Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019115.1 Corchorus olitorius cultivar O-4 contig19148, 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: 37184
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:786 original size:2 final size:2
Alignment explanation
Indices: 779--809 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
769 TTGGTGCTGA
779 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
810 TATGAGTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2697 original size:335 final size:327
Alignment explanation
Indices: 1934--2718 Score: 887
Period size: 332 Copynumber: 2.3 Consensus size: 327
1924 TTTAGTCAGC
* * * * *
1934 AATATGAAAAATGATATTAGAAGCGTGAAAAAGGCTTTGAATTTTTTTAGCGTTGAATTATATAT
1 AATATGAAAAATGATATTAAAAG-TTG--AAA-GCCTTCAATTTTTTTGGCGTTGAATTATATAT
* * * *
1999 TTTTTATGAGTATTGTCGCTAGAAATTGAGGAAAAATCTTTCGGGTCAATTTTCGCAAAATTTTA
62 TTTTTATGAGTATTTTAGC-AAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTA
* * * *
2064 GCCAAAATCGTGTACTAACCATCACGGTTTTCGGCTAGAAATGTGTTCCGGGCGTAGCTCAGTTT
126 GCCAAAATCGTGTACTAACCATCACGGTTTTCGGCTAAAAACGCGTTCCGGGCGCAGCTCAGTTT
* *
2129 TGCATGATTTTTGGTGCCAAGACTCCTTGAAATGTCTATATTCATCTCAACAAATCTCACCCACA
191 TGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTCAACAAATCTCACCCACA
* * *
2194 TTGGATTTAAGGATTTGTTTTTACGAGAATATGAATCTTCTTTCGATTTAATTAGAAATTAATTC
256 TTAGATTTAAGGATTTGTTTTTACGAGAATATGAATCTTCGTTCGATTTAATTAGAAATCAATTC
2259 GGATAAAA
321 -GATAAAA
* ** * * * ** **
2267 AATAGGAAAAACAATATTAGAAGCGTTAAAAGCCCTTCAATCTTTTTGATGTCAAATTATATATT
1 AATATGAAAAATGATATTA-AA-AGTTGAAAG-CCTTCAATTTTTTTGGCGTTGAATTATATATT
* *
2332 TTTTATGAGTAGTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAG
63 TTTTATGAGTATTTTAG-CAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAG
** * *
2397 CTGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGC-CACGGCTCTGT
127 CCAAAATCGTGTACTAACCATCACGGTTTTCGGCTAAAAACGCGTTCCGG-GCGCA--GCTCAGT
* * * * **
2461 TTTGCATGATTTTTGGCGCCACA-ACTCCTTGAAAATATCTTTATTCATCTGATCGAATCTCGGC
189 TTTGCATGATTTTTGGCGCCA-AGACTCCTTG-AAATATCTATATTCATCTCAACAAATCTCACC
* * * *
2525 CACATTAGATTTAATGATTTGTTTTTACGTGCATCTGAATCTT-GTTCGATTTAATTAGAAATCA
252 CACATTAGATTTAAGGATTTGTTTTTACGAGAATATGAATCTTCGTTCGATTTAATTAGAAATCA
*
2589 ATTC-ATAAAT
317 ATTCGATAAAA
*
2599 AATATGAAAAATGATATTAAAAGTATGAAAGTCTTCCAATTTTTTTGGCGTTGAATTTTATATAT
1 AATATGAAAAATGATATTAAAAGT-TGAAAGCCTT-CAATTTTTTTGGCGTTGAA--TTATATAT
* * * *
2664 ATATATTATGGGTATTTTTGTCAAAAATTGAGGAAAAATCTTTCAGGTC-ATTTTT
62 -T-TTTTATGAGTATTTTAG-CAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTT
2719 ACCATCATGG
Statistics
Matches: 374, Mismatches: 63, Indels: 29
0.80 0.14 0.06
Matches are distributed among these distances:
330 5 0.01
331 22 0.06
332 150 0.40
333 27 0.07
334 66 0.18
335 104 0.28
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (327 bp):
AATATGAAAAATGATATTAAAAGTTGAAAGCCTTCAATTTTTTTGGCGTTGAATTATATATTTTT
TATGAGTATTTTAGCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCAA
AATCGTGTACTAACCATCACGGTTTTCGGCTAAAAACGCGTTCCGGGCGCAGCTCAGTTTTGCAT
GATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTCAACAAATCTCACCCACATTAGA
TTTAAGGATTTGTTTTTACGAGAATATGAATCTTCGTTCGATTTAATTAGAAATCAATTCGATAA
AA
Found at i:4573 original size:22 final size:22
Alignment explanation
Indices: 4529--4575 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
4519 AAAAGGTGTT
* *
4529 AAAAAATTTATAAGATTATTAA
1 AAAAAACTTATAAGATTACTAA
