Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015324.1 Kokia drynarioides strain JFW-HI SEQ_130370, 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: 507159
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 280 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:539 original size:45 final size:44
Alignment explanation
Indices: 462--587 Score: 162
Period size: 45 Copynumber: 2.8 Consensus size: 44
452 GCATAGCTCA
* *
462 TCAAGCCAAGGATATCAGCCTCAGGTTAACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAG-CTCAGTTTGACGAGCCACCGCAATAC
*
507 TCAAGCCAAGGATATCAGCTTCATTTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGC-TCAGTTTGACGAGCCACCGCAATAC
** * *
552 TCAAGGGAATGATATCAGGCTGAGTTTGACGAGCCA
1 TCAAGCCAAGGATATCA-GCTCAGTTTGACGAGCCA
588 TCACGATACT
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
44 1 0.01
45 68 0.96
46 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.20
Consensus pattern (44 bp):
TCAAGCCAAGGATATCAGCTCAGTTTGACGAGCCACCGCAATAC
Found at i:626 original size:21 final size:21
Alignment explanation
Indices: 593--635 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
583 AGCCATCACG
* * *
593 ATACTTTATTCCTCCCGGGCA
1 ATACTCTACTCCTCCAGGGCA
614 ATACTCTACTCCTCCAGGGCA
1 ATACTCTACTCCTCCAGGGCA
635 A
1 A
636 ATGGACCCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.35, G:0.14, T:0.28
Consensus pattern (21 bp):
ATACTCTACTCCTCCAGGGCA
Found at i:9670 original size:24 final size:22
Alignment explanation
Indices: 9617--9672 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
9607 TGTACGATTG
9617 TAAAAATTTAATTTTATTATTT
1 TAAAAATTTAATTTTATTATTT
*
9639 TAATAATTTATATATTTATT-TTT
1 TAAAAATTTA-AT-TTTATTATTT
*
9662 TAAAAAATTAA
1 TAAAAATTTAA
9673 ATCAAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 10 0.34
23 13 0.45
24 6 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TAAAAATTTAATTTTATTATTT
Found at i:11371 original size:13 final size:13
Alignment explanation
Indices: 11342--11370 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
11332 CCCCCAGAGC
11342 TTTTCTTTTTTCT
1 TTTTCTTTTTTCT
11355 TTTTCTTTTTT-T
1 TTTTCTTTTTTCT
11367 TTTT
1 TTTT
11371 TACGAAATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTCTTTTTTCT
Found at i:16075 original size:24 final size:23
Alignment explanation
Indices: 16033--16103 Score: 90
Period size: 23 Copynumber: 3.0 Consensus size: 23
16023 TCCTATGCGC
16033 GCAAATGAAAGTGGCACTTCAAT
1 GCAAATGAAAGTGGCACTTCAAT
* *
16056 GCAATTGAAATGTGGCACTT-AGGT
1 GCAAATGAAA-GTGGCACTTCA-AT
*
16080 GCAAATCAAAGTGGCACTTCAAT
1 GCAAATGAAAGTGGCACTTCAAT
16103 G
1 G
16104 TAATACTTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
23 21 0.52
24 19 0.47
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (23 bp):
GCAAATGAAAGTGGCACTTCAAT
Found at i:16462 original size:30 final size:30
Alignment explanation
Indices: 16428--16522 Score: 145
Period size: 30 Copynumber: 3.2 Consensus size: 30
16418 ACTTATTTTA
* *
16428 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTGTTACTATTTTAAAGACAT
*
16458 TTGTTAATTTTGTTACTATTTTAAAGGCAT
1 TTGTTAATTTTGTTACTATTTTAAAGACAT
*
16488 TTGTTAATTTTGTTACTATTTTAAAGGCAT
1 TTGTTAATTTTGTTACTATTTTAAAGACAT
*
16518 ATGTT
1 TTGTT
16523 TGTTAAGTTG
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 61 1.00
ACGTcount: A:0.26, C:0.05, G:0.14, T:0.55
Consensus pattern (30 bp):
TTGTTAATTTTGTTACTATTTTAAAGACAT
Found at i:18755 original size:14 final size:13
Alignment explanation
Indices: 18728--18769 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
18718 ACGAACCTTA
18728 AAGATTT-GGATTT
1 AAGATTTAGG-TTT
18741 AAGATTTCAGGTTT
1 AAGATTT-AGGTTT
18755 AAGATTTAGGTTT
1 AAGATTTAGGTTT
18768 AA
1 AA
18770 AGTTCAAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 15 0.56
14 10 0.37
15 2 0.07
ACGTcount: A:0.33, C:0.02, G:0.21, T:0.43
Consensus pattern (13 bp):
AAGATTTAGGTTT
Found at i:35406 original size:15 final size:15
Alignment explanation
Indices: 35382--35415 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
35372 TCTTGAACAA
35382 AAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAG
*
35397 AAAAAGAAAAAAAAG
1 AAAAAAAAAAAAAAG
35412 AAAA
1 AAAA
35416 GGGAAACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAG
Found at i:41741 original size:15 final size:15
Alignment explanation
Indices: 41717--41761 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
41707 AAGTGTTGGA
*
41717 GGAGGGGGAGGGGGC
1 GGAGGTGGAGGGGGC
* *
41732 GGAGGTGGAGGAGGA
1 GGAGGTGGAGGGGGC
*
41747 GGTGGTGGAGGGGGC
1 GGAGGTGGAGGGGGC
41762 TCCATCAACA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.16, C:0.04, G:0.73, T:0.07
Consensus pattern (15 bp):
GGAGGTGGAGGGGGC
Found at i:42365 original size:18 final size:18
Alignment explanation
Indices: 42327--42365 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
42317 ATGTTTCCCA
* * *
42327 GGTGTTTGATCAGATGTT
1 GGTGTTTGACCAGAAGCT
42345 GGTGTTTGACCAGAAGCT
1 GGTGTTTGACCAGAAGCT
42363 GGT
1 GGT
42366 ACTACAGAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.10, G:0.36, T:0.36
Consensus pattern (18 bp):
GGTGTTTGACCAGAAGCT
Found at i:46852 original size:42 final size:42
Alignment explanation
Indices: 46805--46896 Score: 184
Period size: 42 Copynumber: 2.2 Consensus size: 42
46795 TTCAAGGTAA
46805 TATTGCATTTGAGTGAAAGCCACCGTTGTGAATTACTCTCTT
1 TATTGCATTTGAGTGAAAGCCACCGTTGTGAATTACTCTCTT
46847 TATTGCATTTGAGTGAAAGCCACCGTTGTGAATTACTCTCTT
1 TATTGCATTTGAGTGAAAGCCACCGTTGTGAATTACTCTCTT
46889 TATTGCAT
1 TATTGCAT
46897 GCGTGCACGC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (42 bp):
TATTGCATTTGAGTGAAAGCCACCGTTGTGAATTACTCTCTT
Found at i:55050 original size:2 final size:2
Alignment explanation
Indices: 55043--55079 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
55033 AGTACTGCAT
55043 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55080 GCCTCCTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:62560 original size:51 final size:50
Alignment explanation
Indices: 62456--62560 Score: 113
Period size: 51 Copynumber: 2.1 Consensus size: 50
62446 TATGTTTCTT
* * * * * * *
62456 TTAATTTTTAGAATTATGATCAAATTGAGCTCATTTGTAAACGTTGAGGG
1 TTAATTTTTAGAATTAGGATCAAATTGAGATAATATGTAAAAGATGAGAG
*
62506 TTAATTTTTTAGAATTAGGA-CTAAATTGATATAATATGTAAAAGATGAGAG
1 TTAA-TTTTTAGAATTAGGATC-AAATTGAGATAATATGTAAAAGATGAGAG
62557 TTAA
1 TTAA
62561 ATTCGTTATT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
50 5 0.11
51 40 0.89
ACGTcount: A:0.38, C:0.05, G:0.18, T:0.39
Consensus pattern (50 bp):
TTAATTTTTAGAATTAGGATCAAATTGAGATAATATGTAAAAGATGAGAG
Found at i:67061 original size:15 final size:15
Alignment explanation
Indices: 67041--67070 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
67031 CTTTTAAATT
67041 CAGAAATTAAAACGA
1 CAGAAATTAAAACGA
67056 CAGAAATTAAAACGA
1 CAGAAATTAAAACGA
67071 ATCTAATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.13, G:0.13, T:0.13
Consensus pattern (15 bp):
CAGAAATTAAAACGA
Found at i:67464 original size:22 final size:23
Alignment explanation
Indices: 67414--67464 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
67404 AAATTATAAA
67414 TATAA-TTTATATTTAAAAATAT
1 TATAATTTTATATTTAAAAATAT
* *
67436 T-TAAATTTTATATTT-CATATAT
1 TAT-AATTTTATATTTAAAAATAT
67458 TATAATT
1 TATAATT
67465 ATTTAAACTC
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
21 1 0.04
22 13 0.54
23 10 0.42
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
TATAATTTTATATTTAAAAATAT
Found at i:69550 original size:6 final size:6
Alignment explanation
Indices: 69517--69553 Score: 53
Period size: 5 Copynumber: 6.7 Consensus size: 6
69507 AACTCAAACC
69517 CTTTTT -TTTTT -TTTTT CTTTTT C-TTTT CTTTTT CTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTT
69554 GTTTCGATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 15 0.52
6 14 0.48
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
CTTTTT
Found at i:70505 original size:2 final size:2
