Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1809
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: 34154
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1837 original size:200 final size:199
Alignment explanation
Indices: 1469--1841 Score: 486
Period size: 202 Copynumber: 1.9 Consensus size: 199
1459 TTTTTTTATT
* *
1469 TTTGTAATTAATTTTGCATTAATATTAAAATAATAAATTTTATAATTATTTAATATATTTTGCAC
1 TTTGTAATTAATTTTGCATTAATATTAAAATAATAAATTGTATAATTATTTAATATAATTTGCAC
* * *
1534 ATGAAACAAATTTGACATTTTACTGCAAAATTTTTTTAATATGCACTTTATTAATTTATTTATGT
66 ATGAAACAAATTTGACA-TTGAATGC-AAATTTTTTAAATAT-CACTTTATTAATTTATTTATGT
* *
1599 TTAAAATATATAATTATATATTCAAAAATAAGTAAATCAATCAGCATTCACATGTGAATGCATGT
128 TTAAAATATAAAATTATATATTCAAAAATAAATAAATCAATCAGCATTCACATGTGAATGCATGT
1664 GGTAATA
193 GGTAATA
* * * * *
1671 TTTGTAATTAATTTTGCATTAGTTTTAAAATAATAAATTGTATTA-TACTTTGATATAATTTGTA
1 TTTGTAATTAATTTTGCATTAATATTAAAATAATAAATTGTATAATTA-TTTAATATAATTTGCA
* * *
1735 CATGTAACAAAGTTT-ACA-TGAATGC-AATTTTGAGTTAAATAT-ATTTTATTAGTTTCATTTA
65 CATGAAACAAA-TTTGACATTGAATGCAAATTTT---TTAAATATCACTTTATTAATTT-ATTTA
*
1796 TTTTTAAAATATAAAATTATATATTCAAAAATAAATAAATCAATCA
125 TGTTTAAAATATAAAATTATATATTCAAAAATAAATAAATCAATCA
1842 TTCAAATGCA
Statistics
Matches: 149, Mismatches: 16, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
198 6 0.04
199 11 0.07
200 53 0.36
201 9 0.06
202 67 0.45
203 3 0.02
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (199 bp):
TTTGTAATTAATTTTGCATTAATATTAAAATAATAAATTGTATAATTATTTAATATAATTTGCAC
ATGAAACAAATTTGACATTGAATGCAAATTTTTTAAATATCACTTTATTAATTTATTTATGTTTA
AAATATAAAATTATATATTCAAAAATAAATAAATCAATCAGCATTCACATGTGAATGCATGTGGT
AATA
Found at i:3088 original size:14 final size:14
Alignment explanation
Indices: 3069--3098 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3059 AAGAATGCCA
*
3069 TTTTTTCTTTTTAT
1 TTTTTTCTTTATAT
3083 TTTTTTCTTTATAT
1 TTTTTTCTTTATAT
3097 TT
1 TT
3099 CAACTTTTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.07, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTTCTTTATAT
Found at i:4718 original size:154 final size:156
Alignment explanation
Indices: 4250--4721 Score: 400
Period size: 155 Copynumber: 3.0 Consensus size: 156
4240 ACTAGAAAAA
* * ** *
4250 GATGAACCTATCCTAAA--CACATTCCTTTTG-CATAAAAGTATCCCGGTGACAA-CTAGGACTC
1 GATGAACCTATCCTAAATGCACA--CC-TTCGACATAAAAGCATCCTAGTGACAACCTAGGACTT
* * * * * * * *
4311 AGTTTTAGGAAAAATTACTAAAATACCACGTATGGATGTACCTTCAACATGAAAGTATCCCGGTA
63 AGTTATAAG-AAAATTACAAAAATACCTC-TAAGG-TATACCTTTAACATGAAAGTAT-CTGGTA
*
4376 ACTCTAATTGACAT--TAAAATGATCATAAATGG
124 ACCCTAA-TGACATACTAAAATGATCATAAATGG
* *
4408 GGTGAACCTATCCTAAATGCACACCTTCGACATAAAAGTATCCTAGTGACAACCTAGGACTTAGT
1 GATGAACCTATCCTAAATGCACACCTTCGACATAAAAGCATCCTAGTGACAACCTAGGACTTAGT
* * * * * * * *
4473 TCTAAGAAAATTACAAAAATATCTCTAAGGTATACTTTTGATATAAAAGTATCTAGTAATCCTAA
66 TATAAGAAAATTACAAAAATACCTCTAAGGTATACCTTTAACATGAAAGTATCTGGTAACCCTAA
4538 TAGAC--ACTAAAATGATCATAAATGG
131 T-GACATACTAAAATGATCATAAATGG
*
