Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016503.1 Corchorus olitorius cultivar O-4 contig16536, 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: 149924
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3253 original size:33 final size:33
Alignment explanation
Indices: 3201--3283 Score: 141
Period size: 33 Copynumber: 2.5 Consensus size: 33
3191 GAGAACCCAC
*
3201 AAAATCAAAATT-CAAAATTCTCAATTAAACGAG
1 AAAA-CAAAATTATAAAATTCTCAATTAAACGAG
3234 AAAACAAAATTATAAAATTCTCAATTAAACGAG
1 AAAACAAAATTATAAAATTCTCAATTAAACGAG
3267 AAAACAAAATTATAAAA
1 AAAACAAAATTATAAAA
3284 AAGAAAGAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
32 7 0.15
33 41 0.85
ACGTcount: A:0.60, C:0.12, G:0.05, T:0.23
Consensus pattern (33 bp):
AAAACAAAATTATAAAATTCTCAATTAAACGAG
Found at i:19633 original size:60 final size:58
Alignment explanation
Indices: 19544--19709 Score: 181
Period size: 60 Copynumber: 2.8 Consensus size: 58
19534 ATTTTCGATG
* * * *
19544 TCAGGCCCTTATTTGAGTATTTGGGCAAACGTTAGGCCCTTGTTTGGTCAAATTAA-AGGA
1 TCAGACCCTTATTTGAGCATTT-TGCAAACGTTAGGCCCTTGTTTGCT-AAATTAAGA-GA
* * * *
19604 TCGGACTCTTATTTGAGCATTTTGACAAACGTTAGACCCTTAGTTAGCTAAATTAAGAGA
1 TCAGACCCTTATTTGAGCATTTTG-CAAACGTTAGGCCCTT-GTTTGCTAAATTAAGAGA
* *
19664 TCAGACCCTTATTTGAGCATTTTTGCAAATGTTAGGCCCTTATTTG
1 TCAGACCCTTATTTGAGCA-TTTTGCAAACGTTAGGCCCTTGTTTG
19710 AGCAATTAGC
Statistics
Matches: 88, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
59 4 0.05
60 73 0.83
61 11 0.12
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (58 bp):
TCAGACCCTTATTTGAGCATTTTGCAAACGTTAGGCCCTTGTTTGCTAAATTAAGAGA
Found at i:20170 original size:32 final size:31
Alignment explanation
Indices: 20129--20189 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 31
20119 TCGTCATGCC
*
20129 AAGAGGTAAATTGACCTAAATTTCTAAATCA
1 AAGAGGTAAATTGACCAAAATTTCTAAATCA
*
20160 AAGAGGGTAAATTGGCCAAAATTTCTAAAT
1 AAGA-GGTAAATTGACCAAAATTTCTAAAT
20190 TCAAGGGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 4 0.15
32 23 0.85
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.28
Consensus pattern (31 bp):
AAGAGGTAAATTGACCAAAATTTCTAAATCA
Found at i:31521 original size:30 final size:31
Alignment explanation
Indices: 31446--31521 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 31
31436 TACCGTACAG
* * * *
31446 GTCCCTCTACTTACAAAGAGGGATCAGTTTG
1 GTCCCTCTACTTACAAAAACGGATCAATTTA
* *
31477 GTCCCCCTAC-TACAAAAACTG-TCAATTTA
1 GTCCCTCTACTTACAAAAACGGATCAATTTA
31506 GTCCCTCTACTTACAA
1 GTCCCTCTACTTACAA
31522 TTTGGTGTCA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 15 0.41
30 13 0.35
31 9 0.24
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (31 bp):
GTCCCTCTACTTACAAAAACGGATCAATTTA
Found at i:31623 original size:113 final size:113
Alignment explanation
Indices: 31420--31646 Score: 400
Period size: 113 Copynumber: 2.0 Consensus size: 113
31410 ATAGTCATAG
*
31420 TACAAATCGGTCAAAATACCGTACAGGTCCCTCTACTTACAAAGAGGGATCAGTTTGGTCCCCCT
1 TACAAATCGGTCAAAATACCGTACAGGTCCCTCTACTTACAAAGAGGGATCAATTTGGTCCCCCT
*
31485 ACTACAAAAACTGTCAATTTAGTCCCTCTACTTACAATTTGGTGTCAA
66 ACTACAAAAACTGTCAACTTAGTCCCTCTACTTACAATTTGGTGTCAA
* *
