Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008042.1 Corchorus capsularis cultivar CVL-1 contig08063, 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: 36703
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--33 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1 TA TA TA 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 TA TA TA T
34 GGGTGATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1298 original size:3 final size:3
Alignment explanation
Indices: 1290--1318 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1280 AAATAGAGTT
1290 AGC AGC AGC AGC AGC AGC AGC AGC AGC AG
1 AGC AGC AGC AGC AGC AGC AGC AGC AGC AG
1319 GCCGGTATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.31, G:0.34, T:0.00
Consensus pattern (3 bp):
AGC
Found at i:1583 original size:3 final size:3
Alignment explanation
Indices: 1575--1617 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
1565 GGTCTAACCC
*
1575 ATT ATT ATT ATT ATT ATT ATC ATT ATT ATT A-T ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1618 ACTGTTAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:7306 original size:20 final size:20
Alignment explanation
Indices: 7269--7307 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
7259 GCATTGGATT
*
7269 ATAAATTTCATTACAATTAA
1 ATAAAGTTCATTACAATTAA
* *
7289 ATAAAGTTCTTTATAATTA
1 ATAAAGTTCATTACAATTA
7308 TGCCCAAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.44
Consensus pattern (20 bp):
ATAAAGTTCATTACAATTAA
Found at i:16057 original size:19 final size:18
Alignment explanation
Indices: 16024--16060 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
16014 TTGAAATAAT
16024 TCTTCAATGATCTTCAAG
1 TCTTCAATGATCTTCAAG
*
16042 TCTTCAAATTATCTTCAAG
1 TCTTC-AATGATCTTCAAG
16061 AAATCTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.41
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAG
Found at i:16656 original size:41 final size:40
Alignment explanation
Indices: 16611--16690 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 40
16601 ATGTTTTCAT
*
16611 TTTCATCTCACCTAGGGTTTA-ATGTGTTTTTTGAGGGTTTC
1 TTTCATCTCACCTAGGGTTTATAT-TGTTTGTT-AGGGTTTC
*
16652 TTTCATCTCACTTAGGGTTTATATTGTTTGTTAGGGTTT
1 TTTCATCTCACCTAGGGTTTATATTGTTTGTTAGGGTTT
16691 GAGTTTCATA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 7 0.19
41 27 0.75
42 2 0.06
ACGTcount: A:0.15, C:0.12, G:0.21, T:0.51
Consensus pattern (40 bp):
TTTCATCTCACCTAGGGTTTATATTGTTTGTTAGGGTTTC
Found at i:21507 original size:21 final size:20
Alignment explanation
Indices: 21481--21531 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
21471 TTACACTTGA
*
21481 AGAATTAAACACTATGAAACT
1 AGAATTAAA-ACAATGAAACT
21502 AGAATTAAGAACAATGAAACT
1 AGAATTAA-AACAATGAAACT
*
21523 ATAATTAAA
1 AGAATTAAA
21532 TGCTATCTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 1 0.04
21 25 0.93
22 1 0.04
ACGTcount: A:0.57, C:0.10, G:0.10, T:0.24
Consensus pattern (20 bp):
AGAATTAAAACAATGAAACT
Found at i:25093 original size:17 final size:17
Alignment explanation
Indices: 25049--25097 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
25039 TTAGGAACAT
*
25049 ATTTGCAACAAAACTTTTT
1 ATTTGCAAC-AAA-TTTTG
25068 ATTTG--ACAAATTTTG
1 ATTTGCAACAAATTTTG
25083 ATTTGCAACAAATTT
1 ATTTGCAACAAATTT
25098 AATTTAATAC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 9 0.33
16 3 0.11
17 10 0.37
19 5 0.19
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.43
Consensus pattern (17 bp):
ATTTGCAACAAATTTTG
Found at i:26145 original size:74 final size:74
Alignment explanation
Indices: 26064--26203 Score: 237
Period size: 74 Copynumber: 1.9 Consensus size: 74
26054 GAAGGGAAAT
* *
26064 GTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAAT-GGTTGAAACTCATAGAGGGGCTTTTTAGT
1 GTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAGG-GGAAACTCATAGAGAGGCTTTTTAGT
26128 CATTCAAAAA
65 CATTCAAAAA
*
26138 GTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATGGAGAGGCTTTTTAGTC
1 GTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAGAGGCTTTTTAGTC
26203 A
66 A
26204 CCCGAAAAGT
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
74 60 0.97
75 2 0.03
ACGTcount: A:0.40, C:0.08, G:0.29, T:0.23
Consensus pattern (74 bp):
GTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAGAGGCTTTTTAGTC
ATTCAAAAA
Found at i:26212 original size:74 final size:74
Alignment explanation
Indices: 26059--26215 Score: 235
Period size: 74 Copynumber: 2.1 Consensus size: 74
26049 TTAAGGAAGG
* * *
26059 GAAATGTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATGGTTGAAACTCATAGAGGGGCTTTT
1 GAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATGGTGGAAACTCATAGAGAGGCTTTT
**
26124 TAGTCATTC
66 TAGTCACCC
* *
26133 AAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAGG-GGAAACTCATGGAGAGGCTTT
1 GAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAAT-GGTGGAAACTCATAGAGAGGCTTT
26197 TTAGTCACCC
65 TTAGTCACCC
26207 GAAAAGTGT
1 GAAAAGTGT
26216 GAAAAGACCA
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
74 72 0.97
75 2 0.03
ACGTcount: A:0.40, C:0.09, G:0.29, T:0.22
Consensus pattern (74 bp):
GAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATGGTGGAAACTCATAGAGAGGCTTTT
TAGTCACCC
Found at i:26841 original size:19 final size:18
Alignment explanation
Indices: 26804--26852 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
26794 AGAAGTATAA
26804 AAAATATAAATAAAGAGG
1 AAAATATAAATAAAGAGG
* *
26822 AAAATATATATAGAATAGG
1 AAAATATAAATA-AAGAGG
*
26841 -AAAGATAAATAA
1 AAAATATAAATAA
26853 TGGAAATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 1 0.04
18 20 0.77
19 5 0.19
ACGTcount: A:0.65, C:0.00, G:0.14, T:0.20
Consensus pattern (18 bp):
AAAATATAAATAAAGAGG
Found at i:30154 original size:12 final size:12
Alignment explanation
Indices: 30137--30162 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
30127 TTTCTTTTCA
30137 AATTTTGATGGT
1 AATTTTGATGGT
30149 AATTTTGATGGT
1 AATTTTGATGGT
30161 AA
1 AA
30163 GCGATCAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (12 bp):
AATTTTGATGGT
Done.