Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019085.1 Corchorus olitorius cultivar O-4 contig19118, 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: 15038
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Found at i:2687 original size:32 final size:32
Alignment explanation
Indices: 2646--2706 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
2636 AAATATGTTT
*
2646 GAAAAATAAGGATATAATGGTCGATTCAATTA
1 GAAAAATAAGGATATAATAGTCGATTCAATTA
*
2678 GAAAAATAAGGGTATAATAGTCGATTCAA
1 GAAAAATAAGGATATAATAGTCGATTCAA
2707 AAGTTTTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.48, C:0.07, G:0.20, T:0.26
Consensus pattern (32 bp):
GAAAAATAAGGATATAATAGTCGATTCAATTA
Found at i:2965 original size:59 final size:58
Alignment explanation
Indices: 2902--3027 Score: 150
Period size: 57 Copynumber: 2.2 Consensus size: 58
2892 GTAAAAATTT
* * *
2902 TCAAATAAGTATCTAAAGAAA-AAAATGTTCAAATAAGGACCCAACATTACG-AAAATTGC
1 TCAAATAAGTA-ATAAAAAAACAAAATGCTCAAATAAGGACCCAACATT--GTAAAATTGC
* **
2961 TCAAATAAG-AATAAAAAAACAAAATGCTCAAATCAGGGTCCAACATTGTAAAATTGC
1 TCAAATAAGTAATAAAAAAACAAAATGCTCAAATAAGGACCCAACATTGTAAAATTGC
3018 TCAAATAAGT
1 TCAAATAAGT
3028 CACTGTCGTC
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
56 1 0.02
57 24 0.41
58 24 0.41
59 9 0.16
ACGTcount: A:0.51, C:0.15, G:0.12, T:0.22
Consensus pattern (58 bp):
TCAAATAAGTAATAAAAAAACAAAATGCTCAAATAAGGACCCAACATTGTAAAATTGC
Found at i:3215 original size:28 final size:30
Alignment explanation
Indices: 3175--3242 Score: 122
Period size: 28 Copynumber: 2.3 Consensus size: 30
3165 AATGTTGGGT
3175 CCTTATTTGAGTATTTTTTTTCTTT-GG-C
1 CCTTATTTGAGTATTTTTTTTCTTTGGGAC
3203 CCTTATTTGAGTATTTTTTTTCTTTGGGAC
1 CCTTATTTGAGTATTTTTTTTCTTTGGGAC
3233 CCTTATTTGA
1 CCTTATTTGA
3243 ACATTTTCGT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
28 25 0.66
29 2 0.05
30 11 0.29
ACGTcount: A:0.13, C:0.15, G:0.15, T:0.57
Consensus pattern (30 bp):
CCTTATTTGAGTATTTTTTTTCTTTGGGAC
Found at i:3717 original size:57 final size:56
Alignment explanation
Indices: 3629--3743 Score: 221
Period size: 57 Copynumber: 2.0 Consensus size: 56
3619 TATCTGTTTC
3629 CTTTCACACAATAAATGTTATAATAAATCATATCCCCTCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCATATCCCC-CTATCTCTACTTAATTATT
3686 CTTTCACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTATT
3742 CT
1 CT
3744 ACAAAATAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
56 21 0.36
57 37 0.64
ACGTcount: A:0.35, C:0.23, G:0.02, T:0.40
Consensus pattern (56 bp):
CTTTCACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTATT
Found at i:3834 original size:21 final size:21
Alignment explanation
Indices: 3810--3876 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
3800 AAGGCTTAGG
3810 ATTTGAGTTGAGTATTTCTTA
1 ATTTGAGTTGAGTATTTCTTA
*** * *
3831 ATTT-A-CAAAGAATTTTCTATG
1 ATTTGAGTTGAGTA-TTTCT-TA
3852 ATTTGAGTTGAGTATTTCTTA
1 ATTTGAGTTGAGTATTTCTTA
3873 ATTT
1 ATTT
3877 ATAGAGAATT
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
