Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022733.1 Corchorus olitorius cultivar O-4 contig22766, 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: 47203
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:6839 original size:19 final size:18
Alignment explanation
Indices: 6815--6850 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
6805 TGAAGATTTA
6815 TTGAAGACCATTTGAAGAT
1 TTGAAGACCA-TTGAAGAT
*
6834 TTGAAGACTATTGAAGA
1 TTGAAGACCATTGAAGA
6851 ATTATTTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (18 bp):
TTGAAGACCATTGAAGAT
Found at i:8675 original size:24 final size:25
Alignment explanation
Indices: 8648--8694 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
8638 TTGTGTTTGC
8648 GTTTT-AGAAAAAAAAAAGTTTTCG
1 GTTTTGAGAAAAAAAAAAGTTTTCG
*
8672 GTTTTGCGAAAAAAAAAAGTTTT
1 GTTTTGAGAAAAAAAAAAGTTTT
8695 TGCGTCATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.45, C:0.04, G:0.17, T:0.34
Consensus pattern (25 bp):
GTTTTGAGAAAAAAAAAAGTTTTCG
Found at i:11637 original size:33 final size:33
Alignment explanation
Indices: 11599--11665 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
11589 GCCCGGCCAC
*
11599 CCGAGCCTCATGCCCGGCAATCAGCGCTACCCT
1 CCGAGCCACATGCCCGGCAATCAGCGCTACCCT
* * *
11632 CCGAGCCACATGCCCGGCCATCTGCGCTATCCT
1 CCGAGCCACATGCCCGGCAATCAGCGCTACCCT
11665 C
1 C
11666 TACACCAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.16, C:0.46, G:0.21, T:0.16
Consensus pattern (33 bp):
CCGAGCCACATGCCCGGCAATCAGCGCTACCCT
Found at i:13838 original size:11 final size:11
Alignment explanation
Indices: 13824--13871 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
13814 TGAAGATTTA
13824 TTGAAGACTAT
1 TTGAAGACTAT
13835 TTGAA-A--AT
1 TTGAAGACTAT
13843 TTGAAGACTA-
1 TTGAAGACTAT
*
13853 TTGAAGAATTAT
1 TTGAAG-ACTAT
13865 TTGAAGA
1 TTGAAGA
13872 GCAAGAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
8 7 0.23
9 1 0.03
10 7 0.23
11 10 0.32
12 6 0.19
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.35
Consensus pattern (11 bp):
TTGAAGACTAT
Found at i:13844 original size:22 final size:21
Alignment explanation
Indices: 13812--13871 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
13802 GAAGTTCATG
*
13812 TTTGAAGATTTATTGAAGACTA
1 TTTGAA-AATTATTGAAGACTA
13834 TTTGAAAA-T-TTGAAGACTA
1 TTTGAAAATTATTGAAGACTA
13853 -TTGAAGAATTATTTGAAGA
1 TTTGAA-AATTA-TTGAAGA
13872 GCAAGAATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 5 0.15
19 12 0.36
20 2 0.06
21 1 0.03
22 13 0.39
ACGTcount: A:0.40, C:0.03, G:0.18, T:0.38
Consensus pattern (21 bp):
TTTGAAAATTATTGAAGACTA
Found at i:14753 original size:41 final size:41
Alignment explanation
Indices: 14707--14970 Score: 160
