Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011366.1 Kokia drynarioides strain JFW-HI SEQ_126347, whole genome shotgun sequence
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: 227116
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 58 characters in sequence are not A, C, G, or T
Found at i:20457 original size:147 final size:147
Alignment explanation
Indices: 20190--20483 Score: 579
Period size: 147 Copynumber: 2.0 Consensus size: 147
20180 TTAAAACCAA
20190 GTTTGAGAGTGTGCAATGATTAGGGTCTTGTATATAGTAGTCGGTTGCAGCAGATGCACTAGTTT
1 GTTTGAGAGTGTGCAATGATTAGGGTCTTGTATATAGTAGTCGGTTGCAGCAGATGCACTAGTTT
20255 AATGGTATCATGGTTTTAGGAGTGGCCATGTTGATTGTGGAGGGGCTTTTCTGATTCATATGATT
66 AATGGTATCATGGTTTTAGGAGTGGCCATGTTGATTGTGGAGGGGCTTTTCTGATTCATATGATT
20320 AACTCCGTACTGCTTAG
131 AACTCCGTACTGCTTAG
*
20337 GTTTGAGAGTGTGTAATGATTAGGGTCTTGTATATAGTAGTCGGTTGCAGCAGATGCACTAGTTT
1 GTTTGAGAGTGTGCAATGATTAGGGTCTTGTATATAGTAGTCGGTTGCAGCAGATGCACTAGTTT
20402 AATGGTATCATGGTTTTAGGAGTGGCCATGTTGATTGTGGAGGGGCTTTTCTGATTCATATGATT
66 AATGGTATCATGGTTTTAGGAGTGGCCATGTTGATTGTGGAGGGGCTTTTCTGATTCATATGATT
20467 AACTCCGTACTGCTTAG
131 AACTCCGTACTGCTTAG
20484 CGTACAGTTG
Statistics
Matches: 146, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
147 146 1.00
ACGTcount: A:0.22, C:0.12, G:0.29, T:0.37
Consensus pattern (147 bp):
GTTTGAGAGTGTGCAATGATTAGGGTCTTGTATATAGTAGTCGGTTGCAGCAGATGCACTAGTTT
AATGGTATCATGGTTTTAGGAGTGGCCATGTTGATTGTGGAGGGGCTTTTCTGATTCATATGATT
AACTCCGTACTGCTTAG
Found at i:31898 original size:6 final size:6
Alignment explanation
Indices: 31889--31920 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
31879 CCGGATTCGG
31889 ATTTGA ATTTGA ATTTGA ATTTGA ATTTGA AT
1 ATTTGA ATTTGA ATTTGA ATTTGA ATTTGA AT
31921 AATTTTTGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (6 bp):
ATTTGA
Found at i:32803 original size:15 final size:15
Alignment explanation
Indices: 32780--32815 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
32770 GCAATAAAAA
* *
32780 TTCAATACTTAATTT
1 TTCAGTACTTAAATT
32795 TTCAGTACTTAAATT
1 TTCAGTACTTAAATT
32810 TTCAGT
1 TTCAGT
32816 TTATCAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.50
Consensus pattern (15 bp):
TTCAGTACTTAAATT
Found at i:33161 original size:23 final size:20
Alignment explanation
Indices: 33115--33155 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
33105 CATGTGTTTA
33115 AATGTGTTTAAATATGCTTG
1 AATGTGTTTAAATATGCTTG
33135 AATGATGTTTAGAATATGCTT
1 AATG-TGTTTA-AATATGCTT
33156 TTAATGTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.21
21 6 0.32
22 9 0.47
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.44
Consensus pattern (20 bp):
AATGTGTTTAAATATGCTTG
Found at i:35479 original size:13 final size:13
Alignment explanation
Indices: 35440--35487 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
35430 TATTTAAGTT
35440 TTTAATATATTTTA
1 TTTAAT-TATTTTA
* * *
35454 TTTTATAAATTTA
1 TTTAATTATTTTA
35467 TTTAATTATTTTA
1 TTTAATTATTTTA
*
35480 CTTAATTA
1 TTTAATTA
35488 ACTAATTATT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
13 22 0.81
14 5 0.19
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTAATTATTTTA
Found at i:46116 original size:24 final size:23
Alignment explanation
Indices: 46069--46150 Score: 98
Period size: 21 Copynumber: 3.7 Consensus size: 23
46059 TAATTAAAAA
*
46069 TTTTAAAT-TAAATTATAATTAT
1 TTTTAAATGTGAATTATAATTAT
* *
46091 TTTTAAATGTGTAATTATCATAAT
1 TTTTAAATGTG-AATTATAATTAT
*
46115 TTTT-TAT-TGAATTATAATTAT
1 TTTTAAATGTGAATTATAATTAT
46136 TTTTAAATGTGAATT
1 TTTTAAATGTGAATT
46151 TAGTAATATG
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
21 14 0.29
22 12 0.24
23 9 0.18
24 14 0.29
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.55
Consensus pattern (23 bp):
TTTTAAATGTGAATTATAATTAT
Found at i:46713 original size:24 final size:25
Alignment explanation
Indices: 46654--46706 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
46644 TAGAATTATA
**
46654 TTAA-AATAATATCTCTATTTTTTT
1 TTAAGAATAATATCTCTATTTTAAT
46678 TTGAAGAATAATATCTCTATTTTAAT
1 TT-AAGAATAATATCTCTATTTTAAT
46704 TTA
1 TTA
46707 TAATAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 2 0.08
25 3 0.12
26 20 0.80
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.53
Consensus pattern (25 bp):
TTAAGAATAATATCTCTATTTTAAT
Found at i:46788 original size:16 final size:15
Alignment explanation
Indices: 46767--46800 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
46757 TTATCATAAT
46767 TTTTTTCATTATAAAA
1 TTTTTT-ATTATAAAA
*
46783 TTTTTTATTTTAAAA
1 TTTTTTATTATAAAA
46798 TTT
1 TTT
46801 AAATTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTTTATTATAAAA
Found at i:48697 original size:2 final size:2
Alignment explanation
Indices: 48690--48716 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
48680 AAAGGGAAAT
48690 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
48717 AGATGGGGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:59056 original size:176 final size:177
Alignment explanation
Indices: 58750--59078 Score: 488
Period size: 176 Copynumber: 1.9 Consensus size: 177
58740 TATATTGCTC
* *
58750 ATGTTTATTTTATTTTATTTAAGAGTTAACAAACTTTAAATAGAGGTGAAAACAACAAATAAGAT
1 ATGTTTATTTTATTTTATTTAAGAATTAACAAACTTTAAATAGAGGTGAAAACAACAAATAAGAC
**
58815 AATAGAAACACTACATTAGATCTTAAAGTTAATCAAACACTACGTAAGTCTTGAAAACAAAAAAA
66 AATAGAAACACTACATTAGATCTTAAAGTTAATCAAACACTAAATAAGTCTTGAAAACAAAAAAA