Alignment explanation
Indices: 70500--70531 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
70490 TGCTTTTTTT
70500 TA TA TA 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 TA TA TA
70532 ATAGAATGAC
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):
TA
Found at i:79924 original size:24 final size:24
Alignment explanation
Indices: 79897--79964 Score: 109
Period size: 24 Copynumber: 2.8 Consensus size: 24
79887 ATCTTTCAGT
*
79897 TAAACTCTGTTTAATTGTTTCAAA
1 TAAACTCTGTTTATTTGTTTCAAA
**
79921 TAAACTCTGTTTATTTGTTTCAGT
1 TAAACTCTGTTTATTTGTTTCAAA
79945 TAAACTCTGTTTATTTGTTT
1 TAAACTCTGTTTATTTGTTT
79965 GAGTCAAACT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.25, C:0.12, G:0.10, T:0.53
Consensus pattern (24 bp):
TAAACTCTGTTTATTTGTTTCAAA
Found at i:79973 original size:24 final size:23
Alignment explanation
Indices: 79897--79976 Score: 97
Period size: 24 Copynumber: 3.3 Consensus size: 23
79887 ATCTTTCAGT
* *
79897 TAAACTCTGTTTAATTGTTTCAAA
1 TAAACTCTGTTTATTTGTTT-AAG
*
79921 TAAACTCTGTTTATTTGTTTCAG
1 TAAACTCTGTTTATTTGTTTAAG
*
79944 TTAAACTCTGTTTATTTGTTTGAG
1 -TAAACTCTGTTTATTTGTTTAAG
79968 TCAAACTCT
1 T-AAACTCT
79977 TATTAGTCTA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
23 2 0.04
24 48 0.96
ACGTcount: A:0.26, C:0.14, G:0.11, T:0.49
Consensus pattern (23 bp):
TAAACTCTGTTTATTTGTTTAAG
Found at i:81489 original size:76 final size:76
Alignment explanation
Indices: 81363--81513 Score: 293
Period size: 76 Copynumber: 2.0 Consensus size: 76
81353 GATGTTAGGT
*
81363 ATGTACCTGATTTATGATAGAATCTCATCTCCTTAAGTATTTTAGACTCAAAAGGTTGTAGAATC
1 ATGTACCTGATTTACGATAGAATCTCATCTCCTTAAGTATTTTAGACTCAAAAGGTTGTAGAATC
81428 AACATCGAGTC
66 AACATCGAGTC
81439 ATGTACCTGATTTACGATAGAATCTCATCTCCTTAAGTATTTTAGACTCAAAAGGTTGTAGAATC
1 ATGTACCTGATTTACGATAGAATCTCATCTCCTTAAGTATTTTAGACTCAAAAGGTTGTAGAATC
81504 AACATCGAGT
66 AACATCGAGT
81514 TGAGTGCCAA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 74 1.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (76 bp):
ATGTACCTGATTTACGATAGAATCTCATCTCCTTAAGTATTTTAGACTCAAAAGGTTGTAGAATC
AACATCGAGTC
Found at i:84110 original size:13 final size:12
Alignment explanation
Indices: 84061--84113 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 12
84051 CGTCAGCATT
84061 AATTATTTTTCAA
1 AATTATTTTT-AA
84074 AATATAATTTTTTAA
1 AAT-T-A-TTTTTAA
84089 AATTA-TTTTAA
1 AATTATTTTTAA
84100 AATTAATTTTTAA
1 AATT-ATTTTTAA
84113 A
1 A
84114 TATAAAATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
11 10 0.29
12 1 0.03
13 11 0.31
14 2 0.06
15 6 0.17
16 5 0.14
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (12 bp):
AATTATTTTTAA
Found at i:84186 original size:7 final size:7
Alignment explanation
Indices: 84174--84206 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
84164 TCTCCTTCTC
84174 CTTCCCT
1 CTTCCCT
84181 CTTCCCT
1 CTTCCCT
*
84188 CTTCCCC
1 CTTCCCT
84195 CTTCCC-
1 CTTCCCT
84201 CTTCCC
1 CTTCCC
84207 CACCACTTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (7 bp):
CTTCCCT
Found at i:84193 original size:14 final size:13
Alignment explanation
Indices: 84167--84207 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
84157 TTTCTGCTCT
*
84167 CCTTCTCCTTCCC
1 CCTTCCCCTTCCC
*
84180 TCTTCCCTCTTCCC
1 CCTTCCC-CTTCCC
84194 CCTTCCCCTTCCC
1 CCTTCCCCTTCCC
84207 C
1 C
84208 ACCACTTGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (13 bp):
CCTTCCCCTTCCC
Found at i:84778 original size:12 final size:12
Alignment explanation
Indices: 84738--84789 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
84728 AAACCCTAGG
* *
84738 GAAGGGGAAGGG
1 GAAGGGGAAAGA
*
84750 GAAGGGGAAGAGG
1 GAAGGGGAA-AGA
84763 GAAGGGGAAAGA
1 GAAGGGGAAAGA
* *
84775 GAAGGAGAATGA
1 GAAGGGGAAAGA
84787 GAA
1 GAA
84790 TGAGAGCAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
12 24 0.69
13 11 0.31
ACGTcount: A:0.44, C:0.00, G:0.54, T:0.02
Consensus pattern (12 bp):
GAAGGGGAAAGA
Found at i:84778 original size:19 final size:18
Alignment explanation
Indices: 84738--84779 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
84728 AAACCCTAGG
* *
84738 GAAGGGGAAGGGGAAGGG
1 GAAGGGGAAGGGGAAAGA
84756 GAAGAGGGAAGGGGAAAGA
1 GAAG-GGGAAGGGGAAAGA
84775 GAAGG
1 GAAGG
84780 AGAATGAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (18 bp):
GAAGGGGAAGGGGAAAGA
Found at i:84783 original size:6 final size:6
Alignment explanation
Indices: 84736--84771 Score: 63
Period size: 6 Copynumber: 5.8 Consensus size: 6
84726 AGAAACCCTA
84736 GGGAAG GGGAAG GGGAAG GGGAAG AGGGAAG GGGAA
1 GGGAAG GGGAAG GGGAAG GGGAAG -GGGAAG GGGAA
84772 AGAGAAGGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (6 bp):
GGGAAG
Found at i:84888 original size:11 final size:11
Alignment explanation
Indices: 84847--84887 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
84837 ATAATTTTAT
*
84847 ATTTAAAAATA
1 ATTTTAAAATA
*
84858 ATTTTAAATTA
1 ATTTTAAAATA
84869 ATTTTAAAAT-
1 ATTTTAAAATA
84879 ATTTTAAAA
1 ATTTTAAAA
84888 AATAATTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATTTTAAAATA
Found at i:88125 original size:3 final size:3
Alignment explanation
Indices: 88117--88159 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
88107 TCTTCATTAT
* * *
88117 TTC TTC TTC TTC TTC TTC TTC TTA TCC TTT TTC -TC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
88160 TTATTGCTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:96825 original size:23 final size:22
Alignment explanation
Indices: 96799--96845 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
96789 ATTTAAAAGG
96799 TAAAA-GAATTAAATCTCTAAAAT
1 TAAAAGGAA-TAAATCTC-AAAAT
*
96822 TAAAAGGGATAAATCTCAAAAT
1 TAAAAGGAATAAATCTCAAAAT
96844 TA
1 TA
96846 TACATAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 13 0.59
24 2 0.09
ACGTcount: A:0.55, C:0.09, G:0.09, T:0.28
Consensus pattern (22 bp):
TAAAAGGAATAAATCTCAAAAT
Found at i:97150 original size:29 final size:30
Alignment explanation
Indices: 97088--97150 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
97078 AATTTACAAG
* *
97088 AATTGGATCAAATCAAAATTTCATGTATAA
1 AATTGCATAAAATCAAAATTTCATGTATAA
*
97118 AATTGCATAAAATCAAAA-TTCATGTATAC
1 AATTGCATAAAATCAAAATTTCATGTATAA
97147 AATT
1 AATT
97151 ACACATTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 14 0.47
30 16 0.53
ACGTcount: A:0.48, C:0.11, G:0.08, T:0.33
Consensus pattern (30 bp):
AATTGCATAAAATCAAAATTTCATGTATAA
Found at i:101588 original size:3 final size:3
Alignment explanation
Indices: 101582--101631 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
101572 AGTAACATAG
101582 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
101630 AT
1 AT
101632 CCATGGCTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:101833 original size:20 final size:20
Alignment explanation
Indices: 101810--101847 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
101800 TTTATCTGCA
101810 TACTATTTATTTAT-TTTTGT
1 TACT-TTTATTTATATTTTGT
101830 TACTTTTATTTATATTTT
1 TACTTTTATTTATATTTT
101848 TAGGCATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (20 bp):
TACTTTTATTTATATTTTGT
Found at i:106498 original size:10 final size:10
Alignment explanation
Indices: 106483--106535 Score: 52
Period size: 11 Copynumber: 5.0 Consensus size: 10
106473 GGTATCTTTT
106483 AAAAAAGAAA
1 AAAAAAGAAA
106493 AAAAAAGAAA
1 AAAAAAGAAA
**
106503 AGAAGTAGAAA
1 A-AAAAAGAAA
*
106514 AGAAAAAGGAAG
1 A-AAAAA-GAAA
106526 AAAAAAGAAA
1 AAAAAAGAAA
106536 GTCAAGATGA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
10 14 0.40
11 17 0.49
12 4 0.11
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:107689 original size:7 final size:7
Alignment explanation
Indices: 107661--107707 Score: 60
Period size: 7 Copynumber: 6.6 Consensus size: 7
107651 AAATGTTTTG
107661 ATAATTA
1 ATAATTA
107668 ATAA-TA
1 ATAATTA
107674 ATAATATTA
1 AT-A-ATTA
*
107683 AAAATTA
1 ATAATTA
107690 ATAATTA
1 ATAATTA
107697 ATAATTA
