Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012454.1 Corchorus olitorius cultivar O-4 contig12487, 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: 17230
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Found at i:14301 original size:22 final size:22
Alignment explanation
Indices: 14275--14323 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
14265 GAATTTCGAG
* *
14275 AACCTTTTTAT-AAATTTTTTTT
1 AACCTTCTTATGAAA-TTTTGTT
14297 AACCTTCTTATGAAATTTTGTT
1 AACCTTCTTATGAAATTTTGTT
14319 AACCT
1 AACCT
14324 CACTAAGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.29, C:0.14, G:0.04, T:0.53
Consensus pattern (22 bp):
AACCTTCTTATGAAATTTTGTT
Found at i:14428 original size:22 final size:22
Alignment explanation
Indices: 14296--14827 Score: 187
Period size: 22 Copynumber: 24.3 Consensus size: 22
14286 AAATTTTTTT
* * *
14296 TAACCTTCTTATGAAATTTTGT
1 TAACCTCCATATGAAATTTTGA
* *
14318 TAACCT-CACTAAGGAATTTTGA
1 TAACCTCCA-TATGAAATTTTGA
14340 -AGACCT-CACTATGAAATTTTGA
1 TA-ACCTCCA-TATGAAATTTTGA
*
14362 TAACTTCCCA-ATGAAATTTTGA
1 TAACCT-CCATATGAAATTTTGA
** * *
14384 TAACCAACACTATGAGATGTTGA
1 TAACCTCCA-TATGAAATTTTGA
* *
14407 TAACCTCCATATGATATATTGA
1 TAACCTCCATATGAAATTTTGA
* ** * *
14429 TAACCACGTTATGAAAATTTAA
1 TAACCTCCATATGAAATTTTGA
* * *
14451 AAACCTCCAAATGAAATATT-A
1 TAACCTCCATATGAAATTTTGA
*
14472 GTAA--TCACACTCTGAAATTTTGA
1 -TAACCTC-CA-TATGAAATTTTGA
* *
14495 TAA--TCACACTATAAAATTGTGA
1 TAACCTC-CA-TATGAAATTTTGA
*
14517 TAACCTCGC-TATGAAATTTTAA
1 TAACCTC-CATATGAAATTTTGA
*
14539 TAAACCTTCC-TATAAAATTTTGA
1 T-AACC-TCCATATGAAATTTTGA
* * *
14562 TAACCTCCCTATAAAATTTTAA
1 TAACCTCCATATGAAATTTTGA
* *
14584 TAACCTCCTTATGAAATCTTGA
1 TAACCTCCATATGAAATTTTGA
*
14606 TAA----C-TA-CAAATTTTGA
1 TAACCTCCATATGAAATTTTGA
* * **
14622 TAACCACCTTATGATTTTTTGA
1 TAACCTCCATATGAAATTTTGA
*
14644 TAACCT-CATTATGAAATTTTGT
1 TAACCTCCA-TATGAAATTTTGA
* * *
14666 TAATCTTCTTATGAAATTTTGA
1 TAACCTCCATATGAAATTTTGA
* * * *
14688 TCTACATAC-TATTAAATTTTGA
1 T-AACCTCCATATGAAATTTTGA
*
14710 TAACC-CTC-TCATGCAATTTTGA
1 TAACCTC-CAT-ATGAAATTTTGA
* **
14732 -AAACTAAACTATGAAATTTTGATAA
1 TAACCTCCA-TATGAAATTTTG---A
* *
14757 TTAACCTTCATATGAAATATTGA
1 -TAACCTCCATATGAAATTTTGA
* *
14780 TATCCTCC--CTGAAATTTTGA
1 TAACCTCCATATGAAATTTTGA
* * * *
14800 TTA-CTCCATAATAAAAGTTTAA
1 TAACCTCCAT-ATGAAATTTTGA
14822 TAACCT
1 TAACCT
14828 TCCTAATCCG
Statistics
Matches: 381, Mismatches: 90, Indels: 77
0.70 0.16 0.14
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
18 1 0.00
19 4 0.01
20 14 0.04
21 20 0.05
22 261 0.69
23 44 0.12
24 7 0.02
25 1 0.00
26 11 0.03
27 5 0.01
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (22 bp):
TAACCTCCATATGAAATTTTGA
Found at i:14931 original size:22 final size:22
Alignment explanation
Indices: 14906--15302 Score: 242
Period size: 22 Copynumber: 17.9 Consensus size: 22
14896 ATTCACATTT
*
14906 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTCTA
*
14928 TGAAATTTTAATAACCTCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * * *
14950 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * *
14972 TGAAATTTTCATAATCACAT-TA
1 TGAAATTTTGATAACCTC-TCTA
* * * *
14994 TGTAATTTTGATAACATCGCTT
1 TGAAATTTTGATAACCTCTCTA
** *
15016 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTCTCTA
*
15038 TGAAATTTTGATAATCT-TCCTA
1 TGAAATTTTGATAACCTCT-CTA
15060 T-AAATTTTGATAATCCGATCTCTA
1 TGAAATTTTGATAA-CC--TCTCTA
* * *
15084 TGAAATTTTGATAATCACTATA
1 TGAAATTTTGATAACCTCTCTA
*
15106 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTCTA
* *
15126 TCAAATTTT-ATTA-CTC-CTTA
1 TGAAATTTTGATAACCTCTC-TA
*
