAAGACATGTTAC
1 ACCACAGTCAAGACATGTTAC
288693 ACCACAGTCAAGACATGTTAC
1 ACCACAGTCAAGACATGTTAC
288714 ACCACAGTCAAGACA
1 ACCACAGTCAAGACA
288729 AATGGGCCCT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 2 0.04
21 49 0.96
ACGTcount: A:0.38, C:0.31, G:0.13, T:0.18
Consensus pattern (21 bp):
ACCACAGTCAAGACATGTTAC
Found at i:290857 original size:130 final size:129
Alignment explanation
Indices: 290624--290882 Score: 500
Period size: 130 Copynumber: 2.0 Consensus size: 129
290614 ATCCACCAAT
290624 ACAGCAGACACACGGTTACCAATCACACTGGACATTTTACAAACCATTATCCCAAACCTTCAATT
1 ACAGCAGACACACGGTTACCAATCACACTGGACATTTTACAAACCATTATCCCAAACCTTCAATT
*
290689 TGTTTGCTCTAGCAATTATGAAACCTCATTGTATAAGGCTGCCTTTTCCCTTGCATTCCATGCA
66 TGTTTGCTATAGCAATTATGAAACCTCATTGTATAAGGCTGCCTTTTCCCTTGCATTCCATGCA
290753 NACAGCAGACACACGGTTACCAATCACACTGGACATTTTACAAACCATTATCCCAAACCTTCAAT
1 -ACAGCAGACACACGGTTACCAATCACACTGGACATTTTACAAACCATTATCCCAAACCTTCAAT
290818 TTGTTTGCTATAGCAATTATGAAACCTCATTGTATAAGGCTGCCTTTTCCCTTGCATTCCATGCA
65 TTGTTTGCTATAGCAATTATGAAACCTCATTGTATAAGGCTGCCTTTTCCCTTGCATTCCATGCA
290883 TTACTTAGGA
Statistics
Matches: 128, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
130 128 1.00
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.30
Consensus pattern (129 bp):
ACAGCAGACACACGGTTACCAATCACACTGGACATTTTACAAACCATTATCCCAAACCTTCAATT
TGTTTGCTATAGCAATTATGAAACCTCATTGTATAAGGCTGCCTTTTCCCTTGCATTCCATGCA
Found at i:291956 original size:15 final size:16
Alignment explanation
Indices: 291936--291966 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
291926 TCAACCTCCT
291936 TGCTAGTGCTA-TAGG
1 TGCTAGTGCTAGTAGG
291951 TGCTAGTGCTAGTAGG
1 TGCTAGTGCTAGTAGG
291967 AGTGTGGCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.19, C:0.13, G:0.35, T:0.32
Consensus pattern (16 bp):
TGCTAGTGCTAGTAGG
Found at i:297368 original size:62 final size:62
Alignment explanation
Indices: 297271--297443 Score: 346
Period size: 62 Copynumber: 2.8 Consensus size: 62
297261 TACCGTATCT
297271 ACTACCTATATATATCTGCATGGTGAACTGGAATCAATTTATATAGGCCAAAAGAGCAGAGC
1 ACTACCTATATATATCTGCATGGTGAACTGGAATCAATTTATATAGGCCAAAAGAGCAGAGC
297333 ACTACCTATATATATCTGCATGGTGAACTGGAATCAATTTATATAGGCCAAAAGAGCAGAGC
1 ACTACCTATATATATCTGCATGGTGAACTGGAATCAATTTATATAGGCCAAAAGAGCAGAGC
297395 ACTACCTATATATATCTGCATGGTGAACTGGAATCAATTTATATAGGCC
1 ACTACCTATATATATCTGCATGGTGAACTGGAATCAATTTATATAGGCC
297444 CAGTAGCAGA
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 111 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (62 bp):
ACTACCTATATATATCTGCATGGTGAACTGGAATCAATTTATATAGGCCAAAAGAGCAGAGC
Found at i:304247 original size:43 final size:43
Alignment explanation
Indices: 304199--304316 Score: 123
Period size: 43 Copynumber: 2.7 Consensus size: 43
304189 TCGTTACTAG
* * *
304199 GAGAAAAGAT-TACGTAAATACGA-TTTGATTATCTCTTTATTAC
1 GAGAAAAGATCT-CGTAAATACGAGTTT-ATTATCTCGTAAATAC
* * *
304242 GAGAAAAGATCTCGTTATTACGAGTTTATTATGTCGTAAATAC
1 GAGAAAAGATCTCGTAAATACGAGTTTATTATCTCGTAAATAC
* * *
304285 GAGAAAAGATCTCGTAATTACCAGTTAATTAT
1 GAGAAAAGATCTCGTAAATACGAGTTTATTAT
304317 TTCGATATTA
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
43 60 0.94
44 4 0.06
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (43 bp):
GAGAAAAGATCTCGTAAATACGAGTTTATTATCTCGTAAATAC
Found at i:304316 original size:86 final size:86
Alignment explanation
Indices: 304159--304316 Score: 192
Period size: 86 Copynumber: 1.8 Consensus size: 86
304149 AGGACCACCA
* * * * * *
304159 AAAAAATCTCGTTATTATGAGTTAATCATCTCGTTACTAGGAGAAAAGATTACGTAAATACGATT
1 AAAAAATCTCGTTATTACGAGTTAATCATCTCGTAAATACGAGAAAAGATTACGTAAATACCAGT
*
304224 TGATTATCTCTTTATTACGAG
66 TAATTATCTCTTTATTACGAG
* * * * *
304245 AAAAGATCTCGTTATTACGAGTTTATTATGTCGTAAATACGAGAAAAGATCT-CGTAATTACCAG
1 AAAAAATCTCGTTATTACGAGTTAATCATCTCGTAAATACGAGAAAAGAT-TACGTAAATACCAG
304309 TTAATTAT
65 TTAATTAT
304317 TTCGATATTA
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
86 58 0.98
87 1 0.02
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (86 bp):
AAAAAATCTCGTTATTACGAGTTAATCATCTCGTAAATACGAGAAAAGATTACGTAAATACCAGT
TAATTATCTCTTTATTACGAG
Found at i:308378 original size:19 final size:20
Alignment explanation
Indices: 308354--308394 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
308344 TTACATCATG
308354 TTTGCTTAATGCTTG-TTGC
1 TTTGCTTAATGCTTGCTTGC
**
308373 TTTGCTTTTTGCTTGCTTGC
1 TTTGCTTAATGCTTGCTTGC
308393 TT
1 TT
308395 GTTTTTGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.05, C:0.17, G:0.20, T:0.59
Consensus pattern (20 bp):
TTTGCTTAATGCTTGCTTGC
Found at i:309191 original size:22 final size:22
Alignment explanation
Indices: 309161--309217 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
309151 ACCCAGTGCA
*
309161 TGATTACGTCATATTTGCTTAT
1 TGATAACGTCATATTTGCTTAT
*
309183 TGATAACGTCATATTTGCTTGT
1 TGATAACGTCATATTTGCTTAT
*
309205 TGATGACGTCATA
1 TGATAACGTCATA
309218 ATTACGTCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.44
Consensus pattern (22 bp):
TGATAACGTCATATTTGCTTAT
Found at i:309275 original size:19 final size:20
Alignment explanation
Indices: 309251--309295 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
309241 TTACATCATG
309251 TTTGCTTAATGCTTG-TTGC
1 TTTGCTTAATGCTTGCTTGC
**
309270 TTTGCTTTTTGCTTGCTTGC
1 TTTGCTTAATGCTTGCTTGC
309290 -TTGCTT
1 TTTGCTT
309296 TTGTTGGGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.04, C:0.18, G:0.20, T:0.58
Consensus pattern (20 bp):
TTTGCTTAATGCTTGCTTGC
Found at i:309296 original size:19 final size:19
Alignment explanation
Indices: 309260--309297 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
309250 GTTTGCTTAA
309260 TGCTTGTTGCTTTGCTTTT
1 TGCTTGTTGCTTTGCTTTT
309279 TGCTTGCTTGC-TTGCTTTT
1 TGCTTG-TTGCTTTGCTTTT
309298 GTTGGGGGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.00, C:0.18, G:0.21, T:0.61
Consensus pattern (19 bp):
TGCTTGTTGCTTTGCTTTT
Found at i:310340 original size:22 final size:22
Alignment explanation
Indices: 310313--310383 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
310303 AACTAAATAT
*
310313 TATAAAATCGATGATATTGATA
1 TATAAAATCGATGATATTCATA
* *
310335 TAT-AAAT--ATAATATGTTATA
1 TATAAAATCGATGATAT-TCATA
*
310355 TGATTAAATCGATGATATTCATA
1 T-ATAAAATCGATGATATTCATA
310378 TATAAA
1 TATAAA
310384 TATAATACGA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
19 6 0.15
20 5 0.13
21 6 0.15
22 11 0.28
23 5 0.13
24 6 0.15
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.39
Consensus pattern (22 bp):
TATAAAATCGATGATATTCATA
Found at i:310368 original size:43 final size:43
Alignment explanation
Indices: 310317--310402 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
310307 AAATATTATA
* * *
310317 AAATCGATGATATTGATATATAAATATAATATGTTATATGATT
