Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011970.1 Corchorus olitorius cultivar O-4 contig12003, 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: 11455
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2962 original size:41 final size:40
Alignment explanation
Indices: 2876--3034 Score: 103
Period size: 41 Copynumber: 4.0 Consensus size: 40
2866 AGGGTTTATG
* * * *
2876 TTGT-AAA-TTAGGGTTTCAGATGAAA-GAAATTCAGGGCT
1 TTGTGAAATTTAGGGTTTCTGATGAAATAAAATT-GGGGAT
*
2914 TTTTGAAATTATAGGGTTTCTGATGAAATAAAATTGGGGAT
1 TTGTGAAATT-TAGGGTTTCTGATGAAATAAAATTGGGGAT
*** * * *
2955 TTGTGAAATTT-TCTTTTCCTTATGAAATGAAATTGGCGGGT
1 TTGTGAAATTTAGGGTTT-CTGATGAAATAAAATTGG-GGAT
* * *
2996 TTGTTAAATTTTAGGGTTTATGAT-AAAAATAAATTGGGG
1 TTGTGAAA-TTTAGGGTTTCTGATGAAATA-AAATTGGGG
3035 TTGTTTTGTT
Statistics
Matches: 92, Mismatches: 20, Indels: 15
0.72 0.16 0.12
Matches are distributed among these distances:
38 3 0.03
39 6 0.07
40 18 0.20
41 44 0.48
42 18 0.20
43 3 0.03
ACGTcount: A:0.32, C:0.05, G:0.24, T:0.39
Consensus pattern (40 bp):
TTGTGAAATTTAGGGTTTCTGATGAAATAAAATTGGGGAT
Found at i:4532 original size:18 final size:18
Alignment explanation
Indices: 4509--4543 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4499 ACAAAAATTG
4509 AAATTGTTCATAAACAAA
1 AAATTGTTCATAAACAAA
*
4527 AAATTGTTCATGAACAA
1 AAATTGTTCATAAACAA
4544 TATAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (18 bp):
AAATTGTTCATAAACAAA
Found at i:4779 original size:35 final size:35
Alignment explanation
Indices: 4733--4807 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
4723 TTATATAAAC
*
4733 GAACACTTAAATGAACAATAAACGAGTCTGTTCGT
1 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
4768 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
1 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
4803 GAACA
1 GAACA
4808 TAAACGAACT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (35 bp):
GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
Found at i:5064 original size:3 final size:3
Alignment explanation
Indices: 5056--5117 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
5046 TTCCTTTGCT
5056 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5104 ATA ATA ATA ATA AT
1 ATA ATA ATA ATA AT
5118 CTTCCATTCC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:6601 original size:112 final size:113
Alignment explanation
Indices: 6402--6659 Score: 430
Period size: 112 Copynumber: 2.3 Consensus size: 113
6392 TGTAGCCATA
*
6402 AGTGCCTTTCCTTGTTGATGATTCTGGCCTATGTAGCCCATTGAAAAAAAAATCTATATTTTAAC
1 AGTGCCCTTCCTTGTTGATGATTCTGGCCTATGTAGCCCATTGAAAAAAAAATCTATATTTTAAC
*
6467 TTGGAGTGAGTGCACCCTTAGGAGTGCTGCACTAGTTGCACCTTCAGG
66 TTGGAGTGAGTGCACCCTTAGGAGTGCTGCACTAGTTGCACCTCCAGG
* *
6515 AGTGCCCTTCCTTGTTGATGATTCTGGCCTATGTAGCTCATT-AAAAAAAAATCTATATTTTGAC
1 AGTGCCCTTCCTTGTTGATGATTCTGGCCTATGTAGCCCATTGAAAAAAAAATCTATATTTTAAC
* *
6579 TTGGAGTGAGTGCACCCTTAGGAGTGTTGCACTGGTTGCACCTCCAGG
66 TTGGAGTGAGTGCACCCTTAGGAGTGCTGCACTAGTTGCACCTCCAGG
*
6627 AGTGCCCTTCCTTGTTGAT-ACTTCTAGCCTATG
1 AGTGCCCTTCCTTGTTGATGA-TTCTGGCCTATG
6660 CAACTTAAAA