Period size: 41 Copynumber: 6.2 Consensus size: 41
14697 CGACAAATTA
*
14707 AGTCGTTGCGAAATCTTAAAC-TTTCAGCAGCGACTTTTGTT
1 AGTCGTTGCGAAATCTTAAACTTTTC-GCAACGACTTTTGTT
14748 AGTCGTTGCGAAATCTTAAACTTTTCGCAACGACTTTTGTT
1 AGTCGTTGCGAAATCTTAAACTTTTCGCAACGACTTTTGTT
* * * * **
14789 AGTCGTTGCTCAATATTTGTTACTAATTGATTTTCG-AAGCGAC-CTTGAA
1 AGTCGTTGC-GAA-A--TCTTA--AA---CTTTTCGCAA-CGACTTTTGTT
* * * * * * * *** *
14838 AGTCGCTACAAAAAGCATGATTACTTTT-GAAACGACAGAT-TA
1 AGTCGTTGC-GAAATC-TTA-AACTTTTCGCAACGACTTTTGTT
* *
14880 AGTCGTTGCGAAATCTTAAACTTTCCGCAGCGACTTTTGTT
1 AGTCGTTGCGAAATCTTAAACTTTTCGCAACGACTTTTGTT
* *
14921 AGTCGTTGAGAAATCGTAAACTTTTCGCAACGACTTTTGTT
1 AGTCGTTGCGAAATCTTAAACTTTTCGCAACGACTTTTGTT
*
14962 AGTTGTTGC
1 AGTCGTTGC
14971 TTAATATATG
Statistics
Matches: 169, Mismatches: 38, Indels: 32
0.71 0.16 0.13
Matches are distributed among these distances:
39 5 0.03
40 9 0.05
41 93 0.55
42 19 0.11
43 8 0.05
45 4 0.02
46 2 0.01
47 4 0.02
48 1 0.01
49 14 0.08
50 10 0.06
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (41 bp):
AGTCGTTGCGAAATCTTAAACTTTTCGCAACGACTTTTGTT
Found at i:14781 original size:173 final size:173
Alignment explanation
Indices: 14564--15056 Score: 747
Period size: 173 Copynumber: 2.9 Consensus size: 173
14554 AGTTTTACAA
* * * ** * * **
14564 CGACTTCTATTAGTCGTTGCGAATTCATAGTCTTTTCACAACGACTTTTCTTAGTCGTTTTTTAA
1 CGACTTTTGTTAGTCGTTGCGAAATCATAAACTTTTCGCAACGACTTTTGTTAGTCGTTGCTTAA
*
14629 TATATTTTACAAATTGATTTTCGAAGCGACCTTGAAAGTCGCTACAAAAAACATGATTACTTTTG
66 TATATTTTACTAATTGATTTTCGAAGCGACCTTGAAAGTCGCTACAAAAAACATGATTACTTTTG
14694 AAACGACAAATTAAGTCGTTGCGAAATCTTAAACTTTCAGCAG
131 AAACGACAAATTAAGTCGTTGCGAAATCTTAAACTTTCAGCAG
* *
14737 CGACTTTTGTTAGTCGTTGCGAAATCTTAAACTTTTCGCAACGACTTTTGTTAGTCGTTGCTCAA
1 CGACTTTTGTTAGTCGTTGCGAAATCATAAACTTTTCGCAACGACTTTTGTTAGTCGTTGCTTAA
*
14802 TAT-TTGTTACTAATTGATTTTCGAAGCGACCTTGAAAGTCGCTACAAAAAGCATGATTACTTTT
66 TATATT-TTACTAATTGATTTTCGAAGCGACCTTGAAAGTCGCTACAAAAAACATGATTACTTTT
* *
14866 GAAACGACAGATTAAGTCGTTGCGAAATCTTAAACTTTCCGCAG
130 GAAACGACAAATTAAGTCGTTGCGAAATCTTAAACTTTCAGCAG
* * *
14910 CGACTTTTGTTAGTCGTTGAGAAATCGTAAACTTTTCGCAACGACTTTTGTTAGTTGTTGCTTAA
1 CGACTTTTGTTAGTCGTTGCGAAATCATAAACTTTTCGCAACGACTTTTGTTAGTCGTTGCTTAA
* * * *
14975 TATATGTTACTAATTGATTTTCGCAGCAACCTTGAAAGTCGCTAC-AAAAACATAATTACTTTTG
66 TATATTTTACTAATTGATTTTCGAAGCGACCTTGAAAGTCGCTACAAAAAACATGATTACTTTTG
* *
15039 AAGCCACAAATTAAGTCG
131 AAACGACAAATTAAGTCG
15057 CAATGACAAA
Statistics
Matches: 291, Mismatches: 27, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
172 34 0.12
173 256 0.88
174 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (173 bp):
CGACTTTTGTTAGTCGTTGCGAAATCATAAACTTTTCGCAACGACTTTTGTTAGTCGTTGCTTAA
