Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr10
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: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31
Warning! 2980117 characters in sequence are not A, C, G, or T
File 85 of 284
Found at i:28273744 original size:92 final size:92
Alignment explanation
Indices: 28273538--28274046 Score: 655
Period size: 92 Copynumber: 5.5 Consensus size: 92
28273528 CTTCGGAGAT
* * * * * * * * *
28273538 TCTAACGTGTCCTCGATTGGAATAACTTTTATGAGTAATTTGGCATGTTATCAGGGGAGAATATT
1 TCTAACATGTTCTCGGTTGGAATAGCTCTTATGAGCAATCTGGCGTGTTATCGGGGGAGAATATT
* *
28273603 TAGCTTACGGG-TTCTACAC-ATGTGCA
66 TAGCCTACGGGCTT-TGCACTATGTGCA
* ** * *
28273629 TCTAACGTGTTCTCGGTTGGAATAAATCTTATGAGCAATCTGGTGTATTATCGGGGGAGAATATT
1 TCTAACATGTTCTCGGTTGGAATAGCTCTTATGAGCAATCTGGCGTGTTATCGGGGGAGAATATT
*
28273694 TAGCCTACAGGCTTTGCACTATGTGCA
66 TAGCCTACGGGCTTTGCACTATGTGCA
*
28273721 TCTAACATGTTCTCGGTTGGAATAGCTCTTATGAGCAATCTGGTGTGTTATCGGGGGAGAATATT
1 TCTAACATGTTCTCGGTTGGAATAGCTCTTATGAGCAATCTGGCGTGTTATCGGGGGAGAATATT
*
28273786 TAGCCTACGGGCTTTGTACTATGTGCA
66 TAGCCTACGGGCTTTGCACTATGTGCA
* *
28273813 TCTAACGTGTTCTCGGTTGGAATAGCTCTTATGAGCAATCTGGCATGTTATCGGGGGAGAATATT
1 TCTAACATGTTCTCGGTTGGAATAGCTCTTATGAGCAATCTGGCGTGTTATCGGGGGAGAATATT
28273878 TAGCCTACGGGCTTTGCACTATGTGCA
66 TAGCCTACGGGCTTTGCACTATGTGCA
* * * * * * * *
28273905 TCTAGCATGTTATTGATTAGAATAGCTCTTATGAGCAA-CATGACGTGTTATCAGGAGAGAATAT
1 TCTAACATGTTCTCGGTTGGAATAGCTCTTATGAGCAATC-TGGCGTGTTATCGGGGGAGAATAT
28273969 TTAGCCTACGGGCTTTGCACTATGTGCA
65 TTAGCCTACGGGCTTTGCACTATGTGCA
** * * * * *
28273997 TCTGGCATGTTCTCGGTTGGAATTGCTTTTATGGGCAAACTGGCATGTTA
1 TCTAACATGTTCTCGGTTGGAATAGCTCTTATGAGCAATCTGGCGTGTTA
28274047 ATGTATGGAT
Statistics
Matches: 371, Mismatches: 43, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
91 69 0.19
92 301 0.81
93 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (92 bp):
TCTAACATGTTCTCGGTTGGAATAGCTCTTATGAGCAATCTGGCGTGTTATCGGGGGAGAATATT
TAGCCTACGGGCTTTGCACTATGTGCA
Found at i:28278587 original size:19 final size:20
Alignment explanation
Indices: 28278565--28278605 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
28278555 TATAAAATAA
28278565 AAAAAT-TACTTA-AAATTTT
1 AAAAATATA-TTAGAAATTTT
28278584 AAAAATATATTAGAAATTTT
1 AAAAATATATTAGAAATTTT
28278604 AA
1 AA
28278606 TATTTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (20 bp):
AAAAATATATTAGAAATTTT
Found at i:28287128 original size:13 final size:13
Alignment explanation
Indices: 28287112--28287141 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
28287102 AGTGCTGCAA
28287112 AAAAATGCTTATG
1 AAAAATGCTTATG
*
28287125 AAAAATGCTTTTG
1 AAAAATGCTTATG
28287138 AAAA
1 AAAA
28287142 GCTTGGTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.07, G:0.13, T:0.30
Consensus pattern (13 bp):
AAAAATGCTTATG
Found at i:28289195 original size:11 final size:11
Alignment explanation
Indices: 28289179--28289204 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
28289169 GTCGCCTCTT
28289179 CCTTCGTTCTA
1 CCTTCGTTCTA
28289190 CCTTCGTTCTA
1 CCTTCGTTCTA
28289201 CCTT
1 CCTT
28289205 TGCCTCCCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.38, G:0.08, T:0.46
Consensus pattern (11 bp):
CCTTCGTTCTA
Found at i:28292232 original size:18 final size:17
Alignment explanation
Indices: 28292204--28292238 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28292194 ATTGTTAAGA
*
28292204 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
28292221 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
28292239 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:28292342 original size:15 final size:15
Alignment explanation
Indices: 28292324--28292371 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
28292314 ATTATTAAGA
28292324 ATTTTATTAAATTAT
1 ATTTTATTAAATTAT
*
28292339 ATTTTTAATTAAAATAT
1 A-TTTT-ATTAAATTAT
*
28292356 ATTTAATTATAATTAT
1 ATTTTATTA-AATTAT
28292372 GTTTAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 5 0.19
16 12 0.44
17 10 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTTATTAAATTAT
Found at i:28292344 original size:16 final size:17
Alignment explanation
Indices: 28292325--28292359 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
28292315 TTATTAAGAA
*
28292325 TTTT-ATTAAATTATAT
1 TTTTAATTAAAATATAT
28292341 TTTTAATTAAAATATAT
1 TTTTAATTAAAATATAT
28292358 TT
1 TT
28292360 AATTATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTAATTAAAATATAT
Found at i:28292349 original size:17 final size:17
Alignment explanation
Indices: 28292325--28292371 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
28292315 TTATTAAGAA
28292325 TTTT-ATTAAATTATAT
1 TTTTAATTAAATTATAT
28292341 TTTTAATTAAA--ATAT
1 TTTTAATTAAATTATAT
*
28292356 ATTTAATTATAATTAT
1 TTTTAATTA-AATTAT
28292372 GTTTAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 12 0.46
16 6 0.23
17 6 0.23
18 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTTAATTAAATTATAT
Found at i:28292587 original size:44 final size:45
Alignment explanation
Indices: 28292522--28292612 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
28292512 ACCTCTATTC
* * *
28292522 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
28292566 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
28292611 CA
1 CA
28292613 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:28292614 original size:16 final size:16
Alignment explanation
Indices: 28292593--28292661 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
28292583 GATTAGCTAT
28292593 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
28292609 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
28292626 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
28292642 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
28292658 TACA
1 TACA
28292662 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:28292635 original size:33 final size:32
Alignment explanation
Indices: 28292593--28292661 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
28292583 GATTAGCTAT
28292593 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
28292626 TACACCTCTAATCCAATACACCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
28292658 TACA
1 TACA
28292662 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 8 0.22
33 28 0.78
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:28292942 original size:21 final size:20
Alignment explanation
Indices: 28292918--28292960 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
28292908 AAAGTAAACC
28292918 TAAAAATATTTTAAACATTTT
1 TAAAAATATTTTAAA-ATTTT
* *
28292939 TAAATATATTTTACAATTTT
1 TAAAAATATTTTAAAATTTT
28292959 TA
1 TA
28292961 GAACTAGAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
TAAAAATATTTTAAAATTTT
Found at i:28293730 original size:15 final size:16
Alignment explanation
Indices: 28293696--28293734 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
28293686 GACCAATTAT
* *
28293696 TATTTGGAACAACTTG
1 TATTTAGAACAACATG
28293712 TATTTAGAACAA-ATG
1 TATTTAGAACAACATG
28293727 TATTTAGA
1 TATTTAGA
28293735 GTCATTATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (16 bp):
TATTTAGAACAACATG
Found at i:28296605 original size:38 final size:38
Alignment explanation
Indices: 28296546--28296620 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 38
28296536 TATATCATTC
* *
28296546 TATTAATAATAAAATTTTAATTTTAAA-ATATATTAAAA
1 TATTAATAATAAAAATGTAATTTTAAATAT-TATTAAAA
*
28296584 TATTAATAA-AAATAATGTAATTTTTAATATTATTAAA
1 TATTAATAATAAA-AATGTAATTTTAAATATTATTAAA
28296621 CATACATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 3 0.09
38 27 0.84
39 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (38 bp):
TATTAATAATAAAAATGTAATTTTAAATATTATTAAAA
Found at i:28297400 original size:25 final size:28
Alignment explanation
Indices: 28297352--28297408 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 28
28297342 TGTAATTTAA
* *
28297352 ATTAAGTTTTCATTATGCATTATTTATT
1 ATTAAGTTTACATTATGCATTATTGATT
28297380 ATTAAGTTTACA-TATG-A-TATTGATT
1 ATTAAGTTTACATTATGCATTATTGATT
28297405 ATTA
1 ATTA
28297409 CAAAATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 11 0.41
26 1 0.04
27 4 0.15
28 11 0.41
ACGTcount: A:0.33, C:0.05, G:0.09, T:0.53
Consensus pattern (28 bp):
ATTAAGTTTACATTATGCATTATTGATT
Found at i:28297440 original size:17 final size:18
Alignment explanation
Indices: 28297403--28297440 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
28297393 ATGATATTGA
*
28297403 TTATTACAAAATATTATT
1 TTATTACAAAATATAATT
*
28297421 TTATTATAAAATA-AATT
1 TTATTACAAAATATAATT
28297438 TTA
1 TTA
28297441 ATTGAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
TTATTACAAAATATAATT
Found at i:28297540 original size:14 final size:14
Alignment explanation
Indices: 28297510--28297538 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
28297500 ATTCACAAAT
28297510 AATAACTTTTAGAA
1 AATAACTTTTAGAA
28297524 AATAA-TTTTAGAA
1 AATAACTTTTAGAA
28297537 AA
1 AA
28297539 ATTTGTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.34
Consensus pattern (14 bp):
AATAACTTTTAGAA
Found at i:28298319 original size:2 final size:2
Alignment explanation
Indices: 28298312--28298343 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
28298302 TCCGTTTTTA
