Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000164.1 Hibiscus syriacus cultivar Beakdansim tig00000290_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: 87424
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:8123 original size:22 final size:22
Alignment explanation
Indices: 8076--8141 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
8066 TAAGAAATTA
*
8076 TATTAAAAATAT-AAATAAAAT
1 TATTAAAAATATAAAATTAAAT
*
8097 T-TTAAGAATATAAAATTAAAT
1 TATTAAAAATATAAAATTAAAT
* *
8118 TATTAATAAA-ATACATTTAAAT
1 TATTAA-AAATATAAAATTAAAT
8140 TA
1 TA
8142 CATAAAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
20 9 0.24
21 10 0.27
22 16 0.43
23 2 0.05
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
TATTAAAAATATAAAATTAAAT
Found at i:8126 original size:33 final size:33
Alignment explanation
Indices: 8057--8129 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
8047 GCTTATAATT
* * *
8057 ATAAATTTTTAAGAAATTATATTAAAAATATAA
1 ATAAAATTTTAAGAAATAAAATTAAAAATATAA
* *
8090 ATAAAATTTTAAGAATATAAAATT-AAATTATTA
1 ATAAAATTTTAAGAA-ATAAAATTAAAAATATAA
8123 ATAAAAT
1 ATAAAAT
8130 ACATTTAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 28 0.82
34 6 0.18
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (33 bp):
ATAAAATTTTAAGAAATAAAATTAAAAATATAA
Found at i:18120 original size:21 final size:22
Alignment explanation
Indices: 18085--18144 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 22
18075 AGAACCTGTG
* *
18085 GGGGGTATCGATTCCC-TC-AA
1 GGGGGAATCGGTTCCCATCAAA
18105 GGAGGGAATCGGTTCCCATTCAAA
1 GG-GGGAATCGGTTCCCA-TCAAA
18129 GGGGGAATCGGTTCCC
1 GGGGGAATCGGTTCCC
18145 CTGCAAGGGG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 2 0.06
21 12 0.35
23 16 0.47
24 4 0.12
ACGTcount: A:0.22, C:0.23, G:0.33, T:0.22
Consensus pattern (22 bp):
GGGGGAATCGGTTCCCATCAAA
Found at i:24059 original size:2 final size:2
Alignment explanation
Indices: 24052--24089 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
24042 ATTGATATTC
24052 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
24090 TCATGTACAT
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:24360 original size:18 final size:18
Alignment explanation
Indices: 24337--24496 Score: 212
Period size: 18 Copynumber: 8.9 Consensus size: 18
24327 GCGTAGAATT
*
24337 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
24355 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
24373 TGTCCCGAATGACCATTA
1 TGTCCCGAAGGACCACTA
* *
24391 TGTCCCAAAGAACCACTA
1 TGTCCCGAAGGACCACTA
* *
24409 TGTCTCGAAGGACCATTA
1 TGTCCCGAAGGACCACTA
*
24427 TGTCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTA
* *
24445 TGTCCCGAAGGACAATTA
1 TGTCCCGAAGGACCACTA
*
24463 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
*
24481 TGTCTCGAAGGACCAC
1 TGTCCCGAAGGACCAC
24497 ATAGACCCTC
Statistics
Matches: 120, Mismatches: 22, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 120 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:32190 original size:3 final size:3
Alignment explanation
Indices: 32182--32225 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
