Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019128.1 Corchorus olitorius cultivar O-4 contig19161, 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: 13607
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
Found at i:1582 original size:16 final size:17
Alignment explanation
Indices: 1545--1582 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
1535 TTCTAATTAT
1545 TATT-TTTAGATTATAA
1 TATTATTTAGATTATAA
1561 TA-TATTTA-ATTATAA
1 TATTATTTAGATTATAA
1576 TATTATT
1 TATTATT
1583 ATTTATAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
TATTATTTAGATTATAA
Found at i:2622 original size:334 final size:332
Alignment explanation
Indices: 1941--3286 Score: 1351
Period size: 334 Copynumber: 4.0 Consensus size: 332
1931 ATACTTTACA
* ** * * *
1941 TCATCTAACCAAATCTCAGAAACATTGGATTTAAGAATTTGTTTTTATGAGCATCTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTAAATATTGT
* * * * * *
2006 TCCCATTTAATAAGAAATTAATTTAG-AAAAAATAAGAAATATGATATTAAAAGCGT-AACAGCC
66 TCCGATTTAATTAGAAATTAATTTAGAAAAAAATATGAAAAACGATATTAAAAGCGTCAAAAGCC
* * * *
2069 CTCCAATCTTTTTGGCATTGAATTATATA-TTTTTATGGGTATTTCAGCCAAAAATTGAGGAGAA
131 CTCCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGAAAAA
* * * * * *
2133 -ATCTCTCGTGTCAATTTTTTCAAAAGTTT-GCCGAAATCGTGTACTAACAAACCATCACAG-TT
196 TATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAAT--TGT-GTAA-TAACCATCACAGTTT
** * * * * * *
2195 TTGTCTAAAAACGCGTTATGAGGACCCGGCTCAATTTTGCATGATTTTTGGCTTCGAGACTACTT
257 TTGGATAAAAACACGTTATG-GGGCCCGACTCAGTTTTGCATGATTTTTGG-TGCGAGACTCCTT
2260 GAAATATCTATAT
320 GAAATATCTATAT
* * *
2273 TCATCTAATCAAATCTCACCCACATTGGATTTAATG-ATTTGTTTTAACGAGAATCTAAATATTG
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAA-GAATTTGTTTTTACGAGCATCTAAATATTG
* * * * *
2337 TTTCGATTTAATTAGAAATTAATTTGGAAAAAAATAGGAAAAACGATATTTGAAA-CGTCAAAAA
65 TTCCGATTTAATTAGAAATTAATTTAGAAAAAAATATGAAAAACGATA-TTAAAAGCGTCAAAAG
** * * *
2401 TTCTTCAATCTTTTTGGCGTTGAGTTATATATTTTTTATGAGTATTTTAGCCAAAAATTGA-AAA
129 CCCTCCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGAAA
* *
2465 AATATCTTTTGGATCAATTTTTACAAAATTTTAGCCGAAATTGTGTAATAACCATCACAGTTTTT
194 AATATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATTGTGTAATAACCATCACAGTTTTT
* *
2530 GGATAAAGAAAACGTTATGGGGCGCCGACTCAGTTTTGCATGATTTTTGGTGCAAAGACTCCTTG
259 GGATAAA-AACACGTTATGGGGC-CCGACTCAGTTTTGCATGATTTTTGGTGC-GAGACTCCTTG
* *
2595 AGATATCAATAT
321 AAATATCTATAT
* * * * *
2607 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGAATTTTTTTTTACAACCATCTAAATCTTCT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTAAATATTGT
* * *
2672 TCCGATTTAATTAGAAATTAATTCAG--AAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTC
66 TCCGATTTAATTAGAAATTAATTTAGAAAAAAATATGAAAAACGATATTAAAAGCGTCAAAAGCC
* * * * *
2735 CTCCAATCTTTTTGCCATTAAATTATATATATATTATGAGTATTTTATCCAAAAATTGAGGAAAA
131 CTCCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGA-GAAAA
* * * * *
2800 AT-T-TTTCGGGTCATTTTTTTTACCAAATTTTAGCCAAAATCGTGTACTAACCATCACAGTTTT
