Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015101.1 Corchorus capsularis cultivar CVL-1 contig15122, 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: 39705
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:390 original size:2 final size:2
Alignment explanation
Indices: 383--411 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
373 ACGACGATTA
383 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
412 CACCTTACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1850 original size:15 final size:15
Alignment explanation
Indices: 1830--1864 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
1820 ATACTTGATT
1830 AGAAAGAGAAGGAAA
1 AGAAAGAGAAGGAAA
1845 AGAAAGAGAAGGAAA
1 AGAAAGAGAAGGAAA
1860 AGAAA
1 AGAAA
1865 AAGTCTAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (15 bp):
AGAAAGAGAAGGAAA
Found at i:3079 original size:2 final size:2
Alignment explanation
Indices: 3072--3103 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3062 AAAGATAAAA
3072 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3104 CAACTTCACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4158 original size:12 final size:11
Alignment explanation
Indices: 4125--4158 Score: 52
Period size: 10 Copynumber: 3.1 Consensus size: 11
4115 CTCGTTCTCC
4125 TTTTTTTTTT-
1 TTTTTTTTTTG
4135 TTTTTTTTTTG
1 TTTTTTTTTTG
4146 TTTTTTTTGTTG
1 TTTTTTTT-TTG
4158 T
1 T
4159 GTGTGTGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.45
11 8 0.36
12 4 0.18
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:6167 original size:35 final size:35
Alignment explanation
Indices: 6117--6187 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
6107 TAATGTTAAA
6117 ATTTCTGATAATTTACCAGTTATTGCATAGTTAGC
1 ATTTCTGATAATTTACCAGTTATTGCATAGTTAGC
*
6152 ATTTCTGATACTTTACCAGTTATTGCATAGTTAGC
1 ATTTCTGATAATTTACCAGTTATTGCATAGTTAGC
6187 A
1 A
6188 CATCCTCTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.42
Consensus pattern (35 bp):
ATTTCTGATAATTTACCAGTTATTGCATAGTTAGC
Found at i:21218 original size:3 final size:3
Alignment explanation
Indices: 21198--21232 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
21188 GGAGAAAGGG
* *
21198 AGA AGA AAA AGA AAA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
21233 GAGGAGGAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:24542 original size:67 final size:67
Alignment explanation
Indices: 24434--24568 Score: 270
Period size: 67 Copynumber: 2.0 Consensus size: 67
24424 AAGCACTTAC
24434 AAAGCAACTATGGTGCAGCTGGCTGGACAAAAAATACCGAAAGGGTTTTGTTTTTATAATCTAAT
1 AAAGCAACTATGGTGCAGCTGGCTGGACAAAAAATACCGAAAGGGTTTTGTTTTTATAATCTAAT
24499 TA
66 TA
24501 AAAGCAACTATGGTGCAGCTGGCTGGACAAAAAATACCGAAAGGGTTTTGTTTTTATAATCTAAT
1 AAAGCAACTATGGTGCAGCTGGCTGGACAAAAAATACCGAAAGGGTTTTGTTTTTATAATCTAAT
24566 TA
66 TA
24568 A
1 A
24569 GCTCCATTCA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (67 bp):
AAAGCAACTATGGTGCAGCTGGCTGGACAAAAAATACCGAAAGGGTTTTGTTTTTATAATCTAAT
TA
Found at i:32304 original size:23 final size:23
Alignment explanation
Indices: 32277--32324 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
32267 AATTAATAAC
32277 ATTAATTATTGATTTATGAAATT
1 ATTAATTATTGATTTATGAAATT
32300 ATTAATTATTGATTTATGAAATT
1 ATTAATTATTGATTTATGAAATT
32323 AT
1 AT
32325 GCAATTACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (23 bp):
ATTAATTATTGATTTATGAAATT
Found at i:35894 original size:32 final size:32
Alignment explanation
