Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009348.1 Hibiscus syriacus cultivar Beakdansim tig00113139_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: 52376
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:10590 original size:164 final size:162
Alignment explanation
Indices: 10236--10871 Score: 832
Period size: 164 Copynumber: 3.9 Consensus size: 162
10226 GAGCGTCGAT
* *
10236 AATTAAATCTTAAAAAGTTAGTACTAGTTCGGACATCGCAAACTCATAATCCCAAGTTCTAACTG
1 AATTAAATCTTAAAAAGTTAGAACTAGTTCGGACATCGCAGACTCATAATCCCAAGTTCTAACTG
* *
10301 CCT-CTAAAGCCATTTCTTTCTTCTCCTAATCAGCTCTCTTGGAAATTCATAGTCGCATTTTAAA
66 CCTAC-AAAGCCTTTTCTTTCTTCTCCTAATCAGCTCTCTTTGAAATTCATAGTCGCATTTTAAA
*
10365 CAGTAGAGCTAATTTTAGCAGAGGTAGCTTACG
130 CAGTAGAGCTAATTTTAGCAGAGGTAGCATACG
* * *
10398 AATTAAATCTTAAAAATGTTTA-AACTAGTTTGGACATCGCAGAGTCATAATCCCACGTTCTAAC
1 AATTAAATCTTAAAAA-G-TTAGAACTAGTTCGGACATCGCAGACTCATAATCCCAAGTTCTAAC
* * * * *
10462 TGCCTACAAAGCCCCTTTTTTTTCTTCTCCTAATCAGCTCTCTTTGAAA-TCTTAATCGTATCTT
64 TGCCTACAAAG--CCTTTTCTTTCTTCTCCTAATCAGCTCTCTTTGAAATTCATAGTCGCATTTT
* * * *
10526 AAACAGTAGAGCTAATCTTATCAGAGGTAGAATACA
127 AAACAGTAGAGCTAATTTTAGCAGAGGTAGCATACG
* * *
10562 AATTAAGTCTTAAAAAAGTTTGAACTAGTTCGGACATCGCAGACTCATAATCCCAAGTTCTAATT
1 AATTAAATCTT-AAAAAGTTAGAACTAGTTCGGACATCGCAGACTCATAATCCCAAGTTCTAACT
* * * * *
10627 GCCAATAAAGCCTTTTTCTTTCTTCTCCTAATCAGCCCTCTATGAAATTCATAGTAGCATTTTAA
65 GCCTACAAAGCC-TTTTCTTTCTTCTCCTAATCAGCTCTCTTTGAAATTCATAGTCGCATTTTAA
* * *
10692 ACAATAGACCTAATTTTAGCAGAGGTAGCATATG
129 ACAGTAGAGCTAATTTTAGCAGAGGTAGCATACG
* * *
10726 AATT-AATCTT-AAAAGTTAGAACTAGTTCAGACATTGCAGACTCATAATCCCAAGTTCTAAATG
1 AATTAAATCTTAAAAAGTTAGAACTAGTTCGGACATCGCAGACTCATAATCCCAAGTTCTAACTG
* * * * *
10789 CCTACAAAGCCACGTCTCCTTCTTCTCCTAATCAGCTCTCTCTGAACTTCATAGTCGCATTTTAA
66 CCTACAAAG-C-CTTTTCTTTCTTCTCCTAATCAGCTCTCTTTGAAATTCATAGTCGCATTTTAA
10854 ACAGTAGAGCTAATTTTA
129 ACAGTAGAGCTAATTTTA
10872 CATCTTAAAA
Statistics
Matches: 407, Mismatches: 56, Indels: 22
0.84 0.12 0.05
Matches are distributed among these distances:
161 56 0.14
162 80 0.20
163 86 0.21
164 147 0.36
165 38 0.09
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (162 bp):
AATTAAATCTTAAAAAGTTAGAACTAGTTCGGACATCGCAGACTCATAATCCCAAGTTCTAACTG
CCTACAAAGCCTTTTCTTTCTTCTCCTAATCAGCTCTCTTTGAAATTCATAGTCGCATTTTAAAC
AGTAGAGCTAATTTTAGCAGAGGTAGCATACG
Found at i:10997 original size:146 final size:142
Alignment explanation
Indices: 10731--11180 Score: 449
Period size: 146 Copynumber: 3.0 Consensus size: 142
10721 ATATGAATTA
* *
10731 ATCTTAAAAGTTAGAACTAGTTCAGACATTGCAGACTCATAATCCCAAGTTCTAAATGCCTACAA
1 ATCTTAAAAGTTAGAACTAGTTCAGAAATCGCAGACTCATAATCCCAAGTTCTAAATGCCTACAA
* *
10796 AGCCACGTCTCCTTCTTCTCCTAATCAGCTCTCTCTGAACTTCATAGTCGCATTTTAAACAGTAG
66 AGCCACGTCTCCTTCTCCTCCTAATCAGCTCTCTCTGAAATTCATAGTCGCATTTTAAACAGTAG
10861 AGCTAATTTTAC
131 AGCTAATTTTAC
*
10873 ATCTTAAAAAGTTAGAACTAGTTCGGAAATCGCAGACTCATAATCCCAAGTTCTAATTAATGCCT