1 AAATCGATGATATTCATATATAAATATAATACGATATATGATT
310360 AAATCGATGATATTCATATATAAATATAATACGATATATGATT
1 AAATCGATGATATTCATATATAAATATAATACGATATATGATT
310403 TAGATCAGCG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (43 bp):
AAATCGATGATATTCATATATAAATATAATACGATATATGATT
Found at i:313474 original size:12 final size:12
Alignment explanation
Indices: 313457--313485 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
313447 TGGTACATTT
313457 TTCCGTTTTCCG
1 TTCCGTTTTCCG
313469 TTCCGTTTTCCG
1 TTCCGTTTTCCG
313481 TTCCG
1 TTCCG
313486 CGTTTCAGCG
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:0.00, C:0.34, G:0.17, T:0.48
Consensus pattern (12 bp):
TTCCGTTTTCCG
Found at i:313754 original size:15 final size:15
Alignment explanation
Indices: 313734--313766 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
313724 GTTTGTTCTG
313734 ACAAAGAGTAAATTT
1 ACAAAGAGTAAATTT
*
313749 ACAAAGAGTAGATTT
1 ACAAAGAGTAAATTT
313764 ACA
1 ACA
313767 TCAAGAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (15 bp):
ACAAAGAGTAAATTT
Found at i:315354 original size:331 final size:331
Alignment explanation
Indices: 314198--315453 Score: 1594
Period size: 331 Copynumber: 3.7 Consensus size: 331
314188 CATCTGGCTG
** * * *
314198 ATTAGTTTCT--G-AGAAGATTTTTAAAGATTTACCCTATATATTCCTTTGTTAAACTTTGACCC
1 ATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTGTATATATTCCTATGTAAAACTTCGA---
* * * * *
314260 CCACCCCCATTTGTGGCCCCACCCTACCCCTGGGGATCATTATTTTCACAACTTTGAATCTACAC
63 --TCCCCCA-TTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAAATTTGAATCTACAC
* * * * *
314325 TACCTGAGGATGCTTTCACACAAATTTCAGCTTTCCTGGCTGATCAGTTTCTGAGAAGAAGATTT
125 TACCTGAGGATGCATCCACACAAGTGTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAAGATTT
* * * * * * *
314390 TTAAAGAATAACTCTGTTTGTTTATTCCTATGTAAAACATCGACCTCCCATTGTGGCCCAAACCT
190 TTAAAGATTTA--CTG--TATATATTCCTATGTAAAACTTCGACC-CCCATTGTGGCCCCACCCT
* * * * * *
314455 ACCCCCAGGGGTCATGATTTTCACAAATTTGAATCTACACTTCCTGAGGATTCTTCCACACAAGT
250 ACCCCCGGGGGTCATGATTTTCACAACTTTGAATTTACACTACCTGAGGATACATCCACACAAGT
* * *
314520 TTTAGCTTTCCTGGCTA
315 GTCAGCTTTCCTGGCGA
*
314537 ATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTGTATATATTCCTATGTTAAACTTCGAT-C
1 ATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTGTATATATTCCTATGTAAAACTTCGATCC
* * * * *
314601 CCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGGTTTTTACAACTTTCAATTTACACTACCTG
66 CCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAAATTTGAATCTACACTACCTG
*
314666 AGGATGCATCCACACAAGTGTCAACTTTCCTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAG
131 AGGATGCATCCACACAAGTGTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAG
* *
314731 ATTTACTGTATATATTCCTATGTAAAACGTCGATCCCCCATTGTGGCCCCACCCTCCCCCCGGGG
196 ATTTACTGTATATATTCCTATGTAAAACTTCGA-CCCCCATTGTGGCCCCACCCTACCCCCGGGG
* *
314796 GTCATGATTTTCACAAATTTGCATTGAATCTT-CACTACCTAAGGATACATCCACACAAGTGTCA
260 GTCATGATTTTCAC-AA----CTTTGAAT-TTACACTACCTGAGGATACATCCACACAAGTGTCA
314860 GCTTTCCTGGCCG-
319 GCTTTCCTGG-CGA
** * *
314873 ATTAGTTTCTGAGAAGAAGATTTTTAAAGAATAAATCTGTTTGTTTATTCCTATGTAAAACATT-
1 ATTAGTTTCTGAGAAGAAGATTTTTAAAG-ATTTA-CTG--TATATATTCCTATGTAAAAC-TTC
* * *
314937 GA-CCTCCCATTGTGGCCCAAACCTACCCCCAGGGGTCATGATTTTCACAAATTTGAATCTACAC
61 GATCC-CCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAAATTTGAATCTACAC
* * * *
315001 TACCTGAGGATGCTTCCACACAAGTTTTAGCTTTCCTGGCTAATTAGTTTCTGAGAAGAAGATTT
125 TACCTGAGGATGCATCCACACAAGTGTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAAGATTT
* *
315066 TTAAAGATTTACTGTATATATTCCTATGTTAAACTTCGATCCCCATTGTGGCCCCACCCTACCCC
190 TTAAAGATTTACTGTATATATTCCTATGTAAAACTTCGACCCCCATTGTGGCCCCACCCTACCCC
*
315131 CGGGGGTCATGATTTTCACAACTTTGAATTTACACTACCTGAGGATGCATCCACACAAGTGTCAG
255 CGGGGGTCATGATTTTCACAACTTTGAATTTACACTACCTGAGGATACATCCACACAAGTGTCAG
*
315196 CTTTGCC-AGCGA
320 CTTT-CCTGGCGA
*
315208 ATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTGTATATATTCCTATGTAAAACGTCGATCC
1 ATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTGTATATATTCCTATGTAAAACTTCGATCC
* * * *
315273 CCCATTGTGGCCCCACCCTCCCCCCGGGGGTCATGATTTTCACAAATTTAAATCTTCACTACCTA
66 CCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAAATTTGAATCTACACTACCTG
*
315338 AGGATGCATCCACACAAGTGTCAGCTTTCCTGGCCGATTAGTTTCTGAGAAGAAGATTTTTAAAG
131 AGGATGCATCCACACAAGTGTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAG
* * * * *
315403 ATTTACTCTATGTATTCATTTGTTAAACTTCGACCCCCCATTGTGGCCCCA
196 ATTTACTGTATATATTCCTATGTAAAACTTCGA-CCCCCATTGTGGCCCCA
315454 TCCTCAGGTG
Statistics
Matches: 808, Mismatches: 85, Indels: 55
0.85 0.09 0.06
Matches are distributed among these distances:
330 1 0.00
331 228 0.28
332 22 0.03
333 6 0.01
334 7 0.01
335 188 0.23
336 78 0.10
337 5 0.01
338 3 0.00
339 12 0.01
340 63 0.08
341 151 0.19
342 44 0.05
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (331 bp):
ATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTGTATATATTCCTATGTAAAACTTCGATCC
CCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAAATTTGAATCTACACTACCTG
AGGATGCATCCACACAAGTGTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAG
ATTTACTGTATATATTCCTATGTAAAACTTCGACCCCCATTGTGGCCCCACCCTACCCCCGGGGG
TCATGATTTTCACAACTTTGAATTTACACTACCTGAGGATACATCCACACAAGTGTCAGCTTTCC
TGGCGA
Found at i:315380 original size:166 final size:166
Alignment explanation
Indices: 314191--315453 Score: 1596
Period size: 165 Copynumber: 7.5 Consensus size: 166
314181 AAAGAATCAT
** * *
314191 CTGGCTGATTAGTTTCT--G-AGAAGATTTTTAAAGATTTACCCTATATATTCCTTTGTTAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTGTATATATTCCTATGTAAAACT
* * * * * *
314253 TTGACCCCCACCCCCATTTGTGGCCCCACCCTACCCCTGGGGATCATTATTTTCACAACTTTGAA
66 TCGA-----TCCCCCA-TTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAAATTTGAA
* * * * *
314318 TCTACACTACCTGAGGATGCTTTCACACAAATTTCAGCTTTC
125 TCTTCACTACCTGAGGATGCATCCACACAAGTGTCAGCTTTC
* * * * *
314360 CTGGCTGATCAGTTTCTGAGAAGAAGATTTTTAAAGAATAACTCTGTTTGTTTATTCCTATGTAA
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTA--CTG--TATATATTCCTATGTAA
* * * *
314425 AACATCGA-CCTCCCATTGTGGCCCAAACCTACCCCCAGGGGTCATGATTTTCACAAATTTGAAT
62 AACTTCGATCC-CCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAAATTTGAAT
* * * * * *
314489 CTACACTTCCTGAGGATTCTTCCACACAAGTTTTAGCTTTC
126 CTTCACTACCTGAGGATGCATCCACACAAGTGTCAGCTTTC
* *
314530 CTGGCTAATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTGTATATATTCCTATGTTAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTGTATATATTCCTATGTAAAACT
* * * *
314595 TCGAT-CCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGGTTTTTACAACTTTCAAT-TTAC
66 TCGATCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAAATTTGAATCTT-C
*
314658 ACTACCTGAGGATGCATCCACACAAGTGTCAACTTTC
