Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000738.1 Corchorus capsularis cultivar CVL-1 contig00738, 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, 724
Length: 1208
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Found at i:153 original size:22 final size:21
Alignment explanation
Indices: 128--618 Score: 206
Period size: 22 Copynumber: 22.6 Consensus size: 21
118 TGATCTCATC
128 ATGAAATTTTGATAACCTTCCT
1 ATGAAATTTTGATAACC-TCCT
* * * *
150 ATGAAATTTTAACAACGATACT
1 ATGAAATTTTGATAAC-CTCCT
* * * * **
172 ATGGAATTTCGAGAATCTTTT
1 ATGAAATTTTGATAACCTCCT
** *
193 AT-AAATTTTTTTTAACCTTCTT
1 ATGAAA-TTTTGATAACC-TCCT
*
215 ATGAAATTTTGTTAACCTCCT
1 ATGAAATTTTGATAACCTCCT
* * ** *
236 AAGGAATTTTGA-AGATATCAAT
1 ATGAAATTTTGATA-ACCTC-CT
* * * *
258 ATAAAATGTTGATAACTTCCCA
1 ATGAAATTTTGATAACCT-CCT
* *
280 ATGAAATTTTGATAACCAACATT
1 ATGAAATTTTGATAACC-TC-CT
* *
303 ATGAGATGTTGATAACCTCCAT
1 ATGAAATTTTGATAACCTCC-T
* * * *
325 ATGATATATTGATAACCACGTT
1 ATGAAATTTTGATAACCTC-CT
* * *
347 ATGAAAATTTAAAAACCTCCAT
1 ATGAAATTTTGATAACCTCC-T
* * *
369 ATG-AATTGTTAATAATCATACT
1 ATGAAATT-TTGATAA-CCTCCT
* * *
391 TTGAAATTTTGATAATCACACT
1 ATGAAATTTTGATAACCTC-CT
*
413 ATGAAATTGTGATAACCTCGCT
1 ATGAAATTTTGATAACCTC-CT
* *
435 ATTAAATTTTGATAAATCTTCCT
1 ATGAAATTTTGAT-AA-CCTCCT
*
458 ATAAAATTTTGATAAACCTCCCT
1 ATGAAATTTTGAT-AACCT-CCT
* * *
481 ATAAAATTTTGATAACTTTCTT
1 ATGAAATTTTGATAAC-CTCCT
*
503 ATGAAATCTTGATAA----CT
1 ATGAAATTTTGATAACCTCCT
*
520 A-CAAATTTTGATAACCTCTCT
1 ATGAAATTTTGATAACCTC-CT
** *
541 ATGATTTTTTGATAACCTCATT
1 ATGAAATTTTGATAACCTC-CT
* *
563 ATGAAATTTTGTTAATCTCCCT
1 ATGAAATTTTGATAACCT-CCT
*
585 ATGAAATTTTGATAACCCTCTT
1 ATGAAATTTTGATAA-CCTCCT
607 ATGAAATTTTGA
1 ATGAAATTTTGA
619 AAACTAAATT
Statistics
Matches: 344, Mismatches: 96, Indels: 58
0.69 0.19 0.12
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
20 3 0.01
21 31 0.09
22 228 0.66
23 66 0.19
24 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.40
Consensus pattern (21 bp):
ATGAAATTTTGATAACCTCCT
Found at i:315 original size:45 final size:44
Alignment explanation
Indices: 263--373 Score: 118
Period size: 45 Copynumber: 2.5 Consensus size: 44
253 TCAATATAAA
* *
263 ATGTTGATAACTTCCCA-ATGAAATTTTGATAACCAACATTATGAG
1 ATGTTGATAACCT-CCATATGAAATATTGATAACC-ACATTATGAG
* * *
308 ATGTTGATAACCTCCATATGATATATTGATAACCACGTTATGAAA
1 ATGTTGATAACCTCCATATGAAATATTGATAACCACATTATG-AG
* *
353 AT-TTAAAAACCTCCATATGAA
1 ATGTTGATAACCTCCATATGAA
374 TTGTTAATAA
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
44 26 0.46
45 30 0.54
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (44 bp):
ATGTTGATAACCTCCATATGAAATATTGATAACCACATTATGAG
Found at i:464 original size:23 final size:23
Alignment explanation
Indices: 433--517 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
423 GATAACCTCG
*
433 CTATTAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAATCTTC
* *
456 CTATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAATCTTC
*
479 CTATAAAATTTTGATAACT-TTC
1 CTATAAAATTTTGATAAATCTTC
* * *
501 TTATGAAATCTTGATAA
1 CTATAAAATTTTGATAA