32172 TATTATGCTT
*
32182 GAA GAA GAA GAA -AA GAA GAA -AA GAA -AA AAA GAA GAA GAA -AA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
32226 AATAGAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
2 8 0.22
3 28 0.78
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:32199 original size:8 final size:8
Alignment explanation
Indices: 32186--32227 Score: 59
Period size: 8 Copynumber: 5.2 Consensus size: 8
32176 ATGCTTGAAG
32186 AAGAAGAA
1 AAGAAGAA
32194 AAGAAGAA
1 AAGAAGAA
*
32202 AAGAAAAA
1 AAGAAGAA
32210 AAGAAGAA
1 AAGAAGAA
32218 GAA-AAGAA
1 -AAGAAGAA
32226 AA
1 AA
32228 TAGAAAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
7 2 0.06
8 27 0.87
9 2 0.06
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (8 bp):
AAGAAGAA
Found at i:32214 original size:27 final size:26
Alignment explanation
Indices: 32183--32235 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 26
32173 ATTATGCTTG
32183 AAGAAGAAGAAAAGAAGAAAAGAAAAA
1 AAGAAGAAGAAAAGAA-AAAAGAAAAA
*
32210 AAGAAGAAGAAAAGAAAATAGAAAAA
1 AAGAAGAAGAAAAGAAAAAAGAAAAA
32236 GGGGGTCAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 9 0.36
27 16 0.64
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (26 bp):
AAGAAGAAGAAAAGAAAAAAGAAAAA
Found at i:32216 original size:24 final size:24
Alignment explanation
Indices: 32186--32236 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
32176 ATGCTTGAAG
32186 AAGAAGAA-AAGAAGAAAAGAAAAA
1 AAGAAGAAGAA-AAGAAAAGAAAAA
* *
32210 AAGAAGAAGAAAAGAAAATAGAAA
1 AAGAAGAAGAAAAGAAAAGAAAAA
32234 AAG
1 AAG
32237 GGGGTCAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (24 bp):
AAGAAGAAGAAAAGAAAAGAAAAA
Found at i:33372 original size:15 final size:15
Alignment explanation
Indices: 33352--33383 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
33342 GAGGAAGAAG
33352 AAGTTCATAATGAGA
1 AAGTTCATAATGAGA
33367 AAGTTCATAATGAGA
1 AAGTTCATAATGAGA
33382 AA
1 AA
33384 AACTTGTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (15 bp):
AAGTTCATAATGAGA
Found at i:34197 original size:18 final size:17
Alignment explanation
Indices: 34164--34197 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
34154 GAATAATTAA
34164 ATAAAATATCAAAATAT
1 ATAAAATATCAAAATAT
*
34181 ATAAAATCATTAAAATA
1 ATAAAAT-ATCAAAATA
34198 ATACAGACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATATCAAAATAT
Found at i:43322 original size:35 final size:35
Alignment explanation
Indices: 43264--43379 Score: 162
Period size: 35 Copynumber: 3.3 Consensus size: 35
43254 TGAATAAGAA
* * *
43264 GAACGAAAGG-AGCATCGGCACTTTCGATTTAAGT
1 GAACGAAAGGAAACATCGACACTTTCGATTCAAGT
43298 GAACGAAAGGAAACATCGACACTTTCGATTCAAGT
1 GAACGAAAGGAAACATCGACACTTTCGATTCAAGT
* *
43333 GAACGGAAGAAAACATCGACACTTTCGATTCAAGT
1 GAACGAAAGGAAACATCGACACTTTCGATTCAAGT
*
43368 CGAACGGAAGGA
1 -GAACGAAAGGA
43380 GGTGTCGTAC
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
34 10 0.14
35 54 0.73
36 10 0.14
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.19
Consensus pattern (35 bp):
GAACGAAAGGAAACATCGACACTTTCGATTCAAGT
Found at i:48502 original size:20 final size:19
Alignment explanation
