Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009590.1 Corchorus olitorius cultivar O-4 contig09622, 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: 4402
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Found at i:869 original size:327 final size:321
Alignment explanation
Indices: 21--1138 Score: 1122
Period size: 327 Copynumber: 3.5 Consensus size: 321
11 TATTTTTCTA
* * *
21 TTTTTTTCCGAATTAATTTCTAATTAAATCGATACAAGATTTAGATGCTCGCAAAAAC-AATCCT
1 TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTAAGATGCTCGTAAAAACAAATCCT
* * * * *
85 TAAATCGAATGTGGCTTGGATTTGGTTAGATGAATATAGATATTTCTAGGAGT-TTTTCTGCCAA
66 TAAATCCAATGTGGCTGGGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTAC-GCCAA
* * *
149 AAATCATGCAAAACTGAGCTGGGACTCCGAAACGCGTTTTTAGCCAAAATCTGTGATGGTTAGTA
130 AAATCATGCAAAACTGAGCCGGGACTCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTA
* * * ** * *
214 CACGATTTCGGCTAAAATCTG----AC--CCGAAACGTTTTTT-CTACATTTTTTGCAAAATATT
195 CACGATTTCGGCTAAATTTTGAAAAACTACCCAAAAATTTTTTCCT-CAATTTTTGCACAATATT
* * * * * *
272 CAGAAAAAATATATAATTAAACGCCAAAAATATTGATGGGCTTTTCATGCTTCTAATATC-TT
259 CAGAAAAAATATATAATTCAACACCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTT
* * * *
334 TTTTTTTAC-AGATTAATTTCTAATTAAAACGACACAAGATTCAA-AT-CTCGTAAATACAAATC
1 TTTTTTTCCGA-ATTAATTTCTAATTAAATCGAAACAAGATT-AAGATGCTCGTAAAAACAAATC
* ** * * * * *
396 TTTGTATCCAATGTGACTGGGATTTGGTTCGATGAATATAGACATTTTAAGGAA-TCTTTGCGCC
64 CTTAAATCCAATGTGGCTGGGATTTGGTTAGATGAATATAGATATTTCAA-GAAGTCTTTACGCC
* * * * * *
460 AAAAATCATGCAAAATTAAGTCGGGACTCCAGAAAGCGTTTTTAGCCAAACACTGTGATGGTTAG
128 AAAAATCATGCAAAACTGAGCCGGGACTCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAG
* *
525 TATATGATTTCGGCTAAATTTTTGAAAAAACTAACCCAAAAATTTTTTCCTCAATTTTTGCCACA
193 TACACGATTTCGGCTAAA-TTTTG-AAAAACT-ACCCAAAAATTTTTTCCTCAATTTTTG-CACA
*
590 ATACTCAGAAAAAAATATATAATTCAACACCAAAAAAATTGAAGGGTTTTTTCACGCTTCTAATA
254 ATATTCAG-AAAAAATATATAATTCAACACCAAAAAAATTGAAGGG-TTTTTCACGCTTCTAATA
*
655 CCGTT
317 TCGTT
* * * * * *
660 TTTTTTTCTGAATCAATTTCCAAGTAAATTGAAACAAGATTAAGATGCTTGTAAAAACAAATCCT
1 TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTAAGATGCTCGTAAAAACAAATCCT
** *
725 TAAATCCAATGTGG-TAGGGATTTAATTTA-ATGAATATAGATATTTCAAGAAGTCTTTACGCAA
66 TAAATCCAATGTGGCT-GGGATTT-GGTTAGATGAATATAGATATTTCAAGAAGTCTTTACGCCA
* * * * * *
788 AAAATAATGCAAAACTGAGGCCGGG-C-CCGGAACTCATTTTTAGCAAAAAAACTATGATGGATA
129 AAAATCATGCAAAACTGA-GCCGGGACTCCGGAACGCGTTTTTAGC-CAAAAACTGTGATGGTTA
* * *
851 GTACACGATTTTGGCTAAAATTTTGTAAAAACTGACCCGAAAAGTTTTTCCTCAATTTTTTGGCA
192 GTACACGATTTCGGCT-AAATTTTG-AAAAACT-ACCCAAAAATTTTTTCCTCAA-TTTTT-GCA
* * * *
916 CAATATTCGGGAAAAATATATGATTCAACACCAAAAAAATTGAATGGTTTTTCACGCTTCTAATA
252 CAATATTCAGAAAAAATATATAATTCAACACCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATA
*
981 TTGTTTTT
317 TCG---TT
* * * **
989 CCATTATTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAGCCAAA
1 ---TT-TTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTAAGATGCTCGTAAAAACAAA
* ** * * *
1054 TCCATAAATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTCCAAGGAGTCTTTATGC
62 TCCTTAAATCCAATGTGGCTGGGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTACGC
* *
