Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015118.1 Corchorus olitorius cultivar O-4 contig15151, 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: 3173
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Found at i:579 original size:14 final size:14
Alignment explanation
Indices: 557--827 Score: 157
Period size: 14 Copynumber: 19.6 Consensus size: 14
547 AGTGTGGTCT
557 TTCTTCAATTTCAA
1 TTCTTCAATTTCAA
*
571 TTTTTCAATTCTTCAA
1 TTCTTCAA-T-TTCAA
* *
587 --ATTCAATCCTTTAA
1 TTCTTCAAT--TTCAA
601 TGT-TTCAATTTCAA
1 T-TCTTCAATTTCAA
*
615 TTCTTAATATTTCAA
1 TTCTTCA-ATTTCAA
630 TTCTTCAATTTCAA
1 TTCTTCAATTTCAA
*
644 TTCTTCAAATTCAA
1 TTCTTCAATTTCAA
*
658 TCCTTCAA--T--A
1 TTCTTCAATTTCAA
668 -T-TTCAATTTCAA
1 TTCTTCAATTTCAA
680 TTCTTC-ATATTCAA
1 TTCTTCAAT-TTCAA
*
694 TCCTTCAATTTCAA
1 TTCTTCAATTTCAA
*
708 TTTTTCAATTTC--
1 TTCTTCAATTTCAA
*
720 TTCAAATTTAATCCTTCAA
1 TTC---TTCAAT--TTCAA
739 -TCTTTCAATTTCAA
1 TTC-TTCAATTTCAA
*
753 TTCTTCAAATTCAA
1 TTCTTCAATTTCAA
*
767 TCCTTCAATGCTTCAA
1 TTCTTCAAT--TTCAA
*
783 TGCTTCAATTTCAA
1 TTCTTCAATTTCAA
*
797 TACTTC----T--A
1 TTCTTCAATTTCAA
805 TTCTTCAATTTCAA
1 TTCTTCAATTTCAA
819 TTCTTCAAT
1 TTCTTCAAT
828 ACATCAATTT
Statistics
Matches: 203, Mismatches: 22, Indels: 64
0.70 0.08 0.22
Matches are distributed among these distances:
8 11 0.05
10 3 0.01
12 5 0.02
13 5 0.02
14 122 0.60
15 23 0.11
16 29 0.14
17 3 0.01
18 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.01, T:0.48
Consensus pattern (14 bp):
TTCTTCAATTTCAA
Found at i:585 original size:22 final size:22
Alignment explanation
Indices: 557--837 Score: 213
Period size: 22 Copynumber: 12.5 Consensus size: 22
547 AGTGTGGTCT
*
557 TTCTTCAATTTCAATTTTTCAA
1 TTCTTCAATTTCAATTCTTCAA
* * *
579 TTCTTCAAATTCAATCCTTTAA
1 TTCTTCAATTTCAATTCTTCAA
601 TGT-TTCAATTTCAATTCTT-AA
1 T-TCTTCAATTTCAATTCTTCAA
622 TAT-TTCAATTCTTCAA-T-TTCAA
1 T-TCTTCAA-T-TTCAATTCTTCAA
* *
644 TTCTTCAAATTCAATCCTTCAA
1 TTCTTCAATTTCAATTCTTCAA
666 TAT-TTCAATTTCAATTCTTCATA
1 T-TCTTCAATTTCAATTCTTCA-A
*
689 TTCAATCCTTCAATTTCAATTTTTCAA
1 -T---T-CTTCAATTTCAATTCTTCAA
*
716 TTTCTTCAAATTT-AATCCTTCAA
1 -TTCTTC-AATTTCAATTCTTCAA
739 -TCTTTCAATTTCAATTCTTCAA
1 TTC-TTCAATTTCAATTCTTCAA
* *
761 --ATTCAATCCTTCAATGCTTCAA
1 TTCTTCAAT--TTCAATTCTTCAA
* * *
783 TGCTTCAATTTCAATACTTCTA
1 TTCTTCAATTTCAATTCTTCAA
805 TTCTTCAATTTCAATTCTTCAA
1 TTCTTCAATTTCAATTCTTCAA
* *
827 TACATCAATTT
1 TTCTTCAATTT
838 ACTTCAACGA
Statistics
Matches: 213, Mismatches: 25, Indels: 42
0.76 0.09 0.15
Matches are distributed among these distances:
20 11 0.05
21 19 0.09
22 128 0.60
23 20 0.09
24 13 0.06
26 2 0.01
27 3 0.01
28 17 0.08
ACGTcount: A:0.30, C:0.21, G:0.01, T:0.48
Consensus pattern (22 bp):
TTCTTCAATTTCAATTCTTCAA
Found at i:617 original size:36 final size:35
Alignment explanation
Indices: 559--826 Score: 276
Period size: 36 Copynumber: 7.8 Consensus size: 35
