Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001135.1 Hibiscus syriacus cultivar Beakdansim tig00002263_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: 162108
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
File 2 of 2
Found at i:146977 original size:23 final size:22
Alignment explanation
Indices: 146933--146981 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
146923 TTTTTATTTC
146933 ATATTTTTATTTATTTAAATATT
1 ATATTTTTATTTATTTAAATA-T
*
146956 ATATTTTTA-TTATTATATATAT
1 ATATTTTTATTTATT-TAAATAT
146978 ATAT
1 ATAT
146982 GTGTGTGTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
ATATTTTTATTTATTTAAATAT
Found at i:147342 original size:20 final size:21
Alignment explanation
Indices: 147317--147361 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
147307 TCCAAATTCA
*
147317 CAACGCGAATTT-GTAAATCG
1 CAACGCGAATTTAGAAAATCG
147337 CAACGCGAATTTAGAAAATCG
1 CAACGCGAATTTAGAAAATCG
147358 CAAC
1 CAAC
147362 AAAGAAGCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (21 bp):
CAACGCGAATTTAGAAAATCG
Found at i:147434 original size:40 final size:40
Alignment explanation
Indices: 147390--147481 Score: 107
Period size: 39 Copynumber: 2.3 Consensus size: 40
147380 ACGCGTTTGC
*
147390 CAAATTCGCAACACTGAATTTCAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACAC-GAATTTCAAATTCGCAACACGAATTT
* ** *
147430 CAAATTCGCAACTCGGTTTTCGAATTCGCAACACGAATTT
1 CAAATTCGCAACACGAATTTCAAATTCGCAACACGAATTT
*
147470 -AATTTCGCAACA
1 CAAATTCGCAACA
147482 GGTTTTAGTT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
39 25 0.57
40 19 0.43
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (40 bp):
CAAATTCGCAACACGAATTTCAAATTCGCAACACGAATTT
Found at i:147481 original size:19 final size:20
Alignment explanation
Indices: 147390--147481 Score: 107
Period size: 19 Copynumber: 4.7 Consensus size: 20
147380 ACGCGTTTGC
147390 CAAATTCGCAACACTGAATTT
1 CAAATTCGCAACAC-GAATTT
*
147411 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACACGAATTT
* **
147430 CAAATTCGCAACTCGGTTTT
1 CAAATTCGCAACACGAATTT
*
147450 CGAATTCGCAACACGAATTT
1 CAAATTCGCAACACGAATTT
*
147470 -AATTTCGCAACA
1 CAAATTCGCAACA
147482 GGTTTTAGTT
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
19 28 0.47
20 20 0.33
21 12 0.20
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (20 bp):
CAAATTCGCAACACGAATTT
Found at i:147657 original size:15 final size:16
Alignment explanation
Indices: 147637--147674 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
147627 TCCCCATCTC
*
147637 TAATTTTGTTT-TACA
1 TAATTTTATTTCTACA
*
147652 TAATTTTATTTCTATA
1 TAATTTTATTTCTACA
147668 TAATTTT
1 TAATTTT
147675 TCAATGATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (16 bp):
TAATTTTATTTCTACA
Found at i:148448 original size:24 final size:24
Alignment explanation
Indices: 148419--148472 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
148409 ATATTCAAAA
148419 TTTGATCTTGGTCAAAACCCAGAC
1 TTTGATCTTGGTCAAAACCCAGAC
*
148443 TTTGATCTTGGTCAAAACCCAGAT
1 TTTGATCTTGGTCAAAACCCAGAC
148467 TTTGAT
1 TTTGAT
148473 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (24 bp):
TTTGATCTTGGTCAAAACCCAGAC
Found at i:150750 original size:18 final size:18
Alignment explanation
Indices: 150717--150752 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
150707 AAGCAAAAGG
**
150717 AAATCAAAATTGCAATCA
1 AAATCAAAATCCCAATCA
150735 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
150753 CAACCAGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:151029 original size:42 final size:43
Alignment explanation
Indices: 150964--151064 Score: 132
Period size: 43 Copynumber: 2.4 Consensus size: 43
150954 AATTCGCAAC
* ** **
150964 GCGAAAGTCAAATTCACGTTGCGATT-TTTTGTTGCGATTGAT
1 GCGAAAGTCAAATTCGCAATGCGATTATCGTGTTGCGATTGAT
*
151006 GCGAAAGTCAAATTCGCAATGCGATTATCGTGTTGCGATTGTT
1 GCGAAAGTCAAATTCGCAATGCGATTATCGTGTTGCGATTGAT
*
151049 GCAAAAGTCAAATTCG
1 GCGAAAGTCAAATTCG
151065 AAACGCGAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 23 0.45
43 28 0.55
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.33
Consensus pattern (43 bp):
GCGAAAGTCAAATTCGCAATGCGATTATCGTGTTGCGATTGAT
Found at i:152746 original size:42 final size:41
Alignment explanation
Indices: 152687--152809 Score: 174
Period size: 42 Copynumber: 2.9 Consensus size: 41
152677 ATGAATCGGG
*
152687 CTCTTGAACTGTGGGAGGGACCTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGG-CCTCTTGAACGATGACAGGGGC
* *
