Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005504.1 Hibiscus syriacus cultivar Beakdansim tig00012685_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: 66788
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Found at i:6720 original size:41 final size:40
Alignment explanation
Indices: 6551--6825 Score: 166
Period size: 41 Copynumber: 6.7 Consensus size: 40
6541 TTTAGTTGTG
* * *
6551 TTTTTATACAAACGCCGCAATATGA-TAAATCTATAGTGTCA
1 TTTTTATACAAACGCCGCAATA-GAGT-AGTATATAGTGGCA
* * * *
6592 TTTTT-TCAACAAACGCCGTAACAGAGTAGTACATTAGTGGCG
1 TTTTTAT--ACAAACGCCGCAATAGAGTAGTATA-TAGTGGCA
* * * **
6634 TTGTTATACAAACGCCGCAATAG-GTTTCA-TAAATATTGGTT
1 TTTTTATACAAACGCCGCAATAGAG--T-AGTATATAGTGGCA
* * *
6675 TTTTTATACAAACGCTGTAATAGGGTACGTATATAGTGGCA
1 TTTTTATACAAACGCCGCAATAGAGTA-GTATATAGTGGCA
* ** * * *
6716 TTTTTTTCAACAAACATCGAAATAGAGTAGTAATTTAGCGGCA
1 TTTTTAT--ACAAACGCCGCAATAGAGTAGT-ATATAGTGGCA
* *
6759 TTTTTATTA-AAACGCCGCAATAGAGTAGTACTTTAGAGGCA
1 TTTTTA-TACAAACGCCGCAATAGAGTAGTA-TATAGTGGCA
*
6800 TTTTTATACAAATGCCGCAAT-GAGTA
1 TTTTTATACAAACGCCGCAATAGAGTA
6826 AAATGTATTT
Statistics
Matches: 182, Mismatches: 35, Indels: 35
0.72 0.14 0.14
Matches are distributed among these distances:
39 1 0.01
40 11 0.06
41 106 0.58
42 32 0.18
43 31 0.17
44 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (40 bp):
TTTTTATACAAACGCCGCAATAGAGTAGTATATAGTGGCA
Found at i:7036 original size:41 final size:41
Alignment explanation
Indices: 6932--7100 Score: 137
Period size: 41 Copynumber: 4.1 Consensus size: 41
6922 TGCTCTTACA
* * * * *
6932 TTAGTGGCGTTTGTATACAAACGCCTCTAAAGACTCAGACT
1 TTAGTGACGTTTTTATACAAACGCCGCTATAGACTCATACT
* * * * *
6973 TTCGTAACATTTGTT-TATAAACGTCGCTATAGACTCATACT
1 TTAGTGACGTTT-TTATACAAACGCCGCTATAGACTCATACT
** *
7014 TTAGTGGTGTTTTTATACAAACGCCGTTATAGACTTC-TACT
1 TTAGTGACGTTTTTATACAAACGCCGCTATAGAC-TCATACT
* * * *
7055 TTAGTGACGTTTTTTTTCAAACGCCGCAATAGTC-CTATACT
1 TTAGTGACGTTTTTATACAAACGCCGCTATAGACTC-ATACT
7096 TTAGT
1 TTAGT
7101 AGCTTTTTGA
Statistics
Matches: 98, Mismatches: 25, Indels: 10
0.74 0.19 0.08
Matches are distributed among these distances:
39 1 0.01
40 2 0.02
41 92 0.94
42 3 0.03
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.38
Consensus pattern (41 bp):
TTAGTGACGTTTTTATACAAACGCCGCTATAGACTCATACT
Found at i:8011 original size:32 final size:32
Alignment explanation
Indices: 7970--8037 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
7960 CCAAGTTATA
*
7970 CCTAGCAGCAGACGCAACATCACAGCAAAATC
1 CCTAGCAGCAGACGCAACATCACAACAAAATC
* * *
8002 CCTAGCAGCAGGCGTAACATCACAACAAAATT
1 CCTAGCAGCAGACGCAACATCACAACAAAATC
8034 CCTA
1 CCTA
8038 AATCCAAGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.40, C:0.32, G:0.15, T:0.13
Consensus pattern (32 bp):
CCTAGCAGCAGACGCAACATCACAACAAAATC
Found at i:9172 original size:18 final size:19
Alignment explanation
Indices: 9149--9186 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
9139 TTGGCCGGTT
9149 CCGACCCGA-CCCGTTGAC
1 CCGACCCGACCCCGTTGAC
9167 CCGACCCGACCCCGTTGAC
1 CCGACCCGACCCCGTTGAC
9186 C
1 C
