Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold16
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5287347
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 8769 characters in sequence are not A, C, G, or T
File 35 of 35
Found at i:5201581 original size:22 final size:23
Alignment explanation
Indices: 5201544--5201586 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
5201534 TTGAATATTA
**
5201544 AAATTAAATTTTTTAT-TGAATT
1 AAATTAAATTGATTATATGAATT
5201566 AAATTAAATTGATTATATGAA
1 AAATTAAATTGATTATATGAA
5201587 ATATTATCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (23 bp):
AAATTAAATTGATTATATGAATT
Found at i:5210500 original size:26 final size:26
Alignment explanation
Indices: 5210441--5210501 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
5210431 AATCTGTAAA
* *
5210441 ATATAAATATTAATATATTAAAATTT
1 ATATAAATATAAATATATTAAAATAT
*
5210467 ATATAAATATAAATATGATTATAATAT
1 ATATAAATATAAATAT-ATTAAAATAT
*
5210494 GTA-AAATA
1 ATATAAATA
5210502 CATAATATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 20 0.67
27 10 0.33
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (26 bp):
ATATAAATATAAATATATTAAAATAT
Found at i:5211184 original size:3 final size:3
Alignment explanation
Indices: 5211178--5211204 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5211168 TTATTTAAAA
5211178 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
5211205 ATTGAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5211748 original size:15 final size:15
Alignment explanation
Indices: 5211713--5211752 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
5211703 GGAGTAGGAG
5211713 AAAAA-AAA-AAA-A
1 AAAAAGAAAGAAAGA
5211725 AAAAAGAAAGAAAGA
1 AAAAAGAAAGAAAGA
*
5211740 AAAAGGAAAGAAA
1 AAAAAGAAAGAAA
5211753 CAAATTTGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 5 0.21
13 3 0.12
14 3 0.12
15 13 0.54
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAGAAAGA
Found at i:5214555 original size:21 final size:21
Alignment explanation
Indices: 5214526--5214603 Score: 59
Period size: 21 Copynumber: 3.6 Consensus size: 21
5214516 TCATATTGCA
*
5214526 TTATTTTAGGTTTTAAAATTT
1 TTATATTAGGTTTTAAAATTT
* ** *
5214547 TTATATTAGG-TTCACGTTATTGCG
1 TTATATTAGGTTTTA--AAATT--T
*
5214571 TTATTTTAGGTTTTAAAATTT
1 TTATATTAGGTTTTAAAATTT
5214592 TTATATTAGGTT
1 TTATATTAGGTT
5214604 CACGTTATTT
Statistics
Matches: 41, Mismatches: 11, Indels: 10
0.66 0.18 0.16
Matches are distributed among these distances:
20 3 0.07
21 20 0.49
22 3 0.07
23 3 0.07
24 9 0.22
25 3 0.07
ACGTcount: A:0.26, C:0.04, G:0.14, T:0.56
Consensus pattern (21 bp):
TTATATTAGGTTTTAAAATTT
Found at i:5214583 original size:45 final size:45
Alignment explanation
Indices: 5214519--5214612 Score: 179
Period size: 45 Copynumber: 2.1 Consensus size: 45
5214509 CTTGATTTCA
5214519 TATTGCATTATTTTAGGTTTTAAAATTTTTATATTAGGTTCACGT
1 TATTGCATTATTTTAGGTTTTAAAATTTTTATATTAGGTTCACGT
*
5214564 TATTGCGTTATTTTAGGTTTTAAAATTTTTATATTAGGTTCACGT
1 TATTGCATTATTTTAGGTTTTAAAATTTTTATATTAGGTTCACGT
5214609 TATT
1 TATT
5214613 TTAAGTTCGG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.26, C:0.06, G:0.14, T:0.54
Consensus pattern (45 bp):
TATTGCATTATTTTAGGTTTTAAAATTTTTATATTAGGTTCACGT
Found at i:5214614 original size:21 final size:21
Alignment explanation
Indices: 5214545--5214615 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
5214535 GTTTTAAAAT
5214545 TTTTATATTAGGTTCACGTTA
1 TTTTATATTAGGTTCACGTTA
* * ***
5214566 TTGCGTTATTTTAGGTTTTAAAAT-
1 TT---TTATATTAGG-TTCACGTTA
5214590 TTTTATATTAGGTTCACGTTA
1 TTTTATATTAGGTTCACGTTA
5214611 TTTTA
1 TTTTA
5214616 AGTTCGGATT
Statistics
Matches: 35, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
20 4 0.11
21 16 0.46
24 11 0.31
25 4 0.11
ACGTcount: A:0.24, C:0.07, G:0.14, T:0.55
Consensus pattern (21 bp):
TTTTATATTAGGTTCACGTTA
Found at i:5214627 original size:16 final size:16
Alignment explanation
Indices: 5214610--5214677 Score: 73
Period size: 16 Copynumber: 4.2 Consensus size: 16
5214600 GGTTCACGTT
* *
5214610 ATTTTAAGTTCGGATT
1 ATTTTAAGTTCGAATC
**
5214626 ATTTCGAGTTCGAATC
1 ATTTTAAGTTCGAATC
* * *
5214642 ATTTAAAGTTTGCATC
1 ATTTTAAGTTCGAATC
5214658 ATTTTAAGTTCGAATC
1 ATTTTAAGTTCGAATC
5214674 ATTT
1 ATTT
5214678 CGATTCGAGT
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.46
Consensus pattern (16 bp):
ATTTTAAGTTCGAATC
Found at i:5215496 original size:16 final size:16
Alignment explanation
Indices: 5215471--5215538 Score: 68
Period size: 16 Copynumber: 4.2 Consensus size: 16
5215461 TATTCGGATC
*
5215471 ATTTCGAGTTTGAATT
1 ATTTCAAGTTTGAATT
*
5215487 ATTTCAAGTTTAAATT
1 ATTTCAAGTTTGAATT
* *
5215503 ATTTC-GGATTTGAATA
1 ATTTCAAG-TTTGAATT
5215519 ATTTCGAA-TTTGAATT
1 ATTTC-AAGTTTGAATT
5215535 ATTT
1 ATTT
5215539 TTAAATTCGG
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
15 1 0.02
16 41 0.98
ACGTcount: A:0.31, C:0.06, G:0.13, T:0.50
Consensus pattern (16 bp):
ATTTCAAGTTTGAATT
Found at i:5215507 original size:32 final size:32
Alignment explanation
Indices: 5215471--5215538 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 32
5215461 TATTCGGATC
*
5215471 ATTTC-GAGTTTGAATTATTTC-AAGTTTAAATT
1 ATTTCGGA-TTTGAATAATTTCGAA-TTTAAATT
*
5215503 ATTTCGGATTTGAATAATTTCGAATTTGAATT
1 ATTTCGGATTTGAATAATTTCGAATTTAAATT
5215535 ATTT
1 ATTT
5215539 TTAAATTCGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 28 0.88
33 4 0.12
ACGTcount: A:0.31, C:0.06, G:0.13, T:0.50
Consensus pattern (32 bp):
ATTTCGGATTTGAATAATTTCGAATTTAAATT
Found at i:5216326 original size:69 final size:69
Alignment explanation
Indices: 5216191--5216328 Score: 197
Period size: 69 Copynumber: 2.0 Consensus size: 69
5216181 CGCCATATCA
* * * *
5216191 TGTGCCGCCGCATCTTCTCCCAATTGAAATTGTTGTGCAGGAATCGGCATACTGGTCAGGTTGCA
1 TGTGCCGCCGCATCTTCTCCCAATTGAAATTGCTGTGCAGGAATCGGCATAATGATCAGGTGGCA
5216256 AACG
66 AACG
* * *
5216260 TGTGCCGCTGCATCTTCTCCCGATTGAAATTGCTGTGCAGGAATCAGG-ATAATGATGAGGTGGC
1 TGTGCCGCCGCATCTTCTCCCAATTGAAATTGCTGTGCAGGAATC-GGCATAATGATCAGGTGGC
5216324 AAACG
65 AAACG
5216329 GACAGTTTGA
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
69 59 0.97
70 2 0.03
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (69 bp):
TGTGCCGCCGCATCTTCTCCCAATTGAAATTGCTGTGCAGGAATCGGCATAATGATCAGGTGGCA
AACG
Found at i:5216397 original size:16 final size:16
Alignment explanation
Indices: 5216376--5216432 Score: 80
Period size: 16 Copynumber: 3.6 Consensus size: 16
5216366 GCTAATTTAA
5216376 AAATTTAAATTATTTT
1 AAATTTAAATTATTTT
*
5216392 AAATTTAAATAATTTT
1 AAATTTAAATTATTTT
* *
5216408 AAAATT-AATTTTTTT
1 AAATTTAAATTATTTT
5216423 AAATTTAAAT
1 AAATTTAAAT
5216433 CACCTTTAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
15 12 0.34
16 23 0.66
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AAATTTAAATTATTTT
Found at i:5216426 original size:31 final size:33
Alignment explanation
Indices: 5216368--5216432 Score: 98
Period size: 31 Copynumber: 2.0 Consensus size: 33
5216358 TTTATTCAGC
5216368 TAATTTAAAAATTTAAATTATTTTAAATTTAAA
1 TAATTTAAAAATTTAAATTATTTTAAATTTAAA
* *
5216401 TAATTTTAAAA-TT-AATTTTTTTAAATTTAAA
1 TAATTTAAAAATTTAAATTATTTTAAATTTAAA
5216432 T
1 T
5216433 CACCTTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 18 0.60
32 2 0.07
33 10 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (33 bp):
TAATTTAAAAATTTAAATTATTTTAAATTTAAA
Found at i:5216455 original size:32 final size:31
Alignment explanation
Indices: 5216381--5216455 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
5216371 TTTAAAAATT
*
5216381 TAAATTATTTTAAATTTAAATAATTTTAAAA
1 TAAATTATTTTAAATTTAAATAACTTTAAAA
* * * *
5216412 TTAATTTTTTTAAATTTAAATCACCTTT-AAG
1 TAAATTATTTTAAATTTAAAT-AACTTTAAAA
5216443 TCAAATTATTTTA
1 T-AAATTATTTTA
5216456 TATACAATTT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
31 22 0.63
32 13 0.37
ACGTcount: A:0.43, C:0.05, G:0.01, T:0.51
Consensus pattern (31 bp):
TAAATTATTTTAAATTTAAATAACTTTAAAA
Found at i:5216660 original size:12 final size:13
Alignment explanation
Indices: 5216643--5216673 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
5216633 AACTCTAAAC
5216643 ATTTATAAATAT-
1 ATTTATAAATATA
5216655 ATTTATAAATATA
1 ATTTATAAATATA
5216668 ATTTAT
1 ATTTAT
5216674 GCTATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTATAAATATA
Found at i:5218359 original size:21 final size:22
Alignment explanation
Indices: 5218310--5218361 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
5218300 AATCTAACAG
*
5218310 ATTTTTATTTTGCTTTTTTAAA
1 ATTTTTATTTTGCTTTATTAAA
5218332 ATTTTTATTTTG-TTTCATT-AA
1 ATTTTTATTTTGCTTT-ATTAAA
*
5218353 TTTTTTATT
1 ATTTTTATT
5218362 GTATTATAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.71
Consensus pattern (22 bp):
ATTTTTATTTTGCTTTATTAAA
Found at i:5220957 original size:16 final size:16
Alignment explanation
Indices: 5220932--5220978 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
5220922 AATTAAATTT
5220932 AAATTAAATAAAAATC
1 AAATTAAATAAAAATC
* * * *
5220948 AATTTTAATAATAATT
1 AAATTAAATAAAAATC
5220964 AAATTAAATAAAAAT
1 AAATTAAATAAAAAT
5220979 GATAATAATA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (16 bp):
AAATTAAATAAAAATC
Found at i:5220996 original size:32 final size:33
Alignment explanation
Indices: 5220923--5220996 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 33
5220913 TGAAGTCAAA
**
5220923 ATTAAATTTAAATTAAATAAAAATCAATTTTAAT
1 ATTAAA-TTAAATTAAATAAAAATCAATAATAAT
* *
5220957 AAT-AATTAAATTAAATAAAAAT-GATAATAAT
1 ATTAAATTAAATTAAATAAAAATCAATAATAAT
5220988 ATTAAATTA
1 ATTAAATTA
5220997 TTTGAATTAG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
31 8 0.24
32 22 0.65
33 2 0.06
34 2 0.06
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (33 bp):
