Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002228.1 Hibiscus syriacus cultivar Beakdansim tig00004534_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: 64493
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:5461 original size:14 final size:14
Alignment explanation
Indices: 5438--5484 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
5428 ACTTTTTTAC
* *
5438 TAACTTCTAACCTT
1 TAACTACTAACTTT
*
5452 TAACTGCTAACTTT
1 TAACTACTAACTTT
5466 TAACTACTAACTTT
1 TAACTACTAACTTT
5480 TAACT
1 TAACT
5485 TATTAATTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.32, C:0.23, G:0.02, T:0.43
Consensus pattern (14 bp):
TAACTACTAACTTT
Found at i:12081 original size:9 final size:9
Alignment explanation
Indices: 12055--12098 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
12045 AGATGCGAGA
12055 AAAAGAAAAG
1 AAAA-AAAAG
12065 AAACAAAAAG
1 AAA-AAAAAG
*
12075 AAAAAAATG
1 AAAAAAAAG
*
12084 AAAAAAATG
1 AAAAAAAAG
12093 AAAAAA
1 AAAAAA
12099 TAAAATATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
9 20 0.62
10 11 0.34
11 1 0.03
ACGTcount: A:0.82, C:0.02, G:0.11, T:0.05
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:20045 original size:21 final size:22
Alignment explanation
Indices: 20010--20052 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
20000 GAGTTTGTTT
20010 TCATTTTTCATTTTT-GAAACA
1 TCATTTTTCATTTTTAGAAACA
20031 TCATTTTT-ATATTTTAGAAACA
1 TCATTTTTCAT-TTTTAGAAACA
20053 ATTTCTCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 2 0.10
21 12 0.60
22 6 0.30
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.51
Consensus pattern (22 bp):
TCATTTTTCATTTTTAGAAACA
Found at i:25185 original size:34 final size:32
Alignment explanation
Indices: 25132--25201 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
25122 ACCTTACAAC
*
25132 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
25164 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
25198 TCCC
1 TCCC
25202 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:25511 original size:21 final size:21
Alignment explanation
Indices: 25486--25527 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
25476 CCAGAATGGG
*
25486 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
25507 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
25528 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:25706 original size:29 final size:31
Alignment explanation
Indices: 25674--25733 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
25664 AAATTTTGAA
*
25674 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
25703 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
25734 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:26509 original size:14 final size:14
Alignment explanation
Indices: 26486--26518 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
26476 ACTTTTTTAC
*
26486 TAACTTCTAACTTT
1 TAACTGCTAACTTT
26500 TAACTGCTAACTTT
1 TAACTGCTAACTTT
26514 TAACT
1 TAACT
26519 TACTAATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.30, C:0.21, G:0.03, T:0.45
Consensus pattern (14 bp):
TAACTGCTAACTTT
Found at i:37971 original size:203 final size:203
Alignment explanation