Indices: 48454--48506 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
48444 AAATAACCAA
* *
48454 CAAATTCGCAACTCGATCT
1 CAAATTCGCAACACGAACT
48473 CAAATTCGCAACACGAACT
1 CAAATTCGCAACACGAACT
*
48492 CTAATTTCGCAACAC
1 C-AAATTCGCAACAC
48507 AGTTTCTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.36, C:0.32, G:0.09, T:0.23
Consensus pattern (19 bp):
CAAATTCGCAACACGAACT
Found at i:48832 original size:22 final size:22
Alignment explanation
Indices: 48782--48825 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
48772 TCACTCTCTA
* *
48782 CGACGACATCCGTCTCCATCTC
1 CGACGACATCCGTCCCCATATC
48804 CGACGACATCCGTCCCCATATC
1 CGACGACATCCGTCCCCATATC
48826 TGGCGACTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.45, G:0.14, T:0.20
Consensus pattern (22 bp):
CGACGACATCCGTCCCCATATC
Found at i:49193 original size:20 final size:20
Alignment explanation
Indices: 49170--49208 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
49160 TTTGAAACTT
49170 AAATTCGCAACACGAAAATG
1 AAATTCGCAACACGAAAATG
*
49190 AAATTCGCAACATGAAAAT
1 AAATTCGCAACACGAAAAT
49209 TGCAACGCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.18, G:0.13, T:0.18
Consensus pattern (20 bp):
AAATTCGCAACACGAAAATG
Found at i:49248 original size:20 final size:18
Alignment explanation
Indices: 49231--49280 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 18
49221 TTAGTTTTCG
49231 CGTTGCGAATTTCA-TTT
1 CGTTGCGAATTTCATTTT
49248 --TTGCGAATTTCATTTT
1 CGTTGCGAATTTCATTTT
*
49264 CAAGTTGCGATTTTCAT
1 C--GTTGCGAATTTCAT
49281 GTTGCGAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
15 12 0.44
16 3 0.11
20 12 0.44
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (18 bp):
CGTTGCGAATTTCATTTT
Found at i:49251 original size:15 final size:15
Alignment explanation
Indices: 49233--49263 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
49223 AGTTTTCGCG
49233 TTGCGAATTTCATTT
1 TTGCGAATTTCATTT
49248 TTGCGAATTTCATTT
1 TTGCGAATTTCATTT
49263 T
1 T
49264 CAAGTTGCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.13, G:0.13, T:0.55
Consensus pattern (15 bp):
TTGCGAATTTCATTT
Found at i:49276 original size:14 final size:14
Alignment explanation
Indices: 49259--49296 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
49249 TGCGAATTTC
49259 ATTTTCAAGTTGCG
1 ATTTTCAAGTTGCG
*
49273 ATTTTCATGTTGCG
1 ATTTTCAAGTTGCG
*
49287 AATTT-AAGTT
1 ATTTTCAAGTT
49297 ACAAGAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.24, C:0.11, G:0.18, T:0.47
Consensus pattern (14 bp):
ATTTTCAAGTTGCG
Found at i:52287 original size:12 final size:12
Alignment explanation
Indices: 52266--52299 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
52256 GGTTGTGGGT
*
52266 TTTGAGATTGTG
1 TTTGATATTGTG
52278 TTTGATATTGTG
1 TTTGATATTGTG
*
52290 TTTGGTATTG
1 TTTGATATTG
52300 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:52927 original size:14 final size:15
Alignment explanation
Indices: 52891--52928 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
52881 GAAATCATTG
52891 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
52906 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
