Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003419.1 Corchorus capsularis cultivar CVL-1 contig03427, 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: 1821
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.36
Found at i:169 original size:22 final size:22
Alignment explanation
Indices: 44--184 Score: 86
Period size: 22 Copynumber: 6.3 Consensus size: 22
34 TTGTCTCTAT
* **
44 GTGGTTATCAAAATTTCATAAA
1 GTGGTTATTAAAATTTCATAGG
* * *
66 ATGGTTATTATAAGTTCAT-GAG
1 GTGGTTATTAAAATTTCATAG-G
* * * * *
88 GAGGTTATCAAAATTCCGTAGT
1 GTGGTTATTAAAATTTCATAGG
**
110 GTGGTTACCAAAATTTCATAGG
1 GTGGTTATTAAAATTTCATAGG
* * *
132 ATCAAGTTATTAAAATTTCTTAGG
1 GT--GGTTATTAAAATTTCATAGG
* *
156 TTGGTTATTGAAATTTCATAGG
1 GTGGTTATTAAAATTTCATAGG
178 GTGGTTA
1 GTGGTTA
185 ATTATCACAA
Statistics
Matches: 86, Mismatches: 29, Indels: 8
0.70 0.24 0.07
Matches are distributed among these distances:
22 68 0.79
23 1 0.01
24 17 0.20
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.38
Consensus pattern (22 bp):
GTGGTTATTAAAATTTCATAGG
Found at i:343 original size:22 final size:21
Alignment explanation
Indices: 295--599 Score: 95
Period size: 22 Copynumber: 13.8 Consensus size: 21
285 TTTCATGGGG
* *
295 AGGTTATCAAAATTTTATAGTG
1 AGGTTATCAAAATTTCATAG-A
*
317 TGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATA-GA
* *
339 AGGTTAT-AAAAGTCTCAATTTCATA
1 AGGTTATCAAAA-TTTC-A--T-AGA
* * * *
364 CGGAGTACCAAAATTTGATAGA
1 AGG-TTATCAAAATTTCATAGA
*
386 AGGTTATC-AAATCTCATAG-
1 AGGTTATCAAAATTTCATAGA
* *
405 AGTTATAATCGAAATTTCATAGA
1 AGGT-T-ATCAAAATTTCATAGA
428 GATCGGATTATCAAAATTT-ATAGAA
1 -A--GG-TTATCAAAATTTCATAG-A
* *
453 AGATTATCAAAATTTCATAGTGT
1 AGGTTATCAAAATTTCATA--GA
* * *
476 TGTGTTATCAAAATTTCAAAGCG
1 AG-GTTATCAAAATTTCATAG-A
* *
499 GGGTTATCAAAATTACATA-A
1 AGGTTATCAAAATTTCATAGA
* *
519 TGTGATTATCAGAATTTCATAG-
1 AG-G-TTATCAAAATTTCATAGA
** * *
541 AGG-GGTCAAAATTTTATAAA
1 AGGTTATCAAAATTTCATAGA
* *
561 GAGGCTATC-AAATTTCATAAA
1 -AGGTTATCAAAATTTCATAGA
*
582 GAGGTTATCAAATTTTCA
1 -AGGTTATCAAAATTTCA
600 AAATGTGATT
Statistics
Matches: 209, Mismatches: 45, Indels: 58
0.67 0.14 0.19
Matches are distributed among these distances:
19 14 0.07
20 11 0.05
21 46 0.22
22 84 0.40
23 5 0.02
24 22 0.11
25 15 0.07
26 7 0.03
27 5 0.02
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.34
Consensus pattern (21 bp):
AGGTTATCAAAATTTCATAGA
Found at i:488 original size:24 final size:22
Alignment explanation
Indices: 416--626 Score: 92
Period size: 22 Copynumber: 9.6 Consensus size: 22
406 GTTATAATCG
*
416 AAATTTCATAGAGATCGGATTATCA
1 AAATTTCATAGTG-T-GG-TTATCA
*** *
441 AAATTT-ATAGAAAGATTATCA
1 AAATTTCATAGTGTGGTTATCA
462 AAATTTCATAGTGTTGTGTTATCA
1 AAATTTCATAGTG-TG-GTTATCA
* * *
486 AAATTTCAAAGCGGGGTTATCA
1 AAATTTCATAGTGTGGTTATCA
* * *
508 AAATTACATAATGTGATTATCA
