Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008866.1 Corchorus capsularis cultivar CVL-1 contig08887, 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: 38140
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:6961 original size:15 final size:15
Alignment explanation
Indices: 6941--6970 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
6931 CAATAGCTAT
6941 AATACACTACTTAAA
1 AATACACTACTTAAA
6956 AATACACTACTTAAA
1 AATACACTACTTAAA
6971 GGCTTCCACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.20, G:0.00, T:0.27
Consensus pattern (15 bp):
AATACACTACTTAAA
Found at i:12387 original size:167 final size:167
Alignment explanation
Indices: 12083--12415 Score: 422
Period size: 167 Copynumber: 2.0 Consensus size: 167
12073 CAGGGTACGT
* * * * ** * *
12083 GACTTTAATAGAGTAGTGGAATTACTAAAAGATCCCTACCAAGGCTTGCTTTTGGAGTTAGATAA
1 GACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCCACCAAGGCTTGATGATGGAGCTAGAAAA
* * *
12148 CTTACTTTTTTCGTCTTTTCCTACTTGGAAGATTACTTAAATGTCCTAACTTTTGATTCTTTAGG
66 CTAACTTTTTTCGTCTTTACCTACTTGGAAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGG
* *
12213 AGATTAAATAAGT-AATTTTTTTGGTCATTTCTCAATG
131 AGATTAAATAACTAAACTTTTTT-GTCATTTCTCAATG
* * * *
12250 GACTTGAATAGAGTATTGGAATTAATAAATGATCCCCATCAAGGATTTGATGAT-GAGCTAGAAA
1 GACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCCACCAAGG-CTTGATGATGGAGCTAGAAA
* *
12314 ACTAACATTTTTT-GTCTTTACCTACTT-GACAGATTACTTAAATGTCCTAATTTTTTATTCTTG
65 ACTAAC-TTTTTTCGTCTTTACCTACTTGGA-AGATTACTTAAATGTCCTAACTTTTGATTCTTG
*
12377 AGGGGATTAAATAACTAAACTTTTTTGTCATTTCTCAAT
128 AGGAGATTAAATAACTAAACTTTTTTGTCATTTCTCAAT
12416 TGACAAATGA
Statistics
Matches: 142, Mismatches: 20, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
166 2 0.01
167 121 0.85
168 19 0.13
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.40
Consensus pattern (167 bp):
GACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCCACCAAGGCTTGATGATGGAGCTAGAAAA
CTAACTTTTTTCGTCTTTACCTACTTGGAAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGG
AGATTAAATAACTAAACTTTTTTGTCATTTCTCAATG
Found at i:13862 original size:15 final size:17
Alignment explanation
Indices: 13828--13864 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
13818 ATTGGAGTAG
13828 GAGTTGGTGTTGAATTT
1 GAGTTGGTGTTGAATTT
*
13845 GAGTTGG-G-TGAGTTT
1 GAGTTGGTGTTGAATTT
13860 GAGTT
1 GAGTT
13865 TAACGAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 11 0.58
16 1 0.05
17 7 0.37
ACGTcount: A:0.16, C:0.00, G:0.41, T:0.43
Consensus pattern (17 bp):
GAGTTGGTGTTGAATTT
Found at i:14804 original size:36 final size:36
Alignment explanation
Indices: 14757--14830 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
14747 CTGAAAAAGG
14757 TAATTTTCTAGATTTGCTAATGCTACAAGCATGGCA
1 TAATTTTCTAGATTTGCTAATGCTACAAGCATGGCA
14793 TAATTTTCTAGATTTGCTAATGCTACAAGCATGGCA
1 TAATTTTCTAGATTTGCTAATGCTACAAGCATGGCA
14829 TA
1 TA
14831 GAGCAGAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.36
Consensus pattern (36 bp):
TAATTTTCTAGATTTGCTAATGCTACAAGCATGGCA
Found at i:18476 original size:45 final size:45
Alignment explanation
