Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014114.1 Corchorus olitorius cultivar O-4 contig14147, 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: 161299
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:13101 original size:20 final size:20
Alignment explanation
Indices: 13065--13103 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
13055 CGACTCGAGA
*
13065 AAAATTCGAGTTCAGCTCGG
1 AAAATTCGAGTCCAGCTCGG
13085 AAAATTCGAG-CCGAGCTCG
1 AAAATTCGAGTCC-AGCTCG
13104 AGTAGTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.21
Consensus pattern (20 bp):
AAAATTCGAGTCCAGCTCGG
Found at i:13851 original size:30 final size:30
Alignment explanation
Indices: 13815--13912 Score: 187
Period size: 30 Copynumber: 3.3 Consensus size: 30
13805 CGAGCTCGGT
13815 CTCGAGCCTCCAAAATGAGGCTCGATCAAA
1 CTCGAGCCTCCAAAATGAGGCTCGATCAAA
*
13845 CTCGAGCCTCCAAAATGAGGCGCGATCAAA
1 CTCGAGCCTCCAAAATGAGGCTCGATCAAA
13875 CTCGAGCCTCCAAAATGAGGCTCGATCAAA
1 CTCGAGCCTCCAAAATGAGGCTCGATCAAA
13905 CTCGAGCC
1 CTCGAGCC
13913 AAGCTTCGAG
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 66 1.00
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.15
Consensus pattern (30 bp):
CTCGAGCCTCCAAAATGAGGCTCGATCAAA
Found at i:17920 original size:117 final size:117
Alignment explanation
Indices: 17846--18123 Score: 396
Period size: 117 Copynumber: 2.4 Consensus size: 117
17836 CTTCTCAAAC
*
17846 CCACCATTCCGCGGCA-CCTTGGGTGGTCTCCCAGGCTTACGCTTGGGCCCCTTCCTCGCTACAC
1 CCACCATTCCCCGG-ATCCTTGGGTGGTCTCCCAGGCTTACGCTTGGGCCCCTTCCTCGCTACAC
* *
17910 CATCTGAGTGATCATGCTCTCCTGTTTGCAGCTCAACTGCCATCTCCTCATAA
65 CATCTGAGTGATCATGCTCTCCTGATTCCAGCTCAACTGCCATCTCCTCATAA
*** * *
17963 CCGTTATTCCCCTGATTCTTGGGTGGTCTCCCAGGCTTACGCTTGGGCCCCTTCCTCGCTACACC
1 CCACCATTCCCCGGATCCTTGGGTGGTCTCCCAGGCTTACGCTTGGGCCCCTTCCTCGCTACACC
* *
18028 ATCTGAGTGATCATGCTCTCCTGTTTGCAGCTCAACTGCCATCTCCTCATAA
66 ATCTGAGTGATCATGCTCTCCTGATTCCAGCTCAACTGCCATCTCCTCATAA
*** * * *
18080 CCGTTATTCCCCTGATTCTTGGGTGGTCTCCCACGCTTACGCTT
1 CCACCATTCCCCGGATCCTTGGGTGGTCTCCCAGGCTTACGCTT
18124 TCTTATATTA
Statistics
Matches: 153, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
116 1 0.01
117 152 0.99
ACGTcount: A:0.14, C:0.36, G:0.19, T:0.31
Consensus pattern (117 bp):
CCACCATTCCCCGGATCCTTGGGTGGTCTCCCAGGCTTACGCTTGGGCCCCTTCCTCGCTACACC
ATCTGAGTGATCATGCTCTCCTGATTCCAGCTCAACTGCCATCTCCTCATAA
Found at i:22345 original size:89 final size:86
Alignment explanation
Indices: 22231--22405 Score: 289
Period size: 89 Copynumber: 2.0 Consensus size: 86
22221 AGTAGCAAGA
22231 AAAGGAGTAGAGGAAAAAGCAGGAAGAAGAGAAGGTATAGTGATTCTGATGACAGTGGGAGTGGT
1 AAAGGAGTAGAGG--AAAGCAGGAAGAAGAGAAGGTATAGTGATTCTGATGACA----GAGTGGT
22296 GAAAGTGAAACTGACTTATCTGATAAG
60 GAAAGTGAAACTGACTTATCTGATAAG
22323 AAAGGAGTAGAGG-AAGCAGGAAGAAGAGAAGGTATAGTGATTCTGATGACAGAGTGGTGAAAGT
1 AAAGGAGTAGAGGAAAGCAGGAAGAAGAGAAGGTATAGTGATTCTGATGACAGAGTGGTGAAAGT
22387 GAAACTGACTTATCTGATA
66 GAAACTGACTTATCTGATA
22406 TAAGTCGGTC
Statistics
Matches: 83, Mismatches: 0, Indels: 7
0.92 0.00 0.08
Matches are distributed among these distances:
85 32 0.39
89 38 0.46
92 13 0.16
ACGTcount: A:0.40, C:0.07, G:0.33, T:0.20
Consensus pattern (86 bp):