4551 AAAAAACTTATAATG-TTACTAA
1 AAAAAACTTATAA-GATTACTAA
4573 AAA
1 AAA
4576 TGCTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (22 bp):
AAAAAACTTATAAGATTACTAA
Found at i:4999 original size:20 final size:20
Alignment explanation
Indices: 4966--5005 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
4956 TATTTTGTAC
*
4966 TAAAAATACTTATATAGTTTA
1 TAAAAAAACTTATATA-TTTA
4987 TAAAAAAAC-TATATATTTA
1 TAAAAAAACTTATATATTTA
5006 CAGACAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 6 0.33
21 8 0.44
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.40
Consensus pattern (20 bp):
TAAAAAAACTTATATATTTA
Found at i:6072 original size:28 final size:29
Alignment explanation
Indices: 6041--6113 Score: 69
Period size: 28 Copynumber: 2.5 Consensus size: 29
6031 CCAAATTGCC
* *
6041 AGTTCAGGGGGCAAACGTCCAAAT-TTA-A
1 AGTTCA-GGGGCAAACGTCAAAATCGTAGA
* *
6069 AGTTTAAGGGCAAGACGTCAAAATCGTAGA
1 AGTTCAGGGGCAA-ACGTCAAAATCGTAGA
6099 AGTTCAAGGGGCAAA
1 AGTTC-AGGGGCAAA
6114 AAGAGCATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
27 6 0.17
28 14 0.40
29 2 0.06
30 6 0.17
31 7 0.20
ACGTcount: A:0.38, C:0.15, G:0.27, T:0.19
Consensus pattern (29 bp):
AGTTCAGGGGCAAACGTCAAAATCGTAGA
Found at i:8208 original size:15 final size:15
Alignment explanation
Indices: 8190--8221 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
8180 ATTAAATAGA
8190 TTTACATTAAGAATT
1 TTTACATTAAGAATT
8205 TTTACATTAAGAATT
1 TTTACATTAAGAATT
8220 TT
1 TT
8222 AAGTGTTCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (15 bp):
TTTACATTAAGAATT
Found at i:17209 original size:17 final size:19
Alignment explanation
Indices: 17185--17221 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
17175 GCCCAATTTT
*
17185 GAAAAAAAA-AAAACAAAA
1 GAAAAAAAACAACACAAAA
17203 GAAAAAAAACAACACAAAA
1 GAAAAAAAACAACACAAAA
17222 TACATGACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.84, C:0.11, G:0.05, T:0.00
Consensus pattern (19 bp):
GAAAAAAAACAACACAAAA
Found at i:17221 original size:13 final size:14
Alignment explanation
Indices: 17186--17214 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17176 CCCAATTTTG
17186 AAAA-AAAAAAAAC
1 AAAAGAAAAAAAAC
17199 AAAAGAAAAAAAAC
1 AAAAGAAAAAAAAC
17213 AA
1 AA
17215 CACAAAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.90, C:0.07, G:0.03, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAAAAC
Found at i:19361 original size:22 final size:23
Alignment explanation
Indices: 19330--19382 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
19320 CGGGGATCAC
19330 TTTAAT-TTTTATTTTAATTT-G
1 TTTAATCTTTTATTTTAATTTCG
* *
19351 TTTTATCTTTTATTTTTATTTCG
1 TTTAATCTTTTATTTTAATTTCG
19374 TTTAATCTT
1 TTTAATCTT
19383 CTTTTTTCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 5 0.19
22 13 0.48
23 9 0.33
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.72
Consensus pattern (23 bp):
TTTAATCTTTTATTTTAATTTCG
Found at i:19367 original size:23 final size:22
Alignment explanation
Indices: 19330--19382 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
19320 CGGGGATCAC
19330 TTTAAT-TTTTATTTTAATTT-G
1 TTTAATCTTTTATTTT-ATTTCG
*
19351 TTTTATCTTTTATTTTTATTTCG
1 TTTAATCTTTTA-TTTTATTTCG
19374 TTTAATCTT
1 TTTAATCTT
19383 CTTTTTTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 5 0.19
22 9 0.33
23 13 0.48
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.72
Consensus pattern (22 bp):
TTTAATCTTTTATTTTATTTCG
Found at i:19388 original size:22 final size:22