1 ATCTT-AAAAGTTAGAACTAGTTCAGAAATCGCAGACTCATAATCCCAAGTTCT-A--AATGCCT
* * * * *
10938 GCAAAGCCCCGTTTCTTTCTCCTCCTAATCAGCTCTCTCTGAAATTCATAGTCTCATTTTAAACA
62 ACAAAGCCACGTCTCCTTCTCCTCCTAATCAGCTCTCTCTGAAATTCATAGTCGCATTTTAAACA
11003 GTAGAGCTAATTTTAGC
127 GTAGAGCTAATTTTA-C
*
11020 AGAGGTAGCATACAAA-TTA-AATCTTAAAAAGTT-AGAACTAGTTCGGGCATCACAGACTCATA
1 --A--T--CTTA-AAAGTTAGAA-C-T----AGTTCAGAA--A--TC--G-----CAGACTCATA
* * * * * * *
11082 ATCCCAAGTTCTAAATGCCTAAAAAGCCCCATTTCTTTCTTCT-CTAATCAGCTTTCTCTGAAAT
42 ATCCCAAGTTCTAAATGCCTACAAAGCCACGTCTCCTTCTCCTCCTAATCAGCTCTCTCTGAAAT
11146 TCATAGTCGCATTTTAAACAGTAGAGCTAATTTTA
107 TCATAGTCGCATTTTAAACAGTAGAGCTAATTTTA
11181 GCAGAGGTAG
Statistics
Matches: 261, Mismatches: 18, Indels: 37
0.83 0.06 0.12
Matches are distributed among these distances:
142 5 0.02
143 45 0.17
144 1 0.00
146 80 0.31
147 1 0.00
149 1 0.00
151 3 0.01
152 5 0.02
153 6 0.02
156 3 0.01
157 4 0.02
158 1 0.00
160 2 0.01
162 1 0.00
163 54 0.21
164 26 0.10
166 1 0.00
167 22 0.08
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (142 bp):
ATCTTAAAAGTTAGAACTAGTTCAGAAATCGCAGACTCATAATCCCAAGTTCTAAATGCCTACAA
AGCCACGTCTCCTTCTCCTCCTAATCAGCTCTCTCTGAAATTCATAGTCGCATTTTAAACAGTAG
AGCTAATTTTAC
Found at i:11176 original size:163 final size:164
Alignment explanation
Indices: 10873--11354 Score: 740
Period size: 163 Copynumber: 2.9 Consensus size: 164
10863 CTAATTTTAC
*
10873 ATCTTAAAAAGTTAGAACTAGTTCGGAAATCGCAGACTCATAATCCCAAGTTCTAATTAATGCCT
1 ATCTTAAAAAGTTAGAACTAGTTCGGACATCGCAGACTCATAATCCCAAGTTCT-A--AATGCCT
* * * *
10938 GCAAAGCCCCGTTTCTTTCTCCTCCTAATCAGCTCTCTCTGAAATTCATAGTCTCATTTTAAACA
63 ACAAAGCCCCGTTTCTTTCTTCTCCTAATCAGCTTTCTCTGAAATTCATAGTCGCATTTTAAACA
11003 GTAGAGCTAATTTTAGCAGAGGTAGCATACAAATTAA
128 GTAGAGCTAATTTTAGCAGAGGTAGCATACAAATTAA
* * *
11040 ATCTTAAAAAGTTAGAACTAGTTCGGGCATCACAGACTCATAATCCCAAGTTCTAAATGCCTAAA
1 ATCTTAAAAAGTTAGAACTAGTTCGGACATCGCAGACTCATAATCCCAAGTTCTAAATGCCTACA
*
11105 AAGCCCCATTTCTTTCTTCT-CTAATCAGCTTTCTCTGAAATTCATAGTCGCATTTTAAACAGTA
66 AAGCCCCGTTTCTTTCTTCTCCTAATCAGCTTTCTCTGAAATTCATAGTCGCATTTTAAACAGTA
11169 GAGCTAATTTTAGCAGAGGTAGCATACAAATTAA
131 GAGCTAATTTTAGCAGAGGTAGCATACAAATTAA
* * ** *
11203 ATCTTAAAAAGTTAGAACTAGTTCGGACTTTGTTGACTCATAATCCCATGTTCT-AATGCCTACA
1 ATCTTAAAAAGTTAGAACTAGTTCGGACATCGCAGACTCATAATCCCAAGTTCTAAATGCCTACA
*
11267 AAGCCCCGTTTCTTTCTTCTCCTAATCAGCTGTGT-TC-GAAATTCTTAGTCGCA-TTTAAACAG
66 AAGCCCCGTTTCTTTCTTCTCCTAATCAGCT-T-TCTCTGAAATTCATAGTCGCATTTTAAACAG
*
11329 TAGAGCTAATTTTAGCAGATGTAGCA
129 TAGAGCTAATTTTAGCAGAGGTAGCA
11355 CATGAATACA
Statistics
Matches: 292, Mismatches: 20, Indels: 11
0.90 0.06 0.03
Matches are distributed among these distances:
162 62 0.21
163 148 0.51
164 29 0.10
165 1 0.00
166 1 0.00
167 51 0.17
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.32
Consensus pattern (164 bp):
ATCTTAAAAAGTTAGAACTAGTTCGGACATCGCAGACTCATAATCCCAAGTTCTAAATGCCTACA
