Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001633.1 Hibiscus syriacus cultivar Beakdansim tig00003255_pilon, 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: 80290
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Found at i:323 original size:55 final size:55
Alignment explanation
Indices: 73--324 Score: 307
Period size: 55 Copynumber: 4.6 Consensus size: 55
63 TCAAAATGGT
* * * *
73 AATTCACAAACTCATTAAGAA-TTATGCGACGTT-ACACACATAGTGCTAATAC-GAA
1 AATTCATAAACTCATTATGAATTTA-GTGAGGTTGA-ACACATAGTGCTAATACAG-A
* ** *
128 AATTCATAAACTCATTATGAATTTCGTGAGGTTTTACACATAGTGCTAATACGGA
1 AATTCATAAACTCATTATGAATTTAGTGAGGTTGAACACATAGTGCTAATACAGA
* *
183 AATTCATAAACTCATTATGAATTTCGTGAGGTTGAACACATAGTGCCAATACA-A
1 AATTCATAAACTCATTATGAATTTAGTGAGGTTGAACACATAGTGCTAATACAGA
* *
237 ATATTTATAAACTCATTATGAATTTCA-TGAGGTTGAACACATAGTGCAAATACAGA
1 A-ATTCATAAACTCATTATGAATTT-AGTGAGGTTGAACACATAGTGCTAATACAGA
*
293 AATTCATAAACTCATTATGAATTTATTGAGGT
1 AATTCATAAACTCATTATGAATTTAGTGAGGT
325 ACACACACAA
Statistics
Matches: 176, Mismatches: 14, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
54 3 0.02
55 168 0.95
56 5 0.03
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (55 bp):
AATTCATAAACTCATTATGAATTTAGTGAGGTTGAACACATAGTGCTAATACAGA
Found at i:323 original size:110 final size:110
Alignment explanation
Indices: 73--331 Score: 346
Period size: 110 Copynumber: 2.4 Consensus size: 110
63 TCAAAATGGT
* * * * *
73 AATTCACAAACTCATTAAGAA-TTATGCGACGTTACACACATAGTGCTAATACGAAAATTCATAA
1 AATTCATAAACTCATTATGAATTTAT-TGAGGTTACACACATAGTGCCAATACGAAAATTCATAA
* ** * *
137 ACTCATTATGAATTTCGTGAGGTTTTACACATAGTGCTAATACGGA
65 ACTCATTATGAATTTCATGAGGTTGAACACATAGTGCAAATACAGA
** *
183 AATTCATAAACTCATTATGAATTTCGTGAGGTTGA-ACACATAGTGCCAATAC-AAATATTTATA
1 AATTCATAAACTCATTATGAATTTATTGAGGTT-ACACACATAGTGCCAATACGAAA-ATTCATA
246 AACTCATTATGAATTTCATGAGGTTGAACACATAGTGCAAATACAGA
64 AACTCATTATGAATTTCATGAGGTTGAACACATAGTGCAAATACAGA
293 AATTCATAAACTCATTATGAATTTATTGAGG-TACACACA
1 AATTCATAAACTCATTATGAATTTATTGAGGTTACACACA
332 CAATGCCCTT
Statistics
Matches: 130, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
108 1 0.01
109 9 0.07
110 117 0.90
111 3 0.02
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (110 bp):
AATTCATAAACTCATTATGAATTTATTGAGGTTACACACATAGTGCCAATACGAAAATTCATAAA
CTCATTATGAATTTCATGAGGTTGAACACATAGTGCAAATACAGA
Found at i:1532 original size:55 final size:55
Alignment explanation
Indices: 1462--1704 Score: 246
Period size: 55 Copynumber: 4.4 Consensus size: 55
1452 GTGTCGACAG
* * *
1462 AATTCACAAACTCATTAAGAATTATGCG-GCGTTACACACATAGTGCCAATACGGA
1 AATTCATAAACTCATTATGAATTATGCGAG-GTTACACACATAGTGCCAATACGAA
* * * **
1517 AATTCATAAGCTCATTATGAATTTTGTGAGGTTTTACACATAGTGCCAATACGAA
1 AATTCATAAACTCATTATGAATTATGCGAGGTTACACACATAGTGCCAATACGAA
* * * *
1572 AATTCATAAACTAATTATGAATT-T-CTTGAGGTTGCACAAATAGTGCCAATACAAA
1 AATTCATAAACTCATTATGAATTATGC--GAGGTTACACACATAGTGCCAATACGAA
* * *
1627 AATTTATAAACTCATTATGAATT-T-CTTGAGGTTGA-ACATATAGTGCAAATACGAA
1 AATTCATAAACTCATTATGAATTATGC--GAGGTT-ACACACATAGTGCCAATACGAA
*
1682 AACTCATAAACTCATTATGAATT
1 AATTCATAAACTCATTATGAATT
1705 TATTGAGGTT
Statistics
Matches: 161, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
54 1 0.01
55 159 0.99
56 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (55 bp):
AATTCATAAACTCATTATGAATTATGCGAGGTTACACACATAGTGCCAATACGAA
Found at i:1705 original size:55 final size:55
Alignment explanation
Indices: 1501--1715 Score: 297
Period size: 55 Copynumber: 3.9 Consensus size: 55
1491 CGTTACACAC
* * ** *
1501 ATAGTGCCAATACGGAAATTCATAAGCTCATTATGAATTT-TGTGAGGTTTTACAC
1 ATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCT-TGAGGTTGAACAA
* *
1556 ATAGTGCCAATACGAAAATTCATAAACTAATTATGAATTTCTTGAGGTTGCACAA
1 ATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTGAGGTTGAACAA
* * *
1611 ATAGTGCCAATACAAAAATTTATAAACTCATTATGAATTTCTTGAGGTTGAACAT
1 ATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTGAGGTTGAACAA
* * *
1666 ATAGTGCAAATACGAAAACTCATAAACTCATTATGAATTTATTGAGGTTG
1 ATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTGAGGTTG
1716 CACACTCAAT
Statistics
Matches: 143, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
55 142 0.99