Indices: 37590--38089 Score: 564
Period size: 203 Copynumber: 2.4 Consensus size: 203
37580 TTTGACGCAC
*** *
37590 TTTCAATTTGTTAGTTGTTTTCTTCTTTTGAATGCACAAAAAATTCTGGGAAATCT--ATATTTT
1 TTTCAATTTGTT-G--GTTTTCTTCTTTTGAATGCATGCAAAATTCTGGGGAATCTGCAT-TTTT
* * * *
37653 TCTGTTTGGGATTGAGGAAAAGTTTTAACTTGAATATCAATTAGCTTGAATCACAATATGTTGCT
62 TCTGTTTGGGATTGAGGGAAAG---T--CTTGAATATCAATTAGATTGAACCACAATATATTGCT
* * * * *
37718 GATTTAGTTGTGTTGTTTTCTGTTGCACGAGAAAAGTTGTTGATTTATAAGTTTAAGTCCCATGC
122 GATTTAGTTGTGTTGTTCTATGTTACACGAGAAAAGTTATTGACTTATAAGTTTAAGTCCCATGC
*
37783 TTGTGTGTGTTGT-TGGT
187 TTGTGTGTGTT-TCTGAT
* * *
37800 TTTCAATTTGTTGGTTTTCTTCTTTTGAATGCATGCAAAATTATGGGGAATCTGCATTTTTTTTT
1 TTTCAATTTGTTGGTTTTCTTCTTTTGAATGCATGCAAAATTCTGGGGAATCTGCATTTTTTCTG
* **
37865 TTTGGGATTGAGGGAAAGTCTTGACTATCAATTTTATTGAACCACAATATATTGCTGATTTAGTT
66 TTTGGGATTGAGGGAAAGTCTTGAATATCAATTAGATTGAACCACAATATATTGCTGATTTAGTT
* ** * * *
37930 GTGTTGTTCTATTTTACGTGAGCAAAGTTATT-AGCTTATAAGTTTTAGTCCCATGCTTGTTTGT
131 GTGTTGTTCTATGTTACACGAGAAAAGTTATTGA-CTTATAAGTTTAAGTCCCATGCTTGTGTGT
37994 GTTTCTGAT
195 GTTTCTGAT
* * *
38003 TTTCAATTTATTTGTTGTTTCTTCTTTTGAATGCATGCAAAATTCTGGGGAATATGCA-TTTTTC
1 TTTCAATTT-GTTGGT-TTTCTTCTTTTGAATGCATGCAAAATTCTGGGGAATCTGCATTTTTTC
38067 TGTTT-GGATTGA-GGATAAGTCTT
64 TGTTTGGGATTGAGGGA-AAGTCTT
38090 AACTTGGCTA
Statistics
Matches: 251, Mismatches: 32, Indels: 21
0.83 0.11 0.07
Matches are distributed among these distances:
202 5 0.02
203 120 0.48
204 13 0.05
205 40 0.16
207 35 0.14
208 23 0.09
209 3 0.01
210 12 0.05
ACGTcount: A:0.23, C:0.11, G:0.20, T:0.46
Consensus pattern (203 bp):
TTTCAATTTGTTGGTTTTCTTCTTTTGAATGCATGCAAAATTCTGGGGAATCTGCATTTTTTCTG
TTTGGGATTGAGGGAAAGTCTTGAATATCAATTAGATTGAACCACAATATATTGCTGATTTAGTT
GTGTTGTTCTATGTTACACGAGAAAAGTTATTGACTTATAAGTTTAAGTCCCATGCTTGTGTGTG
TTTCTGAT
Found at i:38843 original size:36 final size:36
Alignment explanation
Indices: 38793--38868 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
38783 GTTATAGCAA
*
38793 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
38829 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
38865 AAAA
1 AAAA
38869 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:43363 original size:15 final size:15
Alignment explanation
Indices: 43345--43374 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
43335 CCACGGTGCT
43345 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
43360 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
43375 GATTGTGATA
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:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:43839 original size:36 final size:36
Alignment explanation
Indices: 43783--43864 Score: 146
Period size: 36 Copynumber: 2.2 Consensus size: 36
43773 CCGGACTGTT
*
43783 ATAGCAAAAAATCGTCTTTATTCGAATTTTGCCAAAA
1 ATAGC-AAAAATCGTATTTATTCGAATTTTGCCAAAA
43820 ATAGCAAAAATCGTATTTATTCGAATTTTGCCAAAA
1 ATAGCAAAAATCGTATTTATTCGAATTTTGCCAAAA
43856 ATAGCAAAA
1 ATAGCAAAA
43865 TCCCGAAAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
36 39 0.89
37 5 0.11
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (36 bp):
ATAGCAAAAATCGTATTTATTCGAATTTTGCCAAAA
