Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005686.1 Corchorus capsularis cultivar CVL-1 contig05704, 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: 2898
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.29
Found at i:1042 original size:70 final size:70
Alignment explanation
Indices: 952--1291 Score: 475
Period size: 70 Copynumber: 4.8 Consensus size: 70
942 TGGATCAATC
* * * * *
952 GGAAACAGCTGATGAAAAACCGCCCTAGGTCAACTGAATCGATCATTCTGACATAAACTTGGATA
1 GGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGATA
*
1017 AACGT
66 AACTT
* * * * * * *
1022 GGAAACTACTGAAGAAAAACCGCCCTAGGTCAACCGAATCAATCATTCTGACACAAACTTGGATA
1 GGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGATA
1087 AACTT
66 AACTT
1092 GGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGAAT
1 GGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGG-AT
1157 AAACTT
65 AAACTT
* *** *
1163 GAAAACAACT-ATAGAAAGACCGTTTTGGGTCGACTGAATCGATCATTCTGATATAAACTTGGAT
1 GGAAACAACTGA-AGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGAT
1227 AAACTT
65 AAACTT
* *
1233 GAAAACAACTGACGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACT
1 GGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACT
1292 GAAGAAAGAC
Statistics
Matches: 243, Mismatches: 24, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
70 179 0.74
71 64 0.26
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.22
Consensus pattern (70 bp):
GGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGATA
AACTT
Found at i:1239 original size:141 final size:140
Alignment explanation
Indices: 954--1291 Score: 471
Period size: 141 Copynumber: 2.4 Consensus size: 140
944 GATCAATCGG
* * * * *
954 AAACAGCTGATGAAAAACCGCCCTAGGTCAACTGAATCGATCATTCTGACATAAACTTGGATAAA
1 AAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGATAAA
* *
1019 CGTGGAAACTACTGAAGAAAAACCGCCCTAGGTCAACCGAATCAATCATTCTGACACAAACTTGG
66 CGTGAAAACAACTGAAGAAAAACCGCCCTAGGTCAACCGAATCAATCATTCTGACACAAACTTGG
*
1084 ATAAACTTGG
131 ATAAACTTGA
1094 AAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGAATAA
1 AAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGG-ATAA
* * *** * * * * * *
1159 ACTTGAAAACAACT-ATAGAAAGACCGTTTTGGGTCGACTGAATCGATCATTCTGATATAAACTT
65 ACGTGAAAACAACTGA-AGAAAAACCGCCCTAGGTCAACCGAATCAATCATTCTGACACAAACTT
1223 GGATAAACTTGA
129 GGATAAACTTGA
*
1235 AAACAACTGACGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACT
1 AAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACT
1292 GAAGAAAGAC
Statistics
Matches: 176, Mismatches: 20, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
140 56 0.32
141 120 0.68
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.22
Consensus pattern (140 bp):
AAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGATAAA
CGTGAAAACAACTGAAGAAAAACCGCCCTAGGTCAACCGAATCAATCATTCTGACACAAACTTGG
ATAAACTTGA
Found at i:1386 original size:36 final size:36
Alignment explanation
Indices: 1282--1386 Score: 131
Period size: 36 Copynumber: 2.9 Consensus size: 36
1272 CGATCATTCT
*
1282 GACATAAACTGAAGAAAGACCGCCCTGGGTCAA-CC
1 GACATAAACTGAAGAAAGACCACCCTGGGTCAATCC
* * * * *
1317 GAAATAAACTAAAGAAAGACCAACCTCGATCAATCC
1 GACATAAACTGAAGAAAGACCACCCTGGGTCAATCC
* *
1353 GACATAATCTGAAGAAAAACCACCCTGGGTCAAT
1 GACATAAACTGAAGAAAGACCACCCTGGGTCAAT
1387 TGAATCGATC
Statistics
Matches: 56, Mismatches: 13, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
35 27 0.48
36 29 0.52
ACGTcount: A:0.43, C:0.26, G:0.17, T:0.14
Consensus pattern (36 bp):
GACATAAACTGAAGAAAGACCACCCTGGGTCAATCC
Found at i:1454 original size:70 final size:71
Alignment explanation
Indices: 1361--1527 Score: 273
Period size: 70 Copynumber: 2.4 Consensus size: 71
1351 CCGACATAAT
* * * *
1361 CTGAAGAAAAACCACCCTGGGTCAATTGAATCGATCATTCTTACATAAACTTGG-ATAAACTTGA
1 CTGAAGAAAGACCGCCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTGGAATAAACTTGA
1425 AAACAA
66 AAACAA
* *
1431 TTGAAGAAAGACCGCCCTAGGTCAACTGAATCGATCATTCTGACATAAACTTGGAATAAACTTGA
1 CTGAAGAAAGACCGCCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTGGAATAAACTTGA
