Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001745.1 Hibiscus syriacus cultivar Beakdansim tig00003532_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: 68395
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:1486 original size:42 final size:41
Alignment explanation
Indices: 1372--1665 Score: 163
Period size: 41 Copynumber: 7.1 Consensus size: 41
1362 TTTTTTCAAA
* * * ** *
1372 CATCATGCTCGAAGGTCTTACAGATGGCCCGAAAAACTTAT
1 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGATTTAT
* ** * * *
1413 CCCTC-TGCTTAAAAGACATACCGA-GGACTCGAAGGATTTAAT
1 -CATCATGCTCGAAAGACTTACTGATGG-CCCGAAGGATTT-AT
* * * *
1455 CATCATGCTCGAAAGACTAACTGATGGCTCGAATGACTTAT
1 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGATTTAT
* * ** * * *
1496 CA-CTTTGTTAAAAAGACTTACAGATGACCCAAATGG-TTTAAT
1 CATC-ATGCTCGAAAGACTTACTGATGGCCCGAA-GGATTT-AT
* * *
1538 CATCATGCTCGAAAGACTTACTAATGGCCCGAATGACTTAT
1 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGATTTAT
* * *
1579 CA-CTTTGCTCAAAAGACTTA-T-ATAGGACCTGAAGGATTTGAT
1 CATC-ATGCTCGAAAGACTTACTGAT-GG-CCCGAAGGATTT-AT
*
1621 CATCATGCTCGAAAGACTTACTGATGGCCC-AGAGGACTTAT
1 CATCATGCTCGAAAGACTTACTGATGGCCCGA-AGGATTTAT
1662 CATC
1 CATC
1666 GAGAAACCTT
Statistics
Matches: 186, Mismatches: 49, Indels: 35
0.69 0.18 0.13
Matches are distributed among these distances:
39 2 0.01
40 7 0.04
41 85 0.46
42 83 0.45
43 7 0.04
44 2 0.01
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (41 bp):
CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGATTTAT
Found at i:1511 original size:83 final size:81
Alignment explanation
Indices: 1372--1663 Score: 327
Period size: 83 Copynumber: 3.5 Consensus size: 81
1362 TTTTTTCAAA
* * * ** * * * *
1372 CATCATGCTCGAAGGTCTTACAGATGGCCCGAAAAACTTATCCCTCTGCTTAAAAGACATACCGA
1 CATCATGCTCGAAAGACTTACTGATGGCCCGAATGACTTATCACTTTG-TTAAAAGACTTACAGA
1437 GGACTCGAAGGATTTAAT
65 GGAC-CGAAGGATTTAAT
* *
1455 CATCATGCTCGAAAGACTAACTGATGGCTCGAATGACTTATCACTTTGTTAAAAAGACTTACAGA
1 CATCATGCTCGAAAGACTTACTGATGGCCCGAATGACTTATCACTTTGTT-AAAAGACTTACAGA
* *
1520 TGACCCAAATGG-TTTAAT
65 GGA-CCGAA-GGATTTAAT
* * * *
1538 CATCATGCTCGAAAGACTTACTAATGGCCCGAATGACTTATCACTTTGCTCAAAAGACTTATATA
1 CATCATGCTCGAAAGACTTACTGATGGCCCGAATGACTTATCACTTTG-TTAAAAGACTTACAGA
*
1603 GGACCTGAAGGATTTGAT
65 GGACC-GAAGGATTTAAT
*
1621 CATCATGCTCGAAAGACTTACTGATGGCCC-AGAGGACTTATCA
1 CATCATGCTCGAAAGACTTACTGATGGCCCGA-ATGACTTATCA
1664 TCGAGAAACC
Statistics
Matches: 178, Mismatches: 24, Indels: 14
0.82 0.11 0.06
Matches are distributed among these distances:
82 7 0.04
83 167 0.94
84 4 0.02
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (81 bp):
CATCATGCTCGAAAGACTTACTGATGGCCCGAATGACTTATCACTTTGTTAAAAGACTTACAGAG
GACCGAAGGATTTAAT
Found at i:1783 original size:74 final size:74
Alignment explanation
Indices: 1660--2094 Score: 563
Period size: 74 Copynumber: 5.9 Consensus size: 74
1650 CAGAGGACTT
* * * *
1660 ATCATCGAGAAACCTTTGAAAATCAAACTT-GTCTTCTTCAAAAATTCATTTGAAAACATCATAT
1 ATCATCAAGAAACCTCTGAAAATCAGACTTAG-CTTCTTTAAAAATTCATTTGAAAACATCATAT
* *
1724 CAATAAATTA
65 CAATCAAGTA
*
1734 ATCATCAAGAAACCTCTGAAAATTAGACTT-GACTTCTTTAAAACA-TCATTTGAAAACATCATA
1 ATCATCAAGAAACCTCTGAAAATCAGACTTAG-CTTCTTTAAAA-ATTCATTTGAAAACATCATA
1797 TCAATCAAGTA
64 TCAATCAAGTA
* ** * * *
1808 ATCACCAAGAAACCTCAAAAAAATTAGACTTAGGTTATTTAAAAATTCATTTGAAAACATCATAT
1 ATCATCAAGAAACCTC-TGAAAATCAGACTTAGCTTCTTTAAAAATTCATTTGAAAACATCATAT
*
1873 CAATCAATTA
65 CAATCAAGTA
* * **
1883 ATCATCAAGAAACCTCTGAAAATCATACTTAGCTTCTTTAAAAATTCATTTCAAAACATCATGCC
1 ATCATCAAGAAACCTCTGAAAATCAGACTTAGCTTCTTTAAAAATTCATTTGAAAACATCATATC
1948 AATCAAGTA
66 AATCAAGTA
* * *
1957 ATCATCAAGAAACCTCT-AAAACTTAGAATTAGCTTCTTTAAAAATTTATTTGAAAACATCATAT
1 ATCATCAAGAAACCTCTGAAAA-TCAGACTTAGCTTCTTTAAAAATTCATTTGAAAACATCATAT
2021 CAATCAAGTA
65 CAATCAAGTA
* * * * *
2031 ATCATTAAGAAACCTCTAAAAATCATACTTAGATTCTTTAAAACTTCATTTGAAAACATCATAT
1 ATCATCAAGAAACCTCTGAAAATCAGACTTAGCTTCTTTAAAAATTCATTTGAAAACATCATAT
2095 TAGTTGGGTA
Statistics
Matches: 316, Mismatches: 39, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
73 4 0.01
74 242 0.77
75 69 0.22
76 1 0.00
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.31
Consensus pattern (74 bp):
ATCATCAAGAAACCTCTGAAAATCAGACTTAGCTTCTTTAAAAATTCATTTGAAAACATCATATC
AATCAAGTA
Found at i:1951 original size:149 final size:148
Alignment explanation
Indices: 1699--2093 Score: 587
Period size: 149 Copynumber: 2.7 Consensus size: 148
1689 TGTCTTCTTC
* * *
1699 AAAAATTCATTTGAAAACATCATATCAATAAATTAATCATCAAGAAACCTCTGAAAATTAGACTT
1 AAAAATTCATTTGAAAACATCATATCAATCAATTAATCATCAAGAAACCTCTGAAAATCATACTT
*
1764 -GACTTCTTTAAAACA-TCATTTGAAAACATCATATCAATCAAGTAATCACCAAGAAACCTCAAA
66 AG-CTTCTTTAAAA-ATTCATTTGAAAACATCATACCAATCAAGTAATCACCAAGAAACCTC-AA
* *
1827 AAAATTAGACTTAGGTTATTT
128 AAAATTAGAATTAGCTTATTT
1848 AAAAATTCATTTGAAAACATCATATCAATCAATTAATCATCAAGAAACCTCTGAAAATCATACTT
1 AAAAATTCATTTGAAAACATCATATCAATCAATTAATCATCAAGAAACCTCTGAAAATCATACTT
* * * *
1913 AGCTTCTTTAAAAATTCATTTCAAAACATCATGCCAATCAAGTAATCATCAAGAAACCTCTAAAA
66 AGCTTCTTTAAAAATTCATTTGAAAACATCATACCAATCAAGTAATCACCAAGAAACCTCAAAAA
* *
1978 CTTAGAATTAGCTTCTTT
131 ATTAGAATTAGCTTATTT
* * * *
1996 AAAAATTTATTTGAAAACATCATATCAATCAAGTAATCATTAAGAAACCTCTAAAAATCATACTT
1 AAAAATTCATTTGAAAACATCATATCAATCAATTAATCATCAAGAAACCTCTGAAAATCATACTT
* *
2061 AGATTCTTTAAAACTTCATTTGAAAACATCATA
66 AGCTTCTTTAAAAATTCATTTGAAAACATCATA
2094 TTAGTTGGGT
Statistics
Matches: 224, Mismatches: 20, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
148 109 0.49
149 114 0.51
150 1 0.00
ACGTcount: A:0.45, C:0.17, G:0.06, T:0.31
Consensus pattern (148 bp):