31533 TACAAATCGGTCAAAATACCGTACAGGTCCCTCTACTTACAGAGAGGGATTAATTTGGTCCCCCT
1 TACAAATCGGTCAAAATACCGTACAGGTCCCTCTACTTACAAAGAGGGATCAATTTGGTCCCCCT
* *
31598 AGTACAAAAACTGTCAACTTGGTCCCTCTACTTACAATTTGGTGTCAA
66 ACTACAAAAACTGTCAACTTAGTCCCTCTACTTACAATTTGGTGTCAA
31646 T
1 T
31647 CGAGTCCCTC
Statistics
Matches: 108, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
113 108 1.00
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (113 bp):
TACAAATCGGTCAAAATACCGTACAGGTCCCTCTACTTACAAAGAGGGATCAATTTGGTCCCCCT
ACTACAAAAACTGTCAACTTAGTCCCTCTACTTACAATTTGGTGTCAA
Found at i:44538 original size:24 final size:24
Alignment explanation
Indices: 44505--44583 Score: 131
Period size: 24 Copynumber: 3.3 Consensus size: 24
44495 AAGAAAAACG
*
44505 AGTTTAAATTCTTATATGAATTGA
1 AGTTTCAATTCTTATATGAATTGA
*
44529 AGTTTCAATTCTTGTATGAATTGA
1 AGTTTCAATTCTTATATGAATTGA
*
44553 ATTTTCAATTCTTATATGAATTGA
1 AGTTTCAATTCTTATATGAATTGA
44577 AGTTTCA
1 AGTTTCA
44584 TATACTTTTC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.47
Consensus pattern (24 bp):
AGTTTCAATTCTTATATGAATTGA
Found at i:45966 original size:19 final size:20
Alignment explanation
Indices: 45942--45979 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
45932 AAATAGAATA
45942 ATTTTCATATTA-ATTTTTT
1 ATTTTCATATTATATTTTTT
*
45961 ATTTTCATTTTATATTTTT
1 ATTTTCATATTATATTTTT
45980 ACTTAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (20 bp):
ATTTTCATATTATATTTTTT
Found at i:48469 original size:19 final size:20
Alignment explanation
Indices: 48421--48481 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 20
48411 ATCGCTGCTC
48421 TAATAATCTCATCTGTACAG
1 TAATAATCTCATCTGTACAG
*
48441 TACATAATCTAATCTGTACAG
1 TA-ATAATCTCATCTGTACAG
*
48462 T-GTAATCTCATCTGTACAG
1 TAATAATCTCATCTGTACAG
48481 T
1 T
48482 TGGTAAACAG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.46
20 2 0.05
21 18 0.49
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (20 bp):
TAATAATCTCATCTGTACAG
Found at i:48863 original size:3 final size:3
Alignment explanation
Indices: 48857--48894 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
48847 TTTTTTTCAT
*
48857 ATA ATA ATA TTA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
48895 TAAATAGCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:52218 original size:2 final size:2
Alignment explanation
Indices: 52213--52260 Score: 78
Period size: 2 Copynumber: 23.0 Consensus size: 2
52203 TATATGGTAC
52213 AT AT AT AT ACT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52257 AT AT
1 AT AT
52261 TATCAATGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 40 0.91
3 4 0.09
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52236 original size:18 final size:17
Alignment explanation
Indices: 52200--52259 Score: 86
Period size: 16 Copynumber: 3.5 Consensus size: 17
52190 TTGAAATTTC
* *
52200 ATATATATGGTACATAT
1 ATATATATAGTATATAT
52217 ATATACTATAGTATATAT
1 ATATA-TATAGTATATAT
52235 ATATATATA-TATATAT
1 ATATATATAGTATATAT
52251 ATATATATA
1 ATATATATA
52260 TTATCAATGT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
16 16 0.40
17 9 0.22
18 15 0.38
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (17 bp):
ATATATATAGTATATAT