TATATTTTACTAATTGATTTTCGAAGCGACCTTGAAAGTCGCTACAAAAAACATGATTACTTTTG
AAACGACAAATTAAGTCGTTGCGAAATCTTAAACTTTCAGCAG
Found at i:19705 original size:12 final size:12
Alignment explanation
Indices: 19688--19727 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
19678 GTAGCTTTTT
19688 CTCATGGAGGTA
1 CTCATGGAGGTA
*
19700 CTCATGGAGGTC
1 CTCATGGAGGTA
*
19712 CTCATGGAGGTG
1 CTCATGGAGGTA
19724 CTCA
1 CTCA
19728 ATGATCCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.20, C:0.23, G:0.33, T:0.25
Consensus pattern (12 bp):
CTCATGGAGGTA
Found at i:22712 original size:7 final size:7
Alignment explanation
Indices: 22680--22704 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
22670 AAGGAGTAAT
22680 GAAAAAG
1 GAAAAAG
22687 GAAAAAG
1 GAAAAAG
22694 GAAAAAG
1 GAAAAAG
22701 GAAA
1 GAAA
22705 GAAAAAAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (7 bp):
GAAAAAG
Found at i:25235 original size:14 final size:14
Alignment explanation
Indices: 25216--25259 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
25206 ATCCCCATTA
25216 AAAAAAAGAAAGAG
1 AAAAAAAGAAAGAG
25230 AAAAAAA-AAA-AG
1 AAAAAAAGAAAGAG
25242 -AAAAAAGAAAAGAG
1 AAAAAAAG-AAAGAG
25256 AAAA
1 AAAA
25260 GAAAAGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
11 6 0.23
12 2 0.08
13 6 0.23
14 9 0.35
15 3 0.12
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAAGAG
Found at i:25243 original size:12 final size:12
Alignment explanation
Indices: 25216--25283 Score: 64
Period size: 12 Copynumber: 5.2 Consensus size: 12
25206 ATCCCCATTA
25216 AAAAAAAGAAAGAG
1 AAAAAAA-AAA-AG
25230 AAAAAAAAAAAG
1 AAAAAAAAAAAG
25242 AAAAAAGAAAAGAG
1 AAAAAA-AAAA-AG
* *
25256 AAAAGAAAAGAAT
1 AAAA-AAAAAAAG
*
25269 AATAAAAAAAAG
1 AAAAAAAAAAAG
25281 AAA
1 AAA
25284 TAGAAATTGA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
12 16 0.36
13 11 0.24
14 16 0.36
15 2 0.04
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:25253 original size:26 final size:27
Alignment explanation
Indices: 25217--25289 Score: 82
Period size: 26 Copynumber: 2.8 Consensus size: 27
25207 TCCCCATTAA
25217 AAAAAAG-AAAGAGAAAA-AAAAAAAG
1 AAAAAAGAAAAGAGAAAAGAAAAAAAG
* *
25242 AAAAAAGAAAAGAGAAAAGAAAAGAAT
1 AAAAAAGAAAAGAGAAAAGAAAAAAAG
*
25269 AATAAAA-AAAAGA-AATAGAAA
1 AA-AAAAGAAAAGAGAAAAGAAA
25290 TTGAATTGCA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
25 7 0.17
26 17 0.40
27 14 0.33
28 4 0.10
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (27 bp):
AAAAAAGAAAAGAGAAAAGAAAAAAAG
Found at i:25278 original size:32 final size:32
Alignment explanation
Indices: 25217--25283 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
25207 TCCCCATTAA
25217 AAAAAAGAAAGAGAAAAAAAAAAAGAAAAAAG
1 AAAAAAGAAAGAGAAAAAAAAAAAGAAAAAAG
