Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017696.1 Corchorus olitorius cultivar O-4 contig17729, 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: 16698
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:3816 original size:2 final size:2
Alignment explanation
Indices: 3809--3839 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3799 AATTAACGTT
3809 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3840 TTGACTTAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9244 original size:2 final size:2
Alignment explanation
Indices: 9237--9261 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9227 TATAACGTTT
9237 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
9262 TTGACTTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11115 original size:4 final size:4
Alignment explanation
Indices: 11108--11179 Score: 81
Period size: 4 Copynumber: 17.8 Consensus size: 4
11098 AAAGTGATAG
* * * *
11108 ATAA ATAA ATAA ATAA ATAA AAAA ATAA ATAG ATAA ATAA GTAA AAATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA-A
* *
11157 ATAG ATAA ATAA AAAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATA
11180 GGTATATAGA
Statistics
Matches: 55, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
4 52 0.95
5 3 0.05
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (4 bp):
ATAA
Found at i:11222 original size:8 final size:8
Alignment explanation
Indices: 11104--11227 Score: 84
Period size: 8 Copynumber: 16.4 Consensus size: 8
11094 AAAAAAAGTG
11104 ATAGATAA
1 ATAGATAA
*
11112 ATAAATAA
1 ATAGATAA
*
11120 ATAAATAA
1 ATAGATAA
* *
11128 AAAAATAA
1 ATAGATAA
11136 ATAGATAA
1 ATAGATAA
11144 ATA-AGTAA
1 ATAGA-TAA
11152 A-A-AT-A
1 ATAGATAA
11157 ATAGATAA
1 ATAGATAA
11165 ATA-A-AA
1 ATAGATAA
11171 A-A-ATAA
1 ATAGATAA
* *
11177 ATAGGTAT
1 ATAGATAA
11185 ATAGATAA
1 ATAGATAA
*
11193 TTAGATAA
1 ATAGATAA
* * *
11201 AGAGGTAT
1 ATAGATAA
*
11209 AGAGATAA
1 ATAGATAA
11217 ATAGATAA
1 ATAGATAA
11225 ATA
1 ATA
11228 TGTAGGTAAA
Statistics
Matches: 93, Mismatches: 16, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
5 4 0.04
6 8 0.09
7 7 0.08
8 74 0.80
ACGTcount: A:0.65, C:0.00, G:0.11, T:0.24
Consensus pattern (8 bp):
ATAGATAA
Found at i:11263 original size:18 final size:19
Alignment explanation
Indices: 11240--11290 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
11230 TAGGTAAAAA
*
11240 AAATAAGTAGATAATAG-T
1 AAATAAATAGATAATAGCT
*
11258 AAATAAATAGATTATAGCT
1 AAATAAATAGATAATAGCT
* *
11277 AAATTAATAAATAA
1 AAATAAATAGATAA
11291 AAAGATTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.59, C:0.02, G:0.10, T:0.29
Consensus pattern (19 bp):
AAATAAATAGATAATAGCT
Found at i:11287 original size:27 final size:27
Alignment explanation
Indices: 11257--11319 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
11247 TAGATAATAG
*
11257 TAAATAAATAGATT-ATAGCTAAATTAA
1 TAAATAAATAGATTAATAG-TAAATAAA
*
11284 TAAATAAAAAGATTAATAGTAAATAAA
1 TAAATAAATAGATTAATAGTAAATAAA
11311 T-AATAAATA
1 TAAATAAATA
11320 AAGAGTTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 7 0.22
27 21 0.66
28 4 0.12
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (27 bp):