58880 ATATTTCGGTTAATT-GATTAATTATTTGATTTCAAATTGAATTGTTA
131 ATATTTCGGTTAATTAG-TTAATTATTTGATTTCAAATTGAATTGTTA
* * *
58927 ATGTTTATTTT-TTTTATTTAATAATTAACAGACTTTAAATAGAGGTGAAAATAACAAATAAGAC
1 ATGTTTATTTTATTTTATTTAAGAATTAACAAACTTTAAATAGAGGTGAAAACAACAAATAAGAC
* * *
58991 ATTGGAAACACTACATTAG-TTTTGAAAGTTAA-CTAAACACTATAATAAGTCTTGAAAAC-AAA
66 AATAGAAACACTACATTAGATCTT-AAAGTTAATC-AAACACTA-AATAAGTCTTGAAAACAAAA
*
59053 AAAATATTTTGGTTAATTAGTTAATT
128 AAAATATTTCGGTTAATTAGTTAATT
59079 CGGTTAATTA
Statistics
Matches: 137, Mismatches: 11, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
175 4 0.03
176 107 0.78
177 26 0.19
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (177 bp):
ATGTTTATTTTATTTTATTTAAGAATTAACAAACTTTAAATAGAGGTGAAAACAACAAATAAGAC
AATAGAAACACTACATTAGATCTTAAAGTTAATCAAACACTAAATAAGTCTTGAAAACAAAAAAA
ATATTTCGGTTAATTAGTTAATTATTTGATTTCAAATTGAATTGTTA
Found at i:64127 original size:2 final size:2
Alignment explanation
Indices: 64120--64145 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
64110 CTGTCTTAAT
64120 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
64146 AATTAAGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:72429 original size:31 final size:31
Alignment explanation
Indices: 72381--72440 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
72371 GGTGTCTTGA
*
72381 TTGATTTATTAATTATTTTAT-AATGATTTAT
1 TTGATTTATTAAATATTTTATGAA-GATTTAT
72412 TTGATTT-TTAAAATATTTTATGAAGATTT
1 TTGATTTATT-AAATATTTTATGAAGATTT
72441 TTTAGCATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 2 0.08
31 22 0.85
32 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (31 bp):
TTGATTTATTAAATATTTTATGAAGATTTAT
Found at i:72479 original size:16 final size:17
Alignment explanation
Indices: 72458--72497 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 17
72448 TTTAAGCCTA
72458 AAAATATTAAAATATT-
1 AAAATATTAAAATATTC
72474 AAAATA-T-AAATATTC
1 AAAATATTAAAATATTC
*
72489 TAAATATTA
1 AAAATATTA
72498 TTAGCATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
14 7 0.35
15 6 0.30
16 7 0.35
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAATATTAAAATATTC
Found at i:77298 original size:22 final size:22
Alignment explanation
Indices: 77256--77298 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
77246 ATTTAGTGAC
*
77256 TTAAATGAAATTTTTTGAATAA
1 TTAAATGAAATTTTATGAATAA
*
77278 TTAAATTAACATTTTAT-AATA
1 TTAAATGAA-ATTTTATGAATA
77299 TTTTAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (22 bp):
TTAAATGAAATTTTATGAATAA
Found at i:89344 original size:16 final size:16
Alignment explanation
Indices: 89312--89346 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
89302 TATTTGAGTA
*
89312 TTTTTTTTTTACTTTT
1 TTTTTTTTTTACATTT
*
89328 TTTTTTTTTTTCATTT
1 TTTTTTTTTTACATTT
89344 TTT
1 TTT
89347 ATAAAGGAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.06, G:0.00, T:0.89
Consensus pattern (16 bp):
TTTTTTTTTTACATTT
Found at i:92544 original size:2 final size:2
Alignment explanation
Indices: 92537--92581 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
92527 GTAAAGTTGG
*
92537 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
92579 TA T
1 TA T
92582 GGAAGCTTCG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:94035 original size:21 final size:21
Alignment explanation
Indices: 93976--94035 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
93966 TATTTTTTTT
* *
93976 ATTAAAATTTTATATATAGGC
1 ATTATAATTTTATATATTGGC
*
93997 ATCT-TAATTTT-TAATATTTGC
1 AT-TATAATTTTAT-ATATTGGC
94018 ATTATAATTTTATATATT
1 ATTATAATTTTATATATT
94036 ATTATAGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
20 2 0.06
21 28 0.88
22 2 0.06
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (21 bp):
ATTATAATTTTATATATTGGC
Found at i:96665 original size:39 final size:39
Alignment explanation
Indices: 96611--96689 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
96601 GATTTAATGG
96611 AGTGATATTTTGTATTGGCTCAACATCTATTAACTCAGC
1 AGTGATATTTTGTATTGGCTCAACATCTATTAACTCAGC
96650 AGTGATATTTTGTATTGGCTCAACATCTATTAACTCAGC
1 AGTGATATTTTGTATTGGCTCAACATCTATTAACTCAGC
96689 A
1 A
96690 AACAACTCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (39 bp):
AGTGATATTTTGTATTGGCTCAACATCTATTAACTCAGC
Found at i:98138 original size:59 final size:60
Alignment explanation
Indices: 98036--98224 Score: 254
Period size: 61 Copynumber: 3.1 Consensus size: 60
98026 TTAATATAAC
* * * *
98036 ATTTAGTACTTGAACTTGACATTTTTTTCTAATATGATACCTAAACTTTTTTT-GACTCA
1 ATTTGGTACTTGAACTTGACATTTTTTCCTAATTTGGTACCTAAACTTTTTTTAGACTCA
* * * *
98095 ATTTGGTACTTGAACTTGACACTTTTTCCTAATTTGGTGCCTAAACTTTTTTTTGGACCCA
1 ATTTGGTACTTGAACTTGACATTTTTTCCTAATTTGGTACCTAAAC-TTTTTTTAGACTCA
* * * *
98156 ATTTGGTACCTGAACTTGGCATTTTTTCCTAATTTGGTACCTAAGCTTTTTTTAGATTCA
1 ATTTGGTACTTGAACTTGACATTTTTTCCTAATTTGGTACCTAAACTTTTTTTAGACTCA
98216 ATTTGGTAC
1 ATTTGGTAC
98225 CTATATTTAT
Statistics
Matches: 113, Mismatches: 15, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
59 40 0.35
60 27 0.24
61 46 0.41
ACGTcount: A:0.24, C:0.17, G:0.13, T:0.46
Consensus pattern (60 bp):
ATTTGGTACTTGAACTTGACATTTTTTCCTAATTTGGTACCTAAACTTTTTTTAGACTCA
Found at i:98192 original size:31 final size:30
Alignment explanation
Indices: 98036--98197 Score: 102
Period size: 31 Copynumber: 5.4 Consensus size: 30
98026 TTAATATAAC
* * *
98036 ATTTAGTACTTGAACTTGACATTTTTTTCTA
1 ATTTGGTACCTGAACTTG-CATTTTTTCCTA
* * * **
98067 ATATGATACCTAAACTT---TTTTTGACTCA
