Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014463.1 Corchorus olitorius cultivar O-4 contig14496, 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: 51527
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:1880 original size:47 final size:47
Alignment explanation
Indices: 1826--2261 Score: 521
Period size: 47 Copynumber: 9.9 Consensus size: 47
1816 TCATATAGAA
1826 TGGTTAATCTAGTTAATAAAATCTTAACGGCCATACATAATGGTTAT
1 TGGTTAATCTAGTTAATAAAATCTTAACGGCCATACATAATGGTTAT
*
1873 TGATTAATCTAGTTAATAAAATCTTAACGGCCATACATAATGGTTAT
1 TGGTTAATCTAGTTAATAAAATCTTAACGGCCATACATAATGGTTAT
* * *
1920 TGATTAATCTAGTTAATAAAATTTTAACGG---T-CATAA--G--AA
1 TGGTTAATCTAGTTAATAAAATCTTAACGGCCATACATAATGGTTAT
*
1959 TGGTTAATCTAGTTAATAAAATCTTAACGGCCATAC---A--G--AA
1 TGGTTAATCTAGTTAATAAAATCTTAACGGCCATACATAATGGTTAT
*
1999 TGGTTAATCTAGTTAATAAAATCTTAACGGCCATACAAAATGGTTAT
1 TGGTTAATCTAGTTAATAAAATCTTAACGGCCATACATAATGGTTAT
* *
2046 TGGTTAATCTAGTTAATAAAATCTTAACGGTCATAC---A--G--AA
1 TGGTTAATCTAGTTAATAAAATCTTAACGGCCATACATAATGGTTAT
* *
2086 TGGTTAATCTAGTTAATAAAATCTTAACGACCATACAAAATGGTTAT
1 TGGTTAATCTAGTTAATAAAATCTTAACGGCCATACATAATGGTTAT
*
2133 TGGTTAATCTAGTTAATAAAATCTTAACGGCCATACAGAATGGTTAT
1 TGGTTAATCTAGTTAATAAAATCTTAACGGCCATACATAATGGTTAT
* * * *
2180 TGGTTAATCTAGTTAATAAAATCTTAACGGCCTTATATAATTGTCA-
1 TGGTTAATCTAGTTAATAAAATCTTAACGGCCATACATAATGGTTAT
* * *
2226 ---TTAATTTAGTTAATAAAATTTTAACGGTCATA-ATAA
1 TGGTTAATCTAGTTAATAAAATCTTAACGGCCATACATAA
2262 AAACATATTA
Statistics
Matches: 349, Mismatches: 22, Indels: 41
0.85 0.05 0.10
Matches are distributed among these distances:
39 29 0.08
40 75 0.21
41 1 0.00
42 6 0.02
43 36 0.10
44 2 0.01
45 2 0.01
47 198 0.57
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (47 bp):
TGGTTAATCTAGTTAATAAAATCTTAACGGCCATACATAATGGTTAT
Found at i:2105 original size:87 final size:87
Alignment explanation
Indices: 1959--2211 Score: 425
Period size: 87 Copynumber: 2.8 Consensus size: 87
1949 GTCATAAGAA
1959 TGGTTAATCTAGTTAATAAAATCTTAACGGCCATACAGAATGGTTAATCTAGTTAATAAAATCTT
1 TGGTTAATCTAGTTAATAAAATCTTAACGGCCATACAGAATGGTTAATCTAGTTAATAAAATCTT
2024 AACGGCCATACAAAATGGTTAT
66 AACGGCCATACAAAATGGTTAT
*
2046 TGGTTAATCTAGTTAATAAAATCTTAACGGTCATACAGAATGGTTAATCTAGTTAATAAAATCTT
1 TGGTTAATCTAGTTAATAAAATCTTAACGGCCATACAGAATGGTTAATCTAGTTAATAAAATCTT
*
2111 AACGACCATACAAAATGGTTAT
66 AACGGCCATACAAAATGGTTAT
2133 TGGTTAATCTAGTTAATAAAATCTTAACGGCCATACAGAATGGTTATTGGTTAATCTAGTTAATA
1 TGGTTAATCTAGTTAATAAAATCTTAACGGCCATACAG-A-----A-TGGTTAATCTAGTTAATA
2198 AAATCTTAACGGCC
59 AAATCTTAACGGCC
2212 TTATATAATT
Statistics
Matches: 155, Mismatches: 4, Indels: 7
0.93 0.02 0.04
Matches are distributed among these distances:
87 122 0.79
88 1 0.01
93 1 0.01
94 31 0.20
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.33
Consensus pattern (87 bp):
TGGTTAATCTAGTTAATAAAATCTTAACGGCCATACAGAATGGTTAATCTAGTTAATAAAATCTT
AACGGCCATACAAAATGGTTAT
Found at i:3168 original size:159 final size:159
Alignment explanation
Indices: 2865--3211 Score: 617
Period size: 159 Copynumber: 2.2 Consensus size: 159
2855 AAGAAGCACT
*
2865 AAAGCTCTGTTTTAATACAGTGT-GACGCATGTGGTATAAGAAATTTCAAGAAAAGCTAATTTGC
1 AAAGCTCTGTTTTAATACAGTGTAG-CGCATGCGGTATAAGAAATTTCAAGAAAAGCTAATTTGC
*
2929 TTTAGCTTGCCTTGCCTTATGCCGCAGGCATTACACTGCATTCAAATACTGAGCTAATGTTATAT
65 TTTAGCTTGCCTTGCCTTATGCCGCAGGCATTACACTGCATTCAAATACTGAGCTAATGTTATAC
2994 CAAAAGGAGCGAATGAAGCAAATTACAAGG
130 CAAAAGGAGCGAATGAAGCAAATTACAAGG
*
3024 AAAGCTCTGTTTTAATACAGTGTAGCGCATGCGGTATAAGAAATTTCAAGAAAAGCTGATTTGCT
1 AAAGCTCTGTTTTAATACAGTGTAGCGCATGCGGTATAAGAAATTTCAAGAAAAGCTAATTTGCT
*
3089 TTAGCTTGCCTTGCCTTATGCCGCAGGCGTTACACTGCATTCAAATACTGAGCTAATGTTATACC
66 TTAGCTTGCCTTGCCTTATGCCGCAGGCATTACACTGCATTCAAATACTGAGCTAATGTTATACC
*
3154 -AAAGAGAGCTAATGAAGCAAATTACAAGG
131 AAAAG-GAGCGAATGAAGCAAATTACAAGG
3183 AAAGCTCTGTTTTAATACAGTGTAGCGCA
1 AAAGCTCTGTTTTAATACAGTGTAGCGCA
3212 ATGTTATACC
Statistics
Matches: 181, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
158 4 0.02
159 176 0.97
160 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (159 bp):
AAAGCTCTGTTTTAATACAGTGTAGCGCATGCGGTATAAGAAATTTCAAGAAAAGCTAATTTGCT
TTAGCTTGCCTTGCCTTATGCCGCAGGCATTACACTGCATTCAAATACTGAGCTAATGTTATACC
AAAAGGAGCGAATGAAGCAAATTACAAGG
Found at i:3238 original size:67 final size:68
Alignment explanation
Indices: 3143--3278 Score: 265
Period size: 67 Copynumber: 2.0 Consensus size: 68
3133 ATACTGAGCT
3143 AATGTTATACCAAAGAGAGCTAATGAAGCAAATTACAAGGAAAGCTCTGTTTTAATACAGTGTAG
1 AATGTTATACCAAAGAGAGCTAATGAAGCAAATTACAAGGAAAGCTCTGTTTTAATACAGTGTAG
3208 CGC
66 CGC
3211 AATGTTATACCAAA-AGAGCTAATGAAGCAAATTACAAGGAAAGCTCTGTTTTAATACAGTGTAG
1 AATGTTATACCAAAGAGAGCTAATGAAGCAAATTACAAGGAAAGCTCTGTTTTAATACAGTGTAG
3275 CGC
66 CGC
3278 A
1 A
3279 TGCGGTATAA
Statistics
Matches: 68, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
67 54 0.79
68 14 0.21
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (68 bp):
AATGTTATACCAAAGAGAGCTAATGAAGCAAATTACAAGGAAAGCTCTGTTTTAATACAGTGTAG
CGC
Found at i:3399 original size:226 final size:227
Alignment explanation
Indices: 2984--3437 Score: 883
Period size: 226 Copynumber: 2.0 Consensus size: 227
2974 ATACTGAGCT
*
2984 AATGTTATATCAAAAGGAGCGAATGAAGCAAATTACAAGGAAAGCTCTGTTTTAATACAGTGTAG
1 AATGTTATACCAAAAGGAGCGAATGAAGCAAATTACAAGGAAAGCTCTGTTTTAATACAGTGTAG
3049 CGCATGCGGTATAAGAAATTTCAAGAAAAGCTGATTTGCTTTAGCTTGCCTTGCCTTATGCCGCA