Indices: 18402--18487 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
18392 AAAGTAGTGA
*
18402 AATTACTAAAAGATCCATAGCCCGAATTAATGATAAGCTGGGTGG
1 AATTACTAAAAGATCCATACCCCGAATTAATGATAAGCTGGGTGG
* *
18447 AATTACTAAAAGATCCCTACCCCGGATTAATGATAAGCTGG
1 AATTACTAAAAGATCCATACCCCGAATTAATGATAAGCTGG
18488 AGAAGTAATC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (45 bp):
AATTACTAAAAGATCCATACCCCGAATTAATGATAAGCTGGGTGG
Found at i:20446 original size:13 final size:13
Alignment explanation
Indices: 20423--20453 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
20413 TAAATACATG
20423 TATCG-ACGGATA
1 TATCGAACGGATA
20435 TATCGAACGGATA
1 TATCGAACGGATA
20448 TATCGA
1 TATCGA
20454 GGTATCGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (13 bp):
TATCGAACGGATA
Found at i:20629 original size:10 final size:10
Alignment explanation
Indices: 20614--20638 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
20604 TATGTAGACA
20614 TTTTTTTTAT
1 TTTTTTTTAT
20624 TTTTTTTTAT
1 TTTTTTTTAT
20634 TTTTT
1 TTTTT
20639 GTACTACGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTAT
Found at i:21480 original size:10 final size:10
Alignment explanation
Indices: 21465--21498 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
21455 TTTAATATGC
21465 ATATTTACGG
1 ATATTTACGG
*
21475 ATATTTATGG
1 ATATTTACGG
21485 ATATTTACGG
1 ATATTTACGG
21495 ATAT
1 ATAT
21499 ATCGAGATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (10 bp):
ATATTTACGG
Found at i:21488 original size:20 final size:20
Alignment explanation
Indices: 21460--21498 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
21450 TTTAATTTAA
21460 TATGCATATTTACGGATATT
1 TATGCATATTTACGGATATT
*
21480 TATGGATATTTACGGATAT
1 TATGCATATTTACGGATAT
21499 ATCGAGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.44
Consensus pattern (20 bp):
TATGCATATTTACGGATATT
Found at i:21626 original size:12 final size:12
Alignment explanation
Indices: 21609--21647 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
21599 GTACAGATAT
21609 CGGATATATCGA
1 CGGATATATCGA
21621 CGGATATATCGA
1 CGGATATATCGA
21633 -GG---TATCGA
1 CGGATATATCGA
21641 CGGATAT
1 CGGATAT
21648 TTAATTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
8 6 0.26
9 2 0.09
11 2 0.09
12 13 0.57
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (12 bp):
CGGATATATCGA
Found at i:22176 original size:16 final size:16
Alignment explanation
Indices: 22136--22177 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
22126 AAAGTCAAAT
*
22136 ACCCGAACCCGAAAAA
1 ACCCAAACCCGAAAAA
*
22152 A-TCAGAACCCGAAAAA
1 ACCCA-AACCCGAAAAA
22168 ACCCAAACCC
1 ACCCAAACCC
22178 AAATCCAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
15 1 0.05
16 18 0.86
17 2 0.10
ACGTcount: A:0.50, C:0.38, G:0.10, T:0.02
Consensus pattern (16 bp):
ACCCAAACCCGAAAAA
Found at i:22375 original size:32 final size:32
Alignment explanation
Indices: 22339--22413 Score: 107
Period size: 32 Copynumber: 2.3 Consensus size: 32
22329 ACTGAATCCG
*
22339 AATCCGAACCCGAATTAACCTGA-CTCAAATTC
1 AATCCAAACCCGAATTAACCTGATC-CAAATTC
*
22371 AATCCAAACCCGAATTGACCTGATCCAAATTC
