Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022202.1 Corchorus olitorius cultivar O-4 contig22235, 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: 28605
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:1920 original size:19 final size:18
Alignment explanation
Indices: 1887--1922 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1877 TGGAAATAAT
1887 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
1905 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
1923 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:2062 original size:19 final size:18
Alignment explanation
Indices: 2029--2064 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2019 TGGAAATAAT
2029 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
2047 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
2065 TAAGTTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:2103 original size:142 final size:142
Alignment explanation
Indices: 1847--2131 Score: 543
Period size: 142 Copynumber: 2.0 Consensus size: 142
1837 TCCTTCGCAA
*
1847 TTAAAGCTCCATTCTTCAATTCTTGCTTCTTGGAAATAATTCTTCAATGGTCTTCAAATCTTCAA
1 TTAAACCTCCATTCTTCAATTCTTGCTTCTTGGAAATAATTCTTCAATGGTCTTCAAATCTTCAA
1912 ATTGTCTTCAATAAGTCTTCAAACACGAACTTCGAATCTCCAAATATATATTCAAAATTACTTTG
66 ATTGTCTTCAATAAGTCTTCAAACACGAACTTCGAATCTCCAAATATATATTCAAAATTACTTTG
1977 CTCATATATGTG
131 CTCATATATGTG
1989 TTAAACCTCCATTCTTCAATTCTTGCTTCTTGGAAATAATTCTTCAATGGTCTTCAAATCTTCAA
1 TTAAACCTCCATTCTTCAATTCTTGCTTCTTGGAAATAATTCTTCAATGGTCTTCAAATCTTCAA
*
2054 ATTGTCTTCAATAAGTTTTCAAACACGAACTTCGAATCTCCAAATATATATTCAAAATTACTTTG
66 ATTGTCTTCAATAAGTCTTCAAACACGAACTTCGAATCTCCAAATATATATTCAAAATTACTTTG
*
2119 CTCATATCTGTG
131 CTCATATATGTG
2131 T
1 T
2132 AAAAAGTCAT
Statistics
Matches: 140, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
142 140 1.00
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.39
Consensus pattern (142 bp):
TTAAACCTCCATTCTTCAATTCTTGCTTCTTGGAAATAATTCTTCAATGGTCTTCAAATCTTCAA
ATTGTCTTCAATAAGTCTTCAAACACGAACTTCGAATCTCCAAATATATATTCAAAATTACTTTG
CTCATATATGTG
Found at i:2980 original size:49 final size:49
Alignment explanation
Indices: 2875--3027 Score: 243
Period size: 49 Copynumber: 3.1 Consensus size: 49
2865 TTTCATAATA
2875 GGTGATTATATTTATTAACCATATTATCCATATATATATTAGAGATAATTAT
1 GGTGATTATA-TTATTAACCATATTATCC--ATATATATTAGAGATAATTAT
* *
2927 GGTGATTATATTATTAACCATATTATCCATACATATTAAAGATAATTAT
1 GGTGATTATATTATTAACCATATTATCCATATATATTAGAGATAATTAT
**
2976 GGTGATTATATTATTAACCATATTATCTTTATATATTAGAGATAATTAT
1 GGTGATTATATTATTAACCATATTATCCATATATATTAGAGATAATTAT
3025 GGT
1 GGT
3028 ATTTATCAAG
Statistics
Matches: 95, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
49 67 0.71
51 18 0.19
52 10 0.11
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (49 bp):
GGTGATTATATTATTAACCATATTATCCATATATATTAGAGATAATTAT
Found at i:7236 original size:4 final size:4
Alignment explanation
Indices: 7227--7287 Score: 122
Period size: 4 Copynumber: 15.2 Consensus size: 4
7217 TTAACTCTCA
7227 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT
1 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT
7275 ATCT ATCT ATCT A
1 ATCT ATCT ATCT A
7288 AAAAAATTTG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 57 1.00
ACGTcount: A:0.26, C:0.25, G:0.00, T:0.49
Consensus pattern (4 bp):
ATCT
Found at i:8693 original size:17 final size:17
Alignment explanation
Indices: 8668--8702 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
8658 AGTGACAAGC
8668 GAGGGTTTGGGTGAAAG
1 GAGGGTTTGGGTGAAAG
* *
8685 GAGGTTTTGTGTGAAAG
1 GAGGGTTTGGGTGAAAG