1 ATAATTA
107704 ATAA
1 ATAA
107708 AAAAATGGGG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
6 4 0.11
7 26 0.74
8 2 0.06
9 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
ATAATTA
Found at i:107711 original size:26 final size:28
Alignment explanation
Indices: 107661--107713 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
107651 AAATGTTTTG
*
107661 ATAATTAATAATAATAATATTAAAAATTA
1 ATAATTAATAAT-ATAATATAAAAAATTA
107690 ATAATTAATAAT-TAATA-AAAAAAT
1 ATAATTAATAATATAATATAAAAAAT
107714 GGGGAAACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 6 0.26
27 5 0.22
29 12 0.52
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (28 bp):
ATAATTAATAATATAATATAAAAAATTA
Found at i:108898 original size:29 final size:29
Alignment explanation
Indices: 108850--109203 Score: 289
Period size: 29 Copynumber: 12.0 Consensus size: 29
108840 CATTTTTTAC
108850 CTTCCAAAAATTACCATTTTACCCCCGAA
1 CTTCCAAAAATTACCATTTTACCCCCGAA
*
108879 CTTCCAAAAA-TCCCATTTTTGA-CCCCGAA
1 CTTCCAAAAATTACCA-TTTT-ACCCCCGAA
* * *
108908 CTTCCAAAAA-TCCCATTTTTAACCTCGAA
1 CTTCCAAAAATTACCA-TTTTACCCCCGAA
*
108937 CCTTCCAAAAATTACCATTTCACCCCCGAA
1 -CTTCCAAAAATTACCATTTTACCCCCGAA
*
108967 CTTCCAAAAA-T-CTCATTTTTGA-CCCCAAA
1 CTTCCAAAAATTAC-CA-TTTT-ACCCCCGAA
* * **
108996 CCTTTCAAAAATTACCATTTCACACCCTAAA
1 -CTTCCAAAAATTACCATTTTAC-CCCCGAA
* *
109027 CTTCCAAAAA-TCCCATTTTTGA-TCCCGAA
1 CTTCCAAAAATTACCA-TTTT-ACCCCCGAA
* *
109056 CCTTCCAAAAATTACCATTTCACCCTCGAA
1 -CTTCCAAAAATTACCATTTTACCCCCGAA
* *
109086 CTTCCAAAAA-TCCCATTTTTGA-CCTCGAA
1 CTTCCAAAAATTACCA-TTTT-ACCCCCGAA
*
109115 CCTTCCAAAAATTACCATTTTACCACCGAA
1 -CTTCCAAAAATTACCATTTTACCCCCGAA
* * *
109145 CTTCCAAAAA-TCCCATTTTTAACCCAGAA
1 CTTCCAAAAATTACCA-TTTTACCCCCGAA
*
109174 CCTTCCAAAAATTACGATTTTACCCCCGAA
1 -CTTCCAAAAATTACCATTTTACCCCCGAA
109204 TGTTTGAAAT
Statistics
Matches: 265, Mismatches: 34, Indels: 51
0.76 0.10 0.15
Matches are distributed among these distances:
27 1 0.00
28 16 0.06
29 117 0.44
30 105 0.40
31 25 0.09
32 1 0.00
ACGTcount: A:0.34, C:0.33, G:0.04, T:0.28
Consensus pattern (29 bp):
CTTCCAAAAATTACCATTTTACCCCCGAA
Found at i:108971 original size:59 final size:58
Alignment explanation
Indices: 108850--109203 Score: 437
Period size: 59 Copynumber: 6.0 Consensus size: 58
108840 CATTTTTTAC
* * * *
108850 CTTCCAAAAATTACCA-TTTTACCCCCGAA-CTTCCAAAAA-TCCCATTTTTGA-CCCCGAA
1 CTTCCAAAAA-TCCCATTTTTA-ACCCGAACCTTCCAAAAATTACCA--TTTCACCCCCGAA
108908 CTTCCAAAAATCCCATTTTTAACCTCGAACCTTCCAAAAATTACCATTTCACCCCCGAA
1 CTTCCAAAAATCCCATTTTTAACC-CGAACCTTCCAAAAATTACCATTTCACCCCCGAA
* * * * **
108967 CTTCCAAAAATCTCATTTTTGACCCCAAACCTTTCAAAAATTACCATTTCACACCCTAAA
1 CTTCCAAAAATCCCATTTTT-AACCCGAACCTTCCAAAAATTACCATTTCAC-CCCCGAA
* *
109027 CTTCCAAAAATCCCATTTTTGATCCCGAACCTTCCAAAAATTACCATTTCACCCTCGAA
1 CTTCCAAAAATCCCATTTTT-AACCCGAACCTTCCAAAAATTACCATTTCACCCCCGAA
* * *
109086 CTTCCAAAAATCCCATTTTTGACCTCGAACCTTCCAAAAATTACCATTTTACCACCGAA
1 CTTCCAAAAATCCCATTTTTAACC-CGAACCTTCCAAAAATTACCATTTCACCCCCGAA
* *
109145 CTTCCAAAAATCCCATTTTTAACCCAGAACCTTCCAAAAATTACGATTTTACCCCCGAA
1 CTTCCAAAAATCCCATTTTTAACCC-GAACCTTCCAAAAATTACCATTTCACCCCCGAA
109204 TGTTTGAAAT
Statistics
Matches: 262, Mismatches: 25, Indels: 17
0.86 0.08 0.06
Matches are distributed among these distances:
57 6 0.02
58 26 0.10
59 170 0.65
60 60 0.23
ACGTcount: A:0.34, C:0.33, G:0.04, T:0.28
Consensus pattern (58 bp):
CTTCCAAAAATCCCATTTTTAACCCGAACCTTCCAAAAATTACCATTTCACCCCCGAA
Found at i:109103 original size:119 final size:117
Alignment explanation
Indices: 108906--109203 Score: 454
Period size: 119 Copynumber: 2.5 Consensus size: 117
108896 TTTGACCCCG
108906 AACTTCCAAAAATCCCATTTTTAACCTCGAACCTTCCAAAAATTACCATTTCACCCCCGAACTTC
1 AACTTCCAAAAATCCCATTTTTAACC-CGAACCTTCCAAAAATTACCATTTCACCCCCGAACTTC
* *
108971 CAAAAATCTCATTTTTGACCCCAAACCTTTCAAAAATTACCATTTCA-CACCCTA
65 CAAAAATCCCATTTTTGACCCCAAACCTTCCAAAAATTACCATTTCACCA-CC-A
* *
109025 AACTTCCAAAAATCCCATTTTTGATCCCGAACCTTCCAAAAATTACCATTTCACCCTCGAACTTC
1 AACTTCCAAAAATCCCATTTTT-AACCCGAACCTTCCAAAAATTACCATTTCACCCCCGAACTTC
* * * *
109090 CAAAAATCCCATTTTTGACCTCGAACCTTCCAAAAATTACCATTTTACCACCG
65 CAAAAATCCCATTTTTGACCCCAAACCTTCCAAAAATTACCATTTCACCACCA
* *
109143 AACTTCCAAAAATCCCATTTTTAACCCAGAACCTTCCAAAAATTACGATTTTACCCCCGAA
1 AACTTCCAAAAATCCCATTTTTAACCC-GAACCTTCCAAAAATTACCATTTCACCCCCGAA
109204 TGTTTGAAAT
Statistics
Matches: 164, Mismatches: 12, Indels: 7
0.90 0.07 0.04
Matches are distributed among these distances:
117 4 0.02
118 52 0.32
119 103 0.63
120 5 0.03
ACGTcount: A:0.35, C:0.33, G:0.04, T:0.28
Consensus pattern (117 bp):
AACTTCCAAAAATCCCATTTTTAACCCGAACCTTCCAAAAATTACCATTTCACCCCCGAACTTCC
AAAAATCCCATTTTTGACCCCAAACCTTCCAAAAATTACCATTTCACCACCA
Found at i:118714 original size:14 final size:15
Alignment explanation
Indices: 118690--118731 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 15
118680 TCATAAATAA
118690 ATAATTATATTATTT
1 ATAATTATATTATTT
118705 ATAATATATTATTATTTT
1 ATAAT-TA-TATTA-TTT
118723 ATAATTATA
1 ATAATTATA
118732 AAGTTTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 5 0.21
16 4 0.17
17 7 0.29
18 8 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATAATTATATTATTT
Found at i:123046 original size:39 final size:39
Alignment explanation
Indices: 122992--123078 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
122982 AAGGGTTTTT
*
122992 ATATTTTAATCTTTTTATTGAATATCCGGTCATAAATTA
1 ATATTTTAATCTTTTTATTGAATATCCCGTCATAAATTA
*
123031 ATATTTTAATCTTTTTATTGAATATCCCGTCATAAATTT
1 ATATTTTAATCTTTTTATTGAATATCCCGTCATAAATTA
123070 ATATTTTAA
1 ATATTTTAA
123079 ATACGTGATT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.33, C:0.10, G:0.06, T:0.51
Consensus pattern (39 bp):
ATATTTTAATCTTTTTATTGAATATCCCGTCATAAATTA
Found at i:129313 original size:4 final size:4
Alignment explanation
Indices: 129304--129330 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
129294 TTTTCAAGAA
129304 ACAT ACAT ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACA
129331 CACACACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (4 bp):
ACAT
Found at i:130942 original size:3 final size:3
Alignment explanation
Indices: 130936--130970 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
130926 TTCAATCTGC
* *
130936 TCT TCT TCT TCC TCT TCC TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
130971 CTCCTCCTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (3 bp):
TCT
Found at i:130944 original size:18 final size:18
Alignment explanation
Indices: 130921--130973 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
130911 CTCCAACTCC
*
130921 TCTTCTTCAATC-TGCTCT
1 TCTTCTTC-ATCTTCCTCT
*
130939 TCTTCTTCCTCTTCCTCT
1 TCTTCTTCATCTTCCTCT
*
130957 TCTTCTTCTTCTTCCTC
1 TCTTCTTCATCTTCCTC
130974 CTCCTCCTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
17 2 0.06
18 29 0.94
ACGTcount: A:0.04, C:0.40, G:0.02, T:0.55
Consensus pattern (18 bp):
TCTTCTTCATCTTCCTCT
Found at i:130951 original size:6 final size:6
Alignment explanation
Indices: 130935--130979 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
130925 CTTCAATCTG
* * * *
130935 CTCTTC TTCTTC CTCTTC CTCTTC TTCTTC TTCTTC CTCCTC CTC
1 CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTC
130980 CTCTTCCTCC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (6 bp):
CTCTTC
Found at i:138232 original size:50 final size:49
Alignment explanation
Indices: 138170--138310 Score: 158
Period size: 50 Copynumber: 2.8 Consensus size: 49
138160 TTTATTTTTC
*
138170 AGATATGATGTTTTAAATAAATATAAATATTTATTTA-ATTTGTTTTGTTT
1 AGATATGATGTTTTAAATAAACATAAATATTTATTTATA-TTG-TTTGTTT
* *
138220 AGATATGGTGTTTTACATAAACATAAATATTTATTTATATTGTTTGTTT
1 AGATATGATGTTTTAAATAAACATAAATATTTATTTATATTGTTTGTTT
* * * * * **
138269 AGATCTTATATTTTATATAAATAATTTATATTTATTTATATT
1 AGATATGATGTTTTAAATAAA-CATAAATATTTATTTATATT
138311 ACATAAACAT
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
49 23 0.29
50 54 0.69
51 1 0.01