1 AAATTTCATAGTGTGGTTATCA
* * *
530 GAATTTCATAGAG-GG--GTCA
1 AAATTTCATAGTGTGGTTATCA
* ** * *
549 AAATTTTATAAAGAGGCTATC-
1 AAATTTCATAGTGTGGTTATCA
** *
570 AAATTTCATAAAGAGGTTATCA
1 AAATTTCATAGTGTGGTTATCA
* * * *
592 AATTTTCAAAATGTGATTA-CAA
1 AAATTTCATAGTGTGGTTATC-A
614 AAATTTCATAGTG
1 AAATTTCATAGTG
627 GTATTTTTGG
Statistics
Matches: 142, Mismatches: 36, Indels: 19
0.72 0.18 0.10
Matches are distributed among these distances:
19 13 0.09
20 2 0.01
21 33 0.23
22 64 0.45
23 2 0.01
24 22 0.15
25 6 0.04
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (22 bp):
AAATTTCATAGTGTGGTTATCA
Found at i:573 original size:21 final size:21
Alignment explanation
Indices: 549--597 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
539 AGAGGGGTCA
549 AAATTTTATAAAGAGGCTATC
1 AAATTTTATAAAGAGGCTATC
* *
570 AAATTTCATAAAGAGGTTATC
1 AAATTTTATAAAGAGGCTATC
591 AAATTTT
1 AAATTTT
598 CAAAATGTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.37
Consensus pattern (21 bp):
AAATTTTATAAAGAGGCTATC
Found at i:731 original size:20 final size:20
Alignment explanation
Indices: 706--755 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
696 TATGGAGTAG
706 TCAAAATTTCAAGGAGGATA
1 TCAAAATTTCAAGGAGGATA
*
726 TCAAAA-TTCAGGGAGGATA
1 TCAAAATTTCAAGGAGGATA
*
745 ACAAAATTTCA
1 TCAAAATTTCA
756 TAGTTTAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.24
Consensus pattern (20 bp):
TCAAAATTTCAAGGAGGATA
Found at i:792 original size:22 final size:20
Alignment explanation
Indices: 767--838 Score: 81
Period size: 22 Copynumber: 3.3 Consensus size: 20
757 AGTTTAGTTT
767 TCAAAATTTCACAAGAGGGTTA
1 TCAAAATTTCA-AAG-GGGTTA
789 TCAAAATTTCAAAGGGAGATTA
1 TCAAAATTTCAAAGGG-G-TTA
*
811 ACAAAATTTCATAATGGGGTTA
1 TCAAAATTTCA-AA-GGGGTTA
833 TCAAAA
1 TCAAAA
839 AATTATATGG
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
20 2 0.05
21 4 0.09
22 32 0.73
23 3 0.07
24 3 0.07
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (20 bp):
TCAAAATTTCAAAGGGGTTA
Found at i:837 original size:66 final size:61
Alignment explanation
Indices: 697--838 Score: 144
Period size: 66 Copynumber: 2.2 Consensus size: 61
687 AACTTTTATT
*
697 ATGGAG-TAGTCAAAATTTCAAGGAGGATATCAAAATTCAGGGAGGATAACAAAATTTCATA
1 ATGGAGTTA-TCAAAATTTCAAAGAGGATATCAAAATTCAGGGAGGATAACAAAATTTCATA
* ** * *
758 GTTTAGTTTTCAAAATTTCACAAGAGGGTTATCAAAATTTCAAAGGGA-GATTAACAAAATTTCA
1 ATGGAGTTATCAAAATTTCA-AAGA-GGATATCAAAA-TTC--AGGGAGGA-TAACAAAATTTCA
822 TA
60 TA
*
824 ATGGGGTTATCAAAA
1 ATGGAGTTATCAAAA
839 AATTATATGG
Statistics
Matches: 63, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
61 14 0.22
62 4 0.06
63 10 0.16
64 3 0.05
65 2 0.03
66 30 0.48
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.29
Consensus pattern (61 bp):
ATGGAGTTATCAAAATTTCAAAGAGGATATCAAAATTCAGGGAGGATAACAAAATTTCATA
Found at i:860 original size:44 final size:44