AAAAATTCATTTGAAAACATCATATCAATCAATTAATCATCAAGAAACCTCTGAAAATCATACTT
AGCTTCTTTAAAAATTCATTTGAAAACATCATACCAATCAAGTAATCACCAAGAAACCTCAAAAA
ATTAGAATTAGCTTATTT
Found at i:4831 original size:24 final size:24
Alignment explanation
Indices: 4773--4874 Score: 125
Period size: 24 Copynumber: 4.3 Consensus size: 24
4763 GAGTCGAGGG
* *
4773 TTCTACGCGGTCTTTTGGGACAAA
1 TTCTACGCGGTCCTTCGGGACAAA
* * *
4797 -TCTATGTGGTCATTCGGGACAAA
1 TTCTACGCGGTCCTTCGGGACAAA
*
4820 TTCTACGCGGTCCTTCGTGACAAA
1 TTCTACGCGGTCCTTCGGGACAAA
**
4844 TTCTACGCGGTCCTTCATGACAAA
1 TTCTACGCGGTCCTTCGGGACAAA
4868 TTCTACG
1 TTCTACG
4875 TGGCACTTCA
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
23 19 0.28
24 49 0.72
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.31
Consensus pattern (24 bp):
TTCTACGCGGTCCTTCGGGACAAA
Found at i:5009 original size:19 final size:20
Alignment explanation
Indices: 4977--5015 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
4967 ATGGGCTAAA
*
4977 TAAACCAATGGATAT-GAAT
1 TAAACAAATGGATATAGAAT
*
4996 TAAACAAATTGATATAGAAT
1 TAAACAAATGGATATAGAAT
5016 GAAAAGTGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.51, C:0.08, G:0.13, T:0.28
Consensus pattern (20 bp):
TAAACAAATGGATATAGAAT
Found at i:9013 original size:2 final size:2
Alignment explanation
Indices: 9006--9033 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
8996 GACATTTTTC
9006 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9034 TAAACATGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9479 original size:55 final size:55
Alignment explanation
Indices: 9418--9938 Score: 742
Period size: 55 Copynumber: 9.5 Consensus size: 55
9408 TTCCACGGTT
* * * * * *
9418 TTGCACACATAGTGTCGATACGGTAATTCACAAACTCATTATGAATTACATGGGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGGGG
* * *
9473 TTGCACACATAGCGCCAATAC-AAAATTTCATAAACTCATTATCAATTTCGTGGGG
1 TTGCACACATAGTGCCAATACGGAAA-TTCATAAACTCATTATGAATTTCGTGGGG
** *
9528 TTGCACACATAGTGCCAATACATAAATTCATAAACTCATTATGAATTTCGTGAGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGGGG
* *
9583 TTACACATATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGGGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGGGG
* * * * *
9638 TAGCACACATAGTACCAATACAGAAATTCATAAACTCATTATGAATTTTGTGAGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGGGG
* * * * *
9693 ATGCACACATAGTGCCAATACGGAAATTCATGAACTCGTTATGAATTTCATGAGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGGGG
* *
9748 TTGCACACATAGTGCCAATATGGAAATTCATAAACTCATTATGAATTTCGCGGGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGGGG
* *
9803 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATAAATTTTGTGGGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGGGG
* *
9858 TTGCACACATAGTG-CAATACGGAAATTCATAAACTCGTTATGAATTTCATGGGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGGGG
9912 TTGC-CACATAGTGCCAATACGGAAATT
1 TTGCACACATAGTGCCAATACGGAAATT
9939 TCAACATATA
Statistics
Matches: 415, Mismatches: 48, Indels: 7
0.88 0.10 0.01
Matches are distributed among these distances:
53 9 0.02
54 55 0.13
55 348 0.84
56 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (55 bp):
TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGGGG
Found at i:13551 original size:21 final size:20
Alignment explanation
Indices: 13507--13589 Score: 141
Period size: 20 Copynumber: 4.2 Consensus size: 20
13497 CCGTTAGACA
13507 GGGGGGAATCGGTACCCCCT
1 GGGGGGAATCGGTACCCCCT
13527 -GGGGGAATCGGTACCCCCT
1 GGGGGGAATCGGTACCCCCT
13546 GGGGGGGAATCGGTACCCCCT
1 -GGGGGGAATCGGTACCCCCT
*
13567 GGGGGGAATCCGTACCCCCT
1 GGGGGGAATCGGTACCCCCT
13587 GGG
1 GGG
13590 CAATCTGATT
Statistics
Matches: 60, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
19 19 0.32
20 22 0.37
21 19 0.32
ACGTcount: A:0.14, C:0.30, G:0.41, T:0.14
Consensus pattern (20 bp):
GGGGGGAATCGGTACCCCCT
Found at i:15545 original size:3 final size:3
Alignment explanation
Indices: 15537--15574 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
15527 TACGTCCTCA
* *
15537 TTC TTC TTC TTC TTC TTC TTC TTG TTT TTC TTC -TC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
15575 CCTTTCTTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.00, C:0.29, G:0.03, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:17018 original size:19 final size:20
Alignment explanation
Indices: 16982--17078 Score: 98
Period size: 19 Copynumber: 5.0 Consensus size: 20
16972 GTTAGACAGA
*
16982 GGGGAATCGGTATCCCCTGGG
1 GGGGAATCTGTATCCCCT-GG
*
17003 GGGGAATCTGT-T-CCCTAG
1 GGGGAATCTGTATCCCCTGG
17021 GGGGAATC-G-ATACCCCTGG
1 GGGGAATCTGTAT-CCCCTGG
17040 GGGGAATCTGT-TCCCCTGG
1 GGGGAATCTGTATCCCCTGG
* *
17059 GAGGAATATGTA-CCCCTGG
1 GGGGAATCTGTATCCCCTGG
17078 G
1 G
17079 TAATCTGATT
Statistics
Matches: 65, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
17 2 0.03
18 9 0.14
19 41 0.63
20 3 0.05
21 10 0.15
ACGTcount: A:0.18, C:0.24, G:0.37, T:0.22
Consensus pattern (20 bp):
GGGGAATCTGTATCCCCTGG
Found at i:17051 original size:37 final size:39
Alignment explanation
Indices: 16982--17054 Score: 123
Period size: 37 Copynumber: 1.9 Consensus size: 39
16972 GTTAGACAGA
*
16982 GGGGAATCGGTATCCCCTGGGGGGGAATCTGTTCCCTAG
1 GGGGAATCGATATCCCCTGGGGGGGAATCTGTTCCCTAG
17021 GGGGAATCGATA-CCCCT-GGGGGGAATCTGTTCCC
1 GGGGAATCGATATCCCCTGGGGGGGAATCTGTTCCC
17055 CTGGGAGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
37 17 0.52
38 5 0.15
39 11 0.33
ACGTcount: A:0.16, C:0.25, G:0.37, T:0.22
Consensus pattern (39 bp):
GGGGAATCGATATCCCCTGGGGGGGAATCTGTTCCCTAG
Found at i:17065 original size:38 final size:36
Alignment explanation