4563 GATGAACCTATCCTAAATGCACACCCTT-GGCAT-AAAGCCATCGC-A-TGACAACCTAGGACTT
1 GATGAACCTATCCTAAATGCACA-CCTTCGACATAAAAG-CATC-CTAGTGACAACCTAGGACTT
* ** * * * *
4624 GGTTATAA-AAAATTATGAAAATGCC-CTTAGGGTATGCCTTTAACATGAAAGTATTTGGGTAAC
63 AGTTATAAGAAAATTACAAAAATACCTC-TAAGGTATACCTTTAACATGAAAGTATCT-GGTAAC
*
4687 CCTAATGA-ATACTAAAATGAACA-AAGATGG
126 CCTAATGACATACTAAAATGATCATAA-ATGG
4717 GATGA
1 GATGA
4722 CTTTTACCCT
Statistics
Matches: 259, Mismatches: 40, Indels: 34
0.78 0.12 0.10
Matches are distributed among these distances:
152 1 0.00
153 39 0.15
154 58 0.22
155 60 0.23
156 21 0.08
157 7 0.03
158 54 0.21
159 15 0.06
160 4 0.02
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (156 bp):
GATGAACCTATCCTAAATGCACACCTTCGACATAAAAGCATCCTAGTGACAACCTAGGACTTAGT
TATAAGAAAATTACAAAAATACCTCTAAGGTATACCTTTAACATGAAAGTATCTGGTAACCCTAA
TGACATACTAAAATGATCATAAATGG
Found at i:5583 original size:19 final size:18
Alignment explanation
Indices: 5559--5621 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
5549 AAACCGTAAC
5559 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
5578 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
5591 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
5610 TGTATCGATACA
1 TGTATCGATACA
5622 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:5596 original size:13 final size:13
Alignment explanation
Indices: 5578--5602 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5568 ACATAAGTGT
5578 TGTATCGATACAA
1 TGTATCGATACAA
5591 TGTATCGATACA
1 TGTATCGATACA
5603 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5600 original size:32 final size:32
Alignment explanation
Indices: 5559--5629 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
5549 AAACCGTAAC
5559 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
5591 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
5623 TGTATCG
1 TGTATCG
5630 CTACGAAGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:5692 original size:13 final size:13
Alignment explanation
Indices: 5674--5700 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5664 ATTACTCAAA
5674 TGTATCGATACAT
1 TGTATCGATACAT
5687 TGTATCGATACAT
1 TGTATCGATACAT
5700 T
1 T
5701 TGTTCTCTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:9592 original size:164 final size:165
Alignment explanation
Indices: 9207--9601 Score: 413
Period size: 165 Copynumber: 2.4 Consensus size: 165
9197 TTACCTAATA
* * * * * * ** *
9207 AAAACACAAAATTAAACATCCAAGAAATCAAAGT-CAGCATAAAAAAGACATCCA-AAAGTTACA
1 AAAACACAAAATTAAATATCAAACATATCAAAATCCA-CACAAAAATCAGATCCACAAA-TTACA
* * * *
9270 A-AGAAGATTTGGCCATGTAACTTTGGCCTTGGAACAAAATTTCCAATATTTATACTTGAATCCC
64 AGA-AAGATTCGGCCATGTAACTTTGGCCTTAGAACAAAATTTCCAATATTTACACTTAAATCCC
* * * * *
9334 TGAACTTTCTGAAATCATAAATTGGTCTTTATATAACT
128 TAAACTTTCTAAAATCACAAATTAGTCTCTATATAACT
* ** *
9372 AAAACACAAAATTAAATATCAAACCTATCAAAATCCACACAAAAATTTGATCCACAAATTAGAAG
1 AAAACACAAAATTAAATATCAAACATATCAAAATCCACACAAAAATCAGATCCACAAATTACAAG
* * * * **
9437 AAAGATTCGGCCATGT-ACTTTTGGTCTTAGAATAAAATTTTCAATATTTCCACTTAAATGTCTA
