Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007100.1 Hibiscus syriacus cultivar Beakdansim tig00018552_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: 99052
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:2120 original size:31 final size:31
Alignment explanation
Indices: 2048--2108 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
2038 AACTCGGGTG
2048 ACCATATCTTAATTAAATAAAAACGAAAGTA
1 ACCATATCTTAATTAAATAAAAACGAAAGTA
*
2079 ACCGTATCTTAATTAAATAAAAACGAAAGT
1 ACCATATCTTAATTAAATAAAAACGAAAGT
2109 TGTCATATCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.52, C:0.13, G:0.08, T:0.26
Consensus pattern (31 bp):
ACCATATCTTAATTAAATAAAAACGAAAGTA
Found at i:5780 original size:26 final size:26
Alignment explanation
Indices: 5750--5805 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
5740 TATAAATATT
*
5750 ATAATTAAATTTAAATAAAAACT-TAA
1 ATAATTAAATTCAAATAAAAA-TATAA
* *
5776 ATAATTTAATTCAATTAAAAATATAA
1 ATAATTAAATTCAAATAAAAATATAA
5802 ATAA
1 ATAA
5806 GATTAAAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 1 0.04
26 25 0.96
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.36
Consensus pattern (26 bp):
ATAATTAAATTCAAATAAAAATATAA
Found at i:7183 original size:12 final size:12
Alignment explanation
Indices: 7166--7196 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
7156 AATAAATAGT
7166 ATATAAATTAAA
1 ATATAAATTAAA
7178 ATATAAATTAAA
1 ATATAAATTAAA
7190 ATATAAA
1 ATATAAA
7197 CTAATATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATATAAATTAAA
Found at i:12335 original size:36 final size:36
Alignment explanation
Indices: 12285--12410 Score: 117
Period size: 37 Copynumber: 3.4 Consensus size: 36
12275 AAACTGTTTA
* * *
12285 AAGTAAGATGAAATTTATTTCAAGGGAAATTATCTC
1 AAGTGAGATAAAATTTATTTCAAGGAAAATTATCTC
** * * *
12321 AAGTGAGATAAAATTTTATTTTGAGAAAAATTGTCTTT
1 AAGTGAGATAAAA-TTTATTTCAAGGAAAATTATC-TC
** * * *
12359 AAGTGAGACGAAATTTGTTTTAAGGAAAATCATCTC
1 AAGTGAGATAAAATTTATTTCAAGGAAAATTATCTC
12395 AAGTGAGATAAAATTT
1 AAGTGAGATAAAATTT
12411 TTGTTTCGAA
Statistics
Matches: 70, Mismatches: 18, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
36 26 0.37
37 32 0.46
38 12 0.17
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.35
Consensus pattern (36 bp):
AAGTGAGATAAAATTTATTTCAAGGAAAATTATCTC
Found at i:12372 original size:74 final size:74
Alignment explanation
Indices: 12236--12498 Score: 272
Period size: 74 Copynumber: 3.6 Consensus size: 74
12226 TTTTTCATGA
* ** * * * * *
12236 GAAAA-TATCTCAAGTAAGATGCAACTTTTGTTTC-AAGGGAAACTGTTTAAAGTAAGATGAAAT
1 GAAAATTATCTCAAGTGAGATAAAATTTTTGTTTCGAA-AGAAACTGTTTTAAGTGAGACGAAAT
* *
12299 TTATTTCAAG
65 TTGTTTTAAG
* *
12309 GGAAATTATCTCAAGTGAGATAAAATTTTAT-TTT-GAGAA-AAATTGTCTTTAAGTGAGACGAA
1 GAAAATTATCTCAAGTGAGATAAAATTTT-TGTTTCGA-AAGAAACTGT-TTTAAGTGAGACGAA
12371 ATTTGTTTTAAG
63 ATTTGTTTTAAG
* *
12383 GAAAATCATCTCAAGTGAGATAAAATTTTTGTTTCGAAAGAAACTGTTTTGAGTGAGACG-AATT
1 GAAAATTATCTCAAGTGAGATAAAATTTTTGTTTCGAAAGAAACTGTTTTAAGTGAGACGAAATT
12447 TGTTTTAAG
66 TGTTTTAAG
* ** *
12456 GAAAATTATCCCAAGTGAG-GCAAA-TTTTGTTTCGAGAGAAACT