Indices: 16982--17078 Score: 115
Period size: 38 Copynumber: 2.5 Consensus size: 36
16972 GTTAGACAGA
16982 GGGGAATCGGTATCCCCTGGGGGGGAATCTGTTCCCTAG
1 GGGGAATC-GTA-CCCCT-GGGGGGAATCTGTTCCCTAG
17021 GGGGAATCGATACCCCTGGGGGGAATCTGTTCCCCT-G
1 GGGGAATCG-TACCCCTGGGGGGAATCTGTT-CCCTAG
*
17058 GGAGGAATATGTACCCCTGGG
1 GG-GGAAT-CGTACCCCTGGG
17079 TAATCTGATT
Statistics
Matches: 53, Mismatches: 1, Indels: 9
0.84 0.02 0.14
Matches are distributed among these distances:
37 17 0.32
38 25 0.47
39 11 0.21
ACGTcount: A:0.18, C:0.24, G:0.37, T:0.22
Consensus pattern (36 bp):
GGGGAATCGTACCCCTGGGGGGAATCTGTTCCCTAG
Found at i:18904 original size:21 final size:21
Alignment explanation
Indices: 18880--18939 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
18870 ATGCCAAAGT
*
18880 AAAATGAATAGATGCAAATGC
1 AAAATGAATAAATGCAAATGC
*
18901 AAAAGGTAA-AAATGCAAATGC
1 AAAATG-AATAAATGCAAATGC
* *
18922 AAAATGCATATATGCAAA
1 AAAATGAATAAATGCAAA
18940 AGGTACTGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
20 1 0.03
21 29 0.91
22 2 0.06
ACGTcount: A:0.55, C:0.10, G:0.17, T:0.18
Consensus pattern (21 bp):
AAAATGAATAAATGCAAATGC
Found at i:18927 original size:13 final size:15
Alignment explanation
Indices: 18909--18940 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
18899 GCAAAAGGTA
18909 AAAATGCA-A-ATGC
1 AAAATGCATATATGC
18922 AAAATGCATATATGC
1 AAAATGCATATATGC
18937 AAAA
1 AAAA
18941 GGTACTGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 1 0.06
15 8 0.47
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.19
Consensus pattern (15 bp):
AAAATGCATATATGC
Found at i:34241 original size:21 final size:21
Alignment explanation
Indices: 34201--34243 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
34191 AAAACAAAAT
* *
34201 ACAAGAAATTAGTAAATTAAA
1 ACAAGAAATAAATAAATTAAA
*
34222 ACAAGAAATAAATAAGTTAAA
1 ACAAGAAATAAATAAATTAAA
34243 A
1 A
34244 TTCAACTAGA
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:0.65, C:0.05, G:0.09, T:0.21
Consensus pattern (21 bp):
ACAAGAAATAAATAAATTAAA
Found at i:36041 original size:94 final size:96
Alignment explanation
Indices: 35876--36067 Score: 271
Period size: 94 Copynumber: 2.0 Consensus size: 96
35866 CAGAATTCTG
* *
35876 CTACAGAGGAAACAAAGAAACACTAGCTACAAACAAAGGCAACTAATAACCTTATACAACCAATC
1 CTACAGAGGAAACAAAGAAACACTAGCT--AAACAAAGGCAACTAACAACCCTATACAACCAATC
* *
35941 CCAATGAACAACCAATAGCTACACAAACAAGGA
64 CCAATGAACAACCAACAGCTAAACAAACAAGGA
* * *
35974 CTACAGAGGAAACAAATAAACACTAGCT-AAC-AAGGCAACTAACGACCCTATACAACCATTCCC
1 CTACAGAGGAAACAAAGAAACACTAGCTAAACAAAGGCAACTAACAACCCTATACAACCAATCCC
* *
36037 AATGAACAACTAGCAGCTAAACAAACAAGGA
66 AATGAACAACCAACAGCTAAACAAACAAGGA
36068 ATTATAACAA
Statistics
Matches: 85, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
94 55 0.65
95 3 0.04
98 27 0.32
ACGTcount: A:0.49, C:0.26, G:0.12, T:0.12
Consensus pattern (96 bp):
CTACAGAGGAAACAAAGAAACACTAGCTAAACAAAGGCAACTAACAACCCTATACAACCAATCCC
AATGAACAACCAACAGCTAAACAAACAAGGA
Found at i:36421 original size:12 final size:12
Alignment explanation
Indices: 36404--36465 Score: 65
Period size: 12 Copynumber: 5.3 Consensus size: 12
36394 GGTTTTTTTA
*
36404 GGTTTGGGTTTG
1 GGTTCGGGTTTG
*
36416 GGTT-TGGTTT-
1 GGTTCGGGTTTG
36426 GGTTCGGGTTTG
1 GGTTCGGGTTTG
* *
36438 GGTTCGAGTTCG
1 GGTTCGGGTTTG
*
36450 GGTTCGGGTTCG
1 GGTTCGGGTTTG
36462 GGTT
1 GGTT
36466 ACAAAAGATG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
10 4 0.09
11 10 0.23
12 29 0.67
ACGTcount: A:0.02, C:0.08, G:0.47, T:0.44
Consensus pattern (12 bp):
GGTTCGGGTTTG
Found at i:36426 original size:5 final size:6
Alignment explanation
Indices: 36404--36465 Score: 56
Period size: 6 Copynumber: 10.7 Consensus size: 6
36394 GGTTTTTTTA
* * * *
36404 GGTTTG GGTTTG GGTTT- GGTTT- GGTTCG GGTTTG GGTTCG AGTTCG
1 GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG
* *
36450 GGTTCG GGTTCG GGTT
1 GGTTTG GGTTTG GGTT
36466 ACAAAAGATG
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
5 9 0.18
6 41 0.82
ACGTcount: A:0.02, C:0.08, G:0.47, T:0.44
Consensus pattern (6 bp):
GGTTTG
Found at i:36435 original size:6 final size:6
Alignment explanation
Indices: 36426--36465 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
36416 GGTTTGGTTT
* *
36426 GGTTCG GGTTTG GGTTCG AGTTCG GGTTCG GGTTCG GGTT
1 GGTTCG GGTTCG GGTTCG GGTTCG GGTTCG GGTTCG GGTT
36466 ACAAAAGATG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.03, C:0.12, G:0.47, T:0.38
Consensus pattern (6 bp):
GGTTCG
Found at i:36450 original size:18 final size:17
Alignment explanation
Indices: 36410--36462 Score: 63
Period size: 18 Copynumber: 3.1 Consensus size: 17
36400 TTTAGGTTTG
* *
36410 GGTTTGGGTTT-GGTTT
1 GGTTCGGGTTTGGGTTC
36426 GGTTCGGGTTTGGGTTC
1 GGTTCGGGTTTGGGTTC
*
36443 GAGTTCGGGTTCGGGTTC
1 G-GTTCGGGTTTGGGTTC
36461 GG
1 GG
36463 GTTACAAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
16 10 0.31
17 6 0.19
18 16 0.50
ACGTcount: A:0.02, C:0.09, G:0.47, T:0.42
Consensus pattern (17 bp):
GGTTCGGGTTTGGGTTC
Found at i:37654 original size:45 final size:46
Alignment explanation
Indices: 37509--37655 Score: 167
Period size: 46 Copynumber: 3.2 Consensus size: 46
37499 TATAATGCAT
* * * * *
37509 CATTATGCATTTTCATTTATGGCAACCTTT--TACCTTTTTATATAC
1 CATTATACA-TTTCATTTATGGCATCATTTCATGCCTTTTTATACAC
* * *
37554 TATTTTACATTTTATTTATGGCATCATTTCATGCCTTTTTATACAC
1 CATTATACATTTCATTTATGGCATCATTTCATGCCTTTTTATACAC
*
37600 CATTATACATTTCGTTTATGGCATC-TTTCCATGCC-TTTTATACAC
1 CATTATACATTTCATTTATGGCATCATTT-CATGCCTTTTTATACAC
37645 CATTATACATT
1 CATTATACATT
37656 GTTATACATC
Statistics
Matches: 87, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