ATTAAATTAAATTAAATAAAAATCAATAATAAT
Found at i:5221946 original size:2 final size:2
Alignment explanation
Indices: 5221939--5221971 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5221929 GTGAAAATAA
5221939 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5221972 GATCTTAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5222152 original size:21 final size:21
Alignment explanation
Indices: 5222109--5222160 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
5222099 AATCTATATT
*
5222109 AAAAATAAATAGAGAATTTAA
1 AAAAATAAATAGAGAATTGAA
*
5222130 AAAAATAAATATA-AATATGAA
1 AAAAATAAATAGAGAAT-TGAA
*
5222151 AATAATAAAT
1 AAAAATAAAT
5222161 TTCAAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 3 0.11
21 24 0.89
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (21 bp):
AAAAATAAATAGAGAATTGAA
Found at i:5224123 original size:24 final size:25
Alignment explanation
Indices: 5224086--5224138 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
5224076 AAAATTTTAT
* *
5224086 TAAATAATATATTTATATCAAATAA
1 TAAAAAATATATTTATATAAAATAA
*
5224111 TAAAAAAT-TATTTATTTAAAATAA
1 TAAAAAATATATTTATATAAAATAA
5224135 TAAA
1 TAAA
5224139 TTATTTTCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (25 bp):
TAAAAAATATATTTATATAAAATAA
Found at i:5224266 original size:22 final size:22
Alignment explanation
Indices: 5224241--5224282 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
5224231 ATTTTTTATT
5224241 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
5224263 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
5224283 ATATTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:5229827 original size:31 final size:31
Alignment explanation
Indices: 5229789--5229864 Score: 127
Period size: 31 Copynumber: 2.5 Consensus size: 31
5229779 TTTTAACTAG
5229789 ATGTATCGATACATCTGGGTAAA-ATGACAGA
1 ATGTATCGATACATCTGGGTAAATA-GACAGA
5229820 ATGTATCGATACATCTGGGTAAATAGACAGA
1 ATGTATCGATACATCTGGGTAAATAGACAGA
*
5229851 ATGTATCAATACAT
1 ATGTATCGATACAT
5229865 TCATACATGT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
31 42 0.98
32 1 0.02
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (31 bp):
ATGTATCGATACATCTGGGTAAATAGACAGA
Found at i:5229876 original size:20 final size:20
Alignment explanation
Indices: 5229850--5229904 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
5229840 AAATAGACAG
* *
5229850 AATGTATCAATACATTCATA
1 AATGTATCGATACATTCAAA
* *
5229870 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTCAAA
5229890 AATGTATCGATACAT
1 AATGTATCGATACAT
5229905 CTAGGTAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:5231274 original size:28 final size:28
Alignment explanation
Indices: 5230797--5231268 Score: 540
Period size: 28 Copynumber: 16.5 Consensus size: 28
5230787 CATTAACTTG
* * *
5230797 TGTGGGATTTGAAAAGAGTTGCCACCGACTT
1 TGTGGGCTTTG-AAAG-GATGCCACTGAC-T
* *
5230828 GTGTGGGCTTTGAAAGGGTGCCACCGACT
1 -TGTGGGCTTTGAAAGGATGCCACTGACT
5230857 TGTGGGCTTTGAAAAGGTATGCCA-TGGACT
1 TGTGGGCTTTG-AAAGG-ATGCCACT-GACT
* * * *
5230887 TGTAGGCTTTGAAGGGGTACCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
5230915 TGTGGGCTTTGAAAAGG-TGCCATTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* * * *
5230943 TGTGTGCTTTGGAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
5230971 TGTGGGCTTT-AGAAGGGTGCCACTGATT
1 TGTGGGCTTTGA-AAGGATGCCACTGACT
5230999 TGTATGGGCTTTGAAAGGGTATGCCACTGACT
1 TG--TGGGCTTTGAAA-GG-ATGCCACTGACT
* *
5231031 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
5231059 AT-TGGGCTTTTG-AAGAGATGCCACTGACT
1 -TGTGGGC-TTTGAAAG-GATGCCACTGACT
*
5231088 TGTGGGCTTTGAAAGGATGCCACTGACG
1 TGTGGGCTTTGAAAGGATGCCACTGACT
5231116 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
5231144 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
5231172 TGTGGGCTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
5231200 TGTAGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
5231228 TGTAGGCTTTGAAAGGATGCCATTGACC
1 TGTGGGCTTTGAAAGGATGCCACTGACT
5231256 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
5231269 GAGATGAACG
Statistics
Matches: 387, Mismatches: 36, Indels: 38
0.84 0.08 0.08
Matches are distributed among these distances:
27 4 0.01
28 261 0.67
29 41 0.11
30 52 0.13
31 7 0.02
32 22 0.06
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:5232538 original size:9 final size:9
Alignment explanation
Indices: 5232517--5232571 Score: 53
Period size: 9 Copynumber: 6.4 Consensus size: 9
5232507 TCTGGACCCC
5232517 TTTTTGTTT
1 TTTTTGTTT
*
5232526 TTTTT-TTG
1 TTTTTGTTT
* *
5232534 GTTTT-TTA
1 TTTTTGTTT
5232542 TTTTT-TTT
1 TTTTTGTTT
*
5232550 GTTTTGTTT
1 TTTTTGTTT
5232559 TTTTTGTTT
1 TTTTTGTTT
5232568 TTTT
1 TTTT
5232572 GTACGAAGGA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
8 18 0.47
9 20 0.53
ACGTcount: A:0.02, C:0.00, G:0.11, T:0.87
Consensus pattern (9 bp):
TTTTTGTTT
Found at i:5232538 original size:17 final size:16
Alignment explanation
Indices: 5232518--5232573 Score: 69
Period size: 17 Copynumber: 3.4 Consensus size: 16
5232508 CTGGACCCCT
5232518 TTTTGTTTTTTTTTTGG
1 TTTTGTTTTTTTTTT-G
5232535 TTTT-TTATTTTTTTTG
1 TTTTGTT-TTTTTTTTG
*
5232551 TTTTGTTTTTTTTGTTT
1 TTTTGTTTTTTTT-TTG
5232568 TTTTGT
1 TTTTGT
5232574 ACGAAGGATG
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
16 13 0.37
17 22 0.63
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.86
Consensus pattern (16 bp):
TTTTGTTTTTTTTTTG
Found at i:5232554 original size:22 final size:22
Alignment explanation
Indices: 5232517--5232573 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
5232507 TCTGGACCCC
*
5232517 TTTT-TGTTTTTTT-TTTGGTT
1 TTTTATGTTTTTTTGTTTTGTT
5232537 TTTTAT-TTTTTTTGTTTTGTT
1 TTTTATGTTTTTTTGTTTTGTT
*
5232558 TTTTTTGTTTTTTTGT
1 TTTTATGTTTTTTTGT
5232574 ACGAAGGATG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.34
21 12 0.38
22 9 0.28
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.86
Consensus pattern (22 bp):
TTTTATGTTTTTTTGTTTTGTT
Found at i:5237321 original size:20 final size:20
Alignment explanation
Indices: 5237296--5237369 Score: 87
Period size: 20 Copynumber: 3.7 Consensus size: 20
5237286 TCACAATTTG
5237296 TATCGATACATTGTTCATTA
1 TATCGATACATTGTTCATTA
** *
5237316 TATCGATACATTACTCATTG
1 TATCGATACATTGTTCATTA
*
5237336 TATCGATACATTGTATCAATA
1 TATCGATACATTGT-TCATTA
*
5237357 TATTGAT-CATTGT
1 TATCGATACATTGT
5237370 ATCGATACAT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 35 0.78
21 10 0.22
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (20 bp):
TATCGATACATTGTTCATTA
Found at i:5239883 original size:78 final size:76
Alignment explanation
Indices: 5239726--5239910 Score: 282
Period size: 78 Copynumber: 2.4 Consensus size: 76
5239716 CATCTCGGAA
*
5239726 ATACTCCAACCCCGGTTTTATTTCCAAAACATCAATCTTTCATCGGGGATACTCCAACCCTGTTA
1 ATACTCCAACCCCGGTTTTATTTCTAAAACATCAATCTTTCATCGGGGATACTCCAACCCTGTTA
*
5239791 TTTTTGAGGGG
66 TTTTTGAAGGG
* * * *
5239802 ATACTCTAACCCCGATTTTATTTCTAAAACATCAATTTTTCATAATC-GGGATACTCCAATCCTG
1 ATACTCCAACCCCGGTTTTATTTCTAAAACATCAATCTTTC---ATCGGGGATACTCCAACCCTG
5239866 TTATTTTTGAAGGG
63 TTATTTTTGAAGGG
5239880 ATACTCCAACCCCGGTTTTATTTCTAAAACA
1 ATACTCCAACCCCGGTTTTATTTCTAAAACA
5239911 CTAATTCTCC
Statistics
Matches: 98, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
76 37 0.38
78 58 0.59
79 3 0.03
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.35
Consensus pattern (76 bp):
ATACTCCAACCCCGGTTTTATTTCTAAAACATCAATCTTTCATCGGGGATACTCCAACCCTGTTA
TTTTTGAAGGG
Found at i:5239953 original size:51 final size:51
Alignment explanation
Indices: 5239877--5240094 Score: 280
Period size: 51 Copynumber: 4.3 Consensus size: 51
5239867 TATTTTTGAA
* *
5239877 GGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTCTCCACAATTG
1 GGGATACTCCAACCTCGGTTTTATTTCTAAAACACCAATTCTCCACAATTG
* * * *
5239928 GGGATACTCCAACCTCGGTTTTATTTCTAAAACATCAATTTTTCATAATTG
1 GGGATACTCCAACCTCGGTTTTATTTCTAAAACACCAATTCTCCACAATTG
* *
5239979 GGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTCTCCACAATCG
1 GGGATACTCCAACCTCGGTTTTATTTCTAAAACACCAATTCTCCACAATTG
* * * * *
5240030 GGGATACTCCAA-CTCCGATTTTATTT-TCAAAACACCAATTTTTCATAA-TC
1 GGGATACTCCAACCT-CGGTTTTATTTCT-AAAACACCAATTCTCCACAATTG
5240080 GGGATACTCCAACCT
1 GGGATACTCCAACCT
5240095 GTTATCTTAA
Statistics
Matches: 145, Mismatches: 19, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
50 14 0.10
51 131 0.90
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (51 bp):
GGGATACTCCAACCTCGGTTTTATTTCTAAAACACCAATTCTCCACAATTG
Found at i:5240137 original size:28 final size:28
Alignment explanation
Indices: 5240075--5240151 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
5240065 CAATTTTTCA
* *
5240075 TAATCGGGATACTCCAA-CCTGTTATCT
1 TAATGGGGATACTCCAACCCCGTTATCT
*
5240102 TAATGGGGATACTCCAACCCCGTTATTT
1 TAATGGGGATACTCCAACCCCGTTATCT
* *
5240130 CTGA-GGGGATACTCTAACCCCG
1 -TAATGGGGATACTCCAACCCCG
5240152 GTTTTATTTC
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 16 0.37
28 25 0.58
29 2 0.05
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (28 bp):
TAATGGGGATACTCCAACCCCGTTATCT
Found at i:5240212 original size:51 final size:50
Alignment explanation
Indices: 5240134--5240408 Score: 115
Period size: 51 Copynumber: 5.3 Consensus size: 50
5240124 TTATTTCTGA
* * *
5240134 GGGGATACTCTAACCCCGGTTTTATTTCTAAAACACCAATTATCCATAATC
1 GGGGATACTCCAA-CCCGATTTTATTTCTAAAACACCAATTCTCCATAATC
* * * * * * * *
5240185 GAGGATACTTCAACTCTGATTTTATTTCCAAAACATCAATTTTTCACAATC
1 GGGGATACTCCAAC-CCGATTTTATTTCTAAAACACCAATTCTCCATAATC
* ***** * * * * * *
5240236 -GGGATACTCCAACCCCGTTATTTCATCGGGGATACTCTAA--CCCCGTTATTTCC
1 GGGGATACTCCAA-CCCG--ATTTTATTTCTAAAACACCAATTCTCC-ATA-AT-C
* * *
