Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013098.1 Corchorus olitorius cultivar O-4 contig13131, 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: 14600
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2886 original size:23 final size:22
Alignment explanation
Indices: 2859--2919 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 22
2849 AAATTCAAAA
2859 AAATCAATCAATCAAAAA-AAATC
1 AAATCAA--AATCAAAAACAAATC
*
2882 AAATCAAAATCAAAAATCAATTC
1 AAATCAAAATCAAAAA-CAAATC
2905 AAATCAAAATCAAAA
1 AAATCAAAATCAAAA
2920 GAGAATGGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
21 9 0.26
23 26 0.74
ACGTcount: A:0.66, C:0.16, G:0.00, T:0.18
Consensus pattern (22 bp):
AAATCAAAATCAAAAACAAATC
Found at i:2893 original size:6 final size:6
Alignment explanation
Indices: 2858--2919 Score: 53
Period size: 6 Copynumber: 10.7 Consensus size: 6
2848 GAAATTCAAA
*
2858 AAAATC AATCAATC AAAA-- AAAATC -AAATC AAAATC AAAAATC -AATTC
1 AAAATC AA--AATC AAAATC AAAATC AAAATC AAAATC -AAAATC AAAATC
2905 -AAATC AAAATC AAAA
1 AAAATC AAAATC AAAA
2920 GAGAATGGAT
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
4 4 0.09
5 13 0.28
6 18 0.38
7 6 0.13
8 6 0.13
ACGTcount: A:0.66, C:0.16, G:0.00, T:0.18
Consensus pattern (6 bp):
AAAATC
Found at i:3596 original size:50 final size:50
Alignment explanation
Indices: 3517--3666 Score: 230
Period size: 50 Copynumber: 3.0 Consensus size: 50
3507 AGTTTTACAA
* *
3517 TAAAATTGCTTTCCATTTATGAGTTCAAGATCAAAATTCGCTTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAG
*
3567 TAAAATTGCTTTCCATTTGT-AGGTCCAAGATCAAAATTTGCTTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGA-GTCCAAGATCAAAATTCGCTTTTCAAAG
* * *
3617 TAAGATTGCATTCCATTTGTGAATCCAAGATCAAAATTCGCTTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAG
3667 GACATTGAAG
Statistics
Matches: 91, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
49 1 0.01
50 89 0.98
51 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (50 bp):
TAAAATTGCTTTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAG
Found at i:4387 original size:50 final size:50
Alignment explanation
Indices: 4307--4655 Score: 482
Period size: 50 Copynumber: 6.9 Consensus size: 50
4297 CCATCCGAAT
* * *
4307 ACATAGGCTTTTCCCCAAGCCAAACTCGTTTCCATACAAGTCAATTATCA
1 ACATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
* *
4357 ACATGGGCTTTTCCACAAGCCAAAATCGTTTCCATACTAGTCAATTATCA
1 ACATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
4407 ACATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
1 ACATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
4457 ACATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
1 ACATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
* * *
4507 ACATTGGCTTTTCCACAAGCCAAGCTCGTTTCCGTACGAGTCAATTATCA
1 ACATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
* * * * *
4557 ACATAGACTTTTTCACAAGCCAAACTCGTTTCCGTACGAGTCAACTATCCA
1 ACATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTAT-CA
* * * * * *
4608 AGCCATATAGACTTTTCCATAAGTCAAACACGTTTCCATATGAGTCAA
1 A--C--ATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAA
4656 GCCTTGCTTC
Statistics
Matches: 274, Mismatches: 20, Indels: 5
0.92 0.07 0.02
Matches are distributed among these distances:
50 234 0.85
51 3 0.01
53 1 0.00
55 36 0.13
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.29
Consensus pattern (50 bp):
ACATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
Found at i:4994 original size:27 final size:27
Alignment explanation
Indices: 4951--5024 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
4941 AGGGTCATCT
** ** *
4951 AGGGGCATTTTGGTCATTTTTATATTC
1 AGGGGCATTTTAATCATTTGAATATCC
*