9187 GGGTGTTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.16, C:0.53, G:0.21, T:0.11
Consensus pattern (19 bp):
CCGACCCGACCCCGTTGAC
Found at i:9231 original size:29 final size:29
Alignment explanation
Indices: 9187--9337 Score: 180
Period size: 29 Copynumber: 5.2 Consensus size: 29
9177 CCCGTTGACC
*
9187 GGGTGTTAGTTTTGTAATTATTTTTAAAA
1 GGGTGTTAGTTTTGTAAATATTTTTAAAA
*
9216 GCGTGTTAGTTTTGTAAATATTTTTAAAA
1 GGGTGTTAGTTTTGTAAATATTTTTAAAA
* *
9245 GGGTGTTA-TTTTCGTTAATAATTTTAAAA
1 GGGTGTTAGTTTT-GTAAATATTTTTAAAA
* * * *
9274 GGGTGTTA-TTTTCTTATTTTTTTTAAAAA
1 GGGTGTTAGTTTTGTAAATATTTTT-AAAA
*
9303 TGGTGTTAGTTTTGTAAATATTTCTTAAAA
1 GGGTGTTAGTTTTGTAAATATTT-TTAAAA
9333 GGGTG
1 GGGTG
9338 ATAATTGTGT
Statistics
Matches: 103, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
28 12 0.12
29 71 0.69
30 18 0.17
31 2 0.02
ACGTcount: A:0.28, C:0.03, G:0.19, T:0.50
Consensus pattern (29 bp):
GGGTGTTAGTTTTGTAAATATTTTTAAAA
Found at i:15682 original size:29 final size:32
Alignment explanation
Indices: 15632--15703 Score: 98
Period size: 29 Copynumber: 2.4 Consensus size: 32
15622 TGAAAAAAAA
*
15632 ATTTAATT-AAATATTTTGGCGAAATTTGAGG
1 ATTTAATTGAAATATTTTGGCGAAATTGGAGG
15663 ATTTAATTGAAA-A-TTT-GCGAAATTGGAGG
1 ATTTAATTGAAATATTTTGGCGAAATTGGAGG
*
15692 ATTTAAATGAAA
1 ATTTAATTGAAA
15704 GTTTTCAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 23 0.61
30 3 0.08
31 9 0.24
32 3 0.08
ACGTcount: A:0.40, C:0.03, G:0.19, T:0.38
Consensus pattern (32 bp):
ATTTAATTGAAATATTTTGGCGAAATTGGAGG
Found at i:16374 original size:19 final size:20
Alignment explanation
Indices: 16347--16390 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
16337 AATTGTTTTT
*
16347 AACCGGTTTGACCGG-TCCG
1 AACCCGTTTGACCGGTTCCG
*
16366 AACCCGTTTGGCCGGTTCCG
1 AACCCGTTTGACCGGTTCCG
16386 -ACCCG
1 AACCCG
16391 ACCCTACCCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.14, C:0.36, G:0.30, T:0.20
Consensus pattern (20 bp):
AACCCGTTTGACCGGTTCCG
Found at i:16409 original size:23 final size:23
Alignment explanation
Indices: 16383--16436 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
16373 TTGGCCGGTT
16383 CCGACCCGACCCT-ACCCGCTGAC
1 CCGACCCGA-CCTGACCCGCTGAC
* *
16406 CCGACTCGACCTGACCCGTTGAC
1 CCGACCCGACCTGACCCGCTGAC
16429 CCGACCCG
1 CCGACCCG
16437 TTGACCTGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 3 0.11
23 24 0.89
ACGTcount: A:0.17, C:0.52, G:0.20, T:0.11
Consensus pattern (23 bp):
CCGACCCGACCTGACCCGCTGAC
Found at i:16434 original size:13 final size:13
Alignment explanation
Indices: 16413--16442 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
16403 GACCCGACTC
*
16413 GACCTGACCCGTT
1 GACCCGACCCGTT
16426 GACCCGACCCGTT
1 GACCCGACCCGTT
16439 GACC
1 GACC
16443 TGGTGTTAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:16486 original size:29 final size:29
Alignment explanation
Indices: 16444--16651 Score: 330
Period size: 29 Copynumber: 7.1 Consensus size: 29
16434 CCGTTGACCT
* *
16444 GGTGTTAGTTTTGTAATTATTTTCAAAAG
1 GGTGTTAGTTTTGTAAATATTTTTAAAAG
16473 GGTGTTAGTTTTGTAAATATTTTTAAAAG