44 17 0.20
45 30 0.34
46 40 0.46
ACGTcount: A:0.24, C:0.20, G:0.07, T:0.48
Consensus pattern (46 bp):
CATTATACATTTCATTTATGGCATCATTTCATGCCTTTTTATACAC
Found at i:37876 original size:68 final size:68
Alignment explanation
Indices: 37676--37881 Score: 272
Period size: 68 Copynumber: 3.0 Consensus size: 68
37666 TAGTCTTTTA
* * * * **
37676 CTCAAAGTCATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTA
1 CTCAAAGGCACTTAACCTTTCATCTAACTGGCATAATTGAAACCTTTCTGTCAAATGCACAGTTA
37741 GGC
66 GGC
* * *
37744 CTCAAAGG-AGCTTAACCTTTCATCTAGCTGGCATAATT-AACACATTTCTGTCAAATGCAGAGT
1 CTCAAAGGCA-CTTAACCTTTCATCTAACTGGCATAATTGAA-ACCTTTCTGTCAAATGCACAGT
*
37807 TAGGT
64 TAGGC
* *
37812 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGAAACCTTTCTGTCAAATGCATAGTTA
1 CTCAAAGGCACTTAACCTTTCATCTAACTGGCATAATTGAAACCTTTCTGTCAAATGCACAGTTA
37877 GGC
66 GGC
37880 CT
1 CT
37882 TTAACTTTTT
Statistics
Matches: 119, Mismatches: 15, Indels: 8
0.84 0.11 0.06
Matches are distributed among these distances:
67 2 0.02
68 114 0.96
69 3 0.03
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.31
Consensus pattern (68 bp):
CTCAAAGGCACTTAACCTTTCATCTAACTGGCATAATTGAAACCTTTCTGTCAAATGCACAGTTA
GGC
Found at i:38301 original size:59 final size:59
Alignment explanation
Indices: 38232--38640 Score: 640
Period size: 59 Copynumber: 6.9 Consensus size: 59
38222 TTTCTCATAA
* * * ** * *
38232 GGAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGTGCAC-AAGGTGCCCCATTT
1 GGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAA-GTGCCCTATAT
* * * *
38291 AGAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACGAAGTGCCCTATAT
1 GGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATAT
* * **
38350 GAAAATTCATACGCTTAGTATGAATTTATTCTCATGTTAGCACACGAAGTGCCCTATAT
1 GGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATAT
*
38409 GGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAACACACGAAGTGCCCTATAT
1 GGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATAT
38468 GGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATAT
1 GGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATAT
*
38527 GGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCAGACGAAGTGCCCTATAT
1 GGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATAT
*
38586 GGAAATTCATACACTTAGTATGAATTCCTTCTCGTGTTAGCACACGAAGTGCCCT
1 GGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCT
38641 TTTGGTAATC
Statistics
Matches: 329, Mismatches: 20, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
59 327 0.99
60 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (59 bp):
GGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATAT
Found at i:39069 original size:93 final size:94
Alignment explanation
Indices: 38972--39171 Score: 251
Period size: 94 Copynumber: 2.1 Consensus size: 94
38962 ACTACTACCC
* * * * *** *
38972 TGGTACCGATACTTCTATGCTATGGTACCAATA-CCCTTTTTGTATCGATACCAATTTTAGGTTC
1 TGGTATCGATACTCCTATACCATGGTACCAATACCCCTTCCGGTATCGATACCAATTTTAGATTC
* *
39036 GATGTTACCTGGTATCGATACCTTTA-CTA
66 GATGTTACCTGGTATAGATACCCTTATC-A
* * *
39065 TGGTATCGATACCCCTATACCATGGTACCGATACCCCTTCCGGTATCGATACCAATTTTTGATTC
1 TGGTATCGATACTCCTATACCATGGTACCAATACCCCTTCCGGTATCGATACCAATTTTAGATTC
*
39130 GATGTTTCCTGGTATAGATACCCTTATCA
66 GATGTTACCTGGTATAGATACCCTTATCA
39159 TGGTATCGATACT
1 TGGTATCGATACT
39172 ACCTCTTCGG
Statistics
Matches: 90, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
93 27 0.30
94 62 0.69
95 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.36
Consensus pattern (94 bp):
TGGTATCGATACTCCTATACCATGGTACCAATACCCCTTCCGGTATCGATACCAATTTTAGATTC
GATGTTACCTGGTATAGATACCCTTATCA
Found at i:39114 original size:18 final size:21
Alignment explanation
Indices: 39041--39117 Score: 65
Period size: 22 Copynumber: 3.8 Consensus size: 21
39031 GGTTCGATGT
* *
39041 TACCTGGTATCGATA--CCTT
1 TACCAGGTATCGATACCCCTA
*
39060 TACTATGGTATCGATACCCCTA
1 TACCA-GGTATCGATACCCCTA
*
39082 TACCATGGTACCGATACCCCT-
1 TACCA-GGTATCGATACCCCTA
39103 T-CC-GGTATCGATACC
1 TACCAGGTATCGATACC
39118 AATTTTTGAT
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
18 11 0.22
19 3 0.06
20 12 0.24
21 1 0.02
22 22 0.45
ACGTcount: A:0.23, C:0.31, G:0.16, T:0.30
Consensus pattern (21 bp):
TACCAGGTATCGATACCCCTA
Found at i:40294 original size:20 final size:20
Alignment explanation
Indices: 40269--40307 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
40259 TTCATCCCTA
40269 TATAATTTATATTAATAAAC
1 TATAATTTATATTAATAAAC
40289 TATAATTTATATTAATAAA
1 TATAATTTATATTAATAAA
40308 TTATTTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (20 bp):
TATAATTTATATTAATAAAC
Found at i:40362 original size:29 final size:30
Alignment explanation
Indices: 40325--40492 Score: 97
Period size: 30 Copynumber: 5.8 Consensus size: 30
40315 ATTAATAGAT
*
40325 TTAATATAAACTATCA-TTTAT-AATTAATA
1 TTAATATAAAATAT-AGTTTATAAATTAATA
40354 TTAATATAAAATATAGTTTATAAAATTAATA
1 TTAATATAAAATATAGTTTAT-AAATTAATA
** * * *
40385 TTAATATAGTATAT-GATATATAGACT-ATAA
1 TTAATATAAAATATAG-TTTATAAATTAAT-A
* *
40415 TTAATAT-TAATACTA---TAT--ACT-ATA
1 TTAATATAAAATA-TAGTTTATAAATTAATA
* **
40439 TTAATATAAAATATAGTTAATATGTTAATA
1 TTAATATAAAATATAGTTTATAAATTAATA
* *
40469 TTAATGTAAACTATAGTTTATAAA
1 TTAATATAAAATATAGTTTATAAA
40493 ACATCTACTA
Statistics
Matches: 108, Mismatches: 17, Indels: 27
0.71 0.11 0.18
Matches are distributed among these distances:
24 10 0.09
25 9 0.08
27 5 0.05
28 1 0.01
29 24 0.22
30 35 0.32
31 24 0.22
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.43
Consensus pattern (30 bp):
TTAATATAAAATATAGTTTATAAATTAATA