1 GAAAATTATCTCAAGTGAGATAAAATTTTTGTTTCGAAAGAAACT
12499 ATCTCAAATA
Statistics
Matches: 161, Mismatches: 21, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
71 18 0.11
72 3 0.02
73 41 0.25
74 89 0.55
75 10 0.06
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (74 bp):
GAAAATTATCTCAAGTGAGATAAAATTTTTGTTTCGAAAGAAACTGTTTTAAGTGAGACGAAATT
TGTTTTAAG
Found at i:12387 original size:38 final size:38
Alignment explanation
Indices: 12345--12460 Score: 89
Period size: 36 Copynumber: 3.1 Consensus size: 38
12335 TTTATTTTGA
12345 GAAAAATTGTCTTTAAGTGAGACGAAATTTGTTTTAAG
1 GAAAAATTGTCTTTAAGTGAGACGAAATTTGTTTTAAG
** * ** **
12383 G-AAAATCATC-TCAAGTGAGATAAAATTT-TTGTTTCG
1 GAAAAATTGTCTTTAAGTGAGACGAAATTTGTT-TTAAG
* * *
12419 AAAGAAACTGT-TTTGAGTGAGACG-AATTTGTTTTAAG
1 GAA-AAATTGTCTTTAAGTGAGACGAAATTTGTTTTAAG
12456 GAAAA
1 GAAAA
12461 TTATCCCAAG
Statistics
Matches: 55, Mismatches: 18, Indels: 12
0.65 0.21 0.14
Matches are distributed among these distances:
35 2 0.04
36 20 0.36
37 18 0.33
38 15 0.27
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.34
Consensus pattern (38 bp):
GAAAAATTGTCTTTAAGTGAGACGAAATTTGTTTTAAG
Found at i:12589 original size:37 final size:37
Alignment explanation
Indices: 12477--12595 Score: 105
Period size: 37 Copynumber: 3.1 Consensus size: 37
12467 CAAGTGAGGC
*
12477 AAATTTTGTTTCGAGAGAAACTATCTCAAATACTGAGA-T
1 AAATTTTGTTTCGAGAGAAACTATCT-TAA-A-TGAGACT
* * * * *
12516 AAAATTTTTGTTTTGAGGGAAACTATATTGAGTGAGACT
1 -AAA-TTTTGTTTCGAGAGAAACTATCTTAAATGAGACT
* * *
12555 AAATTTCGTTTCGAGAGAAACCATCTTAAATGAGACA
1 AAATTTTGTTTCGAGAGAAACTATCTTAAATGAGACT
12592 AAAT
1 AAAT
12596 CGGTGTTTCA
Statistics
Matches: 63, Mismatches: 14, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
37 30 0.48
38 8 0.13
39 1 0.02
40 4 0.06
41 20 0.32
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.33
Consensus pattern (37 bp):
AAATTTTGTTTCGAGAGAAACTATCTTAAATGAGACT
Found at i:23623 original size:49 final size:49
Alignment explanation
Indices: 23486--23630 Score: 227
Period size: 49 Copynumber: 3.0 Consensus size: 49
23476 GAAAACACGG
* *
23486 ATCGTCATCTTCGTCTTCGATGAACCTTTGACATATATGAAAAGCGCGT
1 ATCGTCATCTTCGTCTTCGATGAACCTTTGACATATATGGAAGGCGCGT
*
23535 ATTGTCATCTTCGTCTTCGATGAACCTTTGACATATATGGAAGGCGCGT
1 ATCGTCATCTTCGTCTTCGATGAACCTTTGACATATATGGAAGGCGCGT
* * * *
23584 ATCGTCATCATCGTCTTCGTTAAACCTCTGACATATATGGAAGGCGC
1 ATCGTCATCTTCGTCTTCGATGAACCTTTGACATATATGGAAGGCGC
23631 AAATCATGGT
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 88 1.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (49 bp):
ATCGTCATCTTCGTCTTCGATGAACCTTTGACATATATGGAAGGCGCGT
Found at i:28309 original size:59 final size:59
Alignment explanation
Indices: 28234--28482 Score: 207
Period size: 59 Copynumber: 4.1 Consensus size: 59
28224 TGTTTTAGTA
* * *
28234 CTTTAAATTTCTG-TTTTGCTTTGTTAGTCCCTTAACTTTCGGTTTTTACTATCTTAGCC
1 CTTTAAGTTTCTGTTTTTGCTTT-TTAGTCCCTTAACTTTCTGTTTTTACTATGTTAGCC
* * * * *
28293 CTTTAAGTTTCTGTTTTTGTCTTTTTATTCCTTTAATTTTCTG-TTTTGCTTTGTTAGCC
1 CTTTAAGTTTCTGTTTTTG-CTTTTTAGTCCCTTAACTTTCTGTTTTTACTATGTTAGCC