66 CGCATGCGGTATAAGAAATTTCAAGAAAAGCTGATTTGCTTTAGCTTGCCTTGCCTTATGCCGCA
3114 GGCGTTACACTGCATTCAAATACTGAGCTAATGTTATACCAAAGAGAGCTAATGAAGCAAATTAC
131 GGCGTTACACTGCATTCAAATACTGAGCTAATGTTATACCAAAGAGAGCTAATGAAGCAAATTAC
3179 AAGGAAAGCTCTGTTTTAATACAGTGTAGCGC
196 AAGGAAAGCTCTGTTTTAATACAGTGTAGCGC
*
3211 AATGTTATACCAAAA-GAGCTAATGAAGCAAATTACAAGGAAAGCTCTGTTTTAATACAGTGTAG
1 AATGTTATACCAAAAGGAGCGAATGAAGCAAATTACAAGGAAAGCTCTGTTTTAATACAGTGTAG
3275 CGCATGCGGTATAAGAAATTTCAAGAAAAGCTGATTTGCTTTAGCTTGCCTTGCCTTATGCCGCA
66 CGCATGCGGTATAAGAAATTTCAAGAAAAGCTGATTTGCTTTAGCTTGCCTTGCCTTATGCCGCA
3340 GGCGTTACACTGCATTCAAATACTGAGCTAATGTTATACCAAAGAGAGCTAATGAAGCAAATTAC
131 GGCGTTACACTGCATTCAAATACTGAGCTAATGTTATACCAAAGAGAGCTAATGAAGCAAATTAC
3405 AAGGAAAGCTCTGTTTTAATACAGTGTAGCGC
196 AAGGAAAGCTCTGTTTTAATACAGTGTAGCGC
3437 A
1 A
3438 TGCGGTATAA
Statistics
Matches: 225, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
226 211 0.94
227 14 0.06
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (227 bp):
AATGTTATACCAAAAGGAGCGAATGAAGCAAATTACAAGGAAAGCTCTGTTTTAATACAGTGTAG
CGCATGCGGTATAAGAAATTTCAAGAAAAGCTGATTTGCTTTAGCTTGCCTTGCCTTATGCCGCA
GGCGTTACACTGCATTCAAATACTGAGCTAATGTTATACCAAAGAGAGCTAATGAAGCAAATTAC
AAGGAAAGCTCTGTTTTAATACAGTGTAGCGC
Found at i:3514 original size:159 final size:158
Alignment explanation
Indices: 3211--3531 Score: 624
Period size: 159 Copynumber: 2.0 Consensus size: 158
3201 AGTGTAGCGC
3211 AATGTTATACCAAAAGAGCTAATGAAGCAAATTACAAGGAAAGCTCTGTTTTAATACAGTGTAGC
1 AATGTTATACCAAAAGAGCTAATGAAGCAAATTACAAGGAAAGCTCTGTTTTAATACAGTGTAGC
3276 GCATGCGGTATAAGAAATTTCAAGAAAAGCTGATTTGCTTTAGCTTGCCTTGCCTTATGCCGCAG
66 GCATGCGGTATAAGAAATTTCAAGAAAAGCTGATTTGCTTTAGCTTGCCTTGCCTTATGCCGCAG
3341 GCGTTACACTGCATTCAAATACTGAGCT
131 GCGTTACACTGCATTCAAATACTGAGCT
3369 AATGTTATACCAAAGAGAGCTAATGAAGCAAATTACAAGGAAAGCTCTGTTTTAATACAGTGTAG
1 AATGTTATACCAAA-AGAGCTAATGAAGCAAATTACAAGGAAAGCTCTGTTTTAATACAGTGTAG
*
3434 CGCATGCGGTATAAGAAATTTCAAGAAAAGCTGATTTGCTTTAGCTTGTCTTGCCTTATGCCGCA
65 CGCATGCGGTATAAGAAATTTCAAGAAAAGCTGATTTGCTTTAGCTTGCCTTGCCTTATGCCGCA
3499 GGCGTTACACTGCATTCAAATACTGAGCT
130 GGCGTTACACTGCATTCAAATACTGAGCT
3528 AATG
1 AATG
3532 AAGGATTCTC
Statistics
Matches: 161, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
158 14 0.09
159 147 0.91
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.29
Consensus pattern (158 bp):
AATGTTATACCAAAAGAGCTAATGAAGCAAATTACAAGGAAAGCTCTGTTTTAATACAGTGTAGC
GCATGCGGTATAAGAAATTTCAAGAAAAGCTGATTTGCTTTAGCTTGCCTTGCCTTATGCCGCAG
GCGTTACACTGCATTCAAATACTGAGCT
Found at i:5331 original size:84 final size:84
Alignment explanation
Indices: 5040--5322 Score: 422
Period size: 84 Copynumber: 3.4 Consensus size: 84
