Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012887.1 Corchorus olitorius cultivar O-4 contig12920, 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: 35747
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:54 original size:22 final size:22
Alignment explanation
Indices: 29--86 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
19 CACACTATGG
*
29 AATTTTGATAACC-TCCTCATGA
1 AATTTTAATAACCAT-CTCATGA
* *
51 AATTATAATAACCATCTTATGA
1 AATTTTAATAACCATCTCATGA
73 AATTTTAATAACCA
1 AATTTTAATAACCA
87 CACAGAGACA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 30 0.97
23 1 0.03
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
AATTTTAATAACCATCTCATGA
Found at i:2683 original size:25 final size:25
Alignment explanation
Indices: 2637--2685 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
2627 AGACATGAAT
* *
2637 AAAAGGTCCAAATGCATAAAGGAAC
1 AAAAGGCCCAAATGCACAAAGGAAC
* *
2662 AAAAGGCCCAAGTGCACCAAGGAA
1 AAAAGGCCCAAATGCACAAAGGAA
2686 TTTAAAAGCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.49, C:0.20, G:0.22, T:0.08
Consensus pattern (25 bp):
AAAAGGCCCAAATGCACAAAGGAAC
Found at i:5080 original size:26 final size:26
Alignment explanation
Indices: 5044--5202 Score: 101
Period size: 27 Copynumber: 5.9 Consensus size: 26
5034 TTAAGAGTGG
**
5044 ACTTAAAATGACCAACGTGCCCCTGA
1 ACTTAAAATGACCAAAATGCCCCTGA
5070 ACTTAAAATGACCAAAATGCCCCTGA
1 ACTTAAAATGACCAAAATGCCCCTGA
* * *
5096 A-TGTGCAAATGACTAAAATGCCCCTGG
1 ACT-T-AAAATGACCAAAATGCCCCTGA
* *
5123 A-TGTGCAAATGACTAAAATGCCCCTGA
1 ACT-T-AAAATGACCAAAATGCCCCTGA
* **
5150 A-TGTGCAAATGATTAAAATGCCCCT-A
1 ACT-T-AAAATGACCAAAATGCCCCTGA
* *
5176 TATTTTGAAAATGACCGAAATGCCCCT
1 -A-CTT-AAAATGACCAAAATGCCCCT
5203 AGTTGATCCT
Statistics
Matches: 117, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
25 1 0.01
26 27 0.23
27 70 0.60
28 18 0.15
29 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.23
Consensus pattern (26 bp):
ACTTAAAATGACCAAAATGCCCCTGA
Found at i:5113 original size:27 final size:27
Alignment explanation
Indices: 5075--5174 Score: 173
Period size: 27 Copynumber: 3.7 Consensus size: 27
5065 CCTGAACTTA
*
5075 AAATGACCAAAATGCCCCTGAATGTGC
1 AAATGACTAAAATGCCCCTGAATGTGC
*
5102 AAATGACTAAAATGCCCCTGGATGTGC
1 AAATGACTAAAATGCCCCTGAATGTGC
5129 AAATGACTAAAATGCCCCTGAATGTGC
1 AAATGACTAAAATGCCCCTGAATGTGC
*
5156 AAATGATTAAAATGCCCCT
1 AAATGACTAAAATGCCCCT
5175 ATATTTTGAA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 69 1.00
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (27 bp):
AAATGACTAAAATGCCCCTGAATGTGC
Found at i:7831 original size:15 final size:16
Alignment explanation
Indices: 7800--7831 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
7790 CCTGTAAAGA
7800 ACAATTAATTCCTATC
1 ACAATTAATTCCTATC
7816 ACAATTAATT-CTATC
1 ACAATTAATTCCTATC
7831 A
1 A
7832 AGAAGGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.41, C:0.22, G:0.00, T:0.38
Consensus pattern (16 bp):
ACAATTAATTCCTATC
Found at i:10656 original size:24 final size:25
Alignment explanation
Indices: 10623--10669 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
