Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005133.1 Corchorus capsularis cultivar CVL-1 contig05151, 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: 7925
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33
Found at i:177 original size:69 final size:69
Alignment explanation
Indices: 1--511 Score: 673
Period size: 70 Copynumber: 7.4 Consensus size: 69
* ** * * * *
1 GAAACGAGTTTGGCTAGTGGAAAAGCCTTTACTGCTTGGATGGAACCAAGGC-TAAATTGACTCG
1 GAAACGAGTTTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTAACTCG
*
65 TGTG
66 TATG
** * *
69 GAAACGAGTTTGGCTTGTGGAAAAGCCCCTAAATGCTTGGATGGAACCAAAGCTTGAGCTAACTC
1 GAAACGAGTTTGGCTTGTGGAAAAGCCCCT-GCTGCTTGGATGGAACCAAGGCTTGAACTAACTC
134 GTATG
65 GTATG
* *
139 GAAACGAGTTTGGCTTGTGGAAAAGCCGCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCG
1 GAAACGAGTTTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTAACTCG
204 TATG
66 TATG
* ** * *
208 GAAACGAGTTTTGCTTGTGGAAAAGCCGTTGCTGCTTGGATGAAACCAAGGCTTGAACTGACTCG
1 GAAACGAGTTTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTAACTCG
273 TATG
66 TATG
* ** * **
277 GAAACGAGTTTGTCTTGTGGAAAAGCCCCTAAATGTTTGGATGGAACCAAGGCTTGAACTCTCTC
1 GAAACGAGTTTGGCTTGTGGAAAAGCCCCT-GCTGCTTGGATGGAACCAAGGCTTGAACTAACTC
*
342 GTACG
65 GTATG
* * *
347 GAAACGAGTTTGGCTTATGGAAAAGCCCCTGCATGCTTGGATGGAACCAAAGCTTGAACTATCTC
1 GAAACGAGTTTGGCTTGTGGAAAAGCCCCTGC-TGCTTGGATGGAACCAAGGCTTGAACTAACTC
412 GTATG
65 GTATG
* * *
417 GAAACGAGTTTAGCTTGTGGAAAAGCCCCTGCATGCTTGGATGGAACCAAAGCTTGAACTATCTC
1 GAAACGAGTTTGGCTTGTGGAAAAGCCCCTGC-TGCTTGGATGGAACCAAGGCTTGAACTAACTC
482 GTATG
65 GTATG
* *
487 GAAACGAGTTTGACTTATGGAAAAG
1 GAAACGAGTTTGGCTTGTGGAAAAG
512 TCAAAGCATT
Statistics
Matches: 396, Mismatches: 43, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
68 27 0.07
69 146 0.37
70 223 0.56
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (69 bp):
GAAACGAGTTTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTAACTCG
TATG
Found at i:1067 original size:41 final size:41
Alignment explanation
Indices: 1022--1103 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
1012 TTTTGAAAAG
* * *
1022 CGAATTTTGATCTTGGACTCACAAATGGA-ATGCAATCTTAT
1 CGAATTTTGATATTGGACCCACAAAT-AACATGCAATCTTAT
1063 CGAATTTTGATATTGGACCCACAAATAACATGCAATCTTAT
1 CGAATTTTGATATTGGACCCACAAATAACATGCAATCTTAT
1104 TATAAAACTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 1 0.03
41 36 0.97
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (41 bp):
CGAATTTTGATATTGGACCCACAAATAACATGCAATCTTAT
Found at i:1414 original size:11 final size:10
Alignment explanation
Indices: 1386--1450 Score: 71
Period size: 10 Copynumber: 6.4 Consensus size: 10
1376 TTTTCTTCAT
1386 TTTC-TTTT-
1 TTTCTTTTTC
1394 TTTCTTTTTC
1 TTTCTTTTTC
1404 TTTCATTTTTC
1 TTTC-TTTTTC
*
1415 TCTCTTTTTTTC
1 T-T-TCTTTTTC
*
1427 TTTCTTTTTT