1 GGTGTTAGTTTTGTAAATATTTTTAAAAG
*
16502 GGTGTTATTTTTGTAAATATTTTTAAAAG
1 GGTGTTAGTTTTGTAAATATTTTTAAAAG
*
16531 GGTATTA-TTTTCGTAAATATTTTTAAAAG
1 GGTGTTAGTTTT-GTAAATATTTTTAAAAG
16560 GGTGTTA-TTTTCGTAAATATTTTTAAAAG
1 GGTGTTAGTTTT-GTAAATATTTTTAAAAG
16589 GGTGTTAGTTTTGTAAATATTTTTAAAAG
1 GGTGTTAGTTTTGTAAATATTTTTAAAAG
*
16618 GGTGTTAGTTTTATAAATATTTCTTAAAAG
1 GGTGTTAGTTTTGTAAATATTT-TTAAAAG
16648 GGTG
1 GGTG
16652 ATAATTGTGT
Statistics
Matches: 170, Mismatches: 6, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
28 4 0.02
29 151 0.89
30 15 0.09
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (29 bp):
GGTGTTAGTTTTGTAAATATTTTTAAAAG
Found at i:19979 original size:2 final size:2
Alignment explanation
Indices: 19972--20006 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
19962 GAACATGTGA
19972 AT AT 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 AT AT A
20007 GATAAGACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20458 original size:23 final size:23
Alignment explanation
Indices: 20394--20458 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
20384 CTTATATAGA
*
20394 ACTTCGGTGCATTTCTATGCGGC
1 ACTTCGGTGCATTTCTACGCGGC
* *
20417 ACTAT-GGTGCAATTCTACGTGGC
1 ACT-TCGGTGCATTTCTACGCGGC
*
20440 ACTTCGGTGCATTTATACG
1 ACTTCGGTGCATTTCTACG
20459 AGCTGTGGTG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 1 0.03
23 33 0.94
24 1 0.03
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.34
Consensus pattern (23 bp):
ACTTCGGTGCATTTCTACGCGGC
Found at i:26639 original size:23 final size:22
Alignment explanation
Indices: 26613--26655 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
26603 ATAAATGTTC
26613 TTTG-TTTTCTTTTACAAGAATTT
1 TTTGTTTTTC-TTTA-AAGAATTT
26636 TTTGTTTTTCTTTAAAGAAT
1 TTTGTTTTTCTTTAAAGAAT
26656 GAAAAACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.32
23 8 0.42
24 5 0.26
ACGTcount: A:0.23, C:0.07, G:0.09, T:0.60
Consensus pattern (22 bp):
TTTGTTTTTCTTTAAAGAATTT
Found at i:43243 original size:18 final size:18
Alignment explanation
Indices: 43220--43271 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
43210 ATATAACACA
*
43220 TATGTCCCAAAGGACCAC
1 TATGTCCCGAAGGACCAC
43238 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
43256 TATGTCCCGAAGGACC
1 TATGTCCCGAAGGACC
43272 GCGTAGACCC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.29, C:0.33, G:0.21, T:0.17
Consensus pattern (18 bp):
TATGTCCCGAAGGACCAC
Found at i:43386 original size:25 final size:26
Alignment explanation
Indices: 43335--43386 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
43325 ATAACATGGG
*
43335 CATTTTCACTTATCTCATTTCACTATA
1 CATTTTCAC-TATCACATTTCACTATA
43362 CATTTTCA-TATCACATGTTCA-TATA
1 CATTTTCACTATCACAT-TTCACTATA
43387 AGCTCATAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 11 0.48
26 4 0.17
27 8 0.35
ACGTcount: A:0.29, C:0.23, G:0.02, T:0.46
Consensus pattern (26 bp):
CATTTTCACTATCACATTTCACTATA
Found at i:43857 original size:13 final size:13
Alignment explanation
Indices: 43839--43875 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
