Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015124.1 Corchorus olitorius cultivar O-4 contig15157, 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: 54328
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:457 original size:25 final size:25
Alignment explanation
Indices: 427--474 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
417 ATGCAATGTC
427 AAATTAGATTTGAGCTACATGAATG
1 AAATTAGATTTGAGCTACATGAATG
*
452 AAATTAGCTTTGAGCTACATGAA
1 AAATTAGATTTGAGCTACATGAA
475 CGCAAAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (25 bp):
AAATTAGATTTGAGCTACATGAATG
Found at i:652 original size:27 final size:29
Alignment explanation
Indices: 618--693 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
608 AAGTGGACTC
*
618 AAAATGACCAACATGCCCCT-GA-ATATG
1 AAAATGACCAAAATGCCCCTGGATATATG
* * *
645 CAAATGACCAAAATGCCCCTGGATTTTTG
1 AAAATGACCAAAATGCCCCTGGATATATG
674 AAAATGACCAAAATGCCCCT
1 AAAATGACCAAAATGCCCCT
694 AAGTGATCCT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
27 18 0.43
28 2 0.05
29 22 0.52
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.21
Consensus pattern (29 bp):
AAAATGACCAAAATGCCCCTGGATATATG
Found at i:7778 original size:2 final size:2
Alignment explanation
Indices: 7771--7809 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
7761 CTTCATTTGG
*
7771 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7810 TAGATATCTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10268 original size:31 final size:31
Alignment explanation
Indices: 10227--10313 Score: 113
Period size: 31 Copynumber: 2.8 Consensus size: 31
10217 TTTGATTCTC
* *
10227 CCTTGGGAGGCCGTCGGCCTCAACCAATTCA
1 CCTTGAGAGGCCGTCGGCCTCAACCAACTCA
*
10258 CCTTGCGAGGCCGTCGGCCTCAACCAACTCA
1 CCTTGAGAGGCCGTCGGCCTCAACCAACTCA
* * *
10289 TCTTGAGAGGCTG-CGACCTCAACCA
1 CCTTGAGAGGCCGTCGGCCTCAACCA
10314 TTAATTTTCT
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
30 11 0.22
31 39 0.78
ACGTcount: A:0.21, C:0.37, G:0.24, T:0.18
Consensus pattern (31 bp):
CCTTGAGAGGCCGTCGGCCTCAACCAACTCA
Found at i:10776 original size:11 final size:11
Alignment explanation
Indices: 10760--10797 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
10750 TAAGAAATGA
10760 AATTTATAATT
1 AATTTATAATT
10771 AATTTATAATT
1 AATTTATAATT
10782 -ATTTGATAATT
1 AATTT-ATAATT
*
10793 TATTT
1 AATTT
10798 TATATAATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:11282 original size:21 final size:19
Alignment explanation
Indices: 11257--11314 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
11247 GCTGCTCTAA
11257 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* *
11278 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
11297 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
11315 TGCTAAACAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.36
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:11710 original size:13 final size:14
Alignment explanation
Indices: 11692--11725 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
11682 AGGGACAGAG
11692 AGAGTATAAA-ATA
1 AGAGTATAAACATA
11705 AGAGTATAAACATA
1 AGAGTATAAACATA
*
11719 AGTGTAT
1 AGAGTAT
11726 TTGGAATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.53, C:0.03, G:0.18, T:0.26
Consensus pattern (14 bp):
AGAGTATAAACATA
Found at i:12126 original size:23 final size:23