549 TGTGGTCTTT
559 CTTCAA-TTTCAATTTTTCAATTCTTCAAATTCAATC
1 CTTCAATTTTCAA--TTTCAATTCTTCAAATTCAATC
*
595 CTTTAATGTTTCAATTTCAATTCTT--AA-T--AT-
1 CTTCAAT-TTTCAATTTCAATTCTTCAAATTCAATC
625 -TTCAATTCTTCAATTTCAATTCTTCAAATTCAATC
1 CTTCAATT-TTCAATTTCAATTCTTCAAATTCAATC
*
660 CTTCAATATTTCAATTTCAATTCTTCATATTCAATC
1 CTTCAAT-TTTCAATTTCAATTCTTCAAATTCAATC
*
696 CTTCAA-TTTCAATTTTTCAATTTCTTCAAATTTAATC
1 CTTCAATTTTCAA--TTTCAA-TTCTTCAAATTCAATC
733 CTTCAATCTTTCAATTTCAATTCTTCAAATTCAATC
1 CTTCAAT-TTTCAATTTCAATTCTTCAAATTCAATC
* * * *
769 CTTCAA--TGC---TTCAATGCTTCAATTTCAATA
1 CTTCAATTTTCAATTTCAATTCTTCAAATTCAATC
*
799 CTTCTATTCTTCAATTTCAATTCTTCAA
1 CTTCAATT-TTCAATTTCAATTCTTCAA
827 TACATCAATT
Statistics
Matches: 197, Mismatches: 13, Indels: 44
0.78 0.05 0.17
Matches are distributed among these distances:
28 1 0.01
29 21 0.11
30 23 0.12
31 4 0.02
32 1 0.01
33 5 0.03
34 10 0.05
36 93 0.47
37 27 0.14
38 6 0.03
39 6 0.03
ACGTcount: A:0.30, C:0.22, G:0.01, T:0.47
Consensus pattern (35 bp):
CTTCAATTTTCAATTTCAATTCTTCAAATTCAATC
Found at i:642 original size:73 final size:72
Alignment explanation
Indices: 559--775 Score: 299
Period size: 73 Copynumber: 3.1 Consensus size: 72
549 TGTGGTCTTT
* *
559 CTTCAATTTCAATTTTTCAATTCTTCAAATTCAATCCTTTAATGTTTCAATTTCAATTCTTAATA
1 CTTCAATTTCAATTTTTCAATTCTTCAAATTCAATCCTTCAATATTTCAATTTCAATTCTTAATA
624 TTTCAA--
66 -TTCAATC
*
630 -TTC---TTCAA--TTTCAATTCTTCAAATTCAATCCTTCAATATTTCAATTTCAATTCTTCATA
1 CTTCAATTTCAATTTTTCAATTCTTCAAATTCAATCCTTCAATATTTCAATTTCAATTCTTAATA
689 TTCAATC
66 TTCAATC
* *
696 CTTCAATTTCAATTTTTCAATTTCTTCAAATTTAATCCTTCAATCTTTCAATTTCAATTCTTCAA
1 CTTCAATTTCAATTTTTCAA-TTCTTCAAATTCAATCCTTCAATATTTCAATTTCAATTCTT-AA
761 -ATTCAATC
64 TATTCAATC
769 CTTCAAT
1 CTTCAAT
776 GCTTCAATGC
Statistics
Matches: 130, Mismatches: 6, Indels: 18
0.84 0.04 0.12
Matches are distributed among these distances:
64 5 0.04
65 48 0.37
67 8 0.06
70 8 0.06
72 6 0.05
73 54 0.42
74 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.00, T:0.48
Consensus pattern (72 bp):
CTTCAATTTCAATTTTTCAATTCTTCAAATTCAATCCTTCAATATTTCAATTTCAATTCTTAATA
TTCAATC
Found at i:876 original size:57 final size:56
Alignment explanation
Indices: 805--997 Score: 278
Period size: 56 Copynumber: 3.4 Consensus size: 56
795 AATACTTCTA
* *
805 TTCTTCAATTTCAATTCTTCAATACATCAATTTACTTCAACGATCTAGTGTGGTCT
1 TTCTTCAATTTCAATTCTTCAATGCATCAATTTACTTCAACGATCCAGTGTGGTCT
* * *
861 TTCTTCAATTTTCAATTTTTCAATGCTTCAATTTACTCCAACGATCCAGTGTGGTCT
1 TTCTTCAA-TTTCAATTCTTCAATGCATCAATTTACTTCAACGATCCAGTGTGGTCT
* * *
918 TTCTTCAATTTCAACTCTTCAATGCATCAATTTACTTCAACGATCCAGGGTGATCT
1 TTCTTCAATTTCAATTCTTCAATGCATCAATTTACTTCAACGATCCAGTGTGGTCT
*
974 TTCTTCAACTATTCAAATCTTCAA
1 TTCTTCAA-T-TTCAATTCTTCAA
998 AATATCCAAT
Statistics
Matches: 122, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
56 58 0.48
57 52 0.43