Found at i:46664 original size:85 final size:85
Alignment explanation
Indices: 46516--46679 Score: 197
Period size: 85 Copynumber: 1.9 Consensus size: 85
46506 TACAATCACG
* * * * * * * *
46516 ACACACGAATGTGTGTCATCTTTTTTAATGGCGTGTGCTTCAATGACACGCAATATAAGTCATAC
1 ACACACAAATGTATGTCATCTTATTTAATGACGGGGGCTTCAATGACACGCAATATAAATCATAA
*
46581 ATGCGTGTCATAAATTTATA
66 ATGCGCGTCATAAATTTATA
*
46601 ACACACAAATGTATGTCATCTTAATTT-ATGACGGGGGCTTCAATGACGCGCAATA-AACATCAT
1 ACACACAAATGTATGTCATCTT-ATTTAATGACGGGGGCTTCAATGACACGCAATATAA-ATCAT
*
46664 AAATGTGCGTCATAAA
64 AAATGCGCGTCATAAA
46680 ATGCGTGTCA
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
84 2 0.03
85 61 0.92
86 3 0.05
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (85 bp):
ACACACAAATGTATGTCATCTTATTTAATGACGGGGGCTTCAATGACACGCAATATAAATCATAA
ATGCGCGTCATAAATTTATA
Found at i:46678 original size:13 final size:13
Alignment explanation
Indices: 46660--46707 Score: 69
Period size: 13 Copynumber: 3.6 Consensus size: 13
46650 GCAATAAACA
*
46660 TCATAAATGTGCG
1 TCATAAATGCGCG
*
46673 TCATAAAATGCGTG
1 TCAT-AAATGCGCG
46687 TCATAAATGCGCG
1 TCATAAATGCGCG
46700 TCATAAAT
1 TCATAAAT
46708 TCATTACGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
13 20 0.65
14 11 0.35
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (13 bp):
TCATAAATGCGCG
Found at i:47396 original size:25 final size:24
Alignment explanation
Indices: 47365--47419 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
47355 TTATTGATTA
* *
47365 TTTAATTTCGCATAT-TGTAAAATT
1 TTTAATTTCACACATCT-TAAAATT
47389 TTATAATTTCACACATCTTAAAATT
1 TT-TAATTTCACACATCTTAAAATT
47414 TTTAAT
1 TTTAAT
47420 ATAAATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 6 0.22
25 20 0.74
26 1 0.04
ACGTcount: A:0.36, C:0.11, G:0.04, T:0.49
Consensus pattern (24 bp):
TTTAATTTCACACATCTTAAAATT
Found at i:48790 original size:19 final size:19
Alignment explanation
Indices: 48766--48810 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
48756 GCCTGCATAA
48766 AACCGGTTTGACCGATCTG
1 AACCGGTTTGACCGATCTG
* *
48785 AACCGGGTTGACCGGTCTG
1 AACCGGTTTGACCGATCTG
*
48804 AATCGGT
1 AACCGGT
48811 CCGACCCGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.20, C:0.24, G:0.31, T:0.24
Consensus pattern (19 bp):
AACCGGTTTGACCGATCTG
Found at i:48938 original size:28 final size:29
Alignment explanation
Indices: 48842--48993 Score: 189
Period size: 29 Copynumber: 5.2 Consensus size: 29
48832 ACCGTTGACC
* *
48842 GGGTGTTAGTTTCCTAATTATTTTTAAAA
1 GGGTGATAGTTTCGTAATTATTTTTAAAA
48871 GGGTGATAGTTTCGTAATTATTTTTAAAAA
1 GGGTGATAGTTTCGTAATTATTTTT-AAAA
**
48901 ATGTGATAGTTTCGTAATTATTTTTAAAA
1 GGGTGATAGTTTCGTAATTATTTTTAAAA
*
48930 -GGTGATAGTTTAGTAATTATTTTTAAAA
1 GGGTGATAGTTTCGTAATTATTTTTAAAA
* * * * *
48958 GGGTGGTATTTTTGTAAATATTTCTAAAAA
1 GGGTGATAGTTTCGTAATTATTT-TTAAAA
48988 GGGTGA
1 GGGTGA
48994 AAATTATATA
Statistics
Matches: 108, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
28 26 0.24
29 45 0.42
30 37 0.34
ACGTcount: A:0.32, C:0.03, G:0.20, T:0.45
Consensus pattern (29 bp):
GGGTGATAGTTTCGTAATTATTTTTAAAA
Found at i:56181 original size:17 final size:18
Alignment explanation