1 ATTTGGTACCTGAACTTGCATTTTTTCCT-A
* *
98095 ATTTGGTACTTGAACTTGACACTTTTTCCTA
1 ATTTGGTACCTGAACTTG-CATTTTTTCCTA
* * *
98126 ATTTGGTGCCTAAACTT---TTTTTTGGACCCA
1 ATTTGGTACCTGAACTTGCATTTTTT---CCTA
98156 ATTTGGTACCTGAACTTGGCATTTTTTCCTA
1 ATTTGGTACCTGAACTT-GCATTTTTTCCTA
98187 ATTTGGTACCT
1 ATTTGGTACCT
98198 AAGCTTTTTT
Statistics
Matches: 97, Mismatches: 22, Indels: 24
0.68 0.15 0.17
Matches are distributed among these distances:
27 12 0.12
28 14 0.14
30 18 0.19
31 41 0.42
32 6 0.06
34 6 0.06
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.46
Consensus pattern (30 bp):
ATTTGGTACCTGAACTTGCATTTTTTCCTA
Found at i:98473 original size:30 final size:30
Alignment explanation
Indices: 98433--98561 Score: 106
Period size: 31 Copynumber: 4.3 Consensus size: 30
98423 CCCAAAAAGA
*
98433 TTAAGTACCAACTTTAA-AAAAGTGTCAAAT
1 TTAAGTACCAA-ATTAAGAAAAGTGTCAAAT
* *
98463 TTAGGTACCAAATTAAGGAAAAGTGTCAAGT
1 TTAAGTACCAAATTAA-GAAAAGTGTCAAAT
* *
98494 TTAAGTACCAAATTGAACAAAA----AAAAGT
1 TTAAGTACCAAATT-AAGAAAAGTGTCAAA-T
* * *
98522 TTAGGTACCAAATTAGGAAAAGTGTCAAGT
1 TTAAGTACCAAATTAAGAAAAGTGTCAAAT
*
98552 TTAGGTACCA
1 TTAAGTACCA
98562 TATGTTATAT
Statistics
Matches: 79, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
27 7 0.09
28 14 0.18
29 4 0.05
30 21 0.27
31 31 0.39
32 2 0.03
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.26
Consensus pattern (30 bp):
TTAAGTACCAAATTAAGAAAAGTGTCAAAT
Found at i:98487 original size:31 final size:31
Alignment explanation
Indices: 98450--98561 Score: 119
Period size: 31 Copynumber: 3.7 Consensus size: 31
98440 CCAACTTTAA
98450 AAAAGTGTCAAATTTAGGTACCAAATTAAGG
1 AAAAGTGTCAAATTTAGGTACCAAATTAAGG
* * *
98481 AAAAGTGTCAAGTTTAAGTACCAAATTGAA-C
1 AAAAGTGTCAAATTTAGGTACCAAATT-AAGG
*
98512 AAAA----AAAAGTTTAGGTACCAAATT-AGG
1 AAAAGTGTCAAA-TTTAGGTACCAAATTAAGG
*
98539 AAAAGTGTCAAGTTTAGGTACCA
1 AAAAGTGTCAAATTTAGGTACCA
98562 TATGTTATAT
Statistics
Matches: 65, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
26 1 0.02
27 6 0.09
28 14 0.22
30 11 0.17
31 31 0.48
32 2 0.03
ACGTcount: A:0.46, C:0.11, G:0.19, T:0.25
Consensus pattern (31 bp):
AAAAGTGTCAAATTTAGGTACCAAATTAAGG
Found at i:98530 original size:89 final size:89
Alignment explanation
Indices: 98374--98561 Score: 211
Period size: 89 Copynumber: 2.1 Consensus size: 89
98364 TTTAAAAAAA
* * * ***
98374 TTAGATACCAAATTAGGAAAAAGAGTCAAGTTAAGGAATCAAATTGGACCCCAAAAAGATTAAGT
1 TTAGGTACCAAATTAGGAAAAAGAGTCAAGTTAAGGAACCAAATTGAACAAAAAAAAGATTAAGT
*
98439 ACCAACTTTA-AAAAAGTGTCAAAT
66 ACCAA-ATTAGAAAAAGTGTCAAAT
* * * *
98463 TTAGGTACCAAATTAAGG-AAAAGTGTCAAGTTTAA-GTACCAAATTGAACAAAAAAAAGTTTAG
1 TTAGGTACCAAATT-AGGAAAAAGAGTCAAG-TTAAGGAACCAAATTGAACAAAAAAAAGATTAA
* *
98526 GTACCAAATTAGGAAAAGTGTCAAGT
64 GTACCAAATTAGAAAAAGTGTCAAAT
98552 TTAGGTACCA
1 TTAGGTACCA
98562 TATGTTATAT
Statistics
Matches: 83, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
88 3 0.04
89 73 0.88
90 7 0.08
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.24
Consensus pattern (89 bp):
TTAGGTACCAAATTAGGAAAAAGAGTCAAGTTAAGGAACCAAATTGAACAAAAAAAAGATTAAGT
ACCAAATTAGAAAAAGTGTCAAAT
Found at i:99746 original size:18 final size:18
Alignment explanation
Indices: 99725--99759 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
99715 TTTATATTCA
* *
99725 ATTTTTATTTTCTTTTAT
1 ATTTTGATTTTATTTTAT
99743 ATTTTGATTTTATTTTA
1 ATTTTGATTTTATTTTA
99760 GTTTTTATCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (18 bp):
ATTTTGATTTTATTTTAT
Found at i:99765 original size:18 final size:16
Alignment explanation
Indices: 99725--99767 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 16
99715 TTTATATTCA
*
99725 ATTTTTATTTTCTTTT
1 ATTTTTATTTTATTTT
99741 ATATTTTGATTTTATTTT
1 AT-TTTT-ATTTTATTTT
99759 AGTTTTTAT
1 A-TTTTTAT
99768 CTGCCTATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 2 0.09
17 6 0.26
18 14 0.61
19 1 0.04
ACGTcount: A:0.19, C:0.02, G:0.05, T:0.74
Consensus pattern (16 bp):
ATTTTTATTTTATTTT
Found at i:100130 original size:9 final size:9
Alignment explanation
Indices: 100116--100157 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
100106 TGATGTTTCG
100116 TTTTTTAGT
1 TTTTTTAGT
100125 TTTTTTAGT
1 TTTTTTAGT
*
100134 TTTTCTTTGT
1 TTTT-TTAGT
*
100144 TTTGTTA-T
1 TTTTTTAGT
100152 TTTTTT
1 TTTTTT
100158 CTTACATTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
8 6 0.21
9 15 0.54
10 7 0.25
ACGTcount: A:0.07, C:0.02, G:0.10, T:0.81
Consensus pattern (9 bp):
TTTTTTAGT
Found at i:113044 original size:3 final size:3
Alignment explanation
Indices: 113038--113070 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
113028 TCCAGCAGCT
*
113038 CAA CAA CAG CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
113071 ACCAAGATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.33, G:0.03, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:115635 original size:36 final size:35
Alignment explanation
Indices: 115581--115653 Score: 94
Period size: 36 Copynumber: 2.1 Consensus size: 35
115571 TAAAAAAATA
* *
115581 TTTATTTGCTAAAATAATA-TACAAAAATTATTTAT
1 TTTATTTACTAAAATAATATTA-AAAAATTATTAAT
*
115616 TTTATTTCACTAAAGTAATATTAAAAAATTATTAAT
1 TTTATTT-ACTAAAATAATATTAAAAAATTATTAAT
115652 TT
1 TT
115654 AATAAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
35 7 0.21
36 24 0.73
37 2 0.06
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (35 bp):
TTTATTTACTAAAATAATATTAAAAAATTATTAAT
Found at i:116763 original size:28 final size:28