28298312 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28298344 TATGTTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28300339 original size:25 final size:25
Alignment explanation
Indices: 28300311--28300382 Score: 65
Period size: 26 Copynumber: 2.8 Consensus size: 25
28300301 CCCAATATAT
28300311 GGCTCTTCGAAGCTTCTCGATTAAA
1 GGCTCTTCGAAGCTTCTCGATTAAA
* * *
28300336 GGCTCTT-TATGAGCTTCTTGATTAAT
1 GGCTCTTCGA--AGCTTCTCGATTAAA
* * *
28300362 GGCTCCTCGGAGCTTCCCGAT
1 GGCTCTTCGAAGCTTCTCGAT
28300383 ATTGGCTCGC
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
24 1 0.03
25 16 0.44
26 19 0.53
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (25 bp):
GGCTCTTCGAAGCTTCTCGATTAAA
Found at i:28300448 original size:25 final size:25
Alignment explanation
Indices: 28300309--28300464 Score: 99
Period size: 25 Copynumber: 6.3 Consensus size: 25
28300299 ATCCCAATAT
* *
28300309 ATGGCTCTTCGAAGCTTCTCGATTA
1 ATGGCTCTTCGGAGCTTCCCGATTA
* ** **
28300334 AAGGCTCTTTATGAGCTTCTTGATTA
1 ATGGCTC-TTCGGAGCTTCCCGATTA
*
28300360 ATGGCTCCTCGGAGCTTCCCGA-TA
1 ATGGCTCTTCGGAGCTTCCCGATTA
* *
28300384 TTGGCTCGCTT--GAACTTCCCGA-TA
1 ATGGCT--CTTCGGAGCTTCCCGATTA
* *
28300408 TATGGCT-ATCTAGAGCTTCCCGATTA
1 -ATGGCTCTTC-GGAGCTTCCCGATTA
*
28300434 ATGGCTCTTCGGAGCTACCC-ATTA
1 ATGGCTCTTCGGAGCTTCCCGATTA
*
28300458 TTGGCTC
1 ATGGCTC
28300465 ACATGAGCTT
Statistics
Matches: 101, Mismatches: 21, Indels: 19
0.72 0.15 0.13
Matches are distributed among these distances:
22 1 0.01
24 29 0.29
25 45 0.45
26 26 0.26
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.34
Consensus pattern (25 bp):
ATGGCTCTTCGGAGCTTCCCGATTA
Found at i:28300476 original size:74 final size:73
Alignment explanation
Indices: 28300342--28300502 Score: 191
Period size: 74 Copynumber: 2.2 Consensus size: 73
28300332 TAAAGGCTCT
** * * * *
28300342 TTATGAGCTTCTTGATTAATGGCTCCTCGGAGCTTCCCGATATTGGCTCGCTTGAACTTCCCGAT
1 TTATGAGCTTCCCGATTAATGGCTCCTCGGAGCTACCCGATATTGGCTCACATGAACTTCCCAAT
28300407 ATATGGCTA
66 -TATGGCTA
* * *
28300416 TCTA-GAGCTTCCCGATTAATGGCTCTTCGGAGCTACCC-ATTATTGGCTCACATGAGCTTCCTA
1 T-TATGAGCTTCCCGATTAATGGCTCCTCGGAGCTACCCGA-TATTGGCTCACATGAACTTCCCA
*
28300479 ATTATGGCTC
64 ATTATGGCTA
28300489 TTATGAGCTTCCCG
1 TTATGAGCTTCCCG
28300503 TTATACAGCC
Statistics
Matches: 74, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
72 2 0.03
73 19 0.26
74 51 0.69
75 2 0.03
ACGTcount: A:0.19, C:0.26, G:0.20, T:0.34
Consensus pattern (73 bp):
TTATGAGCTTCCCGATTAATGGCTCCTCGGAGCTACCCGATATTGGCTCACATGAACTTCCCAAT
TATGGCTA
Found at i:28300486 original size:24 final size:25
Alignment explanation
Indices: 28300454--28300500 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
28300444 GGAGCTACCC
28300454 ATTATTGGCTCACATGAGCTTCCTA
1 ATTATTGGCTCACATGAGCTTCCTA
**
28300479 ATTA-TGGCTCTTATGAGCTTCC
1 ATTATTGGCTCACATGAGCTTCC
28300501 CGTTATACAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (25 bp):
ATTATTGGCTCACATGAGCTTCCTA
Found at i:28300547 original size:25 final size:25
Alignment explanation
Indices: 28300371--28300564 Score: 84
Period size: 25 Copynumber: 7.9 Consensus size: 25
28300361 TGGCTCCTCG
* *
28300371 GAGCTTCCCGA-TAT-TGGCTCGCTT
1 GAGCTTCCC-ATTATATGGCTCACGT
*
28300395 GAACTTCCCGA-TATATGGCT-ATC-T
1 GAGCTTCCC-ATTATATGGCTCA-CGT
*
28300419 AGAGCTTCCCGATTA-ATGGCTCTTCG-
1 -GAGCTTCCC-ATTATATGGCTC-ACGT
* *
28300445 GAGCTACCCATTAT-TGGCTCACAT
1 GAGCTTCCCATTATATGGCTCACGT
* * ***
28300469 GAGCTTCCTAAT-TATGGCTCTTAT
1 GAGCTTCCCATTATATGGCTCACGT
* ** **
28300493 GAGCTTCCCGTTATACAGC-CTGGAT
1 GAGCTTCCCATTATATGGCTCACG-T
*
28300518 AAGCTTCCCATTATATGGCTCACGT
1 GAGCTTCCCATTATATGGCTCACGT
* *
28300543 GAGCTTCCTACTATATGGCTCA
1 GAGCTTCCCATTATATGGCTCA
28300565 AGAGAGAGCT
Statistics
Matches: 129, Mismatches: 28, Indels: 25
0.71 0.15 0.14
Matches are distributed among these distances:
23 2 0.02
24 52 0.40
25 70 0.54
26 5 0.04
ACGTcount: A:0.21, C:0.27, G:0.20, T:0.32
Consensus pattern (25 bp):
GAGCTTCCCATTATATGGCTCACGT
Found at i:28312970 original size:25 final size:24
Alignment explanation
Indices: 28312938--28312989 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
28312928 CTAATCAATT
*
28312938 GCTCCTTAGAGCTTCCCGATAT-TG
1 GCTCCTTA-AACTTCCCGATATATG
*
28312962 GCTCGCTTAAACTTCGCGATATATG
1 GCTC-CTTAAACTTCCCGATATATG
28312987 GCT
1 GCT
28312990 ATCCAGAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.19, C:0.27, G:0.21, T:0.33
Consensus pattern (24 bp):
GCTCCTTAAACTTCCCGATATATG
Found at i:28313119 original size:25 final size:25
Alignment explanation
Indices: 28313091--28313138 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
28313081 TACAGCCTGG
*
28313091 ATAAGCTTCCCATTATGTGGCTCAC
1 ATAAGCTTCCCATTATATGGCTCAC
*
28313116 ATAAGCTTCCTATTATATGGCTC
1 ATAAGCTTCCCATTATATGGCTC
28313139 GAGAGAGTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (25 bp):
ATAAGCTTCCCATTATATGGCTCAC
Found at i:28319497 original size:42 final size:45
Alignment explanation
Indices: 28319434--28319645 Score: 132
Period size: 49 Copynumber: 4.6 Consensus size: 45
28319424 CTTCGTTTAC
** * *
28319434 TCGATGTCATAGTTCAACTATGGTCTTACACAT-C-T-TCATATA
1 TCGATGTCATAGCCCAGCTATGGTCTTACACATACATATCACATA
28319476 TCGATGTCATAGCCCAGCTATGGTCTTATGCGTA-ATCACATATCACATA
1 TCGATGTCATAGCCCAGCTATGGTCTTA--C--ACAT-ACATATCACATA
* * *
28319525 TCGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCTCA-C
1 TCGATGTCATAGCCCAGCTATGGTCTTACAC--AT-ACATATCACATA
* * * * *
28319572 T-GATGCCATATCCCAGATATGGTCTTATACAGTAGCATAT-ATCACA
1 TCGATGTCATAGCCCAGCTATGGTCTTACACA-TA-CATATCA-CATA
* * * *
28319618 CCGATGCCATATCCCAGATATGGTCTTA
1 TCGATGTCATAGCCCAGCTATGGTCTTA
28319646 TACGGAAATC
Statistics
Matches: 141, Mismatches: 13, Indels: 27
0.78 0.07 0.15
Matches are distributed among these distances:
42 25 0.18
44 3 0.02
45 11 0.08
46 27 0.19
47 29 0.21
48 13 0.09
49 33 0.23
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (45 bp):
TCGATGTCATAGCCCAGCTATGGTCTTACACATACATATCACATA
Found at i:28319536 original size:49 final size:48
Alignment explanation
Indices: 28319475--28319649 Score: 196
Period size: 47 Copynumber: 3.7 Consensus size: 48
28319465 ATCTTCATAT
* * *
28319475 ATCGATGTCATAGCCCAGCTATGGTCTTATGCGTAATCACATATCACA
1 ATCGATGCCATAGCCCAGATATGGTCTTATACGTAATCACATATCACA
* * *
28319523 TATCGATGCCATAGCCCAGCTATGGTCTTACACG-AATCACATATCTCA
1 -ATCGATGCCATAGCCCAGATATGGTCTTATACGTAATCACATATCACA
* * * *
28319571 CT-GATGCCATATCCCAGATATGGTCTTATACAGT-AGCATATATCAC-
1 ATCGATGCCATAGCCCAGATATGGTCTTATAC-GTAATCACATATCACA
* *
28319617 ACCGATGCCATATCCCAGATATGGTCTTATACG
1 ATCGATGCCATAGCCCAGATATGGTCTTATACG
28319650 GAAATCACTT
Statistics
Matches: 110, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
46 27 0.25
47 40 0.36
48 13 0.12
49 30 0.27
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (48 bp):
ATCGATGCCATAGCCCAGATATGGTCTTATACGTAATCACATATCACA
Found at i:28319702 original size:31 final size:31
Alignment explanation
Indices: 28319667--28319815 Score: 226
Period size: 31 Copynumber: 4.8 Consensus size: 31
28319657 CTTGTCACTT
*
28319667 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
28319698 GTAGCCGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
28319729 GTAGTCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* **
28319760 GTAACAAAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
28319791 GTAGCCGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
28319816 TGTCCTTAAT
Statistics
Matches: 105, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 105 1.00
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.27
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:28319859 original size:44 final size:44
Alignment explanation
Indices: 28319791--28319912 Score: 145
Period size: 50 Copynumber: 2.6 Consensus size: 44
28319781 CACTGATCAG
* *
28319791 GTAGCCGAAGCTACCACTTTTCACTTGTCCTTAATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCCTTAATCAGATAAGT
* * *
28319835 GTAGCCGAAGTTATTACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCA----C--TTGTCCTTAATCAGATAAGT
28319885 GTAGCCGAAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
28319913 TGTCATGGTC
Statistics
Matches: 65, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
44 23 0.35
46 1 0.02
48 1 0.02
50 40 0.62
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.35
Consensus pattern (44 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCCTTAATCAGATAAGT
Found at i:28319881 original size:50 final size:50
Alignment explanation
Indices: 28319809--28319910 Score: 168
Period size: 50 Copynumber: 2.0 Consensus size: 50
28319799 AGCTACCACT
* *
28319809 TTTCACTTGTCCTTAATCAGATAAGTGTAGCCGAAGTTATTACTTATCAC
1 TTTCACTTGTCCTTAATCAGATAAGTGTAGCCGAAGCTATCACTTATCAC
* *
28319859 TTTCATTTGTCCTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCAC
1 TTTCACTTGTCCTTAATCAGATAAGTGTAGCCGAAGCTATCACTTATCAC
28319909 TT
1 TT
28319911 GTTGTCATGG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (50 bp):
TTTCACTTGTCCTTAATCAGATAAGTGTAGCCGAAGCTATCACTTATCAC
Found at i:28324534 original size:46 final size:46
Alignment explanation
Indices: 28324469--28324696 Score: 343
Period size: 46 Copynumber: 5.0 Consensus size: 46
28324459 TTATCTTTGA
* * * * * *
28324469 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATAT
28324515 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
28324561 CA-GTTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATG-TTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* * *
28324607 CAGGCTGCCATGGTTTCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
28324653 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
28324697 TTCAGAAAGC
Statistics
Matches: 168, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
45 5 0.03
46 162 0.96
47 1 0.01
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.39
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
Found at i:28327132 original size:49 final size:48
Alignment explanation
Indices: 28327067--28327223 Score: 237
Period size: 49 Copynumber: 3.3 Consensus size: 48
28327057 AGGGTGTTAT
*
28327067 AGCTATGGCCTTACACGAAATCACATATCACATATCGATGCCATAGCCC
1 AGCTATGGTCTTACACG-AATCACATATCACATATCGATGCCATAGCCC
28327116 AGCTATGGTCTTACACGTAATCACATATCACATATCGATGCCATAGCCC
1 AGCTATGGTCTTACACG-AATCACATATCACATATCGATGCCATAGCCC
* * *
28327165 AGCTATGGTCTTACACGAATCACATATCTCA-CT-GATGCCATATCCC
1 AGCTATGGTCTTACACGAATCACATATCACATATCGATGCCATAGCCC
*
28327211 AGATATGGTCTTA
1 AGCTATGGTCTTA
28327224 TACAGTAGCA
Statistics
Matches: 102, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
46 24 0.24
47 1 0.01
48 13 0.13
49 64 0.63
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.27
Consensus pattern (48 bp):
AGCTATGGTCTTACACGAATCACATATCACATATCGATGCCATAGCCC
Found at i:28327273 original size:47 final size:46
Alignment explanation
Indices: 28327070--28327270 Score: 204
Period size: 49 Copynumber: 4.2 Consensus size: 46
28327060 GTGTTATAGC
* * * *
28327070 TATGGCCTTACACGAAATCACATATCACATATCGATGCCATAGCCCAGC
1 TATGGTCTTACACG-TATCACATATCAC--ACCGATGCCATAGCCCAGA
* *
28327119 TATGGTCTTACACGTAATCACATATCACATATCGATGCCATAGCCCAGC
1 TATGGTCTTACACGT-ATCACATATCAC--ACCGATGCCATAGCCCAGA
* * * *
28327168 TATGGTCTTACACGAATCACATATCTCACTGATGCCATATCCCAGA
1 TATGGTCTTACACGTATCACATATCACACCGATGCCATAGCCCAGA
* * * * *
28327214 TATGGTCTTATACAGTAGCATATATCACACCGATGCCATATCCCAAA
1 TATGGTCTTACAC-GTATCACATATCACACCGATGCCATAGCCCAGA
28327261 TATGGTCTTA
1 TATGGTCTTA
28327271 TACGGAAATC
Statistics
Matches: 135, Mismatches: 15, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
46 27 0.20
47 37 0.27
48 11 0.08
49 60 0.44
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.27
Consensus pattern (46 bp):
TATGGTCTTACACGTATCACATATCACACCGATGCCATAGCCCAGA
Found at i:28327281 original size:95 final size:97
Alignment explanation
Indices: 28327070--28327282 Score: 247
Period size: 95 Copynumber: 2.2 Consensus size: 97
28327060 GTGTTATAGC
* *
28327070 TATGGCCTTACACGAAATCACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGTA
1 TATGGTCTTACACGAAATCACATATCACATATCGATGCCATAGCCCAGATATGGTCTTACACGTA
* * **
28327135 ATCACATATCACATATCGATGCCATAGCCCAGC
66 AGCACATATCACA-ACCGATGCCATAGCCCAAA
* * * *
28327168 TATGGTCTTACACG-AATCACATATCTCA-CT-GATGCCATATCCCAGATATGGTCTTATACAGT
1 TATGGTCTTACACGAAATCACATATCACATATCGATGCCATAGCCCAGATATGGTCTTACAC-GT
* *
28327230 -AGCATATATCAC-ACCGATGCCATATCCCAAA
65 AAGCACATATCACAACCGATGCCATAGCCCAAA
*
28327261 TATGGTCTTATACGGAAATCAC
1 TATGGTCTTACAC-GAAATCAC
28327283 TTGTCACTTG
Statistics
Matches: 99, Mismatches: 13, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
93 27 0.27
94 1 0.01
95 42 0.42
96 3 0.03
97 13 0.13
98 13 0.13
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (97 bp):
TATGGTCTTACACGAAATCACATATCACATATCGATGCCATAGCCCAGATATGGTCTTACACGTA
AGCACATATCACAACCGATGCCATAGCCCAAA
Found at i:28327421 original size:32 final size:31
Alignment explanation
Indices: 28327292--28327441 Score: 212
Period size: 31 Copynumber: 4.8 Consensus size: 31
28327282 CTTGTCACTT
*
28327292 GTAGCC-GAAGCTACCACTATTCACTGATCAG
1 GTAGCCAG-AGCTACCACTTTTCACTGATCAG
*
28327323 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCAGAGCTACCACTTTTCACTGATCAG
*
28327354 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCAGAGCTACCACTTTTCACTGATCAG
* *
28327385 GTAGCCAGAGCTACCACTTTTTGACTGATCAA
1 GTAGCCAGAGCTACCAC-TTTTCACTGATCAG
* *
28327417 GTAGCAAAAGCTACCACTTTTCACT
1 GTAGCCAGAGCTACCACTTTTCACT
28327442 TGTCATTTGT
Statistics
Matches: 110, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
31 82 0.75
32 28 0.25
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (31 bp):
GTAGCCAGAGCTACCACTTTTCACTGATCAG
Found at i:28327515 original size:50 final size:51
Alignment explanation
Indices: 28327424--28327545 Score: 201
Period size: 50 Copynumber: 2.4 Consensus size: 51
28327414 CAAGTAGCAA
* * *
28327424 AAGCTACCACTTTTCACTTGTCATTTGTCCTTGATCAGATAAGTGTAGCCG
1 AAGCTATCACTTATCACTTGTCATTTGTCCTTGATCAGATAAGTATAGCCG
*
28327475 AAGCTATCACTTATCACTT-TCATTTGTCCTTGATCAGATAAGTATAGCGG
1 AAGCTATCACTTATCACTTGTCATTTGTCCTTGATCAGATAAGTATAGCCG
28327525 AAGCTATCACTTATCACTTGT
1 AAGCTATCACTTATCACTTGT
28327546 TGCCATGGTC
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
50 48 0.73
51 18 0.27
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (51 bp):
AAGCTATCACTTATCACTTGTCATTTGTCCTTGATCAGATAAGTATAGCCG
Found at i:28336118 original size:13 final size:13
Alignment explanation
Indices: 28336102--28336172 Score: 65
Period size: 13 Copynumber: 5.4 Consensus size: 13
28336092 ATAAAAATAA
28336102 TATATGAAATGAT
1 TATATGAAATGAT
28336115 TATATG-AATCGAT
1 TATATGAAAT-GAT
*
28336128 TATATAGAAATAAT
1 TATAT-GAAATGAT
*
28336142 TATAT-AAAGTGTT
1 TATATGAAA-TGAT
* *
28336155 TATACGAAATGTT
1 TATATGAAATGAT
28336168 TATAT
1 TATAT
28336173 AGATAGATCT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
12 6 0.12
13 28 0.58
14 11 0.23
15 3 0.06
ACGTcount: A:0.44, C:0.03, G:0.13, T:0.41
Consensus pattern (13 bp):
TATATGAAATGAT
Found at i:28336158 original size:40 final size:39
Alignment explanation
Indices: 28336089--28336175 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 39
28336079 GAAATGGTTA
* *
28336089 TATATAAAAATAATATATGAAATGATTATATG-AATCGAT
1 TATATAGAAATAATATATGAAATGATTATACGAAAT-GAT
* *
28336128 TATATAGAAATAATTATAT-AAAGTGTTTATACGAAATGTT
1 TATATAGAAATAA-TATATGAAA-TGATTATACGAAATGAT
28336168 TATATAGA
1 TATATAGA
28336176 TAGATCTATA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
39 15 0.37
40 23 0.56
41 3 0.07
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.38
Consensus pattern (39 bp):
TATATAGAAATAATATATGAAATGATTATACGAAATGAT
Found at i:28336359 original size:72 final size:73
Alignment explanation
Indices: 28336219--28336362 Score: 236
Period size: 73 Copynumber: 2.0 Consensus size: 73
28336209 TTTAAAATGG
* *
28336219 GAAATGTTAAATGAATAGATGTTGAATGAATTGTATATCTAATGTGATTACTTGTATAAGTTTTA
1 GAAATGTTAAATGAATAGATGTTGAATAAATGGTATATCTAATGTGATTACTTGTATAAGTTTTA
28336284 TAACATGT
66 TAACATGT
* * *
28336292 GAAATGTTAAATGAATAGATGTTGAATAAATGGTATGTC-AATGTGTTTACTTGTATATGTTTTA
1 GAAATGTTAAATGAATAGATGTTGAATAAATGGTATATCTAATGTGATTACTTGTATAAGTTTTA
28336356 TAACATG
66 TAACATG
28336363 AAAAGGTTAT
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
72 30 0.45
73 36 0.55
ACGTcount: A:0.36, C:0.04, G:0.19, T:0.41
Consensus pattern (73 bp):
GAAATGTTAAATGAATAGATGTTGAATAAATGGTATATCTAATGTGATTACTTGTATAAGTTTTA
TAACATGT
Found at i:28336999 original size:21 final size:21
Alignment explanation
Indices: 28336973--28337014 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
28336963 AGAATAGTTA
28336973 ATATTTGTTTGGCTTGGCACT
1 ATATTTGTTTGGCTTGGCACT
28336994 ATATTTGTTTGGCTTGGCACT
1 ATATTTGTTTGGCTTGGCACT
28337015 TAAGGAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.24, T:0.48
Consensus pattern (21 bp):
ATATTTGTTTGGCTTGGCACT
Found at i:28337505 original size:23 final size:22
Alignment explanation
Indices: 28337479--28337532 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
28337469 TTTTGGTGAC
*
28337479 TAAAATGATAACAAATTAAAAA-
1 TAAAATGATAA-AAATGAAAAAG
* *
28337501 TTAAATGATTAAAATGAAAAAG
1 TAAAATGATAAAAATGAAAAAG
28337523 TAAATATGAT
1 TAAA-ATGAT
28337533 GTAACATGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 9 0.35
22 12 0.46
23 5 0.19
ACGTcount: A:0.61, C:0.02, G:0.09, T:0.28
Consensus pattern (22 bp):
TAAAATGATAAAAATGAAAAAG
Found at i:28337520 original size:21 final size:22
Alignment explanation
Indices: 28337481--28337527 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
28337471 TTGGTGACTA
* *
28337481 AAATGATAACAAATTAAAAATT
1 AAATGATAACAAATGAAAAAGT
*
28337503 AAATGATTA-AAATGAAAAAGT
1 AAATGATAACAAATGAAAAAGT
28337524 AAAT
1 AAAT
28337528 ATGATGTAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.26
Consensus pattern (22 bp):
AAATGATAACAAATGAAAAAGT
Found at i:28355283 original size:33 final size:33
Alignment explanation
Indices: 28355236--28355302 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
28355226 GAGTTAGCAT
*
28355236 ATAGTAGACTGCAAGACCTAAGAGGCGACCCAG
1 ATAGTAGACCGCAAGACCTAAGAGGCGACCCAG
*
28355269 ATAGTAGACCGCAAGACCTAAGAGGCGATCCAG
1 ATAGTAGACCGCAAGACCTAAGAGGCGACCCAG
28355302 A
1 A
28355303 ACGGCACACG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.37, C:0.24, G:0.27, T:0.12
Consensus pattern (33 bp):
ATAGTAGACCGCAAGACCTAAGAGGCGACCCAG
Found at i:28359956 original size:43 final size:43
Alignment explanation
Indices: 28359895--28359981 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
