Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004916.1 Corchorus capsularis cultivar CVL-1 contig04934, 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: 3236
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Found at i:273 original size:30 final size:32
Alignment explanation
Indices: 214--284 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 32
204 GAGGAAACTT
*
214 TATATTTTCCGATTGTACCCTTATTTTT-AAAA
1 TATA-TTTCCAATTGTACCCTTATTTTTAAAAA
* *
246 TATATTTCCAATTGTA-TCTTTTTTTTAAAAA
1 TATATTTCCAATTGTACCCTTATTTTTAAAAA
*
277 CATATTTC
1 TATATTTC
285 TAAATTGCCA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 8 0.24
31 22 0.65
32 4 0.12
ACGTcount: A:0.30, C:0.14, G:0.04, T:0.52
Consensus pattern (32 bp):
TATATTTCCAATTGTACCCTTATTTTTAAAAA
Found at i:366 original size:105 final size:106
Alignment explanation
Indices: 249--462 Score: 385
Period size: 105 Copynumber: 2.0 Consensus size: 106
239 TTTAAAATAT
* *
249 ATTTCCAATTGTATCTTTTTTTTAAAAACATATTTCTAAATTGCCATTACTAAATAATATTTTAA
1 ATTTCCAATTGTACCCTTTTTTTAAAAACATATTTCTAAATTGCCATTACTAAATAATATTTTAA
314 TTATTCCATTA-TTTTTCAATCATAAATTATTTCATTATTA
66 TTATTCCATTATTTTTTCAATCATAAATTATTTCATTATTA
*
354 ATTTCCAATTGTACCCTTTTTTTAAAAATATATTTCTAAATTGCCATTACTAAATAATATTTTAA
1 ATTTCCAATTGTACCCTTTTTTTAAAAACATATTTCTAAATTGCCATTACTAAATAATATTTTAA
*
419 TTATTCCATTATTTTTTTAATCATAAATTATTTCATTATTA
66 TTATTCCATTATTTTTTCAATCATAAATTATTTCATTATTA
460 ATT
1 ATT
463 ATATAATACT
Statistics
Matches: 104, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
105 73 0.70
106 31 0.30
ACGTcount: A:0.35, C:0.12, G:0.02, T:0.51
Consensus pattern (106 bp):
ATTTCCAATTGTACCCTTTTTTTAAAAACATATTTCTAAATTGCCATTACTAAATAATATTTTAA
TTATTCCATTATTTTTTCAATCATAAATTATTTCATTATTA
Found at i:917 original size:19 final size:20
Alignment explanation
Indices: 890--927 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
880 TACTATTATT
890 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
910 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
928 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:1194 original size:46 final size:44
Alignment explanation
Indices: 1101--1216 Score: 117
Period size: 46 Copynumber: 2.6 Consensus size: 44
1091 TCTCTATGTA
* * *
1101 GTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGGAG
1 GTTATCAAAATTTCATAGGATGGTTATTAAAATCTCATGAGGAG
* * *
1145 GTTACCAAAATTTCATAGGATTAGGTTATTAAAATCTC-TTAGGTTG
1 GTTATCAAAATTTCATAGGA-T-GGTTATTAAAATCTCATGAGG-AG
** *
1191 GTTATTGAAATTTCATAGGGTGGTTA
1 GTTATCAAAATTTCATAGGATGGTTA
1217 ATTATCACAA
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
44 23 0.39
45 6 0.10
46 30 0.51
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.40
Consensus pattern (44 bp):
GTTATCAAAATTTCATAGGATGGTTATTAAAATCTCATGAGGAG
Found at i:1196 original size:22 final size:22
Alignment explanation
Indices: 1101--1216 Score: 63
Period size: 22 Copynumber: 5.2 Consensus size: 22
1091 TCTCTATGTA
* * * *
1101 GTTATCAAAATTTCATAAGATG
1 GTTATTAAAATCTCATAGGGTG
* * *
1123 GTTATTATAATTTCAT-GAGGAG
1 GTTATTAAAATCTCATAG-GGTG
** * *
1145 GTTACCAAAATTTCATAGGATTAG
1 GTTATTAAAATCTCATAGG-GT-G
* *
1169 GTTATTAAAATCTCTTAGGTTG
1 GTTATTAAAATCTCATAGGGTG
* *
1191 GTTATTGAAATTTCATAGGGTG
1 GTTATTAAAATCTCATAGGGTG
1213 GTTA
1 GTTA
1217 ATTATCACAA
Statistics
Matches: 72, Mismatches: 18, Indels: 8
0.73 0.18 0.08
Matches are distributed among these distances:
22 53 0.74
23 3 0.04
24 16 0.22
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.40
Consensus pattern (22 bp):
GTTATTAAAATCTCATAGGGTG
Found at i:1362 original size:22 final size:21
Alignment explanation
Indices: 1252--1621 Score: 144