Alignment explanation
Indices: 116723--116788 Score: 132
Period size: 28 Copynumber: 2.4 Consensus size: 28
116713 CTTCTGGGGC
116723 ACACATGTCGCTTATAGACCCCGATGCG
1 ACACATGTCGCTTATAGACCCCGATGCG
116751 ACACATGTCGCTTATAGACCCCGATGCG
1 ACACATGTCGCTTATAGACCCCGATGCG
116779 ACACATGTCG
1 ACACATGTCG
116789 AGTTCATGGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.26, C:0.32, G:0.21, T:0.21
Consensus pattern (28 bp):
ACACATGTCGCTTATAGACCCCGATGCG
Found at i:118890 original size:14 final size:15
Alignment explanation
Indices: 118857--118894 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
118847 AATGATATAG
*
118857 AGTTTTGAAATTTAG
1 AGTTTTGAAATTTAA
*
118872 GGTTTT-AAATTTAA
1 AGTTTTGAAATTTAA
118886 AGTTTTGAA
1 AGTTTTGAA
118895 GAAAAGGGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.47
Consensus pattern (15 bp):
AGTTTTGAAATTTAA
Found at i:119281 original size:45 final size:45
Alignment explanation
Indices: 119212--119303 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 45
119202 CGGAGGAGTA
*
119212 GAGTATTACGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
1 GAGTATTACGGTGGCTCGTAAAACTGAGGCTGATATCCTTGGCTT
* *
119257 GAGTATTGCGGTGGCTCGTAAAACTGAGGCTGATATCTTTGGCTT
1 GAGTATTACGGTGGCTCGTAAAACTGAGGCTGATATCCTTGGCTT
119302 GA
1 GA
119304 TGAGCTAGGC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.32
Consensus pattern (45 bp):
GAGTATTACGGTGGCTCGTAAAACTGAGGCTGATATCCTTGGCTT
Found at i:119393 original size:12 final size:12
Alignment explanation
Indices: 119373--119408 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
119363 ATGTCTTTTC
* *
119373 CTCTTGCTCTTG
1 CTCTGGCTCTAG
119385 CTCTGGCTCTAG
1 CTCTGGCTCTAG
119397 CTCTGGCTCTAG
1 CTCTGGCTCTAG
119409 GGCAAGAGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.06, C:0.33, G:0.22, T:0.39
Consensus pattern (12 bp):
CTCTGGCTCTAG
Found at i:120039 original size:58 final size:58
Alignment explanation
Indices: 119975--120092 Score: 236
Period size: 58 Copynumber: 2.0 Consensus size: 58
119965 ACATACCCCT
119975 TCCCCGATATATTGCTCGAGCATCAAACGATATAAGGGAACTGTAAGCTGCCTTCCGA
1 TCCCCGATATATTGCTCGAGCATCAAACGATATAAGGGAACTGTAAGCTGCCTTCCGA
120033 TCCCCGATATATTGCTCGAGCATCAAACGATATAAGGGAACTGTAAGCTGCCTTCCGA
1 TCCCCGATATATTGCTCGAGCATCAAACGATATAAGGGAACTGTAAGCTGCCTTCCGA
120091 TC
1 TC
120093 TTCGATTTTG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (58 bp):
TCCCCGATATATTGCTCGAGCATCAAACGATATAAGGGAACTGTAAGCTGCCTTCCGA
Found at i:121278 original size:14 final size:14
Alignment explanation
Indices: 121261--121292 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
121251 CAAAATAAAT
121261 ATTTATTTTGTACC
1 ATTTATTTTGTACC
121275 ATTTATTTTGTACC
1 ATTTATTTTGTACC
121289 ATTT
1 ATTT
121293 TAGTAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.22, C:0.12, G:0.06, T:0.59
Consensus pattern (14 bp):
ATTTATTTTGTACC
Found at i:121336 original size:16 final size:16
Alignment explanation
Indices: 121315--121363 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
121305 AGATGGGGAT
121315 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
121331 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
*
121346 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
121361 ATT
1 ATT
121364 TAAAATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 9 0.33
15 6 0.22
16 12 0.44
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:122056 original size:16 final size:16
Alignment explanation
Indices: 122020--122072 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 16
122010 ATTACTTTTC
122020 TCTTCTTCTCCTTCTCTTT
1 TCTTCTTCTCC-T-TC-TT
122039 TCTTCTTCTCCTTCTT
1 TCTTCTTCTCCTTCTT
*
122055 TCTTTCTT-TCTTTCTT
1 TC-TTCTTCTCCTTCTT
122071 TC
1 TC
122073 AATACCCGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
16 13 0.41
17 7 0.22
18 1 0.03
19 11 0.34
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (16 bp):
TCTTCTTCTCCTTCTT
Found at i:125352 original size:3 final size:3
Alignment explanation
Indices: 125346--125384 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
125336 GGTTATGATG
125346 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
125385 TCAATGGTGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:127445 original size:38 final size:38
Alignment explanation
Indices: 127394--127472 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
127384 AACTAATTTT
127394 GAACATTGCTGACATTATTAGACACTATAAAGGAAGAA
1 GAACATTGCTGACATTATTAGACACTATAAAGGAAGAA
127432 GAACATTGCTGACATTATTAGACACTATAAAGGAAGAA
1 GAACATTGCTGACATTATTAGACACTATAAAGGAAGAA
127470 GAA
1 GAA
127473 AGAGAAAAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.46, C:0.13, G:0.19, T:0.23
Consensus pattern (38 bp):
GAACATTGCTGACATTATTAGACACTATAAAGGAAGAA
Found at i:130140 original size:39 final size:39
Alignment explanation
Indices: 130062--130158 Score: 122
Period size: 39 Copynumber: 2.5 Consensus size: 39
130052 CATTACTAAG
* * * *
130062 CTGACGATAACACTGTAAATACCGTAAAGTAATATTGAA
1 CTGACGGTAACACTGTAAATACCATAAAGCAATACTGAA
* *
130101 CTGACGGTAACACTGTAAATACCATAATGCAGTACTGAA
1 CTGACGGTAACACTGTAAATACCATAAAGCAATACTGAA
* *
130140 CTAATGGTAACACTGTAAA
1 CTGACGGTAACACTGTAAA
130159 CATCGTGATA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.25
Consensus pattern (39 bp):
CTGACGGTAACACTGTAAATACCATAAAGCAATACTGAA
Found at i:130727 original size:30 final size:29
Alignment explanation
Indices: 130691--130771 Score: 108
