Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013387.1 Corchorus olitorius cultivar O-4 contig13420, 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: 43473
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Found at i:1440 original size:24 final size:24
Alignment explanation
Indices: 1405--1464 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
1395 AATAGAAACA
1405 ACCACATAGTGGTCGTGAGATTCG
1 ACCACATAGTGGTCGTGAGATTCG
* * *
1429 GCCACATGGTGGTCGTGGGATTCG
1 ACCACATAGTGGTCGTGAGATTCG
1453 ACCACATAGTGG
1 ACCACATAGTGG
1465 CCGTTAGAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.22, C:0.22, G:0.33, T:0.23
Consensus pattern (24 bp):
ACCACATAGTGGTCGTGAGATTCG
Found at i:5006 original size:3 final size:3
Alignment explanation
Indices: 5000--5038 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
4990 ATCTTTTTTT
5000 TTA TTA TTA TTA -TA TATA TTA TTA TTA TTA -TA TTA TTA T
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA T
5039 ACCCTCTTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.12
3 26 0.79
4 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:5023 original size:18 final size:17
Alignment explanation
Indices: 5000--5038 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 17
4990 ATCTTTTTTT
5000 TTATTATTATTATATATA
1 TTATTATTATTATAT-TA
5018 TTATTATTATTATATTA
1 TTATTATTATTATATTA
5035 TTAT
1 TTAT
5039 ACCCTCTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATTATTATTATATTA
Found at i:8683 original size:13 final size:13
Alignment explanation
Indices: 8665--8689 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8655 ATTCTCTCTC
8665 TCTTTTTTTTTTA
1 TCTTTTTTTTTTA
8678 TCTTTTTTTTTT
1 TCTTTTTTTTTT
8690 GTTCTAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.08, G:0.00, T:0.88
Consensus pattern (13 bp):
TCTTTTTTTTTTA
Found at i:10125 original size:436 final size:436
Alignment explanation
Indices: 9166--10098 Score: 1053
Period size: 436 Copynumber: 2.1 Consensus size: 436
9156 AACGCTTTAG
* * ** * * * * * *
9166 CTTTTTTTTTTTTTTCTATTTGTCTGATTAAGGTGATTCA-AGTGTCTATTAAAAGGTAATTTCA
1 CTTTATTTTTTTGTTCTATTTGTCCAATGAAGGTAATTCAGA-AGTCGATCAAAAGCTAATTTCA
* ** * * * ** * *
9230 TGAT-TTACAACTTTCATGAAGGACTTAAAAGTCAATTTTTATGTTTCAATTCAA-AAAAATACT
65 TGATCTCA-AACTTTCATGAAAAACTCAAAAGCCAACTTTTACATTTCAATTCAAGAAAACTGCT
*** * * * * *
9293 TTTGAAATTTGGTGATTTTGATTGCCAATTTATTTAATATCATATAATTTTCGATCAACATGTCT
129 TCCCAAATTTAGTGATTTTGATTGCCAATCTATTTAATACCATATAATTTTAGATCAACATGTCC
* * * *
9358 GATTAATGTTTCTTAAGTGTCAGTTAAAAGGTTATTGCATGATCTACGACTTTCATGAAGGACCC
194 AATTAAAGTTTCTTAAGTGTCAGCTAAAAGGTTATTACATGATCTACGACTTTCATGAAGGACCC
* * * * * *
9423 AAAAGCTAAATTTGATTTACGAGTTTCATTAAGCGTTCAAATGGAATTTTTATGTTTCAAGATCT
259 AAAAGCTAAATTTGATGTACAAGTTTCATGAAGCGTTCAAAGGGAATTTTGATGGTTCAAGATCT
* * * *
9488 TCATCAACAAACAATTTTTTTTATTTTGAGTATTTATGAAATGACCCTCATATTTTTCTACTTTA
324 TCATCAACAAACAATTTTTCTTATTTGGAGTATTTATCAAACGACCCTCATATTTTTCTACTTTA
* *
9553 TACTACTTAGTCCTTTACTAATTCTATCTTAATCGTTTTAAAGCGTAA
389 TACTACTTAGTCCTTTACAAATTCTATCTTAATCGATTTAAAGCGTAA
* * * * *
9601 CCTTTATTTTTTTGTTCTATTTGTCCGATGAAGGTGATTCAGATGTCGATTAAAAGGTAATTTCA
1 -CTTTATTTTTTTGTTCTATTTGTCCAATGAAGGTAATTCAGAAGTCGATCAAAAGCTAATTTCA
9666 TGATCTCAAACTTTCATGAAAAACTCAAAAGCCAACTTTTACATTTCAATTCAAGAAAACTGCTT