66 AAAGATTCGGCCATGTAAC-TTTGGCCTTAGAACAAAATTTCCAATATTTACACTTAAATCCCTA
*
9501 AACTTTCTAAAATTACAAATTAGTCTCTATATAA-T
130 AACTTTCTAAAATCACAAATTAGTCTCTATATAACT
* * * * *
9536 TAAACACAAAATTAAATATCGAACATATCAAAATTCAGACAAAAATCAGTTCCACAAATTACAAG
1 AAAACACAAAATTAAATATCAAACATATCAAAATCCACACAAAAATCAGATCCACAAATTACAAG
9601 A
66 A
9602 GTTCGGCCAA
Statistics
Matches: 189, Mismatches: 37, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
164 60 0.32
165 123 0.65
166 6 0.03
ACGTcount: A:0.45, C:0.17, G:0.09, T:0.28
Consensus pattern (165 bp):
AAAACACAAAATTAAATATCAAACATATCAAAATCCACACAAAAATCAGATCCACAAATTACAAG
AAAGATTCGGCCATGTAACTTTGGCCTTAGAACAAAATTTCCAATATTTACACTTAAATCCCTAA
ACTTTCTAAAATCACAAATTAGTCTCTATATAACT
Found at i:11318 original size:153 final size:154
Alignment explanation
Indices: 10962--11357 Score: 417
Period size: 153 Copynumber: 2.6 Consensus size: 154
10952 AAACTATTAG
* * * *
10962 AATAAATTGAATTTTCACAAACTAATTTAATATAAATTTAATAAAAATATTTGATGAATTTT-AA
1 AATAAATTGAATTTTCA-AAACTGATTTAATATAAATTAAACAAAAATATTTGAAGAATTTTGAA
* * * *
11026 AATTTTTAAACTGAGAAAAAT-CTAACCGAAAAAATTTATAGAGTAGAAAACTCTATATCTTAAG
65 AA-TTATAAACTAAGAAAAATCCTAACCGAAAAAATTTAGAGAGTAAAAAACTCTATATCTTAAG
**
11090 AACAAGAAAAATTCTAAAACTTATAA
129 AACAAGAAAAATTCTAAAACACATAA
* * * * * ** * * *
11116 AACATATTGAATTTTTTAAAATTGAATTAATACGAATTAGACAACAATATTTGAAGAATTTTGGA
1 AATAAATTGAA-TTTTCAAAACTGATTTAATATAAATTAAACAAAAATATTTGAAGAATTTTGAA
* * * * **
11181 AATTATAAATTTAGAAAAATCCT-TCTGAAAAAATTTACGA-AGTAAAAAACTCTATAT-TTGGG
65 AATTATAAACTAAGAAAAATCCTAACCGAAAAAATTTA-GAGAGTAAAAAACTCTATATCTTAAG
* *
11243 TAA-TAGAAAAATTTTAAAACACATAA
129 -AACAAGAAAAATTCTAAAACACATAA
* *
11269 AATAAATTGAATTATTCAAAACTGATTTAATATAAATTAAACAATAATATTTAAAGAATTTTGAA
1 AATAAATTGAATT-TTCAAAACTGATTTAATATAAATTAAACAAAAATATTTGAAGAATTTTGAA
*
11334 AATTATAAACTAAAAAAAATCCTA
65 AATTATAAACTAAGAAAAATCCTA
11358 CAAGAAAAAT
Statistics
Matches: 194, Mismatches: 41, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
152 2 0.01
153 93 0.48
154 88 0.45
155 11 0.06
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.33
Consensus pattern (154 bp):
AATAAATTGAATTTTCAAAACTGATTTAATATAAATTAAACAAAAATATTTGAAGAATTTTGAAA
ATTATAAACTAAGAAAAATCCTAACCGAAAAAATTTAGAGAGTAAAAAACTCTATATCTTAAGAA
CAAGAAAAATTCTAAAACACATAA
Found at i:12347 original size:20 final size:20
Alignment explanation
Indices: 12323--12368 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
12313 TCAGATTTGC
*
12323 TTAATTGAATTAAAATATAAA
1 TTAATTGAATAAAAAT-TAAA
*
12344 -TAATTTAATAAAAATTAAA
1 TTAATTGAATAAAAATTAAA
12363 TTAATT
1 TTAATT
12369 ACATGCATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
TTAATTGAATAAAAATTAAA
Found at i:13713 original size:155 final size:155
Alignment explanation
Indices: 13423--13723 Score: 401
Period size: 155 Copynumber: 1.9 Consensus size: 155
13413 CAAAGTTTAA
* * * *
13423 GAAAAATTATGAAAATGCCCTTAGGGGATACCTTTGATGTAAAAGTGCCTTATACCCCTAAATGA
1 GAAAAATTATGAAAATGCCCTTAGGGGAGACCTTTGATGTAAAAATGACTTATACCCCTAAAGGA
* * * * ** *