56 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.33
Consensus pattern (55 bp):
ATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTGAGGTTGAACAA
Found at i:2857 original size:55 final size:55
Alignment explanation
Indices: 2764--3053 Score: 325
Period size: 55 Copynumber: 5.3 Consensus size: 55
2754 TCAGTGGTTT
* * * * * *
2764 TTGCACACGTAGTTCCGAA-ACGGTAATTCACAACCTCATTATGAATTTCGT-AGCG
1 TTGCACACATAGTGCC-AATACGGAAATTCATAAACTCATTATGAATTTCATGAG-G
* * * *
2819 TTGCAGACATAATGCCAATACGGAAGTTCATAAACTCATTAGGAATTTCATGAGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCATGAGG
* * *
2874 TTTCACACATGGTGCCAATACGGAAATTCAGAAACTCATTATGAATTTCATGAGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCATGAGG
* * * * * *
2929 TTACACATATAGTGCCAATAC-GAAATTCGTAAACTCATTATAAATTTCTTAAGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCATGAGG
* **
2983 TTGCACACATAGTGCCAATATGGAAATTCATAAACTCATTATGAATTTTTTGAGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCATGAGG
* *
3038 TTACACACACAGTGCC
1 TTGCACACATAGTGCC
3054 CTTTCGGTAA
Statistics
Matches: 198, Mismatches: 34, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
54 48 0.24
55 148 0.75
56 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (55 bp):
TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCATGAGG
Found at i:2998 original size:109 final size:110
Alignment explanation
Indices: 2764--3053 Score: 334
Period size: 109 Copynumber: 2.6 Consensus size: 110
2754 TCAGTGGTTT
* * * * * * *
2764 TTGCACACGTAGTTCCGAA-ACGGTAATTCACAACCTCATTATGAATTTCGT-AGCGTTGCAGAC
1 TTGCACACATAGTGCC-AATACGGAAATTCACAAACTCATTATGAATTTCATGAG-GTTACACAC
* * * *
2827 ATAATGCCAATACGGAAGTTCATAAACTCATTAGGAATTTCATGAGG
64 ATAGTGCCAATACGGAAATTCATAAACTCATTAGAAATTTCATAAGG
* * * *
2874 TTTCACACATGGTGCCAATACGGAAATTCAGAAACTCATTATGAATTTCATGAGGTTACACATAT
1 TTGCACACATAGTGCCAATACGGAAATTCACAAACTCATTATGAATTTCATGAGGTTACACACAT
* * *
2939 AGTGCCAATAC-GAAATTCGTAAACTCATTATAAATTTCTTAAGG
66 AGTGCCAATACGGAAATTCATAAACTCATTAGAAATTTCATAAGG
* * ** *
2983 TTGCACACATAGTGCCAATATGGAAATTCATAAACTCATTATGAATTTTTTGAGGTTACACACAC
1 TTGCACACATAGTGCCAATACGGAAATTCACAAACTCATTATGAATTTCATGAGGTTACACACAT
3048 AGTGCC
66 AGTGCC
3054 CTTTCGGTAA
Statistics
Matches: 152, Mismatches: 26, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
109 92 0.61
110 58 0.38
111 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (110 bp):
TTGCACACATAGTGCCAATACGGAAATTCACAAACTCATTATGAATTTCATGAGGTTACACACAT
AGTGCCAATACGGAAATTCATAAACTCATTAGAAATTTCATAAGG
Found at i:4165 original size:55 final size:55
Alignment explanation
Indices: 4058--4371 Score: 325
Period size: 55 Copynumber: 5.7 Consensus size: 55
4048 TTGATATTTC
* * * * ** *
4058 AACTCATTATAAA-TTCAGTG-GTTTTCGCACACGTATTGCCGATACGGTAATTCACA
1 AACTCATTATAAATTTC-GTGAG-GTT-GCACACATAGTGCCAATACGAAAATTCATA
* * * * *
4114 AACTAATTATAAATTACGTGGGGTTGCACACATAGTGCTAATAGGAAAATTCATA
1 AACTCATTATAAATTTCGTGAGGTTGCACACATAGTGCCAATACGAAAATTCATA
* * * *
4169 AACTCATTATGAATTTCGTGAGGCTGCACACAT-GATGCCAATACGGAAATTCAGA
1 AACTCATTATAAATTTCGTGAGGTTGCACACATAG-TGCCAATACGAAAATTCATA
* *
4224 AACTCATTATGAATTTCGTGCGGTTGCACACATAGTG-CAATACGAAAATTCATA
1 AACTCATTATAAATTTCGTGAGGTTGCACACATAGTGCCAATACGAAAATTCATA
* *
4278 AACTCATTATAAATTTCTTGTG-GGTT-CAGACATAGTGCCAATACAAAAATTCATA
1 AACTCATTATAAATTTC--GTGAGGTTGCACACATAGTGCCAATACGAAAATTCATA
* **
4333 AACTCATTATTAATTTTTTGAGGTTGCACACATAGTGCC
1 AACTCATTATAAATTTCGTGAGGTTGCACACATAGTGCC
4372 CTTTTTGTAA
Statistics
Matches: 218, Mismatches: 31, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
53 2 0.01
54 46 0.21
55 146 0.67
56 21 0.10
57 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Consensus pattern (55 bp):
AACTCATTATAAATTTCGTGAGGTTGCACACATAGTGCCAATACGAAAATTCATA
Found at i:4328 original size:109 final size:110
Alignment explanation
Indices: 4106--4370 Score: 336
Period size: 109 Copynumber: 2.4 Consensus size: 110
4096 CCGATACGGT
* * * *
4106 AATTCACAAACTAATTATAAATTACGTGGGGTTGCACACATAGTGCTAATAGGAAAATTCATAAA
1 AATTCACAAACTCATTATAAATTTCGTGAGGTTGCACACATAGTGCTAATACGAAAATTCATAAA
* **
4171 CTCATTATGAATTTCGTGAGGCTGCACACATGATGCCAATACGGA
66 CTCATTATAAATTTCGTGAGGCTGCACACATGATGCCAATACAAA
* * *