43829 CTAATTTCCA
43839 TATAATCATATAC
1 TATAATCATATAC
43852 TATAATCATATAC
1 TATAATCATATAC
43865 TATAATCATAT
1 TATAATCATAT
43876 GCACTCACCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.41
Consensus pattern (13 bp):
TATAATCATATAC
Found at i:53085 original size:20 final size:21
Alignment explanation
Indices: 53060--53102 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
53050 ATTGATCATT
*
53060 ACATATA-ATGTTTATCATGA
1 ACATATAGATATTTATCATGA
53080 ACATATATGATATTTATCATGA
1 ACATATA-GATATTTATCATGA
53102 A
1 A
53103 TGATATTTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
22 13 0.65
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (21 bp):
ACATATAGATATTTATCATGA
Found at i:53260 original size:30 final size:30
Alignment explanation
Indices: 53220--53364 Score: 139
Period size: 30 Copynumber: 4.7 Consensus size: 30
53210 GTGTAAGGAT
* *
53220 ACTATAGTGTATAAGGACACTTAGTGCAGC
1 ACTATAGTGTGTAAGGACACTTAGTGCAAC
* * *
53250 ACTATGGTGTATTAAGGACACTTAGTGCATAGGT
1 ACTATAGTGT-GTAAGGACACTTAGTGCA-A--C
*
53284 ACTATAGTGTGTAAGGACACTTAGTACAAC
1 ACTATAGTGTGTAAGGACACTTAGTGCAAC
* * * *
53314 ATTATAGTGTGTAAGGACGCTCAATGCAAC
1 ACTATAGTGTGTAAGGACACTTAGTGCAAC
*
53344 ACTGT-GATGTGTAAGGACACT
1 ACTATAG-TGTGTAAGGACACT
53365 CAATGCATAT
Statistics
Matches: 94, Mismatches: 16, Indels: 10
0.78 0.13 0.08
Matches are distributed among these distances:
29 1 0.01
30 50 0.53
31 17 0.18
32 1 0.01
33 16 0.17
34 9 0.10
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.28
Consensus pattern (30 bp):
ACTATAGTGTGTAAGGACACTTAGTGCAAC
Found at i:54026 original size:27 final size:27
Alignment explanation
Indices: 53990--54050 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
53980 TAAGATTGGA
53990 TTTGAATTAGAAGTTGAAATATTATAT
1 TTTGAATTAGAAGTTGAAATATTATAT
54017 TTTGAATTAGAAGTTGAAATATTATAT
1 TTTGAATTAGAAGTTGAAATATTATAT
54044 TTTGAAT
1 TTTGAAT
54051 CCCTCTTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.46
Consensus pattern (27 bp):
TTTGAATTAGAAGTTGAAATATTATAT
Found at i:55995 original size:182 final size:182
Alignment explanation
Indices: 54605--55980 Score: 2037
Period size: 182 Copynumber: 7.6 Consensus size: 182
54595 ATTAAAGTAC
* * * ** * * * *
54605 CGACACTTTCAACATAACTGGTAGCGCTTTACCGGTTTTGTCATTTCGATATCGGTTTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
* * * *
54670 TTTTTACCTATTATATT-ATCATGGATCGATACATTT-TCATAAAGTATCTACACTTTTTAGGCG
66 TTATTACCTGTTATATTGCT-ATGGATCGATACATTTGT-ATAAAGTATCGACACTTTTTAGGCG
* * * *
54733 CTATAATTTATTCTCTTTTAAATTACGAAAGTATCGATACTTATATTAATTTAT
129 CTATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
* *
54787 CGACACTTTCAATATAACCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTATCATA
1 CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
* * * * * **
54852 TTATTACCTATTATATTTCTATAGATCGATACATTTATATAAAATATCGACACTTTTTAGGTTCT
66 TTATTACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCT
* *
54917 ATAACTTCTTCTCTTTCAAATATA-AAAAGTGTCGATAATTATATTAATTTAT
131 ATAACTTCTTCTCTTTTAAAT-TACAAAAGTGTCGATACTTATATTAATTTAT
* *
