Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010124.1 Corchorus capsularis cultivar CVL-1 contig10145, 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: 18757
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Found at i:302 original size:27 final size:27
Alignment explanation
Indices: 228--296 Score: 138
Period size: 27 Copynumber: 2.6 Consensus size: 27
218 AAGTGACCTT
228 AAAATGACCAAAATGCCCTTGAATGCA
1 AAAATGACCAAAATGCCCTTGAATGCA
255 AAAATGACCAAAATGCCCTTGAATGCA
1 AAAATGACCAAAATGCCCTTGAATGCA
282 AAAATGACCAAAATG
1 AAAATGACCAAAATG
297 GTCTTGGATG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.17
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCTTGAATGCA
Found at i:590 original size:17 final size:17
Alignment explanation
Indices: 570--603 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
560 TTTTTTTGCG
570 ATTTGATTGATTTTTTT
1 ATTTGATTGATTTTTTT
**
587 ATTTTTTTGATTTTTTT
1 ATTTGATTGATTTTTTT
604 TAGACCTTCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.09, T:0.76
Consensus pattern (17 bp):
ATTTGATTGATTTTTTT
Found at i:711 original size:47 final size:47
Alignment explanation
Indices: 654--984 Score: 493
Period size: 47 Copynumber: 7.0 Consensus size: 47
644 AAAACCCGTT
* ** *
654 GACCAACTTTGGTCACTAAATTGAAAACTCATGTGGAAGCGAGAGAA
1 GACCATCTTTGGTCACTAAATTGAAAACTCGCGTGGAAGCGAGAAAA
* *
701 GACCATCTTTGGTAACTAAATTGAAAACCCGCGTGGAAGCGAGAAAA
1 GACCATCTTTGGTCACTAAATTGAAAACTCGCGTGGAAGCGAGAAAA
* * *
748 GACCATCTTTGATCACTAGATTGATAACTCGCAG-GGAAGCGAGAAAA
1 GACCATCTTTGGTCACTAAATTGAAAACTCGC-GTGGAAGCGAGAAAA
* * *
795 GACCATCTTTGGTCACCAAATTGAAAACTCGTGTGGAAACGAGAAAA
1 GACCATCTTTGGTCACTAAATTGAAAACTCGCGTGGAAGCGAGAAAA
* *
842 GACCATCTTTGGTTACTAAATTGAAAATTCGCGTGGAAGCGAGAAAA
1 GACCATCTTTGGTCACTAAATTGAAAACTCGCGTGGAAGCGAGAAAA
*
889 GACCATCTTTGGTCACCAAATTGAAAACTCGCGTGGAAGCGAGAAAA
1 GACCATCTTTGGTCACTAAATTGAAAACTCGCGTGGAAGCGAGAAAA
* *
936 GACCATCTTTGGTCACTAAATTGAAAATTCGCGTGGAAGCGAGAGAA
1 GACCATCTTTGGTCACTAAATTGAAAACTCGCGTGGAAGCGAGAAAA
983 GA
1 GA
985 TTGCCTGGAT
Statistics
Matches: 254, Mismatches: 28, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
46 1 0.00
47 252 0.99
48 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.21
Consensus pattern (47 bp):
GACCATCTTTGGTCACTAAATTGAAAACTCGCGTGGAAGCGAGAAAA
Found at i:1235 original size:69 final size:68
Alignment explanation
Indices: 1095--1385 Score: 279
Period size: 69 Copynumber: 4.2 Consensus size: 68
1085 CTCACTAAAC
* * * * * **
1095 TTGGCTTATGGAAAAGCCCCTGAATGCTCGGATGGAACCAAATCTTA-AACT-ATCTCGCATGGA
1 TTGGCTTGTGGAAAAGCCTCTG-TTGCT-GGATGGAACCAAAGC-TAGATCTGA-CTCGTGTGGA
* *
1158 AGCAAGT
62 AACGAGT
* * * * *
1165 TTGGCTTATGGAAAAGCCTCTCTTGCCTGGATGGAATCGAAGCTGGATCTGACTCGTGTGGAAAC
1 TTGGCTTGTGGAAAAGCCTCTGTTG-CTGGATGGAACCAAAGCTAGATCTGACTCGTGTGGAAAC
1230 GAGT
65 GAGT
* * * *
1234 TTCGCTTGTGGAAAAGCCTCTGTT--TGGATGGAACCAAAACTTA-AACT-ATCTCGTATGGAAA
1 TTGGCTTGTGGAAAAGCCTCTGTTGCTGGATGGAACCAAAGC-TAGATCTGA-CTCGTGTGGAAA
*
1295 AGAGT
64 CGAGT
* *