58 12 0.10
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.41
Consensus pattern (56 bp):
TTCTTCAATTTCAATTCTTCAATGCATCAATTTACTTCAACGATCCAGTGTGGTCT
Found at i:1070 original size:24 final size:24
Alignment explanation
Indices: 1043--1090 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1033 AGTGGTCTTC
* *
1043 CTTCAGTTCTTCCATGCTTCAATT
1 CTTCAATTCTTCAATGCTTCAATT
*
1067 CTTCAATTCTTCAATGCTTTAATT
1 CTTCAATTCTTCAATGCTTCAATT
1091 TACTACAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.21, C:0.25, G:0.06, T:0.48
Consensus pattern (24 bp):
CTTCAATTCTTCAATGCTTCAATT
Found at i:1090 original size:16 final size:16
Alignment explanation
Indices: 1043--1081 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1033 AGTGGTCTTC
* *
1043 CTTCAGTTCTTCCATG
1 CTTCAATTCTTCAATG
*
1059 CTTCAATTCTTCAATT
1 CTTCAATTCTTCAATG
1075 CTTCAAT
1 CTTCAAT
1082 GCTTTAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.21, C:0.28, G:0.05, T:0.46
Consensus pattern (16 bp):
CTTCAATTCTTCAATG
Found at i:1173 original size:20 final size:20
Alignment explanation
Indices: 1148--1188 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1138 GAAACAGGCC
1148 ATCTTTTCAGCATTTATCAA
1 ATCTTTTCAGCATTTATCAA
1168 ATCTTTTCAGCATTTATCAA
1 ATCTTTTCAGCATTTATCAA
1188 A
1 A
1189 GTTGGTTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.44
Consensus pattern (20 bp):
ATCTTTTCAGCATTTATCAA
Found at i:1204 original size:59 final size:59
Alignment explanation
Indices: 1112--1224 Score: 217
Period size: 59 Copynumber: 1.9 Consensus size: 59
1102 TACAGCTCAT
*
1112 TTTTCAGCGTTTATCAAAGTTGGTTGGAAACAGGCCATCTTTTCAGCATTTATCAAATC
1 TTTTCAGCATTTATCAAAGTTGGTTGGAAACAGGCCATCTTTTCAGCATTTATCAAATC
1171 TTTTCAGCATTTATCAAAGTTGGTTGGAAACAGGCCATCTTTTCAGCATTTATC
1 TTTTCAGCATTTATCAAAGTTGGTTGGAAACAGGCCATCTTTTCAGCATTTATC
1225 GAAGTTGGTT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.38
Consensus pattern (59 bp):
TTTTCAGCATTTATCAAAGTTGGTTGGAAACAGGCCATCTTTTCAGCATTTATCAAATC
Found at i:1516 original size:39 final size:39
Alignment explanation
Indices: 1168--1517 Score: 522
Period size: 39 Copynumber: 9.0 Consensus size: 39
1158 CATTTATCAA
*
1168 ATCTTTTCAGCATTTATCAAAGTTGGTTGGAAACAGGCC
1 ATCTTTTCAGCATTTATCAAAGTTGGTTGGAAACAGGTC
*
1207 ATCTTTTCAGCATTTATCGAAGTTGGTTGGAAACAGGTC
1 ATCTTTTCAGCATTTATCAAAGTTGGTTGGAAACAGGTC
* *
1246 ATCTTTTCAGCATTTATCGAAGTTGGTTGGAAACAGGCC
1 ATCTTTTCAGCATTTATCAAAGTTGGTTGGAAACAGGTC
* *
1285 ATCTTTTCAGCATTTATCGAAGTTGGTTGGAAACAGGCC
1 ATCTTTTCAGCATTTATCAAAGTTGGTTGGAAACAGGTC
* *
1324 ATCTTTTCAGCATTTATCGAAGTTGGTTGGAAACAGGCC
1 ATCTTTTCAGCATTTATCAAAGTTGGTTGGAAACAGGTC
**
1363 ATCTTTTCAGCATTTATCAAAGTTGACTGGAAACAGGTC
1 ATCTTTTCAGCATTTATCAAAGTTGGTTGGAAACAGGTC
**
1402 ATCTTTTCAGCATTTATCAAAG-TGACTGGAAACAGGTC
1 ATCTTTTCAGCATTTATCAAAGTTGGTTGGAAACAGGTC
* * * **
1440 CTCTTTTTAGCGTTTATCAAAGTTGACTGGAAACAGGTC