1119 C-AAAACCATGCAAAATTGAG
127 CAAAAATCATGCAAAACTGAG
1139 TCGCCCCGAA
Statistics
Matches: 652, Mismatches: 114, Indels: 60
0.79 0.14 0.07
Matches are distributed among these distances:
312 10 0.02
313 158 0.24
314 10 0.02
319 2 0.00
322 19 0.03
323 12 0.02
324 33 0.05
325 19 0.03
326 72 0.11
327 168 0.26
328 25 0.04
329 3 0.00
331 1 0.00
332 20 0.03
333 99 0.15
334 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (321 bp):
TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTAAGATGCTCGTAAAAACAAATCCT
TAAATCCAATGTGGCTGGGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTACGCCAAA
AATCATGCAAAACTGAGCCGGGACTCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTAC
ACGATTTCGGCTAAATTTTGAAAAACTACCCAAAAATTTTTTCCTCAATTTTTGCACAATATTCA
GAAAAAATATATAATTCAACACCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTT
Found at i:1385 original size:2 final size:2
Alignment explanation
Indices: 1378--1415 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1368 GGTTCGATGA
1378 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1416 TTTTAAGAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2414 original size:15 final size:16
Alignment explanation
Indices: 2394--2423 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2384 TTAGTATTTA
2394 TTCATATAAT-AATTG
1 TTCATATAATGAATTG
2409 TTCATATAATGAATT
1 TTCATATAATGAATT
2424 TTAGCAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (16 bp):
TTCATATAATGAATTG
Found at i:2765 original size:22 final size:22
Alignment explanation
Indices: 2737--3196 Score: 197
Period size: 22 Copynumber: 21.0 Consensus size: 22
2727 TGATAATCAC
2737 TATAAAATTTTGATAACCTCCA
1 TATAAAATTTTGATAACCTCCA
* *
2759 TATAAAATTTTGATAA-TTACA
1 TATAAAATTTTGATAACCTCCA
* * * * *
2780 CTATAAAGTTTTTATGACGATAC-
1 -TATAAAATTTTGATAAC-CTCCA
* *
2803 TATAAAATTTCGAGAACCTCCA
1 TATAAAATTTTGATAACCTCCA
* * * *
2825 TATAAAATTGTGTTAACTTCCC
1 TATAAAATTTTGATAACCTCCA
*
2847 TATAAAATTTTG-TTACACTACC-
1 TATAAAATTTTGATAAC-CT-CCA
** *
2869 TATAAAATTTAAATAACCACC-
1 TATAAAATTTTGATAACCTCCA
* * *
2890 TAATGAAATTTTGATAACCACCC
1 T-ATAAAATTTTGATAACCTCCA
*
2913 TATGAAATTTTGATAACCTCCCA
1 TATAAAATTTTGATAACCT-CCA
* * * * *
2936 -ATGAAATGTTGGTAAGCGCACA
1 TATAAAATTTTGATAACCTC-CA
* *
2958 TTATGAAATTTCGATAACCTTCC-
1 -TATAAAATTTTGATAACC-TCCA
* * *
2981 GATAAAATATTGGTAA--TCACA
1 TATAAAATTTTGATAACCTC-CA
3002 TTATAAAATTTTGATAACCAT--A
1 -TATAAAATTTTGATAACC-TCCA
* * *
3024 TCATGAAATTGTGAT-ACCT-TA
1 T-ATAAAATTTTGATAACCTCCA
*
3045 CTATGAAAATTTT-ATAAACCTCCT
1 -TAT-AAAATTTTGAT-AACCTCCA
3069 TATAAAATTTTGATAACCTCCA
1 TATAAAATTTTGATAACCTCCA
* *
3091 TTTGAAATTTTGATAACCT-C-
1 TATAAAATTTTGATAACCTCCA
* *
3111 -ATGAAATTTTGATAACCAT-CT
1 TATAAAATTTTGATAACC-TCCA
* *
3132 TATAAAATTATGATAACATACC-
1 TATAAAATTTTGATAACCT-CCA
* *
3154 TAT-AAATTTTCTATAA-CTTCA
1 TATAAAATTTT-GATAACCTCCA
*
3175 TTATAAAATTTTGTTAACCTCC
1 -TATAAAATTTTGATAACCTCC
3197 TAGAGAACTA
Statistics
Matches: 332, Mismatches: 68, Indels: 75
0.70 0.14 0.16
Matches are distributed among these distances:
19 18 0.05
20 5 0.02
21 30 0.09
22 232 0.70
23 28 0.08
24 17 0.05
25 2 0.01
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (22 bp):
TATAAAATTTTGATAACCTCCA
Found at i:2786 original size:44 final size:43