1300 TTGGCTTGTAGAAAAGCCTCTGTTGCTTGGATGGAACCAAAGCTAGATCTGACTTGTGTGGAAAC
1 TTGGCTTGTGGAAAAGCCTCTGTTGC-TGGATGGAACCAAAGCTAGATCTGACTCGTGTGGAAAC
1365 GAGT
65 GAGT
1369 TTGGCTTGTGGAAAAGC
1 TTGGCTTGTGGAAAAGC
1386 TGAAGCATTC
Statistics
Matches: 181, Mismatches: 30, Indels: 21
0.78 0.13 0.09
Matches are distributed among these distances:
65 1 0.01
66 53 0.29
67 1 0.01
68 3 0.02
69 99 0.55
70 24 0.13
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (68 bp):
TTGGCTTGTGGAAAAGCCTCTGTTGCTGGATGGAACCAAAGCTAGATCTGACTCGTGTGGAAACG
AGT
Found at i:1366 original size:135 final size:135
Alignment explanation
Indices: 1124--1385 Score: 400
Period size: 135 Copynumber: 1.9 Consensus size: 135
1114 CTGAATGCTC
* * *
1124 GGATGGAACCAAATCTTAAACTATCTCGCATGGAAGCAAGTTTGGCTTATGGAAAAGCCTCTCTT
1 GGATGGAACCAAAACTTAAACTATCTCGCATGGAAGAAAGTTTGGCTTATAGAAAAGCCTCTCTT
* * *
1189 GCCTGGATGGAATCGAAGCTGGATCTGACTCGTGTGGAAACGAGTTTCGCTTGTGGAAAAGCCTC
66 GCCTGGATGGAACCAAAGCTAGATCTGACTCGTGTGGAAACGAGTTTCGCTTGTGGAAAAGCCTC
1254 TGTTT
131 TGTTT
* * *
1259 GGATGGAACCAAAACTTAAACTATCTCGTATGGAA-AAGAGTTTGGCTTGTAGAAAAGCCTCTGT
1 GGATGGAACCAAAACTTAAACTATCTCGCATGGAAGAA-AGTTTGGCTTATAGAAAAGCCTCTCT
* * *
1323 TGCTTGGATGGAACCAAAGCTAGATCTGACTTGTGTGGAAACGAGTTTGGCTTGTGGAAAAGC
65 TGCCTGGATGGAACCAAAGCTAGATCTGACTCGTGTGGAAACGAGTTTCGCTTGTGGAAAAGC
1386 TGAAGCATTC
Statistics
Matches: 114, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
134 1 0.01
135 113 0.99
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.27
Consensus pattern (135 bp):
GGATGGAACCAAAACTTAAACTATCTCGCATGGAAGAAAGTTTGGCTTATAGAAAAGCCTCTCTT
GCCTGGATGGAACCAAAGCTAGATCTGACTCGTGTGGAAACGAGTTTCGCTTGTGGAAAAGCCTC
TGTTT
Found at i:2446 original size:5 final size:5
Alignment explanation
Indices: 2420--2490 Score: 56
Period size: 6 Copynumber: 13.2 Consensus size: 5
2410 CCCTAGAGCC
*
2420 TCTTT TCTTCAT TCTCT T-TTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTT
1 TCTTT TCTT--T TCTTT TCTTT TC-TTT TC-TTT TC-TTT TC-TTT TCTTT
2470 TCTTT TCTTT T-TTT TCCTTT T
1 TCTTT TCTTT TCTTT T-CTTT T
2491 TATATGCACT
Statistics
Matches: 58, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
4 7 0.12
5 20 0.34
6 27 0.47
7 4 0.07
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (5 bp):
TCTTT
Found at i:2490 original size:6 final size:6
Alignment explanation
Indices: 2437--2481 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
2427 TTCATTCTCT
2437 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC -TTTTC -TTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
2482 TTTCCTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 10 0.26
6 28 0.74
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTC
Found at i:2829 original size:20 final size:22
Alignment explanation
Indices: 2806--2853 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 22
2796 CCACTTTCAT
2806 TTTTTTCCTCCTC-TTTT-TTC
1 TTTTTTCCTCCTCTTTTTCTTC
* *
2826 TTTTTTCTTCTTCTTTTTCTTC
1 TTTTTTCCTCCTCTTTTTCTTC
2848 TTTTTT
1 TTTTTT