130 ACTACCTGAGGATGCATCCACACAAGTGTCAGCTTTC
*
314695 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTGTATATATTCCTATGTAAAACG
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTGTATATATTCCTATGTAAAACT
*
314760 TCGATCCCCCATTGTGGCCCCACCCTCCCCCCGGGGGTCATGATTTTCACAAATTTGCATTGAAT
66 TCGATCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAAA--T---TTGAAT
* *
314825 CTTCACTACCTAAGGATACATCCACACAAGTGTCAGCTTTC
126 CTTCACTACCTGAGGATGCATCCACACAAGTGTCAGCTTTC
* ** * *
314866 CTGGCCGATTAGTTTCTGAGAAGAAGATTTTTAAAGAATAAATCTGTTTGTTTATTCCTATGTAA
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAG-ATTTA-CTG--TATATATTCCTATGTAA
* * *
314931 AACATT-GA-CCTCCCATTGTGGCCCAAACCTACCCCCAGGGGTCATGATTTTCACAAATTTGAA
62 AAC-TTCGATCC-CCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAAATTTGAA
* * * *
314994 TCTACACTACCTGAGGATGCTTCCACACAAGTTTTAGCTTTC
125 TCTTCACTACCTGAGGATGCATCCACACAAGTGTCAGCTTTC
* *
315036 CTGGCTAATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTGTATATATTCCTATGTTAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTGTATATATTCCTATGTAAAACT
*
315101 TCGAT-CCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAAT-TTAC
66 TCGATCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAAATTTGAATCTT-C
315164 ACTACCTGAGGATGCATCCACACAAGTGTCAGCTTTGC
130 ACTACCTGAGGATGCATCCACACAAGTGTCAGCTTT-C
*
315202 C-AGC-GAATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTGTATATATTCCTATGTAAAAC
1 CTGGCTG-ATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTGTATATATTCCTATGTAAAAC
* * *
315265 GTCGATCCCCCATTGTGGCCCCACCCTCCCCCCGGGGGTCATGATTTTCACAAATTTAAATCTTC
65 TTCGATCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAAATTTGAATCTTC
*
315330 ACTACCTAAGGATGCATCCACACAAGTGTCAGCTTTC
130 ACTACCTGAGGATGCATCCACACAAGTGTCAGCTTTC
* * * * * *
315367 CTGGCCGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATGTATTCATTTGTTAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTGTATATATTCCTATGTAAAACT
*
315432 TCGACCCCCCATTGTGGCCCCA
66 TCGATCCCCCATTGTGGCCCCA
315454 TCCTCAGGTG
Statistics
Matches: 959, Mismatches: 103, Indels: 67
0.85 0.09 0.06
Matches are distributed among these distances:
164 2 0.00
165 295 0.31
166 249 0.26
167 3 0.00
168 7 0.01
169 19 0.02
170 192 0.20
171 80 0.08
172 23 0.02
173 4 0.00
174 3 0.00
175 62 0.06
176 20 0.02
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.33
Consensus pattern (166 bp):
CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTGTATATATTCCTATGTAAAACT
TCGATCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAAATTTGAATCTTCA
CTACCTGAGGATGCATCCACACAAGTGTCAGCTTTC
Found at i:317824 original size:8 final size:8
Alignment explanation
Indices: 317813--317862 Score: 75
Period size: 8 Copynumber: 6.4 Consensus size: 8
317803 TAAAAAGTTT
317813 ACAGACGG
1 ACAGACGG
*
317821 ACAGACAG
1 ACAGACGG
317829 ACAGACGG
1 ACAGACGG
*
317837 ACGGACGG
1 ACAGACGG
317845 ACAGACGG
1 ACAGACGG
317853 AC-GACGG
1 ACAGACGG
317860 ACA
1 ACA
317863 AAATGTGATC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
7 7 0.19
8 30 0.81
ACGTcount: A:0.38, C:0.26, G:0.36, T:0.00
Consensus pattern (8 bp):
ACAGACGG
Found at i:320899 original size:46 final size:47
Alignment explanation
Indices: 320849--320946 Score: 171
Period size: 47 Copynumber: 2.1 Consensus size: 47
320839 TAGGCATTAA
**
320849 ATGCTTATTTTTAGATATCCAAACCT-AACATTAAATGCTTAAATAT
1 ATGCTTATTTTTAGATATCCAAAAATAAACATTAAATGCTTAAATAT
320895 ATGCTTATTTTTAGATATCCAAAAATAAACATTAAATGCTTAAATAT
1 ATGCTTATTTTTAGATATCCAAAAATAAACATTAAATGCTTAAATAT
320942 ATGCT
1 ATGCT
320947 CAATCAACTC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
46 24 0.49
47 25 0.51
ACGTcount: A:0.41, C:0.13, G:0.07, T:0.39
Consensus pattern (47 bp):
ATGCTTATTTTTAGATATCCAAAAATAAACATTAAATGCTTAAATAT
Found at i:321997 original size:8 final size:8
Alignment explanation
Indices: 321984--322049 Score: 62
Period size: 8 Copynumber: 7.8 Consensus size: 8
321974 GTTAACGTCT
321984 TTTTTTTC
1 TTTTTTTC
321992 TTTTTTTC
1 TTTTTTTC
322000 TTTTGTTTAC
1 TTTT-TTT-C
*
322010 TGTTTTTC
1 TTTTTTTC
322018 TTTTCTTGT-
1 TTTT-TT-TC
*
322027 TTTTTTTT
1 TTTTTTTC
322035 TCTTTTTTC
1 T-TTTTTTC
322044 TTTTTT
1 TTTTTT
322050 GCTCATCAGT
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
7 1 0.02
8 24 0.49
9 19 0.39
10 5 0.10
ACGTcount: A:0.02, C:0.11, G:0.05, T:0.83
Consensus pattern (8 bp):
TTTTTTTC
Found at i:322015 original size:26 final size:25
Alignment explanation
Indices: 321985--322050 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 25
321975 TTAACGTCTT
321985 TTTTTTCTTTTTT-TCTTTTGTTTAC
1 TTTTTTCTTTTTTGT-TTTTGTTTAC
* *
322010 TGTTTTTCTTTTCTTGTTTTTTTTTTC
1 T-TTTTTCTTTT-TTGTTTTTGTTTAC
322037 TTTTTTCTTTTTTG
1 TTTTTTCTTTTTTG
322051 CTCATCAGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
25 4 0.11
26 20 0.56
27 11 0.31
28 1 0.03
ACGTcount: A:0.02, C:0.11, G:0.06, T:0.82
Consensus pattern (25 bp):
TTTTTTCTTTTTTGTTTTTGTTTAC
Found at i:322034 original size:19 final size:18
Alignment explanation
Indices: 321981--322049 Score: 61
Period size: 18 Copynumber: 3.8 Consensus size: 18
321971 TAAGTTAACG
*
321981 TCTTTTTT-TTCTTTTTT
1 TCTTTTTTCTTTTTTTTT
** *
321998 TCTTTTGTT-TACTGTTTT
1 TCTTTT-TTCTTTTTTTTT
*
322016 TCTTTTCTTGTTTTTTTTT
1 TCTTTT-TTCTTTTTTTTT
322035 TCTTTTTTCTTTTTT
1 TCTTTTTTCTTTTTT
322050 GCTCATCAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
17 6 0.14
18 25 0.58
19 12 0.28
ACGTcount: A:0.01, C:0.12, G:0.04, T:0.83
Consensus pattern (18 bp):
TCTTTTTTCTTTTTTTTT
Found at i:326247 original size:2 final size:2
Alignment explanation
Indices: 326240--326269 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
326230 ACGTGTCACA
*
326240 TG TG TG TG GG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
326270 ATAAACAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.53, T:0.47
Consensus pattern (2 bp):
TG
Found at i:332409 original size:4 final size:4
Alignment explanation
Indices: 332400--332457 Score: 107
Period size: 4 Copynumber: 14.5 Consensus size: 4
332390 AATTAATATG
332400 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
*
332448 TAAA TAGA TA
1 TAGA TAGA TA
332458 TGAAGTTATA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 52 1.00
ACGTcount: A:0.52, C:0.00, G:0.22, T:0.26
Consensus pattern (4 bp):
TAGA
Found at i:340944 original size:326 final size:327
Alignment explanation
Indices: 340345--340985 Score: 1011
Period size: 326 Copynumber: 2.0 Consensus size: 327
340335 ATGGTTAACC
*
340345 CCCGCCTTTCATCCCTATATCATTGTGAAATGCTAAAATATGACAGAGTTTGGGTGAGCTAACTG
1 CCCGCCTTTCATCCCTATATCATTGTGAAATGCTAAAATATGACAAAGTTTGGGTGAGCTAACTG
** * * * * *
340410 AACCCTTGTTTGGGGTCATAGGTGCCCTTTAACGCTTATTATGAATACTTTTTGAGGTCCTCTAC
66 AACCCTTGTCAGGGGTCATAGGTGCCCTTTAACGCTTATGATGAATACCTTCTGAGGCCCTCGAC