28359885 GGTGGGCACT
28359895 TTAACATTGTTCCTATGTATCCGTATCTTGACAACATCTATTA
1 TTAACATTGTTCCTATGTATCCGTATCTTGACAACATCTATTA
28359938 TTAACATTGTTCCTATGTATCCGTATCTTGACAACATCTATTA
1 TTAACATTGTTCCTATGTATCCGTATCTTGACAACATCTATTA
28359981 T
1 T
28359982 GATAACAGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.43
Consensus pattern (43 bp):
TTAACATTGTTCCTATGTATCCGTATCTTGACAACATCTATTA
Found at i:28360977 original size:15 final size:16
Alignment explanation
Indices: 28360949--28360989 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
28360939 TATTATTATT
28360949 AAAAGTAAAGTAAATA-A
1 AAAAG-AAAGTAAA-AGA
28360966 AAAAGAAA-TAAAAGA
1 AAAAGAAAGTAAAAGA
28360981 AAAAGAAAG
1 AAAAGAAAG
28360990 ATAGAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 1 0.05
15 13 0.59
16 3 0.14
17 5 0.23
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.10
Consensus pattern (16 bp):
AAAAGAAAGTAAAAGA
Found at i:28379607 original size:33 final size:32
Alignment explanation
Indices: 28379560--28379624 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
28379550 AAATAATAGT
28379560 CAAATTAATAATAATACAAAAATTATACAATATA
1 CAAATTAATAATAATA-AAAAATTA-ACAATATA
* *
28379594 CAAA-TAATAATAATAAAATATTAATAATATA
1 CAAATTAATAATAATAAAAAATTAACAATATA
28379625 ATAGTGAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 7 0.24
32 7 0.24
33 11 0.38
34 4 0.14
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (32 bp):
CAAATTAATAATAATAAAAAATTAACAATATA
Found at i:28379613 original size:11 final size:11
Alignment explanation
Indices: 28379599--28379650 Score: 59
Period size: 11 Copynumber: 4.7 Consensus size: 11
28379589 ATATACAAAT
28379599 AATAATAATAA
1 AATAATAATAA
*
28379610 AATATTAATAA
1 AATAATAATAA
* * *
28379621 TATAATAGTGA
1 AATAATAATAA
*
28379632 AATGATAATAA
1 AATAATAATAA
28379643 AATAATAA
1 AATAATAA
28379651 GAATGAAGTT
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (11 bp):
AATAATAATAA
Found at i:28388430 original size:10 final size:10
Alignment explanation
Indices: 28388415--28388464 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
28388405 GAATTTTAGG
28388415 ATTTAT-TTT
1 ATTTATCTTT
28388424 CATTTATCTTT
1 -ATTTATCTTT
*
28388435 AATTATCTTT
1 ATTTATCTTT
*
28388445 ATTTAT-TTGC
1 ATTTATCTT-T
28388455 ATTTATCTTT
1 ATTTATCTTT
28388465 TAGACTTTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
9 2 0.06
10 26 0.79
11 5 0.15
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.66
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:28392152 original size:10 final size:10
Alignment explanation
Indices: 28392137--28392186 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
28392127 TAATTTTAGG
28392137 ATTTAT-TTT
1 ATTTATCTTT
28392146 CATTTATCTTT
1 -ATTTATCTTT
*
28392157 AATTATCTTT
1 ATTTATCTTT
*
28392167 ATTTAT-TTGC
1 ATTTATCTT-T
28392177 ATTTATCTTT
1 ATTTATCTTT
28392187 TAGAATTTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
9 2 0.06
10 26 0.79
11 5 0.15
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.66
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:28398610 original size:6 final size:6
Alignment explanation
Indices: 28398599--28398661 Score: 54
Period size: 6 Copynumber: 9.8 Consensus size: 6
28398589 CCAATCTTTA
* * * *
28398599 ATTTTT ATTTTT ACTTTT ATTTGT ATTTGT ATTTGTAT TTTTTT ATTTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTT-T-T ATTTTT A-TTTTT
28398650 ATTTATT ATTTT
1 ATTT-TT ATTTT
28398662 ATTATTTTCA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
6 30 0.64
7 13 0.28
8 4 0.09
ACGTcount: A:0.17, C:0.02, G:0.05, T:0.76
Consensus pattern (6 bp):
ATTTTT
Found at i:28398618 original size:12 final size:11
Alignment explanation
Indices: 28398601--28398664 Score: 60
Period size: 12 Copynumber: 5.6 Consensus size: 11
28398591 AATCTTTAAT
28398601 TTTTATTTTTA
1 TTTTATTTTTA
*
28398612 CTTTTATTTGTA
1 -TTTTATTTTTA
*
28398624 TTTGTATTTGTA
1 TTT-TATTTTTA
28398636 TTTT-TTTATT-
1 TTTTATTT-TTA
28398646 TTTTATTTATTA
1 TTTTATTT-TTA
28398658 TTTTATT
1 TTTTATT
28398665 ATTTTCAGAT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
10 7 0.15
11 11 0.24
12 28 0.61
ACGTcount: A:0.17, C:0.02, G:0.05, T:0.77
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:28398666 original size:15 final size:14
Alignment explanation
Indices: 28398603--28398669 Score: 57
Period size: 14 Copynumber: 4.5 Consensus size: 14
28398593 TCTTTAATTT
28398603 TTATTTTTACTTTTA
1 TTATTTTTA-TTTTA
*
28398618 TTTGTATTTGTATTTGTA
1 --T-TATTTTTATTT-TA
28398636 TT-TTTTTATTTT-
1 TTATTTTTATTTTA
28398648 TTATTTATTATTTTA
1 TTATTT-TTATTTTA
28398663 TTATTTT
1 TTATTTT
28398670 CAGATATTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
12 2 0.05
13 4 0.09
14 16 0.37
15 7 0.16
16 1 0.02
17 4 0.09
18 9 0.21
ACGTcount: A:0.18, C:0.01, G:0.04, T:0.76
Consensus pattern (14 bp):
TTATTTTTATTTTA
Found at i:28398666 original size:22 final size:21
Alignment explanation
Indices: 28398600--28398669 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 21
28398590 CAATCTTTAA
28398600 TTTTTATTTTTACTTTTATT-T
1 TTTTTATTTTTA-TTTTATTAT
* *
28398621 GTATTTGTATTTGTATTTTTTTAT
1 -T-TTT-TATTTTTATTTTATTAT
28398645 TTTTTATTTATTATTTTATTAT
1 TTTTTATTT-TTATTTTATTAT
28398667 TTT
1 TTT
28398670 CAGATATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
21 5 0.12
22 17 0.43
23 10 0.25
24 8 0.20
ACGTcount: A:0.17, C:0.01, G:0.04, T:0.77
Consensus pattern (21 bp):
TTTTTATTTTTATTTTATTAT
Found at i:28402481 original size:20 final size:20
Alignment explanation
Indices: 28402456--28402513 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
28402446 TGCATATGTA
* *
28402456 CAGGCCATACGGGCATGTTC
1 CAGGCCACACGGGCATGTCC
*
28402476 CAGGCCACACGGGCGTGTCC
1 CAGGCCACACGGGCATGTCC
*
28402496 CAAGCCACACGGGCATGT
1 CAGGCCACACGGGCATGT
28402514 GCCCCTATCT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.21, C:0.34, G:0.31, T:0.14
Consensus pattern (20 bp):
CAGGCCACACGGGCATGTCC
Found at i:28408970 original size:93 final size:93
Alignment explanation
Indices: 28408858--28409028 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
28408848 GCCCATAAGT
* *
28408858 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
28408923 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
28408951 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
28409016 CGAGTTCGGATGC
66 CGAGTTCGGATGC
28409029 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:28409025 original size:46 final size:46
Alignment explanation
Indices: 28408850--28409025 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
28408840 TGTAACCCGC
* * *
28408850 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
28408896 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
28408946 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
28408989 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
28409026 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 64 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:28415573 original size:21 final size:21
Alignment explanation
Indices: 28415549--28415591 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
28415539 ATGATATATA
28415549 TTAGGTAAAAATCTAGAGTTT
1 TTAGGTAAAAATCTAGAGTTT
28415570 TTAGGTAAAAATCTAGAGTTT
1 TTAGGTAAAAATCTAGAGTTT
28415591 T
1 T
28415592 CTTCAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.40
Consensus pattern (21 bp):
TTAGGTAAAAATCTAGAGTTT
Found at i:28424470 original size:39 final size:38
Alignment explanation
Indices: 28424427--28424520 Score: 100
Period size: 39 Copynumber: 2.4 Consensus size: 38
28424417 ACCAATATGG
*
28424427 CACCCAGTGCCTCATCGG-ATAGTTCGAAGTAATAGTTGA
1 CACCCAGTGCCTCATCGGCATAG-CCGAAGTAA-AGTTGA
* * * *
28424466 CACCCAGTGTCTCCTCGGCCTAGCCGAAGTAAAGTTGG
1 CACCCAGTGCCTCATCGGCATAGCCGAAGTAAAGTTGA
* *
28424504 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
28424521 AATCTATCCG
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
38 18 0.40
39 24 0.53
40 3 0.07
ACGTcount: A:0.24, C:0.30, G:0.22, T:0.23
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCATAGCCGAAGTAAAGTTGA
Found at i:28425480 original size:12 final size:12
Alignment explanation
Indices: 28425465--28425495 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
28425455 TTCTCTTTTA
28425465 TTTTTCTTTCCC
1 TTTTTCTTTCCC
*
28425477 TTTTTCTTTCTC
1 TTTTTCTTTCCC
28425489 TTTTTCT
1 TTTTTCT
28425496 CCCCTGCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTCTTTCCC
Found at i:28427594 original size:96 final size:96
Alignment explanation
Indices: 28427430--28427803 Score: 642
Period size: 96 Copynumber: 3.9 Consensus size: 96
28427420 TTTAAGAATG
28427430 TGTTGGGCTGAGTAACCGAGGTGAGGTGCTTGGCTGTCAAATCTCTTCGCGTCAAAAGGTTCGAT
1 TGTTGGGCTGAGTAACCGAGGTGAGGTGCTTGGCTGTCAAATCTCTTCGCGTCAAAAGGTTCGAT
28427495 ATGTTCTTAAGAAAAATAAAAATTAGGAGTA
66 ATGTTCTTAAGAAAAATAAAAATTAGGAGTA
28427526 TGTTGGGCTGAGTAACCGAGGTGAGGTGCTTGGCTGTCAAATCTCTTCGCGTCAAAAGGTTCGAT
1 TGTTGGGCTGAGTAACCGAGGTGAGGTGCTTGGCTGTCAAATCTCTTCGCGTCAAAAGGTTCGAT
28427591 ATGTTCTTAAGAAAAATAAAAATTAGGAGTA
66 ATGTTCTTAAGAAAAATAAAAATTAGGAGTA
28427622 TGTTGGGCTGAGTAACCGAGGTGAGGTGCTTGGCTGTCAAATCTCTTCGCGTCAAAAGGTTCGAT
1 TGTTGGGCTGAGTAACCGAGGTGAGGTGCTTGGCTGTCAAATCTCTTCGCGTCAAAAGGTTCGAT
28427687 ATGTTCTTAAGAAAAATAAAAATTAGGAGTA