* *
25249 AAAAGAGAAA-AGAAAAGAATAATAA-AAAAAAG
1 AAAAAAGAAAGAGAAAA-AA-AAAAAGAAAAAAG
25281 AAA
1 AAA
25284 TAGAAATTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 6 0.19
32 21 0.68
33 4 0.13
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (32 bp):
AAAAAAGAAAGAGAAAAAAAAAAAGAAAAAAG
Found at i:25372 original size:14 final size:14
Alignment explanation
Indices: 25348--25404 Score: 59
Period size: 14 Copynumber: 4.3 Consensus size: 14
25338 CAAGAGACGT
*
25348 TTTTCAA-AAATTG
1 TTTTCAAGAAATGG
25361 TTTTCAAGAAATGG
1 TTTTCAAGAAATGG
*
25375 TTTTCGAG-AATGAG
1 TTTTCAAGAAATG-G
25389 TTTTCAA-AAA-GG
1 TTTTCAAGAAATGG
25401 TTTT
1 TTTT
25405 AAGTTTTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
12 5 0.13
13 12 0.32
14 21 0.55
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (14 bp):
TTTTCAAGAAATGG
Found at i:25984 original size:25 final size:25
Alignment explanation
Indices: 25954--26055 Score: 88
Period size: 25 Copynumber: 4.1 Consensus size: 25
25944 CAGTTCGAAG
25954 GATAAGCAGAAGACGGTCCTTTTAA
1 GATAAGCAGAAGACGGTCCTTTTAA
* *
25979 GATAAGCGGAAGACGGTCTTTTTAA
1 GATAAGCAGAAGACGGTCCTTTTAA
* *
26004 GATGAATTG-A-AAGACAG---TTTGAA
1 GAT-AA--GCAGAAGACGGTCCTTTTAA
*
26027 GGATAAGCAGAAGACGATCCTTTTAA
1 -GATAAGCAGAAGACGGTCCTTTTAA
26053 GAT
1 GAT
26056 CGAATTGGAA
Statistics
Matches: 60, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
21 1 0.02
22 1 0.02
23 12 0.20
24 3 0.05
25 29 0.48
26 13 0.22
28 1 0.02
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.25
Consensus pattern (25 bp):
GATAAGCAGAAGACGGTCCTTTTAA
Found at i:26034 original size:49 final size:50
Alignment explanation
Indices: 25979--26099 Score: 165
Period size: 50 Copynumber: 2.4 Consensus size: 50
25969 GTCCTTTTAA
* * **
25979 GATAAGCGGAAGACGGTCTTTTTAAGAT-GAATTGAAAGACAGTTTGAAG
1 GATAAGCGGAAGACGATCCTTTTAAGATCGAATTGAAAGACAGTTCAAAG
* *
26028 GATAAGCAGAAGACGATCCTTTTAAGATCGAATTGGAAGACAGTTCAAAG
1 GATAAGCGGAAGACGATCCTTTTAAGATCGAATTGAAAGACAGTTCAAAG
26078 GATAAGCGGAAGAC-AGTCCTTT
1 GATAAGCGGAAGACGA-TCCTTT
26100 GAGATTGAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
49 26 0.41
50 37 0.59
ACGTcount: A:0.37, C:0.12, G:0.26, T:0.24
Consensus pattern (50 bp):
GATAAGCGGAAGACGATCCTTTTAAGATCGAATTGAAAGACAGTTCAAAG
Found at i:26071 original size:50 final size:49
Alignment explanation
Indices: 25979--26114 Score: 168
Period size: 49 Copynumber: 2.8 Consensus size: 49
25969 GTCCTTTTAA
* * * **
25979 GATAAGCGGAAGACGGTCTTTTTAAGATGAATTGAAAGACAGTTTGAAG
1 GATAAGCGGAAGACGATCCTTTTAAGATGAATTGGAAGACAGTTCAAAG
*
26028 GATAAGCAGAAGACGATCCTTTTAAGATCGAATTGGAAGACAGTTCAAAG
1 GATAAGCGGAAGACGATCCTTTTAAGAT-GAATTGGAAGACAGTTCAAAG
*
26078 GATAAGCGGAAGAC-AGTCC-TTTGAGATTGAATTGGAA