19 3 0.09
20 6 0.19
21 14 0.44
22 6 0.19
23 3 0.09
ACGTcount: A:0.28, C:0.06, G:0.15, T:0.51
Consensus pattern (21 bp):
ATTTGAGTTGAGTATTTCTTA
Found at i:3868 original size:42 final size:42
Alignment explanation
Indices: 3809--3889 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
3799 TAAGGCTTAG
3809 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
* *
3851 GATTTGAGTTGAGTATTTCTTAATTTATAGAGAATTTTC
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
3890 AAGACTTAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.30, C:0.06, G:0.16, T:0.48
Consensus pattern (42 bp):
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Found at i:8293 original size:16 final size:16
Alignment explanation
Indices: 8264--8306 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
8254 ACCGGTCATT
8264 TTCCAATT-AAAATTA
1 TTCCAATTAAAAATTA
8279 TTCCAATTAAAAATTA
1 TTCCAATTAAAAATTA
*
8295 TTCAAATTAAAA
1 TTCCAATTAAAA
8307 TGCACCCCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 8 0.31
16 18 0.69
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (16 bp):
TTCCAATTAAAAATTA
Found at i:8380 original size:13 final size:13
Alignment explanation
Indices: 8362--8393 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
8352 TGCTACATGA
8362 CCCTCCAAGTTGT
1 CCCTCCAAGTTGT
*
8375 CCCTCCAATTTGT
1 CCCTCCAAGTTGT
8388 CCCTCC
1 CCCTCC
8394 TGACGTGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.12, C:0.47, G:0.09, T:0.31
Consensus pattern (13 bp):
CCCTCCAAGTTGT
Found at i:8544 original size:41 final size:41
Alignment explanation
Indices: 8493--8574 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
8483 TTTATAATTA
*
8493 GGGGCTAAACCTGGATTTAATTTCTTACCTTAATTATTAGG
1 GGGGCTAAACCTGAATTTAATTTCTTACCTTAATTATTAGG
* *
8534 GGGGCTAAACCTGAATTTAATTTGTTTCCTTAATTATTAGG
1 GGGGCTAAACCTGAATTTAATTTCTTACCTTAATTATTAGG
8575 AGGGTTAAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (41 bp):
GGGGCTAAACCTGAATTTAATTTCTTACCTTAATTATTAGG
Found at i:8591 original size:13 final size:13
Alignment explanation
Indices: 8573--8609 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
8563 TTAATTATTA
*
8573 GGAGGGTTAAGTT
1 GGAGGGTTAAATT
*
8586 GGAGGGATAAATT
1 GGAGGGTTAAATT
8599 GGAGGGTTAAA
1 GGAGGGTTAAA
8610 AAGAATTATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.43, T:0.24
Consensus pattern (13 bp):
GGAGGGTTAAATT
Found at i:10118 original size:15 final size:14
Alignment explanation
Indices: 10092--10135 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
10082 TGCCGGCTCC
10092 TATTATCTAATTAAT
1 TATTA-CTAATTAAT
10107 ATATTACTAATTAAT
1 -TATTACTAATTAAT
*
10122 TAATTAATAATTAA
1 T-ATTACTAATTAA
10136 AGGTTTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 1 0.04
15 20 0.77
16 5 0.19
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (14 bp):
TATTACTAATTAAT
Found at i:11515 original size:47 final size:48
Alignment explanation
Indices: 11455--11562 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