54969 CGACACTTTCAATATATCCGGTAGCTTTTTACCGATTTTATCATTTTGAGACCTGTTTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
*
55034 TTATTACATGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCT
66 TTATTACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCT
*
55099 ATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTCT
131 ATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
* *
55151 CGACACTTTCAATATATTCGGTATCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
55216 TTATTACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCT
66 TTATTACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCT
*
55281 ATAACTTTTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
131 ATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
*
55333 CGACACTTTCAATATATCCGGTAGTTTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCAT
1 CGACACTTTCAATATATCCGGTAG-CTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCAT
* * *
55398 ATTATTACATGTTATATTGATATGGATCGATACATTTGTATAAAATATCGACACTTTTTAGGCGC
65 ATTATTACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGC
*
55463 TATAACTTATTCTCTTTTAAA-TATCAAAAGTGTCGATACTTATATTAATTTAT
130 TATAACTTCTTCTCTTTTAAATTA-CAAAAGTGTCGATACTTATATTAATTTAT
*
55516 CGACACTTTCAATATATCCGGTAGCTTTTTA-TGAGTTTTATCATTTCGAGACCTGTTTTGTCAT
1 CGACACTTTCAATATATCCGGTAGCTTTTTACCG-GTTTTATCATTTCGAGACCTGTTTTGTCAT
*
55580 ATTATTACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAAGCGC
65 ATTATTACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGC
*
55645 TATAACTTCTTCTCTTTTAAATTACAAAAGTGTCAATACTTATATTAATTTAT
130 TATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
* * *** * * * *
55698 TGACACTTTCAATATATTCGGTAGAGGTTTACCGGTTTTATCATAAT-GACATCGGTTTTGTCAT
1 CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCAT-TTCGAGACCTGTTTTGTCAT
* * *
55762 ATCATTACATGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTATAGGCGC
65 ATTATTACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGC
* *
55827 TATAACTTCTTCACTTTTAAATTACAAAAGTGTCGATATTTATATTAATTTAT
130 TATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
* ** * * * *
55880 CGACACTTTCAATATATTCGGTAGCGGTTTACCGGTTTTATCATAAT-GACACCGGTTTTATCAT
1 CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCAT-TTCGAGACCTGTTTTGTCAT
* *
55944 ATTTTTACCTGTTATATTGCTATAGATCGATACATTT
65 ATTATTACCTGTTATATTGCTATGGATCGATACATTT
55981 TTCATTTGTA
Statistics
Matches: 1100, Mismatches: 84, Indels: 20
0.91 0.07 0.02
Matches are distributed among these distances:
181 3 0.00
182 915 0.83
183 182 0.17
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (182 bp):
CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
TTATTACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCT
ATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
Found at i:57153 original size:2 final size:2
Alignment explanation
Indices: 57146--57172 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
57136 TACCAATAAC
57146 TA 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 TA T
57173 TAATTTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.