Indices: 56159--56196 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
56149 AACCGGTCCT
56159 ACCCGACCCGA-CCGTTG
1 ACCCGACCCGACCCGTTG
56176 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
56194 ACC
1 ACC
56197 GTTGACCGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.18, C:0.50, G:0.21, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:56252 original size:29 final size:29
Alignment explanation
Indices: 56210--56354 Score: 213
Period size: 29 Copynumber: 5.0 Consensus size: 29
56200 GACCGGTTTT
56210 TAGTTTCGTAATTATTTTTAAAAGGGTGA
1 TAGTTTCGTAATTATTTTTAAAAGGGTGA
*
56239 TAGTTTCGTAATTATTTTTAAAAAAGGTGA
1 TAGTTTCGTAATTATTTTT-AAAAGGGTGA
*
56269 TAGTTTTGTAATTATTTTTAAAA-GGTGA
1 TAGTTTCGTAATTATTTTTAAAAGGGTGA
*
56297 TAGTTTAGTAATTATTTTTAAAAGGGTGA
1 TAGTTTCGTAATTATTTTTAAAAGGGTGA
* *
56326 T-TTTTCGTAAATATTTCTTAAAAGGGTGA
1 TAGTTTCGTAATTATTT-TTAAAAGGGTGA
56355 AAATTGTGTA
Statistics
Matches: 107, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
28 39 0.36
29 41 0.38
30 27 0.25
ACGTcount: A:0.33, C:0.03, G:0.19, T:0.46
Consensus pattern (29 bp):
TAGTTTCGTAATTATTTTTAAAAGGGTGA
Found at i:56300 original size:28 final size:28
Alignment explanation
Indices: 56210--56350 Score: 194
Period size: 28 Copynumber: 4.9 Consensus size: 28
56200 GACCGGTTTT
56210 TAGTTTCGTAATTATTTTTAAAAGGGTGA
1 TAGTTTCGTAATTATTTTTAAAA-GGTGA
56239 TAGTTTCGTAATTATTTTTAAAAAAGGTGA
1 TAGTTTCGTAATTATTTTT--AAAAGGTGA
*
56269 TAGTTTTGTAATTATTTTTAAAAGGTGA
1 TAGTTTCGTAATTATTTTTAAAAGGTGA
*
56297 TAGTTTAGTAATTATTTTTAAAAGGGTGA
1 TAGTTTCGTAATTATTTTTAAAA-GGTGA
* *
56326 T-TTTTCGTAAATATTTCTTAAAAGG
1 TAGTTTCGTAATTATTT-TTAAAAGG
56351 GTGAAAATTG
Statistics
Matches: 103, Mismatches: 5, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
28 45 0.44
29 31 0.30
30 23 0.22
31 4 0.04
ACGTcount: A:0.33, C:0.03, G:0.18, T:0.46
Consensus pattern (28 bp):
TAGTTTCGTAATTATTTTTAAAAGGTGA
Found at i:57910 original size:2 final size:2
Alignment explanation
Indices: 57903--57940 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
57893 ATTAAATAAG
57903 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57941 GGGTTAGTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58607 original size:35 final size:34
Alignment explanation
Indices: 58561--58663 Score: 91
Period size: 35 Copynumber: 2.8 Consensus size: 34
58551 AATTAAAGAA
* *
58561 AAAATATAAAAATAAACTAAAAATAGTAAACTAAAT
1 AAAA-ATAAAAATAAA-TAAAAATAGTAAACAAAAC
* *
58597 AAAAATAAAAATAAATAATAA-AGTCAAAAGAAAAC
1 AAAAATAAAAATAAATAAAAATAGT--AAACAAAAC
58632 AAAAATAACTAGAATAAAATAAAAATAGTAAA
1 AAAAATAA--A-AAT-AAATAAAAATAGTAAA
58664 AACACTAAAC
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
33 3 0.05
34 5 0.09
35 25 0.45
36 4 0.07
37 1 0.02
38 6 0.11
39 8 0.15
40 3 0.05
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.18
Consensus pattern (34 bp):
AAAAATAAAAATAAATAAAAATAGTAAACAAAAC
Found at i:58625 original size:19 final size:16
Alignment explanation
Indices: 58561--58614 Score: 63
Period size: 18 Copynumber: 3.1 Consensus size: 16
58551 AATTAAAGAA
58561 AAAATATAAAAATAAACT
1 AAAA-ATAAAAATAAA-T
*
58579 AAAAATAGTAAACTAAAT
1 AAAAATA--AAAATAAAT