11445 CCTCGAAAAT
* * ** * * * *
11455 ATGGTTAGTCTTTGGA-TTTAGTCCATTTTTGGCATCTAAAAGGCGTG
1 ATGGTTAGCCTTTGAATTTTAGAACAATTTTGACACCTAAAAGCCGTG
* *
11502 ATGGTTAGCCTTTGAATTTTCGAACAATTTTGACACCTGAAAGCCGTG
1 ATGGTTAGCCTTTGAATTTTAGAACAATTTTGACACCTAAAAGCCGTG
11550 ATGGTTAGCCTTT
1 ATGGTTAGCCTTT
11563 CGGTAAATTT
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
47 14 0.28
48 36 0.72
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (48 bp):
ATGGTTAGCCTTTGAATTTTAGAACAATTTTGACACCTAAAAGCCGTG
Found at i:11693 original size:48 final size:45
Alignment explanation
Indices: 11629--11801 Score: 134
Period size: 48 Copynumber: 3.6 Consensus size: 45
11619 TTGGCCACCA
* *
11629 AAAGTCGTGATTGTTAGCCTTTTGATTTTCGACCAATTTTTATCCTCG
1 AAAGTCGTGATGGTTAG-CTTTTGATTTTAGA-CAATTTTTA-CCTCG
* **
11677 AAAGTCGTGATGGTTAGCTTTTGGATTTTAGGTC-ATATTTGGCCTCCG
1 AAAGTCGTGATGGTTAGCTTTT-GATTTTA-GACAAT-TTTTACCT-CG
* * *
11725 ATAGTCGTGATGTTTAGCATTTGAATTTTAGGACAATTTTGGTACC-CG
1 AAAGTCGTGATGGTTAGCTTTTG-ATTTTA-GACAATTTT--TACCTCG
* *
11773 AAAGTCGTGATGGATAGCCTTTAGATTTT
1 AAAGTCGTGATGGTTAG-CTTTTGATTTT
11802 TTGTCAATAT
Statistics
Matches: 100, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
47 11 0.11
48 80 0.80
49 7 0.07
50 2 0.02
ACGTcount: A:0.23, C:0.14, G:0.23, T:0.40
Consensus pattern (45 bp):
AAAGTCGTGATGGTTAGCTTTTGATTTTAGACAATTTTTACCTCG
Found at i:11829 original size:48 final size:46
Alignment explanation
Indices: 11675--11935 Score: 147
Period size: 48 Copynumber: 5.5 Consensus size: 46
11665 TTTTTATCCT
* * * *
11675 CGAAAGTCGTGATGGTTAGCTTTTGGATTTTAGGTCATATTTG-GCCTC
1 CGAAAGTCGTGATGGATAGCCTTTAGATTTTTGGT-A-ATTTGAGCC-C
* ** * * * *
11723 CGATAGTCGTGATGTTTAGCATTT-GAATTTTAGGACAATTTTG-GTACC
1 CGAAAGTCGTGATGGATAGCCTTTAG-ATTTTTGG-TAA-TTTGAG-CCC
*
11771 CGAAAGTCGTGATGGATAGCCTTTAGATTTTTTGTCAATATTG-GCCTC
1 CGAAAGTCGTGATGGATAGCCTTTAGATTTTTGGT-AAT-TTGAGCC-C
* * * * * *
11819 TGAAATTCGTGATTGACAGCCTTTGGCTTTTTGGTAATTTGAGCCC
1 CGAAAGTCGTGATGGATAGCCTTTAGATTTTTGGTAATTTGAGCCC
* * * *
11865 CAAAAGTCGTGATGGTTAGCCTTTA-ACTTTTCGGTAAATTT-TGCCC
1 CGAAAGTCGTGATGGATAGCCTTTAGA-TTTTTGGT-AATTTGAGCCC
* *
11911 CTGAAAGTCATGATGGTTAGCCTTT
1 C-GAAAGTCGTGATGGATAGCCTTT
11936 GACTTTTCGG
Statistics
Matches: 169, Mismatches: 32, Indels: 25
0.75 0.14 0.11
Matches are distributed among these distances:
46 34 0.20
47 36 0.21
48 97 0.57
49 2 0.01
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.38
Consensus pattern (46 bp):
CGAAAGTCGTGATGGATAGCCTTTAGATTTTTGGTAATTTGAGCCC
Found at i:12174 original size:19 final size:19
Alignment explanation
Indices: 12139--12183 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
12129 TGAAATTAAT
12139 TAATTA-TTAATTAAATAA
1 TAATTATTTAATTAAATAA
* *
12157 TAATTATTTTATTGAATAA
1 TAATTATTTAATTAAATAA
*
12176 TCATTATT
1 TAATTATT
12184 AAAAATACCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (19 bp):
TAATTATTTAATTAAATAA
Found at i:14063 original size:48 final size:47
Alignment explanation
