Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010397.1 Corchorus capsularis cultivar CVL-1 contig10418, 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: 51859
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:5937 original size:4 final size:4
Alignment explanation
Indices: 5928--5954 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5918 TACTGTGATC
5928 AATT AATT AATT AATT AATT AATT AAT
1 AATT AATT AATT AATT AATT AATT AAT
5955 AACAATATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:8321 original size:2 final size:2
Alignment explanation
Indices: 8314--8342 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
8304 ACTATTTATT
8314 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8343 TATCCCCTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22519 original size:27 final size:27
Alignment explanation
Indices: 22489--22545 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
22479 ACATAGAAGA
22489 TTGTGATTTCATTTTACTCTTTCTATT
1 TTGTGATTTCATTTTACTCTTTCTATT
22516 TTGTGATTTCATTTTACTCTTTCTATT
1 TTGTGATTTCATTTTACTCTTTCTATT
22543 TTG
1 TTG
22546 GTCTTTACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.14, C:0.14, G:0.09, T:0.63
Consensus pattern (27 bp):
TTGTGATTTCATTTTACTCTTTCTATT
Found at i:22538 original size:13 final size:14
Alignment explanation
Indices: 22495--22544 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
22485 AAGATTGTGA
22495 TTTC-ATTTTACTC
1 TTTCTATTTTACTC
* *
22508 TTTCTATTTT-GTGA
1 TTTCTATTTTACT-C
22522 TTTC-ATTTTACTC
1 TTTCTATTTTACTC
22535 TTTCTATTTT
1 TTTCTATTTT
22545 GGTCTTTACT
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
13 14 0.48
14 15 0.52
ACGTcount: A:0.14, C:0.16, G:0.04, T:0.66
Consensus pattern (14 bp):
TTTCTATTTTACTC
Found at i:22930 original size:44 final size:44
Alignment explanation
Indices: 22867--22955 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
22857 CAGGCATCAG
22867 GCAAACGTGATTAGATTGAAGGAGATTTAAATTTTGGTTGTATT
1 GCAAACGTGATTAGATTGAAGGAGATTTAAATTTTGGTTGTATT
22911 GCAAACGTGATTAGATTGAAGGAGATTTAAATTTTGGTTGTATT
1 GCAAACGTGATTAGATTGAAGGAGATTTAAATTTTGGTTGTATT
22955 G
1 G
22956 TCTTGCAGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.31, C:0.04, G:0.26, T:0.38
Consensus pattern (44 bp):
GCAAACGTGATTAGATTGAAGGAGATTTAAATTTTGGTTGTATT
Found at i:25924 original size:27 final size:27
Alignment explanation
Indices: 25578--25911 Score: 431
Period size: 27 Copynumber: 12.5 Consensus size: 27
25568 CACTACAATT
** *
25578 CCAAGCTTTTCTATGGGCACCACAACT
1 CCAAGCTTTTCTCCGGGCACCACAACC
* *
25605 ACAAGCTTTTCTCCGGGCACCACAACA
1 CCAAGCTTTTCTCCGGGCACCACAACC
* *
25632 GCAAGCTTTTCTTCGGG---CACAACC
1 CCAAGCTTTTCTCCGGGCACCACAACC
* * *
25656 TCAAGCTTTTCTCTGGGAACCACAACC
1 CCAAGCTTTTCTCCGGGCACCACAACC
25683 CCAAGCTTTTCTCCGGGCACCACAACC
1 CCAAGCTTTTCTCCGGGCACCACAACC
25710 CCAAGCTTTTCTCCGGGCACCACAACC
1 CCAAGCTTTTCTCCGGGCACCACAACC
* * *
25737 ACAAGCTTTTCTCCGGGCTCCACAACA
1 CCAAGCTTTTCTCCGGGCACCACAACC
* *
25764 GCAAGCTTTTCTCCAGGCACCACAACC