65 TGATCTCAAACTTTCATGAAAAACTCAAAAGCCAACTTTTACATTTCAATTCAAGAAAACTGCTT
* * *
9731 CCCAAATTTAGTGGTTTTGATTGCC-GTCTATTTAATACCATATAATTTTAGATCCACATGTCCA
130 CCCAAATTTAGTGATTTTGATTGCCAATCTATTTAATACCATATAATTTTAGATCAACATGTCCA
* * * *
9795 ATTAAAGTTAT-TTAAGTGTCGGCTAAAAGGTTATTACGTGATCTATGACTTTCATGAAGTACCC
195 ATTAAAGTT-TCTTAAGTGTCAGCTAAAAGGTTATTACATGATCTACGACTTTCATGAAGGACCC
* *
9859 GAAAGCTAAATTTGATGTACAAGTTTCATGAAG-GTTCAAAAGGGAATTTTGATGGTTGAAGATC
259 AAAAGCTAAATTTGATGTACAAGTTTCATGAAGCGTTC-AAAGGGAATTTTGATGGTTCAAGATC
*
9923 -TCTATCAACAAAC-A-TTTTCTTATTTGGATTATTTATCAAACGACCCTCATATATACTTTTCT
323 TTC-ATCAACAAACAATTTTTCTTATTTGGAGTATTTATCAAACGACCCTC--ATAT--TTTTCT
* * * *
9985 ACTTTATACTATTTAGTCCTTTACAAATTCTATTTTACTCGATTTAAAGCTTCAA
383 ACTTTATACTACTTAGTCCTTTACAAATTCTATCTTAATCGATTTAAAGCGT-AA
* * *
10040 -TTTTTTTGTCTTTGTTCTATTTGTCCAATTATGGTAATTCATGAAG-C-ACTCAAAAGCTA
1 CTTTATTT-T-TTTGTTCTATTTGTCCAATGAAGGTAATTCA-GAAGTCGA-TCAAAAGCTA
10099 TTTTTTATGT
Statistics
Matches: 421, Mismatches: 61, Indels: 27
0.83 0.12 0.05
Matches are distributed among these distances:
434 29 0.07
435 7 0.02
436 252 0.60
437 38 0.09
438 54 0.13
439 38 0.09
440 3 0.01
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (436 bp):
CTTTATTTTTTTGTTCTATTTGTCCAATGAAGGTAATTCAGAAGTCGATCAAAAGCTAATTTCAT
GATCTCAAACTTTCATGAAAAACTCAAAAGCCAACTTTTACATTTCAATTCAAGAAAACTGCTTC
CCAAATTTAGTGATTTTGATTGCCAATCTATTTAATACCATATAATTTTAGATCAACATGTCCAA
TTAAAGTTTCTTAAGTGTCAGCTAAAAGGTTATTACATGATCTACGACTTTCATGAAGGACCCAA
AAGCTAAATTTGATGTACAAGTTTCATGAAGCGTTCAAAGGGAATTTTGATGGTTCAAGATCTTC
ATCAACAAACAATTTTTCTTATTTGGAGTATTTATCAAACGACCCTCATATTTTTCTACTTTATA
CTACTTAGTCCTTTACAAATTCTATCTTAATCGATTTAAAGCGTAA
Found at i:19114 original size:22 final size:22
Alignment explanation
Indices: 19072--19114 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
19062 TTTTTCTGTT
* *
19072 TTTTGTTTTTGTTTCGTTGTCG
1 TTTTGTTTTTGTTGCGCTGTCG
19094 TTTTGTTTTTGTTGCGCTGTC
1 TTTTGTTTTTGTTGCGCTGTC
19115 AATTTTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.23, T:0.65
Consensus pattern (22 bp):
TTTTGTTTTTGTTGCGCTGTCG
Found at i:21335 original size:19 final size:19
Alignment explanation
Indices: 21285--21335 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
21275 GTGGGATTTT
21285 TTAATAA-TAATTATTTAA
1 TTAATAATTAATTATTTAA
* *
21303 TAAAATGATT-ATTATTTAA
1 T-TAATAATTAATTATTTAA
21322 TTAATAATTAATTA
1 TTAATAATTAATTA
21336 ATTTCAGCCC
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
18 7 0.27
19 18 0.69
20 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
TTAATAATTAATTATTTAA
Found at i:21706 original size:13 final size:13
Alignment explanation
Indices: 21688--21713 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21678 AAGGTAACAA
21688 CAAAAATCATCAC
1 CAAAAATCATCAC
21701 CAAAAATCATCAC
1 CAAAAATCATCAC
21714 TCATGCCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (13 bp):
CAAAAATCATCAC
Found at i:28663 original size:73 final size:73
Alignment explanation
Indices: 28573--28722 Score: 264
Period size: 73 Copynumber: 2.1 Consensus size: 73
28563 CCCTTTTTTC
28573 CCCCCTAAATTATGAAAATCCACTGAAAAAGTCCTATAACGGCGTTTAGTAATAATGAACGCCGT
1 CCCCCTAAATTATGAAAATCCACTGAAAAAGTCCTATAACGGCGTTTAGTAATAATGAACGCCGT
28638 TATAGGTT
66 TATAGGTT
* * * *
28646 CCCCCTAAATTGTGAAAATCCACTGAAAAAGTCCTATAACGGCGTTTATTAGTAATGAACGTCGT
