Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022431.1 Corchorus olitorius cultivar O-4 contig22464, 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: 43175
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1200 original size:28 final size:28
Alignment explanation
Indices: 1175--1227 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
1165 TCCAAATTGT
1175 AAGTTTA-GGG-CAAAACGTCTAAAATTA
1 AAGTTTATGGGACAAAACGTC-AAAATTA
*
1202 AAGTTTATGGGACAAAATGTCAAAAT
1 AAGTTTATGGGACAAAACGTCAAAAT
1228 CATACAAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 7 0.30
28 8 0.35
29 8 0.35
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.26
Consensus pattern (28 bp):
AAGTTTATGGGACAAAACGTCAAAATTA
Found at i:1217 original size:29 final size:26
Alignment explanation
Indices: 1175--1242 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 26
1165 TCCAAATTGT
1175 AAGTTTAGGGCAAAACGTCTAAAATTA
1 AAGTTTAGGGCAAAACGTC-AAAATTA
*
1202 AAGTTTATGGGACAAAATGTCAAAATCATA
1 AAGTTTA-GGG-CAAAACGTCAAAAT--TA
1232 CAAGTTTAGGG
1 -AAGTTTAGGG
1243 GGCAAAATGA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
27 7 0.20
28 8 0.23
29 8 0.23
30 5 0.14
31 7 0.20
ACGTcount: A:0.43, C:0.10, G:0.21, T:0.26
Consensus pattern (26 bp):
AAGTTTAGGGCAAAACGTCAAAATTA
Found at i:1237 original size:31 final size:27
Alignment explanation
Indices: 1175--1251 Score: 75
Period size: 31 Copynumber: 2.6 Consensus size: 27
1165 TCCAAATTGT
*
1175 AAGTTTAGGGCAAAACGTCTAAAATTA
1 AAGTTTAGGGCAAAATGTCTAAAATTA
1202 AAGTTTATGGGACAAAATGTC-AAAATCATA
1 AAGTTTA-GGG-CAAAATGTCTAAAAT--TA
1232 CAAGTTTAGGGGGCAAAATG
1 -AAGTTTA--GGGCAAAATG
1252 AGCATTAAGC
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
27 7 0.17
28 8 0.19
29 8 0.19
30 2 0.05
31 14 0.33
32 3 0.07
ACGTcount: A:0.43, C:0.10, G:0.22, T:0.25
Consensus pattern (27 bp):
AAGTTTAGGGCAAAATGTCTAAAATTA
Found at i:1921 original size:64 final size:64
Alignment explanation
Indices: 1820--2012 Score: 368
Period size: 64 Copynumber: 3.0 Consensus size: 64
1810 TATTTAAAAA
*
1820 AAAATCGAACCCTTTCTACTTGACTTAACATACAATAGTGATTTTATATATAATTTTGAATTTG
1 AAAATCGAACCCTTTCTACTCGACTTAACATACAATAGTGATTTTATATATAATTTTGAATTTG
1884 AAAATCGAACCCTTTCTACTCGACTTAACATACAATAGTGATTTTATATATAATTTTGAATTTG
1 AAAATCGAACCCTTTCTACTCGACTTAACATACAATAGTGATTTTATATATAATTTTGAATTTG
*
1948 AAAATCGAACCTTTTCTACTCGACTTAACATACAATAGTGATTTTATATATAATTTTGAATTTG
1 AAAATCGAACCCTTTCTACTCGACTTAACATACAATAGTGATTTTATATATAATTTTGAATTTG
2012 A
1 A
2013 TGTGATAGGG
Statistics
Matches: 127, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 127 1.00
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (64 bp):
AAAATCGAACCCTTTCTACTCGACTTAACATACAATAGTGATTTTATATATAATTTTGAATTTG
Found at i:25206 original size:151 final size:151
Alignment explanation
Indices: 24932--25221 Score: 411