2854 TTTTCCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 11 0.46
21 4 0.17
22 9 0.38
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTTTTCCTCCTCTTTTTCTTC
Found at i:2830 original size:22 final size:20
Alignment explanation
Indices: 2800--2863 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 20
2790 TTCCTTCCAC
*
2800 TTTCATTTTTTTCCTCCTCTTT
1 TTTC-TTTTTTTTCTCCT-TTT
*
2822 TTTCTTTTTTCTTCTTCTTTT
1 TTTCTTTTTT-TTCTCCTTTT
*
2843 TCTTCTTTTTTTTTTCCTTTT
1 T-TTCTTTTTTTTCTCCTTTT
2864 CTTCCCTTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
21 18 0.50
22 18 0.50
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTCTTTTTTTTCTCCTTTT
Found at i:2842 original size:12 final size:11
Alignment explanation
Indices: 2805--2854 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
2795 TCCACTTTCA
*
2805 TTTTTTTCCTC
1 TTTTTTTCTTC
* *
2816 CTCTTTT-TTC
1 TTTTTTTCTTC
2826 -TTTTTTCTTC
1 TTTTTTTCTTC
2836 TTCTTTTTCTTC
1 TT-TTTTTCTTC
2848 TTTTTTT
1 TTTTTTT
2855 TTTCCTTTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
9 5 0.16
10 5 0.16
11 11 0.34
12 11 0.34
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTTTCTTC
Found at i:2846 original size:26 final size:26
Alignment explanation
Indices: 2817--2866 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
2807 TTTTTCCTCC
2817 TCTT-TTTTCTTTTTT-CTTCTTCTTTT
1 TCTTCTTTT-TTTTTTCCTT-TTCTTTT
2843 TCTTCTTTTTTTTTTCCTTTTCTT
1 TCTTCTTTTTTTTTTCCTTTTCTT
2867 CCCTTCTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (26 bp):
TCTTCTTTTTTTTTTCCTTTTCTTTT
Found at i:2855 original size:12 final size:12
Alignment explanation
Indices: 2826--2855 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2816 CTCTTTTTTC
2826 TTTTTTCTTCTT
1 TTTTTTCTTCTT
*
2838 CTTTTTCTTCTT
1 TTTTTTCTTCTT
2850 TTTTTT
1 TTTTTT
2856 TTCCTTTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTTTCTTCTT
Found at i:2863 original size:20 final size:22
Alignment explanation
Indices: 2818--2867 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 22
2808 TTTTCCTCCT
2818 CTTTT-TTCTTTTTTCTTCTTC
1 CTTTTCTTCTTTTTTCTTCTTC
*
2839 TTTTTCTTCTTTTTT-TT-TTC
1 CTTTTCTTCTTTTTTCTTCTTC
2859 CTTTTCTTC
1 CTTTTCTTC
2868 CCTTCTTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 11 0.42
21 6 0.23
22 9 0.35
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (22 bp):
CTTTTCTTCTTTTTTCTTCTTC
Found at i:3257 original size:46 final size:45
Alignment explanation
Indices: 3215--3332 Score: 150
Period size: 46 Copynumber: 2.6 Consensus size: 45
3205 ACCCTTTAAA
* *
3215 AAAAACATGCCTCTTTTTGAAAAACCGTTTTATGAAAACCTTTTG
1 AAAACCATGCCTCTTTTTGAAAAACCATTTTATGAAAACCTTTTG
* * *
3260 AGAACCATGACTCTTTTTTTG-AAAACCATTTTATCAAAACCTTTTG
1 AAAACCATG-C-CTCTTTTTGAAAAACCATTTTATGAAAACCTTTTG
*
3306 AAAACCATGACTCTTTTTG-AAAACCAT
1 AAAACCATGCCTCTTTTTGAAAAACCAT
3333 CATTGCTTCT
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
44 16 0.25
45 7 0.11
46 32 0.51
47 8 0.13
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (45 bp):
AAAACCATGCCTCTTTTTGAAAAACCATTTTATGAAAACCTTTTG