66 ATGTTCTTAAGAAAAATAAAAATTAGGAGTA
* * * ** * * *
28427718 TGTTGGGCTGAGTAACCGGGGCGGGGTGCTTGGCTGTCATCTCTCTTTGCGTCAAATGGTTCAAT
1 TGTTGGGCTGAGTAACCGAGGTGAGGTGCTTGGCTGTCAAATCTCTTCGCGTCAAAAGGTTCGAT
*
28427783 ATATT-TCTAAGTAAAAATAAA
66 ATGTTCT-TAAG-AAAAATAAA
28427804 TAAATAAAAC
Statistics
Matches: 267, Mismatches: 9, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
95 1 0.00
96 257 0.96
97 9 0.03
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (96 bp):
TGTTGGGCTGAGTAACCGAGGTGAGGTGCTTGGCTGTCAAATCTCTTCGCGTCAAAAGGTTCGAT
ATGTTCTTAAGAAAAATAAAAATTAGGAGTA
Found at i:28428458 original size:10 final size:10
Alignment explanation
Indices: 28428445--28428494 Score: 75
Period size: 10 Copynumber: 5.0 Consensus size: 10
28428435 ATTTTTTTTC
28428445 ATTTATCTTT
1 ATTTATCTTT
28428455 ATTTATCTTT
1 ATTTATCTTT
*
28428465 AATTATCTTT
1 ATTTATCTTT
28428475 ATTTAT-TTGT
1 ATTTATCTT-T
28428485 ATTTATCTTT
1 ATTTATCTTT
28428495 TAGAATTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
9 2 0.06
10 32 0.89
11 2 0.06
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:28435522 original size:16 final size:17
Alignment explanation
Indices: 28435498--28435530 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
28435488 TGAACTCATC
*
28435498 ATACTTTATTC-TTTCA
1 ATACATTATTCATTTCA
28435514 ATACATTATTCATTTCA
1 ATACATTATTCATTTCA
28435531 TCTCATAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.30, C:0.18, G:0.00, T:0.52
Consensus pattern (17 bp):
ATACATTATTCATTTCA
Found at i:28435791 original size:57 final size:58
Alignment explanation
Indices: 28435730--28435925 Score: 159
Period size: 57 Copynumber: 3.6 Consensus size: 58
28435720 TTGTGTCCAA
* *
28435730 CATATGCTCATAAGAGTTTA-ATCAGGATTACCTGTTCGGGCTAAATTCTATCTATCT
1 CATATGCTCATAAGAGCTTATATTAGGATTACCTGTTCGGGCTAAATTCTATCTATCT
* * * * *
28435787 CATATGTTCA-AGAGGGCTTATATTAGGATTA---------GCTAAA-TCT-TGTGTCCAA
1 CATATGCTCATA-AGAGCTTATATTAGGATTACCTGTTCGGGCTAAATTCTATCTAT-C-T
*
28435836 CATATGCTCATAAGAGCTTA-ATTAGGATTACCTGTTCGGGCTAAATCCTATCTATCT
1 CATATGCTCATAAGAGCTTATATTAGGATTACCTGTTCGGGCTAAATTCTATCTATCT
* * * *
28435893 CATATGTTCAAAAGGGTTTATATTAGGATTACC
1 CATATGCTCATAAGAGCTTATATTAGGATTACC
28435926 AGTCTAGGCT
Statistics
Matches: 105, Mismatches: 17, Indels: 33
0.68 0.11 0.21
Matches are distributed among these distances:
47 3 0.03
48 14 0.13
49 22 0.21
50 1 0.01
56 1 0.01
57 37 0.35
58 24 0.23
59 3 0.03
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (58 bp):
CATATGCTCATAAGAGCTTATATTAGGATTACCTGTTCGGGCTAAATTCTATCTATCT
Found at i:28435899 original size:106 final size:106
Alignment explanation
Indices: 28435714--28435923 Score: 375
Period size: 106 Copynumber: 2.0 Consensus size: 106
28435704 TTGTCCAAGA
* *
28435714 TAAATCTTGTGTCCAACATATGCTCATAAGAGTTTAATCAGGATTACCTGTTCGGGCTAAATTCT
1 TAAATCTTGTGTCCAACATATGCTCATAAGAGCTTAATCAGGATTACCTGTTCGGGCTAAATCCT
*
28435779 ATCTATCTCATATGTTCAAGAGGGCTTATATTAGGATTAGC
66 ATCTATCTCATATGTTCAAAAGGGCTTATATTAGGATTAGC
*
28435820 TAAATCTTGTGTCCAACATATGCTCATAAGAGCTTAATTAGGATTACCTGTTCGGGCTAAATCCT
1 TAAATCTTGTGTCCAACATATGCTCATAAGAGCTTAATCAGGATTACCTGTTCGGGCTAAATCCT
*
28435885 ATCTATCTCATATGTTCAAAAGGGTTTATATTAGGATTA
66 ATCTATCTCATATGTTCAAAAGGGCTTATATTAGGATTA
28435924 CCAGTCTAGG
Statistics
Matches: 99, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
106 99 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (106 bp):
TAAATCTTGTGTCCAACATATGCTCATAAGAGCTTAATCAGGATTACCTGTTCGGGCTAAATCCT
ATCTATCTCATATGTTCAAAAGGGCTTATATTAGGATTAGC
Found at i:28437504 original size:7 final size:8
Alignment explanation
Indices: 28437486--28437526 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
28437476 AGGAGGACTT
28437486 GATTGAAA
1 GATTGAAA
28437494 GATTG-AA
1 GATTGAAA
28437501 GATTGAAA
1 GATTGAAA
28437509 GATT-AAA
1 GATTGAAA
*
28437516 GATTCAAA
1 GATTGAAA
28437524 GAT
1 GAT
28437527 GACTGGATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 14 0.45
8 17 0.55
ACGTcount: A:0.49, C:0.02, G:0.22, T:0.27
Consensus pattern (8 bp):
GATTGAAA
Found at i:28437506 original size:15 final size:15
Alignment explanation
Indices: 28437486--28437526 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
28437476 AGGAGGACTT
*
28437486 GATTGAAAGATTGAA
1 GATTGAAAGATTAAA
28437501 GATTGAAAGATTAAA
1 GATTGAAAGATTAAA
*
28437516 GATTCAAAGAT
1 GATTGAAAGAT
28437527 GACTGGATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.49, C:0.02, G:0.22, T:0.27
Consensus pattern (15 bp):
GATTGAAAGATTAAA
Found at i:28437678 original size:13 final size:13
Alignment explanation
Indices: 28437660--28437714 Score: 71
Period size: 13 Copynumber: 4.5 Consensus size: 13
28437650 AATTTAAAAT
*
28437660 TATTTAGTGATAA
1 TATTTAGTAATAA
28437673 TATTTAGTAATAA
1 TATTTAGTAATAA
*
28437686 TATTTA--AA-AT
1 TATTTAGTAATAA
28437696 TATTTAGTAATAA
1 TATTTAGTAATAA
28437709 TATTTA
1 TATTTA
28437715 AGAAAAATCT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
10 7 0.19
11 2 0.06
12 2 0.06
13 25 0.69
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (13 bp):
TATTTAGTAATAA
Found at i:28438602 original size:23 final size:22
Alignment explanation
Indices: 28438542--28438602 Score: 54
Period size: 23 Copynumber: 2.7 Consensus size: 22
28438532 TTATTTATAC
28438542 ATTTATTTTATTTTCTTAAATTT
1 ATTTATTTTATTTT-TTAAATTT
* *
28438565 ATTTATTTGCA-TTTTTGAATCTGT
1 ATTTATTT-TATTTTTTAAAT-T-T
28438589 -TTTATTTTATTTTT
1 ATTTATTTTATTTTT
28438603 CATATTTTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
22 6 0.19
23 23 0.74
24 2 0.06
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.69
Consensus pattern (22 bp):
ATTTATTTTATTTTTTAAATTT
Found at i:28442249 original size:43 final size:43
Alignment explanation
Indices: 28442201--28442428 Score: 294
Period size: 43 Copynumber: 5.3 Consensus size: 43
28442191 GAACACATAG
*
28442201 TTCGCCCATTGGCAAATACTATACACAAGCAGACTTTATACAA
1 TTCGCCCATTGGCGAATACTATACACAAGCAGACTTTATACAA
*** *
28442244 TTCGCCCATTAATGAATACTATACACAAGCATACTTTATACAA
1 TTCGCCCATTGGCGAATACTATACACAAGCAGACTTTATACAA
* * * * *
28442287 TTCGCCTATTGGTGAATACTATACACAAACAGACTGTATACAG
1 TTCGCCCATTGGCGAATACTATACACAAGCAGACTTTATACAA
* * * * *
28442330 TTTGCCAATTGGTGAATACTATACATAAGCAAACTTTATACAA
1 TTCGCCCATTGGCGAATACTATACACAAGCAGACTTTATACAA
*
28442373 TTCGCCCATTGGCGAATACTATACACAAGCATACTTTATACAA
1 TTCGCCCATTGGCGAATACTATACACAAGCAGACTTTATACAA
* *
28442416 TTCACCTATTGGC
1 TTCGCCCATTGGC
28442429 AAAATACAGA
Statistics
Matches: 159, Mismatches: 26, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 159 1.00
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.29
Consensus pattern (43 bp):
TTCGCCCATTGGCGAATACTATACACAAGCAGACTTTATACAA
Found at i:28442542 original size:47 final size:47
Alignment explanation
Indices: 28442488--28442582 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
28442478 CTTACATTAC
28442488 ACCTATACATTTAGGTAGACAACCTTCTTTGTGTTGGCCAAAACCCT
1 ACCTATACATTTAGGTAGACAACCTTCTTTGTGTTGGCCAAAACCCT
28442535 ACCTATACATTTAGGTAGACAACCTTCTTTGTGTTGGCCAAAACCCT
1 ACCTATACATTTAGGTAGACAACCTTCTTTGTGTTGGCCAAAACCCT
28442582 A
1 A
28442583 GTCCATGCTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (47 bp):
ACCTATACATTTAGGTAGACAACCTTCTTTGTGTTGGCCAAAACCCT
Found at i:28442787 original size:15 final size:15
Alignment explanation
Indices: 28442767--28442796 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28442757 AAACCAAAAT
*
28442767 AATATTAATGGTCCA
1 AATATTAAGGGTCCA
28442782 AATATTAAGGGTCCA
1 AATATTAAGGGTCCA
28442797 TTTACAACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (15 bp):
AATATTAAGGGTCCA
Found at i:28444566 original size:10 final size:10
Alignment explanation
Indices: 28444551--28444595 Score: 56
Period size: 10 Copynumber: 4.3 Consensus size: 10
28444541 ATTATTTCAT
28444551 TTTTTTATTA
1 TTTTTTATTA
28444561 TTTTTTATTA
1 TTTTTTATTA
28444571 TTTTATT-TTA
1 TTTT-TTATTA
28444581 TTTGTTATATTA
1 TTT-TT-TATTA
28444593 TTT
1 TTT
28444596 CTCTCACTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
10 21 0.68
11 4 0.13
12 6 0.19
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (10 bp):
TTTTTTATTA
Found at i:28444702 original size:19 final size:19
Alignment explanation
Indices: 28444665--28444707 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
28444655 CTTGTTATGG
*
28444665 ATATTAGTATTATAATTTA
1 ATATTACTATTATAATTTA
* **
28444684 TTATTACTATTATTCTTTA
1 ATATTACTATTATAATTTA
28444703 ATATT
1 ATATT
28444708 TTATTGCGGA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (19 bp):
ATATTACTATTATAATTTA
Found at i:28445118 original size:30 final size:30
Alignment explanation
Indices: 28445082--28445142 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
28445072 TCAAATGTCG
28445082 TGTCCTAACTTACGGGATGTGACATTCGAT
1 TGTCCTAACTTACGGGATGTGACATTCGAT
*
28445112 TGTCCTAACTTATGGGATGTGACATTCGAT
1 TGTCCTAACTTACGGGATGTGACATTCGAT
28445142 T
1 T
28445143 ATCTCGATAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (30 bp):
TGTCCTAACTTACGGGATGTGACATTCGAT
Found at i:28449250 original size:6 final size:6
Alignment explanation
Indices: 28449230--28449264 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
28449220 ATGGAATTTT
*
28449230 AAAT-A AAATAG AAATAA AAATAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
