Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020448.1 Corchorus olitorius cultivar O-4 contig20481, 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: 30380
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:621 original size:5 final size:5
Alignment explanation
Indices: 609--661 Score: 51
Period size: 5 Copynumber: 10.8 Consensus size: 5
599 ATGAAATCAT
609 ATAT- ATATC ATATC ATATC ATCAT- ATATC ATATATC ATATC ATAT-
1 ATATC ATATC ATATC ATATC AT-ATC ATATC --ATATC ATATC ATATC
654 ATAT- ATAT
1 ATATC ATAT
662 TGATAACAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
4 14 0.32
5 23 0.52
6 2 0.05
7 5 0.11
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.43
Consensus pattern (5 bp):
ATATC
Found at i:641 original size:27 final size:24
Alignment explanation
Indices: 607--661 Score: 83
Period size: 27 Copynumber: 2.2 Consensus size: 24
597 AAATGAAATC
607 ATATATATATCATATCATATCATCAT
1 ATATATATATCATATCATAT-AT-AT
633 ATATCATATATCATATCATATATAT
1 ATAT-ATATATCATATCATATATAT
658 ATAT
1 ATAT
662 TGATAACAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 6 0.21
26 6 0.21
27 16 0.57
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.44
Consensus pattern (24 bp):
ATATATATATCATATCATATATAT
Found at i:1159 original size:15 final size:15
Alignment explanation
Indices: 1141--1179 Score: 55
Period size: 13 Copynumber: 2.7 Consensus size: 15
1131 AATTATTTTT
1141 CCATGAATTATCAAA
1 CCATGAATTATCAAA
*
1156 CCATG-ATT-TCCAA
1 CCATGAATTATCAAA
1169 CCATGAATTAT
1 CCATGAATTAT
1180 TTTTTCAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 9 0.43
14 6 0.29
15 6 0.29
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (15 bp):
CCATGAATTATCAAA
Found at i:8893 original size:12 final size:12
Alignment explanation
Indices: 8862--8893 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
8852 ACCTGGCAAT
*
8862 TCGTGTTCCGTG
1 TCGTGTTTCGTG
8874 TCGTGTTTCGTG
1 TCGTGTTTCGTG
8886 TCGTGTTT
1 TCGTGTTT
8894 ACATAGGGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.19, G:0.31, T:0.50
Consensus pattern (12 bp):
TCGTGTTTCGTG
Found at i:9476 original size:18 final size:19
Alignment explanation
Indices: 9453--9497 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
9443 AATCGTGTCC
9453 GACACGAT-TCAAACACGA
1 GACACGATATCAAACACGA
9471 GACACGATAAGTCAAACACGA
1 GACACGAT-A-TCAAACACGA
9492 -ACACGA
1 GACACGA
9498 CTAAACGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.33
20 6 0.25
21 10 0.42
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.09
Consensus pattern (19 bp):
GACACGATATCAAACACGA
Found at i:15661 original size:35 final size:35
Alignment explanation
Indices: 15609--15739 Score: 176
Period size: 35 Copynumber: 3.7 Consensus size: 35
15599 GGGTTGCGTA
*
15609 GGCCAAGGCCATA-CGCTGGCCTACTGGGCCGCGCG
1 GGCCAAGGCCA-AGCGCTGGCCTGCTGGGCCGCGCG
15644 GGCCAAGGCCAAGCGCTGGCCTGCTGGGCCGCGCG
1 GGCCAAGGCCAAGCGCTGGCCTGCTGGGCCGCGCG
* * *
15679 GGCCAAGGCCATGCGCTGGCCTGCTGGGCTGCGCA
1 GGCCAAGGCCAAGCGCTGGCCTGCTGGGCCGCGCG
*
15714 GGCC-AGGCCCTAGCGCTAGGCCTGCT
1 GGCCAAGG-CCAAGCGCT-GGCCTGCT
15740 TTCTTTTTTT
Statistics
Matches: 87, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
34 4 0.05
35 75 0.86
36 8 0.09
ACGTcount: A:0.12, C:0.37, G:0.39, T:0.12
Consensus pattern (35 bp):
GGCCAAGGCCAAGCGCTGGCCTGCTGGGCCGCGCG
Found at i:26138 original size:23 final size:24
