Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021539.1 Corchorus olitorius cultivar O-4 contig21572, 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: 20744
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:270 original size:30 final size:30
Alignment explanation
Indices: 234--294 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
224 TTAGTAAGAT
234 ATTAAAATTTGAGGGTATAAGAGGAAAGTC
1 ATTAAAATTTGAGGGTATAAGAGGAAAGTC
264 ATTAAAATTTGAGGGTATAAGAGGAAAGTC
1 ATTAAAATTTGAGGGTATAAGAGGAAAGTC
294 A
1 A
295 AGATAAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.44, C:0.03, G:0.26, T:0.26
Consensus pattern (30 bp):
ATTAAAATTTGAGGGTATAAGAGGAAAGTC
Found at i:1271 original size:269 final size:269
Alignment explanation
Indices: 464--1271 Score: 1451
Period size: 269 Copynumber: 3.0 Consensus size: 269
454 CAAACGCAAC
* * *
464 TGTATTTTATTTTCTGTGTTTATCTACTTATATTATGGTCTACAATCTACATGTTGTTTTTTCTT
1 TGTATTTTATTTT-TGTGTTTATCTACTTATGTTATGGTCTACAATCTACTTGCTGTTTTTTCTT
* * *
529 TTAGTTTTTACCATTTTTCATCTATTTGAGGAATCAATACCAAAAAAGAATCTTAATAAAATACA
65 TTAGTTTTTATCATTTGTCATCTATTTGAGGAATCAATA-CAAAAAAAAATCTTAATAAAATACA
594 ATAACTCTATAACCTCACTAAAAGTCTACTGTGGCCATGATTTGCAAGAATTAGGAATAAAATGC
129 ATAACTCTATAACCTCACTAAAAGTCTACTGTGGCCATGATTTGCAAGAATTAGGAATAAAATGC
*
659 AAACCAAGGAAAAGGTAAGGCAAAAAAAGAACTAGGCCAAAATTGCTTACCCAGCCAAGATTAAA
194 AAACCAAGGAAAAGGTAAGGCAAAAAAAGAACTAGGCCAAAATTGCTTACCCAGCCAAGATTGAA
724 GTTTTGCCTAT
259 GTTTTGCCTAT
735 TGTATTTTATTTTTGTGTTTATCTACTTATGTTATGGTCTACAATCTACTTGCTGTTTTTTCTTT
1 TGTATTTTATTTTTGTGTTTATCTACTTATGTTATGGTCTACAATCTACTTGCTGTTTTTTCTTT
* * *
800 TAGTATTTATCATTTGTCATCTATTTGAGGAACCAATACAAAAAAAAAAAATCTTAATAAAATGC
66 TAGTTTTTATCATTTGTCATCTATTTGAGGAATCAATAC---AAAAAAAAATCTTAATAAAATAC
865 AATAACTCTATAACCTCACTAAAAGTCTACTGTGGCCATGATTTGCAAGAATTAGGAATAAAATG
128 AATAACTCTATAACCTCACTAAAAGTCTACTGTGGCCATGATTTGCAAGAATTAGGAATAAAATG
930 CAAACCAAGGAAAA-GTAAGGCAAAAAAAGAACTAGGCCAAAATTGCTTACCCAGCCAAGATTGA
193 CAAACCAAGGAAAAGGTAAGGCAAAAAAAGAACTAGGCCAAAATTGCTTACCCAGCCAAGATTGA
994 AG--TTGCCTAT
258 AGTTTTGCCTAT
*
1004 TGTATTTTATTTTTATGTTTATCTACTTATGTTATGGTCTACAATCTACTTGCTGTTTTTTCTTT
1 TGTATTTTATTTTTGTGTTTATCTACTTATGTTATGGTCTACAATCTACTTGCTGTTTTTTCTTT
1069 TAGTTTTTATCATTTGTCATCTATTTGAGGAATCAATACAAAAAAAAATCTTAATAAAATACAAT
66 TAGTTTTTATCATTTGTCATCTATTTGAGGAATCAATACAAAAAAAAATCTTAATAAAATACAAT
1134 AACTCTATAACCTCACTAAAAGTCTACTGTGGCCATGATTTGCAAGAATTAGGAATAAAATGCAA
131 AACTCTATAACCTCACTAAAAGTCTACTGTGGCCATGATTTGCAAGAATTAGGAATAAAATGCAA
1199 ACCAAGGAAAAGGTAAGGCAAAAAAAGAACTAGGCCAAAATTGCTTACCCAGCCAAGATTGAAGT
196 ACCAAGGAAAAGGTAAGGCAAAAAAAGAACTAGGCCAAAATTGCTTACCCAGCCAAGATTGAAGT
1264 TTTGCCTA
261 TTTGCCTA
1272 GGTTATGTTT