Alignment explanation
Indices: 2725--3198 Score: 238
Period size: 44 Copynumber: 10.9 Consensus size: 43
2715 TCTTATGAAA
2725 TTTGATAA-T-CACTATAAAATTTTGATAACCTCCATATAAAAT
1 TTTGATAACTACACTATAAAATTTTGATAACCTCC-TATAAAAT
* * * * * *
2767 TTTGATAATTACACTATAAAGTTTTTATGACGATACTATAAAAT
1 TTTGATAACTACACTATAAAATTTTGATAAC-CTCCTATAAAAT
* * * * * *
2811 TTCGAGAACCTCCA-TATAAAATTGTGTTAACTTCCCTATAAAAT
1 TTTGATAA-CTACACTATAAAATTTTGATAACCT-CCTATAAAAT
* ** * *
2855 TTTGTTACACTAC-CTATAAAATTTAAATAACCACCTAATGAAAT
1 TTTGATA-ACTACACTATAAAATTTTGATAACCTCCT-ATAAAAT
* * * * *
2899 TTTGATAACCACCCTATGAAATTTTGATAACCTCCCAATGAAAT
1 TTTGATAACTACACTATAAAATTTTGATAACCT-CCTATAAAAT
* * * * * * *
2943 GTTGGTAAGCGCACATTATGAAATTTCGATAACCTTCCGATAAAAT
1 TTTGATAA-C-TACACTATAAAATTTTGATAACC-TCCTATAAAAT
* * * * *
2989 ATTGGTAA-TCACATTATAAAATTTTGATAACCAT-ATCATGAAAT
1 TTTGATAACT-ACACTATAAAATTTTGATAACC-TCCT-ATAAAAT
* * *
3033 TGTGATACCT-TACTATGAAAATTTT-ATAAACCTCCTTATAAAAT
1 TTTGATAACTACACTAT-AAAATTTTGAT-AACCTCC-TATAAAAT
* * * *
3077 TTTGATAACCTCCA-TTTGAAATTTTGATAACCT-C-ATGAAAT
1 TTTGATAA-CTACACTATAAAATTTTGATAACCTCCTATAAAAT
* *
3118 TTTGATAAC--CATCTTATAAAATTATGATAACATACCTAT-AAAT
1 TTTGATAACTACA-C-TATAAAATTTTGATAACCT-CCTATAAAAT
* * * *
3161 TTTCTATAACTTCATTATAAAATTTTGTTAACCTCCTA
1 TTT-GATAACTACACTATAAAATTTTGATAACCTCCTA
3199 GAGAACTATT
Statistics
Matches: 328, Mismatches: 72, Indels: 63
0.71 0.16 0.14
Matches are distributed among these distances:
38 2 0.01
40 1 0.00
41 29 0.09
42 8 0.02
43 29 0.09
44 203 0.62
45 17 0.05
46 38 0.12
47 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (43 bp):
TTTGATAACTACACTATAAAATTTTGATAACCTCCTATAAAAT
Found at i:2974 original size:46 final size:44
Alignment explanation
Indices: 2913--3020 Score: 135
Period size: 46 Copynumber: 2.4 Consensus size: 44
2903 ATAACCACCC
* *
2913 TATGAAATTTTGATAACCTCCCAATGAAATGTTGGTAAGCGCACAT
1 TATGAAATTTTGATAACCTCCCAATAAAATATTGGTAA--GCACAT
* * * *
2959 TATGAAATTTCGATAACCTTCCGATAAAATATTGGTAATCACAT
1 TATGAAATTTTGATAACCTCCCAATAAAATATTGGTAAGCACAT
*
3003 TATAAAATTTTGATAACC
1 TATGAAATTTTGATAACC
3021 ATATCATGAA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
44 21 0.39
46 33 0.61
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (44 bp):
TATGAAATTTTGATAACCTCCCAATAAAATATTGGTAAGCACAT
Found at i:3170 original size:63 final size:63
Alignment explanation
Indices: 3002--3163 Score: 149
Period size: 63 Copynumber: 2.5 Consensus size: 63
2992 GGTAATCACA
* *
3002 TTATAAAATTTTGATAACCAT--ATCATGAAATTGTGAT-ACCTTACTATGAAAATTTTATAAAC
1 TTATAAAATTATGATAA-CATCCAT-ATGAAATTTTGATAACC-T-C-ATG-AAATTTTATAAAC
3064 CTCC
60 CTCC
* * *
3068 TTATAAAATTTTGATAACCTCCATTTGAAATTTTGATAACCTCATGAAATTTTGAT-AACCAT-C
1 TTATAAAATTATGATAACATCCATATGAAATTTTGATAACCTCATGAAATTTT-ATAAACC-TCC
3131 TTATAAAATTATGATAACATACC-TAT-AAATTTT
1 TTATAAAATTATGATAACAT-CCATATGAAATTTT
3164 CTATAACTTC
Statistics
Matches: 84, Mismatches: 6, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
62 7 0.08
63 32 0.38
64 8 0.10
65 3 0.04
66 29 0.35
67 5 0.06
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.40
Consensus pattern (63 bp):
TTATAAAATTATGATAACATCCATATGAAATTTTGATAACCTCATGAAATTTTATAAACCTCC
Done.