Alignment explanation
Indices: 12098--12145 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
12088 TTAATAAGAT
12098 CTAAGTACACTATAATATACTCC
1 CTAAGTACACTATAATATACTCC
12121 CTAAGTACACTATAATATACTCC
1 CTAAGTACACTATAATATACTCC
12144 CT
1 CT
12146 CTGTTACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.27, G:0.04, T:0.31
Consensus pattern (23 bp):
CTAAGTACACTATAATATACTCC
Found at i:14310 original size:17 final size:17
Alignment explanation
Indices: 14285--14317 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
14275 TATTTTTATG
*
14285 AAATTTTGATAACCACC
1 AAATGTTGATAACCACC
14302 AAATGTTGATAACCAC
1 AAATGTTGATAACCAC
14318 ACTATGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.27
Consensus pattern (17 bp):
AAATGTTGATAACCACC
Found at i:14332 original size:22 final size:21
Alignment explanation
Indices: 14281--14464 Score: 99
Period size: 22 Copynumber: 8.5 Consensus size: 21
14271 TAAATATTTT
14281 TATGAAATTTTGATAACCACC
1 TATGAAATTTTGATAACCACC
*
14302 ----AAATGTTGATAACCACAC
1 TATGAAATTTTGATAACCAC-C
* **
14320 TATGAAATTTTGATGATTACC
1 TATGAAATTTTGATAACCACC
*
14341 TTATGAAATTGTGATAAACTC-CC
1 -TATGAAATTTTGAT-AAC-CACC
* ** *
14364 AATGAAATACTGATAACCTAAC
1 TATGAAATTTTGATAACC-ACC
* **
14386 TATGAAATTTTAATAAACCTTTC
1 TATGAAATTTTGAT-AACC-ACC
*
14409 TATGAAATTTTGATAACCTCC
1 TATGAAATTTTGATAACCACC
** *
14430 ATATGATTTTTTTGATAACCTCTC
1 -TATGA-AATTTTGATAACCAC-C
14454 TATGAAATTTT
1 TATGAAATTTT
14465 ATTCATTTCC
Statistics
Matches: 124, Mismatches: 25, Indels: 27
0.70 0.14 0.15
Matches are distributed among these distances:
17 15 0.12
18 1 0.01
20 1 0.01
21 6 0.05
22 60 0.48
23 40 0.32
24 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.38
Consensus pattern (21 bp):
TATGAAATTTTGATAACCACC
Found at i:14464 original size:23 final size:22
Alignment explanation
Indices: 14302--14464 Score: 109
Period size: 22 Copynumber: 7.3 Consensus size: 22
14292 GATAACCACC
* * *
14302 AAATGTTGATAACCACACTATG
1 AAATTTTGATAACCTCTCTATG
14324 AAATTTTGATGATTA-C-CT-TATG
1 AAATTTTGAT-A--ACCTCTCTATG
* * * *
14346 AAATTGTGATAAACTCCCAATG
1 AAATTTTGATAACCTCTCTATG
** **
14368 AAATACTGATAACCTAACTATG
1 AAATTTTGATAACCTCTCTATG
* *
14390 AAATTTTAATAAACCTTTCTATG
1 AAATTTTGAT-AACCTCTCTATG
14413 AAATTTTGATAACCTC-CATATG
1 AAATTTTGATAACCTCTC-TATG
**
14435 ATTTTTTTGATAACCTCTCTATG
1 A-AATTTTGATAACCTCTCTATG
14458 AAATTTT
1 AAATTTT
14465 ATTCATTTCC
Statistics
Matches: 109, Mismatches: 22, Indels: 20
0.72 0.15 0.13
Matches are distributed among these distances:
19 1 0.01
20 1 0.01
21 3 0.03
22 62 0.57
23 39 0.36
24 2 0.02
25 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (22 bp):
AAATTTTGATAACCTCTCTATG
Found at i:15203 original size:24 final size:23
Alignment explanation
Indices: 15176--15227 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
15166 TTTTATGTCA
*
15176 ATATTAT-ATATTTTCATATTTTTT
1 ATATTATCATATTAT-AT-TTTTTT
15200 ATATTATCGATATTATATTTTTTT
1 ATATTATC-ATATTATATTTTTTT
15224 ATAT
1 ATAT
15228 AATTTAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 17 0.68
25 2 0.08
26 6 0.24
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (23 bp):
ATATTATCATATTATATTTTTTT
Found at i:36215 original size:15 final size:16
Alignment explanation
Indices: 36191--36230 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