28449265 TAGTAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:28449257 original size:18 final size:17
Alignment explanation
Indices: 28449230--28449275 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
28449220 ATGGAATTTT
*
28449230 AAATAAAATAGAAATAA
1 AAATAAAATAAAAATAA
28449247 AAATAAAAATAAAAATAA
1 AAAT-AAAATAAAAATAA
* *
28449265 TAGTAAAATAA
1 AAATAAAATAA
28449276 GCACACCCGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (17 bp):
AAATAAAATAAAAATAA
Found at i:28460222 original size:20 final size:20
Alignment explanation
Indices: 28460157--28460224 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
28460147 ACAAGAGCAT
*
28460157 CGAAGTGTAGACAGGGGCA-
1 CGAAGTGTACACAGGGGCAC
* * * *
28460176 CAAATGTGCACACAGGGACCCC
1 CGAA-GTGTACACAGGG-GCAC
*
28460198 CGAAGTGTATACAGGGGCAC
1 CGAAGTGTACACAGGGGCAC
28460218 CGAAGTG
1 CGAAGTG
28460225 CAAATCCCGT
Statistics
Matches: 36, Mismatches: 10, Indels: 5
0.71 0.20 0.10
Matches are distributed among these distances:
19 3 0.08
20 19 0.53
21 11 0.31
22 3 0.08
ACGTcount: A:0.31, C:0.24, G:0.34, T:0.12
Consensus pattern (20 bp):
CGAAGTGTACACAGGGGCAC
Found at i:28463516 original size:43 final size:43
Alignment explanation
Indices: 28463468--28463621 Score: 125
Period size: 43 Copynumber: 3.6 Consensus size: 43
28463458 TAATTGCATA
* * *
28463468 TAAGACCATGTCTGGTACATTGGCATTG-TATTGAGATTACGTG
1 TAAGACCATGTCTGGGACATTGGCATCGTTAAT-AGATTACGTG
** * * *
28463511 TAAGACTGTATCTGGGACATTGGCATCGTTAATCGATTTCGTG
1 TAAGACCATGTCTGGGACATTGGCATCGTTAATAGATTACGTG
* * * * * *
28463554 TAAGACCCTGTCTGGGACAGTGGCATCGATATGTA-ATAACATG
1 TAAGACCATGTCTGGGACATTGGCATCGTTA-ATAGATTACGTG
* *
28463597 TAAGACCATATCTGGGATA-TGGCAT
1 TAAGACCATGTCTGGGACATTGGCAT
28463622 TGTTCGAGCT
Statistics
Matches: 88, Mismatches: 21, Indels: 5
0.77 0.18 0.04
Matches are distributed among these distances:
42 6 0.07
43 78 0.89
44 4 0.05
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.31
Consensus pattern (43 bp):
TAAGACCATGTCTGGGACATTGGCATCGTTAATAGATTACGTG
Found at i:28468791 original size:3 final size:3
Alignment explanation
Indices: 28468783--28468807 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
28468773 GGTCCACTTC
28468783 GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT G
28468808 TACCCTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:28470817 original size:31 final size:31
Alignment explanation
Indices: 28470779--28470854 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
28470769 GAGATTTAAT
* *
28470779 AGTTGAGTGACTAAAACGAAAATACCCTAAA
1 AGTTGAGTGACCAAAACGAAAACACCCTAAA
*
28470810 AGTTGAGTGACCAAAATGAAAACACCCTAAA
1 AGTTGAGTGACCAAAACGAAAACACCCTAAA
* *
28470841 AGTAGAGTTACCAA
1 AGTTGAGTGACCAA
28470855 CTAGATAGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.18
Consensus pattern (31 bp):
AGTTGAGTGACCAAAACGAAAACACCCTAAA
Found at i:28471574 original size:23 final size:22
Alignment explanation
Indices: 28471546--28471606 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 22
28471536 TTTATTAAAA
28471546 ATATTTATTTTAATATTTTTAGT
1 ATATTTATTTTAATATTTTT-GT
* * * *
28471569 ATATTTGTTGTATTATTTTTTT
1 ATATTTATTTTAATATTTTTGT
* *
28471591 AAATTTATTTTTATAT
1 ATATTTATTTTAATAT
28471607 ATAAAAAATT
Statistics
Matches: 29, Mismatches: 9, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
22 12 0.41
23 17 0.59
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (22 bp):
ATATTTATTTTAATATTTTTGT
Found at i:28471775 original size:3 final size:3
Alignment explanation
Indices: 28471767--28471798 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
28471757 CTTGCCCTGC
*
28471767 TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
28471799 TATCTTTCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:28473742 original size:24 final size:24
Alignment explanation
Indices: 28473715--28473768 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
28473705 AAAATAAAGC
28473715 TTTGTTAATTATATTCTCATACAA
1 TTTGTTAATTATATTCTCATACAA
28473739 TTTGTTAATTATATTCTCATACAA
1 TTTGTTAATTATATTCTCATACAA
*
28473763 TCTGTT
1 TTTGTT
28473769 CTTCATTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.30, C:0.13, G:0.06, T:0.52
Consensus pattern (24 bp):
TTTGTTAATTATATTCTCATACAA
Found at i:28477322 original size:2 final size:2
Alignment explanation
Indices: 28477315--28477344 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
28477305 CAGCTGCAGT
28477315 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
28477345 CTGAGAGTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:28477895 original size:31 final size:31
Alignment explanation
Indices: 28477827--28477895 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
28477817 CTTAACAACC
* *
28477827 CAATAACTTAAATAAAAATTTTTGAATAATT
1 CAATAATTTAAATAAAAATTTTCGAATAATT
* *
28477858 TAATAATTTAAATAAAAATTTTCGAATAGTT
1 CAATAATTTAAATAAAAATTTTCGAATAATT
28477889 CAATAAT
1 CAATAAT
28477896 CAAATTGTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (31 bp):
CAATAATTTAAATAAAAATTTTCGAATAATT
Found at i:28484646 original size:28 final size:28
Alignment explanation
Indices: 28484578--28484637 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
28484568 TCGGATTTAG
28484578 AAATGTTACCTTTTTAGAGTAAAATCTT
1 AAATGTTACCTTTTTAGAGTAAAATCTT
28484606 AAATGTTACCTTTTTAGAGTAAAATCTT
1 AAATGTTACCTTTTTAGAGTAAAATCTT
28484634 AAAT
1 AAAT
28484638 CCGTACTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (28 bp):
AAATGTTACCTTTTTAGAGTAAAATCTT
Found at i:28487731 original size:84 final size:86
Alignment explanation
Indices: 28487586--28487780 Score: 234
Period size: 84 Copynumber: 2.3 Consensus size: 86
28487576 AAAAGTTTTT
* * **
28487586 AAAATTTTTCAAAAAAAGCAATTAAGTCTTTTTTTTTTACACTCAATTGAACACTTAAACTTTCA
1 AAAATTCTTCAAAAAAAGCAATTAAGACTTAATTTTTTACACTCAATTGAACACTTAAACTTTCA
* * **
28487651 AAATATATCGAAAAGGTCCTC
66 AAATACATCAAAAAGACCCTC
* *** *
28487672 AAACTTCTTCAAAAAAAGCAATTAAGAC-TAATTTTTT-CACTCAATTGGGTACTTGAACTTTCA
1 AAAATTCTTCAAAAAAAGCAATTAAGACTTAATTTTTTACACTCAATTGAACACTTAAACTTTCA
*
28487735 AAATGCATCAAAAAGACCCTC
66 AAATACATCAAAAAGACCCTC
*
28487756 AAAATTTTTCAAAAAAA-CAATTAAG
1 AAAATTCTTCAAAAAAAGCAATTAAG
28487781 TCCATGCTCT
Statistics
Matches: 93, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
83 8 0.09
84 53 0.57
85 7 0.08
86 25 0.27
ACGTcount: A:0.43, C:0.17, G:0.08, T:0.32
Consensus pattern (86 bp):
AAAATTCTTCAAAAAAAGCAATTAAGACTTAATTTTTTACACTCAATTGAACACTTAAACTTTCA
AAATACATCAAAAAGACCCTC
Found at i:28487855 original size:19 final size:20
Alignment explanation
Indices: 28487825--28487872 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
28487815 AATAAATAAT
28487825 AAATAA-TAAATTTT-AGAA
1 AAATAATTAAATTTTAAGAA
*
28487843 AAATAATTAAATTTTAATAA
1 AAATAATTAAATTTTAAGAA
28487863 AAAT-ATTAAA
1 AAATAATTAAA
28487873 AATTAGGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 6 0.22
19 14 0.52
20 7 0.26
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (20 bp):
AAATAATTAAATTTTAAGAA
Found at i:28488142 original size:10 final size:10
Alignment explanation
Indices: 28488127--28488217 Score: 52
Period size: 9 Copynumber: 9.6 Consensus size: 10
28488117 TTCTTACGAC
28488127 TTTATAAATT
1 TTTATAAATT
28488137 TTTAT-AATT
1 TTTATAAATT
* *
28488146 TTTTTATATT
1 TTTATAAATT
* *
28488156 TCTATATA-T
1 TTTATAAATT
28488165 TTTAT-AATT
1 TTTATAAATT
* *
28488174 TTTTTATGATT
1 TTTATA-AATT
28488185 TTTATAAGA-T
1 TTTATAA-ATT
28488195 TTTAT--ATT
1 TTTATAAATT
*
28488203 TTTA-CAATT
1 TTTATAAATT
28488212 TTTATA
1 TTTATA
28488218 TTTCTTTCTA
Statistics
Matches: 61, Mismatches: 11, Indels: 18
0.68 0.12 0.20
Matches are distributed among these distances:
7 1 0.02
8 6 0.10
9 25 0.41
10 20 0.33
11 9 0.15
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (10 bp):
TTTATAAATT
Found at i:28488161 original size:29 final size:27
Alignment explanation
Indices: 28488127--28488205 Score: 97
Period size: 28 Copynumber: 2.8 Consensus size: 27
28488117 TTCTTACGAC
28488127 TTTATAAATTTTTATAATTTTTTTATAT
1 TTTATAAA-TTTTATAATTTTTTTATAT
*
28488155 TTCTATATATTTTATAATTTTTTTATGATT
1 TT-TATAAATTTTATAATTTTTTTAT-A-T
28488185 TTTATAAGATTTTAT-ATTTTT
1 TTTATAA-ATTTTATAATTTTT
28488206 ACAATTTTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
28 19 0.42
29 16 0.36
30 10 0.22
ACGTcount: A:0.29, C:0.01, G:0.03, T:0.67
Consensus pattern (27 bp):
TTTATAAATTTTATAATTTTTTTATAT
Found at i:28488176 original size:28 final size:30
Alignment explanation
Indices: 28488110--28488205 Score: 103
Period size: 29 Copynumber: 3.3 Consensus size: 30
28488100 TTACATTTTG
* * *
28488110 TATAATTTTCTTACGACTT-TATAA-ATTTT
1 TATAATTTTTTTATGATTTCTATAAGA-TTT
*
28488139 TATAATTTTTTTAT-ATTTCTAT-ATATTT
1 TATAATTTTTTTATGATTTCTATAAGATTT
*
28488167 TATAATTTTTTTATGATTTTTATAAGATTT
1 TATAATTTTTTTATGATTTCTATAAGATTT
28488197 TAT-ATTTTT
1 TATAATTTTT
28488206 ACAATTTTTA
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
28 21 0.36
29 29 0.50
30 8 0.14
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.64
Consensus pattern (30 bp):
TATAATTTTTTTATGATTTCTATAAGATTT
Found at i:28488232 original size:19 final size:17
Alignment explanation
Indices: 28488133--28488240 Score: 63
Period size: 19 Copynumber: 5.8 Consensus size: 17
28488123 CGACTTTATA