Found at i:40384 original size:31 final size:29
Alignment explanation
Indices: 40325--40392 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
40315 ATTAATAGAT
*
40325 TTAATATAAACTATCATTTATAATTAATA
1 TTAATATAAAATATCATTTATAATTAATA
40354 TTAATATAAAATAT-AGTTTATAAAATTAATA
1 TTAATATAAAATATCA-TTTAT--AATTAATA
40385 TTAATATA
1 TTAATATA
40393 GTATATGATA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
28 1 0.03
29 18 0.51
31 16 0.46
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (29 bp):
TTAATATAAAATATCATTTATAATTAATA
Found at i:40520 original size:36 final size:36
Alignment explanation
Indices: 40480--40558 Score: 106
Period size: 36 Copynumber: 2.2 Consensus size: 36
40470 TAATGTAAAC
*
40480 TATAGTTTATAAAAC-ATCTACTACATTAATACAAAT
1 TATAGTTTAT-AAACTATATACTACATTAATACAAAT
* * *
40516 TATAGTTTATAAACTATATACTATATTGATATAAAT
1 TATAGTTTATAAACTATATACTACATTAATACAAAT
40552 TATAGTT
1 TATAGTT
40559 AAGATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
35 4 0.11
36 34 0.89
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (36 bp):
TATAGTTTATAAACTATATACTACATTAATACAAAT
Found at i:40555 original size:15 final size:15
Alignment explanation
Indices: 40537--40587 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
40527 AACTATATAC
*
40537 TATATTGATATAAAT
1 TATATTAATATAAAT
*
40552 TATAGTTAAGAT-AAT
1 TATA-TTAATATAAAT
*
40567 TAACATTAATATAAAT
1 T-ATATTAATATAAAT
40583 TATAT
1 TATAT
40588 AGTACATTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (15 bp):
TATATTAATATAAAT
Found at i:40628 original size:21 final size:21
Alignment explanation
Indices: 40604--40654 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
40594 TTAATATAAA
* *
40604 ATAAATTATATATTATAGTTT
1 ATAAATTATATACTATAGGTT
40625 ATAAATTATATACTATAGGTT
1 ATAAATTATATACTATAGGTT
40646 ATAAATTAT
1 ATAAATTAT
40655 TTAGTACACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (21 bp):
ATAAATTATATACTATAGGTT
Found at i:40794 original size:24 final size:23
Alignment explanation
Indices: 40728--40806 Score: 63
Period size: 24 Copynumber: 3.4 Consensus size: 23
40718 TATATACATA
* *
40728 ATATATATAC-TATAAGTTACA-T
1 ATATATATACATATAA-ATAGATT
*
40750 ATATAGTTTACATATAAATAGATT
1 ATATA-TATACATATAAATAGATT
* * *
40774 GTATATATACATATACTATAGGTT
1 ATATATATACATATA-AATAGATT
40798 ATATATATA
1 ATATATATA
40807 TAGGTTATAT
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
22 5 0.11
23 16 0.36
24 24 0.53
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (23 bp):
ATATATATACATATAAATAGATT
Found at i:40802 original size:20 final size:20
Alignment explanation
Indices: 40777--40855 Score: 62
Period size: 20 Copynumber: 4.1 Consensus size: 20
40767 ATAGATTGTA
40777 TATATACATATACTATAGG-
1 TATATACATATACTATAGGT
40796 T-TAT--ATATA-TATAGGT
1 TATATACATATACTATAGGT
* *
40812 TATATATACTATAC-ATAGTT
1 TATATACA-TATACTATAGGT
*
40832 TATACATACATATACTATAAGT
1 TAT--ATACATATACTATAGGT
40854 TA
1 TA
40856 CATATATAGT
Statistics
Matches: 47, Mismatches: 4, Indels: 15
0.71 0.06 0.23
Matches are distributed among these distances:
15 6 0.13
16 6 0.13
17 3 0.06
18 3 0.06
19 2 0.04
20 12 0.26
21 5 0.11
22 10 0.21
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.42
Consensus pattern (20 bp):
TATATACATATACTATAGGT
Found at i:40808 original size:15 final size:16
Alignment explanation
Indices: 40784--40824 Score: 75
Period size: 15 Copynumber: 2.6 Consensus size: 16
40774 GTATATATAC
40784 ATATACTATAGGTTAT
1 ATATACTATAGGTTAT
40800 ATATA-TATAGGTTAT
1 ATATACTATAGGTTAT
40815 ATATACTATA
1 ATATACTATA
40825 CATAGTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (16 bp):
ATATACTATAGGTTAT
Found at i:40859 original size:16 final size:16
Alignment explanation
Indices: 40838--40898 Score: 52
Period size: 16 Copynumber: 3.5 Consensus size: 16
40828 AGTTTATACA
40838 TACATATACTATAAGT
1 TACATATACTATAAGT
40854 TACATATA-TAGTTTACATGT
1 TACATATACTA---TA-A-GT
*
40874 ATACATATACTATATGT
1 -TACATATACTATAAGT
40891 TACATATA
1 TACATATA
40899 TTAACTATTG
Statistics
Matches: 37, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
15 2 0.05
16 16 0.43
17 2 0.05
18 2 0.05
19 3 0.08
20 2 0.05
21 8 0.22
22 2 0.05
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (16 bp):
TACATATACTATAAGT
Found at i:40865 original size:35 final size:36
Alignment explanation
Indices: 40826--40899 Score: 105
Period size: 37 Copynumber: 2.1 Consensus size: 36
40816 TATACTATAC
40826 ATAGTTT-ATACATACATATACTATAAGTTACATAT
1 ATAGTTTAATACATACATATACTATAAGTTACATAT
** *
40861 ATAGTTTACATGTATACATATACTATATGTTACATAT
1 ATAGTTTA-ATACATACATATACTATAAGTTACATAT
40898 AT
1 AT
40900 TAACTATTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 7 0.21
37 27 0.79
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.42
Consensus pattern (36 bp):
ATAGTTTAATACATACATATACTATAAGTTACATAT
Found at i:40877 original size:57 final size:58
Alignment explanation
Indices: 40758--40883 Score: 141
Period size: 57 Copynumber: 2.2 Consensus size: 58
40748 ATATATAGTT
* * * *
40758 TACATATAAATAGATTGTATATATACATATACTATAGGTTATATATATATAGGTTATATA
1 TACATATACATAG-TT-TATACATACATATACTATAAGTTATACATATATAGGTTATATA
* *
40818 TAC-TATACATAGTTTATACATACATATACTATAAG-T-TACATATATAGTTTACATGTA
1 TACATATACATAGTTTATACATACATATACTATAAGTTATACATATATAGGTT--ATATA
40875 TACATATAC
1 TACATATAC
40884 TATATGTTAC
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
55 12 0.21
56 1 0.02
57 26 0.46
58 7 0.12
59 8 0.14
60 3 0.05
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (58 bp):
TACATATACATAGTTTATACATACATATACTATAAGTTATACATATATAGGTTATATA
Found at i:41064 original size:13 final size:14
