Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020557.1 Corchorus olitorius cultivar O-4 contig20590, 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: 21837
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Found at i:2757 original size:25 final size:25
Alignment explanation
Indices: 2721--2770 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
2711 TTAGTGGATT
2721 AAATCAGATTTGAGCTACATGAATG
1 AAATCAGATTTGAGCTACATGAATG
*
2746 AAATCAGCTTTGAGCTACATGAATG
1 AAATCAGATTTGAGCTACATGAATG
2771 CAAAATACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (25 bp):
AAATCAGATTTGAGCTACATGAATG
Found at i:3424 original size:65 final size:66
Alignment explanation
Indices: 3319--3445 Score: 220
Period size: 65 Copynumber: 1.9 Consensus size: 66
3309 CTCGAGTTTA
* *
3319 GCTTGTGGAAAAGCCTATGTTGATAATTGACTTGTATGGAAATGAGCTTGGCTTGTGGAAAACGG
1 GCTTGTGGAAAAGCCTATGTTGATAATTGACTGGTATGGAAACGAGCTTGGCTTGTGGAAAACGG
3384 G
66 G
*
3385 GCTTGTGG-AAAGCCTATGTTGATAATTGACTGGTATGGAAACGAGTTTGGCTTGTGGAAAA
1 GCTTGTGGAAAAGCCTATGTTGATAATTGACTGGTATGGAAACGAGCTTGGCTTGTGGAAAA
3446 GCCTATGTTG
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
65 50 0.86
66 8 0.14
ACGTcount: A:0.28, C:0.10, G:0.31, T:0.31
Consensus pattern (66 bp):
GCTTGTGGAAAAGCCTATGTTGATAATTGACTGGTATGGAAACGAGCTTGGCTTGTGGAAAACGG
G
Found at i:3454 original size:50 final size:50
Alignment explanation
Indices: 3384--3553 Score: 315
Period size: 50 Copynumber: 3.4 Consensus size: 50
3374 TGGAAAACGG
*
3384 GGCTTGTGG-AAAGCCTATGTTGATAATTGACTGGTATGGAAACGAGTTT
1 GGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGTTT
3433 GGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGTTT
1 GGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGTTT
3483 GGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGTTT
1 GGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGTTT
*
3533 GGCTTATGGAAAAGCCTATGT
1 GGCTTGTGGAAAAGCCTATGT
3554 GGCTTGGATG
Statistics
Matches: 118, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
49 9 0.08
50 109 0.92
ACGTcount: A:0.28, C:0.12, G:0.29, T:0.32
Consensus pattern (50 bp):
GGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGTTT
Found at i:4927 original size:6 final size:7
Alignment explanation
Indices: 4912--4955 Score: 56
Period size: 7 Copynumber: 6.4 Consensus size: 7
4902 AGCTCAATTC
*
4912 TTTCCTT
1 TTTCATT
4919 TTTC-TT
1 TTTCATT
4925 TTTC-TT
1 TTTCATT
4931 TTTCATTT
1 TTTCA-TT
4939 TTTCATT
1 TTTCATT
4946 TTTCATT
1 TTTCATT
4953 TTT
1 TTT
4956 TTGTGCACTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
6 12 0.34
7 16 0.46
8 7 0.20
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTCATT
Found at i:4947 original size:15 final size:14
Alignment explanation
Indices: 4923--4956 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 14
4913 TTCCTTTTTC
4923 TTTTTCTTTTTCAT
1 TTTTTCTTTTTCAT
4937 TTTTTCATTTTTCAT
1 TTTTTC-TTTTTCAT
4952 TTTTT
1 TTTTT
4957 TGTGCACTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTCTTTTTCAT
Found at i:5266 original size:15 final size:15
Alignment explanation
Indices: 5246--5295 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
5236 CAATCAATTC
5246 TTTTTTATTTTGATT
1 TTTTTTATTTTGATT
**
5261 TTTTTTATACTGATT
1 TTTTTTATTTTGATT
*
5276 TTTGATT-TTTTG-TT
1 TTT-TTTATTTTGATT
5290 TTTTTT
1 TTTTTT
5296 TTGGAATTTC
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