4978 AGGGGCATTTTAATCATTTGAATGTCC
1 AGGGGCATTTTAATCATTTGAATATCC
**
5005 AGGGGCATTTTGGTCATTTG
1 AGGGGCATTTTAATCATTTG
5025 CACACTCAAG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.20, C:0.12, G:0.26, T:0.42
Consensus pattern (27 bp):
AGGGGCATTTTAATCATTTGAATATCC
Found at i:5165 original size:18 final size:18
Alignment explanation
Indices: 5142--5180 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
5132 ACGTGGGCAC
5142 CTTTGGCATTTCTGCATT
1 CTTTGGCATTTCTGCATT
5160 CTTTGGCATTTCTGCATT
1 CTTTGGCATTTCTGCATT
5178 CTT
1 CTT
5181 CATAGTTCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.10, C:0.23, G:0.15, T:0.51
Consensus pattern (18 bp):
CTTTGGCATTTCTGCATT
Found at i:13452 original size:68 final size:68
Alignment explanation
Indices: 13244--13887 Score: 646
Period size: 68 Copynumber: 9.7 Consensus size: 68
13234 AGTAAAGCTC
* *
13244 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGATCATTTTCGTCTT-TTGCATTTAAGTT
1 TATTTTATATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGTT
13308 TAG
66 TAG
*
13311 TATTTTATATTTCAAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTC-TGCATTTAAGTT
1 TATTTTATATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGTT
13375 TAG
66 TAG
* * * *
13378 TATTTTATATTTCAAAAAATACCCTTTCGGTCGAAGGGTCGTTTTTGTCTTCTCGCATTTAAGTT
1 TATTTTATATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGTT
13443 TAG
66 TAG
* ** *
13446 TGTTTTATATTTCCAAAAATACCCTTTCGGTCGAAGGGTTGTTTTTGTCTTCTTGCATTTAAGTT
1 TATTTTATATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGTT
13511 TAG
66 TAG
* ** * *
13514 TGTTTTATATTTCCAAAAATACCCTTTCGGTCGAAGGGTTGTTTTTGTCTTCTTGCATTTAAGTA
1 TATTTTATATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGTT
13579 TAG
66 TAG
* * * *
13582 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCGTTTTAGTT
1 TATTTTATATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGTT
13647 TAG
66 TAG
* * * * * * * **
13650 -------TGTTTCCAAAAATGCCCTTTCGGTCGAAAGGTCGTTTTCATCTTTTTGTA-CCAAGTT
1 TATTTTATATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGTT
13707 TAG
66 TAG
** * ** * ** *
13710 TACTTTCCTTTTTCCAAAAATGTCCTTTCGGTCGAAGGGTCAATTTCAACTT-TTCCATGTCTAA
1 TA-TTTTATATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCAT-T-TAA
13774 G-TTAG
63 GTTTAG
* * * * * * *
13779 ---TTTACT-TTTCCCAAAATGCCCTTTCGATCAAATGGTCGATTCT-GTCATTCTTGCATTTGA
1 TATTTTA-TATTTCCAAAAATACCCTTTCGGTCGAAGGGTC-ATTTTCGTC-TTCTTGCATTTAA
13839 GTTTA-
63 GTTTAG
* * *
13844 -CTTTT-GATTTCCAAAAATACCCTTTCGGT-GAAAGGGTCAGTTTC
1 TATTTTATATTTCCAAAAATACCCTTTCGGTCG-AAGGGTCATTTTC
13888 ATCATTCTCG
Statistics
Matches: 493, Mismatches: 61, Indels: 47
0.82 0.10 0.08
Matches are distributed among these distances:
60 7 0.01
61 43 0.09
65 35 0.07
66 35 0.07
67 124 0.25
68 242 0.49
69 4 0.01
70 3 0.01
ACGTcount: A:0.23, C:0.18, G:0.16, T:0.43
Consensus pattern (68 bp):
TATTTTATATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGTT
TAG
Found at i:13717 original size:61 final size:60
Alignment explanation
Indices: 13591--13717 Score: 148
Period size: 61 Copynumber: 2.1 Consensus size: 60
13581 GTATTTTCTA
* * *** *
13591 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCGTTTTAGTTTAGTG
1 TTTCCAAAAATACCCTTTCGGTCGAAAGGTCATTTTCATCTTTTT-CGTCCAAGTTTAGTC
* *
13652 TTTCCAAAAATGCCCTTTCGGTCGAAAGGTCGTTTTCATCTTTTT-GTACCAAGTTTAGTAC
1 TTTCCAAAAATACCCTTTCGGTCGAAAGGTCATTTTCATCTTTTTCGT-CCAAGTTTAGT-C
13713 TTTCC
1 TTTCC
13718 TTTTTCCAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
59 2 0.04
60 8 0.14
61 46 0.82
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.43
Consensus pattern (60 bp):
TTTCCAAAAATACCCTTTCGGTCGAAAGGTCATTTTCATCTTTTTCGTCCAAGTTTAGTC
Done.