Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012769.1 Corchorus olitorius cultivar O-4 contig12802, 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: 24445
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:832 original size:21 final size:19
Alignment explanation
Indices: 794--833 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
784 CAAATCCGGC
*
794 CTTAGAATATCCAATCTAA
1 CTTAGAATATCAAATCTAA
813 CTTAGACATATACAAATCTAA
1 CTTAGA-ATAT-CAAATCTAA
834 AACTACCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 4 0.22
21 8 0.44
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (19 bp):
CTTAGAATATCAAATCTAA
Found at i:1309 original size:22 final size:22
Alignment explanation
Indices: 1283--1353 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 22
1273 TGGTTCAAAA
1283 TTTGTGAGATTTGTGAAAGAAT
1 TTTGTGAGATTTGTGAAAGAAT
* **
1305 TTTGT-AGGATAATGGTTCAA-AA-
1 TTTGTGA-GAT--TTGTGAAAGAAT
1327 TTTGTGAGATTTGTGAAAGAAT
1 TTTGTGAGATTTGTGAAAGAAT
1349 TTTGT
1 TTTGT
1354 AGGATCCGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
20 5 0.14
21 3 0.08
22 21 0.57
23 3 0.08
24 5 0.14
ACGTcount: A:0.31, C:0.01, G:0.25, T:0.42
Consensus pattern (22 bp):
TTTGTGAGATTTGTGAAAGAAT
Found at i:1324 original size:44 final size:44
Alignment explanation
Indices: 1271--1358 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
1261 TAAAGTTTTG
1271 AATGGTTCAAAATTTGTGAGATTTGTGAAAGAATTTTGTAGGAT
1 AATGGTTCAAAATTTGTGAGATTTGTGAAAGAATTTTGTAGGAT
1315 AATGGTTCAAAATTTGTGAGATTTGTGAAAGAATTTTGTAGGAT
1 AATGGTTCAAAATTTGTGAGATTTGTGAAAGAATTTTGTAGGAT
1359 CCGAAACCGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.34, C:0.02, G:0.25, T:0.39
Consensus pattern (44 bp):
AATGGTTCAAAATTTGTGAGATTTGTGAAAGAATTTTGTAGGAT
Found at i:1908 original size:31 final size:29
Alignment explanation
Indices: 1840--1908 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
1830 AGCGAATTTG
* *
1840 AAACGTTTTACCCCGAATCAACCAAATTA
1 AAACGTTTTACCCCAAATCAACCAAAATA
* * *
1869 AAAGGTTTTACCCCAAATTAGTCCGAAAATA
1 AAACGTTTTACCCCAAATCA-ACC-AAAATA
1900 AAACGTTTT
1 AAACGTTTT
1909 GCCCTTAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 17 0.53
30 2 0.06
31 13 0.41
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.28
Consensus pattern (29 bp):
AAACGTTTTACCCCAAATCAACCAAAATA
Found at i:5422 original size:103 final size:106
Alignment explanation
Indices: 5162--5422 Score: 352
Period size: 106 Copynumber: 2.5 Consensus size: 106
5152 AGTTTAGCCT
* * *
5162 TAATTTCATTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGAGTAAATTTCAAAATT
1 TAATTTCACTAAGTTTAG-CCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
* *
5227 AATAATTTATTATCATAGGGTTTTATAAATAAAATACAAAGC
65 AATAATTTATTATCATAGGGATTTAGAAATAAAATACAAAGC
*
5269 TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATTA
1 TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTA
* *
5334 ATAATATT-TT-T-ATAGGGATTTGGAAATAAAATATATAA-C
66 ATAAT-TTATTATCATAGGGATTTAGAAATAAAATACA-AAGC
* ** *
5373 TAA-TTCACTAAGTTTAGCCCAAATTAAAACTAAAATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
5423 TAGAAAAATT
Statistics
Matches: 140, Mismatches: 12, Indels: 8
0.88 0.08 0.05
Matches are distributed among these distances:
103 43 0.31
104 24 0.17
105 3 0.02
106 51 0.36
107 19 0.14
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (106 bp):
TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTA
ATAATTTATTATCATAGGGATTTAGAAATAAAATACAAAGC
Found at i:6497 original size:31 final size:29
Alignment explanation
Indices: 6434--6497 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 29
6424 TTCTTCTTTC
* **
6434 TTTTTTTAAAAAGAAAAGAAAAAATGGTT
1 TTTTTTTAAAAAAAAAAGAAAAAATGAAT
*
6463 TTTTTTTAAAACAAAAAAAGGAAAAATGAAT
1 TTTTTTT-AAA-AAAAAAAGAAAAAATGAAT
6494 TTTT
1 TTTT
6498 AATTTTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 7 0.24
30 3 0.10
31 19 0.66
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.36
Consensus pattern (29 bp):
TTTTTTTAAAAAAAAAAGAAAAAATGAAT
