Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017976.1 Corchorus olitorius cultivar O-4 contig18009, 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: 4177
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Found at i:806 original size:31 final size:29
Alignment explanation
Indices: 770--1050 Score: 264
Period size: 31 Copynumber: 9.8 Consensus size: 29
760 CTACGTGTAA
*
770 ATATAGTTGCATATTTAGTAGAGCCATAATC
1 ATATAGTTGCATATTCAGTAG-G-CATAATC
* * *
801 ATATAGTTGCATATTTAGTAGG----GTG
1 ATATAGTTGCATATTCAGTAGGCATAATC
826 ATATAGTTGCATATTCAGTATGG-----TC
1 ATATAGTTGCATATTCAGTA-GGCATAATC
*
851 ATGTAGTTGCATATTCAGTAGGATCATAATC
1 ATATAGTTGCATATTCAGTAGG--CATAATC
*
882 ATATAGTTGCATATTCAGCAGAGCCATAATC
1 ATATAGTTGCATATTCAGTAG-G-CATAATC
* *
913 ATATAGTTACATATTCAGTAGGGATAATC
1 ATATAGTTGCATATTCAGTAGGCATAATC
*
942 ATATAGTTGCAAATTCAGTAGGATCATAATC
1 ATATAGTTGCATATTCAGTAGG--CATAATC
*
973 ATATAGTTGCAAATTCAGTAGGGTCATAATC
1 ATATAGTTGCATATTCAGTA-GG-CATAATC
1004 ATATAGTTGCATATTCAGTAGG----ATC
1 ATATAGTTGCATATTCAGTAGGCATAATC
* *
1029 ATGTAGTTGCATATTTAGTAGG
1 ATATAGTTGCATATTCAGTAGG
1051 GTCATATAAT
Statistics
Matches: 221, Mismatches: 17, Indels: 30
0.82 0.06 0.11
Matches are distributed among these distances:
24 2 0.01
25 63 0.29
26 2 0.01
29 26 0.12
30 4 0.02
31 121 0.55
32 3 0.01
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (29 bp):
ATATAGTTGCATATTCAGTAGGCATAATC
Found at i:835 original size:25 final size:25
Alignment explanation
Indices: 799--1155 Score: 177
Period size: 25 Copynumber: 13.2 Consensus size: 25
789 AGAGCCATAA
*
799 TCATATAGTTGCATATTTAGTAGGG
1 TCATATAGTTGCATATTCAGTAGGG
* *
824 TGATATAGTTGCATATTCAGTATGG
1 TCATATAGTTGCATATTCAGTAGGG
* *
849 TCATGTAGTTGCATATTCAGTAGGATCATAA
1 TCATATAGTTGCATATTCAGTAGG------G
* *
880 TCATATAGTTGCATATTCAGCAGAGCCATAA
1 TCATATAGTTGCATATTCAGTAG-G-----G
*
911 TCATATAGTTACATATTCAGTAGGG
1 TCATATAGTTGCATATTCAGTAGGG
* *
936 ATAATCATATAGTTGCAAATTCAGTAGGATCATAA
1 ----TCATATAGTTGCATATTCAGTAGG------G
*
971 TCATATAGTTGCAAATTCAGTAGGG
1 TCATATAGTTGCATATTCAGTAGGG
*
996 TCATAATCATATAGTTGCATATTCAGTAGGA
1 ------TCATATAGTTGCATATTCAGTAGGG
* *
1027 TCATGTAGTTGCATATTTAGTAGGG
1 TCATATAGTTGCATATTCAGTAGGG
* * **
1052 TCATATAATTGCATATTCTGTAAAAG
1 TCATATAGTTGCATATTCAGT-AGGG
*
1078 -C--AT-GTT-CTATATTCAGTTGGGCG
1 TCATATAGTTGC-ATATTCAG-TAGG-G
*
1101 TCATATAGTTGCATATT-AGCAGGGG
1 TCATATAGTTGCATATTCAGTA-GGG
*
1126 TCATATAGTTCCATATTCAGTAGGGG
1 TCATATAGTTGCATATTCAGTA-GGG
1152 TCAT
1 TCAT
1156 CTACATTATC
Statistics
Matches: 261, Mismatches: 37, Indels: 67
0.72 0.10 0.18
Matches are distributed among these distances:
21 1 0.00
22 9 0.03
23 4 0.02
24 1 0.00
25 100 0.38
26 19 0.07
27 8 0.03
28 1 0.00
29 22 0.08
30 1 0.00
31 94 0.36
32 1 0.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (25 bp):
