Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020956.1 Corchorus olitorius cultivar O-4 contig20989, 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: 28643
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3935 original size:15 final size:15
Alignment explanation
Indices: 3886--3945 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 15
3876 GACACATGTG
*
3886 TAATTTTTAA-TAA-
1 TAATTATTAATTAAT
* *
3899 TAATTATTCAATAAAA
1 TAATTATT-AATTAAT
*
3915 TAATTATTATTTAAT
1 TAATTATTAATTAAT
3930 TAATTATTAATTAAT
1 TAATTATTAATTAAT
3945 T
1 T
3946 CCAGCCCTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
13 7 0.18
14 2 0.05
15 21 0.55
16 8 0.21
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
TAATTATTAATTAAT
Found at i:5765 original size:30 final size:32
Alignment explanation
Indices: 5729--5791 Score: 94
Period size: 30 Copynumber: 2.0 Consensus size: 32
5719 TCAAATCGCA
5729 ATAATTTATCCT-TAAATTTCC-AAATTCATG
1 ATAATTTATCCTCTAAATTTCCTAAATTCATG
* *
5759 ATAATTTGTCCTCTGAATTTCCTAAATTCATG
1 ATAATTTATCCTCTAAATTTCCTAAATTCATG
5791 A
1 A
5792 CAACTAGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 11 0.38
31 8 0.28
32 10 0.34
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.43
Consensus pattern (32 bp):
ATAATTTATCCTCTAAATTTCCTAAATTCATG
Found at i:11361 original size:178 final size:178
Alignment explanation
Indices: 11039--11368 Score: 486
Period size: 178 Copynumber: 1.9 Consensus size: 178
11029 TAAGCTCAAC
* ** **
11039 TTATGTAATATTAAGTAGACCGTCTATTTTCGTTAACCAAAACAATTAATTCTTTGGAAACAATT
1 TTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCAAAACAACAAATTCTTTGGAAACAATT
11104 TTTATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCTTCGAACAAC
66 TTTATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCTTCGAACAAC
*
11169 CTTTCAAGAGACACTTGAATCATCTCAATCAGACATCTGAAGCAAAAG
131 CTTTCAAGAGACACTTAAATCATCTCAATCAGACATCTGAAGCAAAAG
* * *
11217 TTATATAATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAACAAATT-TTTCGGAAGC-AT
1 TTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCAAAACAACAAATTCTTT-GGAAACAAT
* *
11280 TTTTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTTCTTCATGAAAGTTGTAGATCTTGGAAC
65 TTTT-ATACCTTG-AACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCTTCGAAC
* * *
11344 AATCTTTTAATAGACACTTAAATCA
128 AACCTTTCAAGAGACACTTAAATCA
11369 CCTTAATTGG
Statistics
Matches: 135, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
177 13 0.10
178 122 0.90
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (178 bp):
TTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCAAAACAACAAATTCTTTGGAAACAATT
TTTATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCTTCGAACAAC
CTTTCAAGAGACACTTAAATCATCTCAATCAGACATCTGAAGCAAAAG
Found at i:25570 original size:96 final size:94
Alignment explanation
Indices: 25455--25798 Score: 461
Period size: 96 Copynumber: 3.7 Consensus size: 94
25445 TTGGTTCAAT
* *
25455 CGGTTGAACCGGGAACTGGTGCTCAGTCCTGTACTGGTATATATAAAATCATCTAGTCAACGTAC
1 CGGTTGAACCGGGAACTGGTGCTCAGTCCGGTACCGGTATATATAAAATCATCTAGTCAACGTAC
25520 TGGTGTTGACCCGGTTTCAACACGGTTGAAC
66 TGGTGTTGACCCGGTTTC-A-ACGGTTGAAC
* * *
25551 CGGCTGAACCGGGAACTGGTGCTCAGTCCGGCATCGGTATATATAAAATCATCTAGTCAACGTAC
1 CGGTTGAACCGGGAACTGGTGCTCAGTCCGGTACCGGTATATATAAAATCATCTAGTCAACGTAC
* * ** ** *
25616 CGGTGTTGACGCGGTGACCGGTCGGTTCAAC
66 TGGTGTTGACCCGGT-TTC-AACGGTTGAAC
25647 CGGTTGAACCGGGAACTGGTGCTCAGTCCGGTACCGGTATATATAAAATCATCTAGTCAACGTA-
1 CGGTTGAACCGGGAACTGGTGCTCAGTCCGGTACCGGTATATATAAAATCATCTAGTCAACGTAC
*
25711 TCGGTGTTGACCCAGTTTCAAC----G---
66 T-GGTGTTGACCCGGTTTCAACGGTTGAAC
*
25734 CGGTTGAACCGGGAACTGGTGCTCAGTCCGGTACCAGTATATATAAAATCATCTAGTCAACGTAC
1 CGGTTGAACCGGGAACTGGTGCTCAGTCCGGTACCGGTATATATAAAATCATCTAGTCAACGTAC
25799 CGCGGTTGAA
Statistics
Matches: 220, Mismatches: 25, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
87 63 0.29
94 1 0.00
95 1 0.00
96 154 0.70
97 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (94 bp):
CGGTTGAACCGGGAACTGGTGCTCAGTCCGGTACCGGTATATATAAAATCATCTAGTCAACGTAC
TGGTGTTGACCCGGTTTCAACGGTTGAAC
Found at i:25807 original size:87 final size:86
Alignment explanation
Indices: 25641--25812 Score: 292
Period size: 87 Copynumber: 2.0 Consensus size: 86
25631 GACCGGTCGG
*
25641 TTCAACCGGTTGAACCGGGAACTGGTGCTCAGTCCGGTACCGGTATATATAAAATCATCTAGTCA
1 TTCAACCGGTTGAACCGGGAACTGGTGCTCAGTCCGGTACCAGTATATATAAAATCATCTAGTCA
* *
25706 ACGTATCGGTGTTGACCCAGT
66 ACGTACCGGTGTTGAACCAGT
25727 TTCAACGCGGTTGAACCGGGAACTGGTGCTCAGTCCGGTACCAGTATATATAAAATCATCTAGTC
1 TTCAAC-CGGTTGAACCGGGAACTGGTGCTCAGTCCGGTACCAGTATATATAAAATCATCTAGTC
25792 AACGTACCGCG-GTTGAACCAG
65 AACGTACCG-GTGTTGAACCAG
25813 CTGGTTTACC
Statistics
Matches: 81, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
86 6 0.07
87 74 0.91
88 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (86 bp):
TTCAACCGGTTGAACCGGGAACTGGTGCTCAGTCCGGTACCAGTATATATAAAATCATCTAGTCA
ACGTACCGGTGTTGAACCAGT
Found at i:28207 original size:15 final size:16
Alignment explanation
Indices: 28187--28216 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28177 GGTATAATAC
28187 ATTAATCCA-ATATAA
1 ATTAATCCATATATAA
28202 ATTAATCCATATATA
1 ATTAATCCATATATA
28217 GAATAATACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (16 bp):
ATTAATCCATATATAA
Done.