**
28488133 AATTTTTATAATTTTTTT
1 AATTTTTAT-ATTTTTAC
* *
28488151 ATATTTCTATATATTTTAT
1 A-ATTTTTATAT-TTTTAC
*
28488170 AATTTTTTTATGATTTTTAT
1 AA--TTTTTAT-ATTTTTAC
*
28488190 AAGATTTTATATTTTTAC
1 AA-TTTTTATATTTTTAC
*
28488208 AATTTTTATATTTCTTTC
1 AATTTTTATATTT-TTAC
28488226 TAATTTTTAATATTT
1 -AATTTTT-ATATTT
28488241 GATTTTTTAT
Statistics
Matches: 74, Mismatches: 8, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
17 10 0.14
18 16 0.22
19 26 0.35
20 20 0.27
21 2 0.03
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.66
Consensus pattern (17 bp):
AATTTTTATATTTTTAC
Found at i:28491562 original size:50 final size:51
Alignment explanation
Indices: 28491497--28491599 Score: 154
Period size: 50 Copynumber: 2.0 Consensus size: 51
28491487 CTTTTGTTTG
* * * * *
28491497 TTTCATATTATATTTTAATCATTTATGTTTGAAATGTTATG-TTTAGTCAC
1 TTTCAGATTACATTTTAATCACTTATGTTTGAAATGATACGTTTTAGTCAC
28491547 TTTCAGATTACATTTTAATCACTTATGTTTGAAATGATACGTTTTAGTCAC
1 TTTCAGATTACATTTTAATCACTTATGTTTGAAATGATACGTTTTAGTCAC
28491598 TT
1 TT
28491600 ACATTTTTGT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
50 36 0.77
51 11 0.23
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.50
Consensus pattern (51 bp):
TTTCAGATTACATTTTAATCACTTATGTTTGAAATGATACGTTTTAGTCAC
Found at i:28495905 original size:20 final size:20
Alignment explanation
Indices: 28495880--28495922 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
28495870 TGTGATGAAC
*
28495880 CAGGGTTGAGTATGTTCAAT
1 CAGGGTTGAGTACGTTCAAT
28495900 CAGGGTTGAGTACGTTCAAT
1 CAGGGTTGAGTACGTTCAAT
28495920 CAG
1 CAG
28495923 TGATGAATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.30
Consensus pattern (20 bp):
CAGGGTTGAGTACGTTCAAT
Found at i:28496104 original size:244 final size:244
Alignment explanation
Indices: 28495659--28496119 Score: 780
Period size: 244 Copynumber: 1.9 Consensus size: 244
28495649 GGAAACGCAA
* * * *
28495659 GGTTGAGTACGTTCAATCAGTGATGAATTTATGGATAAGACCATGGTTAAATCATGACATAGTGT
1 GGTTGAGTACGTTCAATCAGTGATGAATTGACGGATAAGACCATGGTTAAACCATGACAAAGTGT
28495724 GAAATGTAAGACCATAATGAAGCTATGGCATTATAGTGCAAAACCATAACTGGGTTATGGCATTG
66 GAAATGTAAGACCATAATGAAGCTATGGCATTATAGTGCAAAACCATAACTGGGTTATGGCATTG
*
28495789 TGAAAGTGAACGTAAGACCATAATTGAATCATGGCAGTTATATGTATCTGCAAAAGTGTAATCAC
131 TGAAAGTGAACGTAAGACCATAATTGAATCATGGCAGTTATATGTATCTGCAAAAGTGCAATCAC
28495854 AGCTAAGCTATGACAATGTGATGAACCAGGGTTGAGTATGTTCAATCAG
196 AGCTAAGCTATGACAATGTGATGAACCAGGGTTGAGTATGTTCAATCAG
*
28495903 GGTTGAGTACGTTCAATCAGTGATGAATTGACGGATAAGACCATGGTTAAACCATGATAAAGTGT
1 GGTTGAGTACGTTCAATCAGTGATGAATTGACGGATAAGACCATGGTTAAACCATGACAAAGTGT
*
28495968 GAAATGTAAGACCATAGTTG-AGCTATGGCATTATAGTGCAAAACCATAACTGGGTTATGGCATT
66 GAAATGTAAGACCATA-ATGAAGCTATGGCATTATAGTGCAAAACCATAACTGGGTTATGGCATT
* * * * *
28496032 GTGAAAGTGAACGTAAGACCATGATTGAATCATGGCATTTATATGTGTGTGCAAGAGTGCAATCA
130 GTGAAAGTGAACGTAAGACCATAATTGAATCATGGCAGTTATATGTATCTGCAAAAGTGCAATCA
* *
28496097 TAGCTAAGCTATGGCAATGTGAT
195 CAGCTAAGCTATGACAATGTGAT
28496120 AAAGTGTGCG
Statistics
Matches: 202, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
244 200 0.99
245 2 0.01
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.28
Consensus pattern (244 bp):
GGTTGAGTACGTTCAATCAGTGATGAATTGACGGATAAGACCATGGTTAAACCATGACAAAGTGT
GAAATGTAAGACCATAATGAAGCTATGGCATTATAGTGCAAAACCATAACTGGGTTATGGCATTG
TGAAAGTGAACGTAAGACCATAATTGAATCATGGCAGTTATATGTATCTGCAAAAGTGCAATCAC
AGCTAAGCTATGACAATGTGATGAACCAGGGTTGAGTATGTTCAATCAG
Found at i:28499229 original size:47 final size:47
Alignment explanation
Indices: 28499163--28499257 Score: 113
Period size: 46 Copynumber: 2.0 Consensus size: 47
28499153 TGGTTTATCC
*
28499163 ACATTTCTGTCTAGCAGCTTGTCTGCAAGTAT-GATGGCTTGACCACAT
1 ACATTTCTGTCTAGCAGCTTGGCTGCAA-TATAG-TGGCTTGACCACAT
* * * *
28499211 ACATTTGT-TCTAGTAGCTTGGCTGTAATATAGTGGTTTGACCACAT
1 ACATTTCTGTCTAGCAGCTTGGCTGCAATATAGTGGCTTGACCACAT
28499257 A
1 A
28499258 TATTCGATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
46 17 0.41
47 17 0.41
48 7 0.17
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (47 bp):
ACATTTCTGTCTAGCAGCTTGGCTGCAATATAGTGGCTTGACCACAT
Found at i:28501735 original size:22 final size:23
Alignment explanation
Indices: 28501675--28501735 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
28501665 TACAAAACAC
* * *
28501675 CAGTAGGCATCAAAATGCTTTAA
1 CAGTAGGCACCAAAGTGCTTGAA
** *
28501698 CAGTAGGCACTGAAGTG-TTGAG
1 CAGTAGGCACCAAAGTGCTTGAA
28501720 CAGTAGGCACCAAAGT
1 CAGTAGGCACCAAAGT
28501736 ACGAATCAGT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
22 17 0.57
23 13 0.43
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.21
Consensus pattern (23 bp):
CAGTAGGCACCAAAGTGCTTGAA
Found at i:28501745 original size:22 final size:23
Alignment explanation
Indices: 28501720--28501774 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
28501710 AAGTGTTGAG
*
28501720 CAGTAGGCAC-CAAAGTACGAAT
1 CAGTAGGCACTCAAAGTACAAAT
*
28501742 CAGTAGGC-CTCGAAGTACAAAT
1 CAGTAGGCACTCAAAGTACAAAT
*
28501764 CAGAAGGCACT
1 CAGTAGGCACT
28501775 ATAGTGCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.04
22 25 0.89
23 2 0.07
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (23 bp):
CAGTAGGCACTCAAAGTACAAAT
Found at i:28515395 original size:51 final size:51
Alignment explanation
Indices: 28515337--28515437 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 51
28515327 TCTTGTTCTT
* *
28515337 CCTCCTCTTATCTTTTTCTTTTCTCGCTTTCTTCCACTAAAATTTTCTATC
1 CCTCCTCTTATCTTTTTCTTTTCCCACTTTCTTCCACTAAAATTTTCTATC
28515388 CCTCCTCTTATCTTTTTCTTTTCCCACTTTCTTCCACTAAAATTTTCTAT
1 CCTCCTCTTATCTTTTTCTTTTCCCACTTTCTTCCACTAAAATTTTCTAT
28515438 TCTTTTCTTG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.15, C:0.32, G:0.01, T:0.52
Consensus pattern (51 bp):
CCTCCTCTTATCTTTTTCTTTTCCCACTTTCTTCCACTAAAATTTTCTATC
Found at i:28518448 original size:42 final size:43
Alignment explanation
Indices: 28518397--28518492 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 43
28518387 TGAGATTTAC
* * * *
28518397 ATGTAAGACCATATCTGGAACATAGGCATCATATCT-AATTTT
1 ATGTAAGACCATATCTGGAACAGAGGCATCAAAACTAAATTAT
* * * *
28518439 GTGTAAGACCCTGTCTGGGACAGAGGCATCAAAACTAAATTAT
1 ATGTAAGACCATATCTGGAACAGAGGCATCAAAACTAAATTAT
28518482 ATGTAAGACCA
1 ATGTAAGACCA
28518493 CATCCGGGAC
Statistics
Matches: 43, Mismatches: 10, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
42 29 0.67
43 14 0.33
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (43 bp):
ATGTAAGACCATATCTGGAACAGAGGCATCAAAACTAAATTAT
Found at i:28525996 original size:42 final size:43
Alignment explanation
Indices: 28525945--28526040 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 43
28525935 TGAGATTTAC
* * * *
28525945 ATGTAAGACCATATCTGGAACATAGGCATCATATCT-AATTTT
1 ATGTAAGACCATATCTGGAACAGAGGCATCAAAACTAAATTAT
* * * *
28525987 GTGTAAGACCCTGTCTGGGACAGAGGCATCAAAACTAAATTAT
1 ATGTAAGACCATATCTGGAACAGAGGCATCAAAACTAAATTAT
28526030 ATGTAAGACCA
1 ATGTAAGACCA
28526041 CATCCGGGAC
Statistics
Matches: 43, Mismatches: 10, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
42 29 0.67
43 14 0.33
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (43 bp):
ATGTAAGACCATATCTGGAACAGAGGCATCAAAACTAAATTAT
Found at i:28529395 original size:22 final size:23
Alignment explanation
Indices: 28529362--28529406 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
28529352 TTCTATAAAT
* *
28529362 TAACTTATTTTTTTAAAACAACA
1 TAACTTATTTTTCTAAAAAAACA
28529385 TAACTTA-TTTTCTAAAAAAACA
1 TAACTTATTTTTCTAAAAAAACA
28529407 ATTTCAATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (23 bp):
TAACTTATTTTTCTAAAAAAACA
Found at i:28529627 original size:20 final size:21
Alignment explanation
Indices: 28529579--28529628 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
28529569 TTTAATATTG
28529579 TAATTTT-ATTTTTATAATAA
1 TAATTTTAATTTTTATAATAA
*
28529599 TAGTTTTAATTTTTA-AATAA
1 TAATTTTAATTTTTATAATAA
28529619 TAATTTTAAT
1 TAATTTTAAT
28529629 ATATTATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 20 0.74
21 7 0.26
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
TAATTTTAATTTTTATAATAA
Found at i:28530032 original size:3 final size:3
Alignment explanation
Indices: 28530024--28530069 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
28530014 TTCCAAAATT
28530024 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
28530070 ATATCTGATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:28530087 original size:6 final size:6
Alignment explanation
Indices: 28530078--28530112 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
28530068 ATATATCTGA
*
28530078 TATGTG TATGTG TATGTG TATGTG TATATG TATGT
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGT
28530113 ATGCTATCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (6 bp):
TATGTG
Found at i:28530647 original size:29 final size:29
Alignment explanation
Indices: 28530614--28530677 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 29
28530604 TTTTTGTTTG
28530614 TTTTGCTAAGA-ATAACATTTAGAAAATGA
1 TTTTGCTAA-ACATAACATTTAGAAAATGA
* *
28530643 TTTTGGTAAACTTTAACATTTAGAAAATGA
1 TTTTGCTAAAC-ATAACATTTAGAAAATGA
28530673 TTTTG
1 TTTTG
28530678 GGAAACTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 1 0.03
29 8 0.26
30 22 0.71