TCATATAGTTGCATATTCAGTAGGG
Found at i:958 original size:60 final size:60
Alignment explanation
Indices: 770--1026 Score: 243
Period size: 60 Copynumber: 4.4 Consensus size: 60
760 CTACGTGTAA
* * * *
770 ATATAGTTGCATATTTAGTA-GAGCCATAATCATATAGTTGCATATTTAGTAGGG----TG
1 ATATAGTTGCATATTCAGCAGGA-CCATAATCATATAGTTGCATATTCAGTAGGGATAATC
* * *
826 ATATAGTTGCATATTCAGTATGG-------TCATGTAGTTGCATATTCAGTAGGATCATAATC
1 ATATAGTTGCATATTCAGCA-GGACCATAATCATATAGTTGCATATTCAGTAGG--GATAATC
*
882 ATATAGTTGCATATTCAGCA-GAGCCATAATCATATAGTTACATATTCAGTAGGGATAATC
1 ATATAGTTGCATATTCAGCAGGA-CCATAATCATATAGTTGCATATTCAGTAGGGATAATC
* * * *
942 ATATAGTTGCAAATTCAGTAGGATCATAATCATATAGTTGCAAATTCAGTAGGGTCATAATC
1 ATATAGTTGCATATTCAGCAGGACCATAATCATATAGTTGCATATTCAGTAGGG--ATAATC
*
1004 ATATAGTTGCATATTCAGTAGGA
1 ATATAGTTGCATATTCAGCAGGA
1027 TCATGTAGTT
Statistics
Matches: 167, Mismatches: 15, Indels: 32
0.78 0.07 0.15
Matches are distributed among these distances:
50 22 0.13
54 1 0.01
56 39 0.23
58 1 0.01
60 52 0.31
61 2 0.01
62 50 0.30
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (60 bp):
ATATAGTTGCATATTCAGCAGGACCATAATCATATAGTTGCATATTCAGTAGGGATAATC
Found at i:1017 original size:122 final size:112
Alignment explanation
Indices: 770--1069 Score: 317
Period size: 112 Copynumber: 2.6 Consensus size: 112
760 CTACGTGTAA
* * * * *
770 ATATAGTTGCATATTTAGTAGAGCCATAATCATATAGTTGCATATTTAGTAGGGTGATATAGTTG
1 ATATAGTTGCATATTCAGCAGAGCCATAATCATATAGTTACATATTCAGTAGGGTCATATAGTTG
* * *
835 CATATTCAGTATGGTCATGTAGTTGCATATTCAGTAGGATCATAATC
66 CAAATTCAGTATGGTCATATAGTTGCAAATTCAGTAGGATCATAATC
882 ATATAGTTGCATATTCAGCAGAGCCATAATCATATAGTTACATATTCAGTAGGGATAATCATATA
1 ATATAGTTGCATATTCAGCAGAGCCATAATCATATAGTTACATATTCAGTAGGG----TCATATA
*
947 GTTGCAAATTCAGTA-GGATCATAATCATATAGTTGCAAATTCAGTAGGGTCATAATC
62 GTTGCAAATTCAGTATGG-------TCATATAGTTGCAAATTCAGTAGGATCATAATC
* * * * *
1004 ATATAGTTGCATATTCAGTAG-G-----ATCATGTAGTTGCATATTTAGTAGGGTCATATAATTG
1 ATATAGTTGCATATTCAGCAGAGCCATAATCATATAGTTACATATTCAGTAGGGTCATATAGTTG
*
1063 CATATTC
66 CAAATTC
1070 TGTAAAAGCA
Statistics
Matches: 162, Mismatches: 15, Indels: 22
0.81 0.08 0.11
Matches are distributed among these distances:
112 66 0.41
115 2 0.01
116 43 0.27
121 1 0.01
122 50 0.31
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (112 bp):
ATATAGTTGCATATTCAGCAGAGCCATAATCATATAGTTACATATTCAGTAGGGTCATATAGTTG
CAAATTCAGTATGGTCATATAGTTGCAAATTCAGTAGGATCATAATC
Found at i:1067 original size:91 final size:88
Alignment explanation
Indices: 826--1056 Score: 331
Period size: 91 Copynumber: 2.6 Consensus size: 88
816 TAGTAGGGTG
*
826 ATATAGTTGCATATTCAGTATGG-TCATGTAGTTGCATATTCAGTAGGATCATAATCATATAGTT
1 ATATAGTTGCATATTCAGTAGGGATCATGTAGTTGCATATTCAGTAGGATCATAATCATATAGTT
*