1 TTTCTTTTTC
1437 TTTCTTTTTC
1 TTTCTTTTTC
1447 TTTC
1 TTTC
1451 ATTATGCACT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
8 4 0.08
9 4 0.08
10 23 0.48
11 8 0.17
12 8 0.17
13 1 0.02
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:1426 original size:19 final size:17
Alignment explanation
Indices: 1385--1447 Score: 69
Period size: 19 Copynumber: 3.7 Consensus size: 17
1375 CTTTTCTTCA
*
1385 TTTTCTTTTTTTCTTTT
1 TTTTCTTTTTCTCTTTT
1402 TCTTTCATTTTTCTCTCTTT
1 T-TTTC-TTTTTCTCT-TTT
1422 TTTTC--TTTCT-TTTT
1 TTTTCTTTTTCTCTTTT
1436 TTTTCTTTTTCT
1 TTTTCTTTTTCT
1448 TTCATTATGC
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
14 8 0.20
15 1 0.03
16 10 0.25
17 1 0.03
18 4 0.10
19 12 0.30
20 4 0.10
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTCTTTTTCTCTTTT
Found at i:1438 original size:14 final size:14
Alignment explanation
Indices: 1386--1443 Score: 59
Period size: 14 Copynumber: 4.2 Consensus size: 14
1376 TTTTCTTCAT
1386 TTTCTTTTTTTCTT-
1 TTTCTTTTTTT-TTC
*
1400 TTTCTTTCATTTTTC
1 TTTCTTT-TTTTTTC
*
1415 --TCTCTTTTTTTC
1 TTTCTTTTTTTTTC
1427 TTTCTTTTTTTTTC
1 TTTCTTTTTTTTTC
1441 TTT
1 TTT
1444 TTCTTTCATT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
12 6 0.17
13 4 0.11
14 23 0.64
15 3 0.08
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTCTTTTTTTTTC
Found at i:2084 original size:28 final size:29
Alignment explanation
Indices: 2042--2096 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
2032 TAGGCGAAGG
*
2042 TTTTTCTTTTCTTTTCTT-TTTCCTTTTT
1 TTTTTCTTTTCTTTTCTTCTTTACTTTTT
2070 TTTTTCTTTGT-TTTTCTTCTTTACTTT
1 TTTTTCTTT-TCTTTTCTTCTTTACTTT
2097 GAATGCGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (29 bp):
TTTTTCTTTTCTTTTCTTCTTTACTTTTT
Found at i:2746 original size:44 final size:44
Alignment explanation
Indices: 2633--2771 Score: 242
Period size: 44 Copynumber: 3.1 Consensus size: 44
2623 AATTTTGGAT
2633 AACCATTTTATCAAAACCTTTTGAAAACCATGACTCTTTTTGAAA
1 AACCATTTTATCAAAACCTTTTGAAAACCATGACTCTTTTTG-AA
*
2678 AACCGTTTTATCAAAACCTTTTGAAAACCATGACTCTTTTTGAA
1 AACCATTTTATCAAAACCTTTTGAAAACCATGACTCTTTTTGAA
* *
2722 AATCATTTTATCAAAACCTTTTGAAAACCATGGCTCTTTTTGAA
1 AACCATTTTATCAAAACCTTTTGAAAACCATGACTCTTTTTGAA
2766 AACCAT
1 AACCAT
2772 CGTTGCTTTT
Statistics
Matches: 89, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
44 48 0.54
45 41 0.46
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.36
Consensus pattern (44 bp):
AACCATTTTATCAAAACCTTTTGAAAACCATGACTCTTTTTGAA
Found at i:2799 original size:17 final size:16
Alignment explanation
Indices: 2777--2849 Score: 69
Period size: 17 Copynumber: 4.4 Consensus size: 16
2767 ACCATCGTTG
2777 CTTTTTCTCTTTTCTTT
1 CTTTTTCT-TTTTCTTT
2794 CTTTTTCTTTTTCTTT
1 CTTTTTCTTTTTCTTT
*
2810 -TATTATTCTTCTTCTTTT
1 CT-TT-TTCTTTTTC-TTT
*
2828 CTTTCTT-TCTTTCTTT
1 CTTT-TTCTTTTTCTTT