1 GATAAGCGGAAGACGA-TCCTTTTAAGA-TGAATTGGAA
26115 AACAACTCAA
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
49 41 0.54
50 35 0.46
ACGTcount: A:0.38, C:0.11, G:0.27, T:0.24
Consensus pattern (49 bp):
GATAAGCGGAAGACGATCCTTTTAAGATGAATTGGAAGACAGTTCAAAG
Found at i:26128 original size:50 final size:50
Alignment explanation
Indices: 25979--26151 Score: 131
Period size: 49 Copynumber: 3.5 Consensus size: 50
25969 GTCCTTTTAA
* * * ** **
25979 GATAAGCGGAAGACGGTCTTTTTAAGAT-GAATT-GAAAGACAGTTTGAAG
1 GATAAGCAGAAGACGATCCTTTTAAGATCGAATTGGAAA-ACAACTCAAAG
* **
26028 GATAAGCAGAAGACGATCCTTTTAAGATCGAATTGGAAGACAGTTCAAAG
1 GATAAGCAGAAGACGATCCTTTTAAGATCGAATTGGAAAACAACTCAAAG
* * *
26078 GATAAGCGGAAGAC-AGTCC-TTTGAGATTGAATTGGAAAACAACTCAAAAG
1 GATAAGCAGAAGACGA-TCCTTTTAAGATCGAATTGGAAAACAACTC-AAAG
* * * *
26128 G-TAATCAGAAAATGATCCTCTTAA
1 GATAAGCAGAAGACGATCCTTTTAA
26152 AAAAATGAGT
Statistics
Matches: 100, Mismatches: 18, Indels: 11
0.78 0.14 0.09
Matches are distributed among these distances:
49 58 0.58
50 39 0.39
51 3 0.03
ACGTcount: A:0.40, C:0.13, G:0.24, T:0.24
Consensus pattern (50 bp):
GATAAGCAGAAGACGATCCTTTTAAGATCGAATTGGAAAACAACTCAAAG
Found at i:30618 original size:20 final size:20
Alignment explanation
Indices: 30593--30644 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
30583 GGGGGCAGTA
*
30593 GATACCAAAAAAAAAGAATT
1 GATACCAAAAAAAAACAATT
*
30613 GATACCAAAAAAACACAATT
1 GATACCAAAAAAAAACAATT
*
30633 CATACCAAAAAA
1 GATACCAAAAAA
30645 CAGTAGATAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.63, C:0.17, G:0.06, T:0.13
Consensus pattern (20 bp):
GATACCAAAAAAAAACAATT
Found at i:38424 original size:19 final size:18
Alignment explanation
Indices: 38387--38425 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
38377 TAATATATAA
*
38387 TTTAACAGTAAACTTCAG
1 TTTAACAGTAAACTGCAG
*
38405 TTTATACAGTAATCTGCAG
1 TTTA-ACAGTAAACTGCAG
38424 TT
1 TT
38426 GAGGCAATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (18 bp):
TTTAACAGTAAACTGCAG
Found at i:40576 original size:2 final size:2
Alignment explanation
Indices: 40528--40558 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
40518 TGTTCAATGG
40528 AT 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 AT A
40559 GATGATGCGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42732 original size:150 final size:150
Alignment explanation
Indices: 42445--42744 Score: 557
Period size: 149 Copynumber: 2.0 Consensus size: 150
42435 AGAGAATTGT
* *
42445 TATGTTTTCAAGATCTCCATCAACAAATACTATCTTACTCGATTTAACGCTTCAATTTTTTTTTC
1 TATGTTTTCAAGATCTCCATCAACAAATACTATCTTACTCGATTTAACACTTCAAGTTTTTTTTC
42510 TTTGTTCTATTTGTCGAATTAAGTTAATTTACGAAGGACTCAAAAGCTATTTTTTATGTTTCAAT
