Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000696.1 Corchorus capsularis cultivar CVL-1 contig00696, 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: 2139
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:641 original size:47 final size:47
Alignment explanation
Indices: 517--871 Score: 317
Period size: 47 Copynumber: 7.6 Consensus size: 47
507 CCGAGGTCTG
* * * * *
517 AAATTGAAGACTCGCGTGGAAGCGAGAAAAAACCAACTTTGGTCA-A
1 AAATTGTAGACTCACGTGGAAGTGAGAAAAGACCAACTTTGGTCACT
* * * *
563 AGACATTGCAAACTCACGTGGAAGTGAGAAAAGGCCAACTTTGGTCACC
1 A-A-ATTGTAGACTCACGTGGAAGTGAGAAAAGACCAACTTTGGTCACT
* *
612 AAATTTTAGACTCACATGGAAGTGAGAAAAGACCAACTTTGGTCACT
1 AAATTGTAGACTCACGTGGAAGTGAGAAAAGACCAACTTTGGTCACT
* * * *
659 AAATTGTAGATTCGCATGGAA-TCGAGAAAAGACTAACTTTGGTCACT
1 AAATTGTAGACTCACGTGGAAGT-GAGAAAAGACCAACTTTGGTCACT
* * *
706 AAATTGTA-ACTCGCGTGGAAGCGAG-AAAGACCAACTTT-GTCAAT
1 AAATTGTAGACTCACGTGGAAGTGAGAAAAGACCAACTTTGGTCACT
* * * * * * *
750 AAATTGCAGAATCGCGTGGAAGCGAGGAAGGACCAACTTTTGTCACT
1 AAATTGTAGACTCACGTGGAAGTGAGAAAAGACCAACTTTGGTCACT
* ** * * *
797 AAATTGCAGGTTCACGTGGAAGTGAGGAAAGGCCAACTTTGGCCACT
1 AAATTGTAGACTCACGTGGAAGTGAGAAAAGACCAACTTTGGTCACT
* * * *
844 ACAA-CGTAGACTCGCATGGAAGCGAGAA
1 A-AATTGTAGACTCACGTGGAAGTGAGAA
872 TAGATTACTT
Statistics
Matches: 258, Mismatches: 42, Indels: 17
0.81 0.13 0.05
Matches are distributed among these distances:
44 12 0.05
45 28 0.11
46 27 0.10
47 150 0.58
48 40 0.16
49 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (47 bp):
AAATTGTAGACTCACGTGGAAGTGAGAAAAGACCAACTTTGGTCACT
Found at i:788 original size:91 final size:94
Alignment explanation
Indices: 517--838 Score: 341
Period size: 91 Copynumber: 3.4 Consensus size: 94
507 CCGAGGTCTG
* * *
517 AAATTGAAGACTCGCGTGGAAGCGAGAAAAAACCAACTTTGGTCAA-AGACATTGCA-AACTCAC
1 AAATTGTAGACTCGCGTGGAAGCGAGAAAAGACCAACTTTGGTCAATA-A-ATTGCAGAA-TCGC
* *
580 GTGGAAGTGAGAAAAGG-CCAACTTTGGTCACC
63 GTGGAAGCGAG-AAAGGACCAACTTTGGTCACT
* * * * * * * *
612 AAATTTTAGACTCACATGGAAGTGAGAAAAGACCAACTTTGGTCACTAAATTGTAGATTCGCATG
1 AAATTGTAGACTCGCGTGGAAGCGAGAAAAGACCAACTTTGGTCAATAAATTGCAGAATCGCGTG
* * *
677 GAATCGAGAAAAGACTAACTTTGGTCACT
66 GAAGCGAGAAAGGACCAACTTTGGTCACT
706 AAATTGTA-ACTCGCGTGGAAGCGAG-AAAGACCAACTTT-GTCAATAAATTGCAGAATCGCGTG
1 AAATTGTAGACTCGCGTGGAAGCGAGAAAAGACCAACTTTGGTCAATAAATTGCAGAATCGCGTG
* *
768 GAAGCGAGGAAGGACCAACTTTTGTCACT
66 GAAGCGAGAAAGGACCAACTTTGGTCACT
* ** * * * *
797 AAATTGCAGGTTCACGTGGAAGTGAGGAAAGGCCAACTTTGG
