Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024781.1 Corchorus olitorius cultivar O-4 contig24814, 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: 38207
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:13328 original size:325 final size:325
Alignment explanation
Indices: 12738--13393 Score: 1312
Period size: 325 Copynumber: 2.0 Consensus size: 325
12728 TGAAGTAATA
12738 AACCTAGAATATTCTAGGTGTCGAACCCACAGAGAACAATTAATTCCTATTATAATTAATTCTAT
1 AACCTAGAATATTCTAGGTGTCGAACCCACAGAGAACAATTAATTCCTATTATAATTAATTCTAT
12803 CAAAAAAGGAAATTAAGAGAAATTATCAAAACAATTAAAAACTAAGAGCAATTGAATTATAAAAG
66 CAAAAAAGGAAATTAAGAGAAATTATCAAAACAATTAAAAACTAAGAGCAATTGAATTATAAAAG
12868 TAGAGAATTAAATAAGATATGAAGACAATAATTGGAAAGCTTAGGGCTTCAGGTTTCACCTAATT
131 TAGAGAATTAAATAAGATATGAAGACAATAATTGGAAAGCTTAGGGCTTCAGGTTTCACCTAATT
12933 GGGAAATTACTACCTAACTTATGAATTAAATTGATGCTAAATTTGAATAGAATTACACTTAATTA
196 GGGAAATTACTACCTAACTTATGAATTAAATTGATGCTAAATTTGAATAGAATTACACTTAATTA
12998 CCTATATGCTCCGTCAAGTCTACACATGAATACCTAACTAATTAGAATCACTATCCGTCGATGTC
261 CCTATATGCTCCGTCAAGTCTACACATGAATACCTAACTAATTAGAATCACTATCCGTCGATGTC
13063 AACCTAGAATATTCTAGGTGTCGAACCCACAGAGAACAATTAATTCCTATTATAATTAATTCTAT
1 AACCTAGAATATTCTAGGTGTCGAACCCACAGAGAACAATTAATTCCTATTATAATTAATTCTAT
13128 CAAAAAAGGAAATTAAGAGAAATTATCAAAACAATTAAAAACTAAGAGCAATTGAATTATAAAAG
66 CAAAAAAGGAAATTAAGAGAAATTATCAAAACAATTAAAAACTAAGAGCAATTGAATTATAAAAG
13193 TAGAGAATTAAATAAGATATGAAGACAATAATTGGAAAGCTTAGGGCTTCAGGTTTCACCTAATT
131 TAGAGAATTAAATAAGATATGAAGACAATAATTGGAAAGCTTAGGGCTTCAGGTTTCACCTAATT
13258 GGGAAATTACTACCTAACTTATGAATTAAATTGATGCTAAATTTGAATAGAATTACACTTAATTA
196 GGGAAATTACTACCTAACTTATGAATTAAATTGATGCTAAATTTGAATAGAATTACACTTAATTA
13323 CCTATATGCTCCGTCAAGTCTACACATGAATACCTAACTAATTAGAATCACTATCCGTCGATGTC
261 CCTATATGCTCCGTCAAGTCTACACATGAATACCTAACTAATTAGAATCACTATCCGTCGATGTC
13388 AACCTA
1 AACCTA
13394 ATTAACTAGA
Statistics
Matches: 331, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
325 331 1.00
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.29
Consensus pattern (325 bp):
AACCTAGAATATTCTAGGTGTCGAACCCACAGAGAACAATTAATTCCTATTATAATTAATTCTAT
CAAAAAAGGAAATTAAGAGAAATTATCAAAACAATTAAAAACTAAGAGCAATTGAATTATAAAAG
TAGAGAATTAAATAAGATATGAAGACAATAATTGGAAAGCTTAGGGCTTCAGGTTTCACCTAATT
GGGAAATTACTACCTAACTTATGAATTAAATTGATGCTAAATTTGAATAGAATTACACTTAATTA
CCTATATGCTCCGTCAAGTCTACACATGAATACCTAACTAATTAGAATCACTATCCGTCGATGTC
Found at i:16615 original size:2 final size:2
Alignment explanation
Indices: 16608--16640 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
16598 TTTTTAGGTA
*
16608 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16641 CACACACATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21395 original size:2 final size:2
Alignment explanation
Indices: 21388--21421 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
21378 CCATGTGATA