518 CTACAAATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 16 0.30
23 37 0.70
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.42
Consensus pattern (23 bp):
CTATAAAATTTTGATAAATCTTC
Found at i:516 original size:45 final size:45
Alignment explanation
Indices: 394--517 Score: 130
Period size: 45 Copynumber: 2.8 Consensus size: 45
384 TCATACTTTG
* * *
394 AAATTTTGAT-AATC-ACACTATGAAATTGTGAT-AACCTCGCTATT
1 AAATTTTGATAAATCTTC-CTATGAAATT-TGATAAACCTCCCTATA
*
438 AAATTTTGATAAATCTTCCTATAAAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAATCTTCCTATGAAA-TTTGATAAACCTCCCTATA
* *
484 AAATTTTGATAACT-TTCTTATGAAATCTTGATAA
1 AAATTTTGATAAATCTTCCTATGAAAT-TTGATAA
518 CTACAAATTT
Statistics
Matches: 68, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
44 11 0.16
45 31 0.46
46 26 0.38
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.40
Consensus pattern (45 bp):
AAATTTTGATAAATCTTCCTATGAAATTTGATAAACCTCCCTATA
Found at i:587 original size:44 final size:44
Alignment explanation
Indices: 205--954 Score: 218
Period size: 44 Copynumber: 17.4 Consensus size: 44
195 AAATTTTTTT
* * * *
205 TAACCTTCTTATGAAATTTTGTTAACCT-CCTAAGGAATTTTGA
1 TAACCCTCTTATGAAATTTTGATAACCTCCCTATGAAATTTTGA
** * * * * *
248 -AGA-TATCAATATAAAATGTTGATAACTTCCCAATGAAATTTTGA
1 TA-ACCCTC-TTATGAAATTTTGATAACCTCCCTATGAAATTTTGA
** * * * * *
292 TAACCAACATTATGAGATGTTGATAACCTCCATATGATATATTGA
1 TAACCCTC-TTATGAAATTTTGATAACCTCCCTATGAAATTTTGA
* * * * * *
337 TAACCAC-GTTATGAAAATTTAAAAACCTCCATATG-AATTGTTAA
1 TAACC-CTCTTATGAAATTTTGATAACCTCCCTATGAAATT-TTGA
* * * * * *
381 TAATCATACTT-TGAAATTTTGATAATCACACTATGAAATTGTGA
1 TAACCCT-CTTATGAAATTTTGATAACCTCCCTATGAAATTTTGA
* * * * *
425 TAA-CCTCGCTATTAAATTTTGATAAATCTTCCTATAAAATTTTGA
1 TAACCCTC-TTATGAAATTTTGAT-AACCTCCCTATGAAATTTTGA
* * * * * * *
470 TAAACCTCCCTATAAAATTTTGATAACTTTCTTATGAAATCTTGA
1 TAACCCT-CTTATGAAATTTTGATAACCTCCCTATGAAATTTTGA
* * **
515 TAA----C-TA-CAAATTTTGATAACCTCTCTATGATTTTTTGA
1 TAACCCTCTTATGAAATTTTGATAACCTCCCTATGAAATTTTGA
* *
553 TAA-CCTCATTATGAAATTTTGTTAATCTCCCTATGAAATTTTGA
1 TAACCCTC-TTATGAAATTTTGATAACCTCCCTATGAAATTTTGA
* ***
597 TAACCCTCTTATGAAATTTTGA-AAACTAAATTATGAAATTTTGA
1 TAACCCTCTTATGAAATTTTGATAACCT-CCCTATGAAATTTTGA
* * * * * * *
641 CT-ACTCC-ATAATAAAAGTTTAATAACCTTCC--T--AA-TTTGG
1 -TAAC-CCTCTTATGAAATTTTGATAACCTCCCTATGAAATTTTGA
* * *
680 TAACCATAC-TAAGAAATTTTGATAACCTCCCCA-G-AA-----A
1 TAACCCT-CTTATGAAATTTTGATAACCTCCCTATGAAATTTTGA
* * * *
717 T-A-CCAC-TATGAAATTTTTG-TAA--TCACATTTGAAAATTTGA
1 TAACCCTCTTATGAAA-TTTTGATAACCTC-CCTATGAAATTTTGA
**
757 TAA-CCTCTTTATGAAATTTTGATAACCTCTTTATGAAATTTTGA
1 TAACCCTC-TTATGAAATTTTGATAACCTCCCTATGAAATTTTGA
* * * *
801 TAA-CCTCTTTATAAAATTTTGTTTGACC-CCTTTATGAAATTCTT-A
1 TAACCCTC-TTATGAAATTTTG-ATAACCTCC-CTATGAAATT-TTGA
* * * * *
846 TAATCAC-ATTATGTAATTTTGATAACCTCGCTTTGAAATTTTGA
1 TAA-CCCTCTTATGAAATTTTGATAACCTCCCTATGAAATTTTGA
* * * * *
890 TAACAACGC-TATGGAATTTTGATAATCTTCCTAT-AAATTTTGA
1 TAAC-CCTCTTATGAAATTTTGATAACCTCCCTATGAAATTTTGA
*
933 TAATCCAATCTCTATGAAATTT
1 TAA-CC-CTCT-TATGAAATTT
955 CAATAATCAC
Statistics
Matches: 519, Mismatches: 128, Indels: 117