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.41
Consensus pattern (29 bp):
TTTTGCTAAACATAACATTTAGAAAATGA
Found at i:28530660 original size:30 final size:30
Alignment explanation
Indices: 28530626--28530687 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
28530616 TTGCTAAGAA
*
28530626 TAACATTTAGAAAATGATTTTGGTAAACTT
1 TAACATTTAGAAAATGATTTTGGGAAACTT
28530656 TAACATTTAGAAAATGATTTTGGGAAACTT
1 TAACATTTAGAAAATGATTTTGGGAAACTT
28530686 TA
1 TA
28530688 CCAAGCGACA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.39
Consensus pattern (30 bp):
TAACATTTAGAAAATGATTTTGGGAAACTT
Found at i:28535615 original size:40 final size:40
Alignment explanation
Indices: 28535540--28535616 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
28535530 AACACATCAG
* *
28535540 TTTGGCACCTAGTGCCTCATCGGATAATTCCAAGTAATAA
1 TTTGACACCTAGTGCCTCATCGGATAATGCCAAGTAATAA
* *
28535580 TTTGACACCTAGTGTCTCATCGGCT-ATGCCGAAGTAA
1 TTTGACACCTAGTGCCTCATCGGATAATGCC-AAGTAA
28535617 ATTGGTACCC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 4 0.12
40 28 0.88
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.30
Consensus pattern (40 bp):
TTTGACACCTAGTGCCTCATCGGATAATGCCAAGTAATAA
Found at i:28537436 original size:16 final size:17
Alignment explanation
Indices: 28537405--28537437 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28537395 ATTAATCAAA
28537405 TTAACTAAATTAATTTT
1 TTAACTAAATTAATTTT
*
28537422 TTAATTAAA-TAATTTT
1 TTAACTAAATTAATTTT
28537438 CTCCACTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
TTAACTAAATTAATTTT
Found at i:28544979 original size:29 final size:27
Alignment explanation
Indices: 28544912--28544979 Score: 64
Period size: 29 Copynumber: 2.3 Consensus size: 27
28544902 CTGGGCATGC
*
28544912 TTTTGTAAAATTGGCCCATTTCTGTCAA
1 TTTT-TAAAATTGGCCCATTTCCGTCAA
* *
28544940 TTTTTACAAAATTGGCCTATTTCCGTTATTA
1 TTTTT--AAAATTGGCCCATTTCCGTCA--A
28544971 TTTTTAAAA
1 TTTTTAAAA
28544980 AATGGCCTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
27 1 0.03
28 4 0.12
29 22 0.67
31 6 0.18
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.47
Consensus pattern (27 bp):
TTTTTAAAATTGGCCCATTTCCGTCAA
Found at i:28545468 original size:33 final size:34
Alignment explanation
Indices: 28545431--28545496 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 34
28545421 ATAAAAGAAC
28545431 TGAATTGAAAATTTTCTTTTTT-GGGTCCAAAGT
1 TGAATTGAAAATTTTCTTTTTTGGGGTCCAAAGT
28545464 TGAATTGAAAATTTTCTTTTTTGGGGTCCAAAG
1 TGAATTGAAAATTTTCTTTTTTGGGGTCCAAAG
28545497 CTCTTACATG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 22 0.69
34 10 0.31
ACGTcount: A:0.27, C:0.09, G:0.20, T:0.44
Consensus pattern (34 bp):
TGAATTGAAAATTTTCTTTTTTGGGGTCCAAAGT
Found at i:28547468 original size:15 final size:16
Alignment explanation
Indices: 28547448--28547477 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28547438 AACTTATATT
28547448 GATCCAATT-AAAATG
1 GATCCAATTCAAAATG
28547463 GATCCAATTCAAAAT
1 GATCCAATTCAAAAT
28547478 CAACTAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.27
Consensus pattern (16 bp):
GATCCAATTCAAAATG
Found at i:28548565 original size:22 final size:22
Alignment explanation
Indices: 28548533--28548580 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
28548523 CACAAATATA
28548533 AAAAAAATAGTTAAAATTTTAG
1 AAAAAAATAGTTAAAATTTTAG
* * *
28548555 AAAAAATTAGTTAAATTTTTTG
1 AAAAAAATAGTTAAAATTTTAG
28548577 AAAA
1 AAAA
28548581 TTTCATAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.35
Consensus pattern (22 bp):
AAAAAAATAGTTAAAATTTTAG
Found at i:28549546 original size:5 final size:5
Alignment explanation
Indices: 28549530--28549563 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
28549520 TTTCGGTCAT
* *
28549530 TCCAC TCAAC TCCAC TCCAC TCCAC TCCTC TCCA
1 TCCAC TCCAC TCCAC TCCAC TCCAC TCCAC TCCA
28549564 TACTCTTAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.21, C:0.56, G:0.00, T:0.24
Consensus pattern (5 bp):
TCCAC
Found at i:28556167 original size:13 final size:13
Alignment explanation
Indices: 28556149--28556173 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28556139 ATTTTGGTAC
28556149 TGATGCTGTTCTA
1 TGATGCTGTTCTA
28556162 TGATGCTGTTCT
1 TGATGCTGTTCT
28556174 CATCCAATCC
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:0.12, C:0.16, G:0.24, T:0.48
Consensus pattern (13 bp):
TGATGCTGTTCTA
Found at i:28558209 original size:19 final size:19
Alignment explanation
Indices: 28558187--28558224 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
28558177 TTTAAAATGA
28558187 TAATTTAACGTGTCACATT
1 TAATTTAACGTGTCACATT
28558206 TAATTTAACGTGTCACATT
1 TAATTTAACGTGTCACATT
28558225 AGCTTACTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.42
Consensus pattern (19 bp):
TAATTTAACGTGTCACATT
Found at i:28558244 original size:31 final size:31
Alignment explanation
Indices: 28558208--28558268 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
28558198 GTCACATTTA
* *
28558208 ATTTAACGTGTCACATTAGCTTACTGTTATG
1 ATTTAACGTGCCACATCAGCTTACTGTTATG
*
28558239 ATTTAACGTGCCACGTCAGCTTACTGTTAT
1 ATTTAACGTGCCACATCAGCTTACTGTTAT
28558269 ACACTTAACG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (31 bp):
ATTTAACGTGCCACATCAGCTTACTGTTATG
Found at i:28565505 original size:513 final size:513
Alignment explanation
Indices: 28564538--28565563 Score: 2052
Period size: 513 Copynumber: 2.0 Consensus size: 513
28564528 TAAGCAGTTT
28564538 TAGAGTATTTATGCAAAGCTTATATAAGTTCGGTTCTAGTGTAAAGGGGGGTAAGAAATATATTC
1 TAGAGTATTTATGCAAAGCTTATATAAGTTCGGTTCTAGTGTAAAGGGGGGTAAGAAATATATTC
28564603 AACAATCAGAGATTAATTCATTCTTCAGTCACAACTTATTGTACTCTCTTTTGTTGTTCTATTGT
66 AACAATCAGAGATTAATTCATTCTTCAGTCACAACTTATTGTACTCTCTTTTGTTGTTCTATTGT
28564668 TTCCCCTTTATCAAATCTATTTTCTTCAACGTTTTACCTTGTTTTTAATATCAGCAATTAGACAT
131 TTCCCCTTTATCAAATCTATTTTCTTCAACGTTTTACCTTGTTTTTAATATCAGCAATTAGACAT
28564733 CCAAGTTGAAATTTAAAACCCATTTGGACTGCCACGTAAGACTTCTGTTGGGGAGGTAATGGATT
196 CCAAGTTGAAATTTAAAACCCATTTGGACTGCCACGTAAGACTTCTGTTGGGGAGGTAATGGATT
28564798 TTAATGGTAGAGTAATTACTTCGTAACAAAACAATAATATAAGTAACTAAAATGTAATATTAAAC
261 TTAATGGTAGAGTAATTACTTCGTAACAAAACAATAATATAAGTAACTAAAATGTAATATTAAAC
28564863 AAATAAAAGTGACTATTTCTTTAGTTTACCCTTTAAGGCTGTGGGTCTTAATTTTCGTTTCCTAT
326 AAATAAAAGTGACTATTTCTTTAGTTTACCCTTTAAGGCTGTGGGTCTTAATTTTCGTTTCCTAT
28564928 TTAAGTTTTTTTATTCACCATTTTTTAAATATACATTTTTCACCTCATCATTTTATGTGGTTTGC
391 TTAAGTTTTTTTATTCACCATTTTTTAAATATACATTTTTCACCTCATCATTTTATGTGGTTTGC
28564993 TTTGTTGGAATGCCACATTGGATAAAATAATCAAGTGGCGCTCTTAAGTGGTGTGCCA
456 TTTGTTGGAATGCCACATTGGATAAAATAATCAAGTGGCGCTCTTAAGTGGTGTGCCA
28565051 TAGAGTATTTATGCAAAGCTTATATAAGTTCGGTTCTAGTGTAAAGGGGGGTAAGAAATATATTC
1 TAGAGTATTTATGCAAAGCTTATATAAGTTCGGTTCTAGTGTAAAGGGGGGTAAGAAATATATTC
28565116 AACAATCAGAGATTAATTCATTCTTCAGTCACAACTTATTGTACTCTCTTTTGTTGTTCTATTGT
66 AACAATCAGAGATTAATTCATTCTTCAGTCACAACTTATTGTACTCTCTTTTGTTGTTCTATTGT
28565181 TTCCCCTTTATCAAATCTATTTTCTTCAACGTTTTACCTTGTTTTTAATATCAGCAATTAGACAT
131 TTCCCCTTTATCAAATCTATTTTCTTCAACGTTTTACCTTGTTTTTAATATCAGCAATTAGACAT
28565246 CCAAGTTGAAATTTAAAACCCATTTGGACTGCCACGTAAGACTTCTGTTGGGGAGGTAATGGATT
196 CCAAGTTGAAATTTAAAACCCATTTGGACTGCCACGTAAGACTTCTGTTGGGGAGGTAATGGATT
28565311 TTAATGGTAGAGTAATTACTTCGTAACAAAACAATAATATAAGTAACTAAAATGTAATATTAAAC
261 TTAATGGTAGAGTAATTACTTCGTAACAAAACAATAATATAAGTAACTAAAATGTAATATTAAAC
28565376 AAATAAAAGTGACTATTTCTTTAGTTTACCCTTTAAGGCTGTGGGTCTTAATTTTCGTTTCCTAT
326 AAATAAAAGTGACTATTTCTTTAGTTTACCCTTTAAGGCTGTGGGTCTTAATTTTCGTTTCCTAT
28565441 TTAAGTTTTTTTATTCACCATTTTTTAAATATACATTTTTCACCTCATCATTTTATGTGGTTTGC
391 TTAAGTTTTTTTATTCACCATTTTTTAAATATACATTTTTCACCTCATCATTTTATGTGGTTTGC
28565506 TTTGTTGGAATGCCACATTGGATAAAATAATCAAGTGGCGCTCTTAAGTGGTGTGCCA
456 TTTGTTGGAATGCCACATTGGATAAAATAATCAAGTGGCGCTCTTAAGTGGTGTGCCA
28565564 CAAATTGACC
Statistics
Matches: 513, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
513 513 1.00
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (513 bp):
TAGAGTATTTATGCAAAGCTTATATAAGTTCGGTTCTAGTGTAAAGGGGGGTAAGAAATATATTC
AACAATCAGAGATTAATTCATTCTTCAGTCACAACTTATTGTACTCTCTTTTGTTGTTCTATTGT
TTCCCCTTTATCAAATCTATTTTCTTCAACGTTTTACCTTGTTTTTAATATCAGCAATTAGACAT
CCAAGTTGAAATTTAAAACCCATTTGGACTGCCACGTAAGACTTCTGTTGGGGAGGTAATGGATT
TTAATGGTAGAGTAATTACTTCGTAACAAAACAATAATATAAGTAACTAAAATGTAATATTAAAC
AAATAAAAGTGACTATTTCTTTAGTTTACCCTTTAAGGCTGTGGGTCTTAATTTTCGTTTCCTAT
TTAAGTTTTTTTATTCACCATTTTTTAAATATACATTTTTCACCTCATCATTTTATGTGGTTTGC
TTTGTTGGAATGCCACATTGGATAAAATAATCAAGTGGCGCTCTTAAGTGGTGTGCCA
Found at i:28567190 original size:21 final size:21
Alignment explanation
Indices: 28567149--28567190 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
28567139 AGATTCATGA
**
28567149 AATTTTAGATTTTTTTTTTAT
1 AATTTTAGATTTTTTCATTAT
28567170 AATTTTATGA-TTTTTCATTAT
1 AATTTTA-GATTTTTTCATTAT
28567191 TGTAATTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (21 bp):
AATTTTAGATTTTTTCATTAT
Found at i:28570067 original size:14 final size:14
Alignment explanation
Indices: 28570048--28570079 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
28570038 ACAATAATAC
28570048 TATATATAAATGTA
1 TATATATAAATGTA
*
28570062 TATATATATATGTA
1 TATATATAAATGTA
28570076 TATA
1 TATA
28570080 ATAGAAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (14 bp):
TATATATAAATGTA
Done.