Period size: 151 Copynumber: 1.9 Consensus size: 151
24922 GTGTAAATGG
* * * * *
24932 GTCAAACTGCTCGTAAGCTACTTAAATTCGACTCGTTTTATGTAAAATTTGGCTTGATTGTGTTT
1 GTCAAACTACTCATAAGCTACTCAAATTCGACTCGTTATATGTAAAATTTGGCTCGATTGTGTTT
** * * *
24997 CATTATAAAAGAAGCTTGAAAATCTTACAATAACTACTAATTGATCTCCAACTAAAGATCATAAT
66 CACCATAAAAGAAACTTAAAAATCTTACAAGAACTACTAATTGATCTCCAACTAAAGATCATAAT
25062 CTCACCTATTATCCCCTCTCA
131 CTCACCTATTATCCCCTCTCA
* *
25083 GTCAAACTACTCATAAGCTACTCGAATTTGACTCGTTATATGTAAAATTTGGCTCGATTGTGTTT
1 GTCAAACTACTCATAAGCTACTCAAATTCGACTCGTTATATGTAAAATTTGGCTCGATTGTGTTT
* * * *
25148 CACCGTAAAA-AAACTTTAAAAATCTTACAAGAACTACTAATTGCTCTCCAAGTGAAGATCATAA
66 CACCATAAAAGAAAC-TTAAAAATCTTACAAGAACTACTAATTGATCTCCAACTAAAGATCATAA
*
25212 TCTCATCTAT
130 TCTCACCTAT
25222 CCCCTTTCAT
Statistics
Matches: 121, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
150 3 0.02
151 118 0.98
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (151 bp):
GTCAAACTACTCATAAGCTACTCAAATTCGACTCGTTATATGTAAAATTTGGCTCGATTGTGTTT
CACCATAAAAGAAACTTAAAAATCTTACAAGAACTACTAATTGATCTCCAACTAAAGATCATAAT
CTCACCTATTATCCCCTCTCA
Found at i:32575 original size:11 final size:11
Alignment explanation
Indices: 32559--32599 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
32549 CGAATCATTA
32559 CCCTCTCTTCC
1 CCCTCTCTTCC
**
32570 CCCTCTCTTTTA
1 CCCTCTC-TTCC
32582 CCCTCTCTTCC
1 CCCTCTCTTCC
32593 CCCTCTC
1 CCCTCTC
32600 CTTTTAATTG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.02, C:0.59, G:0.00, T:0.39
Consensus pattern (11 bp):
CCCTCTCTTCC
Found at i:32586 original size:23 final size:24
Alignment explanation
Indices: 32556--32605 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
32546 GTTCGAATCA
32556 TTACCCTCTCTTCCCCCTCT-CTT
1 TTACCCTCTCTTCCCCCTCTCCTT
32579 TTACCCTCTCTTCCCCCTCTCCTT
1 TTACCCTCTCTTCCCCCTCTCCTT
32603 TTA
1 TTA
32606 ATTGTAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.06, C:0.50, G:0.00, T:0.44
Consensus pattern (24 bp):
TTACCCTCTCTTCCCCCTCTCCTT
Found at i:35113 original size:19 final size:19
Alignment explanation
Indices: 35089--35146 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
35079 TTGTTTAACA
35089 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* *
35108 ACTGTACAGATTAGATTAGAT
1 ACTGTACAGATGAGATT--AC
*
35129 ATTGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
35147 TTAGAGCAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:35859 original size:31 final size:30
Alignment explanation
Indices: 35823--35925 Score: 86
Period size: 31 Copynumber: 3.4 Consensus size: 30
35813 GTCAACAAAG
35823 TTTTAAAAGTTTAGGGTGTAAAATGTCAAGA
1 TTTTAAAAGTTTAGGGTGTAAAATGT-AAGA
* *
35854 TTTTAAACA-TTTA-TGTGGTAAAAAGTAAGA
1 TTTTAAA-AGTTTAGGGT-GTAAAATGTAAGA
* * *
35884 TTTTAGAAGTTTAGGGGGCAAAATGATTAA-A