Found at i:6645 original size:18 final size:19
Alignment explanation
Indices: 6624--6670 Score: 71
Period size: 18 Copynumber: 2.5 Consensus size: 19
6614 AATTTTTAAA
6624 AAAAAAATAT-ATTTTTTT
1 AAAAAAATATAATTTTTTT
6642 AAAAAAA-ATAATTTTTTT
1 AAAAAAATATAATTTTTTT
6660 ATAAAAAATAT
1 A-AAAAAATAT
6671 GATCATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 2 0.08
18 16 0.62
19 6 0.23
20 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AAAAAAATATAATTTTTTT
Found at i:6658 original size:19 final size:21
Alignment explanation
Indices: 6616--6667 Score: 74
Period size: 19 Copynumber: 2.6 Consensus size: 21
6606 CCTCACCCAA
6616 TTTTTAAAAAAAAAATATATT
1 TTTTTAAAAAAAAAATATATT
6637 TTTTT--AAAAAAAATA-ATT
1 TTTTTAAAAAAAAAATATATT
*
6655 TTTTTATAAAAAA
1 TTTTTAAAAAAAA
6668 TATGATCATA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 8 0.28
19 10 0.34
20 6 0.21
21 5 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TTTTTAAAAAAAAAATATATT
Found at i:8512 original size:14 final size:16
Alignment explanation
Indices: 8481--8512 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
8471 AATGAGATTG
8481 TTTCTCCAAAGCCAAA
1 TTTCTCCAAAGCCAAA
8497 TTTC-CCAAAG-CAAA
1 TTTCTCCAAAGCCAAA
8511 TT
1 TT
8513 AGCAAAAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 6 0.38
16 4 0.25
ACGTcount: A:0.38, C:0.28, G:0.06, T:0.28
Consensus pattern (16 bp):
TTTCTCCAAAGCCAAA
Found at i:16349 original size:9 final size:9
Alignment explanation
Indices: 16335--16362 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
16325 ATATAGGCGG
16335 CTAACAAGC
1 CTAACAAGC
16344 CTAACAAGC
1 CTAACAAGC
16353 CTAACAAGC
1 CTAACAAGC
16362 C
1 C
16363 CAAATAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.43, C:0.36, G:0.11, T:0.11
Consensus pattern (9 bp):
CTAACAAGC
Found at i:21839 original size:11 final size:11
Alignment explanation
Indices: 21823--21849 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
21813 TCTTCAATTG
21823 TTTTTTCTTTT
1 TTTTTTCTTTT
21834 TTTTTTCTTTT
1 TTTTTTCTTTT
21845 TTTTT
1 TTTTT
21850 AATGCAGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:23628 original size:16 final size:16
Alignment explanation
Indices: 23593--23683 Score: 98
Period size: 16 Copynumber: 5.8 Consensus size: 16
23583 CTCGGGCGGG
23593 TTCGGGTTCGGGTA-T
1 TTCGGGTTCGGGTATT
23608 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
* *
23624 TTCGGGCTCGGGT-TAA
1 TTCGGGTTCGGGTAT-T
*
23640 GTCGGGTTCGGGT-TAT
1 TTCGGGTTCGGGTAT-T
* *
23656 GTCGGGTTCAGGTATT
1 TTCGGGTTCGGGTATT
23672 TTCGGGTTCGGG
1 TTCGGGTTCGGG
23684 CTCGGGTAGG
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
15 15 0.23
16 49 0.75
17 1 0.02
ACGTcount: A:0.08, C:0.14, G:0.41, T:0.37
Consensus pattern (16 bp):
TTCGGGTTCGGGTATT
Found at i:23683 original size:6 final size:6
Alignment explanation
Indices: 23672--23714 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
23662 TTCAGGTATT
* * *
23672 TTCGGG TTCGGG CTCGGG -TAGGG TTCGGG TTCGGG CTCGGG TT
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TT
23715 TGATTTTGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
5 4 0.13
6 27 0.87
ACGTcount: A:0.02, C:0.19, G:0.49, T:0.30
Consensus pattern (6 bp):
TTCGGG
Found at i:23690 original size:12 final size:12
Alignment explanation
Indices: 23673--23714 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
23663 TCAGGTATTT
23673 TCGGGTTCGGGC
1 TCGGGTTCGGGC
* *
23685 TCGGG-TAGGGT
1 TCGGGTTCGGGC
23696 TCGGGTTCGGGC
1 TCGGGTTCGGGC
23708 TCGGGTT
1 TCGGGTT
23715 TGATTTTGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.02, C:0.19, G:0.50, T:0.29
Consensus pattern (12 bp):
TCGGGTTCGGGC
Found at i:24322 original size:2 final size:2
Alignment explanation
Indices: 24317--24349 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
24307 TTATATAAGT
*
24317 TA TA TA TA TA TA TA TA CA 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 T
24350 TTAGTAGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Done.