Statistics
Matches: 517, Mismatches: 14, Indels: 14
0.95 0.03 0.03
Matches are distributed among these distances:
266 101 0.20
267 52 0.10
269 117 0.23
270 83 0.16
271 64 0.12
272 100 0.19
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (269 bp):
TGTATTTTATTTTTGTGTTTATCTACTTATGTTATGGTCTACAATCTACTTGCTGTTTTTTCTTT
TAGTTTTTATCATTTGTCATCTATTTGAGGAATCAATACAAAAAAAAATCTTAATAAAATACAAT
AACTCTATAACCTCACTAAAAGTCTACTGTGGCCATGATTTGCAAGAATTAGGAATAAAATGCAA
ACCAAGGAAAAGGTAAGGCAAAAAAAGAACTAGGCCAAAATTGCTTACCCAGCCAAGATTGAAGT
TTTGCCTAT
Found at i:1535 original size:30 final size:30
Alignment explanation
Indices: 1499--1555 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
1489 TTAGTAAGAT
1499 ATTAAAATTTGAGGGTATAAGAGGAAAGTC
1 ATTAAAATTTGAGGGTATAAGAGGAAAGTC
1529 ATTAAAATTTGAGGGTATAAGAGGAAA
1 ATTAAAATTTGAGGGTATAAGAGGAAA
1556 TTCAAGATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.46, C:0.02, G:0.26, T:0.26
Consensus pattern (30 bp):
ATTAAAATTTGAGGGTATAAGAGGAAAGTC
Found at i:6542 original size:18 final size:18
Alignment explanation
Indices: 6505--6551 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
6495 GGCCGAAAAT
*
6505 TAATAATTATTTATTAAA
1 TAATAATTATTTATCAAA
6523 TAATAATTATTT-TCAGAA
1 TAATAATTATTTATCA-AA
*
6541 TAATTATTATT
1 TAATAATTATT
6552 AAAATTCCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 2 0.08
18 24 0.92
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (18 bp):
TAATAATTATTTATCAAA
Found at i:7981 original size:51 final size:51
Alignment explanation
Indices: 7879--7981 Score: 120
Period size: 51 Copynumber: 2.0 Consensus size: 51
7869 CGTTCTTAAA
* * * **
7879 TATTTCCTTGTTTCAATCTTGTCTCCGGACAAAAGAACACTCTTTTAGTGT
1 TATTTCCTTGCTCCAATCTTGTCTCCGGACAAAAGAACACTCGTACAGTGT
*
7930 TATTTCCTTGCTCCAATCTTGTCTCCGGACATGAA-AACACT-GTACACGTGT
1 TATTTCCTTGCTCCAATCTTGTCTCCGGACA-AAAGAACACTCGTACA-GTGT
7981 T
1 T
7982 TCTCTCTCAG
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
50 2 0.05
51 40 0.91
52 2 0.05
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.38
Consensus pattern (51 bp):
TATTTCCTTGCTCCAATCTTGTCTCCGGACAAAAGAACACTCGTACAGTGT
Found at i:10730 original size:6 final size:6
Alignment explanation
Indices: 10719--10754 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
10709 GAACTATAAT
10719 TATCTA TATCTA TA--TA TATCTA TATCTA TA-CTA TAT
1 TATCTA TATCTA TATCTA TATCTA TATCTA TATCTA TAT
10755 ATAAAAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
4 4 0.15
5 5 0.19
6 18 0.67
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (6 bp):
TATCTA
Found at i:10736 original size:10 final size:10
Alignment explanation
Indices: 10723--10757 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