Period size: 30 Copynumber: 2.7 Consensus size: 29
130681 ATGAGAGGGG
130691 AGTAAAAGTTTTAGGAGAAAAATGGGAGAA
1 AGTAAAAGTTTT-GGAGAAAAATGGGAGAA
**
130721 AGTAAAAGTTTTGGAAGAAAAATGGGAGGG
1 AGTAAAAGTTTTGG-AGAAAAATGGGAGAA
*
130751 AGTAAAAGTATTGGGAGAAAA
1 AGTAAAAGT-TTTGGAGAAAA
130772 TAAAAAGTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
29 2 0.04
30 40 0.87
31 4 0.09
ACGTcount: A:0.48, C:0.00, G:0.32, T:0.20
Consensus pattern (29 bp):
AGTAAAAGTTTTGGAGAAAAATGGGAGAA
Found at i:130889 original size:20 final size:21
Alignment explanation
Indices: 130864--130902 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
130854 GATGGAAGGG
*
130864 AAGTAA-AAGTTTTGAGAGAA
1 AAGTAATAAGGTTTGAGAGAA
130884 AAGTAATAAGGTTTGAGAG
1 AAGTAATAAGGTTTGAGAG
130903 TTTGGGATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.46, C:0.00, G:0.28, T:0.26
Consensus pattern (21 bp):
AAGTAATAAGGTTTGAGAGAA
Found at i:145732 original size:31 final size:32
Alignment explanation
Indices: 145697--145759 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
145687 GATTCTATAG
*
145697 GTCCCTGTA-TGTTTCATAAATTTAATATTTA
1 GTCCCTGTATTGTTTCATAAATTTAAAATTTA
* *
145728 GTCCCTGTATTTTTTTATAAATTTAAAATTTA
1 GTCCCTGTATTGTTTCATAAATTTAAAATTTA
145760 ATCTCTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 9 0.32
32 19 0.68
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.51
Consensus pattern (32 bp):
GTCCCTGTATTGTTTCATAAATTTAAAATTTA
Found at i:145773 original size:32 final size:32
Alignment explanation
Indices: 145712--145789 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 32
145702 TGTATGTTTC
* * *
145712 ATAAATTTAATATTTAGTCCCTGTATTTTTTT
1 ATAAATTTAAAATTTAATCCCTATATTTTTTT
*
145744 ATAAATTTAAAATTTAAT--CTCTATTTTTTT
1 ATAAATTTAAAATTTAATCCCTATATTTTTTT
**
145774 A-ATTTTTAAAATTTAA
1 ATAAATTTAAAATTTAA
145790 GTTCAATTGT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 13 0.32
30 12 0.29
32 16 0.39
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.55
Consensus pattern (32 bp):
ATAAATTTAAAATTTAATCCCTATATTTTTTT
Found at i:149485 original size:2 final size:2
Alignment explanation
Indices: 149446--149477 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
149436 TGTTACTGTA
149446 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
149478 GGGAGAGACC
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:149874 original size:14 final size:13
Alignment explanation
Indices: 149842--149878 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
149832 ATTCAATTTC
*
149842 AATTTTTTATATT
1 AATTTTTTAAATT
149855 AATTTTTTAAATT
1 AATTTTTTAAATT
*
149868 TATTTTTTAAA
1 AATTTTTTAAA
149879 AAATGAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
AATTTTTTAAATT
Found at i:151345 original size:17 final size:18
Alignment explanation
Indices: 151323--151359 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
151313 TTATAAAAAT
151323 ATAATTTCATA-ATTT-TA
1 ATAATTT-ATATATTTATA
151340 ATAATTTATATATTTATA
1 ATAATTTATATATTTATA
151358 AT
1 AT
151360 TTTTAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.17
17 11 0.61
18 4 0.22
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
ATAATTTATATATTTATA
Found at i:151439 original size:8 final size:8
Alignment explanation
Indices: 151428--151458 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
151418 TTTTTATTAA
151428 TTTAAAAT
1 TTTAAAAT
151436 TTTAAAAT
1 TTTAAAAT
151444 TTTAAAAAT
1 TTT-AAAAT
151453 TTTAAA
1 TTTAAA
151459 TATAAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
TTTAAAAT
Found at i:157045 original size:19 final size:21
Alignment explanation
Indices: 157021--157060 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
157011 CTTTATTAAT
*
157021 TTAAAAT-TTTAAA-AAAAAA
1 TTAAAATACTTAAATAAAAAA
157040 TTAAAATACTTAAATAAAAAA
1 TTAAAATACTTAAATAAAAAA
157061 ATTTTCAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 5 0.28
21 6 0.33
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (21 bp):
TTAAAATACTTAAATAAAAAA
Found at i:160354 original size:17 final size:17
Alignment explanation
Indices: 160332--160365 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
160322 TACTAATTTT
*
160332 TTTTAAAGTAATAAAAA
1 TTTTAAAATAATAAAAA
*
160349 TTTTAAAATATTAAAAA
1 TTTTAAAATAATAAAAA
160366 AATGAAAAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
TTTTAAAATAATAAAAA
Found at i:160973 original size:7 final size:7
Alignment explanation
Indices: 160961--160986 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
160951 CAATATTTGA
160961 GTTTGGG
1 GTTTGGG
160968 GTTTGGG
1 GTTTGGG
160975 GTTTGGG
1 GTTTGGG
160982 GTTTG
1 GTTTG
160987 AGTTTTGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.54, T:0.46
Consensus pattern (7 bp):
GTTTGGG
Found at i:160994 original size:14 final size:13
Alignment explanation
Indices: 160956--160991 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
160946 TGGTTCAATA
160956 TTTGAGTTTGGGG
1 TTTGAGTTTGGGG
*
160969 TTTGGGGTTTGGGG
1 TTT-GAGTTTGGGG
160983 TTTGAGTTT
1 TTTGAGTTT
160992 TGGATTCGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.06, C:0.00, G:0.44, T:0.50
Consensus pattern (13 bp):
TTTGAGTTTGGGG
Found at i:161113 original size:20 final size:24
Alignment explanation
Indices: 161088--161134 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 24
161078 AAATATCATC
161088 AAATAAT-TAA-AAAAA-ATT-AT
1 AAATAATATAAGAAAAAGATTGAT
161108 AAATAATATAAGAAAAAGATTGAT
1 AAATAATATAAGAAAAAGATTGAT