15146 TGAAATTGAGACTTTTATAACCT-TCATA
1 TGAAA-T-----TTTGATAACCTCTC-TA
* *
15174 TGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
* *
15196 TGAAATTTTGATAACCTCCCCA
1 TGAAATTTTGATAACCTCTCTA
*
15218 TGAAATATT-AGTAACCTC-CTTA
1 TGAAATTTTGA-TAACCTCTC-TA
* * *
15240 TGAAATTTTGTTAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
* *
15262 TGAAATTCTT-ATAATCTCGCTA
1 TGAAATT-TTGATAACCTCTCTA
* *
15284 TGACATTTTGATAATCTCT
1 TGAAATTTTGATAACCTCT
15303 TTGATAACCT
Statistics
Matches: 289, Mismatches: 59, Indels: 54
0.72 0.15 0.13
Matches are distributed among these distances:
19 3 0.01
20 15 0.05
21 29 0.10
22 201 0.70
23 5 0.02
24 6 0.02
25 13 0.04
26 3 0.01
27 4 0.01
28 10 0.03
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:15044 original size:88 final size:88
Alignment explanation
Indices: 14881--15047 Score: 210
Period size: 88 Copynumber: 1.9 Consensus size: 88
14871 AGAAAAACCC
** * * * * **
14881 CTATGAAATTTTGGTATTCACATTTTGAAATTTTGATAACCTCTTTATGAAATTTTAATAACCTC
1 CTATGAAATTTTCATAATCACATTATGAAATTTTGATAACATCCTTATGAAATTTTAATAACAAC
*
14946 TCTATAAAATTTTGTTGACCCCT
66 ACTATAAAATTTTGTTGACCCCT
* *
14969 CTATGAAATTTTCATAATCACATTATGTAATTTTGATAACATCGCTT-TGAAATTTTGATAACAA
1 CTATGAAATTTTCATAATCACATTATGAAATTTTGATAACATC-CTTATGAAATTTTAATAACAA
*
15033 CACTATGAAATTTTG
65 CACTATAAAATTTTG
15048 ATAATCTTCC
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
88 64 0.97
89 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.43
Consensus pattern (88 bp):
CTATGAAATTTTCATAATCACATTATGAAATTTTGATAACATCCTTATGAAATTTTAATAACAAC
ACTATAAAATTTTGTTGACCCCT
Found at i:15394 original size:24 final size:22
Alignment explanation
Indices: 15337--15394 Score: 55
Period size: 22 Copynumber: 2.5 Consensus size: 22
15327 GATAACCACA
* *
15337 CTATGAAATTTCAATAACTTTC
1 CTATGAAATTTTAATAACTATC
*
15359 CTA-AAAACTTTTAATAACCTGATC
1 CTATGAAA-TTTTAATAA-CT-ATC
15383 CTATGAAATTTT
1 CTATGAAATTTT
15395 GGTAACCACA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
21 3 0.11
22 11 0.39
23 2 0.07
24 9 0.32
25 3 0.11
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.40
Consensus pattern (22 bp):
CTATGAAATTTTAATAACTATC
Found at i:15468 original size:35 final size:35
Alignment explanation
Indices: 15398--15469 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 35
15388 AAATTTTGGT
*
15398 AACCACACTATAAAATTTGGATAACTTCCATATGA
1 AACCACACTATAAAATTTGGATAACCTCCATATGA
** *
15433 AACCACACTATGGAATTTTGATAACCTCC-TCATGA
1 AACCACACTATAAAATTTGGATAACCTCCAT-ATGA
15468 AA
1 AA
15470 TTATAATAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 1 0.03
35 31 0.97
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.28
Consensus pattern (35 bp):
AACCACACTATAAAATTTGGATAACCTCCATATGA
Found at i:15471 original size:22 final size:22
Alignment explanation
Indices: 15446--15503 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
15436 CACACTATGG
15446 AATTTTGATAACC-TCCTCATGA
1 AATTTTGATAACCAT-CTCATGA
* * *
15468 AATTATAATAACCATCTTATGA
1 AATTTTGATAACCATCTCATGA
*
15490 GATTTTGATAACCA
1 AATTTTGATAACCA
15504 CACAGAGACA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
22 28 0.97
23 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (22 bp):
AATTTTGATAACCATCTCATGA
Found at i:15719 original size:20 final size:20
Alignment explanation
Indices: 15694--15732 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
15684 TATTGACATT
15694 TAAAAAATTGAAATT-AAAAG
1 TAAAAAATT-AAATTCAAAAG
15714 TAAAAAATTAAATTCAAAA
1 TAAAAAATTAAATTCAAAA
15733 AATAACAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.26
Consensus pattern (20 bp):
TAAAAAATTAAATTCAAAAG
Done.