Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004397.1 Corchorus capsularis cultivar CVL-1 contig04405, 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, 658
Length: 1097
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Found at i:146 original size:19 final size:19
Alignment explanation
Indices: 87--153 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
77 TGATGGAGTA
* *
87 ATCAAAATTTTAGGGAGGAT
1 ATCAAAA-TTCAGGGAGAAT
* *
107 ACCAAAATTCAGGGAGGAT
1 ATCAAAATTCAGGGAGAAT
* *
126 ATCAAAATTCAGTGATAAT
1 ATCAAAATTCAGGGAGAAT
145 ATCAAAATT
1 ATCAAAATT
154 TCATATGAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 35 0.85
20 6 0.15
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.27
Consensus pattern (19 bp):
ATCAAAATTCAGGGAGAAT
Found at i:172 original size:22 final size:22
Alignment explanation
Indices: 144--617 Score: 128
Period size: 22 Copynumber: 21.7 Consensus size: 22
134 TCAGTGATAA
144 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
* **
166 TATCAAATTTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
188 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
210 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * *
231 AGATCAAAATTTCATAGGGAA-AT
1 -TATCAAAATTTCATA-TGAAGGT
*
254 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
** * * *
276 TATCAAAAAATCATAAGGAGCT
1 TATCAAAATTTCATATGAAGGT
*
298 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
314 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
336 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* * *
359 TATTAAAATTTTATA-GAAAGATT
1 TATCAAAATTTCATATG-AAG-GT
*
382 TATCAAAATTTCATAGCGATA--T
1 TATCAAAATTTCATA-TGA-AGGT
* * ** *
404 TATCACAATTTCATAGGGTGAT
1 TATCAAAATTTCATATGAAGGT
* * * *
426 TATCAAAATTTTAAAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
*
448 TA-CTAACAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATATGAAGGT
** * *
470 T-TTTAAATTT-TTATAAAGTGGT
1 TATCAAAATTTCATATGAA--GGT
* * *
492 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
514 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
537 TATCAAAATTTCAT-TGGGAA-GT
1 TATCAAAATTTCATAT--GAAGGT
*
559 TATCAAAATTTCATATTG-AGAT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
581 CT-TCAAAATTCCTTAGGGAGGT
1 -TATCAAAATTTCATATGAAGGT
*
603 TAACAAAATTTCATA
1 TATCAAAATTTCATA
618 AGAAAGTTTA
Statistics
Matches: 330, Mismatches: 81, Indels: 82
0.67 0.16 0.17
Matches are distributed among these distances:
16 8 0.02
17 2 0.01
18 2 0.01
20 8 0.02
21 19 0.06
22 219 0.66
23 62 0.19
24 8 0.02
25 2 0.01
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:237 original size:66 final size:66
Alignment explanation
Indices: 144--283 Score: 158
Period size: 66 Copynumber: 2.1 Consensus size: 66
134 TCAGTGATAA
* * *** * **
144 TATCAAAATTTCATATGAAGGTTATCAAATTTTCATAGTTTAGTTTTCAAAATTTCATAA-GAGG
1 TATCAAAATTTCATATGAAGGTGATCAAAATTTCATAGGGAAATTAACAAAATTTCATAATGA-G
208 GT
65 GT
* *
210 TATCAAAATTTCATA-GTATGTAGATCAAAATTTCATAGGGAAATTAACAAAATTTCATAATGAG
1 TATCAAAATTTCATATGAAGGT-GATCAAAATTTCATAGGGAAATTAACAAAATTTCATAATGAG
274 GT
65 GT
276 TATCAAAA
1 TATCAAAA
284 AATCATAAGG
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
65 4 0.06
66 56 0.90
67 2 0.03
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.36
Consensus pattern (66 bp):
TATCAAAATTTCATATGAAGGTGATCAAAATTTCATAGGGAAATTAACAAAATTTCATAATGAGG
T
Found at i:238 original size:44 final size:43
Alignment explanation
Indices: 144--351 Score: 153
Period size: 44 Copynumber: 4.9 Consensus size: 43
134 TCAGTGATAA
* *
144 TATCAAAATTTCATATGAAGGTTATCAAATTTTCATAGTTTAG
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTTTAG
* *
187 TTTTCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGTATGTAG
1 -TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGT-T-TAG
* * * * *
233 -ATCAAAATTTCATAGGGAA-ATTAACAAAATTTCATA-ATGAGG
1 TATCAAAATTTCATA-AGAAGGTTATCAAAATTTCATAGTTTA-G
** * * *
275 TTATCAAAAAATCATAAGGAGCTTATCAAAATTT-GTAG--T--
1 -TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTTTAG
* * *
314 TATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAG
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAG
352 GGAGGTTTAT
Statistics
Matches: 129, Mismatches: 26, Indels: 23
0.72 0.15 0.13
Matches are distributed among these distances:
38 27 0.21
39 3 0.02
41 1 0.01
42 2 0.02
43 4 0.03
44 86 0.67
45 3 0.02
46 3 0.02
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (43 bp):
TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTTTAG
Found at i:366 original size:23 final size:23
Alignment explanation
Indices: 313--397 Score: 84
Period size: 23 Copynumber: 3.7 Consensus size: 23
303 AAATTTGTAG
* *
313 TTATCAAGATTTCATAAGAAAG--
1 TTATCAAAATTTTAT-AGAAAGAT
** *
335 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGAAAGAT
*
358 TTATTAAAATTTTATAGAAAGAT
1 TTATCAAAATTTTATAGAAAGAT
*
381 TTATCAAAATTTCATAG
1 TTATCAAAATTTTATAG
398 CGATATTATC
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
21 4 0.08
22 13 0.25
23 34 0.67
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAGAAAGAT
Found at i:561 original size:45 final size:45
Alignment explanation
Indices: 488--573 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
478 TTTTATAAAG
* * *
488 TGGTTATCAATATATCATATGGAGGTTATCAACATCTCATAGTGT
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
* *
533 TGGTTATCAAAATTTCAT-TGGGAAGTTATCAAAATTTCATA
1 TGGTTATCAAAATATCATAT-GGAAGTTATCAAAATCTCATA
574 TTGAGATCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 1 0.03
45 34 0.97
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
Done.