4216 AATTCAGAAACTCATTATGAATTTCGTGCGGTTGCACACATAGTGC-AATACGAAAATTCATAAA
1 AATTCACAAACTCATTATAAATTTCGTGAGGTTGCACACATAGTGCTAATACGAAAATTCATAAA
* * * * *
4280 CTCATTATAAATTTCTTGTGGGTTCAGACAT-AGTGCCAATACAAA
66 CTCATTATAAATTTCGTGAGGCTGCACACATGA-TGCCAATACAAA
* * **
4325 AATTCATAAACTCATTATTAATTTTTTGAGGTTGCACACATAGTGC
1 AATTCACAAACTCATTATAAATTTCGTGAGGTTGCACACATAGTGC
4371 CCTTTTTGTA
Statistics
Matches: 135, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
108 1 0.01
109 93 0.69
110 41 0.30
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (110 bp):
AATTCACAAACTCATTATAAATTTCGTGAGGTTGCACACATAGTGCTAATACGAAAATTCATAAA
CTCATTATAAATTTCGTGAGGCTGCACACATGATGCCAATACAAA
Found at i:5612 original size:55 final size:55
Alignment explanation
Indices: 5536--5809 Score: 379
Period size: 55 Copynumber: 5.0 Consensus size: 55
5526 TGTAGTACTG
* * * *
5536 ATACGATAATTTATAAACTCATTATGAATTACGTGGGGTTGCACACATAGTGCCA
1 ATACGAAAATTCATAAACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCA
* * * * *
5591 ATATGGAAATTCATAAACTCATTATGAGTTTCGTGAGGTTGTACTCATAGTGCCA
1 ATACGAAAATTCATAAACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCA
* *
5646 ATACGAAAATTCATAAACTCATTATGAATTTCGCGAGGTTGCACACATAGTGTCA
1 ATACGAAAATTCATAAACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCA
* **
5701 ATACGAAAATTCATAAACTCATTATGAATTTCTTGAGGTTGTGCACATAGTGCCA
1 ATACGAAAATTCATAAACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCA
* * *
5756 ATAC-AGAAATTCATAAACTCATTATGAATTTCTTAAGGTTGCACACACAGTGCC
1 ATACGA-AAATTCATAAACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCC
5810 CTTTTGGTAA
Statistics
Matches: 193, Mismatches: 25, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
54 1 0.01
55 192 0.99
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (55 bp):
ATACGAAAATTCATAAACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCA
Found at i:7448 original size:27 final size:27
Alignment explanation
Indices: 7410--7461 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
7400 GATAAGCTAT
7410 TGGTCCTACCCTTTTTAAAATCTCATA
1 TGGTCCTACCCTTTTTAAAATCTCATA
7437 TGGTCCTACCCTTTTTAAAATCTCA
1 TGGTCCTACCCTTTTTAAAATCTCA
7462 CAAGGTCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.27, G:0.08, T:0.40
Consensus pattern (27 bp):
TGGTCCTACCCTTTTTAAAATCTCATA
Found at i:7468 original size:27 final size:27
Alignment explanation
Indices: 7411--7469 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
7401 ATAAGCTATT
* *
7411 GGTCCTACCCTTTTTAAAATCTCATAT
1 GGTCCTACCCTTTTTAAAATCTCACAA
7438 GGTCCTACCCTTTTTAAAATCTCACAA
1 GGTCCTACCCTTTTTAAAATCTCACAA
7465 GGTCC
1 GGTCC
7470 AATGAATCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.25, C:0.29, G:0.10, T:0.36
Consensus pattern (27 bp):
GGTCCTACCCTTTTTAAAATCTCACAA
Found at i:11529 original size:56 final size:55
Alignment explanation
Indices: 11445--11597 Score: 184
Period size: 56 Copynumber: 2.8 Consensus size: 55
11435 TGGTTTTCGT
* * * *
11445 ACACGTAGTGCCAATACAGTAATTCATAAACTCATTATGAATTACATG-GGATTGC
1 ACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTACATGAAG-TTAC
* * * *
11500 ACACATAGTGCCAATACGAGAAATCCATAAACTCGTTATGAATTTCGTGAAGTTAC
1 ACACATAGTGCCAATAC-AGAAATTCATAAACTCATTATGAATTACATGAAGTTAC
* *
11556 ACACATAGTG-CAATACTGAAATTCATAAACACATTATGAATT
1 ACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATT
11598 TTTTGAGGTT
Statistics
Matches: 84, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
54 22 0.26
55 22 0.26
56 39 0.46
57 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.28
Consensus pattern (55 bp):
ACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTACATGAAGTTAC
Found at i:11613 original size:54 final size:55
Alignment explanation
Indices: 11445--11621 Score: 205
Period size: 54 Copynumber: 3.2 Consensus size: 55
11435 TGGTTTTCGT
* * *
11445 ACACGTAGTGCCAATACAGTAATTCATAAACTCATTATGAATTACATG-GGATTGC
1 ACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCATGAGG-TTGC
* * * * *
11500 ACACATAGTGCCAATACGAGAAATCCATAAACTCGTTATGAATTTCGTGAAGTTAC
1 ACACATAGTGCCAATAC-AGAAATTCATAAACTCATTATGAATTTCATGAGGTTGC
* * **
11556 ACACATAGTG-CAATACTGAAATTCATAAACACATTATGAATTTTTTGAGGTTGC
1 ACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCATGAGGTTGC
*