* * * *
340475 CTAATCCAAGTGTTTTCAAGTTCTTGTGGTCAATCTCAAGTCAGATATAAACCCATGAAATGAGC
131 CTAATCCAAGTGTTTCCAAGTTATTGTGATCAAACTCAAGTCAGATATAAACCCATGAAATGAGC
*
340540 CAGAACCACTGGGAGCCACTTGGTGGTACCCCTACAGCCCCAATTTGAGACCGGGAAATAATAGC
196 CAGAACCACTGGGAGCCACTTGGTGGTACCCCTACAGCCCAAATTTGAGACCGGGAAATAATAGC
*
340605 CCCATATGTCCTCTACACTGCCCTGGTATCCGTTTGATGCACACTTCAAAGATAAAAGAGATAAT
261 CCCATAAGTCCTCTACACTGCCCTGGTATCCGTTTGATGCACACTTCAAAGATAAAAGAGATAAT
340670 GG
326 GG
*
340672 CCCGCCTTTCA-CCTCTATATCATTGTGAAATGCTAAAATATGACAAAGTTTTGGTGAGCTTAAC
1 CCCGCCTTTCATCC-CTATATCATTGTGAAATGCTAAAATATGACAAAGTTTGGGTGAGC-TAAC
**
340736 -GGGCCCTT-TCAGGGGTCATAGGTGCCCTCTT-ACGCTTATGATGAATACCTTCTGAGGCCCTC
64 TGAACCCTTGTCAGGGGTCATAGGTGCCCT-TTAACGCTTATGATGAATACCTTCTGAGGCCCTC
* * * *
340798 GACCTAATCCTAGTGTTTCCCAGTTATTGTGATCAAACTCCAGTCAGATATAAACCCCTGAAATG
128 GACCTAATCCAAGTGTTTCCAAGTTATTGTGATCAAACTCAAGTCAGATATAAACCCATGAAATG
* *
340863 AGCCAGAACCCCTGGGAGCCACTTGGTGGTACCCCTACAGCCCAAATTTGAGACCGGGAAATAGT
193 AGCCAGAACCACTGGGAGCCACTTGGTGGTACCCCTACAGCCCAAATTTGAGACCGGGAAATAAT
*
340928 AGCCCCATAAGTCCTCTACACTGCCCTGGTATTCGTTTGATGCACACTTCAAAGATAA
258 AGCCCCATAAGTCCTCTACACTGCCCTGGTATCCGTTTGATGCACACTTCAAAGATAA
340986 GGTAGACGGA
Statistics
Matches: 287, Mismatches: 24, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
326 221 0.77
327 62 0.22
328 4 0.01
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (327 bp):
CCCGCCTTTCATCCCTATATCATTGTGAAATGCTAAAATATGACAAAGTTTGGGTGAGCTAACTG
AACCCTTGTCAGGGGTCATAGGTGCCCTTTAACGCTTATGATGAATACCTTCTGAGGCCCTCGAC
CTAATCCAAGTGTTTCCAAGTTATTGTGATCAAACTCAAGTCAGATATAAACCCATGAAATGAGC
CAGAACCACTGGGAGCCACTTGGTGGTACCCCTACAGCCCAAATTTGAGACCGGGAAATAATAGC
CCCATAAGTCCTCTACACTGCCCTGGTATCCGTTTGATGCACACTTCAAAGATAAAAGAGATAAT
GG
Found at i:341082 original size:116 final size:116
Alignment explanation
Indices: 340877--341101 Score: 414
Period size: 116 Copynumber: 1.9 Consensus size: 116
340867 AGAACCCCTG
340877 GGAGCCACTTGGTGGTACCCCTACAGCCCAAATTTGAGACCGGGAAATAGTAGCCCCATAAGTCC
1 GGAGCCACTTGGTGGTACCCCTACAGCCCAAATTTGAGACCGGGAAATAGTAGCCCCATAAGTCC
340942 TCTACACTGCCCTGGTATTCGTTTGATGCACACTTCAAAGATAAGGTAGAC
66 TCTACACTGCCCTGGTATTCGTTTGATGCACACTTCAAAGATAAGGTAGAC
* *
340993 GGAGCCACTTGGTGGTACCCCTACAGCCCAAATTTGAGACCGGGAAATAGTATCCCCATAGGTCC
1 GGAGCCACTTGGTGGTACCCCTACAGCCCAAATTTGAGACCGGGAAATAGTAGCCCCATAAGTCC
* *
341058 TCTACACTGCCGTGGTATTTGTTTGATGCACACTTCAAAGATAA
66 TCTACACTGCCCTGGTATTCGTTTGATGCACACTTCAAAGATAA
341102 AAGAGATATT
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
116 105 1.00
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.24
Consensus pattern (116 bp):
GGAGCCACTTGGTGGTACCCCTACAGCCCAAATTTGAGACCGGGAAATAGTAGCCCCATAAGTCC
TCTACACTGCCCTGGTATTCGTTTGATGCACACTTCAAAGATAAGGTAGAC
Found at i:341686 original size:13 final size:13
Alignment explanation
Indices: 341668--341692 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
341658 TTCTACGGGC
341668 TTAGTGGCTGCTG
1 TTAGTGGCTGCTG
341681 TTAGTGGCTGCT
1 TTAGTGGCTGCT
341693 AGCATCAGCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.16, G:0.36, T:0.40
Consensus pattern (13 bp):
TTAGTGGCTGCTG
Found at i:345485 original size:16 final size:16
Alignment explanation
Indices: 345464--345497 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
345454 CGTCGCATTG
*
345464 CCATTTGACACGATTA
1 CCATTTGACACAATTA
345480 CCATTTGACACAATTA
1 CCATTTGACACAATTA
345496 CC
1 CC
345498 CAAAGTCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.29, G:0.09, T:0.29
Consensus pattern (16 bp):
CCATTTGACACAATTA
Found at i:347216 original size:2 final size:2
Alignment explanation
Indices: 347209--347260 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
347199 TTACTTAATT
347209 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
347251 TC TC TC TC TC
1 TC TC TC TC TC
347261 GTATATTAAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:354992 original size:13 final size:13
Alignment explanation
Indices: 354974--354999 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
354964 AATAAAAGAG
354974 AGAGAGAATACTA
1 AGAGAGAATACTA
354987 AGAGAGAATACTA
1 AGAGAGAATACTA
355000 CTTACATACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.23, T:0.15
Consensus pattern (13 bp):
AGAGAGAATACTA
Found at i:355312 original size:12 final size:12
Alignment explanation
Indices: 355289--355322 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
355279 ATAATTTGTC
355289 CGTTGTTTGTCGT
1 CGTTG-TTGTCGT
355302 CGTTGTTGTCGT
1 CGTTGTTGTCGT
*
355314 CGTCGTTGT
1 CGTTGTTGT
355323 AAACTTTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.00, C:0.18, G:0.32, T:0.50
Consensus pattern (12 bp):
CGTTGTTGTCGT
Found at i:355317 original size:15 final size:13
Alignment explanation
Indices: 355289--355322 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 13
355279 ATAATTTGTC
355289 CGTTGTTTGTCGT
1 CGTTGTTTGTCGT
355302 CGTTGTTGTCGTCGT
1 CGTTGTT-T-GTCGT
355317 CGTTGT
1 CGTTGT
355323 AAACTTTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.37
14 1 0.05
15 11 0.58
ACGTcount: A:0.00, C:0.18, G:0.32, T:0.50
Consensus pattern (13 bp):
CGTTGTTTGTCGT
Found at i:356001 original size:159 final size:160
Alignment explanation
Indices: 355479--356445 Score: 854
Period size: 159 Copynumber: 6.1 Consensus size: 160
355469 GGTATTTTTC
* * ** * * * * * * *
355479 AAAAATCTTCTTCTTAAAAACTATTCGGCCTGAAAAGCTTAAACTT-GTGTGGAGGCATCCTCAG
1 AAAAATCTTCTTCTCAAAAACAATTAAGCCAGGAAAGCTCAAA-TTAGCGTGTAAGCATCCTCAA
* * * *
355543 GTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGAGGGGCCACAATACGGGG
65 ATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAAT-GGGGG
* ** *
355608 ATCAATTTTAACATAGGAATACATAGAGAAAATCTTT
129 ATAAATTTT----TA-TTATATATAGAGAAAATCTTT
* ** * **
355645 AAAAATCTTCTTCTCAAAAAC---T--GCCAGAAAAGCTCAAATTAAAGTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAAAAACAATTAAGCCAGGAAAGCTCAAATTAGCGTGTAAGCATCCTCAAA
* * * *
355705 TAGTGTAGATTCAAATTTGTTCAAATCATAGTCCCTGGTGGT-TGGTGGGGCCACAATGGGGGAA
66 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATGGGGG-A
**
355769 TGGATTTTTACTTAGGATTATATAGAGAAAATCTTT
130 TAAATTTTTA-TT---A-TATATAGAGAAAATCTTT
* **
355805 AAAAATCTTCTTCTCAAAAACAATTAAGCCAAGAAAGCTCAAATTAGCGTGTAATTATCCTCAAA
1 AAAAATCTTCTTCTCAAAAACAATTAAGCCAGGAAAGCTCAAATTAGCGTGTAAGCATCCTCAAA
* *
355870 TAATGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGCGGGGCCACAATGGGGGAT
66 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATGGGGGAT
*
355935 AAATTTTT-TTATATATAGAGAACATCTTT
131 AAATTTTTATTATATATAGAGAAAATCTTT
* *** *
355964 AAAAATCTTCTTCTCAAAAACTATTAAGCCAGGAAAGCTCAAATTAAAATGGAAGCATCCT-AAG
1 AAAAATCTTCTTCTCAAAAACAATTAAGCCAGGAAAGCTCAAATTAGCGTGTAAGCATCCTCAA-
* * * **