52921 AAAAATTA
1 AAAAATTA
52929 AAGACGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:53141 original size:40 final size:40
Alignment explanation
Indices: 53086--53175 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 40
53076 AATAAAAGTT
* *
53086 GTTGCGAAAATAAAATTCGTATTGCGAATTCGAAAATCGA
1 GTTGCGAAAACAAAATTCGTATTGCGAATTAGAAAATCGA
* * * * **
53126 GTTGTGAAAACAAAATTTGTGTTGCTAATTAGAAAATCTT
1 GTTGCGAAAACAAAATTCGTATTGCGAATTAGAAAATCGA
53166 GTTGCGAAAA
1 GTTGCGAAAA
53176 GGAAACTTGT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (40 bp):
GTTGCGAAAACAAAATTCGTATTGCGAATTAGAAAATCGA
Found at i:53186 original size:40 final size:39
Alignment explanation
Indices: 53084--53241 Score: 102
Period size: 40 Copynumber: 3.9 Consensus size: 39
53074 AAAATAAAAG
* * *
53084 TTGTTGCGAAAATAAAATTCGTATTGCGAATTCGAAAATC
1 TTGTTGCGAAAAAAAAATT-GTGTTGCGAATTAGAAAATC
** * * *
53124 GAGTTGTGAAAACAAAATTTGTGTTGCTAATTAGAAAATC
1 TTGTTGCGAAAA-AAAAATTGTGTTGCGAATTAGAAAATC
* * *
53164 TTGTTGCGAAAAGGAAACTTGTGTTACGAATTTA-AAAATC
1 TTGTTGCGAAAA-AAAAATTGTGTTGCGAA-TTAGAAAATC
*** * * *
53204 ACATTGCTAAAAAGAAATTCGCGTTGCGAATTCAGAAA
1 TTGTTGCGAAAAAAAAATT-GTGTTGCGAATT-AGAAA
53242 TCGAGTTGTG
Statistics
Matches: 88, Mismatches: 25, Indels: 9
0.72 0.20 0.07
Matches are distributed among these distances:
39 6 0.07
40 71 0.81
41 11 0.12
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.30
Consensus pattern (39 bp):
TTGTTGCGAAAAAAAAATTGTGTTGCGAATTAGAAAATC
Found at i:53249 original size:20 final size:21
Alignment explanation
Indices: 53216--53254 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
53206 ATTGCTAAAA
*
53216 AGAAATTCGCGTTGCGAATTC
1 AGAAATTCGAGTTGCGAATTC
*
53237 AGAAA-TCGAGTTGTGAAT
1 AGAAATTCGAGTTGCGAAT
53255 ACCAAATTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (21 bp):
AGAAATTCGAGTTGCGAATTC
Found at i:53641 original size:51 final size:51
Alignment explanation
Indices: 53565--53716 Score: 207
Period size: 51 Copynumber: 3.0 Consensus size: 51
53555 AAAAGTGTGG
* * *
53565 CCCATGCA-TCGCGCCTTACACTGATGTGACGCAACGTGAGGTAAGGCGCGA
1 CCCATGCACT-GCGCCTTACGCTGATGTGATGCCACGTGAGGTAAGGCGCGA
* *
53616 CCCATGCACTGCGCCTTACGCTGATGTGATGCCACGTGAGGTAAGGCGTGG
1 CCCATGCACTGCGCCTTACGCTGATGTGATGCCACGTGAGGTAAGGCGCGA
* * * *
53667 CCCATGCACTGCACCTTACGTTGATGTGGTGCCACGTGGGGTAAGGCGCG
1 CCCATGCACTGCGCCTTACGCTGATGTGATGCCACGTGAGGTAAGGCGCG
53717 GTGCATCAGC
Statistics
Matches: 90, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
51 89 0.99
52 1 0.01
ACGTcount: A:0.19, C:0.28, G:0.32, T:0.20
Consensus pattern (51 bp):
CCCATGCACTGCGCCTTACGCTGATGTGATGCCACGTGAGGTAAGGCGCGA
Found at i:53966 original size:30 final size:30
Alignment explanation
Indices: 53921--53999 Score: 108
Period size: 30 Copynumber: 2.7 Consensus size: 30
53911 GAAGGTAATA
*
53921 TATTATATTTTATTATATTTATTTTTTTAG
1 TATTTTATTTTATTATATTTATTTTTTTAG
* *
53951 TATTTTATTTAATTAT-TTAAATTTTTTTAG
1 TATTTTATTTTATTATATT-TATTTTTTTAG
53981 TATTTTATTTTATT-TATTT
1 TATTTTATTTTATTATATTT
54000 TGTAGTTATA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
29 3 0.07
30 39 0.93