1 AAATTGTAGACTCGCGTGGAAGCGAGAAAAGACCAACTTTGG
839 CCACTACAAC
Statistics
Matches: 186, Mismatches: 35, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
91 51 0.27
92 26 0.14
93 30 0.16
94 37 0.20
95 41 0.22
96 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.22
Consensus pattern (94 bp):
AAATTGTAGACTCGCGTGGAAGCGAGAAAAGACCAACTTTGGTCAATAAATTGCAGAATCGCGTG
GAAGCGAGAAAGGACCAACTTTGGTCACT
Found at i:799 original size:138 final size:140
Alignment explanation
Indices: 517--871 Score: 351
Period size: 138 Copynumber: 2.5 Consensus size: 140
507 CCGAGGTCTG
* * * * * * *
517 AAATTGAAGACTCGCGTGGAAGCGAGAAAAAACCAACTTTGGTCA-AAGACATTGCAAACTCACG
1 AAATTGAAGATTCGCGTGGAATCGAGAAAAGACCAACTTTGGTCACTACA-ATTG-TAACTCGCG
* * * ** * *
581 TGGAAGTGAGAAAAGGCCAACTTTGGTCACCAAATTTTAGACTCACATGGAAGTGAGAAAAGACC
64 TGGAAGCGAG-AAAGACCAACTTTGGTCAACAAATTGCAGAATCACATGGAAGCGAGAAAAGACC
646 AACTTTGGTCACT
128 AACTTTGGTCACT
* * *
659 AAATTGTAGATTCGCATGGAATCGAGAAAAGACTAACTTTGGTCACTA-AATTGTAACTCGCGTG
1 AAATTGAAGATTCGCGTGGAATCGAGAAAAGACCAACTTTGGTCACTACAATTGTAACTCGCGTG
* * * * *
723 GAAGCGAGAAAGACCAACTTT-GTCAATAAATTGCAGAATCGCGTGGAAGCGAGGAAGGACCAAC
66 GAAGCGAGAAAGACCAACTTTGGTCAACAAATTGCAGAATCACATGGAAGCGAGAAAAGACCAAC
*
787 TTTTGTCACT
131 TTTGGTCACT
* * * * * * * *
797 AAATTGCAGGTTCACGTGGAAGT-GAGGAAAGGCCAACTTTGGCCACTACAA-CGTAGACTCGCA
1 AAATTGAAGATTCGCGTGGAA-TCGAGAAAAGACCAACTTTGGTCACTACAATTGTA-ACTCGCG
860 TGGAAGCGAGAA
64 TGGAAGCGAGAA
872 TAGATTACTT
Statistics
Matches: 177, Mismatches: 32, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
138 83 0.47
139 33 0.19
140 16 0.09
141 4 0.02
142 40 0.23
143 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (140 bp):
AAATTGAAGATTCGCGTGGAATCGAGAAAAGACCAACTTTGGTCACTACAATTGTAACTCGCGTG
GAAGCGAGAAAGACCAACTTTGGTCAACAAATTGCAGAATCACATGGAAGCGAGAAAAGACCAAC
TTTGGTCACT
Found at i:861 original size:185 final size:189
Alignment explanation
Indices: 517--871 Score: 456
Period size: 185 Copynumber: 1.9 Consensus size: 189
507 CCGAGGTCTG
517 AAATTGAAGACTCGCGTGGAAGCGAGAAAAAACCAACTTTGGTCAAAGACATTGCAAACTCACGT
1 AAATTGAAGACTCGCGTGGAAGCGAGAAAAAACCAACTTTGGTCAAAGACATTGCAAACTCACGT
* **
582 GGAAGTGAGAAAAGGCCAACTTTGGTCACCAAATTTTAGACTCACATGGAAGTGAGAAAAGACCA
66 GGAAGCGAGAAAAGGCCAACTTTGGTCACCAAATTGCAGACTCACATGGAAGTGAGAAAAGACCA
* * * *
647 ACTTTGGTCACTAAATTGTAGATTCGCATGGAATCGAGAAAAGACTAACTTTGGTCACT
131 ACTTTGGCCACTAAATCGTAGACTCGCATGGAAGCGAGAAAAGACTAACTTTGGTCACT
* * *