* * * * * * **
28352 CTTTAACTTTATGTTTTTGCTATTTTAGTCCTTTAACTGTCTATTTTTACTATTTTAATC
1 CTTTAAGTTTCTGTTTTTGCT-TTTTAGTCCCTTAACTTTCTGTTTTTACTATGTTAGCC
* * * *
28412 CTTTAAGTTTCTATTTTTG-TTTTGCTGTGTTAGCCCTTTAACTTTATGTTTTTGCTATGTTAGC
1 CTTTAAGTTTCTGTTTTTGCTTTT--T-AG-T--CCC-TTAACTTTCTGTTTTTACTATGTTAGC
28476 C
59 C
28477 CTTTAA
1 CTTTAA
28483 CTATTTTTTA
Statistics
Matches: 148, Mismatches: 31, Indels: 16
0.76 0.16 0.08
Matches are distributed among these distances:
58 5 0.03
59 60 0.41
60 48 0.32
61 5 0.03
62 1 0.01
64 2 0.01
65 27 0.18
ACGTcount: A:0.15, C:0.16, G:0.11, T:0.57
Consensus pattern (59 bp):
CTTTAAGTTTCTGTTTTTGCTTTTTAGTCCCTTAACTTTCTGTTTTTACTATGTTAGCC
Found at i:28326 original size:30 final size:30
Alignment explanation
Indices: 28226--28484 Score: 195
Period size: 30 Copynumber: 8.5 Consensus size: 30
28216 TTATTTTGTG
* *
28226 TTTTAGTACTTTAAATTTCTG-TTTTGCT-
1 TTTTAGTCCTTTAACTTTCTGTTTTTGCTA
* * *
28254 TTGTTAGTCCCTTAACTTTCGGTTTTTACTA
1 TT-TTAGTCCTTTAACTTTCTGTTTTTGCTA
* * *
28285 TCTTAGCCCTTTAAGTTTCTGTTTTTGTCT-
1 TTTTAGTCCTTTAACTTTCTGTTTTTG-CTA
* *
28315 TTTTATTCCTTTAATTTTCTG-TTTTGCT-
1 TTTTAGTCCTTTAACTTTCTGTTTTTGCTA
* *
28343 TTGTTAGCCCTTTAACTTTATGTTTTTGCTA
1 TT-TTAGTCCTTTAACTTTCTGTTTTTGCTA
* * *
28374 TTTTAGTCCTTTAACTGTCTATTTTTACTA
1 TTTTAGTCCTTTAACTTTCTGTTTTTGCTA
* * * *
28404 TTTTAATCCTTTAAGTTTCTATTTTTGTTTTGCTG
1 TTTTAGTCCTTTAACTTTC----TGT-TTTTGCTA
* * *
28439 TGTTAGCCCTTTAACTTTATGTTTTTGCTA
1 TTTTAGTCCTTTAACTTTCTGTTTTTGCTA
* *
28469 TGTTAGCCCTTTAACT
1 TTTTAGTCCTTTAACT
28485 ATTTTTTATT
Statistics
Matches: 182, Mismatches: 37, Indels: 22
0.76 0.15 0.09
Matches are distributed among these distances:
28 6 0.03
29 35 0.19
30 112 0.62
31 7 0.04
34 2 0.01
35 20 0.11
ACGTcount: A:0.15, C:0.16, G:0.11, T:0.57
Consensus pattern (30 bp):
TTTTAGTCCTTTAACTTTCTGTTTTTGCTA
Found at i:28369 original size:89 final size:89
Alignment explanation
Indices: 28234--28484 Score: 290
Period size: 89 Copynumber: 2.8 Consensus size: 89
28224 TGTTTTAGTA
* ** *
28234 CTTTAAATTTCTGTTTTGCTTTGTTAGTCCC-TTAACTTTCGGTTTTTACTATCTTAGCCCTTTA
1 CTTTAATTTTCTGTTTTGCTTTGTTAG-CCCTTTAACTTTATGTTTTTGCTATCTTAGCCCTTTA
* * * * *
28298 AGTTTCTGTTTTTGTCT-TTTTATTC
65 ACTGTCTATTTTT-ACTATTTTAATC
* *
28323 CTTTAATTTTCTGTTTTGCTTTGTTAGCCCTTTAACTTTATGTTTTTGCTATTTTAGTCCTTTAA
1 CTTTAATTTTCTGTTTTGCTTTGTTAGCCCTTTAACTTTATGTTTTTGCTATCTTAGCCCTTTAA
28388 CTGTCTATTTTTACTATTTTAATC
66 CTGTCTATTTTTACTATTTTAATC
* * *
28412 CTTTAAGTTTCTATTTTTGTTTTGCTGTGTTAGCCCTTTAACTTTATGTTTTTGCTATGTTAGCC
1 CTTTAA-----T-TTTCTGTTTTGCTTTGTTAGCCCTTTAACTTTATGTTTTTGCTATCTTAGCC
28477 CTTTAACT
60 CTTTAACT
28485 ATTTTTTATT
Statistics
Matches: 139, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
88 5 0.04
89 77 0.55
94 1 0.01
95 56 0.40
ACGTcount: A:0.15, C:0.17, G:0.11, T:0.57
Consensus pattern (89 bp):
CTTTAATTTTCTGTTTTGCTTTGTTAGCCCTTTAACTTTATGTTTTTGCTATCTTAGCCCTTTAA
CTGTCTATTTTTACTATTTTAATC
Found at i:28763 original size:5 final size:5
Alignment explanation
Indices: 28749--28780 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
