Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015615.1 Corchorus olitorius cultivar O-4 contig15648, 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: 45154
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:266 original size:15 final size:15
Alignment explanation
Indices: 248--278 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
238 ATTAAATTGG
*
248 TGACGGTTCAATTCA
1 TGACGATTCAATTCA
263 TGACGATTCAATTCA
1 TGACGATTCAATTCA
278 T
1 T
279 TATTGAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (15 bp):
TGACGATTCAATTCA
Found at i:2245 original size:18 final size:19
Alignment explanation
Indices: 2211--2248 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
2201 GTCTATCGTT
*
2211 ATCTCCATGGTCTCCATGC
1 ATCTCCATGGCCTCCATGC
2230 ATCTCCAT-GCCTCCATGC
1 ATCTCCATGGCCTCCATGC
2248 A
1 A
2249 GCCCATGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.18, C:0.39, G:0.13, T:0.29
Consensus pattern (19 bp):
ATCTCCATGGCCTCCATGC
Found at i:2330 original size:30 final size:30
Alignment explanation
Indices: 2294--2354 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 30
2284 TCTTCAAGTT
2294 CATGATAAGTCCTT-GGCGCATCATTCCCTC
1 CATGATAAG-CCTTGGGCGCATCATTCCCTC
2324 CATGATAAGCCTTGGGCGCATCATTCCCTC
1 CATGATAAGCCTTGGGCGCATCATTCCCTC
2354 C
1 C
2355 CCCTTGAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 4 0.13
30 26 0.87
ACGTcount: A:0.20, C:0.34, G:0.18, T:0.28
Consensus pattern (30 bp):
CATGATAAGCCTTGGGCGCATCATTCCCTC
Found at i:5611 original size:18 final size:19
Alignment explanation
Indices: 5577--5614 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
5567 GTCCATCGTT
*
5577 ATCTCCATGGTCTCCATGC
1 ATCTCCATGGCCTCCATGC
5596 ATCTCCAT-GCCTCCATGC
1 ATCTCCATGGCCTCCATGC
5614 A
1 A
5615 ACCCATGCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.18, C:0.39, G:0.13, T:0.29
Consensus pattern (19 bp):
ATCTCCATGGCCTCCATGC
Found at i:7499 original size:189 final size:184
Alignment explanation
Indices: 7182--7558 Score: 639
Period size: 189 Copynumber: 2.0 Consensus size: 184
7172 TAAATAGCCA
*
7182 CCTCCTATAACACAAATCATATACTTTACATACCTAGACACACATAATTTTCTCTTCATTTTCTT
1 CCTCCTATAACACAAATCATATACTTTACATACCTACACACACATAATTTTCTCTTCATTTTCTT
* *
7247 TAGATCTAGTTTTTTTAATCAAGGGTGCCGCCACCCTCTCTAGCCATAGAGGGGTGTGACATACC
66 TAGATCTAGTTTTTTTAATCAAGGGTGCCGCCACCCTCTCTAGCCATAGAGGAGTGCGACATACC
* *
7312 TAGGTATTTTGCTAGAAAATTTCGTCCCCTTCTAGTTCTGTAAGTATT-TATAAG
131 TAGATATTTTGCTAGAAAATTTCGTCCCCTTCTAGTTCTGTAACTATTCT-TAAG
7366 CCTCCTATAACACAAATCATATACTTTACATACCTACACACACATAATTTTCTCTTCATCTATTT
1 CCTCCTATAACACAAATCATATACTTTACATACCTACACACACATAATTTTCTC-T--TC-A-TT
7431 TTCTTTAGATCTAGTTTTTTTAATCAAGGGTGCCGCCACCCTCTCTAGCCATAGAGGAGTGCGAC
61 TTCTTTAGATCTAGTTTTTTTAATCAAGGGTGCCGCCACCCTCTCTAGCCATAGAGGAGTGCGAC
*
7496 ATACCTAGATATTTTGCTAGGAAATTTCGTCCCCTTCTAGTTCTGTAACTATTCTTAAG
126 ATACCTAGATATTTTGCTAGAAAATTTCGTCCCCTTCTAGTTCTGTAACTATTCTTAAG