Found at i:3280 original size:47 final size:46
Alignment explanation
Indices: 3228--3332 Score: 160
Period size: 46 Copynumber: 2.3 Consensus size: 46
3218 AACATGCCTC
* * *
3228 TTTTTGAAAAACCGTTTTATGAAAACCTTTTGAGAACCATGACTCTT
1 TTTTTG-AAAACCATTTTATCAAAACCTTTTGAAAACCATGACTCTT
3275 TTTTTGAAAACCATTTTATCAAAACCTTTTGAAAACCATGACTC--
1 TTTTTGAAAACCATTTTATCAAAACCTTTTGAAAACCATGACTCTT
3319 TTTTTGAAAACCAT
1 TTTTTGAAAACCAT
3333 CATTGCTTCT
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
44 14 0.25
46 35 0.64
47 6 0.11
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (46 bp):
TTTTTGAAAACCATTTTATCAAAACCTTTTGAAAACCATGACTCTT
Found at i:3414 original size:30 final size:28
Alignment explanation
Indices: 3351--3422 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 28
3341 CTTCTCTTTC
*
3351 CTTTCTTTCTTTTTCTTTTTCCATCATT
1 CTTTCTTTCTTTTTCTTTTTCCATCACT
*
3379 CTTTCTTTCTTCTTCTCTTTTTCCTTCTACT
1 CTTTCTTTCTT-TT-TCTTTTTCCATC-ACT
3410 -TTTC--TCTTTTTCT
1 CTTTCTTTCTTTTTCT
3423 GGGAAACTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
26 3 0.08
27 2 0.05
28 15 0.38
29 2 0.05
30 15 0.38
31 2 0.05
ACGTcount: A:0.04, C:0.28, G:0.00, T:0.68
Consensus pattern (28 bp):
CTTTCTTTCTTTTTCTTTTTCCATCACT
Found at i:12082 original size:34 final size:34
Alignment explanation
Indices: 12039--12108 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
12029 TTTTCCCGTT
*
12039 CGAGCCCTCTAAGGTAATCGAATTTGCTTTTTTC
1 CGAGCCCTCTAAGGTAATCGAATTTGCATTTTTC
*
12073 CGAGCCCTCTAAGGTAATTGAATTTGCATTTTTC
1 CGAGCCCTCTAAGGTAATCGAATTTGCATTTTTC
12107 CG
1 CG
12109 GGACTACACT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (34 bp):
CGAGCCCTCTAAGGTAATCGAATTTGCATTTTTC
Found at i:12289 original size:15 final size:15
Alignment explanation
Indices: 12271--12299 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12261 TCCAATTTGT
12271 AAATCAAATGCCTTA
1 AAATCAAATGCCTTA
12286 AAATCAAATGCCTT
1 AAATCAAATGCCTT
12300 GTATATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.21, G:0.07, T:0.28
Consensus pattern (15 bp):
AAATCAAATGCCTTA
Found at i:15958 original size:7 final size:7
Alignment explanation
Indices: 15911--15954 Score: 70
Period size: 7 Copynumber: 6.3 Consensus size: 7
15901 CGGAGTGAGC
15911 ATGGGCA
1 ATGGGCA
15918 ATGGGCA
1 ATGGGCA
15925 ATGGGCA
1 ATGGGCA
15932 ATGGGCA
1 ATGGGCA
*
15939 ATTGGCA
1 ATGGGCA
*
15946 ATTGGCA
1 ATGGGCA
15953 AT
1 AT
15955 TGGCTGAGTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.30, C:0.14, G:0.36, T:0.20
Consensus pattern (7 bp):
ATGGGCA
Found at i:16439 original size:16 final size:17
Alignment explanation
Indices: 16405--16449 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
16395 GGGGACATCT
16405 ATAATAATTAT-TAATTA
1 ATAAT-ATTATATAATTA
*
16422 ATATTATTATATAA-TA
1 ATAATATTATATAATTA
16438 ATAATA-TATATA
1 ATAATATTATATA
16450 TTGCTTGTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 6 0.24
16 12 0.48
17 7 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATAATATTATATAATTA
Done.