58597 AAAAATAAAAATAAAT
1 AAAAATAAAAATAAAT
58613 AA
1 AA
58615 TAAAGTCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 10 0.31
17 3 0.09
18 12 0.38
19 7 0.22
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.20
Consensus pattern (16 bp):
AAAAATAAAAATAAAT
Found at i:58732 original size:13 final size:13
Alignment explanation
Indices: 58714--58738 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58704 AGATAAAATT
58714 AAAATAATAATAA
1 AAAATAATAATAA
58727 AAAATAATAATA
1 AAAATAATAATA
58739 CTAATGATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAATAATAATAA
Found at i:58958 original size:2 final size:2
Alignment explanation
Indices: 58951--59013 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
58941 AGGTTAGGTA
58951 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58993 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
59014 ATAAGTAAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:60783 original size:84 final size:80
Alignment explanation
Indices: 60695--61207 Score: 444
Period size: 84 Copynumber: 6.3 Consensus size: 80
60685 GTTTGCCTAT
* * * *
60695 GAGCTGAGTGTAATCAAACTCGAAGGTCATCGATTGGTAGATAACCCTTCTCGACTTACGCTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-T---TTGGTAGATAACCCTTCTCGACTTAAGCTATG
*
60760 CTACAAATGATGTGCCTTG
62 CTGCAAATGATGTGCCTTG
* * * * * * *
60779 GAGCTGAGCATGGTCGAACTCGAAGGTCTTTTAGTGACAGATAACCCTTCTAGCCTTGAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTT-G-G-TAGATAACCCTTCTCGACTTAAGCTATG
* *
60844 CTGTAAATGATGTTCCCTTG
62 CTGCAAATGATG-TGCCTTG
* * * * * * *
60864 AAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGC
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTAGATAACCCTTCTCGACTTAAGCTATGCTGC
60929 AAATGATGTGCCTTG
66 AAATGATGTGCCTTG
* * * *
60944 AAGCTGAGCGTAGTCGAACTCAAAAGTCTTTGGTTGTCAGATAACCCTTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-G--GT-AGATAACCCTTCTCGACTTAAGCTATG
*
61009 CTGC---T-A--TGCCTTA
62 CTGCAAATGATGTGCCTTG
* * * * **
61022 GAGTTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCATAGATAACCCTTCTAGCCTTGATTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGG---TAGATAACCCTTCTCGACTTAAGCTATG
* *
61087 CTGTAAATGATGTGCCCTCG
62 CTGCAAATGATGTG-CCTTG
* * * * * * *
61107 AAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGTAGATAGCCCTTCTCGACTTAAGCTATTCTGT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTAGATAACCCTTCTCGACTTAAGCTATGCTGC
61172 AAATGATGTGCCTTG
66 AAATGATGTGCCTTG
*
61187 GAGCTGAGCGTAGTCAAACTC
1 GAGCTGAGCGTAGTCGAACTC
61208 AATTGTCTTT
Statistics
Matches: 343, Mismatches: 67, Indels: 42
0.76 0.15 0.09
Matches are distributed among these distances:
76 1 0.00
78 57 0.17
79 4 0.01
80 54 0.16
81 73 0.21
82 3 0.01
83 3 0.01
84 94 0.27
85 54 0.16
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.31
Consensus pattern (80 bp):
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTAGATAACCCTTCTCGACTTAAGCTATGCTGC
AAATGATGTGCCTTG
Found at i:60940 original size:165 final size:167
Alignment explanation
Indices: 60638--61011 Score: 434
Period size: 165 Copynumber: 2.2 Consensus size: 167
60628 ACTCGACCAA
* * * * * * * *