0.68 0.17 0.15
Matches are distributed among these distances:
32 2 0.00
33 1 0.00
34 11 0.02
35 8 0.02
36 1 0.00
37 1 0.00
38 29 0.06
39 24 0.05
40 5 0.01
41 7 0.01
42 10 0.02
43 52 0.10
44 214 0.41
45 124 0.24
46 28 0.05
47 2 0.00
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.39
Consensus pattern (44 bp):
TAACCCTCTTATGAAATTTTGATAACCTCCCTATGAAATTTTGA
Found at i:840 original size:23 final size:22
Alignment explanation
Indices: 746--954 Score: 167
Period size: 22 Copynumber: 9.4 Consensus size: 22
736 TAATCACATT
*
746 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
768 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
790 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * * *
812 TAAAATTTTGTTTGACCCCTTTA
1 TGAAATTTTG-ATAACCTCTTTA
* * *
835 TGAAATTCTT-ATAATCACATTA
1 TGAAATT-TTGATAACCTCTTTA
* *
857 TGTAATTTTGATAACCTCGCTT-
1 TGAAATTTTGATAACCTC-TTTA
** **
879 TGAAATTTTGATAACAACGCTA
1 TGAAATTTTGATAACCTCTTTA
*
901 TGGAATTTTGATAA--TCTTCCTA
1 TGAAATTTTGATAACCTCTT--TA
*
923 T-AAATTTTGATAATCCAATCTCTA
1 TGAAATTTTGATAA-CC--TCTTTA
947 TGAAATTT
1 TGAAATTT
955 CAATAATCAC
Statistics
Matches: 148, Mismatches: 26, Indels: 23
0.75 0.13 0.12
Matches are distributed among these distances:
20 1 0.01
21 14 0.09
22 102 0.69
23 17 0.11
24 5 0.03
25 6 0.04
26 3 0.02
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:885 original size:67 final size:67
Alignment explanation
Indices: 763--888 Score: 166
Period size: 67 Copynumber: 1.9 Consensus size: 67
753 TTGATAACCT
* * *
763 CTTTATGAAATTTTGATAACCTCTTTATGAAATTTTGATAACCTCTTTATAAAATTTTGTTTGAC
1 CTTTATGAAATTTTGATAACCACATTATGAAATTTTGATAACCTCCTTATAAAATTTTGTTTGAC
828 CC
66 CC
* * *
830 CTTTATGAAATTCTT-ATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTG
1 CTTTATGAAATT-TTGATAACCACATTATGAAATTTTGATAACCTC-CTTATAAAATTTTG
889 ATAACAACGC
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
67 47 0.92
68 4 0.08
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (67 bp):
CTTTATGAAATTTTGATAACCACATTATGAAATTTTGATAACCTCCTTATAAAATTTTGTTTGAC
CC
Found at i:925 original size:111 final size:108
Alignment explanation
Indices: 723--931 Score: 260
Period size: 111 Copynumber: 1.9 Consensus size: 108
713 GAAATACCAC
* * * ** **
723 TATGAAATTTTTGTAATCACATTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTCTT
1 TATGAAATTCTTATAATCACATTTGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAACGC
788 TATGAAATTTTGATAACCTCTTTATAAAATTTTGTTTGACCCCTT
66 TATGAAATTTTGATAA-CTCTTTAT-AAATTTTGTTTGACCCCTT
* *
833 TATGAAATTCTTATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAAC
1 TATGAAATTCTTATAATCACATT-TGAAAATTTGATAACCTC-CTTATGAAATTTTGATAACAAC
*
897 GCTATGGAATTTTGATAA-TCTTCCTATAAATTTTG
64 GCTATGAAATTTTGATAACTCTT--TATAAATTTTG
932 ATAATCCAAT
Statistics
Matches: 85, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
109 4 0.05
110 29 0.34
111 50 0.59
112 2 0.02
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (108 bp):
TATGAAATTCTTATAATCACATTTGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAACGC
TATGAAATTTTGATAACTCTTTATAAATTTTGTTTGACCCCTT
Done.