Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008183.1 Corchorus capsularis cultivar CVL-1 contig08204, 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: 8214
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Found at i:1220 original size:166 final size:163
Alignment explanation
Indices: 747--1233 Score: 586
Period size: 166 Copynumber: 2.9 Consensus size: 163
737 TGAGTCATTT
* * *
747 GTCAATTGAGAAATAACCAAAAAGTTTAGTTATTTAATCCCCTTAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAATTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* * * **
812 TTAAGTAATCTACCAAGTAGATAAAGACGAAAAAGATTAGTTCTCTAACTCATCATCAATCCTTG
65 TTAAGTAATCTACCAAGTGGA-AAAGACGAAAAAAATTAGTTCTCTAACTCCTCATCAATCCGGG
* *
877 ATGGGTATCTTTTA-TAAATTCCGCTACTCTATTCAAA
129 A-GGG-ATCTTTTAGT-AATTCCACAACTCTATTCAAA
* *
914 -TCCATTGAGAAATGACCAAAAAGATTACTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAATTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* * * ** ** * *
978 TTAAGTAATTTGCTAAGTAGGAAAAGAC-AAAAAAAAAAGTTCTCTAACTCCAAAAGCAAGTCTT
65 TTAAGTAATCTACCAAGT-GGAAAAGACGAAAAAAATTAGTTCTCTAACTCC-TCATCAA-TC-C
*
1042 GGTAGGGATCTTTTAGTAATTCCACAACTCTATT-AAA
126 GGGAGGGATCTTTTAGTAATTCCACAACTCTATTCAAA
1079 GTCAATTGAGAAATGACCAAAAAGTCTAATTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAGT-TAATTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* ** *
1144 TTAAGTAATCTACCAAGTGGGAAAAGACGAAAAAAATTAGTTATCTCGCTCCTCATTAATCCGGG
65 TTAAGTAATCTACCAAGT-GGAAAAGACGAAAAAAATTAGTTCTCTAACTCCTCATCAATCC-GG
1209 GAGGAGATCTTTTAGTAATTCCACA
128 GAGG-GATCTTTTAGTAATTCCACA
1234 TGTTTATTCA
Statistics
Matches: 271, Mismatches: 39, Indels: 21
0.82 0.12 0.06
Matches are distributed among these distances:
165 30 0.11
166 214 0.79
167 26 0.10
168 1 0.00
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (163 bp):
GTCAATTGAGAAATGACCAAAAAGTTAATTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATT
TAAGTAATCTACCAAGTGGAAAAGACGAAAAAAATTAGTTCTCTAACTCCTCATCAATCCGGGAG
GGATCTTTTAGTAATTCCACAACTCTATTCAAA
Found at i:2738 original size:20 final size:20
Alignment explanation
Indices: 2713--2752 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2703 TAATCGTGTC
*
2713 AAGACACGATTAACACGTTT
1 AAGACACGAGTAACACGTTT
*
2733 AAGACACGAGTGACACGTTT
1 AAGACACGAGTAACACGTTT
2753 TAATTAACGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (20 bp):
AAGACACGAGTAACACGTTT
Found at i:4215 original size:14 final size:13
Alignment explanation
Indices: 4191--4255 Score: 94
Period size: 14 Copynumber: 4.8 Consensus size: 13
4181 GAAAAGTAGT
4191 TAATTTCATAGAG
1 TAATTTCATAGAG
*
4204 TGATTATCATAGAG
1 TAATT-TCATAGAG
4218 TCAATTTCATAGAG
1 T-AATTTCATAGAG
4232 TAATTTCATAGAG
1 TAATTTCATAGAG
4245 TCAATTTCATA
1 T-AATTTCATA
4256 AGGAGTATCA
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
13 17 0.36
14 27 0.57
15 3 0.06
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (13 bp):
TAATTTCATAGAG
Found at i:4248 original size:27 final size:28
Alignment explanation
Indices: 4192--4255 Score: 112
Period size: 27 Copynumber: 2.3 Consensus size: 28
4182 AAAAGTAGTT
*
4192 AATTTCATAGAGTGATTATCATAGAGTC