8702 G
1 G
8703 CTGCGCTAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.49, T:0.29
Consensus pattern (17 bp):
GAGGGTTTGGGTGAAAG
Found at i:12915 original size:20 final size:20
Alignment explanation
Indices: 12877--12915 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12867 TTAATTGATG
*
12877 GAAATTATGCAATGCAAAAT
1 GAAATTACGCAATGCAAAAT
12897 GAAATTACG-AATGCTAAAA
1 GAAATTACGCAATGC-AAAA
12916 ATAATGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.51, C:0.10, G:0.15, T:0.23
Consensus pattern (20 bp):
GAAATTACGCAATGCAAAAT
Found at i:18496 original size:19 final size:20
Alignment explanation
Indices: 18472--18516 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
18462 TGACGCCAGT
18472 TCAAATT-GGGTCTAAACTC
1 TCAAATTCGGGTCTAAACTC
18491 TCAAATTCGGGTCTAAACTC
1 TCAAATTCGGGTCTAAACTC
*
18511 TAAAAT
1 TCAAAT
18517 ACCAAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (20 bp):
TCAAATTCGGGTCTAAACTC
Found at i:18785 original size:15 final size:15
Alignment explanation
Indices: 18765--18795 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
18755 AACTGCCCCT
18765 TTCTTATAAGTTCAA
1 TTCTTATAAGTTCAA
18780 TTCTTATAAGTTCAA
1 TTCTTATAAGTTCAA
18795 T
1 T
18796 AGTCAAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.06, T:0.48
Consensus pattern (15 bp):
TTCTTATAAGTTCAA
Found at i:19298 original size:23 final size:23
Alignment explanation
Indices: 19272--19325 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
19262 TGACACTAAT
*
19272 AACCAAATTATACAATAATATTA
1 AACCAAATTATACAATAAAATTA
19295 AACCAAATTATACAATAAAATTA
1 AACCAAATTATACAATAAAATTA
19318 AA-CAAATT
1 AACCAAATT
19326 TAGATGTGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 6 0.20
23 24 0.80
ACGTcount: A:0.59, C:0.13, G:0.00, T:0.28
Consensus pattern (23 bp):
AACCAAATTATACAATAAAATTA
Found at i:20762 original size:24 final size:26
Alignment explanation
Indices: 20733--20791 Score: 68
Period size: 28 Copynumber: 2.3 Consensus size: 26
20723 AAAACAATTA
*
20733 AAATTTTTGTT-A-AAAGGAAAGGAT
1 AAATTTTTGTTAACAAAGAAAAGGAT
*
20757 AAATTTTTTTTGAAACAAAGAAAAGGAT
1 AAATTTTTGTT--AACAAAGAAAAGGAT
20785 AAATTTT
1 AAATTTT
20792 AACACATTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 10 0.34
27 1 0.03
28 18 0.62
ACGTcount: A:0.47, C:0.02, G:0.15, T:0.36
Consensus pattern (26 bp):
AAATTTTTGTTAACAAAGAAAAGGAT
Found at i:21117 original size:71 final size:72
Alignment explanation
Indices: 21017--21154 Score: 190
Period size: 72 Copynumber: 1.9 Consensus size: 72
21007 TTTTAATTAT
* * *
21017 AAAACTTAAATATATTATAATTTT-TTTTAATATATTTGTTAAATGACAATT-TTTAAACTTGTA
1 AAAACTTAAATATATTAGAATTTTGTTTAAATATATTTCTTAAATGAC-ATTGTTTAAACTTGTA
21080 CAGATTTA
65 CAGATTTA
* ** *
21088 AAAACTTAGATATATTAGAATTTTGTTTAAATATATTTCTTAAATTTCATTGTTTAAACTTTTAC
1 AAAACTTAAATATATTAGAATTTTGTTTAAATATATTTCTTAAATGACATTGTTTAAACTTGTAC
21153 AG
66 AG
21155 TTTCATTCTA
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
71 25 0.43
72 33 0.57
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.48
Consensus pattern (72 bp):
AAAACTTAAATATATTAGAATTTTGTTTAAATATATTTCTTAAATGACATTGTTTAAACTTGTAC
AGATTTA
Found at i:23185 original size:51 final size:50
Alignment explanation
Indices: 23084--23186 Score: 118
Period size: 51 Copynumber: 2.0 Consensus size: 50
23074 ATTCTTCATA
** *
23084 TTTTTCTTGTTTAGATCTTGTCTCAGGACACCCAAACACTCTTTTAGTGT
1 TTTTTCTTGTTTAGATCTTGTCTCAGGACACAAAAACACTCTATTAGTGT
* * * *
23134 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATAAAAACACTGTATTCGTGT
1 TTTT-TCTTGTTT-AGATCTTGTCTCAGGACACAAAAACACTCTATTAGTGT