11610 ACACACAGTGCC
1 ACACATAGTGCC
11622 CTTTTGGTAA
Statistics
Matches: 102, Mismatches: 17, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
54 39 0.38
55 23 0.23
56 39 0.38
57 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (55 bp):
ACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCATGAGGTTGC
Found at i:16348 original size:21 final size:21
Alignment explanation
Indices: 16324--16374 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
16314 TGAATATTTA
16324 ATTTAAATTAATT-AAATAAAT
1 ATTT-AATTAATTAAAATAAAT
*
16345 ATTTAATTAATTCAAAATAAAA
1 ATTTAATTAATT-AAAATAAAT
16367 ATCTTAAT
1 AT-TTAAT
16375 ACGTTAGGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 8 0.31
21 4 0.15
22 9 0.35
23 5 0.19
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTTAATTAATTAAAATAAAT
Found at i:17642 original size:18 final size:17
Alignment explanation
Indices: 17610--17660 Score: 68
Period size: 17 Copynumber: 2.9 Consensus size: 17
17600 CTCCTTAGAT
17610 ATTTTT-ATTTGTTTTTA
1 ATTTTTAATTT-TTTTTA
*
17627 ATTTTTAAATTTTTTTAA
1 ATTTTT-AATTTTTTTTA
17645 ATTTTTAATTTTTTTT
1 ATTTTTAATTTTTTTT
17661 TTAGTTTCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 15 0.50
18 11 0.37
19 4 0.13
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.75
Consensus pattern (17 bp):
ATTTTTAATTTTTTTTA
Found at i:27026 original size:176 final size:174
Alignment explanation
Indices: 26734--27061 Score: 487
Period size: 176 Copynumber: 1.9 Consensus size: 174
26724 ATGATATCAT
* * *
26734 ATTATTTTTCATTTAAATAATTCCAGAAAAGCAATCATTTAATAAAGACAATTGAGAAAATTAAA
1 ATTATTTTTCATTTAAATAATTCAAGAAAAGAAATCATTTAATAAAGACAAATGAGAAAATTAAA
** * **
26799 CAATTAATTATAGTTATCAATCGATTATGTTCAATTATTTAAAAATATCGAGTCAAAGTCTTTAA
66 CAATTAATTATAACTATCAATCCATTATGTTCAATTATTTAAAAATATCGAGTCAAAACCTTTAA
* *
26864 CTTTCATTAAACGACTTTTCCTCGCTAATTTTAACTAGAAGAAC
131 CTTGCATTAAACAACTTTTCCTCGCTAATTTTAACTAGAAGAAC
* *
26908 ATTATTTTTC-TTTCAAATAATTCAAGAAAAGAAATCATTTAATAAAAAGACAAATGATATAATT
1 ATTATTTTTCATTT-AAATAATTCAAGAAAAGAAATCATTTAAT--AAAGACAAATGAGAAAATT
* * *
26972 AATCAATTATTTCTAACTATCAATCCATTATGTTCAATTATTTAAAAATATCGAGTCAAAACCTT
63 AAACAATTAATTATAACTATCAATCCATTATGTTCAATTATTTAAAAATATCGAGTCAAAACCTT
27037 TAACTTGCATTAAACAACTTTTCCT
128 TAACTTGCATTAAACAACTTTTCCT
27062 GTAACACCCA
Statistics
Matches: 136, Mismatches: 15, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
173 3 0.02
174 37 0.27
176 96 0.71
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (174 bp):
ATTATTTTTCATTTAAATAATTCAAGAAAAGAAATCATTTAATAAAGACAAATGAGAAAATTAAA
CAATTAATTATAACTATCAATCCATTATGTTCAATTATTTAAAAATATCGAGTCAAAACCTTTAA
CTTGCATTAAACAACTTTTCCTCGCTAATTTTAACTAGAAGAAC
Found at i:27908 original size:56 final size:57
Alignment explanation
Indices: 27796--27914 Score: 152
Period size: 59 Copynumber: 2.1 Consensus size: 57
27786 CTAACCTGAG
* * *
27796 TATGACACATAAGGTCGTGCCCACCACCTGCACTAGTTATACTTTAGTGAAGTCCCGAA
1 TATGACACATAAGATCATGCCCACCACATGCACTA--TATACTTTAGTGAAGTCCCGAA
* *
27855 TATGACACGTAAGATCATGCCCACCATATGCACTA-ATACTTTAGTGCAA-TCCCGAA
1 TATGACACATAAGATCATGCCCACCACATGCACTATATACTTTAGTG-AAGTCCCGAA
27911 TATG
1 TATG
27915 CAGCCTGCTA
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
56 22 0.41
57 2 0.04
59 30 0.56
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (57 bp):
TATGACACATAAGATCATGCCCACCACATGCACTATATACTTTAGTGAAGTCCCGAA
Found at i:33716 original size:678 final size:675
Alignment explanation
Indices: 31339--34032 Score: 4487
Period size: 678 Copynumber: 4.0 Consensus size: 675
31329 CAGACTTAAC
* *
31339 TTTAAAGTCTTTAGTTTCACTTTTTTTTCTGCTTGTTCTATCTTTGAAAAGCATGACAATTTTCA
1 TTTAAAGTCTTTAGTTTCACTTTTTTTTCTGCTTGTTCTATCTTTGACAAGCATGAAAATTTTCA
* * * *
31404 TATTTTCTCTAATGATCCTTTATTCGATCTAGCAATATAGGGTTTAGATTTAATCCTATAATCAA
66 TATTTTCTCTGATGATCCTTTATTCGATCTAGCAACATAGGCTTTAAATTTAATCCTATAATCAA
* *
31469 AACACCATCTTTCTTTAAATAAAATCACAAATTCAAAACTCTCAGAATAGAAATGTCTTTCAGCT
131 AACACCATCTTTCTTTAAAGAAAATCACAAATTCAAAACTATCAGAATAGAAATGTCTTTCAGCT
*
31534 TTATCGTATCAGCCACCACATTAGCCTTTCCTATTTGCAGTTGATAAGCACATCATCATTCTTTA
196 TTATCGTATCAGCCACTACATTAGCCTTTCCTATTTGCAGTTGATAAGCACATCATCATTCTTTA
* * *
31599 AGGAATTCAATCCATTTCAATTCTTTTCACTCCTTCGATTCAACACATACTTTTGAATTTTGAGA