1 CCCCCTAAATTATGAAAATCCACTGAAAAAGTCCTATAACGGCGTTTAGTAATAATGAACGCCGT
28711 TATAGGTT
66 TATAGGTT
28719 CCCC
1 CCCC
28723 ACGTAACATA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (73 bp):
CCCCCTAAATTATGAAAATCCACTGAAAAAGTCCTATAACGGCGTTTAGTAATAATGAACGCCGT
TATAGGTT
Found at i:31046 original size:28 final size:27
Alignment explanation
Indices: 31006--31183 Score: 152
Period size: 26 Copynumber: 6.4 Consensus size: 27
30996 TGGTAAGTAA
*
31006 AAACTGTTCCTGTTTTGTAAGTTGCTGC
1 AAACTGTT-TTGTTTTGTAAGTTGCTGC
31034 AAACTGTTTCTGTTTTTGTAAGTTGCTGC
1 AAACTGTTT-TG-TTTTGTAAGTTGCTGC
* *
31063 AACAAATG-TTTGTTTTGTTACAATT--TGC
1 -A-AACTGTTTTGTTTTG-TA-AGTTGCTGC
*
31091 AAACTGTTTT-TTTTGTATGTTGCTGC
1 AAACTGTTTTGTTTTGTAAGTTGCTGC
* ** *
31117 AAACTGTGTTTGTTTTGTTA--CACTAC
1 AAACTGT-TTTGTTTTGTAAGTTGCTGC
31143 AAACTGTTTTTGTTTTGTAAGTTGCTGC
1 AAACTG-TTTTGTTTTGTAAGTTGCTGC
31171 AAACTGTGTTTGT
1 AAACTGT-TTTGT
31184 ACATTGTCTG
Statistics
Matches: 120, Mismatches: 15, Indels: 30
0.73 0.09 0.18
Matches are distributed among these distances:
24 2 0.02
25 2 0.02
26 39 0.32
27 9 0.08
28 38 0.32
29 20 0.17
30 6 0.05
31 4 0.03
ACGTcount: A:0.20, C:0.13, G:0.19, T:0.48
Consensus pattern (27 bp):
AAACTGTTTTGTTTTGTAAGTTGCTGC
Found at i:31127 original size:54 final size:53
Alignment explanation
Indices: 31030--31183 Score: 195
Period size: 54 Copynumber: 2.8 Consensus size: 53
31020 TTGTAAGTTG
**
31030 CTGCAAACTGTTTCTGTTTTTGTAAGTTGCTGC-AACAAATGTTTGTTTTGTTACAA
1 CTGCAAACTGTTT-T-TTTTTGTAAGTTGCTGCAAAC-TGTGTTTGTTTTGTTAC-A
* *
31086 TTTGCAAACTG-TTTTTTTTGTATGTTGCTGCAAACTGTGTTTGTTTTGTTACA
1 -CTGCAAACTGTTTTTTTTTGTAAGTTGCTGCAAACTGTGTTTGTTTTGTTACA
*
31139 CTACAAACTGTTTTTGTTTTGTAAGTTGCTGCAAACTGTGTTTGT
1 CTGCAAACTGTTTTT-TTTTGTAAGTTGCTGCAAACTGTGTTTGT
31184 ACATTGTCTG
Statistics
Matches: 87, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
52 8 0.09
53 5 0.06
54 59 0.68
55 4 0.05
56 2 0.02
57 9 0.10
ACGTcount: A:0.20, C:0.13, G:0.19, T:0.48
Consensus pattern (53 bp):
CTGCAAACTGTTTTTTTTTGTAAGTTGCTGCAAACTGTGTTTGTTTTGTTACA
Found at i:31216 original size:13 final size:13
Alignment explanation
Indices: 31198--31226 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
31188 TGTCTGCAAA
31198 CTGCAAACTGTTT
1 CTGCAAACTGTTT
31211 CTGCAAACTGTTT
1 CTGCAAACTGTTT
31224 CTG
1 CTG
31227 TTTCTGTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (13 bp):
CTGCAAACTGTTT
Found at i:40252 original size:19 final size:19
Alignment explanation
Indices: 40202--40252 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
40192 TGTGGGATTT
40202 TTAATAA-TAATTATTCAA
1 TTAATAATTAATTATTCAA
* * *
40220 TAAAATGATT-ATTATTTAA
1 T-TAATAATTAATTATTCAA
40239 TTAATAATTAATTA
1 TTAATAATTAATTA
40253 ATTTCAGCCC
Statistics
Matches: 25, Mismatches: 5, Indels: 5
0.71 0.14 0.14
Matches are distributed among these distances:
18 7 0.28
19 17 0.68
20 1 0.04
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (19 bp):
TTAATAATTAATTATTCAA
Found at i:42933 original size:16 final size:17
Alignment explanation
Indices: 42912--42943 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
42902 GAGATTGCGT
42912 TTTATTTTTCT-TTTTC
1 TTTATTTTTCTATTTTC
42928 TTTATTTTTCTATTTT
1 TTTATTTTTCTATTTT
42944 AATTTGCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTATTTTTCTATTTTC
Done.