66 TTTGTTCTATTTGTCGAATTAAGTTAATTTACGAAGGACTCAAAAGCTATTTTTTATGTTTCAAT
*
42575 TTTAAAAAAGGCTTCCGACA
131 TTTAAAAAAGGCTTCCAACA
42595 TATGTTTTCAAGATCTCCATCAACAAATACTATCTTACTCGATTTAACACTTC-AGTTTTTTTTC
1 TATGTTTTCAAGATCTCCATCAACAAATACTATCTTACTCGATTTAACACTTCAAGTTTTTTTTC
*
42659 TTTGTTCTATTTGTCGAATTAAGTTAATTTATGAAGGACTCAAAAGCTATTTTTTATGTTTCAAT
66 TTTGTTCTATTTGTCGAATTAAGTTAATTTACGAAGGACTCAAAAGCTATTTTTTATGTTTCAAT
42724 TTTAAAAAAGGCTTCCAACA
131 TTTAAAAAAGGCTTCCAACA
42744 T
1 T
42745 TTTCTAGTTT
Statistics
Matches: 146, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
149 94 0.64
150 52 0.36
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.43
Consensus pattern (150 bp):
TATGTTTTCAAGATCTCCATCAACAAATACTATCTTACTCGATTTAACACTTCAAGTTTTTTTTC
TTTGTTCTATTTGTCGAATTAAGTTAATTTACGAAGGACTCAAAAGCTATTTTTTATGTTTCAAT
TTTAAAAAAGGCTTCCAACA
Found at i:44060 original size:4 final size:4
Alignment explanation
Indices: 44051--44077 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
44041 ATGATATTAA
44051 ATTG ATTG ATTG ATTG ATTG ATTG ATT
1 ATTG ATTG ATTG ATTG ATTG ATTG ATT
44078 TGAATATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
ATTG
Found at i:44127 original size:137 final size:131
Alignment explanation
Indices: 43983--44281 Score: 454
Period size: 137 Copynumber: 2.2 Consensus size: 131
43973 TTATATATAT
* *
43983 TAAATTGATTGATGGATTTGAATATATTTTGATCCAATTAGAATCAATTAGTACTAAAATGATAT
1 TAAATTGATTGATTGATTTGAATATATCTTGATCCAATTAGAATCAATTAGTAC--AAATGATAT
44048 TAAATTGATTGATTGATTGATTGATTGATTTGAATATCTTGATCCAATTAGAATCAATTAGTACT
64 T-AA---ATTGATTGATTGATTGATTGATTTGAATATCTTGATCCAATTAGAATCAATTAGTACT
44113 AATGATA
125 AATGATA
* *
44120 TAAATTGATTGATTGATTGATTGATTTGAATATCTTGATCCAATTAGAATCAATTAGTACCAATG
1 TAAATTGATTGATTGA-T--TTGA-AT--ATATCTTGATCCAATTAGAATCAATTAGTACAAATG
44185 ATATTAAATTGATTGATTGATTGATTGATTTGAATATCTTGATCCAATTAGAATCAATTAGTACT
60 ATATTAAATTGATTGATTGATTGATTGATTTGAATATCTTGATCCAATTAGAATCAATTAGTACT
44250 AATGATA
125 AATGATA
44257 TAAATTGATTGATTGATTTGAATAT
1 TAAATTGATTGATTGATTTGAATAT
44282 TGATCAAATT
Statistics
Matches: 151, Mismatches: 5, Indels: 18
0.87 0.03 0.10
Matches are distributed among these distances:
131 2 0.01
133 1 0.01
134 4 0.03
136 1 0.01
137 96 0.64
138 1 0.01
140 6 0.04
141 10 0.07
143 30 0.20
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (131 bp):
TAAATTGATTGATTGATTTGAATATATCTTGATCCAATTAGAATCAATTAGTACAAATGATATTA
AATTGATTGATTGATTGATTGATTTGAATATCTTGATCCAATTAGAATCAATTAGTACTAATGAT
A
Found at i:44154 original size:68 final size:69
Alignment explanation
Indices: 43986--44274 Score: 465
Period size: 68 Copynumber: 4.1 Consensus size: 69
43976 TATATATTAA
* *
43986 ATTGATTGATGGATTTGAATATATTTTGATCCAATTAGAATCAATTAGTACTAAAATGATATTAA