195 ATATCTTTCGGGTCA--ATTTTTACAAAATTTTAGCCGAAATTGTGTAATAACCATCACAG---T
* * * * * * *
2863 TTTTGGCTAAAAACGCATT-TCGGGGCACC-AGCTCAGTTTTACATTATTTTTGGCGCCGACACT
255 TTTTGGATAAAAACACGTTAT-GGGGC-CCGA-CTCAGTTTTGCATGATTTTTGGTG-CGAGACT
2926 CCTTGAAATATCTATAT
316 CCTTGAAATATCTATAT
* * * * *
2943 TTATCTAATAAAATCTTAGCCACATTGCATTTAAGAATTTGTTTTTACGAGCATCTGAATATTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTAAATATTGT
* * * * * *
3008 TTCGATTGAATTAAAAATTTATTCAGAAAAAAATATGAAAAACGATATTAAAAGC-TCAAAGGCC
66 TCCGATTTAATTAGAAATTAATTTAGAAAAAAATATGAAAAACGATATTAAAAGCGTCAAAAGCC
* * ** * * * * *
3072 CTTCAATTTTTTTGGTGTTGAATTATATATTTTTTATTACTATTATGGCTAAAAATTGAG-AAAA
131 CTCCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGAAAAA
* * ** * **
3136 TATCTTTCGGGTCAGTTTTTGCAAAATTTTAATCGAAATTGTGTAATAATCATCATGGTTTTT-G
196 TATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATTGTGTAATAACCATCACAGTTTTTGG
** * ** * * * *
3200 ACTAAAAACACGTTCCGAGGCCCGGTTCAGTTTTGAATGATTTTTGGCGTTGAGACTCCTTAAAA
261 A-TAAAAACACGTTATGGGGCCCGACTCAGTTTTGCATGATTTTTGGTG-CGAGACTCCTTGAAA
*
3265 TATTTATAT
324 TATCTATAT
*
3274 TCATCTAACCAAA
1 TCATCTAATCAAA
3287 CACAACCATT
Statistics
Matches: 833, Mismatches: 151, Indels: 61
0.80 0.14 0.06
Matches are distributed among these distances:
331 58 0.07
332 191 0.23
333 40 0.05
334 215 0.26
335 90 0.11
336 139 0.17
337 73 0.09
338 27 0.03
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (332 bp):
TCATCTAATCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTAAATATTGT
TCCGATTTAATTAGAAATTAATTTAGAAAAAAATATGAAAAACGATATTAAAAGCGTCAAAAGCC
CTCCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGAAAAA
TATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATTGTGTAATAACCATCACAGTTTTTGG
ATAAAAACACGTTATGGGGCCCGACTCAGTTTTGCATGATTTTTGGTGCGAGACTCCTTGAAATA
TCTATAT
Found at i:11903 original size:58 final size:58
Alignment explanation
Indices: 11807--11919 Score: 167
Period size: 58 Copynumber: 1.9 Consensus size: 58
11797 ATTAATCAAA
*
11807 TATCAAGTGACATGTTCTTTATTAGATGCATAAGAAAAGACGTTTTCGGACCGAGACT
1 TATCAAGTGACATGTTCTTTATTAGATGCATAAGAAAAGACGTTTTAGGACCGAGACT
* *
11865 TATCGAGTGACATGTTTTTTTATTAGATGTC-TAA-AAAAGACGTTTTAGGACCGAG
1 TATCAAGTGACATG-TTCTTTATTAGATG-CATAAGAAAAGACGTTTTAGGACCGAG
11920 GCATGATGCT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
58 33 0.66
59 16 0.32
60 1 0.02
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (58 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAGAAAAGACGTTTTAGGACCGAGACT
Found at i:13239 original size:36 final size:36
Alignment explanation
Indices: 13192--13261 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
13182 TTCAATAACC
* * *
13192 TTACATCTTTTGTGATTTTGGTTATCATATTTCTAA
1 TTACATCTTTTGTAATCTTGATTATCATATTTCTAA
*
13228 TTACATTTTTTGTAATCTTGATTATCATATTTCT
1 TTACATCTTTTGTAATCTTGATTATCATATTTCT
13262 CCAAAATCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.23, C:0.11, G:0.09, T:0.57
Consensus pattern (36 bp):
TTACATCTTTTGTAATCTTGATTATCATATTTCTAA
Done.