356028 GTAGTGTAGATTCAATTTTGTTCAAATCATGGTCCCTGGGGGTATGGTGGGG--ATCAA---GTT
65 ATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGTGGGGCCA-CAATGGGGG
* * **
356088 TTACA----TAGGACTATATAGAGAAAATCTTT
129 ATAAATTTTTATTA-TATATAGAGAAAATCTTT
* * * * *
356117 AAAAATCTTCATCTAAAAAACAATTAGGCCAAGAAAGCTCAAATTGGCGTGTAA-CTATCCTCAA
1 AAAAATCTTCTTCTCAAAAACAATTAAGCCAGGAAAGCTCAAATTAGCGTGTAAGC-ATCCTCAA
* *
356181 ATAATGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGCGGGGCCACAATGGGGGA
65 ATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATGGGGGA
*
356246 TAAA--TTT-TTATATAGAGAGAAAATCTTT
130 TAAATTTTTATTATATATAGAGAAAATCTTT
* * * * * *
356274 AAAAATCTTCTTCTC-AAAACTATTAGGCAAGGAAAGCCCAAATTTGAC-TGGT-AGCATCCCCA
1 AAAAATCTTCTTCTCAAAAACAATTAAGCCAGGAAAGCTCAAATTAG-CGT-GTAAGCATCCTCA
* * * * * * * * *
356336 AATCGTATAGATACAAGTTTGTTTAAATAATAGT-CC-AGGGGTAGGATGAGGCCACAATGGGGG
64 AATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATGGGGG
* * *
356399 ATGAATTTTTACATATATAAATAGAAAAAATCTTT
129 ATAAATTTTT--AT-TATATATAGAGAAAATCTTT
356434 AAAAATCTTCTT
1 AAAAATCTTCTT
356446 TTTAAAGACT
Statistics
Matches: 665, Mismatches: 102, Indels: 74
0.79 0.12 0.09
Matches are distributed among these distances:
151 1 0.00
152 2 0.00
153 113 0.17
154 32 0.05
155 7 0.01
156 66 0.10
157 39 0.06
158 6 0.01
159 124 0.19
160 90 0.14
161 68 0.10
163 4 0.01
165 75 0.11
166 38 0.06
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (160 bp):
AAAAATCTTCTTCTCAAAAACAATTAAGCCAGGAAAGCTCAAATTAGCGTGTAAGCATCCTCAAA
TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATGGGGGAT
AAATTTTTATTATATATAGAGAAAATCTTT
Found at i:356177 original size:153 final size:153
Alignment explanation
Indices: 355946--356224 Score: 400
Period size: 153 Copynumber: 1.8 Consensus size: 153
355936 AATTTTTTTA
* * * * *
355946 TATATAGAGAACATCTTTAAAAATCTTCTTCTCAAAAACTATTAAGCCAGGAAAGCTCAAATTAA
1 TATATAGAGAAAATCTTTAAAAATCTTCATCTAAAAAACAATTAAGCCAAGAAAGCTCAAATTAA
* * *
356011 AATGGAAGCATCCT-AAGGTAGTGTAGATTCAATTTTGTTCAAATCATGGTCCCTGGGGGTATGG
66 AATGGAAGCATCCTCAA-ATAATGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTATGG
356075 TGGGGATCAAGTTTTACATAGGAC
130 TGGGGATCAAGTTTTACATAGGAC
* **
356099 TATATAGAGAAAATCTTTAAAAATCTTCATCTAAAAAACAATTAGGCCAAGAAAGCTCAAATTGG
1 TATATAGAGAAAATCTTTAAAAATCTTCATCTAAAAAACAATTAAGCCAAGAAAGCTCAAATTAA
** *
356164 CGTGTAA-CTATCCTCAAATAATGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTA
66 AATGGAAGC-ATCCTCAAATAATGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTA
356225 GGGCGGGGCC
Statistics
Matches: 110, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
152 1 0.01
153 107 0.97
154 2 0.02
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (153 bp):
TATATAGAGAAAATCTTTAAAAATCTTCATCTAAAAAACAATTAAGCCAAGAAAGCTCAAATTAA
AATGGAAGCATCCTCAAATAATGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTATGGT
GGGGATCAAGTTTTACATAGGAC
Found at i:356202 original size:312 final size:314
Alignment explanation
Indices: 355547--356317 Score: 1069
Period size: 312 Copynumber: 2.4 Consensus size: 314
355537 CCTCAGGTAG
* * * *
355547 TGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGAGGGGCCACAATACGGGGATCA
1 TGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGCGGGGCCACAAT-GGGGGATAA
** * *
355612 ATTTTAACATAGGAATACATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAAC---T-GCCAGA
65 ATTTT----T--TTATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTAGCCAGG
* *
355673 AAAGCTCAAATTAAAGTGGAAGCATCCTCAGGTAGTGTAGATTCAAATTTGTTCAAATCATAGTC
124 AAAGCTCAAATTAAAATGGAAGCATCCTAAGGTAGTGTAGATTCAAATTTGTTCAAATCATAGTC
* * * *
355738 CCTGGTGGTTGGTGGGGCCACAATGGGGGAATGGATTTTTACTTAGGATTATATAGAGAAAATCT
189 CCTGGGGGTTGGTGGGG---C-AT---GCAA-GGA-TTTTACATAGGACTATATAGAGAAAATCT
* * *
355803 TTAAAAATCTTCTTCTCAAAAACAATTAAGCCAAGAAAGCTCAAATTAGCGTGTAATTATCCTCA
245 TTAAAAATCTTCATCTAAAAAACAATTAAGCCAAGAAAGCTCAAATTAGCGTGTAACTATCCTCA
355868 AATAA
310 AATAA
355873 TGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGCGGGGCCACAATGGGGGATAAA
1 TGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGCGGGGCCACAATGGGGGATAAA
*
355938 TTTTTTTATATATAGAGAACATCTTTAAAAATCTTCTTCTCAAAAACTATTAAGCCAGGAAAGCT
66 TTTTTTTATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATT-AGCCAGGAAAGCT
* *
356003 CAAATTAAAATGGAAGCATCCTAAGGTAGTGTAGATTCAATTTTGTTCAAATCATGGTCCCTGGG
130 CAAATTAAAATGGAAGCATCCTAAGGTAGTGTAGATTCAAATTTGTTCAAATCATAGTCCCTGGG
356068 GGTATGGTGGGG-AT-CAA-G-TTTTACATAGGACTATATAGAGAAAATCTTTAAAAATCTTCAT
195 GGT-TGGTGGGGCATGCAAGGATTTTACATAGGACTATATAGAGAAAATCTTTAAAAATCTTCAT
* *
356129 CTAAAAAACAATTAGGCCAAGAAAGCTCAAATTGGCGTGTAACTATCCTCAAATAA
259 CTAAAAAACAATTAAGCCAAGAAAGCTCAAATTAGCGTGTAACTATCCTCAAATAA
356185 TGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGCGGGGCCACAATGGGGGATAAA
1 TGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGCGGGGCCACAATGGGGGATAAA
* * *
356250 --TTTTTATATAGAGAGAAAATCTTTAAAAATCTTCTTCTC-AAAACTATTAGGCAAGGAAAGCC
66 TTTTTTTATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTA-GCCAGGAAAGCT
356312 CAAATT
130 CAAATT
356318 TGACTGGTAG
Statistics
Matches: 412, Mismatches: 26, Indels: 31
0.88 0.06 0.07
Matches are distributed among these distances:
308 1 0.00
309 25 0.06
310 37 0.09
312 157 0.38
314 1 0.00
316 2 0.00
319 38 0.09
320 2 0.00
321 1 0.00
322 1 0.00
324 74 0.18
325 20 0.05
326 53 0.13
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (314 bp):
TGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGCGGGGCCACAATGGGGGATAAA
TTTTTTTATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTAGCCAGGAAAGCTC
AAATTAAAATGGAAGCATCCTAAGGTAGTGTAGATTCAAATTTGTTCAAATCATAGTCCCTGGGG
GTTGGTGGGGCATGCAAGGATTTTACATAGGACTATATAGAGAAAATCTTTAAAAATCTTCATCT
AAAAAACAATTAAGCCAAGAAAGCTCAAATTAGCGTGTAACTATCCTCAAATAA
Found at i:356353 original size:156 final size:157
Alignment explanation
Indices: 356099--356445 Score: 382
Period size: 156 Copynumber: 2.2 Consensus size: 157
356089 TACATAGGAC
* * *
356099 TATATAGAGAAAATCTTTAAAAATCTTCATCTAAAAAACAATTAGGCCAAGAAAGCTCAAATTGG
1 TATATAGAGAAAATCTTTAAAAATCTTCTTCTAAAAAACAATTAGGCCAAGAAAGCCCAAATTGA
* * * * * * *
356164 CGTGTAACTATCCTCAAATAATGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGC
66 CGTGTAACTATCCCCAAATAATATAGATACAAGTTTGTTCAAATAATAGT-CC-AGGGGTAGGAC
*
356229 GGGGCCACAATGGGGGAT-AAATTTT-TA
129 GAGGCCACAATGGGGGATGAAATTTTATA
* * *
356256 TATAGAGAGAAAATCTTTAAAAATCTTCTTCT-CAAAACTATTAGG-CAAGGAAAGCCCAAATTT
1 TATATAGAGAAAATCTTTAAAAATCTTCTTCTAAAAAACAATTAGGCCAA-GAAAGCCCAAA-TT
* ** *
356319 GAC-TGGTAGC-ATCCCCAAATCGTATAGATACAAGTTTGTTTAAATAATAGTCCAGGGGTAGGA
64 GACGT-GTAACTATCCCCAAATAATATAGATACAAGTTTGTTCAAATAATAGTCCAGGGGTAGGA
* *
356382 TGAGGCCACAATGGGGGATGAATTTTTACATA
128 CGAGGCCACAATGGGGGATGAAATTTT--ATA
*
356414 TATAAATAGAAAAAATCTTTAAAAATCTTCTT