5240289 GAGGGGATACTCCAACCCCGGTTTTATTTTTAAAACACCAATTCTCCACAATC
1 G-GG-GATACTCCAA-CCCGATTTTATTTCTAAAACACCAATTCTCCATAATC
** * * * * * *
5240342 AAGGATACTTCAACTCCGATTTTATTTCCAAAACATCAATTTTTCACAATC
1 GGGGATACTCCAAC-CCGATTTTATTTCTAAAACACCAATTCTCCATAATC
5240393 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
5240409 TGTTATTTCA
Statistics
Matches: 156, Mismatches: 55, Indels: 27
0.66 0.23 0.11
Matches are distributed among these distances:
50 17 0.11
51 91 0.58
52 13 0.08
53 2 0.01
54 12 0.08
55 3 0.02
56 18 0.12
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (50 bp):
GGGGATACTCCAACCCGATTTTATTTCTAAAACACCAATTCTCCATAATC
Found at i:5240269 original size:28 final size:28
Alignment explanation
Indices: 5240236--5240308 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
5240226 TTTCACAATC
**
5240236 GGGATACTCCAACCCCGTTATTTCATCG
1 GGGATACTCCAACCCCGTTATTTCAGAG
* *
5240264 GGGATACTCTAACCCCGTTATTTCCGAG
1 GGGATACTCCAACCCCGTTATTTCAGAG
5240292 GGGATACTCCAACCCCG
1 GGGATACTCCAACCCCG
5240309 GTTTTATTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.22, C:0.33, G:0.21, T:0.25
Consensus pattern (28 bp):
GGGATACTCCAACCCCGTTATTTCAGAG
Found at i:5240426 original size:28 final size:28
Alignment explanation
Indices: 5240390--5240466 Score: 111
Period size: 28 Copynumber: 2.8 Consensus size: 28
5240380 ATTTTTCACA
*
5240390 ATCGGGGATACTCCAACCCTGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
5240418 ATCGGGGATACTCCGACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
5240446 -TGAGGGGATACTCCAACCCCG
1 AT-CGGGGATACTCCAACCCCG
5240467 GCTTTATGTC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 1 0.02
28 43 0.98
ACGTcount: A:0.21, C:0.31, G:0.22, T:0.26
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:5240497 original size:158 final size:157
Alignment explanation
Indices: 5239978--5240596 Score: 832
Period size: 158 Copynumber: 3.9 Consensus size: 157
5239968 TTTCATAATT
* *
5239978 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTCTCCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTCTCCACAATCGAGGATACTTCAAC
* * * *
5240043 TCCGATTTTATTTTCAAAACACCAATTTTTCATAATCGGGATACTCCAA-CCTGTTATCTTAAT-
66 TCCGATTTTATTTCCAAAACATCAATTTTTCACAATCGGGATACTCCAACCCTGTTAT-TTCATC
5240106 GGGGATACTCCAACCCCGTTATTTCTGA
130 GGGGATACTCCAACCCCGTTATTTCTGA
* * *
5240134 GGGGATACTCTAACCCCGGTTTTATTTCTAAAACACCAATTATCCATAATCGAGGATACTTCAAC
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTCTCCACAATCGAGGATACTTCAAC
* *
5240199 TCTGATTTTATTTCCAAAACATCAATTTTTCACAATCGGGATACTCCAACCCCGTTATTTCATCG
66 TCCGATTTTATTTCCAAAACATCAATTTTTCACAATCGGGATACTCCAACCCTGTTATTTCATCG
* *
5240264 GGGATACTCTAACCCCGTTATTTCCGA
131 GGGATACTCCAACCCCGTTATTTCTGA
* *
5240291 GGGGATACTCCAACCCCGGTTTTATTTTTAAAACACCAATTCTCCACAATCAAGGATACTTCAAC
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTCTCCACAATCGAGGATACTTCAAC
5240356 TCCGATTTTATTTCCAAAACATCAATTTTTCACAATCGGGGATACTCCAACCCTGTTATTTCATC
66 TCCGATTTTATTTCCAAAACATCAATTTTTCACAATC-GGGATACTCCAACCCTGTTATTTCATC
*
5240421 GGGGATACTCCGACCCCGTTATTTCTGA
130 GGGGATACTCCAACCCCGTTATTTCTGA
* * * * *** *
5240449 GGGGATACTCCAACCCCGGCTTTATGTCCAAAATATTGATT-TCTCACAATCGGGGATACTTCAA
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTCTC-CACAATCGAGGATACTTCAA
* ** * * ** * * ** *
5240513 CCCCGACCTTATTTCTAAAATATTGATTTCTCACAATCGGGGATACTCTAACCCCATTATTT-TT
65 CTCCGATTTTATTTCCAAAACATCAATTTTTCACAATC-GGGATACTCCAACCCTGTTATTTCAT
*
5240577 GAGGGGATACTCCAACCCCG
129 -CGGGGATACTCCAACCCCG
5240597 ATTTTATTTT
Statistics
Matches: 411, Mismatches: 47, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
156 109 0.27
157 132 0.32
158 170 0.41
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (157 bp):
GGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTCTCCACAATCGAGGATACTTCAAC
TCCGATTTTATTTCCAAAACATCAATTTTTCACAATCGGGATACTCCAACCCTGTTATTTCATCG
GGGATACTCCAACCCCGTTATTTCTGA
Found at i:5240516 original size:51 final size:51
Alignment explanation
Indices: 5240449--5240567 Score: 177
Period size: 51 Copynumber: 2.3 Consensus size: 51
5240439 TTATTTCTGA
* * *
5240449 GGGGATACTCCAACCCCGGCTTTATGTCCAAAATATTGATTTCTCACAATC
1 GGGGATACTTCAACCCCGACCTTATGTCCAAAATATTGATTTCTCACAATC
* *
5240500 GGGGATACTTCAACCCCGACCTTATTTCTAAAATATTGATTTCTCACAATC
1 GGGGATACTTCAACCCCGACCTTATGTCCAAAATATTGATTTCTCACAATC
5240551 GGGGATAC-TCTAACCCC
1 GGGGATACTTC-AACCCC
5240568 ATTATTTTTG
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
50 2 0.03
51 60 0.97
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (51 bp):
GGGGATACTTCAACCCCGACCTTATGTCCAAAATATTGATTTCTCACAATC
Found at i:5240713 original size:130 final size:130
Alignment explanation
Indices: 5240579--5240822 Score: 309
Period size: 130 Copynumber: 1.9 Consensus size: 130
5240569 TTATTTTTGA
** *
5240579 GGGGATACTCCAACCCCGATTTTATTT-TCAAAATACCT-ATTT-TCTATAATCAGG-GATACTC
1 GGGGATACTCCAACCCCGACCTTATTTCT-AAAATA-CTGATTTCTC-ACAATC-GGAGATACTC
* * *
5240640 CAACCCCGTTATTTCCTAGGGGATACTCCAACCCC-AGTTTTATTTTCAAAATATTGATTTTTCA
62 CAACCCCATTATTTCCGAGAGGATACTCCAACCCCGA-TTTTATTTTCAAAATATTGATTTTTCA
5240704 CAATC
126 CAATC
* *
5240709 GGGGATACTTCAACCCCGACCTTATTTCTAAAATATTGATTTCTCACAATCGGAGATACTCCAAC
1 GGGGATACTCCAACCCCGACCTTATTTCTAAAATACTGATTTCTCACAATCGGAGATACTCCAAC
* * *
5240774 CCCATTATTTTCGATAGGATACTCCAACTCCGATTTTATTTTCAAAATA
66 CCCATTATTTCCGAGAGGATACTCCAACCCCGATTTTATTTTCAAAATA
5240823 CCAATTTTCT
Statistics
Matches: 98, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
129 3 0.03
130 91 0.93
131 4 0.04
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (130 bp):
GGGGATACTCCAACCCCGACCTTATTTCTAAAATACTGATTTCTCACAATCGGAGATACTCCAAC
CCCATTATTTCCGAGAGGATACTCCAACCCCGATTTTATTTTCAAAATATTGATTTTTCACAATC
Found at i:5240726 original size:79 final size:79
Alignment explanation
Indices: 5240500--5240726 Score: 268
Period size: 79 Copynumber: 2.9 Consensus size: 79
5240490 TCTCACAATC
* ** *
5240500 GGGGATACTTCAACCCCGACCTTA-TTTCTAAAATATTGATTTCTCACAATCGGGGATAC-TCTA
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATATTGATTTTTCACAATCGGGGATACTTC-A
* *
5240563 ACCCCATTATTTTTGA
64 ACCCCGTTATTTCTGA
* * * *
5240579 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCT-A-TTTTCTATAATCAGGGATACTCCA
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATA-TTGATTTTTC-ACAATCGGGGATACTTCA
5240642 ACCCCGTTATTTCCT-A
64 ACCCCGTTATTT-CTGA
5240658 GGGGATACTCCAACCCC-AGTTTTATTTTCAAAATATTGATTTTTCACAATCGGGGATACTTCAA
1 GGGGATACTCCAACCCCGA-TTTTATTTTCAAAATATTGATTTTTCACAATCGGGGATACTTCAA
5240722 CCCCG
65 CCCCG
5240727 ACCTTATTTC
Statistics
Matches: 126, Mismatches: 14, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
78 6 0.05
79 108 0.86
80 12 0.10
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATATTGATTTTTCACAATCGGGGATACTTCAAC
CCCGTTATTTCTGA
Found at i:5240734 original size:51 final size:51
Alignment explanation
Indices: 5240661--5240776 Score: 155
Period size: 51 Copynumber: 2.3 Consensus size: 51
5240651 TTTCCTAGGG
** * *
5240661 GATACTCCAACCCC-AGTTTTATTT-TCAAAATATTGATTTTTCACAATCGGG
1 GATACTCCAACCCCGA-CCTTATTTCT-AAAATATTGATTTCTCACAATCGGA
*
5240712 GATACTTCAACCCCGACCTTATTTCTAAAATATTGATTTCTCACAATCGGA
1 GATACTCCAACCCCGACCTTATTTCTAAAATATTGATTTCTCACAATCGGA
5240763 GATACTCCAACCCC
1 GATACTCCAACCCC
5240777 ATTATTTTCG
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
51 55 0.96
52 2 0.04
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.33
Consensus pattern (51 bp):
GATACTCCAACCCCGACCTTATTTCTAAAATATTGATTTCTCACAATCGGA
Found at i:5240846 original size:79 final size:79
Alignment explanation
Indices: 5240763--5240929 Score: 203
Period size: 79 Copynumber: 2.1 Consensus size: 79
5240753 CACAATCGGA
* * *
5240763 GATACTCCAACCCCATTATTTTCGATA-GGATACTCCAACTCCGATTTTATTTTCAAAATACCAA
1 GATACTCCAACCCCATTATTTCCGA-AGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAA
*
5240827 TTTTCTATAATCA-GG
65 TTTTCCATAAT-AGGG
**** * * *
5240842 GATACTCCAACTTTGTTATTTCCGAAGGGATACTCTAACCCCGATTTTATTTTCAGAACACTAAT
1 GATACTCCAACCCCATTATTTCCGAAGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAAT
5240907 TTTCCATAATAGGG
66 TTTCCATAATAGGG
5240921 GATACTCCA
1 GATACTCCA
5240930 GCAACGTTGT
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
78 2 0.03
79 73 0.97
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (79 bp):
GATACTCCAACCCCATTATTTCCGAAGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAAT
TTTCCATAATAGGG
Found at i:5240892 original size:209 final size:209
Alignment explanation
Indices: 5240422--5240896 Score: 754
Period size: 209 Copynumber: 2.3 Consensus size: 209
5240412 TATTTCATCG
* * ** * *
5240422 GGGATACTCCGACCCCGTTATTTCTGAGGGGATACTCCAACCCCGGCTTTATGTCCAAAATATTG
1 GGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGATTTTATTTTCAAAATATTG
5240487 ATTTCTCACAATCGGGGATACTTCAACCCCGACCTTATTTCTAAAATATTGATTTCTCACAATCG
66 ATTTCTCACAATCGGGGATACTTCAACCCCGACCTTATTTCTAAAATATTGATTTCTCACAATCG
* * * * *
5240552 GGGATACTCTAACCCCATTATTTTTGAGGGGATACTCCAACCCCGATTTTATTTTCAAAATACCT
131 GAGATACTCCAACCCCATTATTTTCGAGAGGATACTCCAACCCCGATTTTATTTTCAAAATACCA
5240617 ATTTTCTATAATCA
196 ATTTTCTATAATCA
*
5240631 GGGATACTCCAACCCCGTTATTTCCTAGGGGATACTCCAACCCC-AGTTTTATTTTCAAAATATT
1 GGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGA-TTTTATTTTCAAAATATT
*
5240695 GATTTTTCACAATCGGGGATACTTCAACCCCGACCTTATTTCTAAAATATTGATTTCTCACAATC
65 GATTTCTCACAATCGGGGATACTTCAACCCCGACCTTATTTCTAAAATATTGATTTCTCACAATC
* *
5240760 GGAGATACTCCAACCCCATTATTTTCGATAGGATACTCCAACTCCGATTTTATTTTCAAAATACC
130 GGAGATACTCCAACCCCATTATTTTCGAGAGGATACTCCAACCCCGATTTTATTTTCAAAATACC
5240825 AATTTTCTATAATCA
195 AATTTTCTATAATCA
*** * *
5240840 GGGATACTCCAACTTTGTTATTTCCGAAGGGATACTCTAACCCCGATTTTATTTTCA
1 GGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGATTTTATTTTCA
5240897 GAACACTAAT
Statistics
Matches: 243, Mismatches: 21, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
209 242 1.00
210 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (209 bp):
GGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGATTTTATTTTCAAAATATTG
ATTTCTCACAATCGGGGATACTTCAACCCCGACCTTATTTCTAAAATATTGATTTCTCACAATCG
GAGATACTCCAACCCCATTATTTTCGAGAGGATACTCCAACCCCGATTTTATTTTCAAAATACCA
ATTTTCTATAATCA
Found at i:5240953 original size:209 final size:209
Alignment explanation
Indices: 5240422--5240953 Score: 627
Period size: 209 Copynumber: 2.5 Consensus size: 209
5240412 TATTTCATCG
* * * * * * * * * *
5240422 GGGATACTCCGACCCCGTTATTTCTGAGGGGATACTCCAACCCCGGCTTTATGTCCAAAATATTG
1 GGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAACCCCAGTTTTATTTTCAAAACACTA
* * ** * *
5240487 A-TTTCTCACAATCGGGGATACTTCAACCCCGACCTTATTTCTAAAATATTGATTTCTCACAATC
66 ATTTTC-CACAATAGGGGATACTCCAACAACGACCTTATCTCCAAAATATTGATTTCTCACAATC
* * * *
5240551 GGGGATACTCTAACCCCATTATTTTTGAGGGGATACTCCAACCCCGATTTTATTTTCAAAATACC
130 GGAGATACTCCAACCCCATTATTTTCGAGAGGATACTCCAACCCCGATTTTATTTTCAAAATACC
*
5240616 TATTTTCTATAATCA
195 AATTTTCTATAATCA
* * * * *
5240631 GGGATACTCCAACCCCGTTATTTCCTAGGGGATACTCCAACCCCAGTTTTATTTTCAAAATATTG
1 GGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAACCCCAGTTTTATTTTCAAAACACTA
* * * ** * *
5240696 ATTTTTCACAATCGGGGATACTTCAACCCCGACCTTATTTCTAAAATATTGATTTCTCACAATCG
66 ATTTTCCACAATAGGGGATACTCCAACAACGACCTTATCTCCAAAATATTGATTTCTCACAATCG
* *
5240761 GAGATACTCCAACCCCATTATTTTCGATAGGATACTCCAACTCCGATTTTATTTTCAAAATACCA
131 GAGATACTCCAACCCCATTATTTTCGAGAGGATACTCCAACCCCGATTTTATTTTCAAAATACCA
5240826 ATTTTCTATAATCA
196 ATTTTCTATAATCA
*** * *
5240840 GGGATACTCCAACTTTGTTATTTCCGAAGGGATACTCTAACCCC-GATTTTATTTTCAGAACACT
1 GGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAACCCCAG-TTTTATTTTCAAAACACT
* * ***
5240904 AATTTTCCATAATAGGGGATACTCCAGCAACGTTGTTATCTCCAAAATAT
65 AATTTTCCACAATAGGGGATACTCCAACAACGACCTTATCTCCAAAATAT
5240954 CAAATTTTTC
Statistics
Matches: 284, Mismatches: 37, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
208 1 0.00
209 280 0.99
210 3 0.01
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (209 bp):
GGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAACCCCAGTTTTATTTTCAAAACACTA
ATTTTCCACAATAGGGGATACTCCAACAACGACCTTATCTCCAAAATATTGATTTCTCACAATCG
GAGATACTCCAACCCCATTATTTTCGAGAGGATACTCCAACCCCGATTTTATTTTCAAAATACCA
ATTTTCTATAATCA
Found at i:5252228 original size:10 final size:9
Alignment explanation
Indices: 5252210--5252278 Score: 79
Period size: 9 Copynumber: 7.7 Consensus size: 9
5252200 ATTCTTTTTC
5252210 AAAAAAACA
1 AAAAAAACA
5252219 AAAAACAAC-
1 AAAAA-AACA
5252228 AAAAAAACA
1 AAAAAAACA
*
5252237 AAAAAAA-T
1 AAAAAAACA
5252245 AAAAAAACA
1 AAAAAAACA
5252254 AAACAAAACA
1 AAA-AAAACA
* *
5252264 AAACAAAGA
1 AAAAAAACA
5252273 AAAAAA
1 AAAAAA
5252279 GAGAAAAGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
8 10 0.20
9 29 0.57
10 12 0.24
ACGTcount: A:0.86, C:0.12, G:0.01, T:0.01
Consensus pattern (9 bp):
AAAAAAACA
Found at i:5252239 original size:5 final size:5
Alignment explanation
Indices: 5252213--5252270 Score: 56
Period size: 5 Copynumber: 12.6 Consensus size: 5
5252203 CTTTTTCAAA
*
5252213 AAAAC AAAA- AACAAC -AAA- AAAAC AAAA- AAAA- TAAA- AAAAC AAAAC
1 AAAAC AAAAC AA-AAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC
5252258 AAAAC AAAAC AAA
1 AAAAC AAAAC AAA
5252271 GAAAAAAAGA
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
4 17 0.37
5 29 0.63
ACGTcount: A:0.84, C:0.14, G:0.00, T:0.02
Consensus pattern (5 bp):
AAAAC
Found at i:5252249 original size:35 final size:36
Alignment explanation
Indices: 5252210--5252278 Score: 106
Period size: 35 Copynumber: 1.9 Consensus size: 36
5252200 ATTCTTTTTC
5252210 AAAAAAACAAAA-AACAACAAAA-AAACAAAAAAAAT
1 AAAAAAACAAAACAA-AACAAAACAAACAAAAAAAAT
*
5252245 AAAAAAACAAAACAAAACAAAACAAAGAAAAAAA
1 AAAAAAACAAAACAAAACAAAACAAACAAAAAAA
5252279 GAGAAAAGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
35 19 0.61
36 12 0.39
ACGTcount: A:0.86, C:0.12, G:0.01, T:0.01
Consensus pattern (36 bp):
AAAAAAACAAAACAAAACAAAACAAACAAAAAAAAT
Found at i:5252278 original size:17 final size:17
Alignment explanation
Indices: 5252209--5252278 Score: 95
Period size: 18 Copynumber: 3.9 Consensus size: 17
5252199 CATTCTTTTT
5252209 CAAAAAAACAAAAAACAA
1 CAAAAAAACAAAAAA-AA
5252227 CAAAAAAACAAAAAAAA
1 CAAAAAAACAAAAAAAA
*
5252244 TAAAAAAACAAAACAAAA
1 CAAAAAAACAAAA-AAAA
*
5252262 CAAAACAAAGAAAAAAA
1 CAAAA-AAACAAAAAAA
5252279 GAGAAAAGAA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
17 14 0.30
18 26 0.55
19 7 0.15
ACGTcount: A:0.84, C:0.13, G:0.01, T:0.01
Consensus pattern (17 bp):
CAAAAAAACAAAAAAAA
Found at i:5252293 original size:10 final size:9
Alignment explanation
Indices: 5252210--5252293 Score: 55
Period size: 9 Copynumber: 9.1 Consensus size: 9
5252200 ATTCTTTTTC
*
5252210 AAAAAAACA
1 AAAAAAAGA
*
5252219 AAAAACAA-C
1 AAAAA-AAGA
*
5252228 AAAAAAACA
1 AAAAAAAGA
*
5252237 AAAAAAATA
1 AAAAAAAGA
5252246 AAAAAACA-A
1 AAAAAA-AGA
* *
5252255 AACAAAACA
1 AAAAAAAGA
*
5252264 AAACAAAGA
1 AAAAAAAGA
5252273 AAAAAAGAGA
1 AAAAAA-AGA
5252283 AAAGAAAAGA
1 AAA-AAAAGA
5252293 A
1 A
5252294 CCTGCTTAAG
Statistics
Matches: 61, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
8 3 0.05
9 42 0.69
10 13 0.21
11 3 0.05
ACGTcount: A:0.83, C:0.10, G:0.06, T:0.01
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:5253426 original size:94 final size:97
Alignment explanation
Indices: 5253254--5253438 Score: 263
Period size: 94 Copynumber: 1.9 Consensus size: 97
5253244 TAAACTTTCT
* *
5253254 CCTTTCACTTTTCAGTCCTCAAAGAGCAGGACACTTTTTCCTTTTAAAGCCCACACAAGTTGGTG
1 CCTTTCACTTTTCAGTCCTCAAAGAGCAGGA-AC--TGTCCTTTCAAAGCCCACACAAGTTGGTG
5253319 GCACCTTCTAGTCCTCAAAGAGCAGGGCGCTCTCC
63 GCACCTTCTAGTCCTCAAAGAGCAGGGCGCTCTCC
5253354 CCTTTCACTCTTT-AGTCCTCAAAGAGCAGG-AC-GT-CTTTCAAAGCCCACACAAGTTGGTGGC
1 CCTTTCACT-TTTCAGTCCTCAAAGAGCAGGAACTGTCCTTTCAAAGCCCACACAAGTTGGTGGC
*
5253415 A-CTTTTCAGTCCTCAAAGAGCAGG
65 ACCTTCT-AGTCCTCAAAGAGCAGG
5253439 ACGCCTTTTA
Statistics
Matches: 80, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
93 4 0.05
94 44 0.55
95 1 0.01
98 2 0.03
100 26 0.32
101 3 0.04
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (97 bp):
CCTTTCACTTTTCAGTCCTCAAAGAGCAGGAACTGTCCTTTCAAAGCCCACACAAGTTGGTGGCA
CCTTCTAGTCCTCAAAGAGCAGGGCGCTCTCC
Found at i:5253432 original size:55 final size:55
Alignment explanation
Indices: 5253367--5253550 Score: 237
Period size: 55 Copynumber: 3.2 Consensus size: 55
5253357 TTCACTCTTT
*
5253367 AGTCCTCAAAGAGCAGGACGTCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
1 AGTCCTCAAAGAGCAGGACGTCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCC
* * *
5253422 AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCTACACAAGTTGGTGGCA-TTTCCC
1 AGTCCTCAAAGAGCAGGACGTCTTTCAAAGCCCACACAAGTTGGTGGCACTTT-CC
*
5253477 AGTCCTCAAAGAGCAGGACGTCTTCTCCTTTTAAAGCCCACATAAGTTGGTGGCAC-TTCC
1 AGTCCTCAAAGAGCAGGACGTCTT-T-C----AAAGCCCACACAAGTTGGTGGCACTTTCC
5253537 TAGTCCTCAAAGAG
1 -AGTCCTCAAAGAG
5253551 TAGGGCGTTC
Statistics
Matches: 112, Mismatches: 8, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
54 3 0.03
55 70 0.62
56 1 0.01
60 2 0.02
61 36 0.32
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACGTCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCC
Found at i:5253617 original size:155 final size:156
Alignment explanation
Indices: 5253422--5253706 Score: 455
Period size: 156 Copynumber: 1.8 Consensus size: 156
5253412 GGCACTTTTC
* *
5253422 AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCTACACAAGTTGGTGGCA-TTTCCCAGTCCTCAA
1 AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCAAACAAGTTGGTGGCACTTTCCCAGTCCTCAA
* *
5253486 AGAGCAGGACGTCTTCTCCTTTTAAAGCCCACATAAGTTGGTGGCACTTCCTAGTCCTCAAAGAG
66 AGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAG
5253551 TAGGGCGTTCTCTCCTTTCGCCCTTT
131 TAGGGCGTTCTCTCCTTTCGCCCTTT
* * *
5253577 AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCAAACAAGTTGGTGGCACTTTTCTATTCCTCAA
1 AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCAAACAAGTTGGTGGCACTTTCCCAGTCCTCAA
* * * * *
5253642 AGAGTAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAG
66 AGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAG
5253707 CATGACGCCT
Statistics
Matches: 117, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
155 47 0.40
156 70 0.60
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.28
Consensus pattern (156 bp):
AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCAAACAAGTTGGTGGCACTTTCCCAGTCCTCAA
AGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAG
TAGGGCGTTCTCTCCTTTCGCCCTTT
Found at i:5253628 original size:210 final size:212
Alignment explanation
Indices: 5253266--5253765 Score: 678
Period size: 210 Copynumber: 2.4 Consensus size: 212
5253256 TTTCACTTTT
*
5253266 CAGTCCTCAAAGAGCAGGACACTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CTAG
1 CAGTCCTCAAAGAGCAGGACGC--TTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCTAG
* *
5253330 TCCTCAAAGAGCAGGGCGCTCTCCCCTTTCACTCTTTAGTCCTCAAAGAGCAGGACGTCTTTCAA
64 TCCTCAAAGAGCAGGGCGCTCTCCCCTTTCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAA
* *
5253395 AGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGA-C-GCCTTTTAAAGCCTAC
129 AGCCCAAACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACCTGCCTTTTAAAGCCCAC
5253457 ACAAGTTGGTGGCATTTCC
194 ACAAGTTGGTGGCATTTCC
*
5253476 CAGTCCTCAAAGAGCAGGACGTCTTCTCCTTTTAAAGCCCACATAAGTTGGTGGCA-CTTCCTAG
1 CAGTCCTCAAAGAGCAGGACG-CTT-TCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCTAG
* * * * *
5253540 TCCTCAAAGAGTAGGGCGTTCTCTCCTTTCGCCCTTTAGTCCTCAAAGAGCAGGACGCCTTTTAA