890 GCATATTCAGCAGAGCCATAATC
66 GCAAATTCAGCAGAGCCATAATC
* * *
913 ATATAGTTACATATTCAGTAGGGATAATCATATAGTTGCAAATTCAGTAGGATCATAATCATATA
1 ATATAGTTGCATATTCAGTAGGG---ATCATGTAGTTGCATATTCAGTAGGATCATAATCATATA
* * *
978 GTTGCAAATTCAGTAGGGTCATAATC
63 GTTGCAAATTCAGCAGAGCCATAATC
* *
1004 ATATAGTTGCATATTCAGTA-GGATCATGTAGTTGCATATTTAGTAGGGTCATA
1 ATATAGTTGCATATTCAGTAGGGATCATGTAGTTGCATATTCAGTAGGATCATA
1057 TAATTGCATA
Statistics
Matches: 127, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
87 48 0.38
90 2 0.02
91 77 0.61
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.35
Consensus pattern (88 bp):
ATATAGTTGCATATTCAGTAGGGATCATGTAGTTGCATATTCAGTAGGATCATAATCATATAGTT
GCAAATTCAGCAGAGCCATAATC
Found at i:2117 original size:20 final size:20
Alignment explanation
Indices: 2092--2133 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
2082 TTATTCTCAG
2092 ATTAGGCATTTCTAGATTTC
1 ATTAGGCATTTCTAGATTTC
2112 ATTAGGCATTTCTAGATTTC
1 ATTAGGCATTTCTAGATTTC
2132 AT
1 AT
2134 ATAGTTCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.45
Consensus pattern (20 bp):
ATTAGGCATTTCTAGATTTC
Found at i:2249 original size:29 final size:28
Alignment explanation
Indices: 2207--2264 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 28
2197 TTGGGCCAAA
2207 AAAATTATCTCTATTAAAACAAACTACTT
1 AAAATTATCTCTATTAAAACAAA-TACTT
2236 AAAATTATCTCTATTAAAACAAATACTT
1 AAAATTATCTCTATTAAAACAAATACTT
2264 A
1 A
2265 GGTTGCGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (28 bp):
AAAATTATCTCTATTAAAACAAATACTT
Found at i:2769 original size:7 final size:7
Alignment explanation
Indices: 2757--2816 Score: 92
Period size: 7 Copynumber: 9.1 Consensus size: 7
2747 TTGATAATTA
2757 GTTTAGG
1 GTTTAGG
2764 GTTTAGG
1 GTTTAGG
2771 G-TTAGG
1 GTTTAGG
2777 GTTTAGG
1 GTTTAGG
2784 GTTTAGG
1 GTTTAGG
2791 G-TTAGG
1 GTTTAGG
2797 GTTTAGG
1 GTTTAGG
2804 G-TTAGG
1 GTTTAGG
2810 G-TTAGG
1 GTTTAGG
2816 G
1 G
2817 ATAGGGTCTA
Statistics
Matches: 51, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
6 24 0.47
7 27 0.53
ACGTcount: A:0.15, C:0.00, G:0.47, T:0.38
Consensus pattern (7 bp):
GTTTAGG
Found at i:2777 original size:6 final size:6
Alignment explanation
Indices: 2759--2823 Score: 85
Period size: 6 Copynumber: 10.2 Consensus size: 6
2749 GATAATTAGT
2759 TTAGGG TTTAGGG TTAGGG TTTAGGG TTTAGGG TTAGGG TTTAGGG TTAGGG
1 TTAGGG -TTAGGG TTAGGG -TTAGGG -TTAGGG TTAGGG -TTAGGG TTAGGG
*
2811 TTAGGG ATAGGG T
1 TTAGGG TTAGGG T
2824 CTATCATTCT
Statistics
Matches: 54, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
6 29 0.54
7 25 0.46
ACGTcount: A:0.17, C:0.00, G:0.46, T:0.37
Consensus pattern (6 bp):
TTAGGG
Found at i:2777 original size:13 final size:13
Alignment explanation
Indices: 2757--2823 Score: 93
Period size: 13 Copynumber: 5.2 Consensus size: 13