1 TAT--ATAGAGAAAATCTTTAAAAATCTTCTT
356446 TTTAAAGACT
Statistics
Matches: 159, Mismatches: 22, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
154 25 0.16
155 11 0.07
156 55 0.35
157 38 0.24
158 5 0.03
160 25 0.16
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (157 bp):
TATATAGAGAAAATCTTTAAAAATCTTCTTCTAAAAAACAATTAGGCCAAGAAAGCCCAAATTGA
CGTGTAACTATCCCCAAATAATATAGATACAAGTTTGTTCAAATAATAGTCCAGGGGTAGGACGA
GGCCACAATGGGGGATGAAATTTTATA
Found at i:360557 original size:31 final size:33
Alignment explanation
Indices: 360499--360565 Score: 102
Period size: 31 Copynumber: 2.1 Consensus size: 33
360489 TCTCAATTTT
360499 AACGTTGAAAAATGACCCCCCGCGTCAATATTC
1 AACGTTGAAAAATGACCCCCCGCGTCAATATTC
* *
360532 AACGTTG-AAAATGA-CCCCCGGGTCAATTTTC
1 AACGTTGAAAAATGACCCCCCGCGTCAATATTC
360563 AAC
1 AAC
360566 CCGGGTCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 18 0.56
32 7 0.22
33 7 0.22
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.22
Consensus pattern (33 bp):
AACGTTGAAAAATGACCCCCCGCGTCAATATTC
Found at i:369079 original size:20 final size:20
Alignment explanation
Indices: 369054--369092 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
369044 TCCAACACAT
369054 GTTATACACT-CGTTATTCAC
1 GTTATACA-TGCGTTATTCAC
369074 GTTATACATGCGTTATTCA
1 GTTATACATGCGTTATTCA
369093 TGTGAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.41
Consensus pattern (20 bp):
GTTATACATGCGTTATTCAC
Found at i:369632 original size:280 final size:280
Alignment explanation
Indices: 369130--369685 Score: 1058
Period size: 280 Copynumber: 2.0 Consensus size: 280
369120 CGCTATTTAA
369130 CACATATGATATGTAAAGAAAGACCTTGCTAATGTCCCTGTTTATTGGTTTAAACTTTACTGTAA
1 CACATATGATATGTAAAGAAAGACCTTGCTAATGTCCCTGTTTATTGGTTTAAACTTTACTGTAA
*
369195 TATATGTAGTCATAAATGAATAAAGATGTTTTATCAACAGAATCCACGTGCCTTCTTAAAAATAA
66 TATATGTAGTCATAAATGAATAAAGATGTTTTATCAACAGAATACACGTGCCTTCTTAAAAATAA
*
369260 TTTGATAACGAATCCGGATTTGAGCCGGAATCGGCTTTAGGTTTGTTGTCGACAAATTATAGTAT
131 TTTGATAACAAATCCGGATTTGAGCCGGAATCGGCTTTAGGTTTGTTGTCGACAAATTATAGTAT
369325 GTCACATTTTAACGTCACGGACTTAAGACATCGAACTGCATGATGAATTAAGCAGAGGTAGAATT
196 GTCACATTTTAACGTCACGGACTTAAGACATCGAACTGCATGATGAATTAAGCAGAGGTAGAATT
369390 TGTCAAGCATTCGATTGTTT
261 TGTCAAGCATTCGATTGTTT
*
369410 CACATATGATATGTGAAGAAAGACCTTGCTAATGTCCCTGTTTATTGGTTTAAACTTTACTGTAA
1 CACATATGATATGTAAAGAAAGACCTTGCTAATGTCCCTGTTTATTGGTTTAAACTTTACTGTAA
369475 TATATGTAGTCATAAATGAATAAAGATGTTTTATCAACAGAATACACGTGCCTTCTTAAAAATAA
66 TATATGTAGTCATAAATGAATAAAGATGTTTTATCAACAGAATACACGTGCCTTCTTAAAAATAA
369540 TTTGATAACAAATCCGGATTTGAGCCGGAATCGGCTTTAGGTTTGTTGTCGACAAATTATAGTAT
131 TTTGATAACAAATCCGGATTTGAGCCGGAATCGGCTTTAGGTTTGTTGTCGACAAATTATAGTAT
* * *
369605 GTCACATTTTAACGTCACGGGCTTAAGAGATCGAACTGCATGATGAATTAAGCAGAGGTAGGATT
196 GTCACATTTTAACGTCACGGACTTAAGACATCGAACTGCATGATGAATTAAGCAGAGGTAGAATT
369670 TGTCAAGCATTCGATT
261 TGTCAAGCATTCGATT
369686 TTTTTTACTT
Statistics
Matches: 270, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
280 270 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (280 bp):
CACATATGATATGTAAAGAAAGACCTTGCTAATGTCCCTGTTTATTGGTTTAAACTTTACTGTAA
TATATGTAGTCATAAATGAATAAAGATGTTTTATCAACAGAATACACGTGCCTTCTTAAAAATAA
TTTGATAACAAATCCGGATTTGAGCCGGAATCGGCTTTAGGTTTGTTGTCGACAAATTATAGTAT
GTCACATTTTAACGTCACGGACTTAAGACATCGAACTGCATGATGAATTAAGCAGAGGTAGAATT
TGTCAAGCATTCGATTGTTT
Found at i:389703 original size:29 final size:29
Alignment explanation
Indices: 389664--389744 Score: 110
Period size: 28 Copynumber: 2.8 Consensus size: 29
389654 ACCTTTCCTT
389664 TGGCATAAGGCCTATCACACCTTTTTTCA
1 TGGCATAAGGCCTATCACACCTTTTTTCA
* *
389693 TGGCATAAGGCCAATTACACC-TTTTTCA
1 TGGCATAAGGCCTATCACACCTTTTTTCA
* * *
389721 TGGTATAAGACCTATCATACCTTT
1 TGGCATAAGGCCTATCACACCTTT
389745 CCTGTGGCAT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 23 0.52
29 21 0.48
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.35
Consensus pattern (29 bp):
TGGCATAAGGCCTATCACACCTTTTTTCA
Found at i:389758 original size:28 final size:28
Alignment explanation
Indices: 389624--389757 Score: 99
Period size: 28 Copynumber: 4.7 Consensus size: 28
389614 AGCTTCCAGA
* * * *
389624 ACCTTTCCTGTGGTATATAGGGCATATCAT
1 ACCTTTCCTATGGCATA-A-GGCCTATCAC
*
389654 ACCTTTCCTTTGGCATAAGGCCTATCAC
1 ACCTTTCCTATGGCATAAGGCCTATCAC
** * *
389682 ACCTTTTTTCATGGCATAAGGCCAATTAC
1 ACCTTTCCT-ATGGCATAAGGCCTATCAC
* * * *
389711 ACCTTT-TTCATGGTATAAGACCTATCAT
1 ACCTTTCCT-ATGGCATAAGGCCTATCAC
*
389739 ACCTTTCCTGTGGCATAAG
1 ACCTTTCCTATGGCATAAG
389758 ATGTCATAAC
Statistics
Matches: 85, Mismatches: 17, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
28 46 0.54
29 24 0.28
30 15 0.18
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.35
Consensus pattern (28 bp):
ACCTTTCCTATGGCATAAGGCCTATCAC
Found at i:392325 original size:3 final size:3
Alignment explanation
Indices: 392317--392354 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
392307 TGACAGTAAG
* *
392317 GAT GAT GAT CAT GAT AAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
392355 ATTTCTTACT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.37, C:0.03, G:0.29, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:392727 original size:2 final size:2
Alignment explanation
Indices: 392714--392758 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
392704 ATACAAACTT
*
392714 TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
392756 TC T
1 TC T
392759 TACCACATAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:392827 original size:2 final size:2
Alignment explanation
Indices: 392820--392867 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
392810 AGTATACAAA
392820 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
392862 CT CT CT
1 CT CT CT
392868 NTAAAAAAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:393115 original size:2 final size:2
Alignment explanation
Indices: 393108--393138 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
393098 AGTATACAAA
393108 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
393139 ACCACATACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:393922 original size:22 final size:22
Alignment explanation
Indices: 393868--393922 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 22
393858 AAAAAATTAA
393868 ATTA-TGAATTCAATATCTATTG
1 ATTATTGAATT-AATATCTATTG
* *
393890 A-TATT-ATATTAATATTTATTT
1 ATTATTGA-ATTAATATCTATTG
393911 ATTATTGAATTA
1 ATTATTGAATTA
393923 TTGAAGTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
21 13 0.48
22 13 0.48
23 1 0.04
ACGTcount: A:0.38, C:0.04, G:0.05, T:0.53
Consensus pattern (22 bp):
ATTATTGAATTAATATCTATTG
Found at i:400216 original size:2 final size:2
Alignment explanation
Indices: 400211--400240 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
