Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012603.1 Corchorus capsularis cultivar CVL-1 contig12624, 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: 16491
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Found at i:534 original size:22 final size:21
Alignment explanation
Indices: 479--651 Score: 113
Period size: 22 Copynumber: 8.0 Consensus size: 21
469 CATAGAAAAA
479 TTATC-AAATTTCATAGT-GTAG
1 TTATCAAAATTTCATA-TAG-AG
500 TTA-CAAAATTTCATATAGAAG
1 TTATCAAAATTTCATATAG-AG
*
521 TTATCAAAACTTCATAGT-GTAG
1 TTATCAAAATTTCATA-TAG-AG
*
543 TTATCAAAATTTCATACAGAG
1 TTATCAAAATTTCATATAGAG
* * *
564 ATTACCAAAATTTCATAAAAAGG
1 -TTATCAAAATTTCATATAGA-G
* * *
587 TTACCAAAATTTCTTAGAGATG
1 TTATCAAAATTTCATATAGA-G
* *
609 TTAAT-AAAATTTCATACGAAAG
1 TT-ATCAAAATTTCATA-TAGAG
* *
631 TTAACAAAATTTCATAGAGAG
1 TTATCAAAATTTCATATAGAG
652 GGAGGTTACC
Statistics
Matches: 125, Mismatches: 17, Indels: 20
0.77 0.10 0.12
Matches are distributed among these distances:
20 2 0.02
21 26 0.21
22 91 0.73
23 6 0.05
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.34
Consensus pattern (21 bp):
TTATCAAAATTTCATATAGAG
Found at i:552 original size:44 final size:43
Alignment explanation
Indices: 461--580 Score: 145
Period size: 44 Copynumber: 2.8 Consensus size: 43
451 ACAATCAAAC
* * * *
461 CAAAATTACATAGAAAAATTATC-AAATTTCATAGTGTAGTTA
1 CAAAATTTCATACAGAAGTTATCAAAATTTCATAGTGTAGTTA
* *
503 CAAAATTTCATATAGAAGTTATCAAAACTTCATAGTGTAGTTA
1 CAAAATTTCATACAGAAGTTATCAAAATTTCATAGTGTAGTTA
*
546 TCAAAATTTCATACAG-AGATTACCAAAATTTCATA
1 -CAAAATTTCATACAGAAG-TTATCAAAATTTCATA
581 AAAAGGTTAC
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
42 19 0.28
43 20 0.30
44 28 0.42
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.33
Consensus pattern (43 bp):
CAAAATTTCATACAGAAGTTATCAAAATTTCATAGTGTAGTTA
Found at i:595 original size:44 final size:43
Alignment explanation
Indices: 498--651 Score: 132
Period size: 44 Copynumber: 3.5 Consensus size: 43
488 TTCATAGTGT
* * * ****
498 AGTT-ACAAAATTTCATATAGAAGTTATCAAAACTTCATAGTGT
1 AGTTAACAAAATTTCATAGAG-AGTTAACAAAATTTCATACAAA
* * *
541 AGTTATCAAAATTTCATACAGAGATTACCAAAATTTCATA-AAA
1 AGTTAACAAAATTTCATAGAGAG-TTAACAAAATTTCATACAAA
* * * *
584 AGGTTACCAAAATTTCTTAGAGATGTTAATAAAATTTCATACGAA
1 A-GTTAACAAAATTTCATAGAGA-GTTAACAAAATTTCATACAAA
629 AGTTAACAAAATTTCATAGAGAG
1 AGTTAACAAAATTTCATAGAGAG
652 GGAGGTTACC
Statistics
Matches: 91, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
43 8 0.09
44 79 0.87
45 4 0.04
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.32
Consensus pattern (43 bp):
AGTTAACAAAATTTCATAGAGAGTTAACAAAATTTCATACAAA
Found at i:595 original size:66 final size:64
Alignment explanation
Indices: 479--646 Score: 157
Period size: 66 Copynumber: 2.6 Consensus size: 64
469 CATAGAAAAA
* * * *
479 TTATC-AAATTTCATA-GTGTAGTTACAAAATTTCATATAGAAGTTATCAAAACTTCATAGTG-T
1 TTATCAAAATTTCATACGAG-A-TTACAAAATTTCATATAAAAGTTACCAAAACTTCATAGAGAT
541 AG
64 -G
* *
543 TTATCAAAATTTCATACAGAGATTACCAAAATTTCATA-AAAAGGTTACCAAAATTTCTTAGAGA
1 TTATCAAAATTTCATAC-GAGATTA-CAAAATTTCATATAAAA-GTTACCAAAACTTCATAGAGA