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.71
Consensus pattern (30 bp):
TATTTTATTTTATTATATTTATTTTTTTAG
Found at i:53969 original size:20 final size:19
Alignment explanation
Indices: 53926--53996 Score: 60
Period size: 20 Copynumber: 3.9 Consensus size: 19
53916 TAATATATTA
* *
53926 TATTT-TATTATATTTATT
1 TATTTATATTTTATTTAAT
*
53944 TTTTTAGTATTTTATTTAAT
1 TATTTA-TATTTTATTTAAT
* *
53964 TATTTAAATTTT-TTT-AG
1 TATTTATATTTTATTTAAT
53981 TATTT-TATTTTATTTA
1 TATTTATATTTTATTTA
53997 TTTTGTAGTT
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
16 5 0.12
17 9 0.21
18 7 0.17
19 5 0.12
20 16 0.38
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (19 bp):
TATTTATATTTTATTTAAT
Found at i:58099 original size:30 final size:31
Alignment explanation
Indices: 58060--58136 Score: 111
Period size: 30 Copynumber: 2.5 Consensus size: 31
58050 GCCCGATGAA
*
58060 TTTTACGGGTTGAGAGGATTGTTGTGTG-ATG
1 TTTT-CGGGTTGAGAGGATTGTTGTGTGAAAG
*
58091 TTTTCGGGTTGACAGGATTGTTGTGTGAAAG
1 TTTTCGGGTTGAGAGGATTGTTGTGTGAAAG
*
58122 TTTACGGGTTGAGAG
1 TTTTCGGGTTGAGAG
58137 CGTCTCATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 22 0.54
31 19 0.46
ACGTcount: A:0.18, C:0.05, G:0.38, T:0.39
Consensus pattern (31 bp):
TTTTCGGGTTGAGAGGATTGTTGTGTGAAAG
Found at i:73754 original size:16 final size:15
Alignment explanation
Indices: 73735--73771 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
73725 AAAAAAATCA
73735 TATTATAATAAATTAT
1 TATTATAATAAATT-T
*
73751 TATTATAATAGATTT
1 TATTATAATAAATTT
73766 TATTAT
1 TATTAT
73772 TAACAAGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (15 bp):
TATTATAATAAATTT
Found at i:75056 original size:16 final size:18
Alignment explanation
Indices: 75035--75076 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
75025 TAAAGGGTTG
*
75035 AAATAAA-AA-TAATAGA
1 AAATAAATAATTAATAAA
75051 AAATAAATAATTTAATAAA
1 AAATAAATAA-TTAATAAA
75070 AAATAAA
1 AAATAAA
75077 GTTAGTGGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 7 0.32
17 2 0.09
19 13 0.59
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (18 bp):
AAATAAATAATTAATAAA
Found at i:77691 original size:103 final size:105
Alignment explanation
Indices: 77556--77744 Score: 285
Period size: 103 Copynumber: 1.8 Consensus size: 105
77546 ATTTCAAAGG
* *
77556 AAACAATCTCAAGTAAGACGAAATTTGATTTAAGAAAAACAATCTCACGTGAGACGAAATTTGCT
1 AAACAATCTCAAGTAAGACGAAATTTCATTTAAGAAAAACAATCTCAAGTGAGACGAAATTTGCT
*
77621 TT-AAGAAAAACAATCTCAAGAGATGACATTTTTTTAAGA
66 TTCAAGAAAAAAAATCTCAAGAGATGACATTTTTTTAAGA
* * * *
77660 AAACAATCTCAAGTGAGAC-AAA-TTCATTTTAAGAAAAATAATCTCAAGTGAGACGAATTTTGT
1 AAACAATCTCAAGTAAGACGAAATTTCA-TTTAAGAAAAACAATCTCAAGTGAGACGAAATTTGC
77723 TTTCAAGAAAAAAAATCTCAAG
65 TTTCAAGAAAAAAAATCTCAAG
77745 TGAGATAAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
102 3 0.04
103 38 0.50
104 35 0.46
ACGTcount: A:0.46, C:0.13, G:0.14, T:0.27
Consensus pattern (105 bp):
AAACAATCTCAAGTAAGACGAAATTTCATTTAAGAAAAACAATCTCAAGTGAGACGAAATTTGCT
TTCAAGAAAAAAAATCTCAAGAGATGACATTTTTTTAAGA
Found at i:77740 original size:37 final size:36
Alignment explanation
Indices: 77556--77749 Score: 245