13 2 0.07
14 5 0.18
15 19 0.68
16 2 0.07
ACGTcount: A:0.12, C:0.02, G:0.08, T:0.78
Consensus pattern (15 bp):
TTTTTTATTTTGATT
Found at i:5586 original size:13 final size:13
Alignment explanation
Indices: 5570--5612 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
5560 AGAAAACAAG
5570 TTTCGAAATCATT
1 TTTCGAAATCATT
5583 TTTCGAAATCAATT
1 TTTCGAAATC-ATT
*
5597 TTATCAAAATC-TT
1 TT-TCGAAATCATT
5610 TTT
1 TTT
5613 GTAAACCATG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 1 0.04
13 14 0.52
14 5 0.19
15 7 0.26
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.49
Consensus pattern (13 bp):
TTTCGAAATCATT
Found at i:5690 original size:7 final size:8
Alignment explanation
Indices: 5676--5711 Score: 65
Period size: 8 Copynumber: 4.6 Consensus size: 8
5666 AGTGCCTTTA
5676 ATTTTTTC
1 ATTTTTTC
5684 A-TTTTTC
1 ATTTTTTC
5691 ATTTTTTC
1 ATTTTTTC
5699 ATTTTTTC
1 ATTTTTTC
5707 ATTTT
1 ATTTT
5712 ATGGGAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (8 bp):
ATTTTTTC
Found at i:9552 original size:40 final size:40
Alignment explanation
Indices: 9405--9704 Score: 399
Period size: 40 Copynumber: 7.6 Consensus size: 40
9395 CTTCTGATGA
** * * *
9405 GGAAGGGCAAACTAAGAATTTAGACAACACTTTCCGGTAG
1 GGAAGGGCAAACTGGGTATTTAGACAACACCTTCCGGTGG
* * *
9445 GGAAAGACAAACT-GGTATTTAAACAACACCTTCCGGTGG
1 GGAAGGGCAAACTGGGTATTTAGACAACACCTTCCGGTGG
* *
9484 GGAAGGG-AAACT-TGTATTTAAACAACACCTTCCGGTGG
1 GGAAGGGCAAACTGGGTATTTAGACAACACCTTCCGGTGG
*
9522 GGAAGGGCAAATTGGGTATTTAGACAACACCTTCCGGTGG
1 GGAAGGGCAAACTGGGTATTTAGACAACACCTTCCGGTGG
* * *
9562 GGAAGGGTAAACTGGGTATTTAAACAACATCTTCCGGTGG
1 GGAAGGGCAAACTGGGTATTTAGACAACACCTTCCGGTGG
* * *
9602 GGAAGGACAAATTGGTTATTTAGACAACACCTTCCGGTGG
1 GGAAGGGCAAACTGGGTATTTAGACAACACCTTCCGGTGG
* *
9642 GGAAGGGCAAACTGGGTAATTAGACAACATCTTCCGGTGG
1 GGAAGGGCAAACTGGGTATTTAGACAACACCTTCCGGTGG
*
9682 GGAAGGGCAAACTGGGAATTTAG
1 GGAAGGGCAAACTGGGTATTTAG
9705 GCTAAACAAG
Statistics
Matches: 228, Mismatches: 30, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
38 37 0.16
39 30 0.13
40 161 0.71
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (40 bp):
GGAAGGGCAAACTGGGTATTTAGACAACACCTTCCGGTGG
Found at i:13555 original size:25 final size:25
Alignment explanation
Indices: 13519--13568 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
13509 TTAGTCGATT
13519 AAATCAGATTTGAGCTACATGAATG
1 AAATCAGATTTGAGCTACATGAATG
*
13544 AAATCAGCTTTGAGCTACATGAATG
1 AAATCAGATTTGAGCTACATGAATG
13569 CAAAATACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (25 bp):
AAATCAGATTTGAGCTACATGAATG
Found at i:13762 original size:26 final size:26
Alignment explanation
Indices: 13706--13803 Score: 83
Period size: 26 Copynumber: 3.6 Consensus size: 26
13696 AGTGGACTCC
* *
13706 AAATGACCAACATGCCCCTGAATATG-C
1 AAATGACCAA-ATG-CCCTGAATGTGAA
* *
13733 AAATGACCGAAATGCCCTTAGTGT-AA
1 AAATGACC-AAATGCCCTGAATGTGAA
13759 AAATGACCATAATGCCACTGAATGTGAA
1 AAATGACCA-AATGCC-CTGAATGTGAA
*
13787 AAATGATCAAAATGCCC
1 AAATGA-CCAAATGCCC
13804 CTGGATTTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
25 1 0.02
26 21 0.36
27 18 0.31
28 16 0.28
29 2 0.03
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.20
Consensus pattern (26 bp):
AAATGACCAAATGCCCTGAATGTGAA
Found at i:17247 original size:124 final size:123
Alignment explanation
Indices: 17005--17395 Score: 592
Period size: 124 Copynumber: 3.2 Consensus size: 123