400201 CCCCCCCCCC
*
400211 CA CA CA CA CA CA CA CA CA CA CA TA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
400241 ATCAAATGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.47, G:0.00, T:0.03
Consensus pattern (2 bp):
CA
Found at i:405433 original size:21 final size:21
Alignment explanation
Indices: 405368--405435 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
405358 ATTAATCTCG
* * *
405368 ACATGCGAGTTACTTATGTTA
1 ACATGTGAGATACTCATGTTA
* * *
405389 ACATGTCAGATA-TCCATCTCA
1 ACATGTGAGATACT-CATGTTA
*
405410 ACATGTGAGATACTGATGTTA
1 ACATGTGAGATACTCATGTTA
405431 ACATG
1 ACATG
405436 CACCTTTTAT
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
20 1 0.03
21 33 0.94
22 1 0.03
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (21 bp):
ACATGTGAGATACTCATGTTA
Found at i:407325 original size:20 final size:20
Alignment explanation
Indices: 407301--407348 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
407291 ATACAATACA
* *
407301 ATATTGTATTATATGATATG
1 ATATTGTATCAAATGATATG
* *
407321 GTATTGTATCAAATGATCTG
1 ATATTGTATCAAATGATATG
407341 ATATTGTA
1 ATATTGTA
407349 AAAATATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (20 bp):
ATATTGTATCAAATGATATG
Found at i:407721 original size:20 final size:20
Alignment explanation
Indices: 407650--407708 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
407640 CTTGTCATAT
*
407650 ATAATACATTATCATATCAA-
1 ATAATACAATATCATAT-AAC
*
407670 ACAATACAATATCATATAAC
1 ATAATACAATATCATATAAC
407690 ATAATACAATATCATATAA
1 ATAATACAATATCATATAA
407709 TATTGTACCA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
19 2 0.06
20 33 0.94
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (20 bp):
ATAATACAATATCATATAAC
Found at i:426816 original size:290 final size:291
Alignment explanation
Indices: 426333--426918 Score: 989
Period size: 290 Copynumber: 2.0 Consensus size: 291
426323 ATGGCTTTAA
** * *
426333 ATTTTGGTTGTTTCGAACCCACGACCTAAAAAGTGTTATCATATAAAACGCTGCAGCACATAAAG
1 ATTTTGGTTGTTTCGAACCCACGACCTAAAAAGCCTGATCATATAAAACGCTACAGCACATAAAG
*
426398 AAAAAACCCTACAATTCAACCGAAATTGCCCAAGTTAAAATAATCCTACATATTATCATTTCTTC
66 AAAAAAACCTACAATTCAACCGAAATTGCCCAAGTTAAAATAATCCTACATATTATCATTTCTTC
426463 TTCCTGTTAATTATAACGCTCAAATATAACATAATACATATATGTTTAGATAATGTGTAAACTCA
131 TTCCTGTTAATTATAACGCTCAAATATAACATAATACATATATGTTTAGATAATGTGTAAACTCA
* * * *
426528 TTTTGTATGAATAATACGAATGTATATTTAT-ATAAAAAAGAATTATGGCCTTTAAAAAAAATAT
196 TTTCGTATGAAAAATACGAATGTATATATATAAAAAAAAAGAATTATGGCCTTTAAAAAAAATAT
426592 TTTACAAAAACTAGCTTACAATATGGAAAAC
261 TTTACAAAAACTAGCTTACAATATGGAAAAC
*
426623 ATTTTGGTTGTTTCGAACCCACGACCTAAAAAGCCTGATCATATAATACGCTACAGCAC-TAAAA
1 ATTTTGGTTGTTTCGAACCCACGACCTAAAAAGCCTGATCATATAAAACGCTACAGCACAT-AAA
*
426687 GAAAAAAACCTACAAATT-AACCGAAATTGCCCAAGTTAAAATAATCGTACATATTATCATTTCT
65 GAAAAAAACCTAC-AATTCAACCGAAATTGCCCAAGTTAAAATAATCCTACATATTATCATTTCT
* * * *
426751 TCTTCCTGTTAATTATTATGCTCGAATATAACGTAATACATATATGTTTAGATAATGTGTAAACT
129 TCTTCCTGTTAATTATAACGCTCAAATATAACATAATACATATATGTTTAGATAATGTGTAAACT
426816 CATTTCGTATGAAAAATACGAATGTATATATATAAAAAAAAAGAATTATGGCCTTTAAAAAAAAT
194 CATTTCGTATGAAAAATACGAATGTATATATATAAAAAAAAAGAATTATGGCCTTTAAAAAAAAT
*
426881 ATTTTACAAAAACTAGCTTACAATATGGAAAAT
259 ATTTTACAAAAACTAGCTTACAATATGGAAAAC
426914 ATTTT
1 ATTTT
426919 CCGCAATTAT
Statistics
Matches: 277, Mismatches: 16, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
289 1 0.00
290 205 0.74
291 71 0.26
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (291 bp):
ATTTTGGTTGTTTCGAACCCACGACCTAAAAAGCCTGATCATATAAAACGCTACAGCACATAAAG
AAAAAAACCTACAATTCAACCGAAATTGCCCAAGTTAAAATAATCCTACATATTATCATTTCTTC
TTCCTGTTAATTATAACGCTCAAATATAACATAATACATATATGTTTAGATAATGTGTAAACTCA
TTTCGTATGAAAAATACGAATGTATATATATAAAAAAAAAGAATTATGGCCTTTAAAAAAAATAT
TTTACAAAAACTAGCTTACAATATGGAAAAC
Found at i:438941 original size:16 final size:16
Alignment explanation
Indices: 438920--438952 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
438910 TGCCAATTTT
438920 CAAACCAATGTTAACA
1 CAAACCAATGTTAACA
438936 CAAACCAATGTTAACA
1 CAAACCAATGTTAACA
438952 C
1 C
438953 TTGTAGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.27, G:0.06, T:0.18
Consensus pattern (16 bp):
CAAACCAATGTTAACA
Found at i:455075 original size:10 final size:10
Alignment explanation
Indices: 455060--455089 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
455050 ATGGTTTTAA
455060 AAAGATTTTT
1 AAAGATTTTT
455070 AAAGATTTTT
1 AAAGATTTTT
455080 AAAGATTTTT
1 AAAGATTTTT
455090 CTCTAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (10 bp):
AAAGATTTTT
Found at i:471361 original size:1 final size:1
Alignment explanation
Indices: 471355--471380 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
471345 CAAAGTCGAA
471355 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
471381 CTGGGGTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:473450 original size:27 final size:27
Alignment explanation
Indices: 473408--473461 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
473398 TAAATACCCA
473408 CTAGTGTGAAGACATTTTAGGAAGTTC
1 CTAGTGTGAAGACATTTTAGGAAGTTC
*
473435 CTAGTGTGAAGGCATTTTAGGAAGTTC
1 CTAGTGTGAAGACATTTTAGGAAGTTC
473462 AAAAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.28, C:0.11, G:0.28, T:0.33
Consensus pattern (27 bp):
CTAGTGTGAAGACATTTTAGGAAGTTC
Found at i:479945 original size:180 final size:180
Alignment explanation
Indices: 479592--480320 Score: 1217
Period size: 180 Copynumber: 4.0 Consensus size: 180
479582 GGCTGCCAAA
479592 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTGTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTGTTTTGCA
* * *
479657 GATCAATTGTACATAATATCAGAGGTGTGCATATTGATAGGATTTTGATTTCTGATAATTAATGA
66 GATCAATTGTACAT-ATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATGA
*
479722 AAAAATTACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
130 AAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
*
479773 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGATGTTGTTGTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTGTTTTGCA
479838 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATGAA
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATGAA
*
479903 AAAAATACTAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
131 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
* **
479953 AGGGTACCCTCATTGTACGGATAACTCCTCCTAAAGTTTTCAAGATAGGAAGTAATTGTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTGTTTTGCA
*
480018 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAGTTTATGAA
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATGAA
* * * *
480083 AAAAATACTAGCATTTGAACTTAGTCA-CTTTTGGCAAGATATTGCATAT
131 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