Period size: 36 Copynumber: 5.5 Consensus size: 36
77546 ATTTCAAAGG
* *
77556 AAACAATCTCAAGTAAGACGAAATTTGATTTAAGAA
1 AAACAATCTCAAGTGAGACGAAATTTGTTTTAAGAA
* *
77592 AAACAATCTCACGTGAGACGAAATTTGCTTTAAGAA
1 AAACAATCTCAAGTGAGACGAAATTTGTTTTAAGAA
* *
77628 AAACAATCTCAA--GAGATGACATTT-TTTTAAG-A
1 AAACAATCTCAAGTGAGACGAAATTTGTTTTAAGAA
**
77660 AAACAATCTCAAGTGAGAC-AAATTCATTTTAAGAA
1 AAACAATCTCAAGTGAGACGAAATTTGTTTTAAGAA
* *
77695 AAATAATCTCAAGTGAGACGAATTTTGTTTTCAAGAA
1 AAACAATCTCAAGTGAGACGAAATTTGTTTT-AAGAA
*
77732 AAAAAATCTCAAGTGAGA
1 AAACAATCTCAAGTGAGA
77750 TAAAATTTTG
Statistics
Matches: 137, Mismatches: 15, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
32 13 0.09
33 10 0.07
34 21 0.15
35 19 0.14
36 52 0.38
37 22 0.16
ACGTcount: A:0.46, C:0.13, G:0.14, T:0.27
Consensus pattern (36 bp):
AAACAATCTCAAGTGAGACGAAATTTGTTTTAAGAA
Found at i:77840 original size:65 final size:67
Alignment explanation
Indices: 77717--77840 Score: 164
Period size: 65 Copynumber: 1.9 Consensus size: 67
77707 GTGAGACGAA
* * *
77717 TTTTGTTTTCAAGAAAAAAAATCTCAAGTGAGATAAAATTTTGTTTCAAGTGAGACAATTTCAAA
1 TTTTGTTTTCAAGAAAAAAAATCTCAAGTGAGATAAAATTTTCTTTCAAGTAAAACAATTTCAAA
77782 GT
66 GT
* * *
77784 TTTTGTTTT-AAGAGAAACAATCTCAAGTGA-ACT-AAATTTTCTTTTAAGTAAAACAAT
1 TTTTGTTTTCAAGAAAAAAAATCTCAAGTGAGA-TAAAATTTTCTTTCAAGTAAAACAAT
77841 CATAAGTAAG
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
65 21 0.42
66 20 0.40
67 9 0.18
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (67 bp):
TTTTGTTTTCAAGAAAAAAAATCTCAAGTGAGATAAAATTTTCTTTCAAGTAAAACAATTTCAAA
GT
Found at i:81073 original size:80 final size:81
Alignment explanation
Indices: 80939--81508 Score: 759
Period size: 80 Copynumber: 7.1 Consensus size: 81
80929 CGTTTTAAAA
* * * * *
80939 TAAAAGATTATTTGCCTAGTTGCGCATTTGACAGAAATGTGTCAATCA-TGTC-AGTTAGATGAA
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAATGTGCCAAT-ATTG-CAAGTTAGATGAA
* *
81002 AGGTTAAATACCTTTGAG
64 AGGCTAAATGCCTTTGAG
* ** * *
81020 TAAAAGATTAATTGCCTAGATGTGCA-TTGATAGAAATGTGTCAATCA-TGTC-AGTTAGATTAA
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAATGTGCCAAT-ATTG-CAAGTTAGATGAA
* * *
81082 AGGTTAAATACCTTTAAG
64 AGGCTAAATGCCTTTGAG
* *
81100 TAAAAGATTAATTGCCTAGCTATGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAATGTGCCAATATTGCAAGTTAGATGAAAG
*
81165 GCCAAATGCCTTTGAG
66 GCTAAATGCCTTTGAG
* * * *
81181 T-AAAGATTAGTTGCCTAGATGTGCATTTGGGAGAAATGTGCCAATA-TGCAAGTTAGATG-AAT
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAATGTGCCAATATTGCAAGTTAGATGAAAG
81243 GCTAAATGCCTTTGAG
66 GCTAAATGCCTTTGAG
* *
81259 TAAAAGATTAA-TG-CTAGCTGTGCATTTGGCAGAAAGGTACCAATATTGCAAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAATGTGCCAATATTGCAAGTTAGATGAAAG
81322 GCTAAATG-CTTTGAG
66 GCTAAATGCCTTTGAG
81337 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAATGTGCCAATATTGCAAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAATGTGCCAATATTGCAAGTTAGATGAAAG
81402 GCTAAATGCC-TTGAG
66 GCTAAATGCCTTTGAG
* * * * *
81417 TAAAAGATTAATTACCTAGCTGTACATTTGACAGAAAGGTGCTAATATTGCAAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAATGTGCCAATATTGCAAGTTAGATGAAAG