10613 TTTTTAGTAG
*
10623 TTTATAAAGTTTTCAGAAACCTTGC
1 TTTATAAAGTTTTAAGAAACCTTGC
10648 TTTA-AAAGTTTTAAGAAACCTT
1 TTTATAAAGTTTTAAGAAACCTT
10670 ATAAACTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (25 bp):
TTTATAAAGTTTTAAGAAACCTTGC
Found at i:12619 original size:55 final size:54
Alignment explanation
Indices: 12558--12697 Score: 226
Period size: 55 Copynumber: 2.5 Consensus size: 54
12548 GTGCCACAAT
* * *
12558 TTAGGAGTTAATTTTGGATTTAAAATGAAATTTGCATTTAAGTATAGCTTGATAA
1 TTAGGAG-AAATTTTGGATCTAAAATGAAATTTGCATTTAAGTATAGCTTAATAA
12613 TTAGGAGAAGATTTTGGATCTAAAATGAAATTTGCATTTAAGTATAGCTTAATAA
1 TTAGGAGAA-ATTTTGGATCTAAAATGAAATTTGCATTTAAGTATAGCTTAATAA
12668 TTAGGAGAAAATTTTGGATCTAAAATGAAA
1 TTAGGAG-AAATTTTGGATCTAAAATGAAA
12698 GATTACATAG
Statistics
Matches: 80, Mismatches: 3, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
54 1 0.01
55 77 0.96
56 2 0.03
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.37
Consensus pattern (54 bp):
TTAGGAGAAATTTTGGATCTAAAATGAAATTTGCATTTAAGTATAGCTTAATAA
Found at i:12863 original size:2 final size:2
Alignment explanation
Indices: 12856--12900 Score: 63
Period size: 2 Copynumber: 21.0 Consensus size: 2
12846 TACAGTTTTA
12856 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT GAT AT GAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT -AT AT -AT
12899 AT
1 AT
12901 GATTTGTAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 34 0.85
3 6 0.15
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (2 bp):
AT
Found at i:13957 original size:26 final size:26
Alignment explanation
Indices: 13895--13962 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 26
13885 TTGTAGTTTC
13895 AAATGGTACAATTTTATTTTCACTAAAA
1 AAATGGTACAATTTTATTTTCAC--AAA
*
13923 AAAAGGTACAATTTTATTTGTGC-C-AA
1 AAATGGTACAATTTTATTT-T-CACAAA
13949 AAATGGTACAATTT
1 AAATGGTACAATTT
13963 GAGTATTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
26 15 0.42
28 18 0.50
29 2 0.06
30 1 0.03
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (26 bp):
AAATGGTACAATTTTATTTTCACAAA
Found at i:14387 original size:18 final size:18
Alignment explanation
Indices: 14364--14398 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
14354 CAGATGGTTA
*
14364 TAAAGTATGAAAATGATG
1 TAAAGTAGGAAAATGATG
*
14382 TAAAGTCGGAAAATGAT
1 TAAAGTAGGAAAATGAT
14399 TTGATCGATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.03, G:0.23, T:0.26
Consensus pattern (18 bp):
TAAAGTAGGAAAATGATG
Found at i:20084 original size:25 final size:25
Alignment explanation
Indices: 20055--20106 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
20045 AAGCTCAAAT
20055 AGGTTCATCCTGTTAGTTCAAACGG
1 AGGTTCATCCTGTTAGTTCAAACGG
20080 AGGTTCATCCTGTTAGTTCAAACGG
1 AGGTTCATCCTGTTAGTTCAAACGG
20105 AG
1 AG
20107 AGTGATTGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (25 bp):
AGGTTCATCCTGTTAGTTCAAACGG
Found at i:31933 original size:18 final size:17
Alignment explanation
Indices: 31910--32096 Score: 77
Period size: 18 Copynumber: 11.4 Consensus size: 17
31900 ATCCGGCAGA
31910 AAACAGGACCGAAAGGTC
