Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018125.1 Corchorus olitorius cultivar O-4 contig18158, 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: 21217
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:9057 original size:15 final size:16
Alignment explanation
Indices: 9037--9068 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
9027 TTTTGTATTC
9037 TGTGTGTGTT-TTGTG
1 TGTGTGTGTTCTTGTG
9052 TGTGTGTGTTCTTGTG
1 TGTGTGTGTTCTTGTG
9068 T
1 T
9069 AAGAGACTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.00, C:0.03, G:0.38, T:0.59
Consensus pattern (16 bp):
TGTGTGTGTTCTTGTG
Found at i:9784 original size:25 final size:25
Alignment explanation
Indices: 9750--9800 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
9740 ACTATGGACC
* * *
9750 AACATTGGATTTCCTACAATGACTT
1 AACATCGGATTTCCCAAAATGACTT
9775 AACATCGGATTTCCCAAAATGACTT
1 AACATCGGATTTCCCAAAATGACTT
9800 A
1 A
9801 GTATTGAGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (25 bp):
AACATCGGATTTCCCAAAATGACTT
Found at i:10187 original size:27 final size:28
Alignment explanation
Indices: 10156--10230 Score: 98
Period size: 28 Copynumber: 2.7 Consensus size: 28
10146 ATGTGAAATT
*
10156 AAAATGACCAGAATGCCCCT-GAATGTG
1 AAAATGACCAAAATGCCCCTGGAATGTG
* * *
10183 CAAATGACCAAAATGCCCCTGGATTTTG
1 AAAATGACCAAAATGCCCCTGGAATGTG
*
10211 AAAATGACCAAAATACCCCT
1 AAAATGACCAAAATGCCCCT
10231 AGTTGATCTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
27 18 0.44
28 23 0.56
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTGGAATGTG
Found at i:10824 original size:12 final size:12
Alignment explanation
Indices: 10809--10833 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10799 CTTCTATTTT
10809 TCTAGTTTTTCC
1 TCTAGTTTTTCC
10821 TCTAGTTTTTCC
1 TCTAGTTTTTCC
10833 T
1 T
10834 AAGGGTGTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.24, G:0.08, T:0.60
Consensus pattern (12 bp):
TCTAGTTTTTCC
Found at i:17372 original size:39 final size:39
Alignment explanation
Indices: 17328--17422 Score: 172
Period size: 39 Copynumber: 2.4 Consensus size: 39
17318 GGCTTCGCAG
**
17328 AGGGTTCCGGTGCAAAATCCTGACTGTTTGGCACTCTTT
1 AGGGTTCCGACGCAAAATCCTGACTGTTTGGCACTCTTT
17367 AGGGTTCCGACGCAAAATCCTGACTGTTTGGCACTCTTT
1 AGGGTTCCGACGCAAAATCCTGACTGTTTGGCACTCTTT
17406 AGGGTTCCGACGCAAAA
1 AGGGTTCCGACGCAAAA
17423 AGGTAGAAGA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.28
Consensus pattern (39 bp):
AGGGTTCCGACGCAAAATCCTGACTGTTTGGCACTCTTT
Found at i:17465 original size:36 final size:36
Alignment explanation
Indices: 17419--17493 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
17409 GTTCCGACGC
17419 AAAAAGGTAGAAGAGAATGGAGAAATCGAAACCCTA
1 AAAAAGGTAGAAGAGAATGGAGAAATCGAAACCCTA
* *