Indices: 35858--35934 Score: 120
Period size: 32 Copynumber: 2.4 Consensus size: 32
35848 CTCGGGGTCA
*
35858 TCGGGTTTGGGTTGAATTT-GGATCAGGTTAAT
1 TCGGGTTCGGGTTGAATTTCGG-TCAGGTTAAT
35890 TCGGGTTCGGGTTGAATTTCGGTCAGGTTAAT
1 TCGGGTTCGGGTTGAATTTCGGTCAGGTTAAT
*
35922 TTGGGTTCGGGTT
1 TCGGGTTCGGGTT
35935 CAGTTTGGGT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
32 40 0.95
33 2 0.05
ACGTcount: A:0.14, C:0.09, G:0.36, T:0.40
Consensus pattern (32 bp):
TCGGGTTCGGGTTGAATTTCGGTCAGGTTAAT
Found at i:35902 original size:16 final size:16
Alignment explanation
Indices: 35883--35934 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
35873 ATTTGGATCA
35883 GGTTAATTCGGGTTCG
1 GGTTAATTCGGGTTCG
*
35899 GGTTGAATTTC-GG-TCA
1 GGTT-AA-TTCGGGTTCG
*
35915 GGTTAATTTGGGTTCG
1 GGTTAATTCGGGTTCG
35931 GGTT
1 GGTT
35935 CAGTTTGGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
14 2 0.07
15 4 0.14
16 16 0.55
17 4 0.14
18 3 0.10
ACGTcount: A:0.13, C:0.10, G:0.37, T:0.40
Consensus pattern (16 bp):
GGTTAATTCGGGTTCG
Found at i:36103 original size:16 final size:16
Alignment explanation
Indices: 36082--36145 Score: 83
Period size: 16 Copynumber: 4.0 Consensus size: 16
36072 TTTTCATAAA
*
36082 TTTTCGGATTCGGGTT
1 TTTTCGGGTTCGGGTT
* * *
36098 TTTTCGGGTTTGAGCT
1 TTTTCGGGTTCGGGTT
36114 TTTTCGGGTTCGGGTT
1 TTTTCGGGTTCGGGTT
*
36130 TTTTCGGGTTCAGGTT
1 TTTTCGGGTTCGGGTT
36146 CAAACGGGTG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.05, C:0.12, G:0.33, T:0.50
Consensus pattern (16 bp):
TTTTCGGGTTCGGGTT
Found at i:38091 original size:156 final size:156
Alignment explanation
Indices: 37706--38091 Score: 367
Period size: 156 Copynumber: 2.5 Consensus size: 156
37696 CATCTAGGTG
* ** * *
37706 AAATTTCATCTCAAACAGACTTAGTATGAAAAACTTATGCTAGTTTTTCAATTGAGGACAGTTTG
1 AAATTTCAGCTCATTCAGACTTAGTATGAAAAACTTATGCTAGTTTTTC-ATTTAGGACAATTTG
** * * * * *
37771 AGGAGTCAAACCAACTTCTCTATGCTAGAGAGTTCGGTTTCACTTAGATTTTTTCCCATATCCTT
65 AGGAGAGAAACCAACTTCACCATGCAAGAGAGCTCGGTTTCACTTAGATTTTTTCACATATCCTT
*
37836 ATGGTGATAATCTAAGTATACTGGTGA
130 ATGGTGATAATCTAAGTATACTGGTCA
* * * * * **
37863 AAA-ATCAGCTTCGTT-GGACTTAGTATGGAAAACTTATGCTAGTTTTTCATTTAAGGACCACCT
1 AAATTTCAGC-TCATTCAGACTTAGTATGAAAAACTTATGCTAGTTTTTCATTT-AGGACAATTT
* * * *
37926 -AGGGAGAGAAACCTAGTTCACCAT-CAAGGGGAGCTCGGTTTTACTTAGAATTTTTT-ACATAG
64 GA-GGAGAGAAACCAACTTCACCATGCAA-GAGAGCTCGGTTTCACTTAG-ATTTTTTCACATA-
* *
37988 T-CTTATGCG-GATATTCTAAGT-TTCTTGG-CA
125 TCCTTATG-GTGATAATCTAAGTATAC-TGGTCA
*
38018 AAATTTCAGCTCATTCAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTATGGACAATTTG
1 AAATTTCAGCTCATTCAGACTTAGTATGAAAAACTTATGCTAGTTTTTCATTTA-GGACAATTTG
*
38083 AGGTGAGAA
65 AGGAGAGAA
38092 GCTCCGTTTA
Statistics
Matches: 182, Mismatches: 35, Indels: 25
0.75 0.14 0.10
Matches are distributed among these distances:
155 17 0.09
156 150 0.82
157 15 0.08
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.35
Consensus pattern (156 bp):
AAATTTCAGCTCATTCAGACTTAGTATGAAAAACTTATGCTAGTTTTTCATTTAGGACAATTTGA
GGAGAGAAACCAACTTCACCATGCAAGAGAGCTCGGTTTCACTTAGATTTTTTCACATATCCTTA
TGGTGATAATCTAAGTATACTGGTCA
Found at i:38624 original size:20 final size:20
Alignment explanation
Indices: 38599--38636 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
38589 AAGAGTTTGC
38599 CTTCCTCAGCAAGTAAATGT
1 CTTCCTCAGCAAGTAAATGT
38619 CTTCCTCAGCAAGTAAAT
1 CTTCCTCAGCAAGTAAAT
38637 CCCGCCAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (20 bp):
CTTCCTCAGCAAGTAAATGT
Done.