Statistics
Matches: 137, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
111 1 0.01
112 96 0.70
113 40 0.29
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (113 bp):
AGTGCCCTTCCTTGTTGATGATTCTGGCCTATGTAGCCCATTGAAAAAAAAATCTATATTTTAAC
TTGGAGTGAGTGCACCCTTAGGAGTGCTGCACTAGTTGCACCTCCAGG
Found at i:7110 original size:25 final size:25
Alignment explanation
Indices: 7075--7163 Score: 79
Period size: 25 Copynumber: 3.4 Consensus size: 25
7065 GGTATTTGCA
*
7075 ATGTGGTATTCGCGACGTCAAAGGC
1 ATGTGGCATTCGCGACGTCAAAGGC
* * ***
7100 ATGTGGCATTCGCGATGTGGTATTTGC
1 ATGTGGCATTCGCGACGT--CAAAGGC
* *
7127 AATGTGGTATTCGCGACGTCAAAGAC
1 -ATGTGGCATTCGCGACGTCAAAGGC
7153 ATGTGGCATTC
1 ATGTGGCATTC
7164 ACGATATGAC
Statistics
Matches: 47, Mismatches: 14, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
25 26 0.55
26 2 0.04
27 3 0.06
28 16 0.34
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.29
Consensus pattern (25 bp):
ATGTGGCATTCGCGACGTCAAAGGC
Found at i:7119 original size:14 final size:14
Alignment explanation
Indices: 7100--7142 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
7090 CGTCAAAGGC
*
7100 ATGTGGCATTCGCG
1 ATGTGGTATTCGCG
* *
7114 ATGTGGTATTTGCA
1 ATGTGGTATTCGCG
7128 ATGTGGTATTCGCG
1 ATGTGGTATTCGCG
7142 A
1 A
7143 CGTCAAAGAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.19, C:0.14, G:0.33, T:0.35
Consensus pattern (14 bp):
ATGTGGTATTCGCG
Found at i:7131 original size:53 final size:53
Alignment explanation
Indices: 7063--7300 Score: 228
Period size: 53 Copynumber: 4.5 Consensus size: 53
7053 AAGGCATGTG
7063 GTGGTATTTGCAATGTGGTATTCGCGACGTCAAAGGCATGTGGCATTCGCGAT
1 GTGGTATTTGCAATGTGGTATTCGCGACGTCAAAGGCATGTGGCATTCGCGAT
* *
7116 GTGGTATTTGCAATGTGGTATTCGCGACGTCAAAGACATGTGGCATTCACGAT
1 GTGGTATTTGCAATGTGGTATTCGCGACGTCAAAGGCATGTGGCATTCGCGAT
* ** * * * ** * * * *
7169 ATGACATTTGCGATGTCGTATTCGCAATTTCAAAAGCATGTAGCGTTCGC-TT
1 GTGGTATTTGCAATGTGGTATTCGCGACGTCAAAGGCATGTGGCATTCGCGAT
**** *** *
7221 CAAACATCAAAGGC-ATGTGGTATTCGCGACGTCAAAGGCATATGGCATTCGCGAT
1 --GTGGT-ATTTGCAATGTGGTATTCGCGACGTCAAAGGCATGTGGCATTCGCGAT
*
7276 GTGGTATTCGCAATGTGGTATTCGC
1 GTGGTATTTGCAATGTGGTATTCGC
7301 AATGTGGTAA
Statistics
Matches: 142, Mismatches: 38, Indels: 10
0.75 0.20 0.05
Matches are distributed among these distances:
52 4 0.03
53 102 0.72
54 32 0.23
55 4 0.03
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.30
Consensus pattern (53 bp):
GTGGTATTTGCAATGTGGTATTCGCGACGTCAAAGGCATGTGGCATTCGCGAT
Found at i:7255 original size:25 final size:25
Alignment explanation
Indices: 7227--7274 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
7217 GCTTCAAACA
* *
7227 TCAAAGGCATGTGGTATTCGCGACG
1 TCAAAGGCATATGGCATTCGCGACG
7252 TCAAAGGCATATGGCATTCGCGA
1 TCAAAGGCATATGGCATTCGCGA
7275 TGTGGTATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (25 bp):
TCAAAGGCATATGGCATTCGCGACG
Found at i:7286 original size:14 final size:14
Alignment explanation
Indices: 7267--7309 Score: 77
Period size: 14 Copynumber: 3.1 Consensus size: 14
7257 GGCATATGGC
*
7267 ATTCGCGATGTGGT
1 ATTCGCAATGTGGT
7281 ATTCGCAATGTGGT
1 ATTCGCAATGTGGT