AAGCCCCGTTTCTTTCTTCTCCTAATCAGCTTTCTCTGAAATTCATAGTCGCATTTTAAACAGTA
GAGCTAATTTTAGCAGAGGTAGCATACAAATTAA
Found at i:14681 original size:154 final size:154
Alignment explanation
Indices: 14387--14670 Score: 356
Period size: 154 Copynumber: 1.8 Consensus size: 154
14377 AGTGAGGTAA
* ** * * ***
14387 AGCCCAAGAGAGAGATTTTGCCTCCCTTCCGTCGTGCATGGTGACTTATATAGTGATTTTTAGTA
1 AGCCCAAGAGAGAGACTTTGCCTCCCTTCCACCATGCATAGTGACTTATATAGTGACCCTTAGTA
* * * *
14452 TTGATGTCAAGTCTAAGGTCATGATAACTACTAATAAATTGACAAATTAAATAAAAAGGGCTGTC
66 TTGATATCAAGTCTAAGGTCATGATAACAACTAATAAATTGACAAATTAAATAAAAACGACTGTC
14517 ATAGATCATGTCACGGTGAAATCG
131 ATAGATCATGTCACGGTGAAATCG
* * *
14541 AGCCCAAGAGAGAGACTTTGCTTCCCTTTCACCATGCATAGTGACTTGTATAGTGACCCTTAGTA
1 AGCCCAAGAGAGAGACTTTGCCTCCCTTCCACCATGCATAGTGACTTATATAGTGACCCTTAGTA
* * * * *
14606 TT-AGTATCAAGT-TTAGAGTCGTGATGACAACTAATAAGTTGACAAGTTAAATAAAAACGACTG
66 TTGA-TATCAAGTCTAAG-GTCATGATAACAACTAATAAATTGACAAATTAAATAAAAACGACTG
14669 TC
129 TC
14671 TAATATCATG
Statistics
Matches: 108, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
153 4 0.04
154 104 0.96
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (154 bp):
AGCCCAAGAGAGAGACTTTGCCTCCCTTCCACCATGCATAGTGACTTATATAGTGACCCTTAGTA
TTGATATCAAGTCTAAGGTCATGATAACAACTAATAAATTGACAAATTAAATAAAAACGACTGTC
ATAGATCATGTCACGGTGAAATCG
Found at i:15745 original size:36 final size:37
Alignment explanation
Indices: 15698--15767 Score: 124
Period size: 36 Copynumber: 1.9 Consensus size: 37
15688 CTCGATTTGC
*
15698 ACTTAAATAAACTTGGGTAC-AAGAAATTTACGTTTA
1 ACTTAAATAAACTTGGGTACAAAAAAATTTACGTTTA
15734 ACTTAAATAAACTTGGGTACAAAAAAATTTACGT
1 ACTTAAATAAACTTGGGTACAAAAAAATTTACGT
15768 ACGCCACTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 20 0.62
37 12 0.38
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.31
Consensus pattern (37 bp):
ACTTAAATAAACTTGGGTACAAAAAAATTTACGTTTA
Found at i:28475 original size:3 final size:3
Alignment explanation
Indices: 28464--28521 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
28454 TTTTTTTCCG
** *
28464 TTA TT- TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28509 TTA TTTA TTA TTA
1 TTA -TTA TTA TTA
28522 CAATTTTTGC
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 5 0.11
3 37 0.82
4 3 0.07
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:28645 original size:25 final size:25
Alignment explanation
Indices: 28616--28715 Score: 173
Period size: 25 Copynumber: 4.0 Consensus size: 25
28606 CCAACAACCC
*
28616 ATCAGATTAGGGTTTTAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
28641 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
*
28666 ATCAGTTTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
*
28691 ATCAGACTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
28716 TCCCCTAACT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 71 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:42304 original size:9 final size:8