Period size: 22 Copynumber: 16.7 Consensus size: 21
1242 ATCAAAAAGA
* * *
1252 TTATCAAAATGTCATAGCGAGA
1 TTATCAAAATTTCATAG-AAGG
**
1274 TTAT-AATAATTTCATAGTGGG
1 TTATCAA-AATTTCATAGAAGG
*
1295 ATT-TACAAAATTTCATTAGGAGG
1 -TTAT-CAAAATTTCA-TAGAAGG
* * *
1318 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCAT-AGAAGG
1340 TTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATA-GAAGG
* * *
1362 TTATGAAAGTTTCAATTTCATAAGG
1 TTATCAAAATTTC-A--T-AGAAGG
* * *
1387 AGTACCAAAATTTGATAGAAGG
1 -TTATCAAAATTTCATAGAAGG
*
1409 TTATC-AAATCTCATAG-AGTG
1 TTATCAAAATTTCATAGAAG-G
*
1429 ATTATCGAAATTTCATAGAGATCGG
1 -TTATCAAAATTTCATAGA-A--GG
*
1454 ATTATCAAAATTT-ATAGAAAGA
1 -TTATCAAAATTTCATAG-AAGG
*
1476 TTATCAAAATTTCATAG-TGTTG
1 TTATCAAAATTTCATAGAAG--G
* *
1498 TTATCAAAATTTCAAAGTGAGG
1 TTATCAAAATTTCATAG-AAGG
* *
1520 TTATCAAAATTACATA-ATGTG
1 TTATCAAAATTTCATAGAAG-G
* * *
1541 ATTACCAGAATTTCATAGAGGGG
1 -TTATCAAAATTTCATAGA-AGG
* * * *
1564 TCAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTCATAGA-AGG
*
1586 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGA-AGG
*
1608 TTATCAAATTTTCA
1 TTATCAAAATTTCA
1622 AAATGTGATT
Statistics
Matches: 267, Mismatches: 49, Indels: 64
0.70 0.13 0.17
Matches are distributed among these distances:
19 2 0.01
20 12 0.04
21 27 0.10
22 176 0.66
23 12 0.04
24 8 0.03
25 20 0.07
26 10 0.04
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.34
Consensus pattern (21 bp):
TTATCAAAATTTCATAGAAGG
Found at i:1553 original size:44 final size:44
Alignment explanation
Indices: 1453--1643 Score: 165
Period size: 44 Copynumber: 4.4 Consensus size: 44
1443 ATAGAGATCG
* * * *
1453 GATTATCAAAATTT-ATAGAAAGATTATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATG-T
* *
1497 G-TTATCAAAATTTCAAAGTGAGGTTATCAAAATTACATAATGT
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
* * * * * * * * *
1540 GATTACCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGA
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
* * *
1584 GGTTATCAAAATTTCATAA-AGAGGTTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAATGT
1628 GATTA-CAGAAATTTCA
1 GATTATCA-AAATTTCA
1644 TAGTGGTATT
Statistics
Matches: 113, Mismatches: 30, Indels: 8
0.75 0.20 0.05
Matches are distributed among these distances:
43 16 0.14
44 96 0.85
45 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.34
Consensus pattern (44 bp):
GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
Found at i:1559 original size:88 final size:87
Alignment explanation
Indices: 1453--1646 Score: 203
Period size: 88 Copynumber: 2.2 Consensus size: 87
1443 ATAGAGATCG
* * * ** ** *
1453 GATTATCAAAATTT-ATAGAAAGATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAGT
1 GATTA-CAGAATTTCATAGAAAGATCAACAAAATTTCATAAAGAGGTTATCAAAATTTCATAA-A
*
1516 GAGGTTATCAAAATTACATAATGT
64 GAGGTTATCAAAATTACAAAATGT
** * *
1540 GATTACCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGAGGTTATCAAAATTTCATAAAG
1 GATTA-CAGAATTTCATAGAAAGATCAACAAAATTTCATAAAGAGGTTATCAAAATTTCATAAAG
* *
1605 AGGTTATCAAATTTTCAAAATGT
65 AGGTTATCAAAATTACAAAATGT
1628 GATTACAGAAATTTCATAG
1 GATTACAG-AATTTCATAG
1647 TGGTATTTCT
Statistics
Matches: 88, Mismatches: 16, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
87 15 0.17
88 71 0.81
89 2 0.02
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.34
Consensus pattern (87 bp):
GATTACAGAATTTCATAGAAAGATCAACAAAATTTCATAAAGAGGTTATCAAAATTTCATAAAGA
GGTTATCAAAATTACAAAATGT
Found at i:1621 original size:66 final size:65
Alignment explanation
Indices: 1392--1618 Score: 167
Period size: 66 Copynumber: 3.4 Consensus size: 65
1382 TAAGGAGTAC
* * * * * * * *