1 AATTTCATAGAGTAATTATCATAGAGTC
4220 AATTTCATAGAGTAATT-TCATAGAGTC
1 AATTTCATAGAGTAATTATCATAGAGTC
4247 AATTTCATA
1 AATTTCATA
4256 AGGAGTATCA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 19 0.54
28 16 0.46
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (28 bp):
AATTTCATAGAGTAATTATCATAGAGTC
Found at i:4316 original size:22 final size:22
Alignment explanation
Indices: 4247--4518 Score: 141
Period size: 22 Copynumber: 12.5 Consensus size: 22
4237 TCATAGAGTC
*
4247 AATTTCATA-AG-GAGTATCAA
1 AATTTCATAGAGTGATTATCAA
*
4267 AATTTGATAGAAG-G-TTATC-A
1 AATTTCATAG-AGTGATTATCAA
* *
4287 AATCTCATAGAGTGATTATCGA
1 AATTTCATAGAGTGATTATCAA
4309 AATTTCATAGAGATCGGATTATCAA
1 AATTTCATAGAG-T--GATTATCAA
**
4334 AATTT-ATAGAAAGATTATCAA
1 AATTTCATAGAGTGATTATCAA
* *
4355 AATTTAATAGTGTTG-TTATCAA
1 AATTTCATAGAG-TGATTATCAA
* * * *
4377 AATTTCAAAGCGAGGTTATCAA
1 AATTTCATAGAGTGATTATCAA
* * * *
4399 AATTACAGA-ATGTAATTATCAG
1 AATTTCATAGA-GTGATTATCAA
* * * *
4421 AATTTCATAGAGGGGTCAACAA
1 AATTTCATAGAGTGATTATCAA
* * * *
4443 AATTTTATAAAGAGATTATAAA
1 AATTTCATAGAGTGATTATCAA
* * *
4465 AATTTCATAAAGAGGTTATCAA
1 AATTTCATAGAGTGATTATCAA
* *
4487 ATTTTCA-AAATGTGATTA-CAAA
1 AATTTCATAGA-GTGATTATC-AA
4509 AATTTCATAG
1 AATTTCATAG
4519 TGGTATTTCA
Statistics
Matches: 191, Mismatches: 45, Indels: 29
0.72 0.17 0.11
Matches are distributed among these distances:
19 2 0.01
20 18 0.09
21 28 0.15
22 121 0.63
23 4 0.02
24 5 0.03
25 13 0.07
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (22 bp):
AATTTCATAGAGTGATTATCAA
Found at i:4646 original size:22 final size:22
Alignment explanation
Indices: 4618--5180 Score: 179
Period size: 22 Copynumber: 25.7 Consensus size: 22
4608 TTAGGGAGGA
4618 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
4640 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
4662 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
4684 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
4705 AGATCAAAATTTCATAAGGAGAT
1 -TATCAAAATTTCATATGAAGGT
*
4728 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
* **
4750 TATAAAAAAATCATA-GAGAGGT
1 TATCAAAATTTCATATGA-AGGT
*
4772 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * * *
4788 TATCAAGATTTTATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
4810 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* * **
4833 TATCAAAATTTTATAGGAATATT
1 TATCAAAATTTCATATGAA-GGT
4856 TATCAAAATTTCATA-GCAAGGT
1 TATCAAAATTTCATATG-AAGGT
* * *
4878 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * *
4900 TATCAAAATTTCAGAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
4922 TA-CTAACAA-TTCATATGGAA-GT
1 TATC-AA-AATTTCATAT-GAAGGT
* * *
4944 T-TTAAAATTTTCATAACG-TGGT
1 TATCAAAA-TTTCAT-ATGAAGGT
* * * *
4966 TATCAATATATCTTATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
4988 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
*
5011 TATCCAAATTTCAT-TGGGAA-GT
1 TATCAAAATTTCATAT--GAAGGT
5033 TATCAAAATTTCATATTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * * * *
5055 CT-TCAAAATTCCTTAGGGATGT
1 -TATCAAAATTTCATATGAAGGT
* *
5077 TAACAAAATTTCATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