7295 ATTCGCAATGTGGT
1 ATTCGCAATGTGGT
7309 A
1 A
7310 ATATAGTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.21, C:0.14, G:0.30, T:0.35
Consensus pattern (14 bp):
ATTCGCAATGTGGT
Found at i:7498 original size:42 final size:42
Alignment explanation
Indices: 7436--7517 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
7426 TGGTATATGA
* * **
7436 TACTCGCGATGTGGTATGGTATTCGCGATGCTAAAGGCATGG
1 TACTCGCGATATGGCATGGTATTCGCGACACTAAAGGCATGG
*
7478 TACTCGCGATATGGCGTGGTATTCGCGACACTAAAGGCAT
1 TACTCGCGATATGGCATGGTATTCGCGACACTAAAGGCAT
7518 TTGGCGTCGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (42 bp):
TACTCGCGATATGGCATGGTATTCGCGACACTAAAGGCATGG
Found at i:7836 original size:78 final size:77
Alignment explanation
Indices: 7714--7858 Score: 238
Period size: 78 Copynumber: 1.9 Consensus size: 77
7704 TCTTTCAATG
* *
7714 TCAATGTCAAAGGCATATGTGTTTGCGAGACTATCACCCTCTTTCAATGTC-AAAGACATATGGT
1 TCAATGTCAAAGGCATATGTGTTCGCGAAACTATCACCCTCTTTCAATGTCAAAAG-CATATGGT
7778 GTTTGTGCCTCTT
65 GTTTGTGCCTCTT
*
7791 TCAATGTGAAAGGCATATGGTGTTCGCGAAACTATCACCCTCTTTCAATGTCAAAAGCATATGGT
1 TCAATGTCAAAGGCATAT-GTGTTCGCGAAACTATCACCCTCTTTCAATGTCAAAAGCATATGGT
7856 GTT
65 GTT
7859 CGCGAGGTAC
Statistics
Matches: 63, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
77 17 0.27
78 42 0.67
79 4 0.06
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (77 bp):
TCAATGTCAAAGGCATATGTGTTCGCGAAACTATCACCCTCTTTCAATGTCAAAAGCATATGGTG
TTTGTGCCTCTT
Found at i:7961 original size:51 final size:50
Alignment explanation
Indices: 7881--8020 Score: 147
Period size: 51 Copynumber: 2.7 Consensus size: 50
7871 CCTCCTTCCA
* *
7881 ATGGTGTTAGCAAAGTCTCACCTGCTTCCAACATCT-TGAAGCCTCTTGCAT
1 ATGGTGTTAGCAAAATATCACCT-CTTCCAACAT-TATGAAGCCTCTTGCAT
* * * *
7932 ATGGTGTTCGCAAAATATCACCTCTTTCCAATATTATGAAGTCTTTTGCAT
1 ATGGTGTTAGCAAAATATCACCTC-TTCCAACATTATGAAGCCTCTTGCAT
* * * *
7983 ATGGTGTTTGCAACATATCACCTCCGTCCAATATTATG
1 ATGGTGTTAGCAAAATATCACCT-CTTCCAACATTATG
8021 TTATGAAGTT
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
50 2 0.03
51 74 0.96
52 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.35
Consensus pattern (50 bp):
ATGGTGTTAGCAAAATATCACCTCTTCCAACATTATGAAGCCTCTTGCAT
Found at i:8146 original size:31 final size:32
Alignment explanation
Indices: 8081--8168 Score: 115
Period size: 31 Copynumber: 2.8 Consensus size: 32
8071 ATGTCGAAGG
* *
8081 GTACATCCTCTTCCATATGGTGTTATCAAGAA
1 GTACACCCTCTTCCATATGGTGTTGTCAAGAA
* *
8113 GTACACCCTCTCCCATATGATGTTGT-AAGAA
1 GTACACCCTCTTCCATATGGTGTTGTCAAGAA
* *
8144 GTACACCATCTTCCACATGGTGTTG
1 GTACACCCTCTTCCATATGGTGTTG
8169 GCAAACTATC
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 26 0.54
32 22 0.46
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (32 bp):
GTACACCCTCTTCCATATGGTGTTGTCAAGAA
Found at i:8444 original size:72 final size:72
Alignment explanation
Indices: 8324--8489 Score: 278
Period size: 72 Copynumber: 2.3 Consensus size: 72
8314 TGCTCTGTTT
*
8324 TTGGCTATAATGCCGATGGCCTAAGTCGCCTAATAATTGGCTACAAAGCCGCTGGCCTTAGTCGC
1 TTGGCTATAATGCCGATGGCCTAAGTCGCCCAATAATTGGCTACAAAGCCGCTGGCCTTAGTCGC