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.54
Consensus pattern (49 bp):
AGATATGATGTTTTAAATAAACATAAATATTTATTTATATTGTTTGTTT
Found at i:143353 original size:14 final size:14
Alignment explanation
Indices: 143336--143394 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
143326 ACATAAAAAT
*
143336 ATTAAATTTAATCA
1 ATTAAATTTAATAA
*
143350 ATTATATTTAATAA
1 ATTAAATTTAATAA
*
143364 ATAATAAATTTAATTA
1 AT--TAAATTTAATAA
* *
143380 ATTATATTCAATAA
1 ATTAAATTTAATAA
143394 A
1 A
143395 GTTGACTAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
14 24 0.67
16 12 0.33
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTAAATTTAATAA
Found at i:143366 original size:30 final size:30
Alignment explanation
Indices: 143332--143394 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
143322 TTTAACATAA
* *
143332 AAATATTAAATTTAATCAATTATATTTAAT
1 AAATAATAAATTTAATCAATTATATTCAAT
*
143362 AAATAATAAATTTAATTAATTATATTCAAT
1 AAATAATAAATTTAATCAATTATATTCAAT
143392 AAA
1 AAA
143395 GTTGACTAAA
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:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (30 bp):
AAATAATAAATTTAATCAATTATATTCAAT
Found at i:143638 original size:22 final size:21
Alignment explanation
Indices: 143611--143661 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
143601 AAAAATAGTT
143611 AAAATTTACAACTTAAAAAAAA
1 AAAATTTACAAC-TAAAAAAAA
* * *
143633 AAAATTGTCCAGCTAAAAAATA
1 AAAATT-TACAACTAAAAAAAA
143655 AAAATTT
1 AAAATTT
143662 GCATATATGC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 20 0.80
23 4 0.16
ACGTcount: A:0.61, C:0.10, G:0.04, T:0.25
Consensus pattern (21 bp):
AAAATTTACAACTAAAAAAAA
Found at i:144485 original size:21 final size:19
Alignment explanation
Indices: 144432--144485 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
144422 AAATTATTTA
144432 AAAATTTAAAAACAAATATT
1 AAAATTTAAAAA-AAATATT
*
144452 AAAATTTACAAAAAAA-CTT
1 AAAATTTA-AAAAAAATATT
144471 ATAAATATTAAAAAA
1 A-AAAT-TTAAAAAA
144486 CGAGTAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
19 3 0.10
20 20 0.67
21 7 0.23
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAATTTAAAAAAAATATT
Found at i:144626 original size:9 final size:9
Alignment explanation
Indices: 144612--144663 Score: 61
Period size: 9 Copynumber: 5.7 Consensus size: 9
144602 CAAAAAACCG
144612 TAAAAACTTA
1 TAAAAA-TTA
*
144622 TAAAACTTA
1 TAAAAATTA
144631 TAATAAATTA
1 TAA-AAATTA
*
144641 TAAAAATCA
1 TAAAAATTA
144650 T-AAAATTA
1 TAAAAATTA
144658 TAAAAA
1 TAAAAA
144664 AATCATTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 7 0.19
9 16 0.44
10 13 0.36
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (9 bp):
TAAAAATTA
Found at i:145139 original size:14 final size:15
Alignment explanation
Indices: 145114--145142 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
145104 GAATCAATAA
145114 ATAAATTTTTATATT
1 ATAAATTTTTATATT
145129 ATAAA-TTTTATATT
1 ATAAATTTTTATATT
145143 TTTATAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATAAATTTTTATATT
Found at i:145191 original size:10 final size:10
Alignment explanation
Indices: 145178--145262 Score: 83
Period size: 10 Copynumber: 9.0 Consensus size: 10
145168 TTTTTATAAG
145178 TTTATATATT
1 TTTATATATT
145188 TTTA-ATATT
1 TTTATATATT
*
145197 TTAATATATT
1 TTTATATATT
*
145207 TTTAGA-ATT
1 TTTATATATT
*
145216 TTTATA-A-G
1 TTTATATATT
145224 TTTATATATT
1 TTTATATATT
145234 TTTCA-ATATT
1 TTT-ATATATT
*
145244 TTTATAAATT
1 TTTATATATT
145254 TTTA-ATATT
1 TTTATATATT
145263 CTTAATAATT
Statistics
Matches: 62, Mismatches: 8, Indels: 11
0.77 0.10 0.14
Matches are distributed among these distances:
8 6 0.10
9 23 0.37
10 32 0.52
11 1 0.02
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.62
Consensus pattern (10 bp):
TTTATATATT
Found at i:145203 original size:19 final size:20
Alignment explanation
Indices: 145181--145261 Score: 59
Period size: 19 Copynumber: 4.2 Consensus size: 20
145171 TTATAAGTTT
145181 ATATATTTTT-AATATTTTA
1 ATATATTTTTAAATATTTTA
145200 ATATATTTTTAGAAT-TTTT-
1 ATATATTTTTA-AATATTTTA
* *
145219 ATA-A-GTTTATATATTTTTCA
1 ATATATTTTTAAATA-TTTT-A
145239 ATAT-TTTTATAAAT-TTTTA
1 ATATATTTT-TAAATATTTTA
145258 ATAT
1 ATAT
145262 TCTTAATAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 18
0.69 0.06 0.25
Matches are distributed among these distances:
16 2 0.04
17 4 0.08
18 5 0.10
19 18 0.37
20 11 0.22
21 5 0.10
22 4 0.08
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.60
Consensus pattern (20 bp):
ATATATTTTTAAATATTTTA
Found at i:145216 original size:46 final size:47
Alignment explanation
Indices: 145159--145258 Score: 166
Period size: 46 Copynumber: 2.1 Consensus size: 47
145149 AAAATGTAAC
*
145159 TTTTTAAAATTTTTATAAGTTTATATATTTTT-AATATTTTAATATA
1 TTTTTAAAATTTTTATAAGTTTATATATTTTTCAATATTTTAATAAA
* *
145205 TTTTTAGAATTTTTATAAGTTTATATATTTTTCAATATTTTTATAAA
1 TTTTTAAAATTTTTATAAGTTTATATATTTTTCAATATTTTAATAAA
145252 TTTTTAA
1 TTTTTAA
145259 TATTCTTAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
46 31 0.63
47 18 0.37
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (47 bp):
TTTTTAAAATTTTTATAAGTTTATATATTTTTCAATATTTTAATAAA
Found at i:145244 original size:28 final size:29
Alignment explanation
Indices: 145178--145250 Score: 82
Period size: 28 Copynumber: 2.6 Consensus size: 29
145168 TTTTTATAAG
* *
145178 TTTATATATTTTTA-ATATTTTAATATATT
1 TTTAGATATTTTTATA-AGTTTAATATATT
145207 TTTAGA-ATTTTTATAAGTTT-ATATATT
1 TTTAGATATTTTTATAAGTTTAATATATT
145234 TTTCA-ATATTTTTATAA
1 TTT-AGATATTTTTATAA
145251 ATTTTTAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
27 11 0.28
28 22 0.56
29 6 0.15
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (29 bp):
TTTAGATATTTTTATAAGTTTAATATATT
Found at i:145262 original size:19 final size:19
Alignment explanation
Indices: 145159--145262 Score: 83
Period size: 18 Copynumber: 5.6 Consensus size: 19
145149 AAAATGTAAC
* *
145159 TTTTTAAAATTTTTATAAG
1 TTTTTAATATTTTTATAAA
* *
145178 TTTAT-ATATTTTTA-ATA
1 TTTTTAATATTTTTATAAA
145195 -TTTTAATATATTTT-TAGAA
1 TTTTTAATAT-TTTTATA-AA
** *
145214 TTTTT-ATAAGTTTATATA
1 TTTTTAATATTTTTATAAA
145232 TTTTTCAATATTTTTATAAA
1 TTTTT-AATATTTTTATAAA
145252 TTTTTAATATT
1 TTTTTAATATT
145263 CTTAATAATT
Statistics
Matches: 65, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
16 3 0.05
17 5 0.08
18 22 0.34
19 16 0.25
20 19 0.29
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTTTAATATTTTTATAAA
Found at i:145273 original size:19 final size:20
Alignment explanation
Indices: 145231--145270 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
145221 AAGTTTATAT
*
145231 ATTTTTCAATATTTTTATAA
1 ATTTTTCAATATTTTAATAA
145251 ATTTTT-AATATTCTTAATAA
1 ATTTTTCAATATT-TTAATAA
145271 TTTACTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTTTCAATATTTTAATAA
Found at i:146094 original size:33 final size:33
Alignment explanation
Indices: 146050--146126 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 33
146040 GCTCACGGCG
*
146050 TCAGCTTGCACACACCAAGGGGAATGCGTGATC
1 TCAGCTCGCACACACCAAGGGGAATGCGTGATC
** *
146083 TCAGCTCGCACACATTAAGGGGAATGTGTGATC
1 TCAGCTCGCACACACCAAGGGGAATGCGTGATC
146116 TCAGCTCGCAC
1 TCAGCTCGCAC
146127 GTACCTAAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.26, C:0.27, G:0.26, T:0.21
Consensus pattern (33 bp):
TCAGCTCGCACACACCAAGGGGAATGCGTGATC
Found at i:150085 original size:14 final size:14
Alignment explanation
Indices: 150066--150092 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
150056 TTAGAGAAAT
150066 GCAAAACTTTTTCA
1 GCAAAACTTTTTCA
150080 GCAAAACTTTTTC
1 GCAAAACTTTTTC
150093 GACAACATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.37
Consensus pattern (14 bp):
GCAAAACTTTTTCA
Found at i:151770 original size:19 final size:21
Alignment explanation
Indices: 151733--151771 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
151723 GACGTTTGGT
*
151733 ATTGATTTATGATATAAAATG
1 ATTGATTTATGATAAAAAATG