Alignment explanation
Indices: 41026--41067 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
41016 TTATATATCA
* *
41026 ACTATTGTTTATAG
1 ACTATAGTTTATAT
*
41040 ACTATAGGTTATAT
1 ACTATAGTTTATAT
41054 A-TATAGTTTATAT
1 ACTATAGTTTATAT
41067 A
1 A
41068 AATTATATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.48
Consensus pattern (14 bp):
ACTATAGTTTATAT
Found at i:41065 original size:54 final size:54
Alignment explanation
Indices: 40996--41128 Score: 189
Period size: 54 Copynumber: 2.5 Consensus size: 54
40986 CTGTGTCTAC
* * * *
40996 ACATATATGGTTTATATAAATTATATATCAACTATTGTTTATAGACTATAGGTT
1 ACATATATAGTTTATATAAATTATATATAAACTATTCTTTATAAACTATAGGTT
*
41050 ATATATATAGTTTATATAAATTATATATAAACTATTCTTTATAAACTATAGGTT
1 ACATATATAGTTTATATAAATTATATATAAACTATTCTTTATAAACTATAGGTT
* *
41104 ACATATATA-TATATATATA-TATATA
1 ACATATATAGTTTATATAAATTATATA
41129 ATTTATAATA
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
52 6 0.08
53 8 0.11
54 57 0.80
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (54 bp):
ACATATATAGTTTATATAAATTATATATAAACTATTCTTTATAAACTATAGGTT
Found at i:41279 original size:13 final size:13
Alignment explanation
Indices: 41215--41463 Score: 105
Period size: 13 Copynumber: 17.9 Consensus size: 13
41205 TTATATAAAC
* *
41215 TATATAGATTACA
1 TATATAGTTTATA
*
41228 TACATAGTTTATACA
1 TATATAGTTTAT--A
* *
41243 TATGTAGCTTATA
1 TATATAGTTTATA
*
41256 TATAGAG--TATA
1 TATATAGTTTATA
41267 TATATAGTTTATA
1 TATATAGTTTATA
* *
41280 TCTATATAGTTGATT
1 --TATATAGTTTATA
*
41295 TATATAATTTATA
1 TATATAGTTTATA
* *
41308 TACATATTTTATACA
1 TATATAGTTTAT--A
*
41323 TATGTAGTTTATATAAA
1 TATATAG-TT-TAT--A
41340 CTATATAGTTTATA
1 -TATATAGTTTATA
*
41354 TATGTAGTTTATATAAA
1 TATATAG-TT-TAT--A
41371 CTATATAGTTTATA
1 -TATATAGTTTATA
41385 TATATAGTTTATAATA
1 TATATAG-TT-T-ATA
*
41401 TCCATATATTTTATA
1 T--ATATAGTTTATA
41416 TATATAGTTTATA
1 TATATAGTTTATA
* *
41429 -ATA-ACTATATA
1 TATATAGTTTATA
*
41440 -ATTTA-TATTATA
1 TATATAGT-TTATA
41452 TATATAGTTTAT
1 TATATAGTTTAT
41464 GCATAGTATT
Statistics
Matches: 181, Mismatches: 30, Indels: 50
0.69 0.11 0.19
Matches are distributed among these distances:
11 19 0.10
12 8 0.04
13 71 0.39
14 7 0.04
15 34 0.19
16 13 0.07
17 12 0.07
18 17 0.09
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (13 bp):
TATATAGTTTATA
Found at i:41360 original size:31 final size:31
Alignment explanation
Indices: 41254--41453 Score: 186
Period size: 31 Copynumber: 6.6 Consensus size: 31
41244 ATGTAGCTTA
**
41254 TATATAGAGTATATATATAGTTTAT-AT--C
1 TATATAGTTTATATATATAGTTTATAATAAC
* * *
41282 TATATAGTTGATTTATATAATTTAT-AT-AC
1 TATATAGTTTATATATATAGTTTATAATAAC
*
41311 -ATAT--TTTATACATATGTAGTTTAT-ATAAAC
1 TATATAGTTTAT--ATATATAGTTTATAAT-AAC
*
41341 TATATAGTTTATATATGTAGTTTAT-ATAAAC
1 TATATAGTTTATATATATAGTTTATAAT-AAC
*
41372 TATATAGTTTATATATATAGTTTATAATATC
1 TATATAGTTTATATATATAGTTTATAATAAC
* *
41403 CATATATTTTATATATATAGTTTATAATAAC
1 TATATAGTTTATATATATAGTTTATAATAAC
*
41434 TATATAATTTATATTATATA
1 TATATAGTTTATA-TATATA
41454 TATAGTTTAT
Statistics
Matches: 146, Mismatches: 16, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
26 4 0.03
28 38 0.26
29 1 0.01
30 2 0.01
31 88 0.60
32 8 0.05
33 5 0.03
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (31 bp):
TATATAGTTTATATATATAGTTTATAATAAC
Found at i:41439 original size:18 final size:16
Alignment explanation
Indices: 41266--41463 Score: 99
Period size: 18 Copynumber: 12.8 Consensus size: 16
41256 TATAGAGTAT
41266 ATATATAGTTTATAT-
1 ATATATAGTTTATATA
* *
41281 CTATATAGTTGAT-T-
1 ATATATAGTTTATATA
*
41295 -TATATAATTTATAT-
1 ATATATAGTTTATATA
* *
41309 ACATAT--TTTATA-C
1 ATATATAGTTTATATA
*
41322 ATATGTAGTTTATATAA
1 ATATATAGTTTATAT-A
41339 ACTATATAG-TT-TAT-
1 A-TATATAGTTTATATA
*
41353 ATATGTAGTTTATATAA
1 ATATATAGTTTATAT-A
41370 ACTATATAG-TT-TAT-
1 A-TATATAGTTTATATA
41384 ATATATAGTTTATA-A
1 ATATATAGTTTATATA
41399 TATCCATATA-TTT-TAT-
1 -AT--ATATAGTTTATATA
41415 ATATATAGTTTATAATA
1 ATATATAGTTTAT-ATA
*
41432 ACTATATAATTTATATTA
1 A-TATATAGTTTATA-TA
41450 TATATATAGTTTAT
1 -ATATATAGTTTAT
41464 GCATAGTATT
Statistics
Matches: 143, Mismatches: 13, Indels: 51
0.69 0.06 0.25
Matches are distributed among these distances:
13 38 0.27
14 11 0.08
15 29 0.20
16 12 0.08
17 11 0.08
18 41 0.29
19 1 0.01
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (16 bp):
ATATATAGTTTATATA
Found at i:41549 original size:111 final size:111
Alignment explanation
Indices: 41318--41550 Score: 239
Period size: 111 Copynumber: 2.1 Consensus size: 111
41308 TACATATTTT
* * *
41318 ATACATATGTAGTTTATATAAACTATATAGTTTATATATGTAGTTTATATAAACTATATAGTTTA
1 ATACATATATAATTTATATAAACTATATAGTTTATATATGTAGTTTATATAAACTATATACTTTA
* * **
41383 TATATATAGTTTATAATATCCATATATTTTATATATATAGTTTATA
66 TATATATAGTATATAATATCCATAGATTACATATATATAGTTTATA
* *
41429 ATA-ACTATATAATTTATATTATA-TATATAGTTTATGCATA-GTA-TTTCTATAAACTATATAC
1 ATACA-TATATAATTTATA-TAAACTATATAGTTTAT--ATATGTAGTTTATATAAACTATATAC
* *
41490 TTTAT-TACTTTA-TATATATATAATCTATAGATTACATATAT-TAG-TTATA
62 TTTATATA-TATAGTATATA-AT-ATCCATAGATTACATATATATAGTTTATA
41539 CATACATATATA
1 -ATACATATATA
41551 TATATACTAT
Statistics
Matches: 102, Mismatches: 11, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
110 13 0.13
111 64 0.63
112 22 0.22
113 3 0.03
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (111 bp):
ATACATATATAATTTATATAAACTATATAGTTTATATATGTAGTTTATATAAACTATATACTTTA
TATATATAGTATATAATATCCATAGATTACATATATATAGTTTATA
Found at i:41621 original size:24 final size:25
Alignment explanation
Indices: 41573--41625 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