AAAGGAGTAGAGGAAAGCAGGAAGAAGAGAAGGTATAGTGATTCTGATGACAGAGTGGTGAAAGT
GAAACTGACTTATCTGATAAG
Found at i:24341 original size:23 final size:23
Alignment explanation
Indices: 24299--24346 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
24289 TTCTTGTAAT
24299 AGTGGTTATGGGATTCATGGCTC
1 AGTGGTTATGGGATTCATGGCTC
24322 AGTGGTTATGGGATTCATGGCTC
1 AGTGGTTATGGGATTCATGGCTC
24345 AG
1 AG
24347 GTTGTTGGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.19, C:0.12, G:0.35, T:0.33
Consensus pattern (23 bp):
AGTGGTTATGGGATTCATGGCTC
Found at i:28349 original size:31 final size:32
Alignment explanation
Indices: 28276--28350 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 32
28266 GCCACATCTG
* * * *
28276 TCAAGAAGTAAAATGTCTTGAATTTGAGGAGT
1 TCAAGAGGTAAAATGTCATGAATCTGAGAAGT
*
28308 TCATGAGGTAAAATGTCATGAATCT-AGAAGT
1 TCAAGAGGTAAAATGTCATGAATCTGAGAAGT
28339 TCAA-AGGGTAAA
1 TCAAGA-GGTAAA
28351 TTATCCTGAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
30 1 0.03
31 14 0.39
32 21 0.58
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (32 bp):
TCAAGAGGTAAAATGTCATGAATCTGAGAAGT
Found at i:91083 original size:18 final size:18
Alignment explanation
Indices: 91060--91094 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
91050 GATGCCCCAA
*
91060 GTCATCTTCAAGTCCATT
1 GTCATCATCAAGTCCATT
91078 GTCATCATCAAGTCCAT
1 GTCATCATCAAGTCCAT
91095 AGTAAGTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.34
Consensus pattern (18 bp):
GTCATCATCAAGTCCATT
Found at i:129857 original size:2 final size:2
Alignment explanation
Indices: 129850--129881 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
129840 GAAACTAACC
129850 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
129882 ACTATAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:142915 original size:30 final size:30
Alignment explanation
Indices: 142881--142939 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
142871 TAATAGAATG
142881 AAAAGGCACCATCTTTTACACCCAAGTCAA
1 AAAAGGCACCATCTTTTACACCCAAGTCAA
142911 AAAAGGCACCATCTTTTACACCCAAGTCA
1 AAAAGGCACCATCTTTTACACCCAAGTCA
142940 CAACCTTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.39, C:0.31, G:0.10, T:0.20
Consensus pattern (30 bp):
AAAAGGCACCATCTTTTACACCCAAGTCAA
Found at i:154558 original size:22 final size:21
Alignment explanation
Indices: 154515--154555 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
154505 TTGGGGAGCC
154515 AAAAAACAGACATCTCATAAT
1 AAAAAACAGACATCTCATAAT
*
154536 AAAAACACAGATAT-TCATAA
1 AAAAA-ACAGACATCTCATAA
154556 ATAGGAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.59, C:0.17, G:0.05, T:0.20
Consensus pattern (21 bp):
AAAAAACAGACATCTCATAAT
Found at i:154884 original size:17 final size:18
Alignment explanation
Indices: 154862--154895 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
154852 GCTCTCCCCT
*
154862 TTCACTTTTC-TTTCATG
1 TTCACTCTTCATTTCATG
154879 TTCACTCTTCATTTCAT
1 TTCACTCTTCATTTCAT
154896 TGCCTTTGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.15, C:0.26, G:0.03, T:0.56
Consensus pattern (18 bp):
TTCACTCTTCATTTCATG
Found at i:160819 original size:320 final size:325
Alignment explanation
Indices: 160316--161183 Score: 983