151754 ATTG-TTTA-GATAAAAAAT
1 ATTGATTTATGATAAAAAAT
151772 CGAGTCGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 4 0.24
21 4 0.24
ACGTcount: A:0.46, C:0.00, G:0.13, T:0.41
Consensus pattern (21 bp):
ATTGATTTATGATAAAAAATG
Found at i:160246 original size:28 final size:27
Alignment explanation
Indices: 160215--160267 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
160205 TTTACAGTAA
* * *
160215 TTTTGAATTTTTTACAACTTTTAATTTT
1 TTTTGAATATTGTA-AAATTTTAATTTT
160243 TTTTGAATATTGTAAAATTTTAATT
1 TTTTGAATATTGTAAAATTTTAATT
160268 ATTTCTTAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (27 bp):
TTTTGAATATTGTAAAATTTTAATTTT
Found at i:164576 original size:69 final size:67
Alignment explanation
Indices: 164449--164582 Score: 205
Period size: 67 Copynumber: 2.0 Consensus size: 67
164439 TTTAATAGAT
*
164449 TTAACATTAAATTAAATTTAATACTTATATTGATAGTATTTATTAATTTAATATTAAAGTGATTA
1 TTAACATTAAATTAAATCTAATACTTATATTGATAGTATTTATTAATTTAATATTAAAGTGATTA
164514 TC
66 TC
* * * *
164516 TTAATATTAAATTTAATCTAATATTTATCTTGATAAGTATTATATTAATTTAATATTAAAGTGAT
1 TTAACATTAAATTAAATCTAATACTTATATTGAT-AGTATT-TATTAATTTAATATTAAAGTGAT
164581 TA
64 TA
164583 AATTTAACAT
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
67 29 0.48
68 6 0.10
69 25 0.42
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.49
Consensus pattern (67 bp):
TTAACATTAAATTAAATCTAATACTTATATTGATAGTATTTATTAATTTAATATTAAAGTGATTA
TC
Found at i:165375 original size:6 final size:6
Alignment explanation
Indices: 165364--165392 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
165354 CAAAATTTTC
165364 CCCTTT CCCTTT CCCTTT CCCTTT CCCTT
1 CCCTTT CCCTTT CCCTTT CCCTTT CCCTT
165393 AGTCAAAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (6 bp):
CCCTTT
Found at i:167898 original size:22 final size:22
Alignment explanation
Indices: 167857--167898 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
167847 TAGTTGATAG
**
167857 AAAAAATTCAAATATTAATACA
1 AAAAAATTCAAATACAAATACA
*
167879 AAAAAATTTAAATACAAATA
1 AAAAAATTCAAATACAAATA
167899 TAAGAGAAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (22 bp):
AAAAAATTCAAATACAAATACA
Found at i:184223 original size:6 final size:6
Alignment explanation
Indices: 184213--184250 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
184203 TTTTAATATA
*
184213 AATTAA AATTAC AATTAC AATTAC AATTAC AAGTTAC A
1 AATTAC AATTAC AATTAC AATTAC AATTAC AA-TTAC A
184251 TATATTCAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
6 25 0.83
7 5 0.17
ACGTcount: A:0.53, C:0.13, G:0.03, T:0.32
Consensus pattern (6 bp):
AATTAC
Found at i:186729 original size:31 final size:29
Alignment explanation
Indices: 186656--186736 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 29
186646 AGAATTGGAT
*
186656 AAAATCAAAATTTCATGTATAAAATTGCAC
1 AAAATC-AAAGTTCATGTATAAAATTGCAC
* *
186686 AAAATCAAAGTTCATGTATACAATTGCAT
1 AAAATCAAAGTTCATGTATAAAATTGCAC
*
186715 ATTAAATCATAGTTCATGTATA
1 A--AAATCAAAGTTCATGTATA
186737 GTTTTGGTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
29 21 0.47
30 6 0.13
31 18 0.40
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (29 bp):
AAAATCAAAGTTCATGTATAAAATTGCAC
Found at i:192755 original size:2 final size:2
Alignment explanation
Indices: 192748--192780 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
192738 AGGTTTCCAT
192748 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
192781 TATGGAACAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:194152 original size:24 final size:23
Alignment explanation
Indices: 194125--194194 Score: 104
Period size: 23 Copynumber: 3.0 Consensus size: 23
194115 TCATCAACAT
194125 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCAATTA-A
* *
194149 TGTTCATGAACATGTTCATTTAA
1 TGTTCGTGAACATGTTCAATTAA
*
194172 TGTTCGAGAACATGTTCAATTAA
1 TGTTCGTGAACATGTTCAATTAA
194195 GTTAAATGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
23 21 0.51
24 20 0.49
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCAATTAA
Found at i:194163 original size:12 final size:12
Alignment explanation
Indices: 194114--194189 Score: 50
Period size: 12 Copynumber: 6.3 Consensus size: 12
194104 TTGTTTATTA
*
194114 TTCATCAACATTG
1 TTCATGAACA-TG
*
194127 TTCGTGAACATG
1 TTCATGAACATG
* *
194139 TTCAAT-TATATG
1 TTC-ATGAACATG
194151 TTCATGAACATG
1 TTCATGAACATG
**
194163 TTCATTTA-ATG
1 TTCATGAACATG
194174 TTCGA-GAACATG
1 TTC-ATGAACATG
194186 TTCA
1 TTCA
194190 ATTAAGTTAA
Statistics
Matches: 48, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
11 10 0.21
12 29 0.60
13 9 0.19
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (12 bp):
TTCATGAACATG
Found at i:194885 original size:20 final size:21
Alignment explanation
Indices: 194860--194942 Score: 111
Period size: 20 Copynumber: 4.0 Consensus size: 21
194850 GAGTAGTGGG
194860 ACAAGTACCTT-TGGAGAAGT
1 ACAAGTACCTTCTGGAGAAGT
194880 ACAAGTA-CTTCATGGGAGAAGT
1 ACAAGTACCTTC-T-GGAGAAGT
*
194902 ACAGGTACC-TCTGGAGAAGT
1 ACAAGTACCTTCTGGAGAAGT
194922 ACAAGTACCTTCT-GAGAAGT
1 ACAAGTACCTTCTGGAGAAGT
194942 A
1 A
194943 TCGATAAAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
19 3 0.05
20 31 0.55
21 5 0.09
22 16 0.29
23 1 0.02
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (21 bp):
ACAAGTACCTTCTGGAGAAGT
Found at i:200004 original size:20 final size:20
Alignment explanation
Indices: 199951--200004 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
199941 ATAACTTTGA
199951 TGTTAGTAGAGGAACATCAG
1 TGTTAGTAGAGGAACATCAG
**
199971 TGTTA-TACTTGGAACATCAG
1 TGTTAGTA-GAGGAACATCAG
199991 TGTTAGTAGAGGAA
1 TGTTAGTAGAGGAA
200005 GGCATTGGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.86
21 2 0.07
ACGTcount: A:0.33, C:0.09, G:0.28, T:0.30
Consensus pattern (20 bp):
TGTTAGTAGAGGAACATCAG
Found at i:200135 original size:30 final size:29
Alignment explanation
Indices: 200092--200159 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 29
200082 AAAGTAAAAA
* * * *
200092 AAAAGTGATGGGATCAAAGTGTGAATATTC
1 AAAAGTTAAGGGATCAAAATGTAAAT-TTC
* *
200122 AAAAGTTAAGGGATTAAAATGTAAATTTG
1 AAAAGTTAAGGGATCAAAATGTAAATTTC
200151 AAAAGTTAA
1 AAAAGTTAA
200160 AGGGCAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 11 0.34
30 21 0.66
ACGTcount: A:0.47, C:0.03, G:0.22, T:0.28
Consensus pattern (29 bp):
AAAAGTTAAGGGATCAAAATGTAAATTTC
Found at i:201078 original size:52 final size:53
Alignment explanation
Indices: 201000--201103 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 53
200990 TGGGAATGTT
201000 AGATGTGTTATGGAATGGTTTATGTTAGTTTAAACTTGGTTTTATAT-TTTTC
1 AGATGTGTTATGGAATGGTTTATGTTAGTTTAAACTTGGTTTTATATGTTTTC
201052 AGATGTGTTATGGAATGGTTTATGTTAGTTTAAACTTGGTTTTATATGTTTT
1 AGATGTGTTATGGAATGGTTTATGTTAGTTTAAACTTGGTTTTATATGTTTT
201104 TGGTAATCTG
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 47 0.92
53 4 0.08
ACGTcount: A:0.23, C:0.03, G:0.22, T:0.52
Consensus pattern (53 bp):
AGATGTGTTATGGAATGGTTTATGTTAGTTTAAACTTGGTTTTATATGTTTTC
Found at i:201988 original size:16 final size:16
Alignment explanation
Indices: 201948--201988 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
201938 GTCAACAAAT
201948 ATTTAAAAAAATAAAA
1 ATTTAAAAAAATAAAA
* *
201964 AATAAAAAAAATAAAA
1 ATTTAAAAAAATAAAA
201980 ATTTTAAAA
1 A-TTTAAAA
201989 TATTATTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
ATTTAAAAAAATAAAA
Found at i:202384 original size:10 final size:10
Alignment explanation
Indices: 202369--202419 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 10
202359 CTAGCGTGAC
202369 TTTTAATAAA
1 TTTTAATAAA
*
202379 TTTTAA-ACA
1 TTTTAATAAA
* *
202388 TTTTTATTAA
1 TTTTAATAAA
*
202398 TTTTAATAAT
1 TTTTAATAAA
*
202408 TTTTTATAAA
1 TTTTAATAAA
202418 TT
1 TT
202420 CTTTTAATTA
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
9 7 0.23
10 24 0.77
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTTAATAAA
Found at i:206736 original size:20 final size:20
Alignment explanation