7555 CCTC
1 CCTC
7559 TAATGGATTT
Statistics
Matches: 181, Mismatches: 6, Indels: 7
0.93 0.03 0.04
Matches are distributed among these distances:
184 53 0.29
185 1 0.01
187 2 0.01
188 1 0.01
189 123 0.68
190 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.36
Consensus pattern (184 bp):
CCTCCTATAACACAAATCATATACTTTACATACCTACACACACATAATTTTCTCTTCATTTTCTT
TAGATCTAGTTTTTTTAATCAAGGGTGCCGCCACCCTCTCTAGCCATAGAGGAGTGCGACATACC
TAGATATTTTGCTAGAAAATTTCGTCCCCTTCTAGTTCTGTAACTATTCTTAAG
Found at i:9055 original size:16 final size:16
Alignment explanation
Indices: 9004--9061 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 16
8994 AAGAAAAAAC
* * *
9004 AAAATAAAAGAAGATT
1 AAAAGAAAACAAGATG
* *
9020 AAAAGAAAAGAA-AAG
1 AAAAGAAAACAAGATG
9035 AAAAGAAAACAAGATG
1 AAAAGAAAACAAGATG
*
9051 AAAAGACAACA
1 AAAAGAAAACA
9062 GATTTTGAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
15 12 0.34
16 23 0.66
ACGTcount: A:0.72, C:0.05, G:0.16, T:0.07
Consensus pattern (16 bp):
AAAAGAAAACAAGATG
Found at i:10109 original size:20 final size:20
Alignment explanation
Indices: 10084--10123 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
10074 CTTGTTTGGT
10084 TGGAGGGTTTTGAAGGGGTG
1 TGGAGGGTTTTGAAGGGGTG
*
10104 TGGAGGGTTTTGGAGGGGTG
1 TGGAGGGTTTTGAAGGGGTG
10124 GGCCCTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.57, T:0.30
Consensus pattern (20 bp):
TGGAGGGTTTTGAAGGGGTG
Found at i:14939 original size:10 final size:10
Alignment explanation
Indices: 14924--14951 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
14914 ACATAATAAC
14924 ACCCCTCCTT
1 ACCCCTCCTT
14934 ACCCCTCCTT
1 ACCCCTCCTT
14944 ACCCCTCC
1 ACCCCTCC
14952 AATGAACCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.11, C:0.64, G:0.00, T:0.25
Consensus pattern (10 bp):
ACCCCTCCTT
Found at i:16137 original size:15 final size:14
Alignment explanation
Indices: 16112--16143 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
16102 AAGTAAATTC
16112 AAAGCAAAGAAAAG
1 AAAGCAAAGAAAAG
16126 AAAGCTAAAGAAAAG
1 AAAGC-AAAGAAAAG
16141 AAA
1 AAA
16144 ACGATACAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.03
Consensus pattern (14 bp):
AAAGCAAAGAAAAG
Found at i:18251 original size:11 final size:10
Alignment explanation
Indices: 18212--18270 Score: 57
Period size: 11 Copynumber: 5.8 Consensus size: 10
18202 TTGTTAATTC
18212 TAAAA-AAAA
1 TAAAAGAAAA
* *
18221 TAAATGAAGA
1 TAAAAGAAAA
*
18231 TAAAACAAAA
1 TAAAAGAAAA
18241 CTAAAAGAAAA
1 -TAAAAGAAAA
18252 TTAAAAGAAAA
1 -TAAAAGAAAA
*
18263 GAAAAGAA
1 TAAAAGAA
18271 TGGTAAAGAA
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
9 4 0.10
10 17 0.43
11 19 0.47
ACGTcount: A:0.75, C:0.03, G:0.10, T:0.12
Consensus pattern (10 bp):
TAAAAGAAAA
Found at i:21646 original size:13 final size:14
Alignment explanation
Indices: 21615--21648 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
