Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013032.1 Corchorus olitorius cultivar O-4 contig13065, 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: 29627
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Found at i:2549 original size:92 final size:92
Alignment explanation
Indices: 2392--2577 Score: 291
Period size: 92 Copynumber: 2.0 Consensus size: 92
2382 TAAAAGTCTT
* * * *
2392 CATCGTTATCCTCGTGATAATAACTATACTATTCATCAAACAAATTTATATGATATAGATAAAAT
1 CATCGTTATCCTCGTAACAATAACTATACTATTCATCAAACAAATTTATACGATATAGACAAAAT
*
2457 ATTTATAATTTTACTTTTAATTTTCTC
66 ATTTATAATTGTACTTTTAATTTTCTC
* * * *
2484 CATCGTTATTCTTGTAACAATAACTATACTATTGATCAAACAAATTTATACGATATATACAAAAT
1 CATCGTTATCCTCGTAACAATAACTATACTATTCATCAAACAAATTTATACGATATAGACAAAAT
2549 ATTTATAATTGTACTTTTAATTTTCTC
66 ATTTATAATTGTACTTTTAATTTTCTC
2576 CA
1 CA
2578 AAATCTCAAG
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
92 85 1.00
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (92 bp):
CATCGTTATCCTCGTAACAATAACTATACTATTCATCAAACAAATTTATACGATATAGACAAAAT
ATTTATAATTGTACTTTTAATTTTCTC
Found at i:2710 original size:72 final size:72
Alignment explanation
Indices: 2593--2737 Score: 272
Period size: 72 Copynumber: 2.0 Consensus size: 72
2583 TCAAGCATAT
* *
2593 AAACCATTCTTCTTCATAATAACATTCCAACCGCGCTATTAAGTAAATAATTGAAAGAATTTTAG
1 AAACCATTCTTCCTCATAATAACATTCCAACAGCGCTATTAAGTAAATAATTGAAAGAATTTTAG
2658 ATAAATG
66 ATAAATG
2665 AAACCATTCTTCCTCATAATAACATTCCAACAGCGCTATTAAGTAAATAATTGAAAGAATTTTAG
1 AAACCATTCTTCCTCATAATAACATTCCAACAGCGCTATTAAGTAAATAATTGAAAGAATTTTAG
2730 ATAAATG
66 ATAAATG
2737 A
1 A
2738 TTAACAAGGA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.31
Consensus pattern (72 bp):
AAACCATTCTTCCTCATAATAACATTCCAACAGCGCTATTAAGTAAATAATTGAAAGAATTTTAG
ATAAATG
Found at i:2847 original size:82 final size:82
Alignment explanation
Indices: 2710--2873 Score: 319
Period size: 82 Copynumber: 2.0 Consensus size: 82
2700 CTATTAAGTA
2710 AATAATTGAAAGAATTTTAGATAAATGATTAACAAGGACTGAGAAAACAAACAGAAGTTTAAAAA
1 AATAATTGAAAGAATTTTAGATAAATGATTAACAAGGACTGAGAAAACAAACAGAAGTTTAAAAA
2775 CAAACTATACACTTATT
66 CAAACTATACACTTATT
*
2792 AATAATTGAAAGAATTTTAGATAAATGATTAACGAGGACTGAGAAAACAAACAGAAGTTTAAAAA
1 AATAATTGAAAGAATTTTAGATAAATGATTAACAAGGACTGAGAAAACAAACAGAAGTTTAAAAA
2857 CAAACTATACACTTATT
66 CAAACTATACACTTATT
2874 TATTGTGATA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.26
Consensus pattern (82 bp):
AATAATTGAAAGAATTTTAGATAAATGATTAACAAGGACTGAGAAAACAAACAGAAGTTTAAAAA
CAAACTATACACTTATT
Found at i:7202 original size:21 final size:22
Alignment explanation
Indices: 7178--7218 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
7168 GTTTTTAAAA
*
7178 TTCTTGGGTCA-TCGGGTTATC
1 TTCTCGGGTCATTCGGGTTATC
*
7199 TTCTCGGGTTATTCGGGTTA
1 TTCTCGGGTCATTCGGGTTA
7219 CGAGTTTGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.10, C:0.17, G:0.29, T:0.44
Consensus pattern (22 bp):
TTCTCGGGTCATTCGGGTTATC
Found at i:7483 original size:20 final size:21
Alignment explanation
Indices: 7458--7511 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
7448 CAATTTTGGT
7458 ATAAAATTAATTTTAGAA-A-A
1 ATAAAATTAATTTTA-AATATA