Found at i:54538 original size:16 final size:18
Alignment explanation
Indices: 54517--54549 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
54507 GATTAGCAAA
54517 AATGAAA-AAA-AAAATG
1 AATGAAAGAAAGAAAATG
54533 AATGAAAGAAAGAAAAT
1 AATGAAAGAAAGAAAAT
54550 TACCATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (18 bp):
AATGAAAGAAAGAAAATG
Found at i:54626 original size:19 final size:19
Alignment explanation
Indices: 54599--54636 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
54589 AGACTGGGTC
54599 AAATGGAATGTAGATGAAA
1 AAATGGAATGTAGATGAAA
*
54618 AAATTGAATGTAGATGAAA
1 AAATGGAATGTAGATGAAA
54637 GTGAGAGCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.24, T:0.24
Consensus pattern (19 bp):
AAATGGAATGTAGATGAAA
Found at i:60227 original size:83 final size:87
Alignment explanation
Indices: 60076--60238 Score: 235
Period size: 83 Copynumber: 1.9 Consensus size: 87
60066 AGATAAGCTG
* * *
60076 AACCCGAACACGACTAAACAGCTTGCGGGTCGTGTTGTGTCGTGTGTAAAATTACTAGGTCTAGA
1 AACCCGAACACGACTAAACAGCTTGCAGGTC-TGTTGTGTCGTGTGCAAAATTACCAGGTCTAGA
*
60141 TTGAGCATACACATTATAAGTTA
65 TTGAGCAAACACATTATAAGTTA
* *
60164 AACCCGAACGCGACTAAACAGCTTGCAGGT-TG-T-T-TCGTGTGCAAAATTACCAGGTCTATAT
1 AACCCGAACACGACTAAACAGCTTGCAGGTCTGTTGTGTCGTGTGCAAAATTACCAGGTCTAGAT
60225 TGAGCAAACACATT
66 TGAGCAAACACATT
60239 GAGACTATAA
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
83 37 0.54
84 1 0.01
85 1 0.01
86 2 0.03
88 28 0.41
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.27
Consensus pattern (87 bp):
AACCCGAACACGACTAAACAGCTTGCAGGTCTGTTGTGTCGTGTGCAAAATTACCAGGTCTAGAT
TGAGCAAACACATTATAAGTTA
Found at i:79166 original size:38 final size:38
Alignment explanation
Indices: 79124--79198 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
79114 GGCCGGTGGA
* *
79124 TCGGTGCACCGGTCAGATGGAGTCTTAGGTGTAATCTC
1 TCGGTGCACCGGTCAGATGGAGCCTTAGATGTAATCTC
79162 TCGGTGCACCGGTCAGATGGAGCCTTAGATGTAATCT
1 TCGGTGCACCGGTCAGATGGAGCCTTAGATGTAATCT
79199 TTGTTTCAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.20, C:0.21, G:0.31, T:0.28
Consensus pattern (38 bp):
TCGGTGCACCGGTCAGATGGAGCCTTAGATGTAATCTC
Found at i:84396 original size:3 final size:3
Alignment explanation
Indices: 84388--84427 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
84378 TTTATTTGTG
84388 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
84428 TATCAGTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:100233 original size:23 final size:21
Alignment explanation
Indices: 100198--100245 Score: 69
Period size: 23 Copynumber: 2.2 Consensus size: 21
100188 GGATCTCTCT
100198 TTTTCTCCTTTTTTTTTAACC
1 TTTTCTCCTTTTTTTTTAACC
*
100219 TTTTCTCTCTCTTTTTTTTTACC
1 TTTTCTC-CT-TTTTTTTTAACC
100242 TTTT
1 TTTT
100246 GCATATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 7 0.29
22 2 0.08
23 15 0.62
ACGTcount: A:0.06, C:0.23, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTCTCCTTTTTTTTTAACC
Found at i:106440 original size:9 final size:9
Alignment explanation
Indices: 106426--106451 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
106416 ATGAAACTGC
106426 AGGAGGTGG
1 AGGAGGTGG
106435 AGGAGGTGG
1 AGGAGGTGG
106444 AGGAGGTG
1 AGGAGGTG