81482 GCTAAATGCCTTTGAG
66 GCTAAATGCCTTTGAG
81498 TAAAAGATTAA
1 TAAAAGATTAA
81509 ATGATTAACA
Statistics
Matches: 442, Mismatches: 37, Indels: 20
0.89 0.07 0.04
Matches are distributed among these distances:
77 28 0.06
78 51 0.12
79 33 0.07
80 248 0.56
81 82 0.19
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.30
Consensus pattern (81 bp):
TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAATGTGCCAATATTGCAAGTTAGATGAAAG
GCTAAATGCCTTTGAG
Found at i:81365 original size:237 final size:240
Alignment explanation
Indices: 80939--81508 Score: 769
Period size: 237 Copynumber: 2.4 Consensus size: 240
80929 CGTTTTAAAA
* * * *
80939 TAAAAGATTATTTGCCTAGTTGCGCATTTGACAGAAATGTGTCAATCATGTC-AGTTAGATGAAA
1 TAAAAGATTAATTGCCTAGATGTGCATTTGACAGAAATGTGCCAAT-ATG-CAAGTTAGATGAAA
* * * * **
81003 GGTTAAATACCTTTGAGTAAAAGATTAATTGCCTAGATGTGCATTGATAGAAATGTGTCAATCAT
64 GGCTAAATGCCTTTGAGTAAAAGATTAATTGCCTAGATGTGCATTGACAGAAAGGTACCAATCAT
* *
81068 GTCAGTTAGATTAAAGGTTAAATACCTTTAAGTAAAAGATTAATTGCCTAGCTATGCATTTGGCA
129 GTCAGTTAGATGAAAGGCTAAATACCTTTAAGTAAAAGATTAATTGCCTAGCTATGCATTTGGCA
81133 GAAAGGTGCCAATATTGCAAGTTAGATGAAAGGCCAAATGCCTTTGAG
194 GAAAGGTGCCAATATTGCAAGTTAGATGAAAGGCCAAATGCC-TTGAG
* ** *
81181 T-AAAGATTAGTTGCCTAGATGTGCATTTGGGAGAAATGTGCCAATATGCAAGTTAGATG-AATG
1 TAAAAGATTAATTGCCTAGATGTGCATTTGACAGAAATGTGCCAATATGCAAGTTAGATGAAAGG
* *
81244 CTAAATGCCTTTGAGTAAAAGATTAA-TG-CTAGCTGTGCATTTGGCAGAAAGGTACCAAT-AT-
66 CTAAATGCCTTTGAGTAAAAGATTAATTGCCTAGATGTGCA-TTGACAGAAAGGTACCAATCATG
* * *
81305 TGCAAGTTAGATGAAAGGCTAAAT-GCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGGC
130 T-C-AGTTAGATGAAAGGCTAAATACCTTTAAGTAAAAGATTAATTGCCTAGCTATGCATTTGGC
* *
81369 AGAAATGTGCCAATATTGCAAGTTAGATGAAAGGCTAAATGCCTTGAG
193 AGAAAGGTGCCAATATTGCAAGTTAGATGAAAGGCCAAATGCCTTGAG
* * * * *
81417 TAAAAGATTAATTACCTAGCTGTACATTTGACAGAAAGGTGCTAATATTGCAAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGATGTGCATTTGACAGAAATGTGCCAATA-TGCAAGTTAGATGAAAG
81482 GCTAAATGCCTTTGAGTAAAAGATTAA
65 GCTAAATGCCTTTGAGTAAAAGATTAA
81509 ATGATTAACA
Statistics
Matches: 290, Mismatches: 31, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
236 7 0.02
237 128 0.44
238 47 0.16
239 57 0.20
240 12 0.04
241 38 0.13
242 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.30
Consensus pattern (240 bp):
TAAAAGATTAATTGCCTAGATGTGCATTTGACAGAAATGTGCCAATATGCAAGTTAGATGAAAGG
CTAAATGCCTTTGAGTAAAAGATTAATTGCCTAGATGTGCATTGACAGAAAGGTACCAATCATGT
CAGTTAGATGAAAGGCTAAATACCTTTAAGTAAAAGATTAATTGCCTAGCTATGCATTTGGCAGA
AAGGTGCCAATATTGCAAGTTAGATGAAAGGCCAAATGCCTTGAG
Found at i:85143 original size:16 final size:16
Alignment explanation
Indices: 85122--85152 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
85112 AATAATAAAT
85122 GAACATAAACGAACAC
1 GAACATAAACGAACAC
85138 GAACATAAACGAACA
1 GAACATAAACGAACA
85153 AATTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:85249 original size:23 final size:24
Alignment explanation
Indices: 85219--85307 Score: 130
Period size: 23 Copynumber: 3.8 Consensus size: 24
85209 TTAATAAATA
85219 AACGAACAT-AACGAACACGAACG
1 AACGAACATAAACGAACACGAACG