28739 TCGTTTTTCA
*
28749 ATTTT ATTTT GTTTT ATTTT ATTTT ATTTT AT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT AT
28781 CTTGGCGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (5 bp):
ATTTT
Found at i:31109 original size:12 final size:12
Alignment explanation
Indices: 31092--31117 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
31082 TTCTCCTAGG
31092 AGTTTCGTGGAC
1 AGTTTCGTGGAC
31104 AGTTTCGTGGAC
1 AGTTTCGTGGAC
31116 AG
1 AG
31118 GTAGATGGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.15, G:0.35, T:0.31
Consensus pattern (12 bp):
AGTTTCGTGGAC
Found at i:37639 original size:17 final size:17
Alignment explanation
Indices: 37596--37627 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
37586 AATTAGTTAT
37596 AAGTATA-ATAAAAATC
1 AAGTATATATAAAAATC
37612 AAGTATATATAAAAAT
1 AAGTATATATAAAAAT
37628 AATTGATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.28
Consensus pattern (17 bp):
AAGTATATATAAAAATC
Found at i:38257 original size:16 final size:16
Alignment explanation
Indices: 38236--38291 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 16
38226 TTCAATATGT
38236 TCGGGTTATTTTTGGA
1 TCGGGTTATTTTTGGA
** ** *
38252 TCGGGTTAAATTCAGT
1 TCGGGTTATTTTTGGA
38268 TCGGGTTATTTTTGGA
1 TCGGGTTATTTTTGGA
38284 TCGGGTTA
1 TCGGGTTA
38292 AATTCAGTTC
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.16, C:0.09, G:0.30, T:0.45
Consensus pattern (16 bp):
TCGGGTTATTTTTGGA
Found at i:38275 original size:32 final size:32
Alignment explanation
Indices: 38234--38368 Score: 155
Period size: 32 Copynumber: 4.2 Consensus size: 32
38224 ATTTCAATAT
38234 GTTCGGGTTATTTTTGGATCGGGTTAAATTCA
1 GTTCGGGTTATTTTTGGATCGGGTTAAATTCA
38266 GTTCGGGTTATTTTTGGATCGGGTTAAATTCA
1 GTTCGGGTTATTTTTGGATCGGGTTAAATTCA
** * * * *
38298 GTTCGGGTTGCTTTCGGATTGGGTTAAAAATCG
1 GTTCGGGTTATTTTTGGATCGGGTT-AAATTCA
** * *
38331 GTTCAAGTT-TCTTTTGGTTCGGGTTAATTTCA
1 GTTCGGGTTAT-TTTTGGATCGGGTTAAATTCA
38363 GTTCGG
1 GTTCGG
38369 TTGCTTTCGG
Statistics
Matches: 84, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
32 61 0.73
33 23 0.27
ACGTcount: A:0.17, C:0.11, G:0.29, T:0.43
Consensus pattern (32 bp):
GTTCGGGTTATTTTTGGATCGGGTTAAATTCA
Found at i:38303 original size:16 final size:16
Alignment explanation
Indices: 38252--38306 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
38242 TATTTTTGGA
38252 TCGGGTTAAATTCAGT
1 TCGGGTTAAATTCAGT
** ** *
38268 TCGGGTTATTTTTGGA
1 TCGGGTTAAATTCAGT
38284 TCGGGTTAAATTCAGT
1 TCGGGTTAAATTCAGT
38300 TCGGGTT
1 TCGGGTT
38307 GCTTTCGGAT
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.18, C:0.11, G:0.29, T:0.42
Consensus pattern (16 bp):
TCGGGTTAAATTCAGT
Found at i:40092 original size:30 final size:30
Alignment explanation
Indices: 40058--40123 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
40048 CGAATATAGA
*
40058 TCGCCAGGTGATCTGGGCGACCAATGAATG
1 TCGCCAGGTGATCTGGGCGACCAATGAAGG
*
40088 TCGCCAGGTGGTCTGGGCGACCAATGAAGG
1 TCGCCAGGTGATCTGGGCGACCAATGAAGG
40118 TCGCCA
1 TCGCCA
40124 TGTATGCTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.21, C:0.26, G:0.35, T:0.18
