Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018447.1 Corchorus olitorius cultivar O-4 contig18480, 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: 41232
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:620 original size:19 final size:19
Alignment explanation
Indices: 596--633 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
586 CCCAAGAAAC
*
596 CTAAATCTAATTTAAACTA
1 CTAAATCTAACTTAAACTA
615 CTAAATCTAACTTAAACTA
1 CTAAATCTAACTTAAACTA
634 GGAAACTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.34
Consensus pattern (19 bp):
CTAAATCTAACTTAAACTA
Found at i:7189 original size:20 final size:18
Alignment explanation
Indices: 7164--7211 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 18
7154 GTAACAACAG
7164 TTTCCTTTATCTTTTCTCTT
1 TTTCCTTT-TCTTTT-TCTT
7184 TTTCCTTTTCTTTTTCTT
1 TTTCCTTTTCTTTTTCTT
*
7202 GTTGCCTTTT
1 -TTTCCTTTT
7212 TAGAGTTCAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 4 0.15
19 14 0.54
20 8 0.31
ACGTcount: A:0.02, C:0.23, G:0.04, T:0.71
Consensus pattern (18 bp):
TTTCCTTTTCTTTTTCTT
Found at i:11764 original size:22 final size:22
Alignment explanation
Indices: 11735--11859 Score: 105
Period size: 22 Copynumber: 5.7 Consensus size: 22
11725 TGAATATTTT
*
11735 TATGAAATTTTGATAATCACCC
1 TATGAAATTTTGATAATCACCA
* *
11757 TATTAAATTTTGATAACCACCA
1 TATGAAATTTTGATAATCACCA
*
11779 TATGAAATTTTGATAATTACC-
1 TATGAAATTTTGATAATCACCA
* *
11800 TAT-AAACTTGTGATAA-AATCCA
1 TATGAAA-TTTTGATAATCA-CCA
* * *
11822 TAAGAAACTTTGATAATCTAAC-
1 TATGAAATTTTGATAATC-ACCA
*
11844 TATGAAATTTTAATAA
1 TATGAAATTTTGATAA
11860 ACTTTCCTAT
Statistics
Matches: 81, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
20 4 0.05
21 13 0.16
22 59 0.73
23 4 0.05
24 1 0.01
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAATCACCA
Found at i:11823 original size:43 final size:44
Alignment explanation
Indices: 11735--11839 Score: 126
Period size: 43 Copynumber: 2.4 Consensus size: 44
11725 TGAATATTTT
* *
11735 TATGAAATTTTGATAATCACCCTATTAAATTTTGATAACCACCA
1 TATGAAATTTTGATAATCACCCTATTAAATTGTGATAACAACCA
*
11779 TATGAAATTTTGATAATTA-CCTA-TAAACTTGTGATAA-AATCCA
1 TATGAAATTTTGATAATCACCCTATTAAA-TTGTGATAACAA-CCA
* *
11822 TAAGAAACTTTGATAATC
1 TATGAAATTTTGATAATC
11840 TAACTATGAA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
42 5 0.09
43 30 0.57
44 18 0.34
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (44 bp):
TATGAAATTTTGATAATCACCCTATTAAATTGTGATAACAACCA
Found at i:21312 original size:14 final size:13
Alignment explanation
Indices: 21293--21323 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
21283 CGGTGTATTG
21293 TATAATTTGCCAT
1 TATAATTTGCCAT
21306 ATATAATTTGCCAT
1 -TATAATTTGCCAT
21320 TATA
1 TATA
21324 CATTATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.45
Consensus pattern (13 bp):
TATAATTTGCCAT
Found at i:23803 original size:2 final size:2
Alignment explanation
Indices: 23755--23788 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
23745 TTGTTAATTA
23755 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23789 GCAATAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25106 original size:39 final size:38