23185 TT
1 TT
23187 CTCTTTCAGA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
50 4 0.09
51 39 0.89
52 1 0.02
ACGTcount: A:0.20, C:0.21, G:0.14, T:0.45
Consensus pattern (50 bp):
TTTTTCTTGTTTAGATCTTGTCTCAGGACACAAAAACACTCTATTAGTGT
Found at i:25101 original size:32 final size:32
Alignment explanation
Indices: 25075--25249 Score: 253
Period size: 32 Copynumber: 5.5 Consensus size: 32
25065 CCACAGACTG
* *
25075 GTGGCGTTTTCATCAATGTACGCCACAAATTA
1 GTGGCGTTTTCTTCAAAGTACGCCACAAATTA
* *
25107 GTGGCGTTTTTTTC-AAGAACGCCACAAATTA
1 GTGGCGTTTTCTTCAAAGTACGCCACAAATTA
*
25138 GTGGCTTTTTCTTCAAAGTACGCCACAAATTA
1 GTGGCGTTTTCTTCAAAGTACGCCACAAATTA
25170 GTGGCGTTTTCTTCAAAGTACGCCACAAATTA
1 GTGGCGTTTTCTTCAAAGTACGCCACAAATTA
* ** *
25202 GTGGCGTTTTCTTCAAAGAACGCCACTGATTT
1 GTGGCGTTTTCTTCAAAGTACGCCACAAATTA
*
25234 GTGGCGTTTTATTCAA
1 GTGGCGTTTTCTTCAA
25250 TAAACACCAT
Statistics
Matches: 129, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
31 27 0.21
32 102 0.79
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (32 bp):
GTGGCGTTTTCTTCAAAGTACGCCACAAATTA
Found at i:26061 original size:33 final size:33
Alignment explanation
Indices: 25945--26061 Score: 139
Period size: 33 Copynumber: 3.5 Consensus size: 33
25935 CAATCTCATT
* *
25945 TCTTCTGTCTTCTTCAAGGCGAGCTAGCTCATT-
1 TCTTCTATCTTCTTCAATGCGAGCTAGCTC-TTG
* *
25978 TCTTCTCTCTTCTTCAACT-CGAGCTAGCTCCTG
1 TCTTCTATCTTCTTCAA-TGCGAGCTAGCTCTTG
* *
26011 TCGTCTATCTTCTTCAATGCGAGCCAGCTCTTG
1 TCTTCTATCTTCTTCAATGCGAGCTAGCTCTTG
*
26044 TCTTCTTTCTTCTTCAAT
1 TCTTCTATCTTCTTCAAT
26062 TCTTGCAAGC
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
32 2 0.03
33 70 0.97
ACGTcount: A:0.14, C:0.31, G:0.14, T:0.42
Consensus pattern (33 bp):
TCTTCTATCTTCTTCAATGCGAGCTAGCTCTTG
Found at i:26073 original size:33 final size:33
Alignment explanation
Indices: 25945--26077 Score: 124
Period size: 33 Copynumber: 4.0 Consensus size: 33
25935 CAATCTCATT
* ** *
25945 TCTTCTGTCTTCTTCAAGGCGAGCTAGCTCATT-
1 TCTTCTATCTTCTTCAATTCGAGCAAGCTC-TTG
* * * *
25978 TCTTCTCTCTTCTTCAACTCGAGCTAGCTCCTG
1 TCTTCTATCTTCTTCAATTCGAGCAAGCTCTTG
* * *
26011 TCGTCTATCTTCTTCAATGCGAGCCAGCTCTTG
1 TCTTCTATCTTCTTCAATTCGAGCAAGCTCTTG
* **
26044 TCTTCTTTCTTCTTCAATTCTTGCAAGCTCTTG
1 TCTTCTATCTTCTTCAATTCGAGCAAGCTCTTG
26077 T
1 T
26078 TGCCTTTCTA
Statistics
Matches: 83, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
32 1 0.01
33 82 0.99
ACGTcount: A:0.14, C:0.30, G:0.14, T:0.42
Consensus pattern (33 bp):
TCTTCTATCTTCTTCAATTCGAGCAAGCTCTTG
Found at i:27148 original size:15 final size:15
Alignment explanation
Indices: 27125--27160 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
27115 CATCTACAAA
*
27125 ATCACCTACATTTGC
1 ATCATCTACATTTGC
27140 ATCATCTACATTTGC
1 ATCATCTACATTTGC
27155 ATCATC
1 ATCATC
27161 ACCAACTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.28, C:0.31, G:0.06, T:0.36
Consensus pattern (15 bp):
ATCATCTACATTTGC
Found at i:27935 original size:32 final size:33
Alignment explanation
Indices: 27892--27988 Score: 121
Period size: 32 Copynumber: 3.0 Consensus size: 33
27882 CTGGATTGCA
*
27892 AATTAGGGGCGTTTT-CTTCATAAAACGCCACT
1 AATTAGTGGCGTTTTACTTCATAAAACGCCACT
*
27924 AATTAGTGGCGTTTTAC-TCA-ATAAATGCCACT
1 AATTAGTGGCGTTTTACTTCATA-AAACGCCACT
**
27956 AATTAGTGGCGTTTTACTGAAT-AAACGCCACT
1 AATTAGTGGCGTTTTACTTCATAAAACGCCACT
27988 A
1 A
27989 TTTGCAAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
31 1 0.02
32 53 0.95
33 2 0.04
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Consensus pattern (33 bp):
AATTAGTGGCGTTTTACTTCATAAAACGCCACT
Done.