Consensus pattern (30 bp):
TCGCCAGGTGATCTGGGCGACCAATGAAGG
Found at i:40782 original size:50 final size:50
Alignment explanation
Indices: 40728--40829 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
40718 AAAATTATTG
40728 AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
1 AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
40778 AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
1 AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
40828 AA
1 AA
40830 ATAGGATAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.57, C:0.16, G:0.02, T:0.25
Consensus pattern (50 bp):
AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
Found at i:41040 original size:30 final size:30
Alignment explanation
Indices: 41004--41079 Score: 116
Period size: 30 Copynumber: 2.5 Consensus size: 30
40994 AACGGCATAG
*
41004 CGCCCAGACCACCTGGTGACCTTCATTGGT
1 CGCCCAGACCACCTGGGGACCTTCATTGGT
41034 CGCCCAGACCACCTGGGGACCTTCATTGGT
1 CGCCCAGACCACCTGGGGACCTTCATTGGT
* * *
41064 TGCCTAGATCACCTGG
1 CGCCCAGACCACCTGG
41080 CGATCTATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.17, C:0.36, G:0.25, T:0.22
Consensus pattern (30 bp):
CGCCCAGACCACCTGGGGACCTTCATTGGT
Found at i:45487 original size:2 final size:2
Alignment explanation
Indices: 45482--45509 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
45472 GTCTTTTTTA
45482 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
45510 TATGATCCAT
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:49980 original size:26 final size:28
Alignment explanation
Indices: 49950--50011 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 28
49940 AAAAATTTTA
49950 AGCTC-GC-GAGTTTTCGAGTCGAGTCG
1 AGCTCTGCAGAGTTTTCGAGTCGAGTCG
*
49976 AGCTCCATTTCAGAGTTTTCGAGTCGAGTCG
1 AGCT-C--TGCAGAGTTTTCGAGTCGAGTCG
50007 AGCTC
1 AGCTC
50012 AGCAATACTC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
26 4 0.13
27 1 0.03
30 2 0.07
31 23 0.77
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (28 bp):
AGCTCTGCAGAGTTTTCGAGTCGAGTCG
Found at i:51306 original size:20 final size:20
Alignment explanation
Indices: 51272--51329 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
51262 TTATATTTTA
* *
51272 TAATTATATATTATTTAAAT
1 TAATTATAAAATATTTAAAT
* **
51292 TAATTATAAACTATTT-TTT
1 TAATTATAAAATATTTAAAT
51311 TGAATTATAAAATATTTAA
1 T-AATTATAAAATATTTAA
51330 TTTTTATATA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 2 0.07
20 28 0.93
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (20 bp):
TAATTATAAAATATTTAAAT
Found at i:53509 original size:13 final size:13
Alignment explanation
Indices: 53491--53518 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
53481 GAATGGTATG
53491 TCTTATGCTCTTT
1 TCTTATGCTCTTT
53504 TCTTATGCTCTTT
1 TCTTATGCTCTTT
53517 TC
1 TC
53519 ACTTCTCTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.07, C:0.25, G:0.07, T:0.61
Consensus pattern (13 bp):
TCTTATGCTCTTT
Found at i:58236 original size:38 final size:38
Alignment explanation
Indices: 58185--58268 Score: 159
Period size: 38 Copynumber: 2.2 Consensus size: 38