Alignment explanation
Indices: 25062--25144 Score: 132
Period size: 39 Copynumber: 2.1 Consensus size: 38
25052 TAATGTCCAC
25062 TTTGTATTTGGCATAAAATTATTT-GAAAAGTGATACTTG
1 TTTGTATTTGGCATAAAATT-TTTGGAAAA-TGATACTTG
25101 TTTGTATTTGGCATAAAATTTTTGGAAAATGATACTTG
1 TTTGTATTTGGCATAAAATTTTTGGAAAATGATACTTG
25139 TGTTGT
1 T-TTGT
25145 GGTTGGATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
38 13 0.31
39 29 0.69
ACGTcount: A:0.30, C:0.05, G:0.19, T:0.46
Consensus pattern (38 bp):
TTTGTATTTGGCATAAAATTTTTGGAAAATGATACTTG
Found at i:25331 original size:24 final size:24
Alignment explanation
Indices: 25295--25342 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
25285 ATCATTTATC
* *
25295 TGGATAGATATTATCAAGTGATAAA
1 TGGAGAGATATTATC-AGAGATAAA
25320 TGGAGAGA-ATTATCAGAGATAAA
1 TGGAGAGATATTATCAGAGATAAA
25343 AGAGAAGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 8 0.38
24 6 0.29
25 7 0.33
ACGTcount: A:0.46, C:0.04, G:0.23, T:0.27
Consensus pattern (24 bp):
TGGAGAGATATTATCAGAGATAAA
Found at i:27953 original size:30 final size:30
Alignment explanation
Indices: 27881--28181 Score: 350
Period size: 31 Copynumber: 9.7 Consensus size: 30
27871 TTAAAGCACA
* *
27881 ATGACAACTTCAGGTGTCAATTGTAAGACC
1 ATGACAACTTCTGGTGTCAATTGTAAGATC
*
27911 ATCGACAACTTCTGATGTCAATTGTAAGATC
1 AT-GACAACTTCTGGTGTCAATTGTAAGATC
* * *
27942 ATGAAAACTTCTGGTTGTCAATTGGAGATTTATC
1 ATGACAACTTCTGG-TGTCAATTGTA-A--GATC
* * *
27976 ATGACAACTTCTGGTGTCATTTGGAAATTTATC
1 ATGACAACTTCTGGTGTCAATT-GTAA--GATC
* *
28009 ATGACAACTTCTAGTGTCAATTGCAAGATC
1 ATGACAACTTCTGGTGTCAATTGTAAGATC
*
28039 ATGACAACTTCTGGTGTCAATTGCAAGATC
1 ATGACAACTTCTGGTGTCAATTGTAAGATC
* *
28069 ATGACAACTTCTAGTGTCAATTGCAAGATC
1 ATGACAACTTCTGGTGTCAATTGTAAGATC
**
28099 ATTGACAACTTCTGGTGTCAATTGTAAGGCC
1 A-TGACAACTTCTGGTGTCAATTGTAAGATC
28130 ATTGACAACTTCTGGTGTCAATTGTAAGATC
1 A-TGACAACTTCTGGTGTCAATTGTAAGATC
*
28161 ATTGACAACTTCTGGTATCAA
1 A-TGACAACTTCTGGTGTCAA
28182 AATATATTAG
Statistics
Matches: 241, Mismatches: 23, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
30 74 0.31
31 111 0.46
32 4 0.02
33 34 0.14
34 18 0.07
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Consensus pattern (30 bp):
ATGACAACTTCTGGTGTCAATTGTAAGATC
Found at i:28393 original size:48 final size:48
Alignment explanation
Indices: 28317--28417 Score: 184
Period size: 48 Copynumber: 2.1 Consensus size: 48
28307 TCATATATAA
28317 ATAGTATCAACTACTCACCAAACAAAGAAGATTCACAAAACCAAGGAG
1 ATAGTATCAACTACTCACCAAACAAAGAAGATTCACAAAACCAAGGAG
* *
28365 ATAGTATCAACTCCTCACCAAACCAAGAAGATTCACAAAACCAAGGAG
1 ATAGTATCAACTACTCACCAAACAAAGAAGATTCACAAAACCAAGGAG
28413 ATAGT
1 ATAGT
28418 TTATCTGCGA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.48, C:0.24, G:0.13, T:0.16
Consensus pattern (48 bp):
ATAGTATCAACTACTCACCAAACAAAGAAGATTCACAAAACCAAGGAG
Found at i:28405 original size:18 final size:18
Alignment explanation
Indices: 28379--28414 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
28369 TATCAACTCC
*
28379 TCACCAAACCAAGAAGAT
1 TCACAAAACCAAGAAGAT
*
28397 TCACAAAACCAAGGAGAT
1 TCACAAAACCAAGAAGAT