1496 AAACAA
66 AAACAA
1502 CTGAAGAAAGACCGCCCTGGGTCAAC
1 CTGAAGAAAGACCGCCCTGGGTCAAC
1528 CGAAATAAAC
Statistics
Matches: 88, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
70 48 0.55
71 40 0.45
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.22
Consensus pattern (71 bp):
CTGAAGAAAGACCGCCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTGGAATAAACTTGA
AAACAA
Found at i:1587 original size:36 final size:35
Alignment explanation
Indices: 1500--1589 Score: 99
Period size: 36 Copynumber: 2.5 Consensus size: 35
1490 ACTTGAAAAC
* * * *
1500 AACTGAAGAAAGACCGCCCTGGGTCAACCGAAATA
1 AACTGAAGAAAAACCACCCTCGATCAACCGAAATA
* * * *
1535 AACTAAAGAAAAACCACCCTCGATCATTCCGACATG
1 AACTGAAGAAAAACCACCCTCGATCA-ACCGAAATA
1571 AACTGAAGAAAAACCACCC
1 AACTGAAGAAAAACCACCC
1590 CGGGTCAACT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
35 21 0.47
36 24 0.53
ACGTcount: A:0.43, C:0.29, G:0.16, T:0.12
Consensus pattern (35 bp):
AACTGAAGAAAAACCACCCTCGATCAACCGAAATA
Found at i:1637 original size:50 final size:50
Alignment explanation
Indices: 1554--1671 Score: 175
Period size: 50 Copynumber: 2.4 Consensus size: 50
1544 AAAACCACCC
* *
1554 TCGATCATTCCGACAT-GAACTGAAGAAAAACCACCCCGGGTCAACTGAA
1 TCGATCATTCTGACATAAAACTGAAGAAAAACCACCCCGGGTCAACTGAA
* * * *
1603 TCGATCATTCTGAAATAAAACTTAAGAAAGACCACCCTGGGTCAACTGAA
1 TCGATCATTCTGACATAAAACTGAAGAAAAACCACCCCGGGTCAACTGAA
1653 TCGATCATTCTGACATAAA
1 TCGATCATTCTGACATAAA
1672 CTTGGATCAA
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
49 14 0.23
50 47 0.77
ACGTcount: A:0.38, C:0.25, G:0.16, T:0.21
Consensus pattern (50 bp):
TCGATCATTCTGACATAAAACTGAAGAAAAACCACCCCGGGTCAACTGAA
Found at i:1785 original size:35 final size:35
Alignment explanation
Indices: 1732--1857 Score: 146
Period size: 35 Copynumber: 3.6 Consensus size: 35
1722 ATCGATCATT
*
1732 CTGAAATAAACTGGAGAAAGACCACCCTAGGTCAA
1 CTGAAATAAACTGAAGAAAGACCACCCTAGGTCAA
* *
1767 CTGAAATAAGCTGAAGAAAGACCACCCTGGGTCAA
1 CTGAAATAAACTGAAGAAAGACCACCCTAGGTCAA
* * * * *
1802 CTGAAATAAATTCAAGAAATATCGCCCT-GGATCAA
1 CTGAAATAAACTGAAGAAAGACCACCCTAGG-TCAA
* *
1837 TTGAAATTAACTGAAGAAAGA
1 CTGAAATAAACTGAAGAAAGA
1858 TCGCCCTGGA
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
34 2 0.03
35 74 0.97
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.18
Consensus pattern (35 bp):
CTGAAATAAACTGAAGAAAGACCACCCTAGGTCAA
Found at i:1861 original size:35 final size:34
Alignment explanation
Indices: 1733--1901 Score: 134
Period size: 35 Copynumber: 5.0 Consensus size: 34
1723 TCGATCATTC
* * * * *
1733 TGAAATAAACTGGAGAAAGACCACCCTAGGTCAAC
1 TGAAATTAACTGAAGAAAGATCGCCCT-GGTCAAT
* * *
1768 TGAAA-TAAGCTGAAGAAAGACCACCCTGGGTCAAC
1 TGAAATTAA-CTGAAGAAAGATCGCCCT-GGTCAAT
* * * *
1803 TGAAATAAATTCAAGAAATATCGCCCTGGATCAAT
1 TGAAATTAACTGAAGAAAGATCGCCCTGG-TCAAT
1838 TGAAATTAACTGAAGAAAGATCGCCCTGG---AT
1 TGAAATTAACTGAAGAAAGATCGCCCTGGTCAAT
*
1869 T--AATTAACTGAAGAAAGATCGCCTTGGATCAAT
1 TGAAATTAACTGAAGAAAGATCGCCCTGG-TCAAT
1902 AAACATTAAC
Statistics
Matches: 112, Mismatches: 15, Indels: 16
0.78 0.10 0.11
Matches are distributed among these distances:
29 25 0.22
31 3 0.03
33 2 0.02
34 4 0.04
35 76 0.68
36 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.21
Consensus pattern (34 bp):
TGAAATTAACTGAAGAAAGATCGCCCTGGTCAAT
Found at i:1874 original size:29 final size:29
Alignment explanation
Indices: 1841--1897 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
1831 GATCAATTGA
1841 AATTAACTGAAGAAAGATCGCCCTGGATT
1 AATTAACTGAAGAAAGATCGCCCTGGATT
*
1870 AATTAACTGAAGAAAGATCGCCTTGGAT
1 AATTAACTGAAGAAAGATCGCCCTGGAT
1898 CAATAAACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.25
Consensus pattern (29 bp):
AATTAACTGAAGAAAGATCGCCCTGGATT
Found at i:2883 original size:15 final size:16
Alignment explanation
Indices: 2863--2893 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2853 TTCTTCATCA
2863 TTTTTTCTT-TTCTTT
1 TTTTTTCTTCTTCTTT
2878 TTTTTTCTTCTTCTTT
1 TTTTTTCTTCTTCTTT
2894 CTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTCTTCTTCTTT
Done.