64 TCCTCAAAGAGCAGGGCGCTCTCCCCTTTCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAA
* * *
5253605 AGCCCAAACAAGTTGGTGGCACTTTTCTATTCCTCAAAGAGTAGGATGCCTTTTCCTTTTAAAGC
129 AGCCCAAACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGA--CC--TGCCTTTTAAAGC
*
5253670 CCACACAAGTTGGTGGCATTTTC
190 CCACACAAGTTGGTGGCATTTCC
* * * **
5253693 TAGTCCTCAAAGAGCATGACG----CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC-AGTC
1 CAGTCCTCAAAGAGCAGGACGCTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCTAGTC
5253753 CTCAAAGAGCAGG
66 CTCAAAGAGCAGG
5253766 ATGCTTTCTC
Statistics
Matches: 258, Mismatches: 21, Indels: 21
0.86 0.07 0.07
Matches are distributed among these distances:
209 5 0.02
210 137 0.53
211 60 0.23
212 4 0.02
214 1 0.00
217 51 0.20
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (212 bp):
CAGTCCTCAAAGAGCAGGACGCTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCTAGTC
CTCAAAGAGCAGGGCGCTCTCCCCTTTCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAG
CCCAAACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACCTGCCTTTTAAAGCCCACAC
AAGTTGGTGGCATTTCC
Found at i:5253815 original size:61 final size:61
Alignment explanation
Indices: 5253597--5253963 Score: 430
Period size: 61 Copynumber: 6.1 Consensus size: 61
5253587 GAGCAGGACG
* * *
5253597 CCTTTTAAAGCCCAAACAAGTTGGTGGCACTTTTCTATTCCTCAAAGAGTAGGATGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
* * *
5253659 CCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCATGACGCC-TTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
* *
5253719 -C----AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATG-CTTTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGATGCCTTT-T
* * * * * *
5253775 CCTTTTAAAGACCACTCGAGTTGGTGGTACCTTCTAGTCCTCAAAGAGTAGGATG-C-TTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
* * * *
5253834 CTCTTTGCAAAGCCCACACAAGTTGATGGTACCTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
1 C-CTTT-TAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
* * *
5253897 -CTTTTCAAAGCCCACACGAGTTGGCGGCACTTTTTAGTCCTCAAAGAGCAGGATGCCTTTT
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
5253958 CCTTTT
1 CCTTTT
5253964 CTCCTTTATC
Statistics
Matches: 262, Mismatches: 30, Indels: 26
0.82 0.09 0.08
Matches are distributed among these distances:
54 1 0.00
55 48 0.18
56 1 0.00
57 1 0.00
59 3 0.01
60 9 0.03
61 162 0.62
62 34 0.13
63 3 0.01
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.31
Consensus pattern (61 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
Found at i:5253977 original size:38 final size:38
Alignment explanation
Indices: 5253929--5254069 Score: 131
Period size: 37 Copynumber: 3.5 Consensus size: 38
5253919 GGCGGCACTT
*
5253929 TTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTCTCC
1 TTTA-TCCTCAAAGAGCAGGATGTCTTTTCCTTTTCTCC
* * *
5253968 TTTATCCTCAAAGAGCAGGACACATTTCATTTCCTTCTTTTCCC
1 TTTATCCTCAAAGAGCAGG----ATGTCTTTTCCTT-TTCT-CC
* * *
5254012 TTTTGTCTTCAAAGAGCAGGACGTCTTTTCCTTTTCTCC
1 -TTTATCCTCAAAGAGCAGGATGTCTTTTCCTTTTCTCC
*
5254051 -TTGTCCTCAAAGAGCAGGA
1 TTTATCCTCAAAGAGCAGGA
5254070 CACACTTCAT
Statistics
Matches: 84, Mismatches: 11, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
37 18 0.21
38 15 0.18
39 6 0.07
40 3 0.04
41 10 0.12
42 10 0.12
43 3 0.04
44 2 0.02
45 17 0.20
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.38
Consensus pattern (38 bp):
TTTATCCTCAAAGAGCAGGATGTCTTTTCCTTTTCTCC
Found at i:5254061 original size:37 final size:38
Alignment explanation
Indices: 5253933--5254248 Score: 150
Period size: 42 Copynumber: 7.9 Consensus size: 38
5253923 GCACTTTTTA
* *
5253933 GTCCTCAAAGAGCAGGATGCCTTTTCCTTTTCTCCTTT
1 GTCCTCAAAGAGCAGGACGTCTTTTCCTTTTCTCCTTT
* * * *
5253971 ATCCTCAAAGAGCAGGACACATTTCATTTCCTTCTTTTCCCTTTT
1 GTCCTCAAAGAGCAGG--AC--GTCTTTTCCTT-TTCT-CC-TTT
*
5254016 GTCTTCAAAGAGCAGGACGTCTTTTCCTTTTCTCC-TT
1 GTCCTCAAAGAGCAGGACGTCTTTTCCTTTTCTCCTTT
** *
5254053 GTCCTCAAAGAGCAGGACACACTTCATTCCCTTCTTTTCCCTTTT
1 GTCCTCAAAGAGCAGGAC-GTCTT--TT-CCTT-TTCT-CC-TTT
* *
5254098 GTCCTCAAAGAGCAGGATGCACTTTATTTTCCTCTTTCT--TTT
1 GTCCTCAAAGAGCA-G--G-AC-GTCTTTTCCT-TTTCTCCTTT
* *
5254140 GTCCTCAAAGAGCAGGACGCATTTTGTTTTCCTTTTTTCCTTT
1 GTCCTCAAAGAGCAGGACG-----TCTTTTCCTTTTCTCCTTT
* *
5254183 GTCCTCGAAA-AGTAGGACGTAC-TTT--TTTTC-ACTTT
1 GTCCTC-AAAGAGCAGGACGT-CTTTTCCTTTTCTCCTTT
*
5254218 GTCCTC-AAGAAGCAGGACAT-TTTT-CTTTTCT
1 GTCCTCAAAG-AGCAGGACGTCTTTTCCTTTTCT
5254249 TTTTTCCTTT
Statistics
Matches: 215, Mismatches: 29, Indels: 70
0.68 0.09 0.22
Matches are distributed among these distances:
33 2 0.01
34 3 0.01
35 23 0.11
36 4 0.02
37 19 0.09
38 24 0.11
39 3 0.01
40 6 0.03
41 18 0.08
42 36 0.17
43 24 0.11
44 5 0.02
45 33 0.15
46 7 0.03
47 3 0.01
48 1 0.00
49 4 0.02
ACGTcount: A:0.19, C:0.26, G:0.14, T:0.40
Consensus pattern (38 bp):
GTCCTCAAAGAGCAGGACGTCTTTTCCTTTTCTCCTTT
Found at i:5254086 original size:82 final size:83
Alignment explanation
Indices: 5253928--5254157 Score: 304
Period size: 82 Copynumber: 2.7 Consensus size: 83
5253918 TGGCGGCACT
* *
5253928 TTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTCTCCTTTATCCTCAAAGAGCAGGACACAT
1 TTTT-GTCCTCAAAGAGCAGGACGCCTTTTCCTTTTCTCCTTTATCCTCAAAGAGCAGGACACAC
*
5253993 TTCATTTCCTTCTTTTCCC
65 TTCATTCCCTTCTTTTCCC
* * *
5254012 TTTTGTCTTCAAAGAGCAGGACGTCTTTTCCTTTTCTCC-TTGTCCTCAAAGAGCAGGACACACT
1 TTTTGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTCTCCTTTATCCTCAAAGAGCAGGACACACT
5254076 TCATTCCCTTCTTTTCCC
66 TCATTCCCTTCTTTTCCC
* *
5254094 TTTTGTCCTCAAAGAGCAGGATGCACTTTATTTTCCTCTTTCT--TTTGTCCTCAAAGAGCAGGA
1 TTTTGTCCTCAAAGAGCAGGACGC-C----TTTTCCT-TTTCTCCTTTATCCTCAAAGAGCAGGA
5254157 C
60 C
5254158 GCATTTTGTT
Statistics
Matches: 130, Mismatches: 9, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
82 61 0.47
83 33 0.25
84 4 0.03
87 27 0.21
88 5 0.04
ACGTcount: A:0.20, C:0.28, G:0.14, T:0.38
Consensus pattern (83 bp):
TTTTGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTCTCCTTTATCCTCAAAGAGCAGGACACACT
TCATTCCCTTCTTTTCCC
Found at i:5254200 original size:43 final size:42
Alignment explanation
Indices: 5253954--5254212 Score: 180
Period size: 45 Copynumber: 6.1 Consensus size: 42
5253944 GCAGGATGCC
* * *
5253954 TTTTCCTTTTCTCCTTTATCCTCAAAGAGCAGGACACA-TTTCA
1 TTTTCCTCTT-TCCTTTGTCCTCAAAGAGCAGGACGCACTTT-A
* *
5253997 -TTTCCTTCTTTTCCCTTTTGTCTTCAAAGAGCAGGACG-----TC
1 TTTTCC-TC-TTT-CC-TTTGTCCTCAAAGAGCAGGACGCACTTTA
* * *
5254037 TTTTCCT-TTTCTCCTTGTCCTCAAAGAGCAGGACACACTTCA
1 TTTTCCTCTTTC-CTTTGTCCTCAAAGAGCAGGACGCACTTTA
* *
5254079 -TTCCCTTCTTTTCCCTTTTGTCCTCAAAGAGCAGGATGCACTTTA
1 TTTTCC-TC-TTT-CC-TTTGTCCTCAAAGAGCAGGACGCACTTTA
* * *
5254124 TTTTCCTCTTTCTTTTGTCCTCAAAGAGCAGGACGCATTTTG
1 TTTTCCTCTTTCCTTTGTCCTCAAAGAGCAGGACGCACTTTA
* * *
5254166 TTTTCCTTTTTTCCTTTGTCCTCGAAA-AGTAGGACGTACTTT-
1 TTTTCC-TCTTTCCTTTGTCCTC-AAAGAGCAGGACGCACTTTA
5254208 TTTTC
1 TTTTC
5254213 ACTTTGTCCT
Statistics
Matches: 172, Mismatches: 25, Indels: 39
0.73 0.11 0.17
Matches are distributed among these distances:
37 20 0.12
38 4 0.02
40 1 0.01
41 10 0.06
42 43 0.25
43 29 0.17
44 14 0.08
45 47 0.27
46 4 0.02
ACGTcount: A:0.18, C:0.27, G:0.13, T:0.42
Consensus pattern (42 bp):
TTTTCCTCTTTCCTTTGTCCTCAAAGAGCAGGACGCACTTTA
Found at i:5254212 original size:42 final size:43
Alignment explanation
Indices: 5253954--5254217 Score: 219
Period size: 42 Copynumber: 6.2 Consensus size: 43
5253944 GCAGGATGCC
* * *
5253954 TTTTCCTTTTCTCCTTTATCCTCAAAGAGCAGGACACA-TTTCA
1 TTTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCACTTT-A
* *
5253997 -TTTCCTTCTTTTCCCTTTTGTCTTCAAAGAGCAGGACG-----TC
1 TTTTCCTT-TTTT-CC-TTTGTCCTCAAAGAGCAGGACGCACTTTA
* * *
5254037 TTTTCCTTTTCTCC-TTGTCCTCAAAGAGCAGGACACACTTCA
1 TTTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCACTTTA
* *
5254079 -TTCCCTTCTTTTCCCTTTTGTCCTCAAAGAGCAGGATGCACTTTA
1 TTTTCCTT-TTTT-CC-TTTGTCCTCAAAGAGCAGGACGCACTTTA
* * * *
5254124 TTTTCC-TCTTTCTTTTGTCCTCAAAGAGCAGGACGCATTTTG
1 TTTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCACTTTA
* *
5254166 TTTTCCTTTTTTCCTTTGTCCTCGAAA-AGTAGGACGTACTTT-
1 TTTTCCTTTTTTCCTTTGTCCTC-AAAGAGCAGGACGCACTTTA
5254208 TTTTCACTTT
1 TTTTC-CTTT
5254218 GTCCTCAAGA
Statistics
Matches: 178, Mismatches: 26, Indels: 34
0.75 0.11 0.14
Matches are distributed among these distances:
37 19 0.11
39 2 0.01
40 3 0.02
41 14 0.08
42 47 0.26
43 36 0.20
44 8 0.04
45 45 0.25
46 4 0.02
ACGTcount: A:0.18, C:0.27, G:0.13, T:0.42
Consensus pattern (43 bp):
TTTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCACTTTA
Found at i:5254247 original size:35 final size:34
Alignment explanation
Indices: 5254172--5254237 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
5254162 TTTGTTTTCC
* *
5254172 TTTTTTCCTTTGTCCTCGAAAAGTAGGACGTACT
1 TTTTTTCCTTTGTCCTCGAAAAGCAGGACATACT
5254206 TTTTTTCACTTTGTCCTC-AAGAAGCAGGACAT
1 TTTTTTC-CTTTGTCCTCGAA-AAGCAGGACAT
5254238 TTTTCTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 9 0.32
35 19 0.68
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (34 bp):
TTTTTTCCTTTGTCCTCGAAAAGCAGGACATACT
Found at i:5254252 original size:41 final size:40
Alignment explanation
Indices: 5254206--5254306 Score: 121
Period size: 41 Copynumber: 2.5 Consensus size: 40
5254196 AGGACGTACT
* * *
5254206 TTTTTTCACTTTGTCCTCAAGAAGCAGGACATTTTTCTTTTC
1 TTTTTTC-CTTTGTCCTCAAGAAGCAAGACATATTTC-ATTC
* * *
5254248 TTTTTTCCTTTGTCCTCATGGAGCAAGACCTATTTCATTC
1 TTTTTTCCTTTGTCCTCAAGAAGCAAGACATATTTCATTC
*
5254288 TCTTTTCCTTTGTCCTCAA
1 TTTTTTCCTTTGTCCTCAA
5254307 AAAGTGGGAC
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
40 20 0.39
41 24 0.47
42 7 0.14
ACGTcount: A:0.17, C:0.25, G:0.11, T:0.48
Consensus pattern (40 bp):