1 ATCTTTTCAGCATTTATCAAAGTTGGTTGGAAACAGGTC
**
1479 ATCTTTTCAGCATTTATCAAAGTTGACTGGAAACAGGTC
1 ATCTTTTCAGCATTTATCAAAGTTGGTTGGAAACAGGTC
1518 TTGGTTGGAA
Statistics
Matches: 297, Mismatches: 13, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
38 35 0.12
39 262 0.88
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.34
Consensus pattern (39 bp):
ATCTTTTCAGCATTTATCAAAGTTGGTTGGAAACAGGTC
Found at i:1553 original size:56 final size:56
Alignment explanation
Indices: 1467--1573 Score: 178
Period size: 56 Copynumber: 1.9 Consensus size: 56
1457 CAAAGTTGAC
* *
1467 TGGAAACAGGTCATCTTTTCAGCATTTATCAAAGTTGACTGGAAACAGGTCTTGGT
1 TGGAAACAGGCCATCTTTTCAGCATTTATCAAAGTTGACTAGAAACAGGTCTTGGT
* *
1523 TGGAAACATGCCATCTTTTCAGCATTTATCAAAGTTGACTAGAAACGGGTC
1 TGGAAACAGGCCATCTTTTCAGCATTTATCAAAGTTGACTAGAAACAGGTC
1574 ATTTTTTCAG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 47 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (56 bp):
TGGAAACAGGCCATCTTTTCAGCATTTATCAAAGTTGACTAGAAACAGGTCTTGGT
Found at i:1729 original size:33 final size:35
Alignment explanation
Indices: 1657--1727 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 35
1647 TGTCTTTATC
* *
1657 TTTCAATTTCAGACCTCAGACAGGTCTTTCTTAGT
1 TTTCAATGTCAGACCACAGACAGGTCTTTCTTAGT
*
1692 TTTCAATGTC-GACCACAGACTGGTC-TTCTTCAGT
1 TTTCAATGTCAGACCACAGACAGGTCTTTCTT-AGT
1726 TT
1 TT
1728 CAGACCTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 5 0.16
34 18 0.56
35 9 0.28
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.39
Consensus pattern (35 bp):
TTTCAATGTCAGACCACAGACAGGTCTTTCTTAGT
Found at i:2123 original size:36 final size:37
Alignment explanation
Indices: 2073--2144 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 37
2063 CATTTATAAG
*
2073 GCTACTTTCTCTTCCATCAT-GAACCAACTGGCTTGA
1 GCTACTTTCCCTTCCATCATCGAACCAACTGGCTTGA
** *
2109 GCTACTTTCCCTTCCATTTTCGAACCAATTGGCTTG
1 GCTACTTTCCCTTCCATCATCGAACCAACTGGCTTG
2145 GAACTCTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 17 0.55
37 14 0.45
ACGTcount: A:0.19, C:0.31, G:0.14, T:0.36
Consensus pattern (37 bp):
GCTACTTTCCCTTCCATCATCGAACCAACTGGCTTGA
Found at i:2251 original size:72 final size:72
Alignment explanation
Indices: 2166--2315 Score: 237
Period size: 72 Copynumber: 2.1 Consensus size: 72
2156 CCTGTTGCAT
* * *
2166 TTGGACTTATATTGCGTCAAGTGGGCTGATCATTTCTTGGCATTGTCTGCTTGGGCTTGTATTGT
1 TTGGACTTATATTGCGTCAAGTGGGCTGATCATTTCTTGGCATTATCTGATTGGCCTTGTATTGT
2231 TAACATC
66 TAACATC
* *
2238 TTGGACTTATATTGCTTCAAGTGGGCTGATCATTTCTTGGCATTATTTGATTGGCCTTGTATTGT
1 TTGGACTTATATTGCGTCAAGTGGGCTGATCATTTCTTGGCATTATCTGATTGGCCTTGTATTGT
*
2303 TAACGTC
66 TAACATC
*
2310 CTGGAC
1 TTGGAC
2316 CTTGGGTCTT
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.17, C:0.17, G:0.24, T:0.42
Consensus pattern (72 bp):
TTGGACTTATATTGCGTCAAGTGGGCTGATCATTTCTTGGCATTATCTGATTGGCCTTGTATTGT
TAACATC
Done.