17455 AAAAAGGTAGAAGATAATGGAGAAATCTAAACCCTA
1 AAAAAGGTAGAAGAGAATGGAGAAATCGAAACCCTA
17491 AAA
1 AAA
17494 CGCAAAGAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.55, C:0.11, G:0.21, T:0.13
Consensus pattern (36 bp):
AAAAAGGTAGAAGAGAATGGAGAAATCGAAACCCTA
Found at i:18177 original size:32 final size:31
Alignment explanation
Indices: 18134--18193 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
18124 TTATATATAG
18134 CGGCGTTGTCATCAGAAACGCCGCTATTTAA
1 CGGCGTTGTCATCAGAAACGCCGCTATTTAA
** *
18165 CGGCGTTTGTCATTTGAAACGCCGTTATT
1 CGGCG-TTGTCATCAGAAACGCCGCTATT
18194 CCCATCAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 5 0.20
32 20 0.80
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.32
Consensus pattern (31 bp):
CGGCGTTGTCATCAGAAACGCCGCTATTTAA
Found at i:18265 original size:122 final size:122
Alignment explanation
Indices: 18042--18385 Score: 562
Period size: 122 Copynumber: 2.8 Consensus size: 122
18032 TTGTATATAG
* *
18042 CGGCATTTGTCATGAGAAACGCCGCTATTCCCATCAAGAAATGGTGTTATTTTTTCACCAAATTT
1 CGGCGTTTGTCATGAGAAACGCCGCTATTCCCATCAAGAAATGGTGTT-TTTTTTCACCAAACTT
*
18107 CTATTCTTTGGAAAACATTATATATAGCGGCGTTGTCATCAGAAACGCCGCTATTTAA
65 CTATTCTTTGGAAAACATTATATATAGCGGCGTTGTCATCAGAAACGCCGCTATTCAA
** *
18165 CGGCGTTTGTCATTTGAAACGCCGTTATTCCCATCAAGAAATGGTGTTTTTTTTCACCAAACTTC
1 CGGCGTTTGTCATGAGAAACGCCGCTATTCCCATCAAGAAATGGTGTTTTTTTTCACCAAACTTC
* * *
18230 TATTCTTTGGAAAACATTATATATAGCGGCGTTGTCATTAGAGACGCCGCTATTCAG
66 TATTCTTTGGAAAACATTATATATAGCGGCGTTGTCATCAGAAACGCCGCTATTCAA
*
18287 CGGCGTTTGTCATGAGAAACGCCGCTATTCCCATCAAGAAATGGTGTTTTTTTTTTACCAAACTT
1 CGGCGTTTGTCATGAGAAACGCCGCTATTCCCATCAAGAAATGGTG-TTTTTTTTCACCAAACTT
* *
18352 CTATTCTTTGGAAAAGATTATATATAGTGGCGTT
65 CTATTCTTTGGAAAACATTATATATAGCGGCGTT
18386 TTACGTGGCA
Statistics
Matches: 205, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
122 112 0.55
123 93 0.45
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.35
Consensus pattern (122 bp):
CGGCGTTTGTCATGAGAAACGCCGCTATTCCCATCAAGAAATGGTGTTTTTTTTCACCAAACTTC
TATTCTTTGGAAAACATTATATATAGCGGCGTTGTCATCAGAAACGCCGCTATTCAA
Found at i:18292 original size:31 final size:32
Alignment explanation
Indices: 18254--18316 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
18244 CATTATATAT
* *
18254 AGCGGCG-TTGTCATTAGAGACGCCGCTATTC
1 AGCGGCGTTTGTCATGAGAAACGCCGCTATTC
18285 AGCGGCGTTTGTCATGAGAAACGCCGCTATTC
1 AGCGGCGTTTGTCATGAGAAACGCCGCTATTC
18317 CCATCAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 7 0.24
32 22 0.76
ACGTcount: A:0.21, C:0.25, G:0.29, T:0.25
Consensus pattern (32 bp):
AGCGGCGTTTGTCATGAGAAACGCCGCTATTC
Found at i:19606 original size:21 final size:21
Alignment explanation
Indices: 19537--19722 Score: 125
Period size: 22 Copynumber: 8.8 Consensus size: 21
