Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012168.1 Corchorus olitorius cultivar O-4 contig12201, 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: 11074
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Found at i:2326 original size:199 final size:199
Alignment explanation
Indices: 1970--2705 Score: 943
Period size: 199 Copynumber: 3.7 Consensus size: 199
1960 TCCACTTCTA
* * * * **
1970 TAATATTAATGCATATTCCCTAATGAGACATATGTCAACCCTTAAACCTTGCACGTGCAGTCTGC
1 TAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGC
* ** * * * * *
2035 TAAACTCCACTGACAATGTATTGTATAATTGTTCTTATAGGATTATCATACAATATATTGTCAAT
66 TAAAATCCACTGACGGTGTATAGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCAAT
* * * * *
2100 GTGAATTTT-GAACTCCATAAGCGGGTTAAGAATTTGACACATACTTCATTTCATGATTAATTAA
131 GTAAATTTTAG-ACTCCATAAACGGGTTAAGAAGTTGACACATACTTCATTTCATAATAAATTAA
2164 ATATT
195 ATATT
* * *
2169 TAATATTAATACATATTCCCTAAGGGGACACATGTCAACCTTTAAACCCCGCACGTGCAGCCCGC
1 TAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGC
* * *
2234 TAAAATCCACTGACGGTGTATTA-TATAATTTTTCTTATAGGATTATTATACAACACGCTGTCAG
66 TAAAATCCACTGACGGTGTA-TAGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCAA
* * *
2298 TGTAAATTTTAGACTCTATAAACGGGTTAAGAAGTTGACACATA-TCTCATTTCATCATCAATTA
130 TGTAAATTTTAGACTCCATAAACGGGTTAAGAAGTTGACACATACT-TCATTTCATAATAAATTA
*
2362 AATATA
194 AATATT
* * *
2368 TAATATTAATACATA-TCTCCTAAGGGGACACATGTTAACCCTTAAACCCTGCACGTCCAGTCTG
1 TAATATTAATACATATTC-CCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTG
* * * ** *
2432 CTAAACTCCACTTACGGTGTATAGTATAATTTTTCTTATAGGATTATTATACAATAAACTACCAG
65 CTAAAATCCACTGACGGTGTATAGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCAA
* * *
2497 TGTAAATTTTGGACTCCATAAACGGGTTAAAAAGTTGACACATACCTCATTTCATAATAAATTAA
130 TGTAAATTTTAGACTCCATAAACGGGTTAAGAAGTTGACACATACTTCATTTCATAATAAATTAA
2562 ATATT
195 ATATT
* * *
2567 TAATATTAATACATATTCCTTAAGGGGACACATGTCAACCCTTAAACCCCGCAAGTGTAGTCTGC
1 TAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGC
**
2632 T--AA---ACTGACGGTGTATAGTATAATTTTTCTTATAGGATTACAATACAATACACAT-TCAA
66 TAAAATCCACTGACGGTGTATAGTATAATTTTTCTTATAGGATTATTATACAATACAC-TGTCAA
2691 TGTAAATTTTAGACT
130 TGTAAATTTTAGACT
2706 TATAGATATT
Statistics
Matches: 468, Mismatches: 61, Indels: 21
0.85 0.11 0.04
Matches are distributed among these distances:
194 62 0.13
195 1 0.00
197 1 0.00
198 5 0.01
199 395 0.84
200 4 0.01
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.34
Consensus pattern (199 bp):
TAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGC
TAAAATCCACTGACGGTGTATAGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCAAT
GTAAATTTTAGACTCCATAAACGGGTTAAGAAGTTGACACATACTTCATTTCATAATAAATTAAA
TATT
Found at i:3532 original size:22 final size:21
Alignment explanation
Indices: 3507--3554 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
3497 TCTCAACCTT
3507 AATCAATCAAAACAACATCAAA
1 AATCAA-CAAAACAACATCAAA
** *
3529 AATCAACCCAACAACATCTAA
1 AATCAACAAAACAACATCAAA
3550 AATCA
1 AATCA
3555 TGGAGGGGCG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.58, C:0.27, G:0.00, T:0.15
Consensus pattern (21 bp):
AATCAACAAAACAACATCAAA
Found at i:5972 original size:2 final size:2
Alignment explanation
Indices: 5965--6023 Score: 73
Period size: 2 Copynumber: 27.0 Consensus size: 2
5955 TTGTTATCAT
5965 TA TA TA TA TA TGA TA TA TGA TA TA TGA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA T-A TA TA T-A TA TA T-A TA TA TA TA TA TA TA TA
6008 TA TGA TA CTA TA TA TA
1 TA T-A TA -TA TA TA TA
6024 AAAGTACGAA
Statistics
Matches: 52, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
2 42 0.81
3 10 0.19
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (2 bp):
TA
Found at i:7597 original size:22 final size:22
Alignment explanation
Indices: 7572--7619 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
7562 TAAAAAAATT
7572 ATAGGG-AGATTAACAAAATCTC
1 ATAGGGAAGATT-ACAAAATCTC
* *
7594 ATAGGGAAGGTTACAAAATTTC
1 ATAGGGAAGATTACAAAATCTC
7616 ATAG
1 ATAG
7620 TCAGGTTATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.25
Consensus pattern (22 bp):
ATAGGGAAGATTACAAAATCTC
Found at i:7708 original size:22 final size:22
Alignment explanation
Indices: 7683--7725 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
7673 AAAAAAAATT
**
7683 ATAGCGTTTTTATCAAAATTTA
1 ATAGCGTAATTATCAAAATTTA
*
7705 ATAGGGTAATTATCAAAATTT
1 ATAGCGTAATTATCAAAATTT
7726 TATAAAAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.42
Consensus pattern (22 bp):
ATAGCGTAATTATCAAAATTTA
Found at i:8190 original size:3 final size:3
Alignment explanation
Indices: 8167--8240 Score: 107
Period size: 3 Copynumber: 25.0 Consensus size: 3
8157 TTACTACTAT
*
8167 ATA A-A ATA AAA ATA TATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
8212 ATA ATA ATA ATA ATA AT- ATA ATG ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
8241 CAACAATATT
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
2 4 0.06
3 57 0.89
4 3 0.05
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:9370 original size:3 final size:3
Alignment explanation
Indices: 9362--9442 Score: 83
Period size: 3 Copynumber: 26.0 Consensus size: 3
9352 ATATATATAT
* * * *
9362 ATA ATA ATA ATA ATA ATA ATA TATA ATA AT- TTCC CTCA AAA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA AT-A AT-A ATA ATA ATA
9409 ATA TATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
9443 CAACAATATC
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
2 1 0.01
3 59 0.87
4 8 0.12
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Done.