Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023595.1 Corchorus olitorius cultivar O-4 contig23628, 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: 14470
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Found at i:656 original size:52 final size:52
Alignment explanation
Indices: 600--698 Score: 162
Period size: 52 Copynumber: 1.9 Consensus size: 52
590 ACCAGTCTCT
* *
600 GTTTACTTCTTCTTTCACTCTTTAGTTTAATTACCCAGGATTAAACTTCTTG
1 GTTTACTTCTTCTTTCACTCTTTAGTCTAATTACCCAGAATTAAACTTCTTG
* *
652 GTTTACTTCTTCTTTTACTTTTTAGTCTAATTACCCAGAATTAAACT
1 GTTTACTTCTTCTTTCACTCTTTAGTCTAATTACCCAGAATTAAACT
699 AATTATTGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.23, C:0.20, G:0.08, T:0.48
Consensus pattern (52 bp):
GTTTACTTCTTCTTTCACTCTTTAGTCTAATTACCCAGAATTAAACTTCTTG
Found at i:822 original size:48 final size:48
Alignment explanation
Indices: 657--963 Score: 289
Period size: 48 Copynumber: 6.6 Consensus size: 48
647 TCTTGGTTTA
** * ** **
657 CTTCTTCTTTTACTTTTTAGTCTAATTACCCAGAATTAAACTAATTATT
1 CTTCTTCTTTTACTAATTAGTTTAATTACCTGGAATTAAACTAA-TCCT
* * * * ** * * **
706 GTTCTTCTCTCAGTACCTAGTTTAATTTCCTAGAATTAAACT-AGGCT
1 CTTCTTCTTTTACTAATTAGTTTAATTACCTGGAATTAAACTAATCCT
* * *
753 CTTCTTCTCTTACGATTTAGTTTAATTACCTGGAATTAAACTAATCCT
1 CTTCTTCTTTTACTAATTAGTTTAATTACCTGGAATTAAACTAATCCT
*
801 CTTCTTCTTTTACTAATTAGTTTTATTA-C-----TT-AACT-A---T
1 CTTCTTCTTTTACTAATTAGTTTAATTACCTGGAATTAAACTAATCCT
* *
838 -TTCTTCTTTTACTATTTAGTTTAATAACCTGGAATTAAACTAATCCT
1 CTTCTTCTTTTACTAATTAGTTTAATTACCTGGAATTAAACTAATCCT
* *
885 CTTCTTCTTTTACAAATTAGTTTAATTACCTGGAATTAAACTAATCTT
1 CTTCTTCTTTTACTAATTAGTTTAATTACCTGGAATTAAACTAATCCT
933 CTTCTTCTTTTACTAATTAGTTTAATTACCT
1 CTTCTTCTTTTACTAATTAGTTTAATTACCT
964 AACTATTTCT
Statistics
Matches: 210, Mismatches: 35, Indels: 27
0.77 0.13 0.10
Matches are distributed among these distances:
36 24 0.11
37 2 0.01
40 1 0.00
41 4 0.02
42 4 0.02
43 4 0.02
44 1 0.00
47 37 0.18
48 101 0.48
49 32 0.15
ACGTcount: A:0.27, C:0.19, G:0.07, T:0.48
Consensus pattern (48 bp):
CTTCTTCTTTTACTAATTAGTTTAATTACCTGGAATTAAACTAATCCT
Found at i:843 original size:36 final size:36
Alignment explanation
Indices: 802--1124 Score: 200
Period size: 36 Copynumber: 8.9 Consensus size: 36
792 ACTAATCCTC
* *
802 TTCTTCTTTTACTAATTAGTTTTATTACTTAACTAT
1 TTCTTCTTTTACTAATTAGTTTAATTACCTAACTAT
* *
838 TTCTTCTTTTACTATTTAGTTTAATAACCTGGAATTAAACTAATCCT
1 TTCTTCTTTTACTAATTAGTTTAATTACC------T-AACT-A---T
*
885 CTTCTTCTTTTACAAATTAGTTTAATTACCTGGAATTAAACTAATCTT
1 -TTCTTCTTTTACTAATTAGTTTAATTACC------T-AACT-A---T
933 CTTCTTCTTTTACTAATTAGTTTAATTACCTAACTAT
1 -TTCTTCTTTTACTAATTAGTTTAATTACCTAACTAT
*