1 AAACAGGACC-AAAGGTC
*
31928 AAACAGGACCAAGGGGTC
1 AAACAGGACCAA-AGGTC
*
31946 AAAACAGG--C--A--TA
1 -AAACAGGACCAAAGGTC
31958 AAACAGGACCGAAAGGTC
1 AAACAGGACC-AAAGGTC
31976 AAACAGGACCAAGAGGTC
1 AAACAGGACCAA-AGGTC
* *
31994 GAACAGG--C--A-G-A
1 AAACAGGACCAAAGGTC
*
32005 AAACATGACCAAAGAGGTC
1 AAACAGGACC-AA-AGGTC
*
32024 AAACAAGACCAAGAGGTC
1 AAACAGGACCAA-AGGTC
*
32042 AAACAGG--C--A-G-A
1 AAACAGGACCAAAGGTC
32053 AAACAGGACCAAAGAGGTC
1 AAACAGGACC-AA-AGGTC
*
32072 AAACAAGACCAAGAGGTC
1 AAACAGGACCAA-AGGTC
32090 AAACAGG
1 AAACAGG
32097 CAGAAAATAG
Statistics
Matches: 128, Mismatches: 15, Indels: 52
0.66 0.08 0.27
Matches are distributed among these distances:
11 19 0.15
12 3 0.02
13 5 0.04
16 3 0.02
17 7 0.05
18 66 0.52
19 25 0.20
ACGTcount: A:0.48, C:0.21, G:0.26, T:0.05
Consensus pattern (17 bp):
AAACAGGACCAAAGGTC
Found at i:31967 original size:48 final size:47
Alignment explanation
Indices: 31881--32121 Score: 324
Period size: 48 Copynumber: 5.1 Consensus size: 47
31871 AAGGGCAAAA
* *
31881 AAACAAGACCGAA-AGGTCAATCCGGCAGAAAACAGGACCGAAAGGTC
1 AAACAAGACC-AAGAGGTCAAACAGGCAGAAAACAGGACCGAAAGGTC
* * *
31928 AAACAGGACCAAGGGGTCAAAACAGGCATAAAACAGGACCGAAAGGTC
1 AAACAAGACCAAGAGGTC-AAACAGGCAGAAAACAGGACCGAAAGGTC
* * * *
31976 AAACAGGACCAAGAGGTCGAACAGGCAGAAAACATGACCAAAGAGGTC
1 AAACAAGACCAAGAGGTCAAACAGGCAGAAAACAGGACCGAA-AGGTC
*
32024 AAACAAGACCAAGAGGTCAAACAGGCAGAAAACAGGACCAAAGAGGTC
1 AAACAAGACCAAGAGGTCAAACAGGCAGAAAACAGGACCGAA-AGGTC
* *
32072 AAACAAGACCAAGAGGTCAAACAGGCAGAAAATA-GAACGAAAGGTC
1 AAACAAGACCAAGAGGTCAAACAGGCAGAAAACAGGACCGAAAGGTC
32118 AAAC
1 AAAC
32122 GGAGCAAACT
Statistics
Matches: 175, Mismatches: 16, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
46 11 0.06
47 38 0.22
48 126 0.72
ACGTcount: A:0.48, C:0.21, G:0.25, T:0.06
Consensus pattern (47 bp):
AAACAAGACCAAGAGGTCAAACAGGCAGAAAACAGGACCGAAAGGTC
Found at i:32033 original size:19 final size:18
Alignment explanation
Indices: 32005--32094 Score: 86
Period size: 18 Copynumber: 5.3 Consensus size: 18
31995 AACAGGCAGA
*
32005 AAACATGACCAAAGAGGTC
1 AAACAAGACC-AAGAGGTC
32024 AAACAAGACCAAGAGGTC
1 AAACAAGACCAAGAGGTC
*
32042 AAAC-AG-GC-AGA----
1 AAACAAGACCAAGAGGTC
*
32053 AAACAGGACCAAAGAGGTC
1 AAACAAGACC-AAGAGGTC
32072 AAACAAGACCAAGAGGTC
1 AAACAAGACCAAGAGGTC
32090 AAACA
1 AAACA
32095 GGCAGAAAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
11 4 0.07
12 1 0.02
13 1 0.02
15 6 0.10
16 1 0.02
17 2 0.03
18 25 0.43
19 18 0.31
ACGTcount: A:0.51, C:0.21, G:0.22, T:0.06
Consensus pattern (18 bp):
AAACAAGACCAAGAGGTC
Found at i:32044 original size:96 final size:95
Alignment explanation
Indices: 31881--32121 Score: 317
Period size: 95 Copynumber: 2.5 Consensus size: 95
31871 AAGGGCAAAA
* * * * *
31881 AAACAAGACCGAA-AGGTCAATCCGGCAGAAAACAGGACCGAAAGGTCAAACAGGACCAAGGGGT
1 AAACAAGACC-AAGAGGTCAAACAGGCAGAAAACAGGACCAAAAGGTCAAACAAGACCAAGAGGT
* *
31945 CAAAACAGGCATAAAACAGGACCGAA-AGGTC
65 C-AAACAGGCAGAAAACAGGACCAAAGAGGTC
* * *
31976 AAACAGGACCAAGAGGTCGAACAGGCAGAAAACATGACCAAAGAGGTCAAACAAGACCAAGAGGT
1 AAACAAGACCAAGAGGTCAAACAGGCAGAAAACAGGACCAAA-AGGTCAAACAAGACCAAGAGGT