106452 CGGATTTGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.65, T:0.12
Consensus pattern (9 bp):
AGGAGGTGG
Found at i:106497 original size:60 final size:60
Alignment explanation
Indices: 106433--106740 Score: 411
Period size: 60 Copynumber: 5.1 Consensus size: 60
106423 TGCAGGAGGT
* *
106433 GGAGGAGGTGGAGGAGGTGCGGATTTGGAAGCTGAATTTTCCTTCAAAGGTGGCATTGGA
1 GGAGGAGGTGGAGGAGGTACGGATTTAGAAGCTGAATTTTCCTTCAAAGGTGGCATTGGA
* * * *
106493 GGAGGAGGTGGAGGAGGTGCAGATATAGAAGCTGAGTTTTCCTTCAAAGGTGGCATTGGA
1 GGAGGAGGTGGAGGAGGTACGGATTTAGAAGCTGAATTTTCCTTCAAAGGTGGCATTGGA
** * * **
106553 GGAGGAGGTGGAGGAGGTACGTTTTTAGAAGCTAAATTTTCATTCATTGGTGGCATTGGA
1 GGAGGAGGTGGAGGAGGTACGGATTTAGAAGCTGAATTTTCCTTCAAAGGTGGCATTGGA
* ** * **
106613 GGAGGAGGTGGAGGAGGCACGTTTTTAGAAGCTGAATTTTCATTCATTGGTGGCATTGGA
1 GGAGGAGGTGGAGGAGGTACGGATTTAGAAGCTGAATTTTCCTTCAAAGGTGGCATTGGA
* * *
106673 GGAGGAGGTGGAGGAGGTATGGATTTAGAAGCTGAGA-TTTCCTTCAGATGTGGCATTGGA
1 GGAGGAGGTGGAGGAGGTACGGATTTAGAAGCTGA-ATTTTCCTTCAAAGGTGGCATTGGA
106733 GGAGGAGG
1 GGAGGAGG
106741 AACTACAGCA
Statistics
Matches: 223, Mismatches: 24, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
60 222 1.00
61 1 0.00
ACGTcount: A:0.25, C:0.09, G:0.40, T:0.27
Consensus pattern (60 bp):
GGAGGAGGTGGAGGAGGTACGGATTTAGAAGCTGAATTTTCCTTCAAAGGTGGCATTGGA
Found at i:116846 original size:6 final size:6
Alignment explanation
Indices: 116835--116876 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
116825 CAACCTTGGG
116835 GTCCAT GTCCAT GTCCAT GTCCAT GTCCAT GTCCAT GTCCAT
1 GTCCAT GTCCAT GTCCAT GTCCAT GTCCAT GTCCAT GTCCAT
116877 CCCATTGCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.17, C:0.33, G:0.17, T:0.33
Consensus pattern (6 bp):
GTCCAT
Found at i:124402 original size:109 final size:109
Alignment explanation
Indices: 124260--124477 Score: 303
Period size: 109 Copynumber: 2.0 Consensus size: 109
124250 TTCGATTCAA
* * * * *
124260 TATTGAGGGGAAGTTCTCTCAATGATATCAAGGTTTCGGACTTGAAATCTTATTTAAAATGTATA
1 TATTGAGGGGAAGTTCTCTAAATGATATCAAGGTTTCGAACTTAAAATCTTATTTAAAAGGAATA
* * * *
124325 AGTGCCGATCACC-TATATCGTCCATAATCATCGATATTTTTGTT
66 AGTGCCGACCACCTTA-ATAGTCCATAATCATCAACATTTTTGTT
* *
124369 TATTGAGGGGAATTTCTCTAAATGATATTAAGGTTTCGAACTTAAAATCTTATTTAAAAGGAATA
1 TATTGAGGGGAAGTTCTCTAAATGATATCAAGGTTTCGAACTTAAAATCTTATTTAAAAGGAATA
* *
124434 AGTGCCGACCATCTTAATAGTCCGTAATCATCAACATTTTTGTT
66 AGTGCCGACCACCTTAATAGTCCATAATCATCAACATTTTTGTT
124478 CTTCACTAGA
Statistics
Matches: 95, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
109 93 0.98
110 2 0.02
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.37
Consensus pattern (109 bp):
TATTGAGGGGAAGTTCTCTAAATGATATCAAGGTTTCGAACTTAAAATCTTATTTAAAAGGAATA
AGTGCCGACCACCTTAATAGTCCATAATCATCAACATTTTTGTT
Found at i:136233 original size:19 final size:20
Alignment explanation
Indices: 136209--136264 Score: 87
Period size: 19 Copynumber: 2.8 Consensus size: 20
136199 CTGTTTAGCA
136209 ACTGTACAGATGAGATTA-T
1 ACTGTACAGATGAGATTAGT
*
136228 ACTGTACAGATTAGATTATGT
1 ACTGTACAGATGAGATTA-GT
136249 ACTGTACAGATGAGAT
1 ACTGTACAGATGAGAT
136265 CATTAGAGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (20 bp):
ACTGTACAGATGAGATTAGT
Done.