28415 AGTTTATCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.14, T:0.11
Consensus pattern (18 bp):
TCACAAAACCAAGAAGAT
Found at i:29364 original size:22 final size:24
Alignment explanation
Indices: 29329--29382 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
29319 ATAAATGTTG
* *
29329 CTGATAA-TCTTCT-CTTTTATCT
1 CTGATAATTCTTCTCCATTTATCA
29351 CTGATAATTC-TCTCCATTTATCA
1 CTGATAATTCTTCTCCATTTATCA
29374 CTTGATAAT
1 C-TGATAAT
29383 ATCTAGCCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 10 0.37
23 10 0.37
24 7 0.26
ACGTcount: A:0.24, C:0.22, G:0.06, T:0.48
Consensus pattern (24 bp):
CTGATAATTCTTCTCCATTTATCA
Found at i:33494 original size:8 final size:8
Alignment explanation
Indices: 33483--33507 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
33473 TTGTTTGTTT
33483 GTTTGGTA
1 GTTTGGTA
33491 GTTTGGTA
1 GTTTGGTA
33499 GTTTGGTA
1 GTTTGGTA
33507 G
1 G
33508 GTAGGTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.40, T:0.48
Consensus pattern (8 bp):
GTTTGGTA
Found at i:34483 original size:21 final size:20
Alignment explanation
Indices: 34442--34485 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
34432 TCTTGTAATC
*
34442 TAAAATTATTAGATAAGTTA
1 TAAAATTATTAAATAAGTTA
34462 TAAAAGTTATTAAAATAA-TTA
1 TAAAA-TTATT-AAATAAGTTA
34483 TAA
1 TAA
34486 TGCTTTTCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 5 0.24
21 11 0.52
22 5 0.24
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.39
Consensus pattern (20 bp):
TAAAATTATTAAATAAGTTA
Found at i:39633 original size:209 final size:209
Alignment explanation
Indices: 39220--39639 Score: 734
Period size: 209 Copynumber: 2.0 Consensus size: 209
39210 ATATAGAGAA
39220 GCACAAAATAGGTAGAAAAGAAATTTACAAATATATAGTTTGCTTTCATATAAATTAATTATATA
1 GCACAAAATAGGTAGAAAAGAAATTTACAAATATATAGTTTGCTTTCATATAAATTAATTATATA
* *
39285 CAACTCTCTCATCCTTCATTTTCCTTCTCTCATTAATTCCCCCCACCCCCTCTTTTTAAATTATT
66 CAACTCTCTCATCCTTCATTTTCCTTCTCTCATCAATTCCCCCCACCCCCTCTTTTTAAATAATT
* *
39350 TTTTAAAATTTTTTATGCTTTGTGTAGGTGAATACAACATCGTCAAATCAAGAAGTGTAGTTGAG
131 TTTTAAAATTTTTTATGCTTTGTGTAGGTGAATACAACATCATCAAATCAAGAAGTGTACTTGAG
39415 CATTTTTTTTTCAT
196 CATTTTTTTTTCAT
* *
39429 GCACAAAATAGGTAGAAACGAAATTTAGAAATATATAGTTTGCTTTCATATAAATTAATTATATA
1 GCACAAAATAGGTAGAAAAGAAATTTACAAATATATAGTTTGCTTTCATATAAATTAATTATATA
* *
39494 CAACTCTCTCATCCTTCCTTTTCCTTCTCTCATCAATTCGCCCCACCCCCTCTTTTTAAA-AATT
66 CAACTCTCTCATCCTTCATTTTCCTTCTCTCATCAATTCCCCCCACCCCCTCTTTTTAAATAATT
39558 TTTTAAAATTTTTTTTATGCTTTGTGTAGGTGAATACAACATCATCAAATCAAGAAGTGTACTTG
131 TTTTAAAA--TTTTTTATGCTTTGTGTAGGTGAATACAACATCATCAAATCAAGAAGTGTACTTG
*
39623 AGTATTTTTTTTTCAT
194 AGCATTTTTTTTTCAT
39639 G
1 G
39640 ACATTGATCG
Statistics
Matches: 200, Mismatches: 9, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
208 11 0.05
209 120 0.60
210 69 0.34
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.40
Consensus pattern (209 bp):
GCACAAAATAGGTAGAAAAGAAATTTACAAATATATAGTTTGCTTTCATATAAATTAATTATATA
CAACTCTCTCATCCTTCATTTTCCTTCTCTCATCAATTCCCCCCACCCCCTCTTTTTAAATAATT
TTTTAAAATTTTTTATGCTTTGTGTAGGTGAATACAACATCATCAAATCAAGAAGTGTACTTGAG
CATTTTTTTTTCAT
Done.