TAAATAAATAGATTAATAGTAAATAAA
Found at i:11334 original size:28 final size:30
Alignment explanation
Indices: 11276--11339 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
11266 AGATTATAGC
*
11276 TAAATTAATAAATAAAAAGATTAATAGTAAA
1 TAAA-TAATAAATAAAAAGATTAATAATAAA
*
11307 TAAATAATAAATAAAGAG-TT-ATAATAAA
1 TAAATAATAAATAAAAAGATTAATAATAAA
*
11335 AAAAT
1 TAAAT
11340 CTTTTTTGGC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 11 0.37
29 2 0.07
30 13 0.43
31 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (30 bp):
TAAATAATAAATAAAAAGATTAATAATAAA
Found at i:12745 original size:54 final size:54
Alignment explanation
Indices: 12673--13306 Score: 496
Period size: 54 Copynumber: 11.7 Consensus size: 54
12663 CAAATTCGAA
* * * **
12673 ATCAACTCTGATCATCGAAAACTTCTTGAAACGACCACACTAAATCATCTGGAG
1 ATCAACTCTGATCTTCGAAAACTTCTTGAAATGACCGCACTGGATCATCTGGAG
*
12727 ATCAACTCTGATCTTCGAAAACTTCTTGAAATGACCGCACTGGATCATCTAGAG
1 ATCAACTCTGATCTTCGAAAACTTCTTGAAATGACCGCACTGGATCATCTGGAG
* * * *
12781 ATCAACTCTGATCTTCGAAAACTTCTTGAAACGATCGCACCGGATCATTTGGAG
1 ATCAACTCTGATCTTCGAAAACTTCTTGAAATGACCGCACTGGATCATCTGGAG
* * * *
12835 ATCAACTCTGGTCTTCGAAAACTTCTTGAAAGGACCGCACCGGATCATTTGGAG
1 ATCAACTCTGATCTTCGAAAACTTCTTGAAATGACCGCACTGGATCATCTGGAG
* * *
12889 ATCAACTCTGATCTTCGAAAACTTCTT-AGAAGGACCGCACCGGATTATCTAGG-G
1 ATCAACTCTGATCTTCGAAAACTTCTTGA-AATGACCGCACTGGATCATCT-GGAG
* * *
12943 ATCAACTCTGATC-TCTAAAAACTTCTTGGAATGACCGCAATGGATCATCTAGG-G
1 ATCAACTCTGATCTTC-GAAAACTTCTTGAAATGACCGCACTGGATCATCT-GGAG
* * * *
12997 ATCAACTCTGATC-TCTAAAAACTTTTTGGAATGACCGCACTGGATCATCTGGGG
1 ATCAACTCTGATCTTC-GAAAACTTCTTGAAATGACCGCACTGGATCATCTGGAG
* ** * *
13051 ATCAACTCTGATC-ACTGAAAACTTCTATGAAA-GACAACACTGGGA-CATCTGAAA
1 ATCAACTCTGATCTTC-GAAAACTTCT-TGAAATGACCGCACT-GGATCATCTGGAG
* * * * * * ** *
13105 ATCAACT-TAGATC-TCTGAAAGCTTCTATGAAA-GATCGTACAGGGTCGTCTTAAA
1 ATCAACTCT-GATCTTC-GAAAACTTCT-TGAAATGACCGCACTGGATCATCTGGAG
* * * * *
13159 ATCAACT-TAGATC-TCTGAAAACTTCTACGAAA-GACCGCACAGGGTTATCTGAAG
1 ATCAACTCT-GATCTTC-GAAAACTTCT-TGAAATGACCGCACTGGATCATCTGGAG
* * * * **
13213 ATCAACT-TAAATC-TCTGAAAACTTTTATGAAA-GACCGCACAGGGTCATCTAAAG
1 ATCAACTCT-GATCTTC-GAAAACTTCT-TGAAATGACCGCACTGGATCATCTGGAG
* * *
13267 ATCAACT-TAAATCTCCGAAAACTTCTACGAAA-GACCGCAC
1 ATCAACTCT-GATCTTCGAAAACTTCT-TGAAATGACCGCAC
13307 AGGGTTATAT
Statistics
Matches: 510, Mismatches: 60, Indels: 20
0.86 0.10 0.03
Matches are distributed among these distances:
53 8 0.02
54 492 0.96
55 10 0.02
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.26
Consensus pattern (54 bp):
ATCAACTCTGATCTTCGAAAACTTCTTGAAATGACCGCACTGGATCATCTGGAG
Found at i:13307 original size:108 final size:108
Alignment explanation
Indices: 13067--13345 Score: 398
Period size: 108 Copynumber: 2.6 Consensus size: 108
13057 TCTGATCACT
* ** * ** * * * *
13067 GAAAACTTCTATGAAAGACAACACTGGGACATCTGAAAATCAACTTAGATCTCTGAAAGCTTCTA
1 GAAAACTTCTACGAAAGACCGCACAGGGTTATCTGAAGATCAACTTAAATCTCTGAAAACTTTTA
* * * * *
13132 TGAAAGATCGTACAGGGTCGTCTTAAAATCAACTTAGATCTCT
66 TGAAAGACCGCACAGGGTCATCTTAAAATCAACTTAAATCTCC