161132 AAA
1 AAA
161135 ATAACCTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.30
21 3 0.13
22 5 0.22
23 3 0.13
24 5 0.22
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (24 bp):
AAATAATATAAGAAAAAGATTGAT
Found at i:168303 original size:16 final size:16
Alignment explanation
Indices: 168273--168321 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
168263 TCAATATAAT
*
168273 TCAAATATAACTTAAAC
1 TCAAA-ATAATTTAAAC
*
168290 TCAAAATAATTTAAAT
1 TCAAAATAATTTAAAC
* *
168306 TCAATATAATTAAAAC
1 TCAAAATAATTTAAAC
168322 CTAAATATTC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
16 22 0.81
17 5 0.19
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (16 bp):
TCAAAATAATTTAAAC
Found at i:168669 original size:19 final size:19
Alignment explanation
Indices: 168645--168684 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
168635 GTAGTAAAAT
* * *
168645 AATAGTGTAATAACAGTAA
1 AATAGTGAAAAAACAATAA
168664 AATAGTGAAAAAACAATAA
1 AATAGTGAAAAAACAATAA
168683 AA
1 AA
168685 AAAACAACAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.20
Consensus pattern (19 bp):
AATAGTGAAAAAACAATAA
Found at i:169495 original size:31 final size:31
Alignment explanation
Indices: 169426--169495 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
169416 TTAATAGTCT
* *
169426 ATATTTTTATAATTTTTAAAAGATTAAATCA
1 ATATTTTAATAATTTTTAAAAGATTAAAACA
*
169457 ATTTTTTAAT-ATTTTTAAAAGGATTAAAACGA
1 ATATTTTAATAATTTTTAAAA-GATTAAAAC-A
169489 A-ATTTTA
1 ATATTTTA
169496 CTTTTACTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
30 10 0.30
31 21 0.64
32 2 0.06
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (31 bp):
ATATTTTAATAATTTTTAAAAGATTAAAACA
Found at i:177592 original size:21 final size:20
Alignment explanation
Indices: 177568--177622 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
177558 GATAACAATA
177568 ATAATTTATATTAAAATGAAT
1 ATAATTTAT-TTAAAATGAAT
* **
177589 ATAATATTATTTAGAATTTAT
1 ATAAT-TTATTTAAAATGAAT
177610 AT-ATTTATTTAAA
1 ATAATTTATTTAAA
177623 TCAATTAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 8 0.28
20 2 0.07
21 15 0.52
22 4 0.14
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (20 bp):
ATAATTTATTTAAAATGAAT
Found at i:177835 original size:2 final size:2
Alignment explanation
Indices: 177828--177853 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
177818 TAAACTTTTA
177828 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
177854 TACTTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:178262 original size:30 final size:30
Alignment explanation
Indices: 178228--178290 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
178218 ACTTAACAAG
* *
178228 CAAATATCTCTAAAATAGTAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
*
178258 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
178288 CAA
1 CAA
178291 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.57, C:0.16, G:0.03, T:0.24
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:181573 original size:23 final size:23
Alignment explanation
Indices: 181547--181615 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
181537 TCCAAACAAT
181547 AACAAAAAAACCAAAACAGCAAC
1 AACAAAAAAACCAAAACAGCAAC
* *
181570 AACAAAAACAA-TAAAATAGCAAC
1 AACAAAAA-AACCAAAACAGCAAC
* *
181593 AA-AAACAACACCAAAACAACAAC
1 AACAAA-AAAACCAAAACAGCAAC
181616 CAAAACAGTA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
22 4 0.11
23 31 0.84
24 2 0.05
ACGTcount: A:0.70, C:0.25, G:0.03, T:0.03
Consensus pattern (23 bp):
AACAAAAAAACCAAAACAGCAAC
Found at i:181621 original size:12 final size:12
Alignment explanation
Indices: 181589--181622 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
181579 AATAAAATAG
*
181589 CAACAAAAACAA
1 CAACCAAAACAA
181601 C-ACCAAAACAA
1 CAACCAAAACAA
181612 CAACCAAAACA
1 CAACCAAAACA
181623 GTAAACAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (12 bp):
CAACCAAAACAA
Found at i:181636 original size:30 final size:28
Alignment explanation
Indices: 181595--181651 Score: 87
Period size: 30 Copynumber: 2.0 Consensus size: 28
181585 ATAGCAACAA
181595 AAACAACACCAAAACAACAACCAAAACAGT
1 AAACAACACCAAAACAACAA--AAAACAGT
*
181625 AAACAATACCAAAACAACAAAAAACAG
1 AAACAACACCAAAACAACAAAAAACAG
181652 CAACTAAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 7 0.27
30 19 0.73
ACGTcount: A:0.67, C:0.26, G:0.04, T:0.04
Consensus pattern (28 bp):
AAACAACACCAAAACAACAAAAAACAGT
Found at i:181649 original size:40 final size:40
Alignment explanation
Indices: 181594--181684 Score: 119
Period size: 40 Copynumber: 2.2 Consensus size: 40
181584 AATAGCAACA
* * * *
181594 AAAACAACACCAAAACAACAACCAAAACAGTAAACAATACC
1 AAAACAACA-AAAAACAACAACCAAAACAGAAAAAAACACC
* *
181635 AAAACAACAAAAAACAGCAACTAAAACAGAAAAAAACACC
1 AAAACAACAAAAAACAACAACCAAAACAGAAAAAAACACC
181675 AAAACAACAA
1 AAAACAACAA
181685 TATAATTTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 35 0.80
41 9 0.20
ACGTcount: A:0.68, C:0.25, G:0.03, T:0.03
Consensus pattern (40 bp):
AAAACAACAAAAAACAACAACCAAAACAGAAAAAAACACC
Found at i:181680 original size:18 final size:18
Alignment explanation
Indices: 181614--181680 Score: 55
Period size: 18 Copynumber: 3.5 Consensus size: 18
181604 CAAAACAACA
* * *
181614 ACCAAAACAGTAAACAAT
1 ACCAAAACAGAAAAAAAC
181632 ACCAAAACA-ACAAAAAAC
1 ACCAAAACAGA-AAAAAAC
181650 AGCAACTAAAACAGAAAAAAAC
1 A-C--C-AAAACAGAAAAAAAC
181672 ACCAAAACA
1 ACCAAAACA
181681 ACAATATAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