*
7478 ATAAAATTTAATTTTAAATATT
1 ATAAAA-TTAATTTTAAATATA
7500 ATAAAATTAATT
1 ATAAAATTAATT
7512 AAGAAATGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 8 0.27
21 16 0.53
22 6 0.20
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
ATAAAATTAATTTTAAATATA
Found at i:11987 original size:11 final size:11
Alignment explanation
Indices: 11973--12006 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
11963 ATGCAGTACG
11973 TGTGTTAATAC
1 TGTGTTAATAC
*
11984 TGTGTTAATAT
1 TGTGTTAATAC
*
11995 TGTTTTAATAC
1 TGTGTTAATAC
12006 T
1 T
12007 TTTTTTTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.26, C:0.06, G:0.15, T:0.53
Consensus pattern (11 bp):
TGTGTTAATAC
Found at i:15718 original size:43 final size:43
Alignment explanation
Indices: 15670--15754 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
15660 GGTCTCAGAT
*
15670 TCAAGTTTTATTAATGAACAAAATATGTATTAGAAAAATTTTA
1 TCAAGTCTTATTAATGAACAAAATATGTATTAGAAAAATTTTA
*
15713 TCAAGTCTTATTAATGAACAAAATATGTATTAGAAGAATTTT
1 TCAAGTCTTATTAATGAACAAAATATGTATTAGAAAAATTTT
15755 TTTCTAAGGG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.39
Consensus pattern (43 bp):
TCAAGTCTTATTAATGAACAAAATATGTATTAGAAAAATTTTA
Found at i:20991 original size:28 final size:26
Alignment explanation
Indices: 20929--20996 Score: 82
Period size: 26 Copynumber: 2.5 Consensus size: 26
20919 TTATTATCGA
*
20929 ATAAATATAATATACTTTTTTAAGGG
1 ATAAATATAATATACTTTTTTAAGCG
* * *
20955 AAAAATATAATATACATTTTTTTAGCT
1 ATAAATATAATATAC-TTTTTTAAGCG
20982 ATAAATTATAATATA
1 ATAAA-TATAATATA
20997 ATCAGATATT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 14 0.40
27 12 0.34
28 9 0.26
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (26 bp):
ATAAATATAATATACTTTTTTAAGCG
Found at i:21052 original size:13 final size:13
Alignment explanation
Indices: 21034--21058 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21024 TAAGACTTTT
21034 TTTAATTTTAAAA
1 TTTAATTTTAAAA
21047 TTTAATTTTAAA
1 TTTAATTTTAAA
21059 CTATAGATAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTAATTTTAAAA
Found at i:21278 original size:21 final size:21
Alignment explanation
Indices: 21254--21317 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
21244 CACTAATATT
21254 TATTAATACTATAACAAGTTA
1 TATTAATACTATAACAAGTTA
*
21275 TATT--TACTCACTAA-TA-TT-
1 TATTAATACT-A-TAACAAGTTA
21293 TATTAATACTATAACAAGTTA
1 TATTAATACTATAACAAGTTA
21314 TATT
1 TATT
21318 TACTTAGAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 14
0.68 0.04 0.28
Matches are distributed among these distances:
18 7 0.21
19 8 0.24
20 8 0.24
21 11 0.32
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.44
Consensus pattern (21 bp):
TATTAATACTATAACAAGTTA
Found at i:21282 original size:19 final size:19
Alignment explanation
Indices: 21260--21321 Score: 58
Period size: 19 Copynumber: 3.2 Consensus size: 19
21250 TATTTATTAA
21260 TACTATAACAAGTTATATT
1 TACTATAACAAGTTATATT
*
21279 TACTCACTAA-TA-TT-TATT
1 TACT-A-TAACAAGTTATATT
21297 AATACTATAACAAGTTATATT
1 --TACTATAACAAGTTATATT
21318 TACT
1 TACT
21322 TAGAAGGAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 14
0.68 0.04 0.28