970 TTCTTCTTTTAC----TA---T--TTA-GTAACTAT
1 TTCTTCTTTTACTAATTAGTTTAATTACCTAACTAT
*
996 TTCTTCTTGTACTAATTAGTTTAATTACCTAACTAT
1 TTCTTCTTTTACTAATTAGTTTAATTACCTAACTAT
*
1032 TTCTTCTTTTAC----TA---T--TTA-GTAACTAT
1 TTCTTCTTTTACTAATTAGTTTAATTACCTAACTAT
*
1058 TTCTTCTTTTACTATTTAGTTTAATTACCTAACTAT
1 TTCTTCTTTTACTAATTAGTTTAATTACCTAACTAT
*
1094 TTCTTCTTTTACTATTTAGTTTAATTACCTA
1 TTCTTCTTTTACTAATTAGTTTAATTACCTA
1125 GAATTAAACT
Statistics
Matches: 240, Mismatches: 15, Indels: 64
0.75 0.05 0.20
Matches are distributed among these distances:
26 37 0.15
27 6 0.03
29 2 0.01
30 4 0.02
32 4 0.02
33 2 0.01
35 6 0.03
36 93 0.39
37 1 0.00
40 1 0.00
41 4 0.02
42 2 0.01
43 4 0.02
44 1 0.00
47 1 0.00
48 72 0.30
ACGTcount: A:0.27, C:0.16, G:0.04, T:0.53
Consensus pattern (36 bp):
TTCTTCTTTTACTAATTAGTTTAATTACCTAACTAT
Found at i:855 original size:84 final size:84
Alignment explanation
Indices: 754--913 Score: 275
Period size: 84 Copynumber: 1.9 Consensus size: 84
744 AACTAGGCTC
* *
754 TTCTTCTCTTACGATTTAGTTTAATTACCTGGAATTAAACTAATCCTCTTCTTCTTTTACTAATT
1 TTCTTCTCTTACGATTTAGTTTAATAACCTGGAATTAAACTAATCCTCTTCTTCTTTTACAAATT
*
819 AGTTTTATTACTTAACTAT
66 AGTTTAATTACTTAACTAT
* *
838 TTCTTCTTTTACTATTTAGTTTAATAACCTGGAATTAAACTAATCCTCTTCTTCTTTTACAAATT
1 TTCTTCTCTTACGATTTAGTTTAATAACCTGGAATTAAACTAATCCTCTTCTTCTTTTACAAATT
903 AGTTTAATTAC
66 AGTTTAATTAC
914 CTGGAATTAA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 71 1.00
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.49
Consensus pattern (84 bp):
TTCTTCTCTTACGATTTAGTTTAATAACCTGGAATTAAACTAATCCTCTTCTTCTTTTACAAATT
AGTTTAATTACTTAACTAT
Found at i:917 original size:132 final size:131
Alignment explanation
Indices: 723--989 Score: 426
Period size: 132 Copynumber: 2.0 Consensus size: 131
713 TCTCAGTACC
** * * *
723 TAGTTTAATTTCCTAGAATTAAACTAGGCTCTTCTTCTCTTACGATTTAGTTTAATTACCTGGAA
1 TAGTTTAATAACCTAGAATTAAACTAGCCTCTTCTTCTCTTACAAATTAGTTTAATTACCTGGAA
* *
788 TTAAACTAATCCTCTTCTTCTTTTACTAATTAGTTTTATTACTTAACTATTTCTTCTTTTACTAT
66 TTAAACTAATCCTCTTCTTCTTTTACTAATTAGTTTAATTACCTAACTATTTCTTCTTTTACTAT
853 T
131 T
* * *
854 TAGTTTAATAACCTGGAATTAAACTAATCCTCTTCTTCTTTTACAAATTAGTTTAATTACCTGGA
1 TAGTTTAATAACCTAGAATTAAACT-AGCCTCTTCTTCTCTTACAAATTAGTTTAATTACCTGGA
*
919 ATTAAACTAATCTTCTTCTTCTTTTACTAATTAGTTTAATTACCTAACTATTTCTTCTTTTACTA
65 ATTAAACTAATCCTCTTCTTCTTTTACTAATTAGTTTAATTACCTAACTATTTCTTCTTTTACTA
984 TT
130 TT
986 TAGT
1 TAGT
990 AACTATTTCT
Statistics
Matches: 124, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
131 22 0.18
132 102 0.82
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.49
Consensus pattern (131 bp):
TAGTTTAATAACCTAGAATTAAACTAGCCTCTTCTTCTCTTACAAATTAGTTTAATTACCTGGAA