21388 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21422 ATTCTAGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22437 original size:111 final size:111
Alignment explanation
Indices: 22243--22460 Score: 409
Period size: 111 Copynumber: 2.0 Consensus size: 111
22233 AATCTTGACC
*
22243 CTATACATATGGTAAAACATCAGCTACAAATTCATTTAAATTGAAGTACAGCCGTGAATTAATAT
1 CTATACATATGGTAAAACATCAGCTACAAATTCATTTAAACTGAAGTACAGCCGTGAATTAATAT
22308 TAGATTTATATATATAATTCGAACTTTCAAAAAGAAAACTTAATTA
66 TAGATTTATATATATAATTCGAACTTTCAAAAAGAAAACTTAATTA
*
22354 CTATACATATGGTAAAACATCAGCTATAAATTCATTTAAACTGAAGTACAGCCGTGAATTAATAT
1 CTATACATATGGTAAAACATCAGCTACAAATTCATTTAAACTGAAGTACAGCCGTGAATTAATAT
*
22419 TTGATTTATATATATAATTCGAACTTTCAAAAAGAAAACTTA
66 TAGATTTATATATATAATTCGAACTTTCAAAAAGAAAACTTA
22461 TGTACAAATT
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 104 1.00
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (111 bp):
CTATACATATGGTAAAACATCAGCTACAAATTCATTTAAACTGAAGTACAGCCGTGAATTAATAT
TAGATTTATATATATAATTCGAACTTTCAAAAAGAAAACTTAATTA
Found at i:26048 original size:31 final size:31
Alignment explanation
Indices: 26013--26179 Score: 156
Period size: 31 Copynumber: 5.4 Consensus size: 31
26003 TTTGTGCACG
*
26013 TGGCATGCCACGTGTCACTTTTTGAAACACA
1 TGGCATGCCACGTGTCACTTTTTGATACACA
* *
26044 TGGCATGCCACGTGTCACTTTTGGGTACACA
1 TGGCATGCCACGTGTCACTTTTTGATACACA
* ** *
26075 TGGCGTGATACGTGTCACTTTTTGATACACG
1 TGGCATGCCACGTGTCACTTTTTGATACACA
* * * *
26106 TGGCGTGCCACATGTCGCTTTTTTG-TACACG
1 TGGCATGCCACGTGTCAC-TTTTTGATACACA
* * ** * * *
26137 TGACGTGCCATATGTCGCTTTTTGGTACACG
1 TGGCATGCCACGTGTCACTTTTTGATACACA
26168 TGGCATGCCACG
1 TGGCATGCCACG
26180 GCGGACACCG
Statistics
Matches: 115, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
30 6 0.05
31 103 0.90
32 6 0.05
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.32
Consensus pattern (31 bp):
TGGCATGCCACGTGTCACTTTTTGATACACA
Found at i:26092 original size:62 final size:63
Alignment explanation
Indices: 26022--26179 Score: 187
Period size: 62 Copynumber: 2.5 Consensus size: 63
26012 GTGGCATGCC
* * *
26022 ACGTGTCACTTTTTGAAACACATGGCATGCCACGTGTCACTTTTGGGTACACATGGCGTG-AT
1 ACGTGTCACTTTTTGATACACGTGGCATGCCACGTGTCACTTTTGGGTACACATGACGTGCAT
* * * ** *
26084 ACGTGTCACTTTTTGATACACGTGGCGTGCCACATGTCGCTTTTTTGTACACGTGACGTGCCAT
1 ACGTGTCACTTTTTGATACACGTGGCATGCCACGTGTCACTTTTGGGTACACATGACGTG-CAT
* *
26148 A--TGTCGCTTTTTGGTACACGTGGCATGCCACG
1 ACGTGTCACTTTTTGATACACGTGGCATGCCACG
26180 GCGGACACCG
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
62 78 0.96
64 3 0.04
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.32
Consensus pattern (63 bp):
ACGTGTCACTTTTTGATACACGTGGCATGCCACGTGTCACTTTTGGGTACACATGACGTGCAT
Found at i:26852 original size:6 final size:6
Alignment explanation
Indices: 26841--26865 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
26831 ATTCTATAGC
26841 ACATCA ACATCA ACATCA ACATCA A
1 ACATCA ACATCA ACATCA ACATCA A
26866 GCAGTTAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (6 bp):