Alignment explanation
Indices: 767--863 Score: 108
Period size: 44 Copynumber: 2.2 Consensus size: 44
757 AGTTTAGTTT
*
767 TCAAAATTTCACAAGAGGGTTATCAAAATTTCAAAGGGAGATTA
1 TCAAAATTTCACAAGAGGGTTATCAAAAATTCAAAGGGAGATTA
* * * * *
811 ACAAAATTTCATAATG-GGGTTATCAAAAAATT-ATATGGAGGTTA
1 TCAAAATTTCACAA-GAGGGTTATC-AAAAATTCAAAGGGAGATTA
855 TCAAAATTT
1 TCAAAATTT
864 GTAGTGATCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
44 37 0.84
45 7 0.16
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.31
Consensus pattern (44 bp):
TCAAAATTTCACAAGAGGGTTATCAAAAATTCAAAGGGAGATTA
Found at i:901 original size:22 final size:22
Alignment explanation
Indices: 870--972 Score: 91
Period size: 23 Copynumber: 4.6 Consensus size: 22
860 ATTTGTAGTG
* *
870 ATCAAGATTTCATAAGAAAGTT
1 ATCAAAATTTCATAGGAAAGTT
* * *
892 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGGAAAG-TT
* *
915 ATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATAGGAA-AGTT
*
938 ATCAAAATTTCATAGCG-AGGTT
1 ATCAAAATTTCATAG-GAAAGTT
*
960 ATCACAATTTCAT
1 ATCAAAATTTCAT
973 TGTGTGACTA
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
22 29 0.44
23 36 0.55
24 1 0.02
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAGGAAAGTT
Found at i:918 original size:23 final size:23
Alignment explanation
Indices: 890--969 Score: 108
Period size: 23 Copynumber: 3.5 Consensus size: 23
880 CATAAGAAAG
890 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* *
913 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGGAGGT
* *
936 TTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTTATAGGGAGGT
*
958 TTATCACAATTT
1 TTATCAAAATTT
970 CATTGTGTGA
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 11 0.22
23 39 0.78
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:999 original size:22 final size:22
Alignment explanation
Indices: 959--1001 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
949 ATAGCGAGGT
* **
959 TATCACAATTTCATTGTGTGAC
1 TATCAAAATTTCAGAGTGTGAC
981 TATCAAAATTTCAGAGTGTGA
1 TATCAAAATTTCAGAGTGTGA
1002 TTACTAACAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCAGAGTGTGAC
Found at i:1071 original size:22 final size:23
Alignment explanation
Indices: 1046--1097 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
1036 CATAACGTAA
*
1046 TTATCAATATATCATA-TGAAGG
1 TTATCAACATATCATAGTGAAGG
* **
1068 TTATCAACATCTCATAGTGTTGG
1 TTATCAACATATCATAGTGAAGG
1091 TTATCAA
1 TTATCAA
1098 AATTTTATTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.38
Consensus pattern (23 bp):
TTATCAACATATCATAGTGAAGG
Found at i:1617 original size:2 final size:2
Alignment explanation
Indices: 1612--1638 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1602 ATCTAGTGTG
1612 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1639 TATTTGTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.