TTTTTTCCTTTGTCCTCAAGAAGCAAGACATATTTCATTC
Found at i:5254926 original size:20 final size:20
Alignment explanation
Indices: 5254901--5254971 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
5254891 TTTTCACAAT
*
5254901 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGCTCA
*
5254921 TTGTATCGATACATTACTCA
1 TTGTATCGATACATTGCTCA
5254941 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATTGCTCA
*
5254961 TTATATCGATA
1 TTGTATCGATA
5254972 TATTATATCG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (20 bp):
TTGTATCGATACATTGCTCA
Found at i:5254978 original size:13 final size:13
Alignment explanation
Indices: 5254960--5254984 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5254950 TACATTGCTC
5254960 ATTATATCGATAT
1 ATTATATCGATAT
5254973 ATTATATCGATA
1 ATTATATCGATA
5254985 CATTCTGGAT
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
ATTATATCGATAT
Found at i:5257505 original size:79 final size:79
Alignment explanation
Indices: 5257327--5257546 Score: 286
Period size: 79 Copynumber: 2.8 Consensus size: 79
5257317 TTTTCATCTT
* * * *
5257327 GGGGATACTCCTACCTCGGTTTTATTTCCAAAACATCAATCTTT--C-ATCGGGGATTCTCCAAC
1 GGGGATACTCCAACCTCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAAC
*
5257389 CCCGTTATTTCCGA
66 CCCATTATTTCCGA
* * * *
5257403 GGGGATACTCTAACCCCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGAGGATACTCCAAT
1 GGGGATACTCCAACCTCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAAC
*
5257468 CCCATTATTTTCGA
66 CCCATTATTTCCGA
* * *
5257482 GGGGATACTCCAACCTCGATTTTATTTCTAAAACA-CTAATTCTCCACAATCGGGGATACTCCAA
1 GGGGATACTCCAACCTCGGTTTTATTTCTAAAACATC-AATTTTTCACAATCGGGGATACTCCAA
5257546 C
65 C
5257547 TCTGATTTTA
Statistics
Matches: 123, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
76 39 0.32
78 2 0.02
79 82 0.67
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (79 bp):
GGGGATACTCCAACCTCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAAC
CCCATTATTTCCGA
Found at i:5257558 original size:51 final size:51
Alignment explanation
Indices: 5257482--5257598 Score: 166
Period size: 51 Copynumber: 2.3 Consensus size: 51
5257472 TTATTTTCGA
5257482 GGGGATACTCCAACCTCGATTTTATTTCTAAAACA-CTAATTCTCCACAATC
1 GGGGATACTCCAACCTCGATTTTATTTCTAAAACATC-AATTCTCCACAATC
* * * *
5257533 GGGGATACTCCAA-CTCTGATTTTATTTCTAAAACATCAATTTTTCATAATT
1 GGGGATACTCCAACCTC-GATTTTATTTCTAAAACATCAATTCTCCACAATC
5257584 GGGGATACTCCAACC
1 GGGGATACTCCAACC
5257599 CCGTTATTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
50 3 0.05
51 54 0.92
52 2 0.03
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCTCGATTTTATTTCTAAAACATCAATTCTCCACAATC
Found at i:5257688 original size:129 final size:128
Alignment explanation
Indices: 5257403--5257756 Score: 505
Period size: 129 Copynumber: 2.7 Consensus size: 128
5257393 TTATTTCCGA
* * *
5257403 GGGGATAC-TCTAACCCCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTTC-AACTCCGATTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAA
* * * *
5257467 TCCCATTATTT-TCGAGGGGATACTCCAACCTCGATTTTATTTCTAAAACACTAATTCTCCACAA
65 CCCCGTTATTTCT-GA-GGGATACTCCAACC-CAATTTTATTTCTAAAACACCAATTCTCCACAA
5257531 TC
127 TC
* * * *
5257533 GGGGATACTCCAACTCTGATTTTATTTCTAAAACATCAATTTTTCATAATTGGGGATACTCCAAC
1 GGGGATACTTCAACTCCGATTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAAC
*
5257598 CCCGTTATTTCTGAGGAGATACTCCAACCCAATTTTATTTTTAAAACACCAATTCTCCACAATC
66 CCCGTTATTTCTGAGG-GATACTCCAACCCAATTTTATTTCTAAAACACCAATTCTCCACAATC
* *
5257662 GGGGATACTTCAACTCCGATTTTATTTCCAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
1 GGGGATACTTCAACTCCGATTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAAC
*
5257727 CCCGTTATTTCATTAGGGATACTCCAACCC
66 CCCGTTATTTC-TGAGGGATACTCCAACCC
5257757 CGTTATTTCC
Statistics
Matches: 201, Mismatches: 19, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
129 117 0.58
130 82 0.41
131 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (128 bp):
GGGGATACTTCAACTCCGATTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAAC
CCCGTTATTTCTGAGGGATACTCCAACCCAATTTTATTTCTAAAACACCAATTCTCCACAATC
Found at i:5257695 original size:51 final size:51
Alignment explanation
Indices: 5257615--5258043 Score: 265
Period size: 51 Copynumber: 8.2 Consensus size: 51
5257605 TTTCTGAGGA
* **
5257615 GATACTCCAA-CCCAATTTTATTTTTAAAACACCAATTCTCCACAATCGGG
1 GATACTCCAACCCCGATTTTATTTCCAAAACACCAATTCTCCACAATCGGG
* * * *
5257665 GATACTTCAACTCCGATTTTATTTCCAAAACACCAATTTTTCACAATCGGG
1 GATACTCCAACCCCGATTTTATTTCCAAAACACCAATTCTCCACAATCGGG
* **** * * * ** *
5257716 GATACTCCAACCCCGTTATTTCATTAGGGATACTCCAA--CCCCGTTATTTCCGAGGG
1 GATACTCCAACCCCG--ATTTTATTTCCAAAACACCAATTCTCC-ACA-AT-C--GGG
* *
5257772 GATACTCTAACCCCGATTTTATTTCTAAAACACCAATTCTCCACAATCGGG
1 GATACTCCAACCCCGATTTTATTTCCAAAACACCAATTCTCCACAATCGGG
* * * * * *
5257823 GATACTTCAACTCCAATTTTATTTTCAAAACACCAATTTTTCACAATCGGG
1 GATACTCCAACCCCGATTTTATTTCCAAAACACCAATTCTCCACAATCGGG
* * ***** * * * * ** *
5257874 GATACTCCAACCCTGTTATTTCATCGGGGATACTCTAA--CCCCGTTATTTCCGAGGG
1 GATACTCCAACCCCG--ATTTTATTTCCAAAACACCAATTCTCC-ACA-AT-C--GGG
* * *
5257930 GATACTCCAACCCCGGTTTTATTTCTAAAACACAAATTCTCCACAATCGGG
1 GATACTCCAACCCCGATTTTATTTCCAAAACACCAATTCTCCACAATCGGG
* * * * *
5257981 GATACTCCAACTCCAATTTTATTTTCAAAACACCAATTTTTCACAATCGGG
1 GATACTCCAACCCCGATTTTATTTCCAAAACACCAATTCTCCACAATCGGG
5258032 GATACTCCAACC
1 GATACTCCAACC
5258044 TTGTTATTTC
Statistics
Matches: 275, Mismatches: 85, Indels: 37
0.69 0.21 0.09
Matches are distributed among these distances:
50 9 0.03
51 163 0.59
52 2 0.01
53 30 0.11
54 29 0.11
55 2 0.01
56 40 0.15
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.31
Consensus pattern (51 bp):
GATACTCCAACCCCGATTTTATTTCCAAAACACCAATTCTCCACAATCGGG
Found at i:5257773 original size:28 final size:29
Alignment explanation
Indices: 5257713--5257786 Score: 107
Period size: 28 Copynumber: 2.6 Consensus size: 29
5257703 TTTCACAATC
**
5257713 GGGGATACTCCAACCCCGTTATTTCATTA
1 GGGGATACTCCAACCCCGTTATTTCACGA
5257742 -GGGATACTCCAACCCCGTTATTTC-CGA
1 GGGGATACTCCAACCCCGTTATTTCACGA
*
5257769 GGGGATACTCTAACCCCG
1 GGGGATACTCCAACCCCG
5257787 ATTTTATTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 1 0.02
28 40 0.98
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (29 bp):
GGGGATACTCCAACCCCGTTATTTCACGA
Found at i:5257900 original size:28 final size:28
Alignment explanation
Indices: 5257868--5257944 Score: 109
Period size: 28 Copynumber: 2.8 Consensus size: 28
5257858 ATTTTTCACA
*
5257868 ATCGGGGATACTCCAACCCTGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
5257896 ATCGGGGATACTCTAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
***
5257924 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
5257945 GTTTTATTTC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.26
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:5258062 original size:28 final size:28
Alignment explanation
Indices: 5258026--5258099 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 28
5258016 ATTTTTCACA
* *
5258026 ATCGGGGATACTCCAACCTTGTTATTT-C
1 ATCGAGGATACTCCAACC-CGTTATTTCC
5258054 ATCGAGGATACTCCAACCCGTTATTTCC
1 ATCGAGGATACTCCAACCCGTTATTTCC
**
5258082 AAGGA-GATACTCCAACCC
1 ATCGAGGATACTCCAACCC
5258100 TGGCTTTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
27 20 0.49
28 21 0.51
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (28 bp):
ATCGAGGATACTCCAACCCGTTATTTCC
Found at i:5258090 original size:27 final size:27
Alignment explanation
Indices: 5258031--5258099 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 27
5258021 TCACAATCGG
* *
5258031 GGATACTCCAACCTTGTTATTTCATCGA
1 GGATACTCCAACC-CGTTATTTCAACGA
*
5258059 GGATACTCCAACCCGTTATTTCCAAGGA
1 GGATACTCCAACCCGTTATTT-CAACGA
5258087 -GATACTCCAACCC
1 GGATACTCCAACCC
5258100 TGGCTTTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 20 0.54
28 17 0.46
ACGTcount: A:0.28, C:0.30, G:0.14, T:0.28
Consensus pattern (27 bp):
GGATACTCCAACCCGTTATTTCAACGA
Found at i:5258150 original size:51 final size:51
Alignment explanation
Indices: 5258087--5258202 Score: 169
Period size: 51 Copynumber: 2.3 Consensus size: 51
5258077 TTTCCAAGGA
* * * *
5258087 GATACTCCAACCCTGGCTTTATTTCCAAAATATTGATTTCTTACAATCGGG
1 GATACTCCAACCCCGACCTTATTTCCAAAATATTGATTTCTCACAATCGGG
* **
5258138 GATACTTCAACCCCGACCTTATTTTTAAAATATTGATTTCTCACAATCGGG
1 GATACTCCAACCCCGACCTTATTTCCAAAATATTGATTTCTCACAATCGGG
5258189 GATACTCCAACCCC
1 GATACTCCAACCCC
5258203 ATTATTTTTG
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.33
Consensus pattern (51 bp):
GATACTCCAACCCCGACCTTATTTCCAAAATATTGATTTCTCACAATCGGG
Found at i:5258199 original size:157 final size:158
Alignment explanation
Indices: 5257586--5258201 Score: 862
Period size: 158 Copynumber: 3.9 Consensus size: 158
5257576 TCATAATTGG
* * *
5257586 GGATACTCCAACCCCGTTATTTCTGAGGAGATACTCCAA-CCCAATTTTATTTTTAAAACACCAA
1 GGATACTCCAACCCCGTTATTTCCGAGGAGATACTCCAACCCCGATTTTATTTCTAAAACACCAA
* *
5257650 TTCTCCACAATCGGGGATACTTCAACTCCGATTTTATTTCCAAAACACCAATTTTTCACAATCGG
66 TTCTCCACAATCGGGGATACTTCAACTCCAATTTTATTTTCAAAACACCAATTTTTCACAATCGG
* *
5257715 GGATACTCCAACCCCGTTATTTCAT-TA
131 GGATACTCCAACCCTGTTATTTCATCGA
* *
5257742 GGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCTAACCCCGATTTTATTTCTAAAACACCA
1 -GGATACTCCAACCCCGTTATTTCCGAGGAGATACTCCAACCCCGATTTTATTTCTAAAACACCA
5257807 ATTCTCCACAATCGGGGATACTTCAACTCCAATTTTATTTTCAAAACACCAATTTTTCACAATCG
65 ATTCTCCACAATCGGGGATACTTCAACTCCAATTTTATTTTCAAAACACCAATTTTTCACAATCG
*
5257872 GGGATACTCCAACCCTGTTATTTCATCGG
130 GGGATACTCCAACCCTGTTATTTCATCGA
* * * *
5257901 GGATACTCTAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACAAA
1 GGATACTCCAACCCCGTTATTTCCGAGGAGATACTCCAACCCCGATTTTATTTCTAAAACACCAA
*