607 TG
63 TG
*
609 TTAAT-AAAATTTCATACGAAAGTTAACAAAATTTCATA
1 TT-ATCAAAATTTCATACGAGA-TT-ACAAAATTTCATA
647 GAGAGGGAGG
Statistics
Matches: 88, Mismatches: 7, Indels: 16
0.79 0.06 0.14
Matches are distributed among these distances:
64 5 0.06
65 19 0.22
66 58 0.66
67 6 0.07
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (64 bp):
TTATCAAAATTTCATACGAGATTACAAAATTTCATATAAAAGTTACCAAAACTTCATAGAGATG
Found at i:717 original size:22 final size:22
Alignment explanation
Indices: 502--731 Score: 70
Period size: 22 Copynumber: 10.5 Consensus size: 22
492 TAGTGTAGTT
* * *
502 ACAAAATTTCATATAGAAGTTA
1 ACAAAATTTTATAGAGAGGTTA
* * * *
524 TCAAAACTTCATAGTGTA-GTTA
1 ACAAAATTTTATAGAG-AGGTTA
* * * *
546 TCAAAATTTCATACAGAGATTA
1 ACAAAATTTTATAGAGAGGTTA
* * * *
568 CCAAAATTTCATAAAAAGGTTA
1 ACAAAATTTTATAGAGAGGTTA
* *
590 CCAAAATTTCT-TAGAGATGTTA
1 ACAAAATTT-TATAGAGAGGTTA
* * *
612 ATAAAATTTCATACGA-AAGTTA
1 ACAAAATTTTATA-GAGAGGTTA
*
634 ACAAAATTTCATAGAGAGGGAGGTTA
1 ACAAAATTT--TATAGA--GAGGTTA
* *
660 CCAAAA-TTTAT-----GCTTA
1 ACAAAATTTTATAGAGAGGTTA
*
676 TCAAAATTTCCTAT-GA-AGGTTA
1 ACAAAATTT--TATAGAGAGGTTA
698 ACAAAATTTTATAGAGAGGTTA
1 ACAAAATTTTATAGAGAGGTTA
720 TA-AAAATTTTAT
1 -ACAAAATTTTAT
732 GCAAAGGCTA
Statistics
Matches: 159, Mismatches: 30, Indels: 38
0.70 0.13 0.17
Matches are distributed among these distances:
16 9 0.06
17 2 0.01
19 3 0.02
20 3 0.02
21 3 0.02
22 117 0.74
23 8 0.05
24 2 0.01
25 2 0.01
26 10 0.06
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (22 bp):
ACAAAATTTTATAGAGAGGTTA
Found at i:747 original size:22 final size:21
Alignment explanation
Indices: 673--747 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 21
663 AAATTTATGC
673 TTATCAAAATTTCCTATG-AAGG
1 TTATCAAAATTT--TATGAAAGG
* *
695 TTAACAAAATTTTATAGAGAGG
1 TTATCAAAATTTTAT-GAAAGG
*
717 TTATAAAAATTTTATGCAAAGG
1 TTATCAAAATTTTATG-AAAGG
*
739 CTATCAAAA
1 TTATCAAAA
748 ATACATAGAG
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
20 3 0.07
21 2 0.05
22 38 0.88
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.33
Consensus pattern (21 bp):
TTATCAAAATTTTATGAAAGG
Found at i:3702 original size:8 final size:8
Alignment explanation
Indices: 3689--3718 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
3679 ATAAGCAAGC
3689 CTTGTAGG
1 CTTGTAGG
3697 CTTGTAGG
1 CTTGTAGG
3705 CTTGTAGG
1 CTTGTAGG
3713 C-TGTAG
1 CTTGTAG
3719 CTCTTCAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 5 0.23
8 17 0.77
ACGTcount: A:0.13, C:0.13, G:0.37, T:0.37
Consensus pattern (8 bp):
CTTGTAGG
Found at i:4889 original size:25 final size:24
Alignment explanation
Indices: 4861--4917 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 24
4851 GTGAATTGTA
*
4861 AAATAAATTGAATAATAAAGATATT
1 AAATAAATTGAATAATAAA-ACATT
* * *
4886 AAATAGATTTAATAATTAAACATT
1 AAATAAATTGAATAATAAAACATT
4910 AAA-AAATT
1 AAATAAATT
4918 CAAAGGCTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 4 0.15
24 7 0.26
25 16 0.59
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (24 bp):
AAATAAATTGAATAATAAAACATT
Done.