152729 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGATATGGGC
1 CTCTTGAACGGTGGGA-GGGCCTCTTGAACGATGACAGGGGC
* *
152771 CTCTTGAACGATAGGAGGCGCCTCTTGAACGATGACAGG
1 CTCTTGAACGGTGGGAGG-GCCTCTTGAACGATGACAGG
152810 TGCATCGGGC
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
41 2 0.03
42 67 0.93
43 3 0.04
ACGTcount: A:0.22, C:0.21, G:0.35, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGCCTCTTGAACGATGACAGGGGC
Found at i:152802 original size:21 final size:21
Alignment explanation
Indices: 152687--152805 Score: 134
Period size: 21 Copynumber: 5.7 Consensus size: 21
152677 ATGAATCGGG
* *
152687 CTCTTGAACTG-TGGGAGGGAC
1 CTCTTGAAC-GATGAGAGGGGC
*
152708 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACGATGAGAGGGGC
* *
152729 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
* *
152750 CTCTTGAACGATGATATGGGC
1 CTCTTGAACGATGAGAGGGGC
*
152771 CTCTTGAACGAT-AGGAGGCGC
1 CTCTTGAACGATGA-GAGGGGC
152792 CTCTTGAACGATGA
1 CTCTTGAACGATGA
152806 CAGGTGCATC
Statistics
Matches: 82, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
20 2 0.02
21 79 0.96
22 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.34, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:154944 original size:19 final size:19
Alignment explanation
Indices: 154885--154944 Score: 66
Period size: 20 Copynumber: 3.1 Consensus size: 19
154875 GTAGTTTCTT
154885 AAACTTAAATTCGCAATGCG
1 AAAC-TAAATTCGCAATGCG
* * *
154905 AAAATGAAAATCGCAACGCG
1 AAACT-AAATTCGCAATGCG
*
154925 AAACTAAATTCGCATTGCG
1 AAACTAAATTCGCAATGCG
154944 A
1 A
154945 TTTTCGTGTT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
19 13 0.41
20 19 0.59
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (19 bp):
AAACTAAATTCGCAATGCG
Found at i:155500 original size:20 final size:20
Alignment explanation
Indices: 155475--155590 Score: 142
Period size: 20 Copynumber: 5.8 Consensus size: 20
155465 ATAAACGCGT
*
155475 TTTGACTTATGTGTTCCGAA
1 TTTGACTTATGTGTTGCGAA
*
155495 TTTGACTTCTGTGTTGCGAA
1 TTTGACTTATGTGTTGCGAA
* *
155515 TTTGAATTAGGTGTTGCGAA
1 TTTGACTTATGTGTTGCGAA
* * *
155535 TTTAACTTATATGTTTCGAA
1 TTTGACTTATGTGTTGCGAA
*
155555 TTTGACTTCTGTGTTGCGAA
1 TTTGACTTATGTGTTGCGAA
* *
155575 TTTAACTTCTGTGTTG
1 TTTGACTTATGTGTTG
155591 TGATTCACAT
Statistics
Matches: 81, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 81 1.00
ACGTcount: A:0.20, C:0.12, G:0.22, T:0.47
Consensus pattern (20 bp):
TTTGACTTATGTGTTGCGAA
Found at i:155535 original size:40 final size:40
Alignment explanation
Indices: 155475--155590 Score: 160
Period size: 40 Copynumber: 2.9 Consensus size: 40
155465 ATAAACGCGT
* *
155475 TTTGACTTATGTGTTCCGAATTTGACTTCTGTGTTGCGAA
1 TTTGACTTATGTGTTGCGAATTTAACTTCTGTGTTGCGAA
* * * * *
155515 TTTGAATTAGGTGTTGCGAATTTAACTTATATGTTTCGAA
1 TTTGACTTATGTGTTGCGAATTTAACTTCTGTGTTGCGAA
*
155555 TTTGACTTCTGTGTTGCGAATTTAACTTCTGTGTTG
1 TTTGACTTATGTGTTGCGAATTTAACTTCTGTGTTG
155591 TGATTCACAT
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 63 1.00
ACGTcount: A:0.20, C:0.12, G:0.22, T:0.47
Consensus pattern (40 bp):
TTTGACTTATGTGTTGCGAATTTAACTTCTGTGTTGCGAA
Found at i:155654 original size:20 final size:20
Alignment explanation
Indices: 155631--155673 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
155621 AACTGGGTTG
*
155631 CGAAATTGGAGTTCGCGTTA
1 CGAAATTGGAGATCGCGTTA
* *
155651 CG-AATTTGAGATCGCGTTG
1 CGAAATTGGAGATCGCGTTA
155670 CGAA
1 CGAA
155674 TTTGTTGGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (20 bp):
CGAAATTGGAGATCGCGTTA
Found at i:155832 original size:9 final size:9
Alignment explanation
Indices: 155818--155855 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
155808 CATTTTATTA
155818 TATATTTTT
1 TATATTTTT
155827 TATATTTTGT
1 TATATTTT-T
*
155837 TTTATTTTT
1 TATATTTTT
155846 TATATTTTT
1 TATATTTTT
155855 T
1 T
155856 TCCTTTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
9 18 0.69
10 8 0.31
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (9 bp):
TATATTTTT
Found at i:155833 original size:21 final size:19
Alignment explanation
Indices: 155809--155853 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
155799 TAAATATTGC
155809 ATTTTATTATATATTTTTTAT
1 ATTTTATT-T-TATTTTTTAT
*
155830 ATTTTGTTTTATTTTTTAT
1 ATTTTATTTTATTTTTTAT
155849 ATTTT
1 ATTTT
155854 TTTCCTTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 15 0.65
20 1 0.04
21 7 0.30
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (19 bp):
ATTTTATTTTATTTTTTAT
Done.