18 21 0.52
19 2 0.05
21 2 0.05
22 14 0.35
23 1 0.03
ACGTcount: A:0.67, C:0.24, G:0.04, T:0.04
Consensus pattern (18 bp):
ACCAAAACAGAAAAAAAC
Found at i:193851 original size:7 final size:7
Alignment explanation
Indices: 193839--193875 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
193829 TTTTCTCATC
193839 GAGAATG
1 GAGAATG
193846 GAGAATG
1 GAGAATG
193853 GAGAATG
1 GAGAATG
193860 GAGAATG
1 GAGAATG
*
193867 GAGTATG
1 GAGAATG
193874 GA
1 GA
193876 TGCTAGTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.43, T:0.16
Consensus pattern (7 bp):
GAGAATG
Found at i:204510 original size:59 final size:59
Alignment explanation
Indices: 204412--204551 Score: 185
Period size: 59 Copynumber: 2.4 Consensus size: 59
204402 TTCGGATGCA
* * * *
204412 CGGGGGCAAAATGGT-AGTTTTAGAGGGTTCGGAGACAAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGAGACAAAAATGGGATTTTTGGAACTT
*
204470 CGGGGGTAAAATGGTAATTTTTAGAAGGTTC-GAGGTCAAAAATGGGATTTTTGGAACTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGA-GACAAAAATGGGATTTTTGGAACTT
** *
204529 TAGGGATAAAATGGTAATTTTTA
1 CGGGGGTAAAATGGTAATTTTTA
204552 AATGGTTTAG
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
58 16 0.22
59 56 0.78
ACGTcount: A:0.31, C:0.06, G:0.31, T:0.31
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGAGACAAAAATGGGATTTTTGGAACTT
Found at i:204520 original size:30 final size:29
Alignment explanation
Indices: 204419--204521 Score: 91
Period size: 30 Copynumber: 3.5 Consensus size: 29
204409 GCACGGGGGC
* * * *
204419 AAAATGGTAGTTTTAGAGGGTTCGGAGACA
1 AAAATGGGATTTTTAGAAGGTTCGG-GTCA
* ***
204449 AAAATGGGATTTTTGGAA-GTTCGGGGGT
1 AAAATGGGATTTTTAGAAGGTTCGGGTCA
*
204477 AAAATGGTAATTTTTAGAAGGTTCGAGGTCA
1 AAAATGG-GATTTTTAGAAGGTTCG-GGTCA
204508 AAAATGGGATTTTT
1 AAAATGGGATTTTT
204522 GGAACTTTAG
Statistics
Matches: 57, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
28 8 0.14
29 15 0.26
30 25 0.44
31 9 0.16
ACGTcount: A:0.32, C:0.05, G:0.31, T:0.32
Consensus pattern (29 bp):
AAAATGGGATTTTTAGAAGGTTCGGGTCA
Found at i:205681 original size:35 final size:36
Alignment explanation
Indices: 205639--205725 Score: 115
Period size: 35 Copynumber: 2.4 Consensus size: 36
205629 TATTTAATAA
205639 TAATAATAATTATTATTAT-ATTAATAATAATAACAT
1 TAATAATAATTATTATTATCATTAATAATAA-AACAT
* *
205675 T-ATAATAATTATTATTGTCATTAATATTAAAACAT
1 TAATAATAATTATTATTATCATTAATAATAAAACAT
*
205710 TAATTAATATTTATTA
1 TAA-TAATAATTATTA
205726 GAACGTTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
35 22 0.49
36 12 0.27
37 11 0.24
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.47
Consensus pattern (36 bp):
TAATAATAATTATTATTATCATTAATAATAAAACAT
Found at i:205685 original size:24 final size:24
Alignment explanation
Indices: 205636--205681 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
205626 TATTATTTAA
* *
205636 TAATAATAATAATTATTATTATAT
1 TAATAATAATAATCATTATAATAT
205660 TAATAATAATAA-CATTATAATA
1 TAATAATAATAATCATTATAATA
205682 ATTATTATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
TAATAATAATAATCATTATAATAT
Found at i:213049 original size:59 final size:59
Alignment explanation
Indices: 212951--213090 Score: 185
Period size: 59 Copynumber: 2.4 Consensus size: 59
212941 TTCGGATGCA
* * * *
212951 CGGGGGCAAAATGGT-AGTTTTAGAGGGTTCGGAGACAAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGAGACAAAAATGGGATTTTTGGAACTT
*
213009 CGGGGGTAAAATGGTAATTTTTAGAAGGTTC-GAGGTCAAAAATGGGATTTTTGGAACTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGA-GACAAAAATGGGATTTTTGGAACTT
** *
213068 TAGGGATAAAATGGTAATTTTTA
1 CGGGGGTAAAATGGTAATTTTTA
213091 AATGGTTTAG
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
58 16 0.22
59 56 0.78
ACGTcount: A:0.31, C:0.06, G:0.31, T:0.31
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGAGACAAAAATGGGATTTTTGGAACTT
Found at i:213059 original size:30 final size:29
Alignment explanation
Indices: 212958--213060 Score: 91
Period size: 30 Copynumber: 3.5 Consensus size: 29
212948 GCACGGGGGC
* * * *
212958 AAAATGGTAGTTTTAGAGGGTTCGGAGACA
1 AAAATGGGATTTTTAGAAGGTTCGG-GTCA
* ***
212988 AAAATGGGATTTTTGGAA-GTTCGGGGGT
1 AAAATGGGATTTTTAGAAGGTTCGGGTCA
*
213016 AAAATGGTAATTTTTAGAAGGTTCGAGGTCA
1 AAAATGG-GATTTTTAGAAGGTTCG-GGTCA
213047 AAAATGGGATTTTT
1 AAAATGGGATTTTT
213061 GGAACTTTAG
Statistics
Matches: 57, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
28 8 0.14
29 15 0.26
30 25 0.44
31 9 0.16
ACGTcount: A:0.32, C:0.05, G:0.31, T:0.32
Consensus pattern (29 bp):
AAAATGGGATTTTTAGAAGGTTCGGGTCA
Found at i:214220 original size:35 final size:36
Alignment explanation
Indices: 214178--214264 Score: 115
Period size: 35 Copynumber: 2.4 Consensus size: 36
214168 TATTTAATAA
214178 TAATAATAATTATTATTAT-ATTAATAATAATAACAT
1 TAATAATAATTATTATTATCATTAATAATAA-AACAT
* *
214214 T-ATAATAATTATTATTGTCATTAATATTAAAACAT
1 TAATAATAATTATTATTATCATTAATAATAAAACAT
*
214249 TAATTAATATTTATTA
1 TAA-TAATAATTATTA
214265 GAACGTTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
35 22 0.49
36 12 0.27
37 11 0.24
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.47
Consensus pattern (36 bp):
TAATAATAATTATTATTATCATTAATAATAAAACAT
Found at i:214224 original size:24 final size:24
Alignment explanation
Indices: 214175--214220 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
214165 TATTATTTAA
* *
214175 TAATAATAATAATTATTATTATAT
1 TAATAATAATAATCATTATAATAT
214199 TAATAATAATAA-CATTATAATA