16995 CTGATGCACA
* **
17005 ACGCCGCTATATATAATGTTTT-C-ATGAATACAAATTTGGTGAAACTAAAAAGGCCATTTCTTT
1 ACGCCGCTATATATAATGTTTTCCGA-GAATAGAAATTTGGTGAAACTAAAAACACCATTTCTTT
*
17068 GTTATGAATA-GGCGTTTCTCATGACAGACGCCGTTAAATAGTGGCGTTTCGATAGTAG
65 GTTATGAATACGGCGTTTCTCATGACAGACGCCGCTAAATAGTGGCGTTTCGATAGTAG
*
17126 ACGCCGCTATATATAATGTTTTCCGAGAATAGAAATTTGATGAAACTAAAAACACCATTTCTTTG
1 ACGCCGCTATATATAATGTTTTCCGAGAATAGAAATTTGGTGAAACTAAAAACACCATTTCTTTG
17191 TTATGAATAGCGGCGTTTCTCATGACAGACGCCGCTAAATAGTGGCGTTTCGATAGTAG
66 TTATGAATA-CGGCGTTTCTCATGACAGACGCCGCTAAATAGTGGCGTTTCGATAGTAG
*
17250 ACG-CGCTATATATAATGTTTTCCGAAGAATAGAAATGTGGTGAAACTAAAAACACCATTTCTTT
1 ACGCCGCTATATATAATGTTTTCCG-AGAATAGAAATTTGGTGAAACTAAAAACACCATTTCTTT
**** * *
17314 GTTATGAATAACGGCGTTTAGGGTGACAGACGCCGCTAAATAGTGGCATTTCGATAGTAA
65 GTTATGAAT-ACGGCGTTTCTCATGACAGACGCCGCTAAATAGTGGCGTTTCGATAGTAG
* *
17374 ACGCCGCTATATTTAATTTTTT
1 ACGCCGCTATATATAATGTTTT
17396 TCCGCTACAA
Statistics
Matches: 248, Mismatches: 15, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
121 22 0.09
122 45 0.18
123 22 0.09
124 142 0.57
125 17 0.07
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.32
Consensus pattern (123 bp):
ACGCCGCTATATATAATGTTTTCCGAGAATAGAAATTTGGTGAAACTAAAAACACCATTTCTTTG
TTATGAATACGGCGTTTCTCATGACAGACGCCGCTAAATAGTGGCGTTTCGATAGTAG
Found at i:21183 original size:33 final size:33
Alignment explanation
Indices: 21142--21270 Score: 213
Period size: 33 Copynumber: 3.9 Consensus size: 33
21132 AAAAAAACCA
* * * *
21142 AAATAGCGGCGTTTTTTATACAGAAACGCCATT
1 AAATAGCGGCGTTTCTTGTACGGAAACGCCACT
*
21175 AAATAGCGGCGTTTCTTGTACGGAAACGCCAGT
1 AAATAGCGGCGTTTCTTGTACGGAAACGCCACT
21208 AAATAGCGGCGTTTCTTGTACGGAAACGCCACT
1 AAATAGCGGCGTTTCTTGTACGGAAACGCCACT
21241 AAATAGCGGCGTTTCTTGTACGGAAACGCC
1 AAATAGCGGCGTTTCTTGTACGGAAACGCC
21271 GCCATTTGTA
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 91 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.26
Consensus pattern (33 bp):
AAATAGCGGCGTTTCTTGTACGGAAACGCCACT
Found at i:21502 original size:25 final size:25
Alignment explanation
Indices: 21474--21521 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
21464 TTTAAAAACA
21474 CCGCCATATGCAAAAAAAAAAAATG
1 CCGCCATATGCAAAAAAAAAAAATG
21499 CCGCCATATGCAAAAAAAAAAAA
1 CCGCCATATGCAAAAAAAAAAAA
21522 AAACGCCGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.58, C:0.21, G:0.10, T:0.10
Consensus pattern (25 bp):
CCGCCATATGCAAAAAAAAAAAATG
Found at i:21528 original size:25 final size:25
Alignment explanation
Indices: 21475--21528 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
21465 TTAAAAACAC
***
21475 CGCCATATGCAAAAAAAAAAAATGC
1 CGCCATATGCAAAAAAAAAAAAAAA
21500 CGCCATATGCAAAAAAAAAAAAAAA
1 CGCCATATGCAAAAAAAAAAAAAAA
21525 CGCC
1 CGCC
21529 GCTATATCAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.57, C:0.22, G:0.11, T:0.09
Consensus pattern (25 bp):
CGCCATATGCAAAAAAAAAAAAAAA
Found at i:21530 original size:28 final size:25
Alignment explanation
Indices: 21467--21521 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
21457 AGCGGCGTTT
*
21467 AAAAACACCGCCATATGCAAAAAAA
1 AAAAACGCCGCCATATGCAAAAAAA
*
21492 AAAAATGCCGCCATATGCAAAAAAA
1 AAAAACGCCGCCATATGCAAAAAAA
21517 AAAAA
1 AAAAA
21522 AAACGCCGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.62, C:0.20, G:0.09, T:0.09
Consensus pattern (25 bp):
AAAAACGCCGCCATATGCAAAAAAA
Done.