Alignment explanation
Indices: 26079--26138 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
26069 GTACATATGT
26079 ATATATGTTAACTTTGAAATCATA
1 ATATATGTTAACTTTGAAATCATA
**
26103 ATATATGACAACTTTGAAATCA-A
1 ATATATGTTAACTTTGAAATCATA
* *
26126 TTGTATGTTAACT
1 ATATATGTTAACT
26139 AGCTTGAATG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 10 0.33
24 20 0.67
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (24 bp):
ATATATGTTAACTTTGAAATCATA
Found at i:26539 original size:250 final size:250
Alignment explanation
Indices: 26098--26599 Score: 934
Period size: 250 Copynumber: 2.0 Consensus size: 250
26088 AACTTTGAAA
*
26098 TCATAATATATGACAACTTTGAAATCAATTGTATGTTAACTAGCTTGAATGATGCTTCTGAAAAT
1 TCATAATAAATGACAACTTTGAAATCAATTGTATGTTAACTAGCTTGAATGATGCTTCTGAAAAT
*
26163 CAATTACCATCAAATCATGCAAATGGCCGGACAACATCAATTAGCATTAAGTTAATTGATATCTA
66 CAATTACCATCAAATCATGCAAATGGCCGGACAAAATCAATTAGCATTAAGTTAATTGATATCTA
*
26228 AATTACTCCTAAATCAAATTCTAACTAAATGAAATAGTAACTTAAAGAACTATTCCAACAGTATA
131 AATTACTCCTAAATCAAATTCTAACTAAATGAAATAGTAACGTAAAGAACTATTCCAACAGTATA
*
26293 TATATTGTA-TAACTATGATAAAAAGACCACATAAACTCAAGGTTTGGTATTCTTT
196 TATAATGTAGT-ACTATGATAAAAAGACCACATAAACTCAAGGTTTGGTATTCTTT
26348 TCATAATAAATGACAACTTTGAAATCAATTGTATGTTAACTAGCTTGAATGATGCTTCTGAAAAT
1 TCATAATAAATGACAACTTTGAAATCAATTGTATGTTAACTAGCTTGAATGATGCTTCTGAAAAT
26413 CAATTACCATCAAATCATGCAAATGGCCGGACAAAATCAATTAGCATTAAGTTAATTGATATCTA
66 CAATTACCATCAAATCATGCAAATGGCCGGACAAAATCAATTAGCATTAAGTTAATTGATATCTA
26478 AATTACTCCTAAATCAAATTCTAACTAAATGAAATAGTAACGTAAAGAACTATTCCAACAGTATA
131 AATTACTCCTAAATCAAATTCTAACTAAATGAAATAGTAACGTAAAGAACTATTCCAACAGTATA
* *
26543 TATAATGTAGTTCTATGATAAAAAGACCACCTAAACTCAAGGTTTGGTATTCTTT
196 TATAATGTAGTACTATGATAAAAAGACCACATAAACTCAAGGTTTGGTATTCTTT
26598 TC
1 TC
26600 TTTTGATAAT
Statistics
Matches: 245, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
250 244 1.00
251 1 0.00
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.32
Consensus pattern (250 bp):
TCATAATAAATGACAACTTTGAAATCAATTGTATGTTAACTAGCTTGAATGATGCTTCTGAAAAT
CAATTACCATCAAATCATGCAAATGGCCGGACAAAATCAATTAGCATTAAGTTAATTGATATCTA
AATTACTCCTAAATCAAATTCTAACTAAATGAAATAGTAACGTAAAGAACTATTCCAACAGTATA
TATAATGTAGTACTATGATAAAAAGACCACATAAACTCAAGGTTTGGTATTCTTT
Found at i:30262 original size:113 final size:114
Alignment explanation
Indices: 30064--30292 Score: 442
Period size: 113 Copynumber: 2.0 Consensus size: 114
30054 AAATGAAGTA
30064 TGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATATACACTGACAGTGTATTGTATAATAAT
1 TGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATATACACTGACAGTGTATTGTATAATAAT
30129 ATCATATAAAAAAATTATACAATACACCATCAGTGGAGTTT-AGCAGAC
66 ATCATATAAAAAAATTATACAATACACCATCAGTGGAGTTTAAGCAGAC
30177 TGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATATACACTGACAGTGTATTGTATAATAAT
1 TGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATATACACTGACAGTGTATTGTATAATAAT
*
30242 ATCATATAAAAAAATTATACAATACACCGTCAGTGGAGTTTAAGCAGAC
66 ATCATATAAAAAAATTATACAATACACCATCAGTGGAGTTTAAGCAGAC
30291 TG
1 TG
30293 CACGCGTAGG
Statistics
Matches: 114, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
113 105 0.92
114 9 0.08
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (114 bp):
TGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATATACACTGACAGTGTATTGTATAATAAT
ATCATATAAAAAAATTATACAATACACCATCAGTGGAGTTTAAGCAGAC
Done.