60638 TTTATTGACAGATAGCCCTTATTGGCTTGAGTTATTCTGTAAATTTGGTTTGCCTATGAGCTGAG
1 TTTAGTGACAGATAACCCTTCTAGACTTGAGTTATGCTGTAAATATGGTTTCCCTATGAGCTGAG
* * *
60703 TGTAATCAAACTCGAAGGTCATCGATTGGTAGATAACCCTTCTCGACTTACGCTATGCTACAAAT
66 TGTAATCAAACTCGAAGGTCAT--ATTGGCAGATAACCCTTCTCGACTTAAGCTATACTACAAAT
* * * *
60768 GATGTGCCTTGGAGCTGAGCATGGTCGAACTCGAAGGTC
129 GATGTGCCTTGAAGCTGAGCATAGTCGAACTCAAAAGTC
*
60807 TTTTAGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGAT-G-TTCCCT-TGAAGCT
1 -TTTAGTGACAGATAACCCTTCTAGACTTGAGTTATGCTGTAAAT-ATGGTTTCCCTATG-AGCT
* * * *
60869 GAGTGTAATCGAACTCGAGGGTC-T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAA
63 GAGTGTAATCAAACTCGAAGGTCATATTGGCAGATAACCCTTCTCGACTTAAGCTATACTACAAA
*
60932 TGATGTGCCTTGAAGCTGAGCGTAGTCGAACTCAAAAGTC
128 TGATGTGCCTTGAAGCTGAGCATAGTCGAACTCAAAAGTC
* * * *
60972 TTTGGTTGTCAGATAACCCTTCTCGACTTAAGTTATGCTG
1 TTTAG-TGACAGATAACCCTTCTAGACTTGAGTTATGCTG
61012 CTATGCCTTA
Statistics
Matches: 176, Mismatches: 25, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
164 4 0.02
165 99 0.56
168 3 0.02
169 30 0.17
170 39 0.22
171 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (167 bp):
TTTAGTGACAGATAACCCTTCTAGACTTGAGTTATGCTGTAAATATGGTTTCCCTATGAGCTGAG
TGTAATCAAACTCGAAGGTCATATTGGCAGATAACCCTTCTCGACTTAAGCTATACTACAAATGA
TGTGCCTTGAAGCTGAGCATAGTCGAACTCAAAAGTC
Found at i:61066 original size:243 final size:242
Alignment explanation
Indices: 60772--61253 Score: 766
Period size: 243 Copynumber: 2.0 Consensus size: 242
60762 ACAAATGATG
* * *
60772 TGCCTTGGAGCTGAGCATGGTCGAACTCGAAGGTCTTTTAGTGACAGATAACCCTTCTAGCCTTG
1 TGCCTTAGAGCTGAGCATAGTCGAACTCGAAGGTCTTTTAGTCACAGATAACCCTTCTAGCCTTG
* *
60837 AGTTATGCTGTAAATGATGTTCCCTTGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGAT
66 AGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGAT
*
60902 AGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAACTCAA
131 AGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCAAACTCAA
* *
60967 AAGTCTTTGGTTGTCAGATAACCCTTCTCGACTTAAGTTATGCTGCTA
196 AAGTCTTT-GTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCTA
* * * *
61015 TGCCTTAGAGTTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCATAGATAACCCTTCTAGCCTTG
1 TGCCTTAGAGCTGAGCATAGTCGAACTCGAAGGTCTTTTAGTCACAGATAACCCTTCTAGCCTTG
* *
61080 ATTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGTAGAT
66 AGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGAT
* * *
61145 AGCCCTTCTCGACTTAAGCTATTCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCAA
131 AGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCAAACTCAA
** * *
61210 TTGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTG
196 AAGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTG
61254 TGAATAAATA
Statistics
Matches: 218, Mismatches: 21, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
242 32 0.15
243 186 0.85
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (242 bp):
TGCCTTAGAGCTGAGCATAGTCGAACTCGAAGGTCTTTTAGTCACAGATAACCCTTCTAGCCTTG
AGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGAT
AGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCAAACTCAA
AAGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCTA
Done.