Alignment explanation
Indices: 42279--42304 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
42269 AAAAAAAAGG
42279 AAATGAAA
1 AAATGAAA
42287 AAATGAAA
1 AAATGAAA
42295 AAATGAAA
1 AAATGAAA
42303 AA
1 AA
42305 GAAGAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAATGAAA
Found at i:42314 original size:16 final size:16
Alignment explanation
Indices: 42279--42313 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
42269 AAAAAAAAGG
*
42279 AAATGAAAAAATGAAA
1 AAATGAAAAAAAGAAA
42295 AAATGAAAAAGAAGAAA
1 AAATGAAAAA-AAGAAA
42312 AA
1 AA
42314 TAAATAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (16 bp):
AAATGAAAAAAAGAAA
Found at i:43528 original size:89 final size:89
Alignment explanation
Indices: 43267--43561 Score: 362
Period size: 89 Copynumber: 3.2 Consensus size: 89
43257 CCAGACTTCC
* *
43267 TCATCACGTAGGAGCCGTGTCAACATTAGGATAACCAGCCGTCCTTATCACGTAGGAACCGAGTT
1 TCATCACGTAGGAGCCGTGTCAAC-CTA-GATAACCAGCCGTCCTCATCACGTAGGAACCGAGTT
*
43332 ATCACCCTTCCTAAAGGTGGCCAGAGT-TCT
64 ATCA----TCCTAAAGATGGCCAGA-TCTCT
* * *
43362 TCATCATGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
1 TCATCACGTAGGAGCCGTGTCAACC-TAGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTA
**
43427 TCA-CCTTTAGATGGCCAGATCTCT
65 TCATCCTAAAGATGGCCAGATCTCT
* * *
43451 TCATCACGTAAGAGCCGTGTCAACCT-GATAACCAGTCGTCCTCATTACGTAGGAACCGAGTTAT
1 TCATCACGTAGGAGCCGTGTCAACCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTAT
* *
43515 CATCCCTAAAGATGACCAGATCTCC
66 CAT-CCTAAAGATGGCCAGATCTCT
*
43540 TCATCACGTAGGAGCCATGTCA
1 TCATCACGTAGGAGCCGTGTCA
43562 CCCTTAGACG
Statistics
Matches: 177, Mismatches: 19, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
87 37 0.21
88 2 0.01
89 76 0.43
94 38 0.21
95 24 0.14
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (89 bp):
TCATCACGTAGGAGCCGTGTCAACCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTAT
CATCCTAAAGATGGCCAGATCTCT
Found at i:43773 original size:3 final size:3
Alignment explanation
Indices: 43762--43824 Score: 58
Period size: 3 Copynumber: 21.0 Consensus size: 3
43752 TTTTTTTCCG
** * *
43762 TTA TT- TTA TTA TTTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TTT
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
43806 TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA
43825 CAATTTTTGC
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
2 3 0.06
3 39 0.81
4 6 0.12
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:43801 original size:23 final size:22
Alignment explanation
Indices: 43770--43824 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 22
43760 CGTTATTTTA
43770 TTATTTATTATTATTATTATCG
1 TTATTTATTATTATTATTATCG
*
43792 TTATCTTATTATTTTTATTA---
1 TTAT-TTATTATTATTATTATCG
43812 TTATTTATTATTA
1 TTATTTATTATTA
43825 CAATTTTTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 8 0.27
20 4 0.13
22 4 0.13
23 14 0.47
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