85242 AACGAACATAAACG-ACACGAACG
1 AACGAACATAAACGAACACGAACG
**
85265 AACGAACATAAACGAACAC-AATA
1 AACGAACATAAACGAACACGAACG
85288 AACGAGACATAAACGAACAC
1 AACGA-ACATAAACGAACAC
85308 AATAAAAAAC
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
23 39 0.64
24 22 0.36
ACGTcount: A:0.55, C:0.25, G:0.15, T:0.06
Consensus pattern (24 bp):
AACGAACATAAACGAACACGAACG
Found at i:85255 original size:10 final size:11
Alignment explanation
Indices: 85242--85313 Score: 51
Period size: 13 Copynumber: 6.2 Consensus size: 11
85232 AACACGAACG
85242 AACGA-ACATA
1 AACGACACATA
85252 AACGACACGA-A
1 AACGACAC-ATA
85263 CGAACGA-ACATA
1 --AACGACACATA
85275 AACGAACACAATA
1 AACG-ACAC-ATA
*
85288 AACGAGACATA
1 AACGACACATA
85299 AACGAACACAATA
1 AACG-ACAC-ATA
85312 AA
1 AA
85314 AAACTTATTA
Statistics
Matches: 50, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
10 9 0.18
11 12 0.24
12 12 0.24
13 17 0.34
ACGTcount: A:0.58, C:0.22, G:0.12, T:0.07
Consensus pattern (11 bp):
AACGACACATA
Found at i:85280 original size:14 final size:13
Alignment explanation
Indices: 85261--85305 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 13
85251 AAACGACACG
85261 AACGAACGAACATA
1 AACGAACG-ACATA
85275 AACGAAC-ACAATA
1 AACGAACGAC-ATA
85288 AACG-A-GACATA
1 AACGAACGACATA
85299 AACGAAC
1 AACGAAC
85306 ACAATAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
11 7 0.26
12 6 0.22
13 7 0.26
14 7 0.26
ACGTcount: A:0.58, C:0.22, G:0.13, T:0.07
Consensus pattern (13 bp):
AACGAACGACATA
Found at i:85288 original size:13 final size:13
Alignment explanation
Indices: 85272--85313 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
85262 ACGAACGAAC
85272 ATAAACGAACACA
1 ATAAACGAACACA
*
85285 ATAAACG-AGAC-
1 ATAAACGAACACA
85296 ATAAACGAACACA
1 ATAAACGAACACA
85309 ATAAA
1 ATAAA
85314 AAACTTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 7 0.28
12 6 0.24
13 12 0.48
ACGTcount: A:0.62, C:0.19, G:0.10, T:0.10
Consensus pattern (13 bp):
ATAAACGAACACA
Found at i:85297 original size:24 final size:24
Alignment explanation
Indices: 85215--85313 Score: 125
Period size: 23 Copynumber: 4.2 Consensus size: 24
85205 TTAATTAATA
85215 AATAAACGAACAT-AACGAACACG
1 AATAAACGAACATAAACGAACACG
**
85238 AACGAACGAACATAAACG-ACACG
1 AATAAACGAACATAAACGAACACG
**
85261 AACGAACGAACATAAACGAACAC-
1 AATAAACGAACATAAACGAACACG
85284 AATAAACGAGACATAAACGAACAC-
1 AATAAACGA-ACATAAACGAACACG
85308 AATAAA
1 AATAAA
85314 AAACTTATTA
Statistics
Matches: 69, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
23 41 0.59
24 28 0.41
ACGTcount: A:0.58, C:0.22, G:0.13, T:0.07
Consensus pattern (24 bp):
AATAAACGAACATAAACGAACACG
Found at i:85582 original size:24 final size:24
Alignment explanation
Indices: 85554--85607 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
85544 CTCTGTTTTA
*
85554 AACATAAATGAACGAACATAAACG
1 AACATAAATGAACAAACATAAACG
* *
85578 AACATAAATGAATAAATATAAACG
1 AACATAAATGAACAAACATAAACG
*
85602 ATCATA
1 AACATA
85608 TAATCAAGCG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.59, C:0.13, G:0.09, T:0.19
Consensus pattern (24 bp):
AACATAAATGAACAAACATAAACG
Done.