10713 TATAATTATC
10723 TATATCTATA
1 TATATCTATA
10733 TATATCTATA
1 TATATCTATA
*
10743 TCTATACTATA
1 TATAT-CTATA
10754 TATA
1 TATA
10758 AAAAAAGTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 14 0.64
11 8 0.36
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (10 bp):
TATATCTATA
Found at i:10738 original size:16 final size:17
Alignment explanation
Indices: 10719--10754 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
10709 GAACTATAAT
10719 TATCTATATCTATA-TA
1 TATCTATATCTATACTA
10735 TATCTATATCTATACTA
1 TATCTATATCTATACTA
10752 TAT
1 TAT
10755 ATAAAAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (17 bp):
TATCTATATCTATACTA
Found at i:11586 original size:20 final size:23
Alignment explanation
Indices: 11563--11639 Score: 74
Period size: 25 Copynumber: 3.5 Consensus size: 23
11553 AGGAGTACCA
*
11563 AAATTTGATAGAAG-G-TTATC-
1 AAATTTCATAGAAGTGATTATCG
11583 AAATTTCATAG-AGTGATTATCG
1 AAATTTCATAGAAGTGATTATCG
* *
11605 AAATTTCATAGAAATCGGATTATCA
1 AAATTTCATAGAAGT--GATTATCG
11630 AAATTT-ATAG
1 AAATTTCATAG
11640 GAAGATAATC
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
19 2 0.04
20 11 0.23
21 5 0.10
22 11 0.23
23 2 0.04
24 4 0.08
25 13 0.27
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.35
Consensus pattern (23 bp):
AAATTTCATAGAAGTGATTATCG
Found at i:11633 original size:25 final size:21
Alignment explanation
Indices: 11563--11661 Score: 78
Period size: 21 Copynumber: 4.5 Consensus size: 21
11553 AGGAGTACCA
* *
11563 AAATTTGATAGAA-GGTTATC
1 AAATTTCATAGAATGATTATC
*
11583 AAATTTCATAGAGTGATTATC
1 AAATTTCATAGAATGATTATC
11604 GAAATTTCATAGAAATCGGATTATC
1 -AAATTTCATAG-AAT--GATTATC
*
11629 AAAATTT-ATAGGAA-GATAATC
1 -AAATTTCATA-GAATGATTATC
11650 AAAGTTTCATAG
1 AAA-TTTCATAG
11662 TGTTGTTATC
Statistics
Matches: 65, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
20 14 0.22
21 16 0.25
22 14 0.22
23 2 0.03
24 5 0.08
25 14 0.22
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.33
Consensus pattern (21 bp):
AAATTTCATAGAATGATTATC
Found at i:11740 original size:22 final size:22
Alignment explanation
Indices: 11715--11770 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
11705 ATGTGATTAT
11715 CAAAATTTCATAGAG-GGCTCAA
1 CAAAATTTCATAGAGAGG-TCAA
* * * *
11737 CAAACTTTTATAGAGAGGTTAT
1 CAAAATTTCATAGAGAGGTCAA
11759 CAAAATTTCATA
1 CAAAATTTCATA
11771 AAAAAGTTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
22 25 0.93
23 2 0.07
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (22 bp):
CAAAATTTCATAGAGAGGTCAA
Found at i:12115 original size:23 final size:22
Alignment explanation
Indices: 11896--12367 Score: 263
Period size: 22 Copynumber: 21.6 Consensus size: 22
11886 TTATGGAGTA