261 AGGAATTCAATCCATTTCATTTCTTTTCACTCTTTCGAGTCAACACATACTTTTGAATTTTGAGA
*
31664 TCCGCATAAATATAGACTCACTCACCATATAGATAGTGGTGATATATCAACAAAGTAAACAAAAT
326 TCCGCATAAATATAGAGTCACTCACCATATAGATAGTGGTGATATATCAACAAAGTAAACAAAAT
*
31729 TGTTGTCAACTAGAGATCATGAGCCATATAATTTATTTCATGAATTTGTAGTTGCTTTAAAGCAT
391 TGTTGTCAACTAGAGATCATGAGCCATATAATTTATTTCATGATTTTGTAGTTGCTTTAAAGCAT
* *
31794 AAACCAAAATTTTTCCAATTGTACAAACAATCATCTCAAACCATTAGGAGATGCATTACTATAAT
456 AAACCAAAACTTTTCCAATTGTAAAAACAATCATCTCAAACCATTAGGAGATGCATTACTATAAT
*
31859 TCAAATACTCTTTTCTAGATTCTAGTTATACTGACCTTGGAGCTTATGTCGGTATTCTTTTTAAC
521 TCAAATACTCTTTTCTAGATTCTAGTTATACTGACCTTGGAGCTTATGTCGGTATTCATTTTAAC
*
31924 ATCTCAAAGTTTTCTTGGCACTTAACAATCCAAATGAATAACACGTCTTTCTCTAATAGTTTGGT
586 ATCTCAAAGTTTTCTTGGCACTTAACAGTCCAAATGAATAACACGTCTTTCTCTAATAGTTTGGT
*
31989 CAGAGGGAATATAATAAAAAATAAG
651 CAGAGGGAATATAATCAAAAATAAG
* * *
32014 TTTAAACTCTTTAGTTTCACTTTTTTTTCCTTCTTGTTCTATCTTTGACAAGCATGACAATTTTC
1 TTTAAAGTCTTTAGTTTCACTTTTTTTT-CTGCTTGTTCTATCTTTGACAAGCATGAAAATTTTC
* * * *
32079 ATATTTTCTCTGATGATCCTTTATTCAATATAGAAACATAGGCTTTAGATTTAATCCTATAATCA
65 ATATTTTCTCTGATGATCCTTTATTCGATCTAGCAACATAGGCTTTAAATTTAATCCTATAATCA
* *
32144 AAACACCATCTTTATTTAAAGAAAATCACAAATTCAAAACTCTCAGAATAGAAATGTCTTTCAGC
130 AAACACCATCTTTCTTTAAAGAAAATCACAAATTCAAAACTATCAGAATAGAAATGTCTTTCAGC
* *
32209 TTTATCGTATCAGCCACTGCATTAGCCTTTCCTATTTGAAGTTGATAAGCACATCATCATTCTTT
195 TTTATCGTATCAGCCACTACATTAGCCTTTCCTATTTGCAGTTGATAAGCACATCATCATTCTTT
*
32274 AAGGAATTCAATCCATTTCATTTCTTTTCACTCATTCGAGTCAACACATACTTTTGAATTTTGAG
260 AAGGAATTCAATCCATTTCATTTCTTTTCACTCTTTCGAGTCAACACATACTTTTGAATTTTGAG
* *
32339 ATCCGTATAAATAT--AGTCACTCACCATATAGATAGTGGTGATATATCAACATAGTAAACAAAA
325 ATCCGCATAAATATAGAGTCACTCACCATATAGATAGTGGTGATATATCAACAAAGTAAACAAAA
*
32402 TTGTTGTCAACTAGAGATCATGAGCCATATAATTTATTTCATGATTTTGTAGTTGGTTTAAAGCA
390 TTGTTGTCAACTAGAGATCATGAGCCATATAATTTATTTCATGATTTTGTAGTTGCTTTAAAGCA
* * * *
32467 TAAACCAAAACTTTTCCAATTATACAAATAATCATCTCAACCCATTAGGAGATGCATTACTATAA
455 TAAACCAAAACTTTTCCAATTGTAAAAACAATCATCTCAAACCATTAGGAGATGCATTACTATAA
*
32532 TTCAAATACTCTTTTATAGATTCTAGTTATACTGACCTTGGAGCTTATGTCGGTATTCATTTTAA
520 TTCAAATACTCTTTTCTAGATTCTAGTTATACTGACCTTGGAGCTTATGTCGGTATTCATTTTAA
* * * *
32597 AATCTCAAAGTTTTCTTGGCACTTAACAGTCCAAATGAATAACACGTATTTCTTTAATATTTTGG
585 CATCTCAAAGTTTTCTTGGCACTTAACAGTCCAAATGAATAACACGTCTTTCTCTAATAGTTTGG
* *
32662 TCAAAGGGAATATAATCAAAATTAAG
650 TCAGAGGGAATATAATCAAAAATAAG
* *
32688 TTTAAAGTCTTTAGTTTCACTTTTTTTTCTGCTTGTTCTATCTTTGATAGGCATGAAAATTTTCA
1 TTTAAAGTCTTTAGTTTCACTTTTTTTTCTGCTTGTTCTATCTTTGACAAGCATGAAAATTTTCA
* * *
32753 TATTTTCTTTGATGATCCTTTATTCGGTCTAGCAACATAGGCTTTAAATTTAATTCTATAATCAA
66 TATTTTCTCTGATGATCCTTTATTCGATCTAGCAACATAGGCTTTAAATTTAATCCTATAATCAA
* * * *
32818 AACACCATCTTTCTTGAAAGACAATCACACATTCAAAACTATCATAATAGAAATGTCTTTCAGCT
131 AACACCATCTTTCTTTAAAGAAAATCACAAATTCAAAACTATCAGAATAGAAATGTCTTTCAGCT
* * *
32883 TTATCGTATCAGCCACTATATTAGCCTTTCCTGTTTGCAGTTGATAAGAACATCATCATTCTTTA
196 TTATCGTATCAGCCACTACATTAGCCTTTCCTATTTGCAGTTGATAAGCACATCATCATTCTTTA
* *
32948 AGGAATTCGATCCATTTCATTTCTTTTCACTCTTTCGAGTCAAAACATACTTTTGAATTTTGAGA
261 AGGAATTCAATCCATTTCATTTCTTTTCACTCTTTCGAGTCAACACATACTTTTGAATTTTGAGA
* *
33013 TCTGCATAAATATAGAGTCACTCACCATACAGATAGTGGTGATATATCAACAAAGTAAACAAAAT
326 TCCGCATAAATATAGAGTCACTCACCATATAGATAGTGGTGATATATCAACAAAGTAAACAAAAT
* *
33078 TGTTGTCAACTAGAGATCATGAGCCATATAATTTATTTCATGATTTTTTAGTTGCTTTAAACCAT
391 TGTTGTCAACTAGAGATCATGAGCCATATAATTTATTTCATGATTTTGTAGTTGCTTTAAAGCAT
33143 AAACCAAAACTTTTCCAATTGTAAAAACAATCATCTCAAACCATTAGGAGATGCATTACTATAAT
456 AAACCAAAACTTTTCCAATTGTAAAAACAATCATCTCAAACCATTAGGAGATGCATTACTATAAT
*
33208 TCAAATACTCTTTTCTAGATTCTAGTTATACTGACGTTGGAGCTTATGTCGGTATTCATTTTAAC
521 TCAAATACTCTTTTCTAGATTCTAGTTATACTGACCTTGGAGCTTATGTCGGTATTCATTTTAAC
*
33273 ATCTCAAAGTTTTCTTGGCACTTAACATTCCAAATGAATAACACGTCTTTCTCTAATAGTTTGGT
586 ATCTCAAAGTTTTCTTGGCACTTAACAGTCCAAATGAATAACACGTCTTTCTCTAATAGTTTGGT
*
33338 CAGAGAGAATATAATCAAAAATAAG
651 CAGAGGGAATATAATCAAAAATAAG
33363 TTTAAAGTCTTTAGTTTCACTTTTTTTTTTCTGCTTGTGTCTATCTTTGACAAGCATGAAAATTT
1 TTTAAAGTCTTTAGTTTCAC--TTTTTTTTCTGCTTGT-TCTATCTTTGACAAGCATGAAAATTT
* * *