* * * *
480132 AGGGTACCCTCATTGTATGTATAACTCCTCCTACAGATTTCAAGATAGGAAGTTGTTCTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTGTTTTGCA
*
480197 GATCAATTGTACATAGGGTATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTT
66 GATCAATTGTAC--A---TATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTT
*
480262 ATGAAAAAAATACCAGCTTTTGAACTTAGTCACTTTTTGGCAAAATATTGCATAT
126 ATGAAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
480317 AGGG
1 AGGG
480321 GTACACCATT
Statistics
Matches: 515, Mismatches: 27, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
179 90 0.17
180 247 0.48
181 79 0.15
184 75 0.15
185 24 0.05
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.36
Consensus pattern (180 bp):
AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTGTTTTGCA
GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATGAA
AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
Found at i:480305 original size:364 final size:361
Alignment explanation
Indices: 479592--480320 Score: 1219
Period size: 364 Copynumber: 2.0 Consensus size: 361
479582 GGCTGCCAAA
* **
479592 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTGTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTAAAGTTTTCAAGATAGGAAGTAATTGTTTTGCA
*
479657 GATCAATTGTACATAATATCAGAGGTGTGCATATTGATAGGATTTTGATTTCTGATAATTAATGA
66 GATCAATTGTACATAATATCAGAGGTGTGCATATTGATAGGATTTTGATTTCCGATAATTAATGA
* * *
479722 AAAAATTACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCTCATT
131 AAAAAATACCAGCATTTGAACTTAGTCATCTTTTGGCAAAATATTGCATATAGGGTACCCTCATT
* * *
479787 GTACGGATAACTCCTCCTACAGTTTTCAAGATAGGATGTTGTTGTTTTGCAGATCAATTGTACAT
196 GTACGGATAACTCCTCCTACAGATTTCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTACAT
*
479852 ATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATGAAAAAAATACTAGCTT
261 ATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATGAAAAAAATACCAGCTT
*
479917 TTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
326 TTGAACTTAGTCACTTTTTGGCAAAATATTGCATAT
479953 AGGGTACCCTCATTGTACGGATAACTCCTCCTAAAGTTTTCAAGATAGGAAGTAATTGTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTAAAGTTTTCAAGATAGGAAGTAATTGTTTTGCA
* * *
480018 GATCAATTGTACAT-ATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAGTTTATGA
66 GATCAATTGTACATAATATCAGAGGTGTGCATATTGATAGGATTTTGATTTCCGATAATTAATGA
* *
480082 AAAAAATACTAGCATTTGAACTTAGTCA-CTTTTGGCAAGATATTGCATATAGGGTACCCTCATT
131 AAAAAATACCAGCATTTGAACTTAGTCATCTTTTGGCAAAATATTGCATATAGGGTACCCTCATT
* *
480146 GTATGTATAACTCCTCCTACAGATTTCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTACAT
196 GTACGGATAACTCCTCCTACAGATTTCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTAC--
*
480211 AGGGTATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTATGAAAAAAATACC
259 A---TATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATGAAAAAAATACC
480276 AGCTTTTGAACTTAGTCACTTTTTGGCAAAATATTGCATAT
321 AGCTTTTGAACTTAGTCACTTTTTGGCAAAATATTGCATAT
480317 AGGG
1 AGGG
480321 GTACACCATT
Statistics
Matches: 343, Mismatches: 20, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
359 92 0.27
360 71 0.21
361 77 0.22
364 103 0.30
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.36
Consensus pattern (361 bp):
AGGGTACCCTCATTGTACGGATAACTCCTCCTAAAGTTTTCAAGATAGGAAGTAATTGTTTTGCA
GATCAATTGTACATAATATCAGAGGTGTGCATATTGATAGGATTTTGATTTCCGATAATTAATGA
AAAAAATACCAGCATTTGAACTTAGTCATCTTTTGGCAAAATATTGCATATAGGGTACCCTCATT
GTACGGATAACTCCTCCTACAGATTTCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTACAT
ATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATGAAAAAAATACCAGCTT
TTGAACTTAGTCACTTTTTGGCAAAATATTGCATAT
Found at i:480662 original size:2 final size:2
Alignment explanation
Indices: 480655--480747 Score: 186
Period size: 2 Copynumber: 46.5 Consensus size: 2
480645 GTTTGAAATG
480655 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
480697 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
480739 GA GA GA GA G
1 GA GA GA GA G
480748 TTTTGTTTTA
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 91 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:481469 original size:20 final size:20
Alignment explanation
Indices: 481444--481521 Score: 138
Period size: 20 Copynumber: 3.9 Consensus size: 20
481434 CTCAGCACTT
*
481444 TAACTTAAAGTGCTGAGGTC
1 TAACTTAGAGTGCTGAGGTC
481464 TAACTTAGAGTGCTGAGGTC
1 TAACTTAGAGTGCTGAGGTC
481484 TAACTTAGAGTGCTGAGGTC
1 TAACTTAGAGTGCTGAGGTC
*
481504 TAACTTCGAGTGCTGAGG
1 TAACTTAGAGTGCTGAGG
481522 ACCTGGGTTG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (20 bp):
TAACTTAGAGTGCTGAGGTC
Found at i:501642 original size:172 final size:172
Alignment explanation
Indices: 501204--501796 Score: 999
Period size: 172 Copynumber: 3.4 Consensus size: 172
501194 GCAGTATACT
* ** * *
501204 AGTATCGACCAAGGCTGATTTAGGAACTTGACCAAGGTATTTGTGGTATAAACATTTGGTATAAA
1 AGTATCGACCAATGCTGATTTTCGAACTTGACCAAAGTATTAGTGGTATAAACATTTGGTATAAA
* * * *
501269 TTTCATGTAAATCCGTCAAAATTTGTAGGAATGAGAGCGCTTACAAGGTCAATGTTTGGATAAAA
66 TTTAATGAAAATCCGTCAAAGTTTGTAGGCATGAGAGCGCTTACAAGGTCAATGTTTGGATAAAA
* *
501334 CGGAGTCTTTATTGTGGTCAAAGTCCCATTACTCCAACAAAA
131 CGGAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAA
*
501376 AGTCGAT-GATCAATGCTGATTTTCGAACTTGACCAAAGTATTAGTGGTATAAACATTTGGTATA
1 AGT--ATCGACCAATGCTGATTTTCGAACTTGACCAAAGTATTAGTGGTATAAACATTTGGTATA
*
501440 AATTTAATGAAAATCCGTCAAAGTTTGTAGGCATGCGAGCGCTTACAAGGTCAATGTTTGGATAA
64 AATTTAATGAAAATCCGTCAAAGTTTGTAGGCATGAGAGCGCTTACAAGGTCAATGTTTGGATAA
501505 AACGGAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAA
129 AACGGAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAA
* * *
501549 AGTATCGACCAATGCTGATTTTCAAACTTGACCAAAATATTAGTGGTATAAACATTTGGTATTAA
1 AGTATCGACCAATGCTGATTTTCGAACTTGACCAAAGTATTAGTGGTATAAACATTTGGTATAAA
*
501614 TTTAATGAAAATCCGTCAAAGTTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAA
66 TTTAATGAAAATCCGTCAAAGTTTGTAGGCATGAGAGCGCTTACAAGGTCAATGTTTGGATAAAA
501679 CGGAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAA
131 CGGAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAA
501721 AGTATCGACCAATGCTGATTTTCGAACTTGACCAAAGTATTAGTGGTATAAACATTTGGTATAAA
1 AGTATCGACCAATGCTGATTTTCGAACTTGACCAAAGTATTAGTGGTATAAACATTTGGTATAAA
*
501786 TTTAATCAAAA
66 TTTAATGAAAA
501797 ATTTGTAGGC
Statistics
Matches: 395, Mismatches: 23, Indels: 6
0.93 0.05 0.01
Matches are distributed among these distances:
171 2 0.01
172 235 0.59
173 156 0.39
174 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.30
Consensus pattern (172 bp):
AGTATCGACCAATGCTGATTTTCGAACTTGACCAAAGTATTAGTGGTATAAACATTTGGTATAAA
TTTAATGAAAATCCGTCAAAGTTTGTAGGCATGAGAGCGCTTACAAGGTCAATGTTTGGATAAAA
CGGAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAA
Done.