58175 AAATGCACAC
58185 CTCCACTTATATGAAATGCAATTCAATATAGCAATCTT
1 CTCCACTTATATGAAATGCAATTCAATATAGCAATCTT
*
58223 CTCCACTTATATGAAATGCAATTGAATATAGCAATCTT
1 CTCCACTTATATGAAATGCAATTCAATATAGCAATCTT
58261 CTCCACTT
1 CTCCACTT
58269 CTATATATAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.35
Consensus pattern (38 bp):
CTCCACTTATATGAAATGCAATTCAATATAGCAATCTT
Found at i:69917 original size:2 final size:2
Alignment explanation
Indices: 69912--69939 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
69902 TTTTTTTGAA
69912 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
69940 TAAATATTAA
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:71423 original size:14 final size:14
Alignment explanation
Indices: 71404--71442 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
71394 TAATGGGAAT
71404 TAATCCCTGCAAAA
1 TAATCCCTGCAAAA
*
71418 TAATCCCTGCGAAA
1 TAATCCCTGCAAAA
* *
71432 GAATCTCTGCA
1 TAATCCCTGCA
71443 TATAGACAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (14 bp):
TAATCCCTGCAAAA
Found at i:73027 original size:23 final size:21
Alignment explanation
Indices: 72997--73048 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 21
72987 TTATCATTTT
72997 TAAATTATTAATT-TTAAAAAAA
1 TAAATTA-T-ATTATTAAAAAAA
73019 TAAACTTATATTATTAAAAAATA
1 TAAA-TTATATTATTAAAAAA-A
*
73042 TTAATTA
1 TAAATTA
73049 CTAAACATAC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 3 0.12
22 16 0.62
23 7 0.27
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAATTATATTATTAAAAAAA
Found at i:78330 original size:13 final size:13
Alignment explanation
Indices: 78286--78330 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
78276 TATTTTCTAT
78286 ATTAATTATAATC
1 ATTAATTATAATC
*
78299 CTTATATTATAAATC
1 ATTA-ATTAT-AATC
78314 -TTAATTATAATC
1 ATTAATTATAATC
78326 ATTAA
1 ATTAA
78331 ATTAATTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 4 0.14
13 12 0.43
14 8 0.29
15 4 0.14
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTAATTATAATC
Found at i:78508 original size:2 final size:2
Alignment explanation
Indices: 78501--78525 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
78491 TATTTGAAAT
78501 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 T
78526 TCAAAGTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:78909 original size:2 final size:2
Alignment explanation
Indices: 78902--78932 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
78892 AACTATAGAC
78902 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
78933 ACAGTTAAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:84615 original size:17 final size:17
Alignment explanation
Indices: 84590--84644 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
84580 ATGTGTTACG
84590 TATAGATTTTTAAAAAA
1 TATAGATTTTTAAAAAA
* *
84607 TATATA-TTTTAAATAA
1 TATAGATTTTTAAAAAA
*
84623 TATTAGATTTTTTTAAAAA
1 TA-TAGA-TTTTTAAAAAA
84642 TAT
1 TAT
84645 GAACGTGACA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
16 11 0.37
17 8 0.27
18 1 0.03
19 10 0.33
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (17 bp):