33428 TAATATTTTCTTTGATGATCCTTTATTCGATCTAGCAACATAGGCTTTAAATTTAATTCTATAAT
63 TCATATTTTCTCTGATGATCCTTTATTCGATCTAGCAACATAGGCTTTAAATTTAATCCTATAAT
* * * *
33493 CAAAACACCATATTTCTTTAAAGACAATCACACATTCAAAACTATCATAATAGAAATGTCTTTCA
128 CAAAACACCATCTTTCTTTAAAGAAAATCACAAATTCAAAACTATCAGAATAGAAATGTCTTTCA
* *
33558 GCTTTATCGTATCAACCACTATATTAGCCTTTCCTATTTGCAGTTGATAAGCACATCATCATTCT
193 GCTTTATCGTATCAGCCACTACATTAGCCTTTCCTATTTGCAGTTGATAAGCACATCATCATTCT
*
33623 TTGAGGAATTCAATCCATTTCATTTCTTTTCACTCTTTCGAGTCAACACATACTTTTGAATTTTG
258 TTAAGGAATTCAATCCATTTCATTTCTTTTCACTCTTTCGAGTCAACACATACTTTTGAATTTTG
33688 AGATCCGCATAAATATAGAGTCACTCACCATATAGATAGTGGTGATATATCAACAAAGTAAACAA
323 AGATCCGCATAAATATAGAGTCACTCACCATATAGATAGTGGTGATATATCAACAAAGTAAACAA
* * * *
33753 AATTGTTGTCAAATCA-AGATCATAAGGCATATAATTTATTTCATGATTCTGTAGTTGCTTTAAA
388 AATTGTTGTCAACT-AGAGATCATGAGCCATATAATTTATTTCATGATTTTGTAGTTGCTTTAAA
*
33817 GCATAAACCAAAACTTTTCCTATTGTACAAAA-AATCATCTCAAACCATTAGGAGATGCATTACT
452 GCATAAACCAAAACTTTTCCAATTGTA-AAAACAATCATCTCAAACCATTAGGAGATGCATTACT
* * * ** **
33881 ATAATTCAAATAATATTTTCTAGATTCTAATTATACTGACCTTGGAGCTTATGTCAATATTTTTT
516 ATAATTCAAATACTCTTTTCTAGATTCTAGTTATACTGACCTTGGAGCTTATGTCGGTATTCATT
* * *
33946 TTAACATCTCAAAGTTTTATTGGTACTTAACAGTCCAAATGAATAACACGTCTTTTTCTAATAGT
581 TTAACATCTCAAAGTTTTCTTGGCACTTAACAGTCCAAATGAATAACACGTCTTTCTCTAATAGT
34011 TTGGTCAGAGGGAATATAATCA
646 TTGGTCAGAGGGAATATAATCA
34033 TCGAAAAGTT
Statistics
Matches: 1894, Mismatches: 117, Indels: 13
0.94 0.06 0.01
Matches are distributed among these distances:
673 283 0.15
674 344 0.18
675 363 0.19
676 293 0.15
677 16 0.01
678 590 0.31
679 5 0.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (675 bp):
TTTAAAGTCTTTAGTTTCACTTTTTTTTCTGCTTGTTCTATCTTTGACAAGCATGAAAATTTTCA
TATTTTCTCTGATGATCCTTTATTCGATCTAGCAACATAGGCTTTAAATTTAATCCTATAATCAA
AACACCATCTTTCTTTAAAGAAAATCACAAATTCAAAACTATCAGAATAGAAATGTCTTTCAGCT
TTATCGTATCAGCCACTACATTAGCCTTTCCTATTTGCAGTTGATAAGCACATCATCATTCTTTA
AGGAATTCAATCCATTTCATTTCTTTTCACTCTTTCGAGTCAACACATACTTTTGAATTTTGAGA
TCCGCATAAATATAGAGTCACTCACCATATAGATAGTGGTGATATATCAACAAAGTAAACAAAAT
TGTTGTCAACTAGAGATCATGAGCCATATAATTTATTTCATGATTTTGTAGTTGCTTTAAAGCAT
AAACCAAAACTTTTCCAATTGTAAAAACAATCATCTCAAACCATTAGGAGATGCATTACTATAAT
TCAAATACTCTTTTCTAGATTCTAGTTATACTGACCTTGGAGCTTATGTCGGTATTCATTTTAAC
ATCTCAAAGTTTTCTTGGCACTTAACAGTCCAAATGAATAACACGTCTTTCTCTAATAGTTTGGT
CAGAGGGAATATAATCAAAAATAAG
Found at i:37247 original size:7 final size:7
Alignment explanation
Indices: 37235--37284 Score: 77
Period size: 7 Copynumber: 7.4 Consensus size: 7
37225 GTCAAAGAAA
37235 GTCAACG
1 GTCAACG
37242 GTCAACG
1 GTCAACG
37249 GTC-ACG
1 GTCAACG
37255 GTCAACG
1 GTCAACG
37262 GTC-ACG
1 GTCAACG
37268 GTCAACG
1 GTCAACG
*
37275 GTCAATG
1 GTCAACG
37282 GTC
1 GTC
37285 GGGTCGGGTC
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
6 12 0.30
7 28 0.70
ACGTcount: A:0.24, C:0.28, G:0.30, T:0.18
Consensus pattern (7 bp):
GTCAACG
Found at i:37257 original size:13 final size:13
Alignment explanation
Indices: 37239--37278 Score: 80
Period size: 13 Copynumber: 3.1 Consensus size: 13
37229 AAGAAAGTCA
37239 ACGGTCAACGGTC
1 ACGGTCAACGGTC
37252 ACGGTCAACGGTC
1 ACGGTCAACGGTC
37265 ACGGTCAACGGTC
1 ACGGTCAACGGTC
37278 A
1 A
37279 ATGGTCGGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.25, C:0.30, G:0.30, T:0.15
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:37260 original size:20 final size:20
Alignment explanation
Indices: 37235--37284 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
37225 GTCAAAGAAA
37235 GTCAACGGTCAACGGTC-ACG
1 GTCAACGGTC-ACGGTCAACG
37255 GTCAACGGTCACGGTCAACG
1 GTCAACGGTCACGGTCAACG
*
37275 GTCAATGGTC
1 GTCAACGGTC
37285 GGGTCGGGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.24, C:0.28, G:0.30, T:0.18
Consensus pattern (20 bp):
GTCAACGGTCACGGTCAACG
Found at i:37296 original size:17 final size:17
Alignment explanation
Indices: 37274--37331 Score: 80
Period size: 17 Copynumber: 3.4 Consensus size: 17
37264 CACGGTCAAC
* *
37274 GGTCAATGGTCGGGTCG
1 GGTCAACGGTAGGGTCG
37291 GGTCAACGGTAGGGTCG
1 GGTCAACGGTAGGGTCG
* *
37308 GGTCAACAGTTGGGTCG
1 GGTCAACGGTAGGGTCG
37325 GGTCAAC
1 GGTCAAC
37332 CCGGTTCAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.17, C:0.19, G:0.43, T:0.21