ACATCA
Found at i:28453 original size:40 final size:43
Alignment explanation
Indices: 28362--28460 Score: 116
Period size: 40 Copynumber: 2.4 Consensus size: 43
28352 AGAATACAAC
* * * *
28362 AAAGCAAAGACTCTCTGATTAGTTTATTCCTCCAAGATACAACA
1 AAAGCAAAGACTCTCCGATAAG-TTATTCCTCCAAGACACAAAA
*
28406 AAA-CAAAGACTCTCCGA-AAG-TATTCCTCCAGGACA-AAAA
1 AAAGCAAAGACTCTCCGATAAGTTATTCCTCCAAGACACAAAA
28445 AAAGCAAAGACTCTCC
1 AAAGCAAAGACTCTCC
28461 TATTAGAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
39 6 0.12
40 25 0.51
42 2 0.04
43 13 0.27
44 3 0.06
ACGTcount: A:0.42, C:0.25, G:0.12, T:0.20
Consensus pattern (43 bp):
AAAGCAAAGACTCTCCGATAAGTTATTCCTCCAAGACACAAAA
Found at i:28480 original size:31 final size:31
Alignment explanation
Indices: 28442--28507 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
28432 TCCAGGACAA
* *
28442 AAAAAAGCAAAGACTCTCCTATTAGAATTGC
1 AAAAAAGCAAACACTCTCCGATTAGAATTGC
28473 AAAAAAGCAAACACTCTCCGATTAGAATTGC
1 AAAAAAGCAAACACTCTCCGATTAGAATTGC
28504 AAAA
1 AAAA
28508 CTAGTTATGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.48, C:0.20, G:0.12, T:0.20
Consensus pattern (31 bp):
AAAAAAGCAAACACTCTCCGATTAGAATTGC
Found at i:33397 original size:139 final size:137
Alignment explanation
Indices: 33114--33365 Score: 360
Period size: 139 Copynumber: 1.8 Consensus size: 137
33104 ATTTTTTTAA
* *
33114 TTAAATTAGTAAAATGGTAAAAATAAAATAGGTATAAATATTAGATTTAATTAAATAAAAATGGA
1 TTAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAATATTAGATTTAATTAAATAAAAATAGA
* ** **
33179 GCTTTTAGTTGAGTAAAACTATAAAAGTATATTTAAAAGATTCTAATATATATAAGTTTTTCAAT
66 GCTTTTAGTTGAGTAAAACTATAAAAGTATATTTAAAAAAAACTAATATATATAAGTTTAACAAT
33244 TAAAAAT
131 TAAAAAT
* *
33251 TTAAAATAGTAAAATGGTAAAAATTAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATA
1 TTAAAATAGTAAAATGGTAAAAATAAAATAGGTATAA--ATATTAGATTTAATTAAATAAAAATA
* *
33316 GAGTTTTTAGTTGAGTAAAACTATAAAAGTTTATTTCTCAAAAAAAACTA
64 GAGCTTTTAGTTGAGTAAAACTATAAAAGTATA-TT-T-AAAAAAAACTA
33366 TAAAAATTTA
Statistics
Matches: 101, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
137 34 0.34
139 56 0.55
140 2 0.02
141 1 0.01
142 8 0.08
ACGTcount: A:0.50, C:0.03, G:0.11, T:0.36
Consensus pattern (137 bp):
TTAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAATATTAGATTTAATTAAATAAAAATAGA
GCTTTTAGTTGAGTAAAACTATAAAAGTATATTTAAAAAAAACTAATATATATAAGTTTAACAAT
TAAAAAT
Found at i:38073 original size:27 final size:27
Alignment explanation
Indices: 38043--38099 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
38033 ACACATGTCC
* **
38043 ATTTTTTTAATTAATTAAGTTTTAAAT
1 ATTTTTTTAATCAAAAAAGTTTTAAAT
*
38070 A-TTTTTTACTCAAAAAAGTTTTAAAT
1 ATTTTTTTAATCAAAAAAGTTTTAAAT
38096 ATTT
1 ATTT
38100 CAATCTAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 22 0.88
27 3 0.12
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.54
Consensus pattern (27 bp):
ATTTTTTTAATCAAAAAAGTTTTAAAT
Done.