13175 GAAAACTTCTACGAAAGACCGCACAGGGTTATCTGAAGATCAACTTAAATCTCTGAAAACTTTTA
1 GAAAACTTCTACGAAAGACCGCACAGGGTTATCTGAAGATCAACTTAAATCTCTGAAAACTTTTA
13240 TGAAAGACCGCACAGGGTCATC-TAAAGATCAACTTAAATCTCC
66 TGAAAGACCGCACAGGGTCATCTTAAA-ATCAACTTAAATCTCC
*
13283 GAAAACTTCTACGAAAGACCGCACAGGGTTATATGAAGATCAACTTAAATCTCTGAAAACTTT
1 GAAAACTTCTACGAAAGACCGCACAGGGTTATCTGAAGATCAACTTAAATCTCTGAAAACTTT
13346 AAAAGATCGC
Statistics
Matches: 154, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
107 4 0.03
108 150 0.97
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.25
Consensus pattern (108 bp):
GAAAACTTCTACGAAAGACCGCACAGGGTTATCTGAAGATCAACTTAAATCTCTGAAAACTTTTA
TGAAAGACCGCACAGGGTCATCTTAAAATCAACTTAAATCTCC
Found at i:13450 original size:22 final size:22
Alignment explanation
Indices: 13408--13451 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
13398 AACACCTGTA
*
13408 CTTGACTCTTCATCTATCCATT
1 CTTGACTCTTCATCTAGCCATT
*
13430 CTTGACTTCTTC-TTTAGCCATT
1 CTTGAC-TCTTCATCTAGCCATT
13452 ATTGGCTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.16, C:0.30, G:0.07, T:0.48
Consensus pattern (22 bp):
CTTGACTCTTCATCTAGCCATT
Found at i:14765 original size:20 final size:19
Alignment explanation
Indices: 14740--14798 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
14730 GTCTTTTGCT
14740 TTTTCAACTTTTTCTTTTCC
1 TTTTCAA-TTTTTCTTTTCC
*
14760 TTTTCAATTTTT-TTCTTCA
1 TTTTCAATTTTTCTT-TTCC
14779 TTCTTC-ATTTTTCTTTTCC
1 TT-TTCAATTTTTCTTTTCC
14798 T
1 T
14799 CTCCTTTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
18 2 0.06
19 20 0.59
20 12 0.35
ACGTcount: A:0.10, C:0.22, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTCAATTTTTCTTTTCC
Found at i:15171 original size:15 final size:15
Alignment explanation
Indices: 15139--15189 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
15129 CCGATTTTTA
*
15139 GAAAAACCCTTT-TCT
1 GAAAAACACTTTCT-T
15154 GAAAAACACTTTCTT
1 GAAAAACACTTTCTT
*
15169 GAAAAGCCACTTTCTT
1 GAAAA-ACACTTTCTT
15185 GAAAA
1 GAAAA
15190 GCATCTTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
15 17 0.53
16 15 0.47
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (15 bp):
GAAAAACACTTTCTT
Found at i:15197 original size:16 final size:15
Alignment explanation
Indices: 15149--15197 Score: 64
Period size: 16 Copynumber: 3.2 Consensus size: 15
15139 GAAAAACCCT
*
15149 TTTC-TGAAAAACAC
1 TTTCTTGAAAAGCAC
15163 TTTCTTGAAAAGCCAC
1 TTTCTTGAAAAG-CAC
15179 TTTCTTGAAAAGCATC
1 TTTCTTGAAAAGCA-C
15195 TTT
1 TTT
15198 GACTTTTGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 4 0.13
15 8 0.26
16 19 0.61
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (15 bp):
TTTCTTGAAAAGCAC
Found at i:16245 original size:15 final size:16
Alignment explanation
Indices: 16224--16272 Score: 64
Period size: 15 Copynumber: 3.0 Consensus size: 16
16214 AACCTTTAAT
16224 TGAGTTTAATAAAATA
1 TGAGTTTAATAAAATA
16240 -GAGTTTAATAAAAATA
1 TGAGTTTAAT-AAAATA
*
16256 TTAGGTTTAATAAAATA
1 TGA-GTTTAATAAAATA
16273 AAAATAGAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
15 9 0.31
16 6 0.21
17 7 0.24
18 7 0.24
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (16 bp):
TGAGTTTAATAAAATA
Done.