Alignment explanation
Indices: 19330--19394 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
19320 CGGGGATCAC
* *
19330 TTTAAT-TTTTATTTTAATTTG
1 TTTAATCTTCTATTTTTATTTG
* *
19351 TTTTATCTTTTATTTTTATTTCG
1 TTTAATCTTCTATTTTTATTT-G
*
19374 TTTAATCTTCT-TTTTTCTTTG
1 TTTAATCTTCTATTTTTATTTG
19395 ATTTTAGGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 6 0.16
22 21 0.57
23 10 0.27
ACGTcount: A:0.15, C:0.08, G:0.05, T:0.72
Consensus pattern (22 bp):
TTTAATCTTCTATTTTTATTTG
Found at i:21280 original size:18 final size:19
Alignment explanation
Indices: 21247--21282 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
21237 GTACACTTGT
21247 ACTATAATAATTCTCCTAC
1 ACTATAATAATTCTCCTAC
*
21266 ACTATAAT-TTTCTCCTA
1 ACTATAATAATTCTCCTA
21283 TGATCCAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (19 bp):
ACTATAATAATTCTCCTAC
Found at i:22451 original size:21 final size:21
Alignment explanation
Indices: 22292--22507 Score: 114
Period size: 22 Copynumber: 9.8 Consensus size: 21
22282 GAAACCACAT
*
22292 TATGAAATTTTGTTAAT-TTC
1 TATGAAATTTTGATAATCTTC
* * *
22312 ATTCTGAAATTTTGATAACCTCAC
1 --TATGAAATTTTGATAATCT-TC
* * **
22336 TATAAAATTTTTTATAATCACAC
1 TATGAAA-TTTTGATAATC-TTC
* *
22359 TAAG-AATTTTGATAACCTTCC
1 TATGAAATTTTGATAATCTT-C
* *
22380 TATGAAATTTTGACAACCTGATATC
1 TATGAAATTTTGATAA--T-CT-TC
* * * *
22405 AATGATATTTTGATAACCGCTC
1 TATGAAATTTTGATAATC-TTC
22427 TATGAAATTTTGATAATCTTC
1 TATGAAATTTTGATAATCTTC
*
22448 TATGAAATTTT-AGTAATCAATC
1 TATGAAATTTTGA-TAATC-TTC
* *
22470 TGTGAAATTTTGATAAACTTC
1 TATGAAATTTTGATAATCTTC
22491 TTATGAAATTTTGATAA
1 -TATGAAATTTTGATAA
22508 CTACACATAG
Statistics
Matches: 145, Mismatches: 34, Indels: 30
0.69 0.16 0.14
Matches are distributed among these distances:
20 1 0.01
21 33 0.23
22 79 0.54
23 15 0.10
24 1 0.01
25 15 0.10
26 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (21 bp):
TATGAAATTTTGATAATCTTC
Found at i:23672 original size:14 final size:14
Alignment explanation
Indices: 23638--23708 Score: 74
Period size: 14 Copynumber: 5.0 Consensus size: 14
23628 AAGGTCTATC
23638 TAGAATAAATAGAATTA
1 TAGAAT-AA-AGAA-TA
23655 TAGAATAAAGAATA
1 TAGAATAAAGAATA
*
23669 TAGAATAAATAA-A
1 TAGAATAAAGAATA
* *
23682 TAGAATATAGAAAA
1 TAGAATAAAGAATA
23696 TAGAATAAA-AATA
1 TAGAATAAAGAATA
23709 AATTTCGAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
13 14 0.29
14 22 0.46
15 4 0.08
16 2 0.04
17 6 0.12
ACGTcount: A:0.65, C:0.00, G:0.11, T:0.24
Consensus pattern (14 bp):
TAGAATAAAGAATA
Found at i:35954 original size:17 final size:18
Alignment explanation
Indices: 35920--35955 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
35910 TTTGTTTTAG
*
35920 ACATTTTATTCTTTTACC
1 ACATTTTATTCTTATACC
35938 ACATTTTATTC-TATACC
1 ACATTTTATTCTTATACC
35955 A
1 A
35956 AAGAGTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.28, C:0.22, G:0.00, T:0.50
Consensus pattern (18 bp):
ACATTTTATTCTTATACC
Found at i:36959 original size:15 final size:15
Alignment explanation
Indices: 36888--36948 Score: 61
Period size: 15 Copynumber: 3.9 Consensus size: 15
36878 CCGCTATAAT
*
36888 TTTAATTAATAATTTA
1 TTTAATT-ATAATATA
* *
36904 TTT-CTAATAATTATA
1 TTTAATTATAA-TATA
36919 TTTAAATTATAATATA
1 TTT-AATTATAATATA
36935 TTTAATTATAATAT
1 TTTAATTATAATAT
36949 TATTATTTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
14 4 0.11
15 18 0.49
16 10 0.27
17 5 0.14
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTAATTATAATATA
Done.