1 TTTTAAAAGTTTAGGGTGTAAAATG--TAAGA
*
35915 TTTTGAAAGTT
1 TTTTAAAAGTT
35926 CACGTGTCAC
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
29 1 0.02
30 22 0.39
31 30 0.53
32 4 0.07
ACGTcount: A:0.39, C:0.03, G:0.21, T:0.37
Consensus pattern (30 bp):
TTTTAAAAGTTTAGGGTGTAAAATGTAAGA
Found at i:36298 original size:60 final size:60
Alignment explanation
Indices: 36205--36364 Score: 162
Period size: 60 Copynumber: 2.7 Consensus size: 60
36195 CTAATTGCTA
* ** * * * ***
36205 AAATAAGGGTCTAACGTT-TGTTAAAATACTCAAATAAGGGAATGATCTTTTAATTTGGGC
1 AAATAAGGGTCTAACATTATCAT-AAATGCTCAAATAAGGGAACGATCTTTTAAATTAACC
* **
36265 AAATAAGGGTCTAACATTATCATAAATGCTCAAATAAAGGCCCGATCTTTTAAATTAACC
1 AAATAAGGGTCTAACATTATCATAAATGCTCAAATAAGGGAACGATCTTTTAAATTAACC
* *
36325 AAATAAGGGCCTAACATTATCGA-AAATGCTAAAATAAGGG
1 AAATAAGGGTCTAACATTATC-ATAAATGCTCAAATAAGGG
36365 CTTGGCGTCG
Statistics
Matches: 83, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
60 80 0.96
61 3 0.04
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (60 bp):
AAATAAGGGTCTAACATTATCATAAATGCTCAAATAAGGGAACGATCTTTTAAATTAACC
Found at i:36535 original size:60 final size:60
Alignment explanation
Indices: 36410--36539 Score: 140
Period size: 60 Copynumber: 2.2 Consensus size: 60
36400 GAAGCCAGGC
* * * * * *
36410 CCTTATTTGATCAAATTAAAAGATCGGGTCCTTATTTAAGCATTTTCGATAACGTTAGGT
1 CCTTATTTGACCAAATTAAAAGATCAGGCCCTTAATTAAGCATTTTCGATAACATTAGCT
* *
36470 CCTTATTTGGCCAAATTAAAAGATCATGCCCTTAATTAAGCATTTTAAC-A-AACATTAGACT
1 CCTTATTTGACCAAATTAAAAGATCAGGCCCTTAATTAAGCATTTT--CGATAACATTAG-CT
36531 -CTTATTTGA
1 CCTTATTTGA
36540 GTAATTATCC
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
60 55 0.95
61 2 0.03
62 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (60 bp):
CCTTATTTGACCAAATTAAAAGATCAGGCCCTTAATTAAGCATTTTCGATAACATTAGCT
Found at i:37595 original size:2 final size:2
Alignment explanation
Indices: 37588--37617 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
37578 CAAAGCAGAC
37588 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
37618 GAGTCTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41790 original size:67 final size:67
Alignment explanation
Indices: 41681--41811 Score: 228
Period size: 67 Copynumber: 2.0 Consensus size: 67
41671 AAGAGACTAA
*
41681 TTAATCAAGTTACATCGATAGATCTATATAAAATAGGGTTTAATTTGAACCCATTTTCCTATTTT
1 TTAATCAAGTTACATCGATAGATCTATATAAAATAGGGTTTAATTTAAACCCATTTTCCTATTTT
41746 AT
66 AT
*
41748 TTAATCAAGTTACATCGATA-ATCTATATAAAATAGGGTTTTAATTTAAACTCATTTTCCTATTT
1 TTAATCAAGTTACATCGATAGATCTATATAAAATAGGG-TTTAATTTAAACCCATTTTCCTATTT
41812 AAATTTAGGT
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
66 17 0.28
67 44 0.72
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (67 bp):
TTAATCAAGTTACATCGATAGATCTATATAAAATAGGGTTTAATTTAAACCCATTTTCCTATTTT
AT
Done.