2844 CTTTTT
1 CTTTTT
2850 TCCTTCTATT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
15 3 0.06
16 17 0.35
17 20 0.42
18 7 0.15
19 1 0.02
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.77
Consensus pattern (16 bp):
CTTTTTCTTTTTCTTT
Found at i:2807 original size:23 final size:22
Alignment explanation
Indices: 2777--2851 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 22
2767 ACCATCGTTG
2777 CTTTTTCTCTTTTCTTTCTTTTT
1 CTTTTTCT-TTTTCTTTCTTTTT
*
2800 CTTTTTCTTTTAT-TATTCTTCTT
1 CTTTTTCTTTT-TCT-TTCTTTTT
*
2823 C-TTTTCTTTCTTTCTTTCTTTCT
1 CTTTTTC-TT-TTTCTTTCTTTTT
2846 -TTTTTC
1 CTTTTTC
2852 CTTCTATTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
22 9 0.21
23 31 0.72
24 3 0.07
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (22 bp):
CTTTTTCTTTTTCTTTCTTTTT
Found at i:2840 original size:12 final size:11
Alignment explanation
Indices: 2780--2862 Score: 67
Period size: 12 Copynumber: 6.9 Consensus size: 11
2770 ATCGTTGCTT
*
2780 TTTCTCTTTTC
1 TTTCTTTTTTC
*
2791 TTTCTTTTTCTT
1 TTTCTTTTT-TC
*
2803 TTTCTTTTATTAT
1 TTTCTTTT-TT-C
2816 TCTTCTTCTTTTC
1 T-TTCTT-TTTTC
2829 TTTCTTTCTTTC
1 TTTCTTT-TTTC
2841 TTTCTTTTTTC
1 TTTCTTTTTTC
*
2852 CTTCTATTTTT
1 TTTCT-TTTTT
2863 TCTGGGAAAC
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
11 17 0.28
12 31 0.51
13 4 0.07
14 7 0.11
15 2 0.03
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:3350 original size:75 final size:75
Alignment explanation
Indices: 3240--3461 Score: 338
Period size: 75 Copynumber: 3.0 Consensus size: 75
3230 TGGATTCAAT
* * * * * *
3240 CACCTTGAAATCATTGCTTTGACTAAAACTGATTTTGAAACATCTTTTGATTAAAACTCATCATT
1 CACCTCGAAACCATTGCTTTGATTGAAACTGATTTTGAAACTTGTTTTGATTAAAACTCATCATT
3305 CTTTTGCTCA
66 CTTTTGCTCA
* *
3315 CACCTCGAAACCATTTCTTTGATTGAAACTAATTTTGAAACTTGTTTTGATTAAAACTCATCATT
1 CACCTCGAAACCATTGCTTTGATTGAAACTGATTTTGAAACTTGTTTTGATTAAAACTCATCATT
*
3380 CTTTTGCCCA
66 CTTTTGCTCA
*
3390 CACCTCGAAACCATTGCTTTGATTGAAACTGA-TTTGAAACTTGTTTTGATTAAAACCCATCATT
1 CACCTCGAAACCATTGCTTTGATTGAAACTGATTTTGAAACTTGTTTTGATTAAAACTCATCATT
*
3454 CCTTTGCT
66 CTTTTGCT
3462 TACAGTCTAG
Statistics
Matches: 133, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
74 37 0.28
75 96 0.72
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.39
Consensus pattern (75 bp):
CACCTCGAAACCATTGCTTTGATTGAAACTGATTTTGAAACTTGTTTTGATTAAAACTCATCATT
CTTTTGCTCA
Found at i:3610 original size:3 final size:3
Alignment explanation
Indices: 3602--3669 Score: 91
Period size: 3 Copynumber: 22.7 Consensus size: 3
3592 TTTTATCCCT
* * * * *
3602 TTA TTA TTA TTA TTA TTA TTG TTG TTG TTG TTG TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3650 TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
3670 TAATTCAAAT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (3 bp):
TTA
Done.