36181 AGAGGTTGAA
*
36191 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
36206 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
36222 AGAAAACAA
1 AGAAAACAA
36231 AGCAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:38160 original size:31 final size:30
Alignment explanation
Indices: 38122--38229 Score: 114
Period size: 31 Copynumber: 3.5 Consensus size: 30
38112 TAAGAACAAT
38122 TGCTCAAATAAGGGCCTAACGTTTTCCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTT-CAAAA
* * **
38153 TGCTCAAATAAGGGCTTGATC-TTTT-AATT
1 TGCTCAAATAAGGGCCT-AACGTTTTCAAAA
38182 TGGC-CAAATTAAGGGCCTAACGTTTTCTAAAA
1 T-GCTCAAA-TAAGGGCCTAACGTTTTC-AAAA
38214 TGCTCAAATAAGGGCC
1 TGCTCAAATAAGGGCC
38230 CGATCTTTAA
Statistics
Matches: 62, Mismatches: 8, Indels: 14
0.74 0.10 0.17
Matches are distributed among these distances:
29 9 0.15
30 14 0.23
31 30 0.48
32 9 0.15
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAACGTTTTCAAAA
Found at i:38225 original size:61 final size:60
Alignment explanation
Indices: 38126--38259 Score: 223
Period size: 61 Copynumber: 2.2 Consensus size: 60
38116 AACAATTGCT
** *
38126 CAAATAAGGGCCTAACGTTTTCCAAAATGCTCAAATAAGGGCTTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTTCCAAAATGCTCAAATAAGGGCCCGATCTTTAAATTTGGC
*
38186 CAAATTAAGGGCCTAACGTTTTCTAAAATGCTCAAATAAGGGCCCGATCTTTAAATTTGGC
1 CAAA-TAAGGGCCTAACGTTTTCCAAAATGCTCAAATAAGGGCCCGATCTTTAAATTTGGC
38247 CAAATAAGGGCCT
1 CAAATAAGGGCCT
38260 GGCGTCGAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
60 13 0.19
61 56 0.81
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTTCCAAAATGCTCAAATAAGGGCCCGATCTTTAAATTTGGC
Found at i:38251 original size:29 final size:29
Alignment explanation
Indices: 38157--38258 Score: 84
Period size: 29 Copynumber: 3.4 Consensus size: 29
38147 CCAAAATGCT
** *
38157 CAAATAAGGGCTTGATCTTTTAATTTGGC
1 CAAATAAGGGCCCGATCTTTAAATTTGGC
* *
38186 CAAATTAAGGGCCTAACG-TTTTCTAAA-AT-GC
1 CAAA-TAAGGGCC---CGATCTT-TAAATTTGGC
38217 TCAAATAAGGGCCCGATCTTTAAATTTGGC
1 -CAAATAAGGGCCCGATCTTTAAATTTGGC
38247 CAAATAAGGGCC
1 CAAATAAGGGCC
38259 TGGCGTCGAA
Statistics
Matches: 57, Mismatches: 7, Indels: 18
0.70 0.09 0.22
Matches are distributed among these distances:
28 6 0.11
29 20 0.35
30 9 0.16
31 10 0.18
32 8 0.14
33 4 0.07
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (29 bp):
CAAATAAGGGCCCGATCTTTAAATTTGGC
Found at i:38378 original size:60 final size:60
Alignment explanation
Indices: 38300--38462 Score: 229
Period size: 60 Copynumber: 2.7 Consensus size: 60
38290 CTGATGCCAC
* *
38300 GCCCTTATTTGAGTATTTTCGATAACATTAGGCCCTTATTTGACCAAATTTAAAGATCGG
1 GCCCTTATTTGAGCATTTTCGATAACATTAGGCCCTTATTTGACCAAATTAAAAGATCGG
* * * *
38360 GCCCTTATTTTAGCATTTTCGATAACAATAGGCCTTTATTTGGCCAAATTAAAAGATCGG
1 GCCCTTATTTGAGCATTTTCGATAACATTAGGCCCTTATTTGACCAAATTAAAAGATCGG
* **
38420 GCCCTTATTTGAGCATTTTGGCA-AATGTTAGGCCCTTATTTGA
1 GCCCTTATTTGAGCATTTTCG-ATAACATTAGGCCCTTATTTGA
38463 GCAATTATCC
Statistics
Matches: 89, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
60 88 0.99
61 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (60 bp):
GCCCTTATTTGAGCATTTTCGATAACATTAGGCCCTTATTTGACCAAATTAAAAGATCGG
Found at i:38427 original size:29 final size:29
Alignment explanation
Indices: 38330--38430 Score: 73
Period size: 29 Copynumber: 3.4 Consensus size: 29