* *
11896 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
**
11918 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG-GGAGGTT
* *
11940 TTCAAAATTTCATA-AGAGGGTT
1 ATCAAAATTTCATAGGGA-GGTT
** * *
11962 ATCAAAATTTCATA-ATATGTAG
1 ATCAAAATTTCATAGGGAGGT-T
*
11984 ATC-AAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGGGAGGTT
* ***
12005 AACAAAATTTCATAATAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
**
12027 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
12049 ATCAAAATTT-AT----A-GTT
1 ATCAAAATTTCATAGGGAGGTT
* *
12065 ATCAAGATTTCATAAGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
*
12087 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
* *
12110 ATCAAAATTTTATAGGAAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
*
12133 ATCAAAATTTCATAGCGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
12155 ATCACAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
*
12177 ATCAAAATTT--TAGGGTGTGATT
1 ATCAAAATTTCATAGGGAG-G-TT
**
12199 AAT-AACAA-TTCATATAGAGGTT
1 -ATCAA-AATTTCATAGGGAGGTT
* * * ***
12221 TTTAAATTTTCA-AAACATGGTT
1 ATCAAAATTTCATAGGGA-GGTT
* * *
12243 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * **
12265 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAG-GGAGGTT
* ***
12288 ATCAAAATTTCATTGGGAAACT
1 ATCAAAATTTCATAGGGAGGTT
* *
12310 ATTAAAATTTCATAGTGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
12332 TTCAAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
*
12354 AACAAAATTTCATA
1 ATCAAAATTTCATA
12368 AGAAGGTCAA
Statistics
Matches: 340, Mismatches: 86, Indels: 48
0.72 0.18 0.10
Matches are distributed among these distances:
16 12 0.04
17 3 0.01
20 7 0.02
21 22 0.06
22 226 0.66
23 66 0.19
24 4 0.01
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:12338 original size:22 final size:22
Alignment explanation
Indices: 12313--12385 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
12303 GGAAACTATT
* **
12313 AAAATTTCATAGTGAGGTTTTC
1 AAAATTTCATAGGGAGGTTAAC
* *
12335 AAAATTCCTTAGGGAGGTTAAC
1 AAAATTTCATAGGGAGGTTAAC
* * * *
12357 AAAATTTCATAAGAAGGTCAAA
1 AAAATTTCATAGGGAGGTTAAC
12379 AAAATTT
1 AAAATTT
12386 ATAAAAAGAT
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (22 bp):
AAAATTTCATAGGGAGGTTAAC
Found at i:13395 original size:339 final size:344
Alignment explanation
Indices: 12748--13423 Score: 925
Period size: 339 Copynumber: 2.0 Consensus size: 344
12738 TTCAAAACAT
**
12748 TCTCCAAGTTGGTTTAGGAGAAGATCAATTCTGTCCAGAAATTTCAAGGGCAAAATCGTCCATCG
1 TCTCCAAGCCGGTTTAGGAGAAGATCAATTCTGTCCAGAAATTTCAAGGGCAAAATCGTCCA-C-
* * * **
12813 GAACTGCAGAATCAGGTCTTGAGGTAAACATAAAAGTTGTAGATCTTGGAATCCTCTTTCCAATG
64 GAACT-----ATCAGGTCTCGAGATAAACATAAAAGTTGTAGATCTTGGAATCCTCTATCCAACA