TTAAACTAATCCTCTTCTTCTTTTACTAATTAGTTTAATTACCTAACTATTTCTTCTTTTACTAT
T
Found at i:992 original size:26 final size:26
Alignment explanation
Indices: 963--1015 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
953 TTTAATTACC
* *
963 TAACTATTTCTTCTTTTACTATTTAG
1 TAACTATTTCTTCTTGTACTAATTAG
989 TAACTATTTCTTCTTGTACTAATTAG
1 TAACTATTTCTTCTTGTACTAATTAG
1015 T
1 T
1016 TTAATTACCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.25, C:0.15, G:0.06, T:0.55
Consensus pattern (26 bp):
TAACTATTTCTTCTTGTACTAATTAG
Found at i:1009 original size:62 final size:62
Alignment explanation
Indices: 934--1113 Score: 342
Period size: 62 Copynumber: 2.9 Consensus size: 62
924 ACTAATCTTC
934 TTCTTCTTTTACTAATTAGTTTAATTACCTAACTATTTCTTCTTTTACTATTTAGTAACTAT
1 TTCTTCTTTTACTAATTAGTTTAATTACCTAACTATTTCTTCTTTTACTATTTAGTAACTAT
*
996 TTCTTCTTGTACTAATTAGTTTAATTACCTAACTATTTCTTCTTTTACTATTTAGTAACTAT
1 TTCTTCTTTTACTAATTAGTTTAATTACCTAACTATTTCTTCTTTTACTATTTAGTAACTAT
*
1058 TTCTTCTTTTACTATTTAGTTTAATTACCTAACTATTTCTTCTTTTACTATTTAGT
1 TTCTTCTTTTACTAATTAGTTTAATTACCTAACTATTTCTTCTTTTACTATTTAGT
1114 TTAATTACCT
Statistics
Matches: 115, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 115 1.00
ACGTcount: A:0.24, C:0.16, G:0.04, T:0.56
Consensus pattern (62 bp):
TTCTTCTTTTACTAATTAGTTTAATTACCTAACTATTTCTTCTTTTACTATTTAGTAACTAT
Found at i:1054 original size:26 final size:26
Alignment explanation
Indices: 1025--1077 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1015 TTTAATTACC
1025 TAACTATTTCTTCTTTTACTATTTAG
1 TAACTATTTCTTCTTTTACTATTTAG
1051 TAACTATTTCTTCTTTTACTATTTAG
1 TAACTATTTCTTCTTTTACTATTTAG
1077 T
1 T
1078 TTAATTACCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.23, C:0.15, G:0.04, T:0.58
Consensus pattern (26 bp):
TAACTATTTCTTCTTTTACTATTTAG
Found at i:1095 original size:47 final size:47
Alignment explanation
Indices: 1086--1471 Score: 583
Period size: 47 Copynumber: 8.4 Consensus size: 47
1076 GTTTAATTAC
1086 CTAACTATTTCTTCTTTTACTATTTAGTTTAATTACCTAGAATTAAA
1 CTAACTATTTCTTCTTTTACTATTTAGTTTAATTACCTAGAATTAAA
*
1133 CTAACTATTTTTTCTTTTACTATTTAGTTTAATTACCTAGAATTAAA
1 CTAACTATTTCTTCTTTTACTATTTAGTTTAATTACCTAGAATTAAA
*
1180 CTAACTATTTCTCCTTTTACTA-TTAGTTTAATTACCTAGAATTAAA
1 CTAACTATTTCTTCTTTTACTATTTAGTTTAATTACCTAGAATTAAA
* * *
1226 CTAACT-TTTCTTCTTTTGCTACTTAGTTTAATAACCTAG-----AA
1 CTAACTATTTCTTCTTTTACTATTTAGTTTAATTACCTAGAATTAAA
1267 CTAACT-TTTCTTCTTTTACTATTTAGTTTAATTACCTAGAATTAAA
1 CTAACTATTTCTTCTTTTACTATTTAGTTTAATTACCTAGAATTAAA
* * *
1313 CTAACTTTTTCTTCTTTTGCTACTTAGTTTAATTACCTAGAATTAAA
1 CTAACTATTTCTTCTTTTACTATTTAGTTTAATTACCTAGAATTAAA
* * *
1360 CTAACTTTTTCTTCTTTTACTATTTAGTATAATTTCCTAGAATTAAA