8389 CCAATAC
66 CCAATAC
* *
8396 TTGGCTATAATGTCGATGGCCTAAGTCGCCCAATAATTGGCTATAAAGCCGCTGGCCTTAGTCGC
1 TTGGCTATAATGCCGATGGCCTAAGTCGCCCAATAATTGGCTACAAAGCCGCTGGCCTTAGTCGC
*
8461 CCAATAT
66 CCAATAC
* *
8468 TTGGCTATAATGCTGCTGGCCT
1 TTGGCTATAATGCCGATGGCCT
8490 TTGATGCCAT
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 87 1.00
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (72 bp):
TTGGCTATAATGCCGATGGCCTAAGTCGCCCAATAATTGGCTACAAAGCCGCTGGCCTTAGTCGC
CCAATAC
Found at i:8490 original size:36 final size:36
Alignment explanation
Indices: 8324--8490 Score: 226
Period size: 36 Copynumber: 4.6 Consensus size: 36
8314 TGCTCTGTTT
* * *
8324 TTGGCTATAATGCCGATGGCCTAAGTCGCCTAATAA
1 TTGGCTATAATGCCGCTGGCCTTAGTCGCCCAATAA
* * *
8360 TTGGCTACAAAGCCGCTGGCCTTAGTCGCCCAATAC
1 TTGGCTATAATGCCGCTGGCCTTAGTCGCCCAATAA
* * *
8396 TTGGCTATAATGTCGATGGCCTAAGTCGCCCAATAA
1 TTGGCTATAATGCCGCTGGCCTTAGTCGCCCAATAA
* *
8432 TTGGCTATAAAGCCGCTGGCCTTAGTCGCCCAATAT
1 TTGGCTATAATGCCGCTGGCCTTAGTCGCCCAATAA
*
8468 TTGGCTATAATGCTGCTGGCCTT
1 TTGGCTATAATGCCGCTGGCCTT
8491 TGATGCCATT
Statistics
Matches: 112, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 112 1.00
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (36 bp):
TTGGCTATAATGCCGCTGGCCTTAGTCGCCCAATAA
Found at i:9214 original size:48 final size:48
Alignment explanation
Indices: 9143--9353 Score: 356
Period size: 48 Copynumber: 4.5 Consensus size: 48
9133 CTCCAAGGCG
*
9143 TTGAACATGGGAGATACACAAATGGTTTTCACCATGACAAAGATCACA
1 TTGAACATAGGAGATACACAAATGGTTTTCACCATGACAAAGATCACA
*
9191 TTGAACATGGGAGATACACAAATGGTTTTCACCATGACAAAGATCACA
1 TTGAACATAGGAGATACACAAATGGTTTTCACCATGACAAAGATCACA
9239 TTGAACATAGGAGATACACAAATGGTTTTCACCATGACAAAGATCACA
1 TTGAACATAGGAGATACACAAATGGTTTTCACCATGACAAAGATCACA
*
9287 TTGAACATAGGAGATACACAAATGGTTTTCACCATGACAAAG-GCAC-
1 TTGAACATAGGAGATACACAAATGGTTTTCACCATGACAAAGATCACA
* *
9333 -TGAACATAAGATATACACAAA
1 TTGAACATAGGAGATACACAAA
9354 ATTATGAGAT
Statistics
Matches: 159, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
45 19 0.12
47 3 0.02
48 137 0.86
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (48 bp):
TTGAACATAGGAGATACACAAATGGTTTTCACCATGACAAAGATCACA
Found at i:10595 original size:13 final size:13
Alignment explanation
Indices: 10577--10621 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
10567 GTTACAAGAC
*
10577 GTATTGTCAGAGG
1 GTATTGTCAGAAG
*
10590 GTATTGAT-AAAAG
1 GTATTG-TCAGAAG
10603 GTATTGTCAGAAG
1 GTATTGTCAGAAG
10616 GTATTG
1 GTATTG
10622 ACACTATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 1 0.04
13 25 0.93
14 1 0.04
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.33
Consensus pattern (13 bp):
GTATTGTCAGAAG
Found at i:10834 original size:14 final size:14
Alignment explanation
Indices: 10815--10845 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
10805 AAAATAAGAG
10815 CTTACCGAAATTAA
1 CTTACCGAAATTAA
10829 CTTACCGAAATTAA
1 CTTACCGAAATTAA
10843 CTT
1 CTT
10846 CCTGACTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.39, C:0.23, G:0.06, T:0.32
Consensus pattern (14 bp):
CTTACCGAAATTAA
Done.