* * * * * * *
12878 GCACCTCATTTGTATTTTTTTGAGCTCTAGATCAAAAGTTATGAATTTTCTTCCAAAATTACTCT
124 GCACCTCATTTGCATTTTTTTGACCTCCAGATAAAAAATTATGAATTTTCTTCAAAAACTACTCT
* * * *
12943 TGTGAAGTCCTCTTTTGAATAGGATTTAACAATGCTGCATTAGGGTGGAATCATTACTGCATCAT
189 TGTGAAGTCCTCCTTCGAATAGGATTTAACAATGCTGCATCAGGCTGGAATCATTACTGCATCAT
* * * * * *
13008 AATTACTGATTGGACTTGAAATCCTTCTTTGAGCTTTCATATTAACGAATTGGGTTTAAGAATAT
254 AATTACTAATTGGACTTGAAATCCTTCTTTGAGCTTCCATAGTAACGAAGTGGGTCTAAAAATAT
13073 CAGATTTAGACTTCAAGACATCTGGC
319 CAGATTTAGACTTCAAGACATCTGGC
* *
13099 TCTCCAAGCCGGTTTAGGAGAATATCAATTCTGTCCAGAAATTTTAAGGGCAAAATCGT-CA-GA
1 TCTCCAAGCCGGTTTAGGAGAAGATCAATTCTGTCCAGAAATTTCAAGGGCAAAATCGTCCACGA
* *
13162 A-T-T-AGGTCTCGAGATAAACATAAAAGTTGTAGATCTTGGAATCCTCTATCCAACAGTACCTG
66 ACTATCAGGTCTCGAGATAAACATAAAAGTTGTAGATCTTGGAATCCTCTATCCAACAGCACCTC
* *
13224 ATTTGCATTTTTTTGACCTCCGGATAAAAAATTATGAATTTTCTTCAAAAACTACTGTTGTGAAG
131 ATTTGCATTTTTTTGACCTCCAGATAAAAAATTATGAATTTTCTTCAAAAACTACTCTTGTGAAG
*
13289 TCCTCCTTCGAATAGGATTTAACAATGTTGCATCAGAGCT-GAATCATTACTGCATCATAATTAC
196 TCCTCCTTCGAATAGGATTTAACAATGCTGCATCAG-GCTGGAATCATTACTGCATCATAATTAC
* *
13353 TAATTGGACTT-AGACTCCTTCTTTGGGCTTCCATAGTAACGAAGTGGGTCTAAAAATATCAGAT
260 TAATTGGACTTGA-AATCCTTCTTTGAGCTTCCATAGTAACGAAGTGGGTCTAAAAATATCAGAT
13417 TTAGACT
324 TTAGACT
13424 CATCTGGCTT
Statistics
Matches: 290, Mismatches: 33, Indels: 16
0.86 0.10 0.05
Matches are distributed among these distances:
338 1 0.00
339 225 0.78
340 3 0.01
346 1 0.00
347 3 0.01
350 2 0.01
351 55 0.19
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (344 bp):
TCTCCAAGCCGGTTTAGGAGAAGATCAATTCTGTCCAGAAATTTCAAGGGCAAAATCGTCCACGA
ACTATCAGGTCTCGAGATAAACATAAAAGTTGTAGATCTTGGAATCCTCTATCCAACAGCACCTC
ATTTGCATTTTTTTGACCTCCAGATAAAAAATTATGAATTTTCTTCAAAAACTACTCTTGTGAAG
TCCTCCTTCGAATAGGATTTAACAATGCTGCATCAGGCTGGAATCATTACTGCATCATAATTACT
AATTGGACTTGAAATCCTTCTTTGAGCTTCCATAGTAACGAAGTGGGTCTAAAAATATCAGATTT
AGACTTCAAGACATCTGGC
Found at i:13673 original size:2 final size:2
Alignment explanation
Indices: 13666--13705 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
13656 CAATTTAGAA
*
13666 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT ACT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A
13706 CTCCCTCCGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:18298 original size:17 final size:17
Alignment explanation
Indices: 18276--18321 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
18266 CCGAAATTAG
18276 TAATAATTATTTTATAA
1 TAATAATTATTTTATAA
18293 TAATAATTATTTTATAA
1 TAATAATTATTTTATAA
* *
18310 TTATTATTATTT
1 TAATAATTATTT
18322 CAGTAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TAATAATTATTTTATAA
Done.