1 CTAACTATTTCTTCTTTTACTATTTAGTTTAATTACCTAGAATTAAA
*
1407 CTAACCT-TTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAA
1 CTAA-CTATTTCTTCTTTTACTATTTAGTTTAATTACCTAGAATTAAA
*
1454 CTAACTTTTTCTTCTTTT
1 CTAACTATTTCTTCTTTT
1472 TTTTGCTCTT
Statistics
Matches: 312, Mismatches: 18, Indels: 18
0.90 0.05 0.05
Matches are distributed among these distances:
41 38 0.12
45 13 0.04
46 56 0.18
47 203 0.65
48 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.49
Consensus pattern (47 bp):
CTAACTATTTCTTCTTTTACTATTTAGTTTAATTACCTAGAATTAAA
Found at i:1299 original size:180 final size:178
Alignment explanation
Indices: 1051--1448 Score: 624
Period size: 180 Copynumber: 2.2 Consensus size: 178
1041 TACTATTTAG
1051 TAACTATTTCTTCTTTTACTATTTAGTTTAATTACCT--AACTATTTCTTCTTTTACTATTTAGT
1 TAACT-TTTCTTCTTTTACTATTTAGTTTAATTACCTAGAACTATTTCTTCTTTTACTATTTAGT
*
1114 TTAATTACCTAGAATTAAACTAACTATTTT-TTCTTTTACTATTTAGTTTAATTACCTAGAATTA
65 TTAATTACCTAGAATTAAACTAACT-TTTTCTTCTTTTACTACTTAGTTTAATTACCTAGAATTA
*
1178 AACTAACTATTTCTCCTTTTACTA-TTAGTTTAATTACCTAGAATTAAAC
129 AACTAACTATTTCTCCTTTTACTATTTAGTATAATTACCTAGAATTAAAC
* * *
1227 TAACTTTTCTTCTTTTGCTACTTAGTTTAATAACCTAGAACTAACTTTTCTTCTTTTACTATTTA
1 TAACTTTTCTTCTTTTACTATTTAGTTTAATTACCTAGAACT-A--TTTCTTCTTTTACTATTTA
*
1292 GTTTAATTACCTAGAATTAAACTAACTTTTTCTTCTTTTGCTACTTAGTTTAATTACCTAGAATT
63 GTTTAATTACCTAGAATTAAACTAACTTTTTCTTCTTTTACTACTTAGTTTAATTACCTAGAATT
* * *
1357 AAACTAACTTTTTCTTCTTTTACTATTTAGTATAATTTCCTAGAATTAAAC
128 AAACTAACTATTTCTCCTTTTACTATTTAGTATAATTACCTAGAATTAAAC
*
1408 TAACCTTTTCTTCTTTTACTATTTAGTTTAATTACCCAGAA
1 TAA-CTTTTCTTCTTTTACTATTTAGTTTAATTACCTAGAA
1449 TTAAACTAAC
Statistics
Matches: 201, Mismatches: 13, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
175 28 0.14
176 5 0.02
177 4 0.02
178 1 0.00
179 4 0.02
180 100 0.50
181 26 0.13
182 33 0.16
ACGTcount: A:0.29, C:0.16, G:0.05, T:0.49
Consensus pattern (178 bp):
TAACTTTTCTTCTTTTACTATTTAGTTTAATTACCTAGAACTATTTCTTCTTTTACTATTTAGTT
TAATTACCTAGAATTAAACTAACTTTTTCTTCTTTTACTACTTAGTTTAATTACCTAGAATTAAA
CTAACTATTTCTCCTTTTACTATTTAGTATAATTACCTAGAATTAAAC
Found at i:4953 original size:26 final size:27
Alignment explanation
Indices: 4894--4963 Score: 97
Period size: 26 Copynumber: 2.6 Consensus size: 27
4884 CCCGCAATCT
* *
4894 TGACCTAAATGCCCCTGAGGCGGAAAA
1 TGACCAAAATGCCCCTGAGGCGAAAAA
*
4921 TGACCAAAATGCCCCTGATGC-AAAAA
1 TGACCAAAATGCCCCTGAGGCGAAAAA
*
4947 TGACCAAAATGTCCCTG
1 TGACCAAAATGCCCCTG
4964 GTAATTTCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
26 20 0.51
27 19 0.49
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.17
Consensus pattern (27 bp):
TGACCAAAATGCCCCTGAGGCGAAAAA
Done.