41563 TAATATAAAT
41573 TATAATTTATAAACTATATACTTTA
1 TATAATTTATAAACTATATACTTTA
* * *
41598 TATAGTTTATACA-TATATAGTTTA
1 TATAATTTATAAACTATATACTTTA
41622 TATA
1 TATA
41626 CATACATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.49
Consensus pattern (25 bp):
TATAATTTATAAACTATATACTTTA
Found at i:41700 original size:13 final size:13
Alignment explanation
Indices: 41682--41733 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
41672 TATACATTTT
*
41682 ATAGTTTATACAC
1 ATAGTTTATAAAC
41695 ATAGTTTATATAAAC
1 ATAG-TT-TATAAAC
* *
41710 ATAGTTTATATAT
1 ATAGTTTATAAAC
*
41723 ATAGCTTATAA
1 ATAGTTTATAA
41734 TAATTATATA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
13 18 0.56
14 4 0.12
15 10 0.31
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (13 bp):
ATAGTTTATAAAC
Found at i:41712 original size:83 final size:82
Alignment explanation
Indices: 41531--41706 Score: 266
Period size: 83 Copynumber: 2.1 Consensus size: 82
41521 TTACATATAT
* *
41531 TAGTTATACATACATATATATATATACTATATTAATATAAATTATAATTTATAAACTATATACTT
1 TAGTT-TATATACATACATATATATACTATATTAATATAAATTATAATTTATAAACTATATACTT
*
41596 TATATAGTTTATACATATA
65 TATATAGTTTATACA-ACA
* *
41615 TAGTTTATATACATACATATATATACTATATTAATATAAATTATAGTTTATAAATTATATACATT
1 TAGTTTATATACATACATATATATACTATATTAATATAAATTATAATTTATAAACTATATAC-TT
41680 T-TATAGTTTATAC-ACA
65 TATATAGTTTATACAACA
41696 TAGTTTATATA
1 TAGTTTATATA
41707 AACATAGTTT
Statistics
Matches: 86, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
81 13 0.15
83 65 0.76
84 8 0.09
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (82 bp):
TAGTTTATATACATACATATATATACTATATTAATATAAATTATAATTTATAAACTATATACTTT
ATATAGTTTATACAACA
Found at i:41723 original size:17 final size:15
Alignment explanation
Indices: 41688--41721 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
41678 TTTTATAGTT
*
41688 TATACACATAGTTTA
1 TATAAACATAGTTTA
41703 TATAAACATAGTTTA
1 TATAAACATAGTTTA
41718 TATA
1 TATA
41722 TATAGCTTAT
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:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (15 bp):
TATAAACATAGTTTA
Found at i:41726 original size:28 final size:29
Alignment explanation
Indices: 41682--41763 Score: 89
Period size: 28 Copynumber: 2.9 Consensus size: 29
41672 TATACATTTT
* *
41682 ATAGTTTATACACATAGTTTATATAA-AC
1 ATAGTTTATATATATAGTTTATATAATAC
* *
41710 ATAGTTTATATATATAGCTTATAATAATTAT
1 ATAGTTTATATATATAGTTTAT-ATAA-TAC
41741 ATAGTTTATATATA-A-TTTATATA
1 ATAGTTTATATATATAGTTTATATA
41764 TAAACTTATA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
28 22 0.48
29 8 0.17
30 1 0.02
31 15 0.33
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (29 bp):
ATAGTTTATATATATAGTTTATATAATAC
Found at i:41743 original size:18 final size:20
Alignment explanation
Indices: 41720--41763 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
41710 ATAGTTTATA
41720 TATATAGCTTATA-ATAA-T
1 TATATAGCTTATATATAATT
*
41738 TATATAGTTTATATATAATT
1 TATATAGCTTATATATAATT
41758 TATATA
1 TATATA
41764 TAAACTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 12 0.52
19 4 0.17
20 7 0.30
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (20 bp):
TATATAGCTTATATATAATT
Found at i:41783 original size:26 final size:26
Alignment explanation
Indices: 41749--41805 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
41739 ATATAGTTTA
41749 TATATAATTTATATATAAACTTATAT
1 TATATAATTTATATATAAACTTATAT
41775 TATATAATTTATATATAAACTTATAT
1 TATATAATTTATATATAAACTTATAT
41801 TATAT
1 TATAT
41806 TAATATAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.51
Consensus pattern (26 bp):
TATATAATTTATATATAAACTTATAT
Found at i:41817 original size:15 final size:15
Alignment explanation
Indices: 41761--41820 Score: 52
Period size: 15 Copynumber: 3.9 Consensus size: 15
41751 TATAATTTAT
41761 ATATAAACTTATATT-
1 ATATAAA-TTATATTA
*
41776 ATATAATTTATATATA
1 ATATAAATTATAT-TA
*
41792 A-ACTTATATTATATTA
1 ATA--TAAATTATATTA
41808 ATATAAATTATAT
1 ATATAAATTATAT
41821 ACTTTAATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 6 0.17
15 17 0.47
16 4 0.11
17 9 0.25
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
ATATAAATTATATTA
Found at i:41835 original size:17 final size:18
Alignment explanation
Indices: 41815--41849 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
41805 TTAATATAAA
41815 TTATATACTTTA-ATATT
1 TTATATACTTTATATATT
*
41832 TTATATAGTTTATATATT
1 TTATATACTTTATATATT
41850 GTTTACACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (18 bp):
TTATATACTTTATATATT
Found at i:42007 original size:21 final size:21
Alignment explanation
Indices: 41978--42024 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
41968 ACATAAATCT
* *
41978 TATATATTATATA-TTTATATA
1 TATAAATTACATAGTTTAT-TA
41999 TATAAATTACATAGTTTATTA
1 TATAAATTACATAGTTTATTA
42020 -ATAAA
1 TATAAA
42025 CTAATTGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 5 0.22
21 13 0.57
22 5 0.22
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
TATAAATTACATAGTTTATTA
Found at i:46054 original size:15 final size:15
Alignment explanation
Indices: 46034--46065 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
46024 TTAGCTGGGT
*
46034 GGGCGGATGTGGGGC
1 GGGCGGATGCGGGGC
46049 GGGCGGATGCGGGGC
1 GGGCGGATGCGGGGC
46064 GG
1 GG
46066 ATAATGTCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.16, G:0.69, T:0.09
Consensus pattern (15 bp):
GGGCGGATGCGGGGC
Found at i:53596 original size:31 final size:30
Alignment explanation
Indices: 53523--53710 Score: 175
Period size: 32 Copynumber: 6.1 Consensus size: 30
53513 GGAGTCGAGG
*