Consensus pattern (17 bp):
GGTCAACGGTAGGGTCG
Found at i:37349 original size:19 final size:19
Alignment explanation
Indices: 37325--37414 Score: 110
Period size: 19 Copynumber: 4.7 Consensus size: 19
37315 AGTTGGGTCG
*
37325 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
*
37344 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
37363 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
* * *
37382 GGTTAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
37402 GGTCAAACCGGTT
1 GGTCAAACCGGTT
37415 TTCCAGCAGC
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
18 1 0.02
19 48 0.76
20 14 0.22
ACGTcount: A:0.26, C:0.30, G:0.26, T:0.19
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:37372 original size:9 final size:9
Alignment explanation
Indices: 37325--37413 Score: 70
Period size: 9 Copynumber: 9.3 Consensus size: 9
37315 AGTTGGGTCG
*
37325 GGTCAACCC
1 GGTCAAACC
*
37334 GGTTCAGACC
1 GG-TCAAACC
*
37344 GGTCAACCC
1 GGTCAAACC
*
37353 GGTTCAGACC
1 GG-TCAAACC
37363 GGTCAAACC
1 GGTCAAACC
*
37372 GGTTCGAACC
1 GG-TCAAACC
*
37382 GGTTAAACC
1 GGTCAAACC
*
37391 GGTTCAAAACT
1 GG-TC-AAACC
37402 GGTCAAACC
1 GGTCAAACC
37411 GGT
1 GGT
37414 TTTCCAGCAG
Statistics
Matches: 62, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
9 31 0.50
10 25 0.40
11 6 0.10
ACGTcount: A:0.26, C:0.30, G:0.26, T:0.18
Consensus pattern (9 bp):
GGTCAAACC
Found at i:44507 original size:13 final size:13
Alignment explanation
Indices: 44489--44534 Score: 83
Period size: 13 Copynumber: 3.5 Consensus size: 13
44479 AAGAAAGTCA
44489 ACGGTCAACGGTC
1 ACGGTCAACGGTC
44502 ACGGTCAACGGTC
1 ACGGTCAACGGTC
44515 ACGGTCAACGGTC
1 ACGGTCAACGGTC
44528 AACGGTC
1 -ACGGTC
44535 GGTCGGGTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 26 0.81
14 6 0.19
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.15
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:44510 original size:20 final size:20
Alignment explanation
Indices: 44485--44534 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
44475 GTCAAAGAAA
44485 GTCAACGGTCAACGGTC-ACG
1 GTCAACGGTC-ACGGTCAACG
44505 GTCAACGGTCACGGTCAACG
1 GTCAACGGTCACGGTCAACG
44525 GTCAACGGTC
1 GTCAACGGTC
44535 GGTCGGGTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 6 0.21
20 23 0.79
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (20 bp):
GTCAACGGTCACGGTCAACG
Found at i:44550 original size:7 final size:7
Alignment explanation
Indices: 44485--44534 Score: 86
Period size: 7 Copynumber: 7.4 Consensus size: 7
44475 GTCAAAGAAA
44485 GTCAACG
1 GTCAACG
44492 GTCAACG
1 GTCAACG
44499 GTC-ACG
1 GTCAACG
44505 GTCAACG
1 GTCAACG
44512 GTC-ACG
1 GTCAACG
44518 GTCAACG
1 GTCAACG
44525 GTCAACG
1 GTCAACG
44532 GTC
1 GTC
44535 GGTCGGGTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
6 12 0.29
7 29 0.71
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:44557 original size:17 final size:16
Alignment explanation
Indices: 44524--44579 Score: 76
Period size: 17 Copynumber: 3.4 Consensus size: 16
44514 CACGGTCAAC
44524 GGTCAACGGTCGGTCG
1 GGTCAACGGTCGGTCG
44540 GGTCAACGGTCGGGTCG
1 GGTCAACGGTC-GGTCG
* *
44557 GGTCAACAGTCTGGTCA
1 GGTCAACGGTC-GGTCG
44574 GGTCAA
1 GGTCAA
44580 ACCGGTCAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
16 11 0.31
17 25 0.69
ACGTcount: A:0.18, C:0.23, G:0.39, T:0.20
Consensus pattern (16 bp):
GGTCAACGGTCGGTCG
Found at i:44606 original size:20 final size:20
Alignment explanation
Indices: 44578--44615 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
44568 TGGTCAGGTC
44578 AAACCGGTCAAACCGGTTCA
1 AAACCGGTCAAACCGGTTCA
*
44598 AAACTGGTCAAACCGGTT
1 AAACCGGTCAAACCGGTT
44616 TTCCAGCAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.18
Consensus pattern (20 bp):
AAACCGGTCAAACCGGTTCA
Found at i:44608 original size:10 final size:9
Alignment explanation
Indices: 44574--44614 Score: 55
Period size: 9 Copynumber: 4.3 Consensus size: 9
44564 AGTCTGGTCA
44574 GGTCAAACC
1 GGTCAAACC
44583 GGTCAAACC
1 GGTCAAACC
*
44592 GGTTCAAAACT
1 GG-TC-AAACC
44603 GGTCAAACC
1 GGTCAAACC
44612 GGT
1 GGT
44615 TTTCCAGCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 18 0.64
10 4 0.14
11 6 0.21