Indices: 206711--206749 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
206701 AAATAATCAT
206711 TTTATTTATTGTATG-TTAAG
1 TTTATTTATT-TATGATTAAG
206731 TTTATTTATTTATGATTAA
1 TTTATTTATTTATGATTAA
206750 AATATTAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (20 bp):
TTTATTTATTTATGATTAAG
Found at i:207455 original size:24 final size:25
Alignment explanation
Indices: 207415--207464 Score: 59
Period size: 24 Copynumber: 2.0 Consensus size: 25
207405 GTTTGTTTAT
**
207415 TATTAATTAATATTGTTTGTGAACA
1 TATTAATTAATATTGTTCATGAACA
207440 TATTCAATT-ATA-TGTTCATGAACA
1 TATT-AATTAATATTGTTCATGAACA
207464 T
1 T
207465 GTTTGTTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 11 0.50
25 7 0.32
26 4 0.18
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (25 bp):
TATTAATTAATATTGTTCATGAACA
Found at i:208267 original size:14 final size:14
Alignment explanation
Indices: 208248--208276 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
208238 ACCAAATTGG
208248 TTTCATGCTCCCTT
1 TTTCATGCTCCCTT
208262 TTTCATGCTCCCTT
1 TTTCATGCTCCCTT
208276 T
1 T
208277 CTCTCTTGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.34, G:0.07, T:0.52
Consensus pattern (14 bp):
TTTCATGCTCCCTT
Found at i:209058 original size:15 final size:15
Alignment explanation
Indices: 209038--209088 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
209028 ACAACACAAT
209038 AACGTAAATAACTAA
1 AACGTAAATAACTAA
**
209053 AACGT-AATATTTAA
1 AACGTAAATAACTAA
**
209067 AATATAAATAACTAA
1 AACGTAAATAACTAA
*
209082 AATGTAA
1 AACGTAA
209089 TTTGAGAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
14 10 0.36
15 18 0.64
ACGTcount: A:0.59, C:0.08, G:0.06, T:0.27
Consensus pattern (15 bp):
AACGTAAATAACTAA
Found at i:209235 original size:22 final size:22
Alignment explanation
Indices: 209209--209255 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
209199 TATTTTTATT
209209 ATTAA-ATTTAATTAAAATAAAA
1 ATTAATATTTAA-TAAAATAAAA
*
209231 ATTAATATTTAATACAATAAAA
1 ATTAATATTTAATAAAATAAAA
209253 ATT
1 ATT
209256 TTAATTACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
ATTAATATTTAATAAAATAAAA
Found at i:212727 original size:18 final size:19
Alignment explanation
Indices: 212697--212746 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
212687 TAAAATATAA
212697 ATTTTGAATTTTT-ATAAA-T
1 ATTTTG-ATTTTTGA-AAATT
212716 ATTTTGATTTTTGAAAATT
1 ATTTTGATTTTTGAAAATT
212735 ATTTTGATTTTT
1 ATTTTGATTTTT
212747 TTTGTAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.31
19 20 0.69
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (19 bp):
ATTTTGATTTTTGAAAATT
Found at i:213154 original size:23 final size:23
Alignment explanation
Indices: 213128--213171 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
213118 ATATTCTAAA
*
213128 ATGATAAAATTATAAATTAATAT
1 ATGATAAAATTACAAATTAATAT
* *
213151 ATGATAAGATTACATATTAAT
1 ATGATAAAATTACAAATTAAT
213172 CTCCAAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (23 bp):
ATGATAAAATTACAAATTAATAT
Found at i:214778 original size:24 final size:24
Alignment explanation
Indices: 214750--214795 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
214740 TCATTAACAT
*
214750 TGTTCGTGAACATGTTCAATTATA
1 TGTTCATGAACATGTTCAATTATA
*
214774 TGTTCATGAACATGTTCGATTA
1 TGTTCATGAACATGTTCAATTA
214796 AGTTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.41
Consensus pattern (24 bp):
TGTTCATGAACATGTTCAATTATA
Found at i:215250 original size:28 final size:28
Alignment explanation
Indices: 215219--215315 Score: 194
Period size: 28 Copynumber: 3.5 Consensus size: 28
215209 AGATGTCTCA
215219 GCGAAGTGGTGAATTGCAAAATGATACC
1 GCGAAGTGGTGAATTGCAAAATGATACC
215247 GCGAAGTGGTGAATTGCAAAATGATACC
1 GCGAAGTGGTGAATTGCAAAATGATACC
215275 GCGAAGTGGTGAATTGCAAAATGATACC
1 GCGAAGTGGTGAATTGCAAAATGATACC
215303 GCGAAGTGGTGAA
1 GCGAAGTGGTGAA
215316 GTGCGAGATG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 69 1.00
ACGTcount: A:0.35, C:0.13, G:0.31, T:0.21
Consensus pattern (28 bp):
GCGAAGTGGTGAATTGCAAAATGATACC
Found at i:218718 original size:80 final size:80
Alignment explanation
Indices: 218623--218783 Score: 322
Period size: 80 Copynumber: 2.0 Consensus size: 80
218613 AAATAAGAAA
218623 TAGAAGGGAGTACAAAAATTATGGCCAGAGCAATGGCTGCACAATGTTTTAAATGGTGAATGAAA
1 TAGAAGGGAGTACAAAAATTATGGCCAGAGCAATGGCTGCACAATGTTTTAAATGGTGAATGAAA
218688 CGAAAAGAAGATAAG
66 CGAAAAGAAGATAAG
218703 TAGAAGGGAGTACAAAAATTATGGCCAGAGCAATGGCTGCACAATGTTTTAAATGGTGAATGAAA
1 TAGAAGGGAGTACAAAAATTATGGCCAGAGCAATGGCTGCACAATGTTTTAAATGGTGAATGAAA
218768 CGAAAAGAAGATAAG
66 CGAAAAGAAGATAAG
218783 T
1 T
218784 TCGTAATGTT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 81 1.00
ACGTcount: A:0.43, C:0.10, G:0.26, T:0.20
Consensus pattern (80 bp):
TAGAAGGGAGTACAAAAATTATGGCCAGAGCAATGGCTGCACAATGTTTTAAATGGTGAATGAAA
CGAAAAGAAGATAAG
Found at i:219510 original size:21 final size:19
Alignment explanation
Indices: 219486--219529 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
219476 ATTAAAATAA
219486 TATTTGTGTGTATGTATTTAT
1 TATTTGTGTGT-T-TATTTAT
* *
219507 TATTTGTTTGTTTGTTTAT
1 TATTTGTGTGTTTATTTAT
219526 TATT
1 TATT
219530 CATTAACATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 10 0.48
20 1 0.05
21 10 0.48
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (19 bp):
TATTTGTGTGTTTATTTAT
Found at i:233606 original size:21 final size:22
Alignment explanation
Indices: 233562--233615 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
233552 GTTTTAAGCA
233562 TTATATAAAAAAATCTTTTAAT
1 TTATATAAAAAAATCTTTTAAT
* * *
233584 TTATATTAAGAAA-CTTTTTATT
1 TTATATAAAAAAATC-TTTTAAT
*
233606 TTAAATAAAA
1 TTATATAAAA
233616 GGGATAATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (22 bp):
TTATATAAAAAAATCTTTTAAT
Found at i:234324 original size:19 final size:18
Alignment explanation
Indices: 234275--234324 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
234265 ATTTACTTCA
*
234275 TAAAAAGTATTTTTATTTT
1 TAAAAA-TATTTTAATTTT
* *
234294 TACAAATTTTTTAATTTT
1 TAAAAATATTTTAATTTT
234312 TAAATAATATTTT
1 TAAA-AATATTTT
234325 TATGTCCTGT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 13 0.52
19 12 0.48
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (18 bp):
TAAAAATATTTTAATTTT
Found at i:234414 original size:20 final size:20
Alignment explanation
Indices: 234389--234426 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
234379 ATTTTTAAAA
*
234389 TTTAAATAGTGTATAAAAGT
1 TTTAAAAAGTGTATAAAAGT
*
234409 TTTAAAAAGTTTATAAAA
1 TTTAAAAAGTGTATAAAA
234427 TAAAAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (20 bp):
TTTAAAAAGTGTATAAAAGT
Found at i:234514 original size:3 final size:3
Alignment explanation
Indices: 234506--234550 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
234496 TTATGGTTAT
234506 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
234551 CCTTCATTCT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:240247 original size:24 final size:24
Alignment explanation
Indices: 240189--240265 Score: 68
Period size: 24 Copynumber: 3.3 Consensus size: 24
240179 TTTAAAAATT
* * ** *
240189 ATAAAAATATATACTATTAAAATA
1 ATAAAAATATATAATTTTATTATG
*
240213 AT-AAAAT-TATATTTTTATTATG
1 ATAAAAATATATAATTTTATTATG
* *
240235 ATAAAAATATATAATTTAATTAGG
1 ATAAAAATATATAATTTTATTATG
240259 ATAAAAA
1 ATAAAAA
240266 AGAATTTTCT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
22 12 0.28
23 10 0.23
24 21 0.49
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (24 bp):
ATAAAAATATATAATTTTATTATG
Found at i:240568 original size:5 final size:6
Alignment explanation
Indices: 240552--240577 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
240542 TGAACCTAGG
240552 CTTTTT CTTTTT CTTTTT CTTTTT CT
1 CTTTTT CTTTTT CTTTTT CTTTTT CT
240578 AACTTATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
CTTTTT
Found at i:244070 original size:7 final size:7
Alignment explanation