1 AATCCAAACCCGAATTAACCTGATCCAAATTC
*
22403 AACCCAAACCC
1 AATCCAAACCC
22414 AAAAATGTCC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
32 38 0.97
33 1 0.03
ACGTcount: A:0.39, C:0.35, G:0.08, T:0.19
Consensus pattern (32 bp):
AATCCAAACCCGAATTAACCTGATCCAAATTC
Found at i:24444 original size:65 final size:65
Alignment explanation
Indices: 24363--24493 Score: 253
Period size: 65 Copynumber: 2.0 Consensus size: 65
24353 AGACTAAAAA
*
24363 TTGTAACCAAGTCTATAACCTCTAAGAATCAGATAAGATATAAAACAACTAGATCAGAAGATTTG
1 TTGTAACCAAGTCTATAACCTCTAAGAATCAGATAACATATAAAACAACTAGATCAGAAGATTTG
24428 TTGTAACCAAGTCTATAACCTCTAAGAATCAGATAACATATAAAACAACTAGATCAGAAGATTTG
1 TTGTAACCAAGTCTATAACCTCTAAGAATCAGATAACATATAAAACAACTAGATCAGAAGATTTG
24493 T
1 T
24494 GTACAAAGTC
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.27
Consensus pattern (65 bp):
TTGTAACCAAGTCTATAACCTCTAAGAATCAGATAACATATAAAACAACTAGATCAGAAGATTTG
Found at i:29782 original size:142 final size:143
Alignment explanation
Indices: 29524--29791 Score: 475
Period size: 142 Copynumber: 1.9 Consensus size: 143
29514 GATTGCCGTG
* * *
29524 ATATTGAAACACATTTATTGTAATGTCAAACAGATTAGGGAGAAATATATTCATATATAATAACT
1 ATATTCAAACACATTTATTGCAATGTCAAACAGATTAGGGAGAAATATATGCA-ATATAATAACT
29589 ATAGACCCATTGCATAACTTGCTATCTGACCGTAAATAAAATTATAAAGTGATTTAGTAAAATTA
65 ATAGACCCATTGCATAACTTGCTATCTGACCGTAAATAAAATTATAAAGTGATTTAGTAAAATTA
29654 TAAAGTGACCATAA
130 TAAAGTGACCATAA
* *
29668 ATATTCAAACAGATTTATTGCAATGTCAAACAGATTAGGGAGAAATATATGC-ATATAATAACTT
1 ATATTCAAACACATTTATTGCAATGTCAAACAGATTAGGGAGAAATATATGCAATATAATAACTA
29732 TAGACCCATTGCATAACTTGCTATCTGACCGTAAATAAAATTATAAAGTGATTTAGTAAA
66 TAGACCCATTGCATAACTTGCTATCTGACCGTAAATAAAATTATAAAGTGATTTAGTAAA
29792 TGACAGGGAA
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
142 71 0.60
144 48 0.40
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (143 bp):
ATATTCAAACACATTTATTGCAATGTCAAACAGATTAGGGAGAAATATATGCAATATAATAACTA
TAGACCCATTGCATAACTTGCTATCTGACCGTAAATAAAATTATAAAGTGATTTAGTAAAATTAT
AAAGTGACCATAA
Found at i:34892 original size:63 final size:63
Alignment explanation
Indices: 34820--34946 Score: 238
Period size: 63 Copynumber: 2.0 Consensus size: 63
34810 GCCAAGCCTT
34820 TTCTTTTCAAACTTGATATAGTTCGAGCTTAT-GTACCCTTAAACAAGATAGTTTTCCATACAA
1 TTCTTTTCAAACTTGATATAGTTCGAGCTTATAGTA-CCTTAAACAAGATAGTTTTCCATACAA
34883 TTCTTTTCAAACTTGATATAGTTCGAGCTTATAGTACCTTAAACAAGATAGTTTTCCATACAA
1 TTCTTTTCAAACTTGATATAGTTCGAGCTTATAGTACCTTAAACAAGATAGTTTTCCATACAA
34946 T
1 T
34947 CCAGTGATTG
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
63 60 0.95
64 3 0.05
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (63 bp):
TTCTTTTCAAACTTGATATAGTTCGAGCTTATAGTACCTTAAACAAGATAGTTTTCCATACAA
Found at i:35058 original size:14 final size:14
Alignment explanation
Indices: 35039--35068 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
35029 ATCAAGTATG
35039 CATTCCATTAAAAC
1 CATTCCATTAAAAC
35053 CATTCCATTAAAAC
1 CATTCCATTAAAAC
35067 CA
1 CA
35069 ATAACATCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.30, G:0.00, T:0.27
Consensus pattern (14 bp):
CATTCCATTAAAAC
Done.