1 CCAAGCTTTTCTCCGGGCACCACAACC
* * *
25791 TCAAGCTTTTCTCTGGGAACCACAACC
1 CCAAGCTTTTCTCCGGGCACCACAACC
* * *
25818 TCAAGCTTTTCTCTGGGAACCACAACC
1 CCAAGCTTTTCTCCGGGCACCACAACC
*
25845 TCAAGCTTTTCTCCGGGCACCACAACC
1 CCAAGCTTTTCTCCGGGCACCACAACC
*
25872 CCAAGCTTTTCTCCAGGCACCACAACC
1 CCAAGCTTTTCTCCGGGCACCACAACC
*
25899 CCTAGCTTTTCTC
1 CCAAGCTTTTCTC
25912 TTGGCACTAC
Statistics
Matches: 275, Mismatches: 29, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
24 20 0.07
27 255 0.93
ACGTcount: A:0.24, C:0.38, G:0.15, T:0.23
Consensus pattern (27 bp):
CCAAGCTTTTCTCCGGGCACCACAACC
Found at i:26023 original size:27 final size:27
Alignment explanation
Indices: 25993--26177 Score: 264
Period size: 27 Copynumber: 6.9 Consensus size: 27
25983 AGCTTCTTCT
*
25993 CAGCTAGTTC-AACTGCAAGCTTTGCAA
1 CAGCTGGTTCAAACT-CAAGCTTTGCAA
*
26020 CAGCTGGTTCAAACTCAAGCTTTGCAG
1 CAGCTGGTTCAAACTCAAGCTTTGCAA
*
26047 CAGCTGGTTCGAACTCAAGCTTTGCAA
1 CAGCTGGTTCAAACTCAAGCTTTGCAA
*
26074 CAGCTGGTTCAAACTTAAGCTTTGCAA
1 CAGCTGGTTCAAACTCAAGCTTTGCAA
*
26101 CAGCTGGTTCGAACTCAAGCTTTGCAA
1 CAGCTGGTTCAAACTCAAGCTTTGCAA
* *
26128 CAGCTGGTTCAAACTCAAGCTTTCCAG
1 CAGCTGGTTCAAACTCAAGCTTTGCAA
** *
26155 CAGCTGGTTTGAACTCAGGCTTT
1 CAGCTGGTTCAAACTCAAGCTTT
26178 ATATTTGGCA
Statistics
Matches: 143, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
27 139 0.97
28 4 0.03
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (27 bp):
CAGCTGGTTCAAACTCAAGCTTTGCAA
Found at i:26051 original size:54 final size:54
Alignment explanation
Indices: 25993--26177 Score: 300
Period size: 54 Copynumber: 3.4 Consensus size: 54
25983 AGCTTCTTCT
*
25993 CAGCTAGTTC-AACTGCAAGCTTTGCAACAGCTGGTTCAAACTCAAGCTTTGCAG
1 CAGCTGGTTCGAACT-CAAGCTTTGCAACAGCTGGTTCAAACTCAAGCTTTGCAG
* *
26047 CAGCTGGTTCGAACTCAAGCTTTGCAACAGCTGGTTCAAACTTAAGCTTTGCAA
1 CAGCTGGTTCGAACTCAAGCTTTGCAACAGCTGGTTCAAACTCAAGCTTTGCAG
*
26101 CAGCTGGTTCGAACTCAAGCTTTGCAACAGCTGGTTCAAACTCAAGCTTTCCAG
1 CAGCTGGTTCGAACTCAAGCTTTGCAACAGCTGGTTCAAACTCAAGCTTTGCAG
* *
26155 CAGCTGGTTTGAACTCAGGCTTT
1 CAGCTGGTTCGAACTCAAGCTTT
26178 ATATTTGGCA
Statistics
Matches: 122, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
54 118 0.97
55 4 0.03
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (54 bp):
CAGCTGGTTCGAACTCAAGCTTTGCAACAGCTGGTTCAAACTCAAGCTTTGCAG
Found at i:28899 original size:66 final size:65
Alignment explanation
Indices: 28762--28897 Score: 186
Period size: 66 Copynumber: 2.1 Consensus size: 65
28752 CCTTCCAAGC
* ** * * *
28762 AATAGACCCGGGTTCGACTCCTGGCAAACGCAGTCTTTCCTCATTTTTTTTTGTAGTTTCTCTTA
1 AATATACCCGGGTTCGACTCCCAGCAAACACAGCCTTTCCTCA-TTTTTTTGGTAGTTTCTCTTA
28827 A
65 A
28828 AATATACCCGGGTTCGACTCCCAGCAAACACAGCCATTT-CTCA-TTTTTTGGTAGTTTCTCTTA
1 AATATACCCGGGTTCGACTCCCAGCAAACACAGCC-TTTCCTCATTTTTTTGGTAGTTTCTCTTA
28891 A
65 A
28892 AATATA
1 AATATA
28898 TAAATACCAA
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
64 26 0.41
66 34 0.54
67 3 0.05
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (65 bp):