Period size: 320 Copynumber: 2.7 Consensus size: 325
160306 ATAATTATTA
* * * *
160316 ACCCGAAAAGAT-TTTTCCTCAATTT-TTGTCAAAAATACTCATAAAATATATATAATTCAACGC
1 ACCCGAAAAG-TCTTATCCTCAATTTCTTG-CCACAATACTCAGAAAATATATATAATTCAACGC
** * * * * *
160379 CAAAAGGATTGAAGGACTTTTCAAGCTTTTAATATCGTTTTTCATATTTTTTTCTGAATTAATTT
64 CAAAAAAATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTC-CA-TTTTTTCCGAATTAATTT
* *
160444 CTAATTAAATC-GAAACAAGATTCAGATGCATGTAAAAACAAATTCTTAAATCCAATGTCGCTGA
127 CTAATTAAATCAGAAACAAGATTCAGATGCATGTAAAAACAAATCCTTAAATCCAATGTGGCTGA
* * * *
160508 TATTTGATTAGTTGAATAAAGATATTTCAAGGAGT-CTCGGTGCCAAAAAT-ATGCAAAACAGAG
192 GATTTGATTAGATGAATAAA-ATATTTCAAGGAGTCCT-GGCGCCAAAAATCATGAAAAACAGAG
* * * *
160571 CAGTGGTCT-CGGAACGCGTTTTTAGTC-AAAACCGTGATGGTTAATACACGATTTCGACT-A-A
255 CAG-GGACTCCGGAACGCATTTTTAGCCAAAAACCGTGATAGTTAATACACGATTTCGACTAATA
160632 AAA-CTG
319 AAAGCTG
* * *
160638 ACCTGAAATGTCTTAT-CTCAATTT-TTCGCCACAATACACAGAAAATATATATAATTCAACGCC
1 ACCCGAAAAGTCTTATCCTCAATTTCTT-GCCACAATACTCAGAAAATATATATAATTCAACGCC
**
160701 AAAAAAATTGGCGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTACCGAATTAATTTCT
65 AAAAAAATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTT-CCGAATTAATTTCT
** *
160766 AATTAAA-CAGAAACAAGATTCAGATGCCCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGA
129 AATTAAATCAGAAACAAGATTCAGATGCATGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGA
* * * * ** *
160830 TTTGCTTCGATGAAT-ATATATTTCAAGGAGTCCTTGCGCCAAAAATCATGAAAAATTGAGCTGG
194 TTTGATTAGATGAATAAAATATTTCAAGGAGTCCTGGCGCCAAAAATCATGAAAAACAGAGCAGG
* * *
160894 GACTCCGGAACGCATTTTTAGCCAAAAACTGTGATAGTTAGTACACGATTTCGGCTAAAATTTTG
259 GACTCCGGAACGCATTTTTAGCCAAAAACCGTGATAGTTAATACACGATTTCGACT--AA---T-
*
160959 CAAAAGTTG
318 -AAAAGCTG
* * * * *
160968 ACCCGAAAAGTTTTTTCCTCAATTTCTTGCCACAATACTCAGAAAAAATATACAATTCAGCGCCA
1 ACCCGAAAAGTCTTATCCTCAATTTCTTGCCACAATACTCAGAAAATATATATAATTCAACGCCA
* * * * *
161033 GAAAAATTGAAGGGTTTTTCACGCTTCAAATATCGTTTTTCCATTTTTTCCGAATTTATTTTTAA
66 AAAAAATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCCGAATTAATTTCTAA
* * * *
161098 TTAAATCA-AAACAAGATTCAGATACTTGGAAAAACAAATCTTTAAATCCAATGTGGCTGAGATT
131 TTAAATCAGAAACAAGATTCAGATGCATGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATT
*
161162 TGGTTAGATGAATATAAATATT
196 TGATTAGATGAATA-AAATATT
161184 CCAGGGATTC
Statistics
Matches: 459, Mismatches: 64, Indels: 36
0.82 0.11 0.06
Matches are distributed among these distances:
318 28 0.06
319 38 0.08
320 110 0.24
321 77 0.17
322 12 0.03
323 1 0.00
329 4 0.01
330 94 0.20
331 87 0.19
332 8 0.02
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Consensus pattern (325 bp):
ACCCGAAAAGTCTTATCCTCAATTTCTTGCCACAATACTCAGAAAATATATATAATTCAACGCCA
AAAAAATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCCGAATTAATTTCTAA
TTAAATCAGAAACAAGATTCAGATGCATGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATT
TGATTAGATGAATAAAATATTTCAAGGAGTCCTGGCGCCAAAAATCATGAAAAACAGAGCAGGGA
CTCCGGAACGCATTTTTAGCCAAAAACCGTGATAGTTAATACACGATTTCGACTAATAAAAGCTG
Found at i:161174 original size:330 final size:321
Alignment explanation
Indices: 160316--161284 Score: 1025
Period size: 331 Copynumber: 3.0 Consensus size: 321