Indices: 244058--244091 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
244048 AGATATAGGA
244058 GGCAATT
1 GGCAATT
244065 GGCAATT
1 GGCAATT
*
244072 TGCAATT
1 GGCAATT
244079 GGCAATT
1 GGCAATT
244086 GGCAAT
1 GGCAAT
244092 GAAAAGGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (7 bp):
GGCAATT
Found at i:248429 original size:14 final size:14
Alignment explanation
Indices: 248410--248437 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
248400 TTGATAATTG
248410 TATGCCCCCACAAC
1 TATGCCCCCACAAC
248424 TATGCCCCCACAAC
1 TATGCCCCCACAAC
248438 GCTGGGGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.50, G:0.07, T:0.14
Consensus pattern (14 bp):
TATGCCCCCACAAC
Found at i:264840 original size:108 final size:110
Alignment explanation
Indices: 264651--264878 Score: 415
Period size: 108 Copynumber: 2.1 Consensus size: 110
264641 AGCCTTTAAC
* *
264651 TTTTGTTGCTTTTAATAATTTTTGAACATTTCTCTTAAGCAAAATAGTGAGCTGTGAGCATCACA
1 TTTTGTTGCTTTTAATAATTTTTGAACATTTCTCTTAAACAAAACAGTGAGCTGTGAGCATCACA
264716 TGTAGTCTTCTAGGTTCTGCTTTCAGCTGATTGTT-ATTTTTT-T
66 TGTAGTCTTCTAGGTTCTGCTTTCAGCTGATTGTTAATTTTTTCT
264759 TTTTGTTGCTTTTAATAATTTTTGAACATTTCTCTTAAACAAAACAGTGAGCTGTGAGCATCACA
1 TTTTGTTGCTTTTAATAATTTTTGAACATTTCTCTTAAACAAAACAGTGAGCTGTGAGCATCACA
264824 TGTAGTCTTCTAGGTTCTGCTTTCAGCTGATTGTTAATTTTTTCCT
66 TGTAGTCTTCTAGGTTCTGCTTTCAGCTGATTGTTAATTTTTT-CT
264870 TTTTGTTGC
1 TTTTGTTGC
264879 ATCCCATTGG
Statistics
Matches: 115, Mismatches: 2, Indels: 3
0.96 0.02 0.03
Matches are distributed among these distances:
108 98 0.85
109 7 0.06
111 10 0.09
ACGTcount: A:0.22, C:0.15, G:0.16, T:0.47
Consensus pattern (110 bp):
TTTTGTTGCTTTTAATAATTTTTGAACATTTCTCTTAAACAAAACAGTGAGCTGTGAGCATCACA
TGTAGTCTTCTAGGTTCTGCTTTCAGCTGATTGTTAATTTTTTCT
Found at i:266201 original size:14 final size:15
Alignment explanation
Indices: 266172--266204 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
266162 ATGTTATTGA
*
266172 AATAATATTTTAATT
1 AATAATATTATAATT
266187 AATAA-ATTATAATT
1 AATAATATTATAATT
266201 AATA
1 AATA
266205 GGCTTGCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATAATATTATAATT
Found at i:271305 original size:6 final size:6
Alignment explanation
Indices: 271279--271322 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
271269 AATGAGAAGA
* * * *
271279 AAAAGG AAGACG AATAGG AAAAGG AAAAGG AAAATG AAAAGG AA
1 AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AA
271323 GTGATTTTTG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.64, C:0.02, G:0.30, T:0.05
Consensus pattern (6 bp):
AAAAGG
Found at i:286971 original size:22 final size:22
Alignment explanation
Indices: 286946--286990 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
286936 TTAAATAAAA
*
286946 AAATAAATTAATTATTCTTATT
1 AAATAAATTAATTATTATTATT
* * *
286968 AAATTATTTATTTATTATTATT
1 AAATAAATTAATTATTATTATT
286990 A
1 A
286991 TTATTTTAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
AAATAAATTAATTATTATTATT
Found at i:293869 original size:5 final size:5
Alignment explanation
Indices: 293859--293894 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
293849 TAGATTATGA
293859 TGATG TGATG TGATG TGATG TGATG TGATG TGATG T
1 TGATG TGATG TGATG TGATG TGATG TGATG TGATG T
293895 CAGTCATCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.19, C:0.00, G:0.39, T:0.42
Consensus pattern (5 bp):
TGATG
Found at i:294821 original size:22 final size:21
Alignment explanation
Indices: 294796--294852 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
294786 GGATCTAAGG
294796 AAAAATAAAAGAAACAGAATT
1 AAAAATAAAAGAAACAGAATT
*
294817 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAG-AAACAGAATT
294839 AAAAA-AAATAGAAA
1 AAAAATAAA-AGAAA
294853 ATAGAGAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
21 17 0.52
22 16 0.48
ACGTcount: A:0.75, C:0.02, G:0.09, T:0.14
Consensus pattern (21 bp):
AAAAATAAAAGAAACAGAATT
Found at i:294846 original size:15 final size:16
Alignment explanation
Indices: 294822--294851 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
294812 GAATTAAAAA
294822 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
294838 TAAAA-AAAATAGAA
1 TAAAAGAAAATAGAA
294852 AATAGAGAAG
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:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:294853 original size:22 final size:22
Alignment explanation
Indices: 294796--294857 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
294786 GGATCTAAGG
*
294796 AAAAATAAAAG-AAACAGAATT
1 AAAAATAAAAGAAAATAGAATT
294817 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
294839 AAAAA-AAATAGAAAATAGA
1 AAAAATAAA-AGAAAATAGA
294858 GAAGTCGAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
21 14 0.37
22 24 0.63
ACGTcount: A:0.74, C:0.02, G:0.10, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:295639 original size:14 final size:14
Alignment explanation
Indices: 295622--295651 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
295612 TTTAAACTCT
*
295622 AAAAGATAAATATA
1 AAAAGATAAACATA
295636 AAAAGATAAACATA
1 AAAAGATAAACATA
295650 AA
1 AA
295652 TTAAATACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.73, C:0.03, G:0.07, T:0.17
Consensus pattern (14 bp):
AAAAGATAAACATA
Found at i:295675 original size:19 final size:19
Alignment explanation
Indices: 295653--295695 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
295643 AAACATAAAT
295653 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
295672 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
295691 TAAAT
1 TAAAT
295696 CCTAATATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:300677 original size:23 final size:24
Alignment explanation
Indices: 300646--300714 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 24
300636 AGTACGTCTT
300646 GTGCTCTCTGTTATTAGCACTGTGA
1 GTGC-CTCTGTTATTAGCACTGTGA
300671 GTGCTCTCTGTTATTAGCACTGTGA
1 GTGC-CTCTGTTATTAGCACTGTGA
300696 GTGCTCTCTG--ATTAGCACT
1 GTGC-CTCTGTTATTAGCACT
300715 TCATGTGCTC
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
23 9 0.20
25 35 0.80
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.39
Consensus pattern (24 bp):
GTGCCTCTGTTATTAGCACTGTGA
Found at i:300704 original size:27 final size:25
Alignment explanation
Indices: 300646--300776 Score: 132
Period size: 23 Copynumber: 5.5 Consensus size: 25
300636 AGTACGTCTT
300646 GTGCTCTCTGTTATTAGCACTGTGA
1 GTGCTCTCTGTTATTAGCACTGTGA
300671 GTGCTCTCTGTTATTAGCACTGTGA
1 GTGCTCTCTGTTATTAGCACTGTGA
*
300696 GTGCTCTCTG--ATTAGCACT-TCA
1 GTGCTCTCTGTTATTAGCACTGTGA
* * * *
300718 TGTGCTCT-T-TGATTAGTACTTTGT
1 -GTGCTCTCTGTTATTAGCACTGTGA
* * *
300742 GTACTCTCTG-T-TTAGCACTATGT
1 GTGCTCTCTGTTATTAGCACTGTGA
300765 GTGCTCTCTGTT
1 GTGCTCTCTGTT
300777 GCCCAGCACT
Statistics
Matches: 90, Mismatches: 9, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
22 3 0.03
23 49 0.54
24 3 0.03
25 35 0.39
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.44
Consensus pattern (25 bp):
GTGCTCTCTGTTATTAGCACTGTGA
Found at i:300742 original size:21 final size:22
Alignment explanation
Indices: 300645--300796 Score: 96
Period size: 25 Copynumber: 6.4 Consensus size: 22
300635 TAGTACGTCT
300645 TGTGCTCTCTGTTATTAGCACTGTGA
1 TGTGCTCTCTG--ATTAGCACT-T-A
300671 -GTGCTCTCTGTTATTAGCACTGTGA
1 TGTGCTCTCTG--ATTAGCACT-T-A
300696 -GTGCTCTCTGATTAGCACTTCA
1 TGTGCTCTCTGATTAGCACTT-A
* *
300718 TGTGCTCTTTGATTAGTACTT-
1 TGTGCTCTCTGATTAGCACTTA
* *
300739 TGTGTACTCTCTGTTTAGCACTATG
1 TGTG--CTCTCTGATTAGCACT-TA
300764 TGTGCTCTCTG-TTGCCCAGCACTTA
1 TGTGCTCTCTGATT----AGCACTTA
300789 TGTGCTCT
1 TGTGCTCT
300797 TTATTAGTGC
Statistics
Matches: 110, Mismatches: 7, Indels: 19
0.81 0.05 0.14
Matches are distributed among these distances:
21 4 0.04
22 4 0.04
23 47 0.43
24 1 0.01
25 48 0.44
26 6 0.05
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.42
Consensus pattern (22 bp):
TGTGCTCTCTGATTAGCACTTA
Found at i:300770 original size:69 final size:66
Alignment explanation