32041 CAAACAGGCAGAAAACAGGACCAAAGAGGTC
65 CAAACAGGCAGAAAACAGGACCAAAGAGGTC
* * *
32072 AAACAAGACCAAGAGGTCAAACAGGCAGAAAATA-GAACGAAAGGTCAAAC
1 AAACAAGACCAAGAGGTCAAACAGGCAGAAAACAGGACCAAAAGGTCAAAC
32122 GGAGCAAACT
Statistics
Matches: 128, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
94 11 0.09
95 60 0.47
96 57 0.45
ACGTcount: A:0.48, C:0.21, G:0.25, T:0.06
Consensus pattern (95 bp):
AAACAAGACCAAGAGGTCAAACAGGCAGAAAACAGGACCAAAAGGTCAAACAAGACCAAGAGGTC
AAACAGGCAGAAAACAGGACCAAAGAGGTC
Found at i:32655 original size:13 final size:13
Alignment explanation
Indices: 32637--32674 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
32627 CTCATGGAGG
32637 TCAAAGTCAACTC
1 TCAAAGTCAACTC
**
32650 TCAAAGTCAACGG
1 TCAAAGTCAACTC
32663 TCAAAGTCAACT
1 TCAAAGTCAACT
32675 AGATGATGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.39, C:0.26, G:0.13, T:0.21
Consensus pattern (13 bp):
TCAAAGTCAACTC
Found at i:32711 original size:29 final size:28
Alignment explanation
Indices: 32667--32746 Score: 97
Period size: 28 Copynumber: 2.8 Consensus size: 28
32657 CAACGGTCAA
* *
32667 AGTCAACTAGATGATGTGGCATGTTGACCC
1 AGTCAAC-GGATGATGTGGCAGGTTGA-CC
*
32697 AGTCAACGGATGATGTGGCAGGTTGACT
1 AGTCAACGGATGATGTGGCAGGTTGACC
* *
32725 GGTCAACGGATGACGTGGCAGG
1 AGTCAACGGATGATGTGGCAGG
32747 AAGATGTGGC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
28 21 0.47
29 17 0.38
30 7 0.16
ACGTcount: A:0.25, C:0.17, G:0.35, T:0.23
Consensus pattern (28 bp):
AGTCAACGGATGATGTGGCAGGTTGACC
Found at i:34998 original size:32 final size:30
Alignment explanation
Indices: 34956--35019 Score: 83
Period size: 32 Copynumber: 2.1 Consensus size: 30
34946 AAATTAATGG
* * *
34956 AACAATATATTTACCCTTGCCAATTTACATGA
1 AACAACATATTTACCCATG-CAA-TCACATGA
34988 AACAACATATTTACCCATGCAATCACATGA
1 AACAACATATTTACCCATGCAATCACATGA
35018 AA
1 AA
35020 TTACATCCGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 9 0.31
31 3 0.10
32 17 0.59
ACGTcount: A:0.42, C:0.23, G:0.06, T:0.28
Consensus pattern (30 bp):
AACAACATATTTACCCATGCAATCACATGA
Found at i:35485 original size:112 final size:110
Alignment explanation
Indices: 35290--35506 Score: 321
Period size: 112 Copynumber: 2.0 Consensus size: 110
35280 ATTTTCTGAA
* **
35290 TTAATTAAATTTTAAATATTTCAATCTAGTCGTTAGGGACACATGTCACCTTTCTAGACCTGTAC
1 TTAATTAAATTTTAAATATTTCAATCTAGTCGTTAGGGACACATGTCACCCTTCTAGACCTACAC
* * *
35355 GTGCAGTTTGCTAAACTCCACTAACGGTGTATTAAATAATTTTCC
66 ATGCAGTTTGCTAAACTCCACTAACGGTGAATCAAATAATTTTCC
35400 TTAATTAAATTATT-AATATTTCAATCTAGTC-TCTAAGGAGACACATGTCACCCTTCTAGACCT
1 TTAATTAAATT-TTAAATATTTCAATCTAGTCGT-T-AGG-GACACATGTCACCCTTCTAGACCT
*
35463 ACACATGCAGTTTGCTAAACTCCACTGACGGTGAATCAAATAAT
62 ACACATGCAGTTTGCTAAACTCCACTAACGGTGAATCAAATAAT
35507 AATTCTAGAT
Statistics
Matches: 96, Mismatches: 7, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
109 1 0.01
110 29 0.30
111 5 0.05
112 61 0.64
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (110 bp):
TTAATTAAATTTTAAATATTTCAATCTAGTCGTTAGGGACACATGTCACCCTTCTAGACCTACAC
ATGCAGTTTGCTAAACTCCACTAACGGTGAATCAAATAATTTTCC
Done.