5030 ACCAAAACAG
* * *
5040 ATAGGTCGGGCACCTATTTGACCTTTTCCGGTGATTAAATAGGTGCCCGACCTATCCATCTTGGA
1 ATAGGTCAGACACCTATTTGACCTTTTCCGGTGATTAAATAGGTGCCCGACCTATCCGTCTTGGA
* * *
5105 TTTAATTGACCCAAATCGT
66 CTTAATTGGCCCAGATCGT
* * * * * * * *
5124 ATAGGTCGGATACTTATTTGACATTTTCTGGTGATTAAATAGATGTCCGACCTATCCGTTTTTGG
1 ATAGGTCAGACACCTATTTGACCTTTTCCGGTGATTAAATAGGTGCCCGACCTATCCG-TCTTGG
5189 ACTTAATTGGCCCAGATCGT
65 ACTTAATTGGCCCAGATCGT
5209 ATAGGTCAGACACCTATTTGACCTTTTCCGGTGATTAAATAGGTGCCCGACCTATCCGTCTTGGA
1 ATAGGTCAGACACCTATTTGACCTTTTCCGGTGATTAAATAGGTGCCCGACCTATCCGTCTTGGA
*
5274 GTTAATTGGCCCAGATCGT
66 CTTAATTGGCCCAGATCGT
5293 ATAGGTCAGACACCTATTTGACCTTTTCCG
1 ATAGGTCAGACACCTATTTGACCTTTTCCG
5323 AACATTAAAC
Statistics
Matches: 177, Mismatches: 21, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
84 104 0.59
85 73 0.41
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (84 bp):
ATAGGTCAGACACCTATTTGACCTTTTCCGGTGATTAAATAGGTGCCCGACCTATCCGTCTTGGA
CTTAATTGGCCCAGATCGT
Found at i:21559 original size:24 final size:24
Alignment explanation
Indices: 21523--21569 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
21513 GCATATAGTC
*
21523 AGATACTAGAGAACAGTATGTAAA
1 AGATACTAAAGAACAGTATGTAAA
21547 AGATACTAAAGAACAGTATGTAA
1 AGATACTAAAGAACAGTATGTAA
21570 GAAAAAGACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.51, C:0.09, G:0.19, T:0.21
Consensus pattern (24 bp):
AGATACTAAAGAACAGTATGTAAA
Found at i:34689 original size:17 final size:17
Alignment explanation
Indices: 34663--34695 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
34653 TTAGATTAAT
34663 GTTTCTTTTTG-GTTTG
1 GTTTCTTTTTGAGTTTG
34679 GTTTCCTTTTTGAGTTT
1 GTTT-CTTTTTGAGTTT
34696 TGACATTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 7 0.47
18 4 0.27
ACGTcount: A:0.03, C:0.09, G:0.21, T:0.67
Consensus pattern (17 bp):
GTTTCTTTTTGAGTTTG
Found at i:42533 original size:5 final size:5
Alignment explanation
Indices: 42508--42567 Score: 97
Period size: 5 Copynumber: 12.4 Consensus size: 5
42498 CCCTGATGCC
*
42508 AAAG- AAAG- AAAGA AAAAA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA
42556 AAAGA AAAGA AA
1 AAAGA AAAGA AA
42568 GGCTTCCTTG
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
4 8 0.15
5 45 0.85
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:48631 original size:26 final size:26
Alignment explanation
Indices: 48602--48651 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
48592 GATGACTAAG
48602 CAGAGAGTTGAAATTCAATTGCCAAT
1 CAGAGAGTTGAAATTCAATTGCCAAT
* *
48628 CAGAGAGTTGATATTCGATTGCCA
1 CAGAGAGTTGAAATTCAATTGCCA
48652 TTCTTTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (26 bp):
CAGAGAGTTGAAATTCAATTGCCAAT
Done.