1 TAATAATAATAATCATTATAATA
214221 ATTATTATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
TAATAATAATAATCATTATAATAT
Found at i:215311 original size:200 final size:201
Alignment explanation
Indices: 215074--215540 Score: 681
Period size: 200 Copynumber: 2.3 Consensus size: 201
215064 CGTTTGTCTT
* * * *
215074 AATCCGCTTCTCTGTACCTCATCAGGAAGATGAATTTGGTTCACTTCTCTGTATCTCATCAGGAA
1 AATCCGCTTCTCAGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAA
* *** *
215139 GCTAACCTTTTATTGCTTTGGCCCGCTTCTCAATGTCTCATCAGGAAGCTGGGGTTCAAAGATTT
66 GCTAACCATTTATTGCTTCCACCCGCTTCTCAATGTCTCATCAGGAAGCTAGGGTTCAAAGATTT
* * *
215204 TGCTC-ATTTCGAGCCTCGTTTGGGTCTTCTCCTTAGTGTCTCATCAGGAAGATG-GTCCCTTC-
131 TGCTCGATTT-GAGCCTCGTTTGGGTCTTCTCCTCAGTGTCTCATCAGGAAGATGACT-CCGTCG
215266 ATCGTTTC
194 ATCGTTTC
* *
215274 AATCCGCTTCTCCGTATCTCATCAGGAAGACGAATTTGGTTCACTTCCCAGTATCTCATCAGGAA
1 AATCCGCTTCTCAGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAA
** *
215339 GCTAACCATTTATTGCTTCCACTTGCTTCTCAGTGTCTCATCAGGAAGCTAGGGTTCAAAGATTT
66 GCTAACCATTTATTGCTTCCACCCGCTTCTCAATGTCTCATCAGGAAGCTAGGGTTCAAAGATTT
* * *
215404 TGCTCGCTTTGAGCCTCGTTTGGGTCTTCTCCTCAGTGTCTCATCAGGAAGATGACTGCGTCGTT
131 TGCTCGATTTGAGCCTCGTTTGGGTCTTCTCCTCAGTGTCTCATCAGGAAGATGACTCCGTCGAT
*
215469 TGTTTC
196 CGTTTC
*
215475 AA-CTCGCTTCTCAGTATCTCATCAGGAAGACAAATTTGGTTCACTTCTCAGTATCTCATCAGGA
1 AATC-CGCTTCTCAGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGA
215539 AG
65 AG
215541 ACAAATTTGG
Statistics
Matches: 240, Mismatches: 23, Indels: 7
0.89 0.09 0.03
Matches are distributed among these distances:
200 169 0.70
201 71 0.30
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.34
Consensus pattern (201 bp):
AATCCGCTTCTCAGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAA
GCTAACCATTTATTGCTTCCACCCGCTTCTCAATGTCTCATCAGGAAGCTAGGGTTCAAAGATTT
TGCTCGATTTGAGCCTCGTTTGGGTCTTCTCCTCAGTGTCTCATCAGGAAGATGACTCCGTCGAT
CGTTTC
Found at i:215522 original size:37 final size:37
Alignment explanation
Indices: 215481--215577 Score: 194
Period size: 37 Copynumber: 2.6 Consensus size: 37
215471 TTTCAACTCG
215481 CTTCTCAGTATCTCATCAGGAAGACAAATTTGGTTCA
1 CTTCTCAGTATCTCATCAGGAAGACAAATTTGGTTCA
215518 CTTCTCAGTATCTCATCAGGAAGACAAATTTGGTTCA
1 CTTCTCAGTATCTCATCAGGAAGACAAATTTGGTTCA
215555 CTTCTCAGTATCTCATCAGGAAG
1 CTTCTCAGTATCTCATCAGGAAG
215578 CTAACCTTTT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (37 bp):
CTTCTCAGTATCTCATCAGGAAGACAAATTTGGTTCA
Found at i:215566 original size:238 final size:237
Alignment explanation
Indices: 215280--215732 Score: 755
Period size: 238 Copynumber: 1.9 Consensus size: 237
215270 TTTCAATCCG
* *
215280 CTTCTCCGTATCTCATCAGGAAGACGAATTTGGTTCACTTCCCAGTATCTCATCAGGAAGCTAAC
1 CTTCTCAGTATCTCATCAGGAAGACAAATTTGGTTCACTTCCCAGTATCTCATCAGGAAGCTAAC
* *
215345 CATTTATTGCTTC-CACTTGCTTCTCAGTGTCTCATCAGGAAGCTAGGGTTCAAAGATTTTGCTC
66 CATTTATTGCTACGCACAT--TTCTCAGTGTCTCATCAGGAAGCTAGGGTTCAAAGATTTTGCTC
* *
215409 GCTTTGAGCCTCGTTTGGGTCTTCTCCTCAGTGTCTCATCAGGAAGATGACTGCGTCGTTTGTTT
129 GCTTTGAGCCTCGTTTGGGTATTCTCCTCAGTGTCTCATCAGGAAGATGACTACGTCGTTTGTTT
215474 CAACTCGCTTCTCAGTATCTCATCAGGAAGACAAATTTGGTTCA
194 CAACTCGCTTCTCAGTATCTCATCAGGAAGACAAATTTGGTTCA
*
215518 CTTCTCAGTATCTCATCAGGAAGACAAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAAC
1 CTTCTCAGTATCTCATCAGGAAGACAAATTTGGTTCACTTCCCAGTATCTCATCAGGAAGCTAAC
* * * *
215583 CTTTTATTGCTACGGCCCATTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCG
66 CATTTATTGCTAC-GCACATTTCTCAGTGTCTCATCAGGAAGCTAGGGTTCAAAGATTTTGCTCG
*
215648 CTTTGAGCCTCGTTTGGGTATTCTCCTCAGTGTCTCATCAGGAAGATGATTACGTCGTTTGTTTC
130 CTTTGAGCCTCGTTTGGGTATTCTCCTCAGTGTCTCATCAGGAAGATGACTACGTCGTTTGTTTC
*
215713 AACTCGCTTCTCTGTATCTC
195 AACTCGCTTCTCAGTATCTC
215733 GAATTTGGTT
Statistics
Matches: 200, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
238 197 0.99
240 3 0.01
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.35
Consensus pattern (237 bp):
CTTCTCAGTATCTCATCAGGAAGACAAATTTGGTTCACTTCCCAGTATCTCATCAGGAAGCTAAC
CATTTATTGCTACGCACATTTCTCAGTGTCTCATCAGGAAGCTAGGGTTCAAAGATTTTGCTCGC
TTTGAGCCTCGTTTGGGTATTCTCCTCAGTGTCTCATCAGGAAGATGACTACGTCGTTTGTTTCA
ACTCGCTTCTCAGTATCTCATCAGGAAGACAAATTTGGTTCA
Found at i:215881 original size:79 final size:79
Alignment explanation
Indices: 215732--215882 Score: 248
Period size: 79 Copynumber: 1.9 Consensus size: 79
215722 CTCTGTATCT
* * * *
215732 CGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGTTACGGCTCATTTCT
1 CGAATTTGGTTCACTTCTCAGTATCTCATCAAGAAGCTAACCTTTTATTGCTACGGCCCACTTCT
215797 CAGTGTCAAGAAGA
66 CAGTGTCAAGAAGA
*
215811 CGAATTTGGTTCACTTCTCAGTATCTCATCAAGAAGCTAACCTTTTATTGCTACGGCCCGCTTCT
1 CGAATTTGGTTCACTTCTCAGTATCTCATCAAGAAGCTAACCTTTTATTGCTACGGCCCACTTCT
*
215876 TAGTGTC
66 CAGTGTC
215883 TCATCAGGAA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 66 1.00
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (79 bp):
CGAATTTGGTTCACTTCTCAGTATCTCATCAAGAAGCTAACCTTTTATTGCTACGGCCCACTTCT
CAGTGTCAAGAAGA
Found at i:216478 original size:27 final size:27
Alignment explanation
Indices: 216448--216502 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
216438 CCAAGAATTC
*
216448 TATTAAAAAGAGGATCGAAGGAAACAA
1 TATTAAAAAGAGGATCAAAGGAAACAA
** *
216475 TATTAAAGGGAGGGTCAAAGGAAACAA
1 TATTAAAAAGAGGATCAAAGGAAACAA
216502 T
1 T
216503 CATCAATTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.51, C:0.07, G:0.25, T:0.16
Consensus pattern (27 bp):
TATTAAAAAGAGGATCAAAGGAAACAA
Done.