Indices: 13977--14104 Score: 118
Period size: 48 Copynumber: 2.7 Consensus size: 47
13967 TTGCCATCCG
* * *
13977 AAAGTCTTAATGGTTAGCTTTAAGATTTTCAGAGAATTTT-GGCACCC-A
1 AAAGTCTTTATGGTTAGCTTTGA-ATTTTCA-ACAATTTTAGGC-CCCGA
*
14025 AAAGTCTTTATGGTTAGCATTTGAATTTTCAACCAATTTTAGTCCCCGA
1 AAAGTCTTTATGGTTAGC-TTTGAATTTTCAA-CAATTTTAGGCCCCGA
* * *
14074 ATA-TCGTTATGGTTAGCCTTTGGATTTTCAA
1 AAAGTCTTTATGGTTAG-CTTTGAATTTTCAA
14105 TCATTTTTTG
Statistics
Matches: 68, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
47 1 0.01
48 57 0.84
49 10 0.15
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (47 bp):
AAAGTCTTTATGGTTAGCTTTGAATTTTCAACAATTTTAGGCCCCGA
Found at i:14478 original size:48 final size:48
Alignment explanation
Indices: 14390--14515 Score: 148
Period size: 48 Copynumber: 2.6 Consensus size: 48
14380 TTGACCCCCA
* * * * *
14390 AAAGTCGTGATGTTTAGCATTTGGCTTTTTGGTA-AATTTTTTTCC-TCG
1 AAAGTCGTGATGGTTAGCCTTTGGATTTTT-G-ACAATTTTTTACCGGCG
*
14438 AAAGTCGTGATGGTTAGCCTTTGGATTTTTGACCATTTTTTACCGGCG
1 AAAGTCGTGATGGTTAGCCTTTGGATTTTTGACAATTTTTTACCGGCG
* *
14486 AAAGTCGTGATAGTTAACCTTTGGATTTTT
1 AAAGTCGTGATGGTTAGCCTTTGGATTTTT
14516 AGTTAATTTT
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
46 1 0.01
47 10 0.15
48 57 0.84
ACGTcount: A:0.21, C:0.13, G:0.22, T:0.44
Consensus pattern (48 bp):
AAAGTCGTGATGGTTAGCCTTTGGATTTTTGACAATTTTTTACCGGCG
Found at i:14821 original size:47 final size:45
Alignment explanation
Indices: 14728--14877 Score: 140
Period size: 47 Copynumber: 3.2 Consensus size: 45
14718 CCAAAAATCG
* * *
14728 TGATGGTTAGCCTTTAGATTTTCGGGCCAATTTTCACCTCGAAAGTCA
1 TGATGGTTAGCCTTT-GCTTTTC-GGCCAATTTGCCCCT-GAAAGTCA
*
14776 TGATGGTTAGCCTTTGCCTTTTCGGCCAATTTGGCCCCTGAAAGTCG
1 TGATGGTTAGCCTTTG-CTTTTCGGCCAATTT-GCCCCTGAAAGTCA
* * * * *
14823 TTATGGTTAGCCTTTAACTTTTTGGTCAATTTCGCCCCCGAAAGTCGA
1 TGATGGTTAGCCTTT-GCTTTTCGGCCAATTT-GCCCCTGAAAGTC-A
14871 T-ATGGTT
1 TGATGGTT
14878 GGCTTTTCAA
Statistics
Matches: 87, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
47 62 0.71
48 25 0.29
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (45 bp):
TGATGGTTAGCCTTTGCTTTTCGGCCAATTTGCCCCTGAAAGTCA
Found at i:14932 original size:47 final size:47
Alignment explanation
Indices: 14881--15026 Score: 127
Period size: 47 Copynumber: 3.1 Consensus size: 47
14871 TATGGTTGGC
* *
14881 TTTTCAATCATTTTTTCC-CTCGAAAGTCATGATGGTTAGCCTTTGTA
1 TTTTCAATCATTTTTTCCTC-CGAAAGTCGTGATGGTTAGCCTTTGAA
* * * * * * * *
14928 TTTTCAGTTATTTTTTGCTACCAAAAATTGTGATGGTTAACCTTTGGA
1 TTTTCAATCATTTTTTCCT-CCGAAAGTCGTGATGGTTAGCCTTTGAA
* *
14976 -TTT-ATTCCATTTTTTGCCTCCGAAAGTCGTGATGGTTAGTCTTTGAA
1 TTTTCAAT-CATTTTTT-CCTCCGAAAGTCGTGATGGTTAGCCTTTGAA
15023 TTTT
1 TTTT
15027 TGGACAATTT
Statistics
Matches: 76, Mismatches: 18, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
46 2 0.03
47 47 0.62
48 26 0.34
49 1 0.01
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.47
Consensus pattern (47 bp):
TTTTCAATCATTTTTTCCTCCGAAAGTCGTGATGGTTAGCCTTTGAA
Done.