706 AAATTGTA-ACTCGCGTGGAAGCGAG-AAAGACCAACTTT-GTCAATA-A-ATTGCAGAA-TCGC
1 AAATTGAAGACTCGCGTGGAAGCGAGAAAAAACCAACTTTGGTCAA-AGACATTGCA-AACTCAC
* * * ** * * *
765 GTGGAAGCGAG-GAAGGACCAACTTTTGTCACTAAATTGCAGGTTCACGTGGAAGTGAGGAAAGG
64 GTGGAAGCGAGAAAAGG-CCAACTTTGGTCACCAAATTGCAGACTCACATGGAAGTGAGAAAAGA
829 CCAACTTTGGCCACTACAA-CGTAGACTCGCATGGAAGCGAGAA
128 CCAACTTTGGCCACTA-AATCGTAGACTCGCATGGAAGCGAGAA
872 TAGATTACTT
Statistics
Matches: 144, Mismatches: 18, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
184 4 0.03
185 93 0.65
186 10 0.07
187 13 0.09
188 17 0.12
189 7 0.05
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (189 bp):
AAATTGAAGACTCGCGTGGAAGCGAGAAAAAACCAACTTTGGTCAAAGACATTGCAAACTCACGT
GGAAGCGAGAAAAGGCCAACTTTGGTCACCAAATTGCAGACTCACATGGAAGTGAGAAAAGACCA
ACTTTGGCCACTAAATCGTAGACTCGCATGGAAGCGAGAAAAGACTAACTTTGGTCACT
Found at i:1090 original size:70 final size:70
Alignment explanation
Indices: 995--1212 Score: 307
Period size: 70 Copynumber: 3.1 Consensus size: 70
985 ACTTGGCTTA
* * *
995 TGGAAAAGCCCTCT-ACTGATTGGATGGAACCAACGCTTAAACTGACTCGTATGGAAACGAGTTT
1 TGGAAAAGCCC-CTGAATGCTTGGATGGAACCAAAGCTTAAACTGACTCGTATGGAAACGAGTTT
1059 GACTTG
65 GACTTG
* *
1065 TGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTAATCT-ACCTCGTATGGAAACGAGGTT
1 TGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTAAACTGA-CTCGTATGGAAACGAGTTT
*
1129 GGCTTG
65 GACTTG
* *
1135 TGGAAAAGCCCCTGGAA-ACTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTT
1 TGGAAAAGCCCCT-GAATGCTTGGATGGAACCAAAGCTTAAACTGACTCGTATGGAAACGAGTTT
*
1199 GACTTA
65 GACTTG
1205 TGGAAAAG
1 TGGAAAAG
1213 TCAAAACATT
Statistics
Matches: 132, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
69 3 0.02
70 125 0.95
71 4 0.03
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (70 bp):
TGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTAAACTGACTCGTATGGAAACGAGTTTG
ACTTG
Found at i:1849 original size:50 final size:50
Alignment explanation
Indices: 1752--1849 Score: 144
Period size: 50 Copynumber: 2.0 Consensus size: 50
1742 TTGAAAAGCA
* *
1752 AATTTTGATTTTGGACTCACAAACAGAATGCAATCTTATCTTGAAACTCG
1 AATTTTGATATTGGACTCACAAACAGAATGCAATCTTATCTTAAAACTCG
**
1802 AATTTTGATATTGGACTCACAAATGGAATGCAATCTTAT-TATAAAACT
1 AATTTTGATATTGGACTCACAAACAGAATGCAATCTTATCT-TAAAACT
1850 TCTTGTTTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
49 1 0.02
50 42 0.98
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (50 bp):
AATTTTGATATTGGACTCACAAACAGAATGCAATCTTATCTTAAAACTCG
Done.