TTATTTATTATTATTATTATCG
Found at i:43802 original size:20 final size:19
Alignment explanation
Indices: 43762--43824 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 19
43752 TTTTTTTCCG
43762 TTATT-TTATTAT--TTA-
1 TTATTATTATTATCATTAT
*
43777 TTATTATTATTATCGTTAT
1 TTATTATTATTATCATTAT
* *
43796 CTTATTATTTTTATTATTAT
1 -TTATTATTATTATCATTAT
43816 TTATTATTA
1 TTATTATTA
43825 CAATTTTTGC
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
15 5 0.13
16 7 0.18
18 3 0.08
19 8 0.21
20 16 0.41
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (19 bp):
TTATTATTATTATCATTAT
Found at i:43948 original size:25 final size:25
Alignment explanation
Indices: 43919--44018 Score: 173
Period size: 25 Copynumber: 4.0 Consensus size: 25
43909 CCAACAACCC
*
43919 ATCAGATTAGGGTTTTAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
43944 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
*
43969 ATCAGTTTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
*
43994 ATCAGACTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
44019 TCCCCTAACT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 71 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:47078 original size:25 final size:25
Alignment explanation
Indices: 47050--47099 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
47040 TATTGAATAT
*
47050 GTTTTATTATTTTTTATTTTTTAAA
1 GTTTTATTATTTATTATTTTTTAAA
47075 GTTTTATTATTTATTATTTTTTAAA
1 GTTTTATTATTTATTATTTTTTAAA
47100 CGTTCATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (25 bp):
GTTTTATTATTTATTATTTTTTAAA
Found at i:47112 original size:25 final size:25
Alignment explanation
Indices: 47050--47113 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
47040 TATTGAATAT
*
47050 GTTTTATTATTTT-TTATTTTTTAAA
1 GTTTCATT-TTTTATTATTTTTTAAA
* *
47075 GTTTTATTATTTATTATTTTTTAAA
1 GTTTCATTTTTTATTATTTTTTAAA
47100 CG-TTCATTTTTTAT
1 -GTTTCATTTTTTAT
47114 ATATAATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 3 0.09
25 30 0.88
26 1 0.03
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (25 bp):
GTTTCATTTTTTATTATTTTTTAAA
Found at i:48960 original size:21 final size:20
Alignment explanation
Indices: 48936--48975 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
48926 AGGCTCTCTA
*
48936 TTTCTATTTTCCTAACTTAAT
1 TTTCAATTTTCCTAA-TTAAT
*
48957 TTTCAATTTTTCTAATTAA
1 TTTCAATTTTCCTAATTAA
48976 CTTATTGAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.28, C:0.15, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTCAATTTTCCTAATTAAT
Found at i:49486 original size:15 final size:15
Alignment explanation
Indices: 49468--49506 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
49458 AGGGAGAAAG
49468 AAAAAAGGAAAAAAA
1 AAAAAAGGAAAAAAA
* * *
49483 AAAAAATGAAGAAGA
1 AAAAAAGGAAAAAAA
49498 AAAAAAGGA
1 AAAAAAGGA
49507 TTTTATAATG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (15 bp):
AAAAAAGGAAAAAAA
Done.