Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005389.1 Corchorus capsularis cultivar CVL-1 contig05407, 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: 2536
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35
Found at i:195 original size:10 final size:9
Alignment explanation
Indices: 170--194 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
160 TTTTCTTTCC
170 TTTTTTTAA
1 TTTTTTTAA
179 TTTTTTTAA
1 TTTTTTTAA
188 TTTTTTT
1 TTTTTTT
195 TGTAATTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:1323 original size:31 final size:30
Alignment explanation
Indices: 1288--1346 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 30
1278 ATATTTTTCG
*
1288 ATTGTACCCTTATTTTTAAA-ACATGTTTCCA
1 ATTGTACCC-T-TTTTTAAAGACATATTTCCA
1319 ATTGTACCCTTTTTTAAAGACATATTTC
1 ATTGTACCCTTTTTTAAAGACATATTTC
1347 TAAATTGCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 8 0.31
30 9 0.35
31 9 0.35
ACGTcount: A:0.29, C:0.19, G:0.07, T:0.46
Consensus pattern (30 bp):
ATTGTACCCTTTTTTAAAGACATATTTCCA
Found at i:1353 original size:31 final size:31
Alignment explanation
Indices: 1288--1353 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
1278 ATATTTTTCG
* *
1288 ATTGTACCCTTATTTTTAAAACATGTTTCCA
1 ATTGTACCCTTATTTTTAAAACATATTTCAA
1319 ATTGTACCC-T-TTTTTAAAGACATATTTCTAA
1 ATTGTACCCTTATTTTTAAA-ACATATTTC-AA
1350 ATTG
1 ATTG
1354 CCATTACTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 8 0.26
30 9 0.29
31 14 0.45
ACGTcount: A:0.30, C:0.17, G:0.08, T:0.45
Consensus pattern (31 bp):
ATTGTACCCTTATTTTTAAAACATATTTCAA
Found at i:1651 original size:22 final size:22
Alignment explanation
Indices: 1623--1745 Score: 74
Period size: 22 Copynumber: 5.6 Consensus size: 22
1613 TGGTCCAATT
1623 TCAAAATTTCA-AA-GCGAAGTTA
1 TCAAAATTTCATAATGCG-A-TTA
* *
1645 TCAAAATTACATAATGTGATTA
1 TCAAAATTTCATAATGCGATTA
* *
1667 TCAAAATTTCATAGAGGCG-TCA
1 TCAAAATTTCATA-ATGCGATTA
* * * *
1689 ACAAAATTTTATAGA-GAGGTTA
1 TCAAAATTTCATA-ATGCGATTA
* * *
1711 TCAAATTTTCAAAATGTGATTA
1 TCAAAATTTCATAATGCGATTA
*
1733 CCAAAATTTCATA
1 TCAAAATTTCATA
1746 GTGGTATTTC
Statistics
Matches: 77, Mismatches: 19, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
21 3 0.04
22 66 0.86
23 6 0.08
24 2 0.03
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (22 bp):
TCAAAATTTCATAATGCGATTA
Found at i:1914 original size:44 final size:44
Alignment explanation
Indices: 1846--1971 Score: 134
Period size: 44 Copynumber: 2.8 Consensus size: 44
1836 CAGGGAGCAT
*
1846 ATCAAAATTTCATATATGAAGGTTATCAAAATTTCATAGT-T-TAG
1 ATCAAAATTTCATA-A-GAGGGTTATCAAAATTTCATAGTATGTAG
* *
1890 TTTTCAAAATTTCATAAGAGGGTTATCAAAATTTTATAGTATGTAG
1 --ATCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGTATGTAG
*
1936 ATCAAAATTTCAT-AG-GGAGATTAACAAAATTTCATA
1 ATCAAAATTTCATAAGAGG-G-TTATCAAAATTTCATA
1972 ATGAGGTAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
42 2 0.03
43 3 0.04
44 47 0.67
45 2 0.03
46 16 0.23
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (44 bp):
ATCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGTATGTAG
Found at i:1918 original size:22 final size:21
Alignment explanation
Indices: 1845--2141 Score: 101
Period size: 22 Copynumber: 13.6 Consensus size: 21
1835 TCAGGGAGCA
*
1845 TATCAAAATTTCATATATGAAGGT
1 TATCAAAATTTC--ATA-GAGGGT
***
1869 TATCAAAATTTCATAGTTTAGT
1 TATCAAAATTTCATAG-AGGGT
*
1891 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCAT-AGAGGGT
* *
1913 TATCAAAATTTTATAGTA-TGT
1 TATCAAAATTTCATAG-AGGGT
*
1934 AGATCAAAATTTCATAG-GGAGAT
1 -TATCAAAATTTCATAGAGG-G-T
*
1957 TAACAAAATTTCATA-ATGAGGT
1 TATCAAAATTTCATAGA-G-GGT
* * ** *
1979 AATAAAAAAATCATAGAGAGAT
1 TATCAAAATTTCATAGAG-GGT
*
2001 TATCAAAATTT--T-TA--GT
1 TATCAAAATTTCATAGAGGGT
* **
2017 CATCAGGATTTCATA-AGGAGGT
1 TATCAAAATTTCATAGA-G-GGT
*
2039 TATCAAAATTTTATAG-GGAGATT
1 TATCAAAATTTCATAGAGG-G--T
* *
2062 TATCAAAATTTTATAGGAAGGTT
1 TATCAAAATTTCATA-G-AGGGT
* *
2085 TATCAAAATTTTATAGCGAGGT
1 TATCAAAATTTCATAGAG-GGT
* * *
2107 TATCACAATTTCATAGTGTGAT
1 TATCAAAATTTCATAGAG-GGT
2129 TATCAAAATTTCA
1 TATCAAAATTTCA
2142 GAGTGTGATT
Statistics
Matches: 204, Mismatches: 43, Indels: 54
0.68 0.14 0.18
Matches are distributed among these distances:
16 9 0.04
18 2 0.01
19 1 0.00
20 2 0.01
21 8 0.04
22 128 0.63
23 38 0.19
24 14 0.07
26 2 0.01
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.36
Consensus pattern (21 bp):
TATCAAAATTTCATAGAGGGT
Found at i:2068 original size:23 final size:23
Alignment explanation
Indices: 2038--2139 Score: 118
Period size: 23 Copynumber: 4.5 Consensus size: 23
2028 CATAAGGAGG
2038 TTATCAAAATTTTATAGGGAGAT
1 TTATCAAAATTTTATAGGGAGAT
* *
2061 TTATCAAAATTTTATAGGAAGGT
1 TTATCAAAATTTTATAGGGAGAT
* *
2084 TTATCAAAATTTTATAGCGAG-G
1 TTATCAAAATTTTATAGGGAGAT
* * * *
2106 TTATCACAATTTCATAGTGTGA-
1 TTATCAAAATTTTATAGGGAGAT
2128 TTATCAAAATTT
1 TTATCAAAATTT
2140 CAGAGTGTGA
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
22 28 0.41
23 40 0.59
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGAT
Found at i:2146 original size:22 final size:22
Alignment explanation
Indices: 2106--2152 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
2096 TATAGCGAGG
* *
2106 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
2128 TTATCAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
2150 TTA
1 TTA
2153 CTGACAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTCAGAGTGTGA
Found at i:2270 original size:22 final size:22
Alignment explanation
Indices: 2218--2301 Score: 80
Period size: 22 Copynumber: 3.8 Consensus size: 22
2208 TTATACTGTT
* **
2218 GGTTATTAAAATTTCATTTGGA
1 GGTTATCAAAATTTCATAGGGA
* *
2240 AGTTATCAAAATTTCATAGTGA
1 GGTTATCAAAATTTCATAGGGA
* *
2262 GGTCT-TCAAAATTCCTTAGGGA
1 GGT-TATCAAAATTTCATAGGGA
*
2284 GGTTAACAAAATTTCATA
1 GGTTATCAAAATTTCATA
2302 AGAAGGTTCA
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
21 1 0.02
22 46 0.96
23 1 0.02
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.37
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGGGA
Done.