1392 CAAAATTTGATAGAAG-G-TTATCAAATCTCATAGAGTGATTATCGAAATTTCATAGAGATCGGA
1 CAAAATTTCATA-AAGAGATTATCAAATTTCATAGAGGGGTCAACAAAATTTCAAAGAGA--GG-
1455 TTAT
62 TTAT
* ** * * *
1459 CAAAATTT-ATAGAA-AGATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCAAAGTGAGGTT
1 CAAAATTTCATA-AAGAGATTATC-AAATTTCATAGAGGGGTCAACAAAATTTCAAAGAGAGGTT
1522 AT
64 AT
* * * * *
1524 CAAAATTACATAATGTGATTACCAGAATTTCATAGAGGGGTCAACAAAATTTTATAA-AGAGGTT
1 CAAAATTTCATAAAGAGATTATCA-AATTTCATAGAGGGGTCAACAAAATTTCA-AAGAGAGGTT
1588 AT
64 AT
*
1590 CAAAATTTCATAAAGAGGTTATCAAATTT
1 CAAAATTTCATAAAGAGATTATCAAATTT
1619 TCAAAATGTG
Statistics
Matches: 130, Mismatches: 23, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
65 18 0.14
66 68 0.52
67 15 0.12
68 29 0.22
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.33
Consensus pattern (65 bp):
CAAAATTTCATAAAGAGATTATCAAATTTCATAGAGGGGTCAACAAAATTTCAAAGAGAGGTTAT
Found at i:1790 original size:22 final size:22
Alignment explanation
Indices: 1765--2302 Score: 202
Period size: 22 Copynumber: 24.7 Consensus size: 22
1755 TCAAGGAGGA
1765 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
* *
1787 TATCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
1809 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* *
1830 AGATCAAAATTTCATATGGAA-AT
1 -TATCAAAATTTCATAT-GAAGGT
* *
1853 TAACAAAATTTCATATGGAA-AT
1 TATCAAAATTTCATAT-GAAGGT
*
1875 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
** * * *
1897 TATCAAAAAATCGTACGGAGGT
1 TATCAAAATTTCATATGAAGGT
*
1919 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
1935 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
1957 TATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATATGAAG-GT
*
1980 TATCAAAATTTCATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
*
2002 TATCACAATTTCATAATGTAA--T
1 TATCAAAATTTCAT-ATG-AAGGT
* * * *
2024 TATCCAAATTTCAGAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
*
2046 TA-CTAACAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATATGAAGGT
* * * **
2068 TTTTAAATTTTCATA-GCGTGGT
1 TATCAAAATTTCATATG-AAGGT
* * *
2090 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
2112 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
* * *
2135 TATCAAATTTTGAT-TGGGAGGT
1 TATCAAAATTTCATAT-GAAGGT
*
2157 TATTAAAATTTCATATTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
2179 CT-TCAAAATTCCTTAGGGAGGT
1 -TATCAAAATTTCATATGAAGGT
* *
2201 TAACAAAATTTCATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
** * **
2223 TAAAAAAAATT-ATAAAAAGGT
1 TATCAAAATTTCATATGAAGGT
* ** * **
2244 TCTTGAAATTCCATA-GTATCGT
1 TATCAAAATTTCATATG-AAGGT
* *
2266 TATTAAAATTTCATAGGAAGGT
1 TATCAAAATTTCATATGAAGGT
2288 TATCAAAATTTCATA
1 TATCAAAATTTCATA
2303 ATGAGATCAT
Statistics
Matches: 390, Mismatches: 90, Indels: 72
0.71 0.16 0.13
Matches are distributed among these distances:
16 9 0.02
17 2 0.01
18 2 0.01
20 2 0.01
21 31 0.08
22 297 0.76
23 42 0.11
24 5 0.01
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:2171 original size:45 final size:44
Alignment explanation
Indices: 2056--2171 Score: 119
Period size: 45 Copynumber: 2.6 Consensus size: 44
2046 TACTAACAAT
* *
2056 TCATATGGAGGTTTTTAAATTTTCATAGCGTGGTTATCAATATA
1 TCATATGGAGGTTATTAAAATTTCATAGCGTGGTTATCAATATA
* * * * *
2100 TCATATGGAGGTTATCAACATCTCATAGTGTTGGTTATCAA-ATTT
1 TCATATGGAGGTTATTAAAATTTCATAGCG-TGGTTATCAATA-TA
*
2145 TGAT-TGGGAGGTTATTAAAATTTCATA
1 TCATAT-GGAGGTTATTAAAATTTCATA
2172 TTGAGGTCTT
Statistics
Matches: 58, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
44 26 0.45
45 32 0.55
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.41
Consensus pattern (44 bp):
TCATATGGAGGTTATTAAAATTTCATAGCGTGGTTATCAATATA
Done.