** *
5099 TAAAAAAAATTT-ATA-AAAGGGT
1 T-ATCAAAATTTCATATGAA-GGT
* ***
5121 TCTCAAAA-TTC-TATAGTATCAT
1 TATCAAAATTTCATAT-G-AAGGT
* * *
5143 TATTAAAATTTCATAGGAAGAT
1 TATCAAAATTTCATATGAAGGT
5165 TATCAAAATTTCATAT
1 TATCAAAATTTCATAT
5181 TGGGATCATA
Statistics
Matches: 402, Mismatches: 92, Indels: 94
0.68 0.16 0.16
Matches are distributed among these distances:
16 9 0.02
17 1 0.00
18 3 0.01
20 9 0.02
21 22 0.05
22 272 0.68
23 82 0.20
24 4 0.01
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:4697 original size:66 final size:63
Alignment explanation
Indices: 4618--4912 Score: 226
Period size: 66 Copynumber: 4.5 Consensus size: 63
4608 TTAGGGAGGA
* *
4618 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAGTTTTCAAAATTTCATAAGAGGG
1 TATCAAAATTTCATA-GAAGGTTATCAAAATTTCATAG--TAGTTATCAAAATTTCATAAGAAGG
4683 T
63 T
* * * * *
4684 TATCAAAATTTCATAGTATGTAGATCAAAATTTCATAAGGAGATTAACAAAATTTCATAATG-AG
1 TATCAAAATTTCATAGAAGGT-TATCAAAATTTCAT-AGTAG-TTATCAAAATTTCATAA-GAAG
4748 GT
62 GT
* ** * * *
4750 TATAAAAAAATCATAGAGAGGTTATCAAAA-TT--T-GTAGTTATCAAGATTTTATAAGAAAGT
1 TATCAAAATTTCATAGA-AGGTTATCAAAATTTCATAGTAGTTATCAAAATTTCATAAGAAGGT
* * * *
4810 TATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGGAATATTTATCAAAATTTCAT-AGCA
1 TATCAAAATTTCATA-GAAGG-TTATCAAAATTTCATA-G--TAGTTATCAAAATTTCATAAG-A
4874 AGGT
60 AGGT
* *
4878 TATCACAATTTCATAG-TGTGATTATCAAAATTTCA
1 TATCAAAATTTCATAGAAG-G-TTATCAAAATTTCA
4913 GAGTGTGATT
Statistics
Matches: 180, Mismatches: 32, Indels: 33
0.73 0.13 0.13
Matches are distributed among these distances:
59 1 0.01
60 31 0.17
61 13 0.07
62 2 0.01
63 1 0.01
64 1 0.01
65 8 0.04
66 68 0.38
67 23 0.13
68 32 0.18
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (63 bp):
TATCAAAATTTCATAGAAGGTTATCAAAATTTCATAGTAGTTATCAAAATTTCATAAGAAGGT
Found at i:5485 original size:16 final size:17
Alignment explanation
Indices: 5423--5485 Score: 60
Period size: 16 Copynumber: 3.8 Consensus size: 17
5413 TCGGCCTATT
*
5423 TTCGGGTTCGGACTTGAA
1 TTCGGGTTCGG-GTTGAA
*
5441 -TCCGGTTCGGGTTGAA
1 TTCGGGTTCGGGTTGAA
* *
5457 TTTGGG-TCAGGTT-AA
1 TTCGGGTTCGGGTTGAA
5472 TTCGGGTTCGGGTT
1 TTCGGGTTCGGGTT
5486 CAGTTTGGGT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
15 7 0.19
16 17 0.47
17 12 0.33
ACGTcount: A:0.13, C:0.14, G:0.37, T:0.37
Consensus pattern (17 bp):
TTCGGGTTCGGGTTGAA
Found at i:5680 original size:16 final size:17
Alignment explanation
Indices: 5646--5689 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
5636 TCGGATTGGT
*
5646 TTTTTCGGG-TCTGAGC
1 TTTTTCGGGTTCGGAGC
5662 TTTTTCGGGTTCGGA-C
1 TTTTTCGGGTTCGGAGC
*
5678 TTTTTCAGGTTC
1 TTTTTCGGGTTC
5690 AGGTTCAAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 21 0.84
17 4 0.16
ACGTcount: A:0.07, C:0.18, G:0.27, T:0.48
Consensus pattern (17 bp):
TTTTTCGGGTTCGGAGC
Found at i:7068 original size:2 final size:2
Alignment explanation
Indices: 7061--7095 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
7051 GATCAGTTTG
7061 TA 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 TA T
7096 GTGCACTCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.