21605 CTCCACCTGA
*
21615 TTTTTTGTGTATTC
1 TTTTTTGAGTATTC
21629 TTTTTTGAGTATTC
1 TTTTTTGAGTATTC
21643 TTTTTT
1 TTTTTT
21649 TCTTCCTAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.09, C:0.06, G:0.12, T:0.74
Consensus pattern (14 bp):
TTTTTTGAGTATTC
Found at i:22702 original size:21 final size:21
Alignment explanation
Indices: 22678--22720 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
22668 TCCATCTGGC
*
22678 ATGTAATTTTTTCATTTGTAA
1 ATGTAATTTTTGCATTTGTAA
22699 ATGTAATTTTTGCATTTGTAA
1 ATGTAATTTTTGCATTTGTAA
22720 A
1 A
22721 ACAACCACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.05, G:0.12, T:0.53
Consensus pattern (21 bp):
ATGTAATTTTTGCATTTGTAA
Found at i:23742 original size:49 final size:49
Alignment explanation
Indices: 23633--23736 Score: 181
Period size: 49 Copynumber: 2.1 Consensus size: 49
23623 CCTCACAAAC
23633 GATGATATTTGGTATCTGAGTCGTCTTTTGGGGTACTAACGATGTGAAT
1 GATGATATTTGGTATCTGAGTCGTCTTTTGGGGTACTAACGATGTGAAT
* *
23682 GGTGATATTTGGTATCTGAGTCGTCTTTTGGGGTACTAACGATGTGCACT
1 GATGATATTTGGTATCTGAGTCGTCTTTTGGGGTACTAACGATGTG-AAT
23732 GATGA
1 GATGA
23737 CTTTGGACCC
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
49 45 0.88
50 6 0.12
ACGTcount: A:0.21, C:0.12, G:0.30, T:0.38
Consensus pattern (49 bp):
GATGATATTTGGTATCTGAGTCGTCTTTTGGGGTACTAACGATGTGAAT
Found at i:25291 original size:31 final size:30
Alignment explanation
Indices: 25237--25311 Score: 105
Period size: 31 Copynumber: 2.5 Consensus size: 30
25227 AATTGCTGCT
*
25237 ATTTGAGGCTTGTTATGTTTGATTGTTACA
1 ATTTGAGGCTTGTTATGTGTGATTGTTACA
*
25267 ATTTGAGGCTTGATTATGTGTGATTGTTTCA
1 ATTTGAGGCTTG-TTATGTGTGATTGTTACA
* *
25298 GTTGGAGGCTTGTT
1 ATTTGAGGCTTGTT
25312 TAAGTTTCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 14 0.35
31 26 0.65
ACGTcount: A:0.17, C:0.07, G:0.28, T:0.48
Consensus pattern (30 bp):
ATTTGAGGCTTGTTATGTGTGATTGTTACA
Found at i:42847 original size:12 final size:13
Alignment explanation
Indices: 42830--42859 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
42820 CTTAAATCAA
42830 TTTTTTAAATTGT
1 TTTTTTAAATTGT
42843 TTTTTTAAATTGT
1 TTTTTTAAATTGT
42856 TTTT
1 TTTT
42860 GGAACTAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (13 bp):
TTTTTTAAATTGT
Found at i:44753 original size:34 final size:34
Alignment explanation
Indices: 44715--44808 Score: 120
Period size: 34 Copynumber: 2.8 Consensus size: 34
44705 AAAAATTGAA
**
44715 TGGGAACTTTCCCAATTTGAAAACTTAAAACCGG
1 TGGGAACTTTCCCAATTACAAAACTTAAAACCGG
* * *
44749 TGGGAACTTTCACGATTACAAAACTTAAAACTGG
1 TGGGAACTTTCCCAATTACAAAACTTAAAACCGG
*
44783 TGGGAACTTTTCCAA-TA-AAAACTTAA
1 TGGGAACTTTCCCAATTACAAAACTTAA
44809 TGATAATCTC
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
32 9 0.17
33 2 0.04
34 41 0.79
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (34 bp):
TGGGAACTTTCCCAATTACAAAACTTAAAACCGG
Done.