ACGTcount: A:0.32, C:0.27, G:0.24, T:0.17
Consensus pattern (9 bp):
GGTCAAACC
Found at i:48745 original size:176 final size:175
Alignment explanation
Indices: 48452--48781 Score: 529
Period size: 176 Copynumber: 1.9 Consensus size: 175
48442 ACAATATAAT
*
48452 ATTATTTTTCTTTTAAATAATTCCAAAGAAGCAATCATTTAAAAAAAGAGAAAAGAGAAAATTAA
1 ATTATTTTTCTTTTAAATAATTCCAAAAAAGCAATCATTTAAAAAAAGAGAAAAGAGAAAATTAA
* ** *
48517 TCAATTAATTCTACTTATCAGTCCATTATGTTCAATTATTTAAAAATATCGAGTCAAAGCCTTTA
66 TCAATTAATTCTAATTATCAACCCATTATGTTAAATTATTTAAAAATATCGAGTCAAAGCCTTTA
48582 ACTTGCATTAAACGACTTTTCCTCGCTAAGTTTAAATAGGAGAAA
131 ACTTGCATTAAACGACTTTTCCTCGCTAAGTTTAAATAGGAGAAA
*
48627 ATTATTTTTCTTTTAAATAATT-CAAGAAAAGCAATCATTTAAAAAAA-AGAAAAATGATAAAAT
1 ATTATTTTTCTTTTAAATAATTCCAA-AAAAGCAATCATTTAAAAAAAGAG-AAAA-GAGAAAAT
* * *
48690 TAATCAATTATTTTTAATTATCAACCCATTATGTTAAATTATTTAAAAATATCGAGTCAAATCCT
63 TAATCAATTAATTCTAATTATCAACCCATTATGTTAAATTATTTAAAAATATCGAGTCAAAGCCT
*
48755 TTAACTTGCATTAAACGAGTTTTCCTC
128 TTAACTTGCATTAAACGACTTTTCCTC
48782 TAACACCCAT
Statistics
Matches: 142, Mismatches: 10, Indels: 5
0.90 0.06 0.03
Matches are distributed among these distances:
174 5 0.04
175 46 0.32
176 91 0.64
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.36
Consensus pattern (175 bp):
ATTATTTTTCTTTTAAATAATTCCAAAAAAGCAATCATTTAAAAAAAGAGAAAAGAGAAAATTAA
TCAATTAATTCTAATTATCAACCCATTATGTTAAATTATTTAAAAATATCGAGTCAAAGCCTTTA
ACTTGCATTAAACGACTTTTCCTCGCTAAGTTTAAATAGGAGAAA
Found at i:58089 original size:21 final size:21
Alignment explanation
Indices: 58060--58099 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
58050 TGATAAAATT
58060 AATCAATTAT-TTCTAATTACA
1 AATCAATTATATTC-AATTACA
*
58081 AATCCATTATATTCAATTA
1 AATCAATTATATTCAATTA
58100 TTTAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (21 bp):
AATCAATTATATTCAATTACA
Found at i:59168 original size:2 final size:2
Alignment explanation
Indices: 59161--59187 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
59151 CAATAAACAT
59161 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
59188 TCATGATAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:61739 original size:21 final size:21
Alignment explanation
Indices: 61710--61750 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
61700 TGATAAAATT
61710 AATCAATTAT-TTCTAATTATC
1 AATCAATTATGTTC-AATTATC
*
61731 AATCCATTATGTTCAATTAT
1 AATCAATTATGTTCAATTAT
61751 TTAAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.37, C:0.15, G:0.02, T:0.46
Consensus pattern (21 bp):
AATCAATTATGTTCAATTATC
Found at i:61984 original size:20 final size:20
Alignment explanation
Indices: 61959--62012 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
61949 AATGCACTTA
61959 GTGCATCGATGCATCCTGAT
1 GTGCATCGATGCATCCTGAT
*
61979 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGAT
*
61999 GTGCATCCATGCAT
1 GTGCATCGATGCAT
62013 GAAGGCTGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.19, C:0.28, G:0.24, T:0.30
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGAT
Found at i:62131 original size:20 final size:22
Alignment explanation
Indices: 62093--62132 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
62083 TTTGAGTAGA
62093 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
62115 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
62133 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:65493 original size:20 final size:20
Alignment explanation
Indices: 65453--65493 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
65443 ATGCACTTAT
* *
65453 TGCATCGATGCATCTTGATG
1 TGCATCGATGCATCATCATG
65473 TGCATCGATGCATCATCATG
1 TGCATCGATGCATCATCATG
65493 T
1 T
65494 ATTAAATTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (20 bp):
TGCATCGATGCATCATCATG
Found at i:65712 original size:23 final size:23
Alignment explanation
Indices: 65682--65731 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
65672 TGATACGACA
65682 TGGTAATTATCATGATTTTATAG
1 TGGTAATTATCATGATTTTATAG
65705 TGGTAATTATCATGATTTTATAG
1 TGGTAATTATCATGATTTTATAG
65728 TGGT
1 TGGT
65732 CAAATGGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.28, C:0.04, G:0.20, T:0.48
Consensus pattern (23 bp):
TGGTAATTATCATGATTTTATAG
Done.