TATAGATTTTTAAAAAA
Found at i:85454 original size:2 final size:2
Alignment explanation
Indices: 85441--85489 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
85431 TTTCTTTTTA
*
85441 AT AT AA 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
85483 AT AT AT A
1 AT AT AT A
85490 ATTTTAATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:86626 original size:21 final size:21
Alignment explanation
Indices: 86600--86641 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
86590 CCAGAATAGG
*
86600 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
*
86621 GGGAATTGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
86642 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:86778 original size:19 final size:19
Alignment explanation
Indices: 86729--86781 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
86719 GCCTCGGGGA
*
86729 TATTGTTCAAACAGTGATT
1 TATTGTTCAAATAGTGATT
* *
86748 TACTGTTCAAATATTGATT
1 TATTGTTCAAATAGTGATT
86767 TATTGTTCAAATAGT
1 TATTGTTCAAATAGT
86782 AAATTACTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.45
Consensus pattern (19 bp):
TATTGTTCAAATAGTGATT
Found at i:86891 original size:29 final size:31
Alignment explanation
Indices: 86859--86918 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
86849 AAATTTTGAA
*
86859 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
86888 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
86919 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:91248 original size:23 final size:23
Alignment explanation
Indices: 91218--91279 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
91208 TCTGAATGAT
91218 TCAGTGCTGATTGATTTAACAAA
1 TCAGTGCTGATTGATTTAACAAA
*
91241 TCAGTGCTGATTTATTTAACAAA
1 TCAGTGCTGATTGATTTAACAAA
* * *
91264 ACAGTGTTGAATGATT
1 TCAGTGCTGATTGATT
91280 CAGTACAGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (23 bp):
TCAGTGCTGATTGATTTAACAAA
Found at i:91399 original size:15 final size:16
Alignment explanation
Indices: 91361--91401 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
91351 ATAGAACTTC
*
91361 TGAATCATTCAGCATT
1 TGAATCATTCAGCACT
*
91377 TGAATCATTCAGCGCT
1 TGAATCATTCAGCACT
91393 T-AATCATTC
1 TGAATCATTC
91402 TGGAATAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAGCACT
Found at i:92592 original size:2 final size:2
Alignment explanation
Indices: 92585--92615 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
92575 ATCACTATGA
92585 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
92616 CTTGTTGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:93197 original size:36 final size:36
Alignment explanation
Indices: 93144--93217 Score: 94
Period size: 36 Copynumber: 2.1 Consensus size: 36
93134 ACATGTTGAT
*
93144 TTAATTTTGAGGGGATGACATGGTCTAATTTAAATA
1 TTAATTTTGAGGGGATGACATAGTCTAATTTAAATA
* * * * *
93180 TTAATTTTTAGGTGATGATATATTTTAATTTAAATA
1 TTAATTTTGAGGGGATGACATAGTCTAATTTAAATA
93216 TT
1 TT
93218 TTTGATGGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.34, C:0.03, G:0.16, T:0.47
Consensus pattern (36 bp):
TTAATTTTGAGGGGATGACATAGTCTAATTTAAATA
Done.