5257966 TTCTCCACAATCGGGGATACTCCAACTCCAATTTTATTTTCAAAACACCAATTTTTCACAATCGG
66 TTCTCCACAATCGGGGATACTTCAACTCCAATTTTATTTTCAAAACACCAATTTTTCACAATCGG
*
5258031 GGATACTCCAACCTTGTTATTTCATCGA
131 GGATACTCCAACCCTGTTATTTCATCGA
* * ** * * ***
5258059 GGATACTCCAA-CCCGTTATTTCCAAGGAGATACTCCAACCCTGGCTTTATTTCCAAAATATTGA
1 GGATACTCCAACCCCGTTATTTCCGAGGAGATACTCCAACCCCGATTTTATTTCTAAAACACCAA
* * * ** * * *** *
5258123 TT-TCTTACAATCGGGGATACTTCAACCCCGACCTTATTTTTAAAATATTGATTTCTCACAATCG
66 TTCTC-CACAATCGGGGATACTTCAACTCCAATTTTATTTTCAAAACACCAATTTTTCACAATCG
5258187 GGGATACTCCAACCC
130 GGGATACTCCAACCC
5258202 CATTATTTTT
Statistics
Matches: 416, Mismatches: 40, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
156 2 0.00
157 143 0.34
158 271 0.65
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.31
Consensus pattern (158 bp):
GGATACTCCAACCCCGTTATTTCCGAGGAGATACTCCAACCCCGATTTTATTTCTAAAACACCAA
TTCTCCACAATCGGGGATACTTCAACTCCAATTTTATTTTCAAAACACCAATTTTTCACAATCGG
GGATACTCCAACCCTGTTATTTCATCGA
Found at i:5258241 original size:79 final size:79
Alignment explanation
Indices: 5258138--5258352 Score: 290
Period size: 79 Copynumber: 2.7 Consensus size: 79
5258128 TACAATCGGG
* * *
5258138 GATACTTCAACCCCGACCTTATTTTTAAAATATTGATTTCTCACAATCGGGGATACTCCAACCCC
1 GATACTCCAACCTCGACTTTATTTTTAAAATATTGATTTCTCACAATCGGGGATACTCCAACCCC
* *
5258203 ATTATTTTTGAG-G
66 ATTATTTTCGAGAA
* ** * *
5258216 GAATACTCCAACCTCGATTTTATTTTTAAAATACCGATTT-TCTATAATCAGGGATACTCCAACC
1 G-ATACTCCAACCTCGACTTTATTTTTAAAATATTGATTTCTC-ACAATCGGGGATACTCCAACC
5258280 CCATTATTTTCGAGAA
64 CCATTATTTTCGAGAA
* *
5258296 GATACTCCAACCTCGGCTTTATTTTCAAAATATTGATTTCTCACAATCGGGGATACT
1 GATACTCCAACCTCGACTTTATTTTTAAAATATTGATTTCTCACAATCGGGGATACT
5258353 TTAACCCCGA
Statistics
Matches: 116, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
78 3 0.03
79 110 0.95
80 3 0.03
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (79 bp):
GATACTCCAACCTCGACTTTATTTTTAAAATATTGATTTCTCACAATCGGGGATACTCCAACCCC
ATTATTTTCGAGAA
Found at i:5258350 original size:209 final size:209
Alignment explanation
Indices: 5258059--5258570 Score: 760
Period size: 209 Copynumber: 2.5 Consensus size: 209
5258049 ATTTCATCGA
* *
5258059 GGATACTCCAA-CCCGTTATTTCCAAGGAGATACTCCAACC-CTGGCTTTATTTCCAAAATATTG
1 GGATACTCCAACCCCATTATTTCCGAGGAGATACTCCAACCTC-GGCTTTATTTCCAAAATATTG
* *
5258122 ATTTCTTACAATCGGGGATACTTCAACCCCGACCTTATTTTTAAAATATTGATTTCTCACAATCG
65 ATTTCTCACAATCGGGGATACTTCAACCCCGACCTTATTTCTAAAATATTGATTTCTCACAATCG
* *
5258187 GGGATACTCCAACCCCATTATTTTTGAGGGAATACTCCAACCTCGATTTTATTTTTAAAATACCG
130 AGGATACTCCAACCCCATTATTTTCGAGGGAATACTCCAACCTCGATTTTATTTTTAAAATACCG
**
5258252 ATTTTCTATAATCAG
195 ATAATCTATAATCAG
* * *
5258267 GGATACTCCAACCCCATTATTTTCGAGAAGATACTCCAACCTCGGCTTTATTTTCAAAATATTGA
1 GGATACTCCAACCCCATTATTTCCGAGGAGATACTCCAACCTCGGCTTTATTTCCAAAATATTGA
*
5258332 TTTCTCACAATCGGGGATACTTTAACCCCGACCTTATTTCTAAAATATTGATTTCTCACAATCGA
66 TTTCTCACAATCGGGGATACTTCAACCCCGACCTTATTTCTAAAATATTGATTTCTCACAATCGA
* *
5258397 GGATACTCCAACCCCATTATTTTCGAGGGGATACTCTAACCTCGATTTTATTTTTAAAATACCGA
131 GGATACTCCAACCCCATTATTTTCGAGGGAATACTCCAACCTCGATTTTATTTTTAAAATACCGA
5258462 TAATCTATAATCAG
196 TAATCTATAATCAG
* ** * * * *
5258476 GGATACTCCAACTCTTTTATTTCCGAGGAGATACTCCAA-CTCCGGTTTTATTTCCAGAACATCG
1 GGATACTCCAACCCCATTATTTCCGAGGAGATACTCCAACCT-CGGCTTTATTTCCAAAATATTG
* * * *
5258540 ATTTTTCATAATCAGGGATACTCCAACCCCG
65 ATTTCTCACAATCGGGGATACTTCAACCCCG
5258571 TTGTTATCTC
Statistics
Matches: 272, Mismatches: 29, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
208 13 0.05
209 258 0.95
210 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (209 bp):
GGATACTCCAACCCCATTATTTCCGAGGAGATACTCCAACCTCGGCTTTATTTCCAAAATATTGA
TTTCTCACAATCGGGGATACTTCAACCCCGACCTTATTTCTAAAATATTGATTTCTCACAATCGA
GGATACTCCAACCCCATTATTTTCGAGGGAATACTCCAACCTCGATTTTATTTTTAAAATACCGA
TAATCTATAATCAG
Found at i:5258352 original size:130 final size:130
Alignment explanation
Indices: 5258218--5258457 Score: 313
Period size: 130 Copynumber: 1.8 Consensus size: 130
5258208 TTTTGAGGGA
* ** * *
5258218 ATACTCCAACCTCGATTTTATTTTTAAAATACCGATTT-TCTATAATC-AGGGATACTCCAACCC
1 ATACTCCAACCCCGACCTTATTTCTAAAATACCGATTTCTC-ACAATCGA-GGATACTCCAACCC
*
5258281 CATTATTTTCGAGAAGATACTCCAACCTCGGCTTTATTTTCAAAATATTGATTTCTCACAATCGG
64 CATTATTTTCGAGAAGATACTCCAACCTCGACTTTATTTTCAAAATATTGATTTCTCACAATCGG
5258346 GG
129 GG
** **
5258348 ATACTTTAACCCCGACCTTATTTCTAAAATATTGATTTCTCACAATCGAGGATACTCCAACCCCA
1 ATACTCCAACCCCGACCTTATTTCTAAAATACCGATTTCTCACAATCGAGGATACTCCAACCCCA
** * * *
5258413 TTATTTTCGAGGGGATACTCTAACCTCGATTTTATTTTTAAAATA
66 TTATTTTCGAGAAGATACTCCAACCTCGACTTTATTTTCAAAATA
5258458 CCGATAATCT
Statistics
Matches: 93, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
130 90 0.97
131 3 0.03
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (130 bp):
ATACTCCAACCCCGACCTTATTTCTAAAATACCGATTTCTCACAATCGAGGATACTCCAACCCCA
TTATTTTCGAGAAGATACTCCAACCTCGACTTTATTTTCAAAATATTGATTTCTCACAATCGGGG
Found at i:5258410 original size:51 final size:51
Alignment explanation
Indices: 5258296--5258411 Score: 162
Period size: 51 Copynumber: 2.3 Consensus size: 51
5258286 TTTTCGAGAA
* * * *
5258296 GATACTCCAACCTCGGCTTTATTTTCAAAATATTGATTTCTCACAATCGGG
1 GATACTCCAACCCCGACCTTATTTTCAAAATATTGATTTCTCACAATCGAG
**
5258347 GATACTTTAACCCCGACCTTA-TTTCTAAAATATTGATTTCTCACAATCGAG
1 GATACTCCAACCCCGACCTTATTTTC-AAAATATTGATTTCTCACAATCGAG
5258398 GATACTCCAACCCC
1 GATACTCCAACCCC
5258412 ATTATTTTCG
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
50 4 0.07
51 52 0.93
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (51 bp):
GATACTCCAACCCCGACCTTATTTTCAAAATATTGATTTCTCACAATCGAG
Found at i:5258480 original size:79 final size:79
Alignment explanation
Indices: 5258397--5258569 Score: 188
Period size: 79 Copynumber: 2.2 Consensus size: 79
5258387 TCACAATCGA
* * * ** *
5258397 GGATACTCCAACCCCATTATTTTCGAGGGGATACTCTAAC-CTCGATTTTATTTTTAAAATACCG
1 GGATACTCCAACCCCATTATTTCCGAGGAGATACTCCAACTC-CGATTTTATTTCCAAAACACCG
5258461 ATAATCT-ATAATCAG
65 AT-ATCTCATAATCAG
* ** * * *
5258476 GGATACTCCAACTCTTTTATTTCCGAGGAGATACTCCAACTCCGGTTTTATTTCCAGAACATCGA
1 GGATACTCCAACCCCATTATTTCCGAGGAGATACTCCAACTCCGATTTTATTTCCAAAACACCGA
* *
5258541 TTTTTCATAATCAG
66 TATCTCATAATCAG
5258555 GGATACTCCAACCCC
1 GGATACTCCAACCCC
5258570 GTTGTTATCT
Statistics
Matches: 76, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
78 2 0.03
79 73 0.96
80 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (79 bp):
GGATACTCCAACCCCATTATTTCCGAGGAGATACTCCAACTCCGATTTTATTTCCAAAACACCGA
TATCTCATAATCAG
Found at i:5267331 original size:10 final size:10
Alignment explanation
Indices: 5267298--5267337 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 10
5267288 GGTAATTTCA
*
5267298 TGAAATATTT
1 TGAAAAATTT
5267308 ATGAAAAATGTT
1 -TGAAAAAT-TT
5267320 TGAAAAATTT
1 TGAAAAATTT
5267330 TGAAAAAT
1 TGAAAAAT
5267338 CATCTAGTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 10 0.37
11 15 0.56
12 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (10 bp):
TGAAAAATTT
Found at i:5269031 original size:20 final size:20
Alignment explanation
Indices: 5269006--5269081 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
5268996 GTAAAAAGAC
*
5269006 AGAATGTATCGATTCATTGA
1 AGAATGTATCGATACATTGA
*
5269026 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
* *
5269046 TA-CATGTACCGATACATTGA
1 -AGAATGTATCGATACATTGA
* *
5269066 AAAATTGCATCGATAC
1 AGAA-TGTATCGATAC
5269082 CTCTAGGTAA
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
19 1 0.02
20 34 0.76
21 10 0.22
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:5269144 original size:20 final size:19
Alignment explanation
Indices: 5269100--5269154 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
5269090 AAAAAGACAG
*
5269100 AATGTATCGATATATTTAT
1 AATGTATCGATACATTTAT
*
5269119 ACATGTATCGATACATTTTT
1 A-ATGTATCGATACATTTAT
*
5269139 CAATGTATCAATACAT
1 -AATGTATCGATACAT
5269155 CTGGGTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (19 bp):
AATGTATCGATACATTTAT
Found at i:5273921 original size:52 final size:52
Alignment explanation
Indices: 5273843--5274023 Score: 317
Period size: 52 Copynumber: 3.5 Consensus size: 52
5273833 CGAAATATGA
* *
5273843 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAATGTATCGATACATCTGGGC
* *
5273895 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATTTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAATGTATCGATACATCTGGGC
*
5273947 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAATGTATCGATACATCTGGGC
5273999 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
5274024 AAGATCAGTG
Statistics
Matches: 124, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 124 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTGTATAATGTATCGATACATCTGGGC
Found at i:5274050 original size:13 final size:13
Alignment explanation
Indices: 5274032--5274056 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5274022 CAAAGATCAG
5274032 TGTATCGATACAA
1 TGTATCGATACAA
5274045 TGTATCGATACA
1 TGTATCGATACA
5274057 TTTAAGTGAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5274114 original size:87 final size:87
Alignment explanation
Indices: 5274012--5274230 Score: 379
Period size: 87 Copynumber: 2.5 Consensus size: 87
5274002 TTTGCCTGCA
5274012 TGTATCGATACAAAGATCAGTGTATCGATACAATGTATCGATACATTTAAGTGATGTATCGATAC
1 TGTATCGATACAAAGATCAGTGTATCGATACAATGTATCGATACATTTAAGTGATGTATCGATAC
5274077 ATTTTTTGGCAGTACCTTAAAT
66 ATTTTTTGGCAGTACCTTAAAT
5274099 TGTATCGATACAAAGATCAGTGTATCGATACAATGTATCGATACATTTAAGTGATGTATCGATAC
1 TGTATCGATACAAAGATCAGTGTATCGATACAATGTATCGATACATTTAAGTGATGTATCGATAC
*
5274164 ATTTTTTGGCAGTAGCTTAAAT
66 ATTTTTTGGCAGTACCTTAAAT
* *
5274186 TGTATCGATACAAAAAAAT-A-TGTATCGATACATTGTATCGATACA