2747 TTGATAATTA
2757 GTTTAGGGTTTAGG
1 GTTTAGGG-TTAGG
2771 G-TTAGGGTTTAGG
1 GTTTAGGG-TTAGG
2784 GTTTAGGGTTAGG
1 GTTTAGGGTTAGG
2797 GTTTAGGGTTAGG
1 GTTTAGGGTTAGG
*
2810 G-TTAGGGATAGG
1 GTTTAGGGTTAGG
2822 GT
1 GT
2824 CTATCATTCT
Statistics
Matches: 50, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
12 11 0.22
13 32 0.64
14 7 0.14
ACGTcount: A:0.16, C:0.00, G:0.46, T:0.37
Consensus pattern (13 bp):
GTTTAGGGTTAGG
Found at i:2782 original size:20 final size:20
Alignment explanation
Indices: 2757--2816 Score: 113
Period size: 20 Copynumber: 3.0 Consensus size: 20
2747 TTGATAATTA
2757 GTTTAGGGTTTAGGGTTAGG
1 GTTTAGGGTTTAGGGTTAGG
2777 GTTTAGGGTTTAGGGTTAGG
1 GTTTAGGGTTTAGGGTTAGG
2797 GTTTAGGG-TTAGGGTTAGG
1 GTTTAGGGTTTAGGGTTAGG
2816 G
1 G
2817 ATAGGGTCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
19 12 0.30
20 28 0.70
ACGTcount: A:0.15, C:0.00, G:0.47, T:0.38
Consensus pattern (20 bp):
GTTTAGGGTTTAGGGTTAGG
Found at i:3817 original size:62 final size:62
Alignment explanation
Indices: 3741--3947 Score: 373
Period size: 62 Copynumber: 3.4 Consensus size: 62
3731 ACACGACAGA
*
3741 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGAAGGAGGCGAGGCCAGCAGG
1 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
3803 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
1 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
*
3865 CACGAAGGTACACGGGAAGAC--AGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
1 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
*
3925 CACGAAGGTACATGAGAAGACAG
1 CACGAAGGTACACGAGAAGACAG
3948 GAAGACAGAC
Statistics
Matches: 139, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
60 58 0.42
62 81 0.58
ACGTcount: A:0.35, C:0.22, G:0.40, T:0.04
Consensus pattern (62 bp):
CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
Found at i:3989 original size:34 final size:33
Alignment explanation
Indices: 3925--4012 Score: 142
Period size: 34 Copynumber: 2.7 Consensus size: 33
3915 GGCCAGCAGG
*
3925 CACGAAGGTACATGAGAAGAC-AGGAAGACAGA
1 CACGAAGGTACACGAGAAGACAAGGAAGACAGA
3957 CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
1 CACGAAGGTACACGAGAAGACA-AGGAAGACAGA
*
3991 CACGAAGGTACACAAGAAGACA
1 CACGAAGGTACACGAGAAGACA
4013 CAGTGGTGCT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
32 20 0.38
34 32 0.62
ACGTcount: A:0.48, C:0.18, G:0.30, T:0.05
Consensus pattern (33 bp):
CACGAAGGTACACGAGAAGACAAGGAAGACAGA
Found at i:4118 original size:2 final size:2
Alignment explanation
Indices: 4113--4176 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
4103 CAGAAACAAC
4113 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
4155 AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG
4177 G
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.