Indices: 300651--300823 Score: 186
Period size: 71 Copynumber: 2.5 Consensus size: 66
300641 GTCTTGTGCT
* * * *
300651 CTCTGTTATTAGCACTGTGAGTGCTCTCTGTTATTAGCACTGTGAGTGCTCTCTGATT-AGCACT
1 CTCT-TTATTAGTACTTTG-GTACTCTCTG-T-TTAGCACTATGAGTGCTCTCTG-TTCAGCACT
300715 TCATGTG
61 T-ATGTG
*
300722 CTCTTTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTATGTGTGCTCTCTGTTGCCCAGCACT
1 CTCTTT-ATTAGTACTTTG-GTACTCTCTGTTTAGCACTATGAGTGCTCTCTGTT---CAGCACT
300787 TATGTG
61 TATGTG
*
300793 CTCTTTATTAGTGCTTTGGTACTCTCTGTTT
1 CTCTTTATTAGTACTTTGGTACTCTCTGTTT
300824 GTTCCGTATA
Statistics
Matches: 90, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
68 2 0.02
69 33 0.37
70 14 0.16
71 34 0.38
72 7 0.08
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.44
Consensus pattern (66 bp):
CTCTTTATTAGTACTTTGGTACTCTCTGTTTAGCACTATGAGTGCTCTCTGTTCAGCACTTATGT
G
Found at i:305414 original size:30 final size:28
Alignment explanation
Indices: 305356--305426 Score: 76
Period size: 30 Copynumber: 2.5 Consensus size: 28
305346 GTATGTTTAA
*
305356 TAATATTAAAAT-TATAATATTTGATAT
1 TAATATTAAAATATATAAAATTTGATAT
305383 TAATATTAAAATATATTTAAAATTT-ATTAT
1 TAATATTAAAATATA--TAAAATTTGA-TAT
305413 TAATA-TAATAATAT
1 TAATATTAA-AATAT
305427 TAGACTTCAT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
27 12 0.32
28 2 0.05
29 4 0.11
30 20 0.53
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (28 bp):
TAATATTAAAATATATAAAATTTGATAT
Found at i:305539 original size:22 final size:19
Alignment explanation
Indices: 305514--305562 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 19
305504 AAAAAGATTG
*
305514 ATTTTTTATTGACTTATAAGTT
1 ATTTTTTATT-AATTA-AA-TT
*
305536 ATTTTTCATTAATTAAATT
1 ATTTTTTATTAATTAAATT
305555 ATTTTTTA
1 ATTTTTTA
305563 ATATAACAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 9 0.38
20 2 0.08
21 4 0.17
22 9 0.38
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (19 bp):
ATTTTTTATTAATTAAATT
Found at i:309031 original size:25 final size:26
Alignment explanation
Indices: 309003--309051 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
308993 ATAATTTGAG
*
309003 TATTTC-ATTTTTTTAGAAATTAATT
1 TATTTCAATTTTTTAAGAAATTAATT
*
309028 TATTTCAATTTTTTAATAAATTAA
1 TATTTCAATTTTTTAAGAAATTAA
309052 AATCGACTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (26 bp):
TATTTCAATTTTTTAAGAAATTAATT
Found at i:313159 original size:131 final size:129
Alignment explanation
Indices: 312927--313163 Score: 386
Period size: 131 Copynumber: 1.8 Consensus size: 129
312917 TAGATAGACT
* *
312927 CACTTTAAAATTCTGACAATTTCTTTTTTTTTATTTAATAAAACATTGAGAGCCTTGAGATGTAA
1 CACTTTAAAATTCTAACAATTTCTTTTTTTTTATTTAATAAAACATTGAGAGACTTGAGATGTAA
* *
312992 TTTTTTCACTTTTTAGTGGTTTTTGAAAAAGTGTGAAAGGGTGCCCCTCCTAGATAGGCAGCAC
66 TTTTTTCAATTTTTAGTGGTTGTTGAAAAAGTGTGAAAGGGTGCCCCTCCTAGATAGGCAGCAC
* *
313056 CACTTTAAAATTCTAATAATTTCTTTTTTTTTTAATTTAATAAAACATTGAGAGACTTGGGATGT
1 CACTTTAAAATTCTAACAATTTC-TTTTTTTTT-ATTTAATAAAACATTGAGAGACTTGAGATGT
313121 AA-TTTTTCTAATTTTTAGTGGTTGTTGAAAAAGTGTGAAAGGG
64 AATTTTTTC-AATTTTTAGTGGTTGTTGAAAAAGTGTGAAAGGG
313164 CGGCACCAAA
Statistics
Matches: 99, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
129 21 0.21
130 15 0.15
131 63 0.64
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (129 bp):
CACTTTAAAATTCTAACAATTTCTTTTTTTTTATTTAATAAAACATTGAGAGACTTGAGATGTAA
TTTTTTCAATTTTTAGTGGTTGTTGAAAAAGTGTGAAAGGGTGCCCCTCCTAGATAGGCAGCAC
Found at i:313300 original size:16 final size:15
Alignment explanation
Indices: 313275--313311 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
313265 CAATTAGTTC
*
313275 AAAAACATTTTTATCA
1 AAAAATATTTTTAT-A
313291 AAAAATATTTTTATA
1 AAAAATATTTTTATA
313306 AAAAAT
1 AAAAAT
313312 TTAATTCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAAATATTTTTATA
Found at i:319812 original size:131 final size:129
Alignment explanation
Indices: 319573--319838 Score: 363
Period size: 131 Copynumber: 2.0 Consensus size: 129
319563 GCTAAAGAAA
*
319573 GTAACCGATTATATCTCATGTCATGGGTTGGGTGAGTTCGGATCCATGCCCACTCTATGTAAGGT
1 GTAACCGATTATATCTCATGTCATGGGTTGGGTGAGTTCGGATCCATG--CACTCTATGTAAAGT
* * * * *
319638 AATTAGATAAAATTTTCCAGTTTGAGTTTGACCTAATCTGAAAAGTGGACTTGAAGTTTTGCTCA
64 AATTAGATAAAATTTTCAAGTTTGAGCTTGACCTAACCTGAAAAATGGACATGAAGTTTTGCTCA
319703 T
129 T
* * *
319704 GTAATCGATTATATCTCATGTCATGGGTTGGGTGAGTTCGGATTCACATTG-GCTTTATGTAAAG
1 GTAACCGATTATATCTCATGTCATGGGTTGGGTGAGTTCGGA-TC-CA-TGCACTCTATGTAAAG
* * * *
319768 TATTTAGATCAATTTTTCAAGTTTGAGCTTGACCTAACCTGAAAAATTGACATGAAGTTTTGCTC
63 TAATTAGATAAAATTTTCAAGTTTGAGCTTGACCTAACCTGAAAAATGGACATGAAGTTTTGCTC
319833 AT
128 AT
319835 GTAA
1 GTAA
319839 ATATGGATCC
Statistics
Matches: 119, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
131 113 0.95
132 2 0.02
133 2 0.02
134 2 0.02
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.36
Consensus pattern (129 bp):
GTAACCGATTATATCTCATGTCATGGGTTGGGTGAGTTCGGATCCATGCACTCTATGTAAAGTAA
TTAGATAAAATTTTCAAGTTTGAGCTTGACCTAACCTGAAAAATGGACATGAAGTTTTGCTCAT
Found at i:319903 original size:17 final size:17
Alignment explanation
Indices: 319883--319917 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
319873 ATTTAGACCA
319883 ATTTTTTATTTAAA-AAT
1 ATTTTTT-TTTAAATAAT
319900 ATTTTTTTTTAAATAAT
1 ATTTTTTTTTAAATAAT
319917 A
1 A
319918 AAATGTAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTTTTTTAAATAAT
Found at i:320718 original size:18 final size:18
Alignment explanation
Indices: 320654--320718 Score: 51
Period size: 18 Copynumber: 3.6 Consensus size: 18
320644 AATTGATCTT
*
320654 AATTCTTAAAAAAATAAAA
1 AATT-TTAAAAATATAAAA
* * *
320673 AATTATAAAAATA-CACA
1 AATTTTAAAAATATAAAA
* *
320690 GATTTTCAAAAATATAATA
1 AATTTT-AAAAATATAAAA
320709 AATTTTAAAA
1 AATTTTAAAA
320719 GCTGCAAAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 5
0.71 0.18 0.10
Matches are distributed among these distances:
17 6 0.17
18 18 0.51
19 11 0.31
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.31
Consensus pattern (18 bp):
AATTTTAAAAATATAAAA
Found at i:324755 original size:11 final size:10
Alignment explanation
Indices: 324729--324780 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
324719 TAAAAAGAGC
324729 AAAAATATAA
1 AAAAATATAA
324739 AAAAATATCAA
1 AAAAATAT-AA
* *
324750 ATAAATTTAA
1 AAAAATATAA
*
324760 AAAAATCAGAAA
1 AAAAAT-A-TAA
324772 AAAAATATA
1 AAAAATATA
324781 CGGAAAGTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
10 16 0.48
11 9 0.27
12 8 0.24
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.21
Consensus pattern (10 bp):
AAAAATATAA
Found at i:325153 original size:10 final size:9
Alignment explanation
Indices: 325110--325158 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
325100 AAATATTAAA
325110 AATAATTTT
1 AATAATTTT
*
325119 TATAATTTT
1 AATAATTTT
*
325128 -ATACTTTTT
1 AATA-ATTTT
325137 AATAATTTT
1 AATAATTTT
325146 AATAAATTTT
1 AAT-AATTTT
325156 AAT
1 AAT
325159 TTTAAAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
8 3 0.09
9 19 0.56
10 12 0.35
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (9 bp):
AATAATTTT
Found at i:325160 original size:16 final size:16
Alignment explanation
Indices: 325139--325169 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
325129 TACTTTTTAA
*
325139 TAATTTTAATAAATTT
1 TAATTTTAAAAAATTT
325155 TAATTTTAAAAAATT
1 TAATTTTAAAAAATT
325170 ATTTTTTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAATTTTAAAAAATTT
Found at i:327578 original size:22 final size:23
Alignment explanation
Indices: 327553--327605 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 23
327543 GAAAATATTT
327553 ATTTATTTTTATAT-ATTTGT-AA
1 ATTTATTTTTATATAATTT-TAAA
*
327575 ATTTATTATTATATAATTTTAAA
1 ATTTATTTTTATATAATTTTAAA
327598 ATTTATTT
1 ATTTATTT
327606 ATTTATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 14 0.52
23 13 0.48
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (23 bp):
ATTTATTTTTATATAATTTTAAA
Done.