38320 GATAACATTA
* *
38330 GGCCCTTATTTGACCAAATTTAAAGATCG
1 GGCCCTTATTTGGCCAAATTAAAAGATCG
* ** *
38359 GGCCCTTATTTTAG-CATTTTCGATAACA-AT-A
1 GGCCCTTA-TTTGGCCAAATT--A-AA-AGATCG
*
38390 GGCCTTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGGCCAAATTAAAAGATCG
38419 GGCCCTTATTTG
1 GGCCCTTATTTG
38431 AGCATTTTGG
Statistics
Matches: 52, Mismatches: 12, Indels: 16
0.65 0.15 0.20
Matches are distributed among these distances:
27 1 0.02
28 4 0.08
29 24 0.46
30 7 0.13
31 11 0.21
32 4 0.08
33 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.35
Consensus pattern (29 bp):
GGCCCTTATTTGGCCAAATTAAAAGATCG
Found at i:48552 original size:27 final size:27
Alignment explanation
Indices: 48485--48578 Score: 100
Period size: 27 Copynumber: 3.4 Consensus size: 27
48475 AGTGGACATA
*
48485 AAATGACCAAAATGCCCCCT-GAATGTGC
1 AAATGACCAAAATG-CCCCTAG-GTGTGC
* * *
48513 AAATTACCGAAATGCCACTAGGTGTGC
1 AAATGACCAAAATGCCCCTAGGTGTGC
**
48540 AAATGACCAAAATGCCCCTAGGCATGC
1 AAATGACCAAAATGCCCCTAGGTGTGC
*
48567 ATATGACCAAAA
1 AAATGACCAAAA
48579 GAAGTAAATT
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
27 42 0.76
28 13 0.24
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTAGGTGTGC
Found at i:52630 original size:18 final size:19
Alignment explanation
Indices: 52591--52630 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
52581 GTGCTCCCGT
52591 TGTGATGCTCCCACTTTTCAA
1 TGTGATGCTCCCA--TTTCAA
52612 TGTGATGCTCCCA-TTCAA
1 TGTGATGCTCCCATTTCAA
52630 T
1 T
52631 TCTGACCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
21 13 0.68
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.38
Consensus pattern (19 bp):
TGTGATGCTCCCATTTCAA
Found at i:52864 original size:24 final size:24
Alignment explanation
Indices: 52835--52883 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
52825 TTTTTTATTT
52835 TTTATTCTCTTCTTCTCCGTTTTC
1 TTTATTCTCTTCTTCTCCGTTTTC
52859 TTTATTCTCTTCTTCTCCGTTTTC
1 TTTATTCTCTTCTTCTCCGTTTTC
52883 T
1 T
52884 GCTTCGTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.04, C:0.29, G:0.04, T:0.63
Consensus pattern (24 bp):
TTTATTCTCTTCTTCTCCGTTTTC
Found at i:53054 original size:15 final size:15
Alignment explanation
Indices: 53034--53062 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
53024 GCTCAAATGT
53034 TTGGGCAAATCGTTG
1 TTGGGCAAATCGTTG
53049 TTGGGCAAATCGTT
1 TTGGGCAAATCGTT
53063 TTTTCTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.31, T:0.34
Consensus pattern (15 bp):
TTGGGCAAATCGTTG
Found at i:53302 original size:20 final size:20
Alignment explanation
Indices: 53279--53316 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
53269 AGTTTTGTTA
53279 TAATGTTGCT-AAATTGCTGT
1 TAAT-TTGCTAAAATTGCTGT
53299 TAATTTGCTAAAATTGCT
1 TAATTTGCTAAAATTGCT
53317 TGCTGTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.45
Consensus pattern (20 bp):
TAATTTGCTAAAATTGCTGT
Found at i:54106 original size:13 final size:15
Alignment explanation
Indices: 54079--54110 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
54069 GTCTTCTCCT
54079 TTTTTTCCTTCTTTC
1 TTTTTTCCTTCTTTC
54094 TTTTTT-CTT-TTTC
1 TTTTTTCCTTCTTTC
54107 TTTT
1 TTTT
54111 CTTTTGGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 3 0.18
15 6 0.35
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTTCCTTCTTTC
Done.