53523 GTATACCTATGTTCTACG-GAACATATGGACA
1 GTATACCTATGTT-TTCGAG-ACATATGGACA
*
53554 GAATTACCTATGTCTTTCGAGACATATGGACA
1 GTA-TACCTATGT-TTTCGAGACATATGGACA
*
53586 GTATACCTATGTTCTACG-GAACATATGGACA
1 GTATACCTATGTT-TTCGAG-ACATATGGACA
*
53617 GAATTACCTATGTCTTTCGAGACATATGGACA
1 GTA-TACCTATGT-TTTCGAGACATATGGACA
***
53649 GTATACCTATGTTAAGGA-ACATATGGACA
1 GTATACCTATGTTTTCGAGACATATGGACA
* * * *
53678 GTTTACCTAGGTTCTTCGAAACCTATGGACA
1 GTATACCTATGTT-TTCGAGACATATGGACA
53709 GT
1 GT
53711 TGCCGAGGAT
Statistics
Matches: 131, Mismatches: 16, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
29 22 0.17
30 7 0.05
31 48 0.37
32 50 0.38
33 4 0.03
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (30 bp):
GTATACCTATGTTTTCGAGACATATGGACA
Found at i:53601 original size:63 final size:63
Alignment explanation
Indices: 53523--53710 Score: 294
Period size: 63 Copynumber: 3.0 Consensus size: 63
53513 GGAGTCGAGG
53523 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
53586 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
* * * * *
53649 GTATACCTATG-T-TAAGGAACATATGGACAG-TTTACCTAGGT-TCTTCGAAACCTATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCT-TTCGAGACATATGGACA
53709 GT
1 GT
53711 TGCCGAGGAT
Statistics
Matches: 119, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
59 1 0.01
60 26 0.22
61 17 0.14
62 1 0.01
63 74 0.62
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (63 bp):
GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
Found at i:53711 original size:31 final size:30
Alignment explanation
Indices: 53526--53711 Score: 167
Period size: 31 Copynumber: 6.0 Consensus size: 30
53516 GTCGAGGGTA
* *
53526 TACCTATGTTCTACGGAACATATGGACAGAAT
1 TACCTATG-TCTACGAAACATATGGACAG-TT
* * *
53558 TACCTATGTCTTTCGAGACATATGGACAGTA
1 TACCTATGTC-TACGAAACATATGGACAGTT
* *
53589 TACCTATGTTCTACGGAACATATGGACAGAAT
1 TACCTATG-TCTACGAAACATATGGACAG-TT
* * *
53621 TACCTATGTCTTTCGAGACATATGGACAGTA
1 TACCTATGTC-TACGAAACATATGGACAGTT
* *
53652 TACCTATGT-TAAGGAACATATGGACAGTT
1 TACCTATGTCTACGAAACATATGGACAGTT
* * *
53681 TACCTAGGTTCTTCGAAACCTATGGACAGTT
1 TACCTATG-TCTACGAAACATATGGACAGTT
53712 GCCGAGGATC
Statistics
Matches: 123, Mismatches: 25, Indels: 13
0.76 0.16 0.08
Matches are distributed among these distances:
29 22 0.18
30 1 0.01
31 52 0.42
32 48 0.39
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (30 bp):
TACCTATGTCTACGAAACATATGGACAGTT
Found at i:56971 original size:21 final size:21
Alignment explanation
Indices: 56945--57000 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
56935 TCTGGGCAGA
56945 GTGCATCGATGCATATTCATT
1 GTGCATCGATGCATATTCATT
56966 GTGCATCGATGCATATTCATT
1 GTGCATCGATGCATATTCATT
56987 GTGCATCGATGCAT
1 GTGCATCGATGCAT
57001 CAAGGTTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (21 bp):
GTGCATCGATGCATATTCATT
Found at i:58463 original size:31 final size:31
Alignment explanation
Indices: 58390--58555 Score: 162
Period size: 32 Copynumber: 5.3 Consensus size: 31
58380 GGAGTCAAGG
58390 GTATACCTATGT-TCTACG-GAACATATGGACA
1 GTATACCTATGTCT-TACGAG-ACATATGGACA
* *
58421 GAATTACCTATGTCTTTCGAGACATATGGACA
1 GTA-TACCTATGTCTTACGAGACATATGGACA
58453 GTATACCTATGT-TCTACG-GAACATATGGACA
1 GTATACCTATGTCT-TACGAG-ACATATGGACA
* *
58484 GAATTACCTATGTCTTTCGAGACATATGGACA
1 GTA-TACCTATGTCTTACGAGACATATGGACA
* * *
58516 GTATACTTATGTTCTAAGGA-ACATATGGACA
1 GTATACCTATG-TCTTACGAGACATATGGACA
*
58547 GTTTACCTA
1 GTATACCTA
58556 GGTTCTTCGA
Statistics
Matches: 113, Mismatches: 13, Indels: 18
0.78 0.09 0.12
Matches are distributed among these distances:
30 2 0.02
31 52 0.46
32 55 0.49
33 4 0.04
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (31 bp):
GTATACCTATGTCTTACGAGACATATGGACA
Found at i:58468 original size:63 final size:63
Alignment explanation
Indices: 58390--58555 Score: 298
Period size: 63 Copynumber: 2.7 Consensus size: 63
58380 GGAGTCAAGG
58390 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
58453 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
* * *
58516 GTATACTTATGTTCTAAGGAACATATGGACAG-TTTACCTA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTA
58556 GGTTCTTCGA
Statistics
Matches: 100, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
62 7 0.07
63 93 0.93
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (63 bp):
GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
Found at i:58561 original size:31 final size:31
Alignment explanation
Indices: 58393--58561 Score: 175
Period size: 31 Copynumber: 5.4 Consensus size: 31
58383 GTCAAGGGTA
*
58393 TACCTATGTTCTACGGAACATATGGACAGAAT
1 TACCTATGTTCTACGGAACATATGGACAG-TT
* *
58425 TACCTATG-TCTTTC-GAGACATATGGACAGTA
1 TACCTATGTTC-TACGGA-ACATATGGACAGTT
*
58456 TACCTATGTTCTACGGAACATATGGACAGAAT
1 TACCTATGTTCTACGGAACATATGGACAG-TT
* *
58488 TACCTATG-TCTTTC-GAGACATATGGACAGTA
1 TACCTATGTTC-TACGGA-ACATATGGACAGTT
* *
58519 TACTTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTT
*
58550 TACCTAGGTTCT
1 TACCTATGTTCT
58562 TCGAAACCTA
Statistics
Matches: 113, Mismatches: 15, Indels: 19
0.77 0.10 0.13
Matches are distributed among these distances:
31 61 0.54
32 52 0.46
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAGTT
Found at i:58610 original size:30 final size:30
Alignment explanation
Indices: 58567--58638 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
58557 GTTCTTCGAA
* * *
58567 ACCTATGGTTAGTTTCCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
58597 ACCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
58627 ACCTCTGGATAG
1 ACCTCTGGATAG
58639 GTCCTTCGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCGAGGATCTTTATG
Done.