1 ATTGATTGATTGATTTG-A-ATATCTTGATCCAATTAGAATCAATTAGTACT--AATGATATT-A
44051 ATTGATTGATTG
61 A---ATTGATTG
44063 ATTGATTGATTGATTTGAATATCTTGATCCAATTAGAATCAATTAGTACTAATGATA-TAAATTG
1 ATTGATTGATTGATTTGAATATCTTGATCCAATTAGAATCAATTAGTACTAATGATATTAAATTG
44127 ATTG
66 ATTG
*
44131 ATTGATTGATTGATTTGAATATCTTGATCCAATTAGAATCAATTAGTACCAATGATATTAAATTG
1 ATTGATTGATTGATTTGAATATCTTGATCCAATTAGAATCAATTAGTACTAATGATATTAAATTG
44196 ATTG
66 ATTG
44200 ATTGATTGATTGATTTGAATATCTTGATCCAATTAGAATCAATTAGTACTAATGATA-TAAATTG
1 ATTGATTGATTGATTTGAATATCTTGATCCAATTAGAATCAATTAGTACTAATGATATTAAATTG
44264 ATTG
66 ATTG
44268 ATTGATT
1 ATTGATT
44275 TGAATATTGA
Statistics
Matches: 207, Mismatches: 4, Indels: 11
0.93 0.02 0.05
Matches are distributed among these distances:
68 82 0.40
69 67 0.32
71 2 0.01
72 1 0.00
73 7 0.03
75 31 0.15
76 1 0.00
77 16 0.08
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.42
Consensus pattern (69 bp):
ATTGATTGATTGATTTGAATATCTTGATCCAATTAGAATCAATTAGTACTAATGATATTAAATTG
ATTG
Found at i:44301 original size:137 final size:140
Alignment explanation
Indices: 44014--44315 Score: 438
Period size: 137 Copynumber: 2.2 Consensus size: 140
44004 ATATATTTTG
44014 ATCCAATTAGAATCAATTAGTACTAAAATGATATTAAATTGATTGATTGATTGATTGATTGATTT
1 ATCCAATTAGAATCAATTAGTAC-AAAATGATATTAAA-T-ATTGATTGATTGATTGATTGATTT
*
44079 GAATATCTTGATCCAATTAGAATCAATTAGTACTAATGATATAAATTGATTGATTGATTGATTGA
63 GAATATCTTGATCCAATTAGAATCAATTAGTACTAATGATATAAATTGATTGATTGATTGAATGA
* **
44144 TTTGAATATCTTG
128 TTTGAAAATCTAA
*
44157 ATCCAATTAGAATCAATTAGTAC-CAATGATATT-AA-ATTGATTGATTGATTGATTGATTTGAA
1 ATCCAATTAGAATCAATTAGTACAAAATGATATTAAATATTGATTGATTGATTGATTGATTTGAA
44219 TATCTTGATCCAATTAGAATCAATTAGTACTAATGATATAAATTGATTGATTGATTTGAAT-A-T
66 TATCTTGATCCAATTAGAATCAATTAGTACTAATGATATAAATTGATTGATTGA-TTGAATGATT
44282 TGATCAAAT-TAAA
130 TGA--AAATCT-AA
*
44295 AT-CAATTAAAATCAATTAGTA
1 ATCCAATTAGAATCAATTAGTA
44316 TTAATATCAT
Statistics
Matches: 149, Mismatches: 6, Indels: 14
0.88 0.04 0.08
Matches are distributed among these distances:
136 4 0.03
137 101 0.68
138 10 0.07
140 2 0.01
141 9 0.06
143 23 0.15
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.40
Consensus pattern (140 bp):
ATCCAATTAGAATCAATTAGTACAAAATGATATTAAATATTGATTGATTGATTGATTGATTTGAA
TATCTTGATCCAATTAGAATCAATTAGTACTAATGATATAAATTGATTGATTGATTGAATGATTT
GAAAATCTAA
Found at i:44303 original size:10 final size:10
Alignment explanation
Indices: 44288--44312 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
44278 ATATTGATCA
44288 AATTAAAATC
1 AATTAAAATC
44298 AATTAAAATC
1 AATTAAAATC
44308 AATTA
1 AATTA
44313 GTATTAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (10 bp):
AATTAAAATC
Done.