160306 ATAATTATTA
* * * *
160316 ACCCGAAAAGATTTTTCCTCAATTTTTGTCAAAAATACTCATAAAATATATATAATTCAACGCCA
1 ACCCGAAAAGTTTTTTCCTCAATTTTTG-CCACAATACTCAGAAAATATATATAATTCAACGCCA
* * * * * *
160381 AAAGGATTGAAGGACTTTTCAAGCTTTTAATATCGTTTTTCATATTTTTTTCTGAATTAATTTCT
65 AAA-AATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTC-CA-TTTTTTCCGAATTAATTTCT
* * *
160446 AATTAAATCGAAACAAGATTCAGATGCATGTAAAAACAAAT-TCTTAAATCCAATGTCGCTGATA
127 AATTAAATCAAAACAAGATTCAGATGCATGTAAAAACAAATCT-TTAAATCCAATGTGGCTGAGA
* * * * ** *
160510 TTTGATTAGTTGAATAAAGATATTTCAAGGAGT-CTCGGTGCCAAAAAT-ATGCAAAACAGAGCA
191 TTTGATTAGATGAAT--ATATATTTCAAGGAGTCCT-TGTGCCAAAAATCATGAAAAATTGAGCT
* * * * *
160573 GTGG-TCTCGGAACGCGTTTTTAGTC-AAAACCGTGATGGTTAATACACGATTTCGACT---AAA
253 GAGGCTC-CGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAAAA
160633 AACTG
317 AACTG
* * * * *
160638 ACCTGAAATGTCTTAT-CTCAATTTTTCGCCACAATACACAGAAAATATATATAATTCAACGCCA
1 ACCCGAAAAGTTTTTTCCTCAATTTTT-GCCACAATACTCAGAAAATATATATAATTCAACGCC-
**
160702 AAAAAATTGGCGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTACCGAATTAATTTCTA
64 AAAAAATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTT-CCGAATTAATTTCTA
** * *
160767 ATTAAA-CAGAAACAAGATTCAGATGCCCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGAT
128 ATTAAATCA-AAACAAGATTCAGATGCATGTAAAAACAAATCTTTAAATCCAATGTGGCTGAGAT
* * *
160831 TTGCTTCGATGAATATATATTTCAAGGAGTCCTTGCGCCAAAAATCATGAAAAATTGAGCTG-GG
192 TTGATTAGATGAATATATATTTCAAGGAGTCCTTGTGCCAAAAATCATGAAAAATTGAGCTGAGG
* *
160895 ACTCCGGAACGCATTTTTAGCCAAAAACTGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGC
257 -CTCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAA------
*
160960 AAAAGTTG
315 AAAA-CTG
* * *
160968 ACCCGAAAAGTTTTTTCCTCAATTTCTTGCCACAATACTCAGAAAAAATATACAATTCAGCGCCA
1 ACCCGAAAAGTTTTTTCCTCAATTT-TTGCCACAATACTCAGAAAATATATATAATTCAACGCCA
* * * *
161033 GAAAAATTGAAGGGTTTTTCACGCTTCAAATATCGTTTTTCCATTTTTTCCGAATTTATTTTTAA
65 -AAAAATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCCGAATTAATTTCTAA
* * *
161098 TTAAATCAAAACAAGATTCAGATACTTGGAAAAACAAATCTTTAAATCCAATGTGGCTGAGATTT
129 TTAAATCAAAACAAGATTCAGATGCATGTAAAAACAAATCTTTAAATCCAATGTGGCTGAGATTT
* * * * * * *
161163 GGTTAGATGAATATAAATATTCCAGGGATTCTTTATGTC-AAAATCAT-ACAAAATTGAG-TCGA
194 GATTAGATGAATAT--ATATTTCAAGGAGTCCTTGTGCCAAAAATCATGA-AAAATTGAGCT-GA
* *
161225 GGCCCCGAAACGCGTTTTTAGCCAAAAA-TCGTGATGGTTAG-ACACGATTTCGGCTAAAAA
255 GGCTCCGGAACGCGTTTTTAGCCAAAAACT-GTGATGGTTAGTACACGATTTCGGCTAAAAA
161285 TTGACTCGAA
Statistics
Matches: 543, Mismatches: 74, Indels: 58
0.80 0.11 0.09
Matches are distributed among these distances:
318 27 0.05
319 37 0.07
320 110 0.20
321 72 0.13
322 16 0.03
323 1 0.00
324 1 0.00
329 4 0.01
330 118 0.22
331 137 0.25
332 20 0.04
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (321 bp):
ACCCGAAAAGTTTTTTCCTCAATTTTTGCCACAATACTCAGAAAATATATATAATTCAACGCCAA
AAAATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCCGAATTAATTTCTAATT
AAATCAAAACAAGATTCAGATGCATGTAAAAACAAATCTTTAAATCCAATGTGGCTGAGATTTGA
TTAGATGAATATATATTTCAAGGAGTCCTTGTGCCAAAAATCATGAAAAATTGAGCTGAGGCTCC
GGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAAAAAACTG
Done.