1 TGTATCGATAC--AAAGATCAGTGTATCGATACAATGTATCGATACA
5274231 ACACTTTATG
Statistics
Matches: 127, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
87 121 0.95
88 1 0.01
89 5 0.04
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (87 bp):
TGTATCGATACAAAGATCAGTGTATCGATACAATGTATCGATACATTTAAGTGATGTATCGATAC
ATTTTTTGGCAGTACCTTAAAT
Found at i:5274137 original size:13 final size:13
Alignment explanation
Indices: 5274119--5274143 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5274109 CAAAGATCAG
5274119 TGTATCGATACAA
1 TGTATCGATACAA
5274132 TGTATCGATACA
1 TGTATCGATACA
5274144 TTTAAGTGAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5274221 original size:33 final size:33
Alignment explanation
Indices: 5274184--5274250 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
5274174 AGTAGCTTAA
5274184 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
5274217 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
5274250 A
1 A
5274251 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:5274224 original size:13 final size:13
Alignment explanation
Indices: 5274206--5274230 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5274196 CAAAAAAATA
5274206 TGTATCGATACAT
1 TGTATCGATACAT
5274219 TGTATCGATACA
1 TGTATCGATACA
5274231 ACACTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5275193 original size:52 final size:52
Alignment explanation
Indices: 5275061--5275272 Score: 199
Period size: 52 Copynumber: 4.2 Consensus size: 52
5275051 GAAAAGTGAT
* * * * * * * *
5275061 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGCTGAGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG-G-A
* * *
5275115 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
*
5275168 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
* * *
5275211 AAAGGTGCCAATGTGCTGATTCAAGGTCGGCTACATTGGACTTAAAGATGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
5275263 AAAGGTGCCA
1 AAAGGTGCCA
5275273 CCGATTTGTG
Statistics
Matches: 129, Mismatches: 19, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
43 37 0.29
44 1 0.01
46 1 0.01
49 1 0.01
51 1 0.01
52 42 0.33
53 6 0.05
54 5 0.04
55 35 0.27
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
Found at i:5275229 original size:43 final size:43
Alignment explanation
Indices: 5275168--5275257 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
5275158 TAAAGATGGA
*
5275168 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* * *
5275211 AAAGGTGCCAATGTGCTGATTCAAGGTCGGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
5275254 AAAG
1 AAAG
5275258 ATGGAAAAGG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.27
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
Found at i:5275359 original size:30 final size:30
Alignment explanation
Indices: 5275295--5275672 Score: 289
Period size: 30 Copynumber: 12.8 Consensus size: 30
5275285 CTTTGAAGGT
**
5275295 TGCCACTGACTTGTGGGCTTTT-AAAGGT-
1 TGCCACTGACTTGTGGGCTTTTGAAAAATA
5275323 TGCCACTGACTTGTGGGCTTTTGAAAAATA
1 TGCCACTGACTTGTGGGCTTTTGAAAAATA
**
5275353 TGCCACTGACTTGTGGGCTTTT-AAAGGT-
1 TGCCACTGACTTGTGGGCTTTTGAAAAATA
5275381 TGCCACTGACTTGTGGGCTTTTGAAAAATA
1 TGCCACTGACTTGTGGGCTTTTGAAAAATA
***
5275411 TGCCACTGACTTGTGGGCTTTTGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTTGAAAAATA
* *
5275441 TGCCACTAACTTGTGGGC---TGAAAAGA-G
1 TGCCACTGACTTGTGGGCTTTTGAAAA-ATA
* * * ** *
5275468 TGCTA-TAGAGTTGTGAGCTTACAAAAGAAAAAGA
1 TGCCACT-GACTTGTGGGCTT----TTGAAAAATA
* * * * *
5275502 GTGCCACGGAGTTGTGGAC-TTTGGAAAAGA
1 -TGCCACTGACTTGTGGGCTTTTGAAAAATA
* ** ***
5275532 TGCCACCGACTTGTGGGCTTCGGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTTGAAAAATA
* * **
5275562 TGCCACTGATTTGTGGAC-TTTG-AAGGT-
1 TGCCACTGACTTGTGGGCTTTTGAAAAATA
* *
5275589 TGCCACTGACTTGTGGGCTTTCGAAAAAAA
1 TGCCACTGACTTGTGGGCTTTTGAAAAATA
*
5275619 TGCCACTGACTTGTGGGC-TTTGAAAAAAA
1 TGCCACTGACTTGTGGGCTTTTGAAAAATA
*
5275648 TGCCACTGACTTGTGGACTTTTGAA
1 TGCCACTGACTTGTGGGCTTTTGAA
5275673 GGGTGATGAA
Statistics
Matches: 282, Mismatches: 47, Indels: 40
0.76 0.13 0.11
Matches are distributed among these distances:
26 1 0.00
27 35 0.12
28 50 0.18
29 58 0.21
30 118 0.42
33 1 0.00
34 6 0.02
35 13 0.05
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (30 bp):
TGCCACTGACTTGTGGGCTTTTGAAAAATA
Found at i:5275369 original size:58 final size:57
Alignment explanation
Indices: 5275266--5275677 Score: 327
Period size: 58 Copynumber: 7.1 Consensus size: 57
5275256 AGATGGAAAA
* * **
5275266 GGTGCCACCGATTTGTGGGCTTTG-AAGGT-TGCCACTGACTTGTGGGCTTTTAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAAATATGCCACTGACTTGTGGGCTTTTAAAG
*
5275321 GTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTAAAG
1 GGTGCCACTGACTTGTGGGC-TTTGAAAAATATGCCACTGACTTGTGGGCTTTTAAAG
*
5275379 GTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAG
1 GGTGCCACTGACTTGTGGGC-TTTGAAAAATATGCCACTGACTTGTGGGCTTTT--AAAG
* * * * * **
5275439 GGTGCCACTAACTTGTGGGC--TGAAAAGA-GTGCTA-TAGAGTTGTGAGCTTACAAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAA-ATATGCCACT-GACTTGTGGGCTT-TTAAAG
* * * * * * **
5275495 AAAAAGAGTGCCACGGAGTTGTGGACTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGGAAAAG
1 -----G-GTGCCACTGACTTGTGGGCTTTGAAAAATATGCCACTGACTTGTGGGCTT--TTAAAG
* * ** * *
5275560 GGTGCCACTGATTTGTGGACTTTG-AAGGT-TGCCACTGACTTGTGGGCTTTCGAAAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAAAATATGCCACTGACTTGTGGGCTTT--TAAAG
** * * *
5275617 AATGCCACTGACTTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGGACTTTTGAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAAATATGCCACTGACTTGTGGGCTTTTAAAG
5275674 GGTG
1 GGTG
5275678 ATGAATGTCT
Statistics
Matches: 288, Mismatches: 46, Indels: 44
0.76 0.12 0.12
Matches are distributed among these distances:
55 17 0.06
56 9 0.03
57 71 0.25
58 85 0.30
59 41 0.14
60 23 0.08
61 1 0.00
62 15 0.05
63 1 0.00
64 20 0.07
65 5 0.02
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (57 bp):
GGTGCCACTGACTTGTGGGCTTTGAAAAATATGCCACTGACTTGTGGGCTTTTAAAG
Found at i:5275545 original size:29 final size:29
Alignment explanation
Indices: 5275496--5275668 Score: 170
Period size: 29 Copynumber: 5.9 Consensus size: 29
5275486 TTACAAAAGA
* *
5275496 AAAAGAGTGCCACGGAGTTGTGGACTTTGG
1 AAAAGA-TGCCACTGACTTGTGGACTTTGG
* * *
5275526 AAAAGATGCCACCGACTTGTGGGCTTCGG
1 AAAAGATGCCACTGACTTGTGGACTTTGG
* *
5275555 AAAAGGGTGCCACTGATTTGTGGACTTT-G
1 AAAA-GATGCCACTGACTTGTGGACTTTGG
* * * *
5275584 -AAGGTTGCCACTGACTTGTGGGCTTTCGA
1 AAAAGATGCCACTGACTTGTGGACTTT-GG
* * *
5275613 AAAAAATGCCACTGACTTGTGGGCTTTGA
1 AAAAGATGCCACTGACTTGTGGACTTTGG
*
5275642 AAAAAATGCCACTGACTTGTGGACTTT
1 AAAAGATGCCACTGACTTGTGGACTTT
5275669 TGAAGGGTGA
Statistics
Matches: 121, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
27 20 0.17
28 2 0.02
29 52 0.43
30 47 0.39
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (29 bp):
AAAAGATGCCACTGACTTGTGGACTTTGG
Found at i:5275603 original size:121 final size:116
Alignment explanation
Indices: 5275381--5275663 Score: 300
Period size: 121 Copynumber: 2.4 Consensus size: 116
5275371 TTTTAAAGGT
* **
5275381 TGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCA
1 TGCCACTGACTTGTGGGC-TTTGAAAAAAATGCCACTGACTTGTGGGCTTCGGAAAAGGGTGCCA
* * * *
5275446 CTAACTTGTGGGCTGAAAAGAGTGCTATAGAGTTGTGAGCTTACAAAAGAAAAAGAG
65 CTAACTTGTGGACTGAAAAGAGTGCCATAGACTTGTGAGCTTAC----GAAAAA-AA
* * * * * *
5275503 TGCCACGGAGTTGTGGACTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCAC
1 TGCCACTGACTTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGGGCTTCGGAAAAGGGTGCCAC
* * *** * *
5275568 TGATTTGTGGACTTTGAAG-GTTGCCACT-GACTTGTGGGCTTTCGAAAAAAA
66 TAACTTGTGGACTGAAAAGAG-TGCCA-TAGACTTGTGAGCTTACGAAAAAAA
5275619 TGCCACTGACTTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGG
1 TGCCACTGACTTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGG
5275664 ACTTTTGAAG
Statistics
Matches: 134, Mismatches: 25, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
116 40 0.30
117 6 0.04
120 1 0.01
121 71 0.53
122 16 0.12
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (116 bp):
TGCCACTGACTTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGGGCTTCGGAAAAGGGTGCCAC
TAACTTGTGGACTGAAAAGAGTGCCATAGACTTGTGAGCTTACGAAAAAAA
Found at i:5277115 original size:1 final size:1
Alignment explanation
Indices: 5277111--5277201 Score: 56
Period size: 1 Copynumber: 91.0 Consensus size: 1
5277101 CCGGACCCCC
* ** ** *** ** **
5277111 TTTTTTTTTTTTGTTTTTTTTTTTTTGGTTTTTCATTTTTCCGTTTTTTTTTTGGTTTTTCATTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
**
5277176 TTTTTCGTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
5277202 GGAGGACGCC
Statistics
Matches: 72, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 72 1.00
ACGTcount: A:0.02, C:0.05, G:0.08, T:0.85
Consensus pattern (1 bp):
T
Found at i:5277157 original size:29 final size:30
Alignment explanation
Indices: 5277125--5277194 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 30
5277115 TTTTTTTTGT
5277125 TTTTTTTTTTTTGGTTTTTCA-TTTTTCCG
1 TTTTTTTTTTTTGGTTTTTCATTTTTTCCG
*
5277154 --TTTTTTTTTTGGTTTTTCATTTTTTTTCG
1 TTTTTTTTTTTTGGTTTTTCA-TTTTTTCCG
5277183 TTTTTTTTTTTT
1 TTTTTTTTTTTT
5277195 TTTTTTTGGA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
27 19 0.53
29 7 0.19
31 10 0.28
ACGTcount: A:0.03, C:0.07, G:0.09, T:0.81
Consensus pattern (30 bp):
TTTTTTTTTTTTGGTTTTTCATTTTTTCCG
Found at i:5286902 original size:10 final size:10
Alignment explanation
Indices: 5286887--5286913 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
5286877 ATGTATCAAG
5286887 CAAAAACAAA
1 CAAAAACAAA
5286897 CAAAAACAAA
1 CAAAAACAAA
5286907 CAAAAAC
1 CAAAAAC
5286914 TTAGTTAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAACAAA
Done.