AATATACCCGGGTTCGACTCCCAGCAAACACAGCCTTTCCTCATTTTTTTGGTAGTTTCTCTTAA
Found at i:33815 original size:11 final size:12
Alignment explanation
Indices: 33788--33819 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
33778 AAGTCTACAT
*
33788 TTTTTTGTTTTC
1 TTTTTTGCTTTC
33800 TTTTTTGCTTTC
1 TTTTTTGCTTTC
33812 TTTTTTGC
1 TTTTTTGC
33820 AAAAATAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.09, T:0.78
Consensus pattern (12 bp):
TTTTTTGCTTTC
Found at i:38089 original size:28 final size:28
Alignment explanation
Indices: 38057--38114 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
38047 ATCCGTACAC
*
38057 CGCTACATGATTAATTACATTATTGAAA
1 CGCTACATGATTAACTACATTATTGAAA
* *
38085 CGCTATATGATTAGCTACATTATTGAAA
1 CGCTACATGATTAACTACATTATTGAAA
38113 CG
1 CG
38115 TTAATCTATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (28 bp):
CGCTACATGATTAACTACATTATTGAAA
Found at i:40749 original size:237 final size:238
Alignment explanation
Indices: 40334--40809 Score: 810
Period size: 237 Copynumber: 2.0 Consensus size: 238
40324 TGCACATGTT
*
40334 TAAATTTCGATCAATAATGAAGTGGACTTTGTTGGCTGGTTATAACTTCTCTTAATGGCAGTTTG
1 TAAATTTCGATCAATAATGAAGTGGACTTTGTTGGCCGGTTATAACTTCTCTTAATGGCAGTTTG
* *
40399 TAATTCTTATCGGTGATTCATTCCAAAATATTAGTTCATTAACTCCGTGTGTTTGTTCGTTATAT
66 TAATTCTTATCGGTGATCCATTCCAAAATATCAGTTCATTAACTCCGTGTGTTTGTTCGTTATAT
* * * *
40464 TAGTTAAGTCAACAAGACTTGAATAGGAAATGTAGCTCTTATGTGCTTAGAGG-CTAATGAGTGT
131 TAGTTAAGTAAACAAGACTTGAATAGGAAATGCAGCTCTTATGTGCTTAGAGGTCTAACGAGTAT
* *
40528 TTATGACGTAATACAGGCTTTGTTGCTTGGCACGTGTACTTGC
196 TTATGACGTAATACAGACTTTGCTGCTTGGCACGTGTACTTGC
40571 TAAATTTCGATCAATAATGAAGTGGACTTTGTTGGCCGGTTATAACTTCTCTTAATGGCAGTTTG
1 TAAATTTCGATCAATAATGAAGTGGACTTTGTTGGCCGGTTATAACTTCTCTTAATGGCAGTTTG
*
40636 TAATTCTTATTGGTGATCCATTCCAAAATATCAGTTCATTAACTCCGTGTGTTTGTTCGTTATAT
66 TAATTCTTATCGGTGATCCATTCCAAAATATCAGTTCATTAACTCCGTGTGTTTGTTCGTTATAT
* *
40701 TAGTTAAGTAAACAAGACTTGAATAGGAAATGCAGCTTTTATGTGCTTAGAGGTGTAACGAGTAT
131 TAGTTAAGTAAACAAGACTTGAATAGGAAATGCAGCTCTTATGTGCTTAGAGGTCTAACGAGTAT
* * *
40766 TTCTGATGTAATACATACTTTGCTGCTTGGCACGTGTACTTGC
196 TTATGACGTAATACAGACTTTGCTGCTTGGCACGTGTACTTGC
40809 T
1 T
40810 TTATTTGAAA
Statistics
Matches: 223, Mismatches: 15, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
237 176 0.79
238 47 0.21
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.39
Consensus pattern (238 bp):
TAAATTTCGATCAATAATGAAGTGGACTTTGTTGGCCGGTTATAACTTCTCTTAATGGCAGTTTG
TAATTCTTATCGGTGATCCATTCCAAAATATCAGTTCATTAACTCCGTGTGTTTGTTCGTTATAT
TAGTTAAGTAAACAAGACTTGAATAGGAAATGCAGCTCTTATGTGCTTAGAGGTCTAACGAGTAT
TTATGACGTAATACAGACTTTGCTGCTTGGCACGTGTACTTGC
Found at i:51441 original size:13 final size:13
Alignment explanation
Indices: 51423--51450 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
51413 TTCTGAATCC
51423 TAGCTCTAGGCAA
1 TAGCTCTAGGCAA
51436 TAGCTCTAGGCAA
1 TAGCTCTAGGCAA
51449 TA
1 TA
51451 CAGTCAAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.25
Consensus pattern (13 bp):
TAGCTCTAGGCAA
Done.