19527 AGAATATTTT
*
19537 TATGAAATTTTGATAACTACC
1 TATGAAATTTTGATAATTACC
* *
19558 GTATTAAATTTTGATAATCACGC
1 -TATGAAATTTTGATAATTAC-C
19581 TATGAAATTTTGATAATTACC
1 TATGAAATTTTGATAATTACC
*
19602 TATGAAATTGTGATAAATT-CC
1 TATGAAATTTTGAT-AATTACC
* * *
19623 ATATGAATTTTTGATAACCTAAC
1 -TATGAAATTTTGATAA-TTACC
**
19646 TATGAAATTTT-A-CCTT-CC
1 TATGAAATTTTGATAATTACC
19664 TATGAAATTTT-ATAACCTT-CC
1 TATGAAATTTTGATAA--TTACC
* * *
19685 TATG-ATTTTTTATAATCTCCC
1 TATGAAATTTTGATAAT-TACC
* *
19706 TATGAGATTTTGTTAAT
1 TATGAAATTTTGATAAT
19723 CTCCCTATAA
Statistics
Matches: 130, Mismatches: 22, Indels: 24
0.74 0.12 0.14
Matches are distributed among these distances:
18 13 0.10
19 2 0.02
20 6 0.05
21 37 0.28
22 70 0.54
23 2 0.02
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (21 bp):
TATGAAATTTTGATAATTACC
Found at i:19696 original size:39 final size:41
Alignment explanation
Indices: 19581--19681 Score: 109
Period size: 43 Copynumber: 2.5 Consensus size: 41
19571 ATAATCACGC
* * **
19581 TATGAAATTTTGATAA-TTACCTATGAAATTGTGATAAATTCCA
1 TATGAAATTTTGATAACCTAACTATGAAATT-T--TACCTTCCA
*
19624 TATGAATTTTTGATAACCTAACTATGAAATTTTACCTTCC-
1 TATGAAATTTTGATAACCTAACTATGAAATTTTACCTTCCA
19664 TATGAAATTTT-ATAACCT
1 TATGAAATTTTGATAACCT
19682 TCCTATGATT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
39 7 0.14
40 10 0.20
41 6 0.12
43 16 0.31
44 12 0.24
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.42
Consensus pattern (41 bp):
TATGAAATTTTGATAACCTAACTATGAAATTTTACCTTCCA
Found at i:19738 original size:22 final size:22
Alignment explanation
Indices: 19683--19742 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
19673 TTATAACCTT
19683 CCTATGATTTTTT-ATAATCTC
1 CCTATGATTTTTTGATAATCTC
** *
19704 CCTATGAGATTTTGTTAATCTC
1 CCTATGATTTTTTGATAATCTC
*
19726 CCTATAATTTTTTGATA
1 CCTATGATTTTTTGATA
19743 CTATAGTATG
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 11 0.35
22 20 0.65
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.50
Consensus pattern (22 bp):
CCTATGATTTTTTGATAATCTC
Found at i:20608 original size:45 final size:45
Alignment explanation
Indices: 20575--20710 Score: 236
Period size: 45 Copynumber: 3.0 Consensus size: 45
20565 GGCAATCTAA
* *
20575 TCCGATTTAGCTCTTATAGTATGATTATACTTTTAAAAATTCAAC
1 TCCGGTTTAGTTCTTATAGTATGATTATACTTTTAAAAATTCAAC
*
20620 TCCGGTTTAGTTCTTATAGTATGATTATACATTTAAAAATTCAAC
1 TCCGGTTTAGTTCTTATAGTATGATTATACTTTTAAAAATTCAAC
*
20665 TCCGGTTTAGTTCTTATAGTATGATTATACATTTAAAAATTCAAC
1 TCCGGTTTAGTTCTTATAGTATGATTATACTTTTAAAAATTCAAC
20710 T
1 T
20711 GCTTCGAAAA
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 88 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (45 bp):
TCCGGTTTAGTTCTTATAGTATGATTATACTTTTAAAAATTCAAC
Done.