Matches are distributed among these distances:
18 7 0.21
19 12 0.35
20 8 0.24
21 7 0.21
ACGTcount: A:0.40, C:0.13, G:0.03, T:0.44
Consensus pattern (19 bp):
TACTATAACAAGTTATATT
Found at i:21292 original size:39 final size:39
Alignment explanation
Indices: 21238--21321 Score: 168
Period size: 39 Copynumber: 2.2 Consensus size: 39
21228 ATAAGGGTGG
21238 TTTACTCACTAATATTTATTAATACTATAACAAGTTATA
1 TTTACTCACTAATATTTATTAATACTATAACAAGTTATA
21277 TTTACTCACTAATATTTATTAATACTATAACAAGTTATA
1 TTTACTCACTAATATTTATTAATACTATAACAAGTTATA
21316 TTTACT
1 TTTACT
21322 TAGAAGGAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.39, C:0.13, G:0.02, T:0.45
Consensus pattern (39 bp):
TTTACTCACTAATATTTATTAATACTATAACAAGTTATA
Found at i:21464 original size:3 final size:3
Alignment explanation
Indices: 21456--21496 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
21446 ATATATATAT
21456 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
21497 CAAAATAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:22589 original size:18 final size:19
Alignment explanation
Indices: 22555--22591 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
22545 GTTAAATTTC
22555 ATTATATGAACAATAAATA
1 ATTATATGAACAATAAATA
*
22574 ATTATAT-AAGAATAAATA
1 ATTATATGAACAATAAATA
22592 CTAAATCAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.32
Consensus pattern (19 bp):
ATTATATGAACAATAAATA
Found at i:23474 original size:19 final size:19
Alignment explanation
Indices: 23450--23487 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
23440 TTTTTATATA
23450 TAGTATGGATAACTATGAT
1 TAGTATGGATAACTATGAT
23469 TAGTATGGATAACTATGAT
1 TAGTATGGATAACTATGAT
23488 AATAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (19 bp):
TAGTATGGATAACTATGAT
Found at i:24751 original size:2 final size:2
Alignment explanation
Indices: 24744--24782 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
24734 TGGAACTTCA
24744 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24783 GGTTCTGACG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25870 original size:72 final size:72
Alignment explanation
Indices: 25751--25890 Score: 246
Period size: 72 Copynumber: 1.9 Consensus size: 72
25741 ATAAATTTTT
25751 TTTTCTAAAAGTTGCTCTCAAACACTAAATTCTTATAGATGTATATCCTTATTTTCTTGACAATG
1 TTTTCTAAAAGTTGCTCTCAAACACTAAATTCTTATAGATGTATATCCTTATTTTCTTGACAATG
25816 CAAAAAA
66 CAAAAAA
* *
25823 TTTTCT-AAAGATTGCTCTCAAACACTAAATTCTTATAGATGTGTATCCTTCTTTTCTTGACAAT
1 TTTTCTAAAAG-TTGCTCTCAAACACTAAATTCTTATAGATGTATATCCTTATTTTCTTGACAAT
25887 GCAA
65 GCAA
25891 TTTTAGTTCC
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
71 4 0.06
72 61 0.94
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.40
Consensus pattern (72 bp):
TTTTCTAAAAGTTGCTCTCAAACACTAAATTCTTATAGATGTATATCCTTATTTTCTTGACAATG
CAAAAAA
Found at i:26933 original size:13 final size:12
Alignment explanation
Indices: 26912--26946 Score: 61
Period size: 13 Copynumber: 2.8 Consensus size: 12
26902 AATAAAGTAA
26912 TAATACTATTAT
1 TAATACTATTAT
26924 TAATTACTATTAT
1 TAA-TACTATTAT
26937 TAATACTATT
1 TAATACTATT
26947 TCAATGTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (12 bp):
TAATACTATTAT
Done.