13488 CTAAAAAAGGATTATAAATGGGATGGACCTATCCTAAATACCCATATTCGGCATAAAAGTGAAAT
66 CTAAAAAAGGATTAGAAACGGAATGAACCTATCCTAAATACCCATATTCGGCATAAAAGCCAAAC
**
13553 CGGTGATGACCTAGGAGTTAAATTT
131 CGGTGACAACCTAGGAGTTAAATTT
*
13578 GAAAAATTATGAAAATGCCCTTAGGTGAGACCTTTGATGTAAAAAT-ACTTGATACCCCTAAAGG
1 GAAAAATTATGAAAATGCCCTTAGGGGAGACCTTTGATGTAAAAATGACTT-ATACCCCTAAAGG
* * *
13642 ATTTAAAAAGGTTTAGAAACGGAATGAACCTATCCTAAATACCCACT-TTCGGCATAAAA-CCAA
65 ACTAAAAAAGGATTAGAAACGGAATGAACCTATCCTAAATACCCA-TATTCGGCATAAAAGCCAA
13705 ACCTGGTGACAACCTAGGA
129 ACC-GGTGACAACCTAGGA
13724 CTCCATTCTA
Statistics
Matches: 126, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
154 7 0.06
155 118 0.94
156 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (155 bp):
GAAAAATTATGAAAATGCCCTTAGGGGAGACCTTTGATGTAAAAATGACTTATACCCCTAAAGGA
CTAAAAAAGGATTAGAAACGGAATGAACCTATCCTAAATACCCATATTCGGCATAAAAGCCAAAC
CGGTGACAACCTAGGAGTTAAATTT
Found at i:13738 original size:155 final size:155
Alignment explanation
Indices: 13424--13768 Score: 383
Period size: 155 Copynumber: 2.2 Consensus size: 155
13414 AAAGTTTAAG
* * * *
13424 AAAAATTATGAAAATGCCCTTAGGGGATACCTTTGATGTAAAAGTGCCTTATACCCCTAAATGAC
1 AAAAATTATGAAAATGCCCTTAGGGGAGACCTTTGATGTAAAAATGACTTATACCCCTAAAGGAC
* * * * ** *
13489 TAAAAAAGGATTATAAATGGGATGGACCTATCCTAAATACCCATATTCGGCATAAAAGTGAAATC
66 TAAAAAAGGATTAGAAACGGAATGAACCTATCCTAAATACCCATATTCGGCATAAAAGCCAAACC
** * *
13554 GGTGATGACCTAGGAGTTAAATTTG
131 GGTGACAACCTAGGAGCTAAATTTA
*
13579 AAAAATTATGAAAATGCCCTTAGGTGAGACCTTTGATGTAAAAAT-ACTTGATACCCCTAAAGGA
1 AAAAATTATGAAAATGCCCTTAGGGGAGACCTTTGATGTAAAAATGACTT-ATACCCCTAAAGGA
* * *
13643 TTTAAAAAGGTTTAGAAACGGAATGAACCTATCCTAAATACCCACT-TTCGGCATAAAA-CCAAA
65 CTAAAAAAGGATTAGAAACGGAATGAACCTATCCTAAATACCCA-TATTCGGCATAAAAGCCAAA
**
13706 CCTGGTGACAACCTAGGA-CTCCATTCTA
129 CC-GGTGACAACCTAGGAGCTAAATT-TA
** * * * *
13734 AAAAATTACAAAAATGCGCATAGAGGATACCTTTG
1 AAAAATTATGAAAATGCCCTTAGGGGAGACCTTTG
13769 TCGTGAAAGT
Statistics
Matches: 158, Mismatches: 28, Indels: 8
0.81 0.14 0.04
Matches are distributed among these distances:
154 11 0.07
155 146 0.92
156 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (155 bp):
AAAAATTATGAAAATGCCCTTAGGGGAGACCTTTGATGTAAAAATGACTTATACCCCTAAAGGAC
TAAAAAAGGATTAGAAACGGAATGAACCTATCCTAAATACCCATATTCGGCATAAAAGCCAAACC
GGTGACAACCTAGGAGCTAAATTTA
Found at i:13824 original size:155 final size:153
Alignment explanation
Indices: 13665--14570 Score: 874
Period size: 151 Copynumber: 5.9 Consensus size: 153
13655 TAGAAACGGA
* * * * ** *
13665 ATGAACCTATCCTAAATACCCACTTTCGGCATAAAACCAAACCTGGTGACAACCTAGGACTCCAT
1 ATGAACCTATCCTAACTACCCACCTTCGGCATAAAAGCAGACCCAGTGACAACCTAGGACTCGAT
* * * * * *
13730 TCTAAAAAATTACAAAAATGCGC-ATAGAGGATACCTTTGTCGT-GAAAGTATCCCGGTACCTTT
66 TCTAAAAAATTACCAAAATGC-CTCTAGAGGATACCTTCGACGTAG-AAGTA-CCCGATACCTCT
* *
13793 AAAGGACTTAAAAAGGATATAGCTGAG
128 AAAGGACTTAAAAAGGA-AAAGTTGAG
* * * ** *
13820 ATGAACTTATCCTAACTACCCACCTTCTGCATGAAAGTGGACCCAGTGACAACCTAAGACTCGAT
1 ATGAACCTATCCTAACTACCCACCTTCGGCATAAAAGCAGACCCAGTGACAACCTAGGACTCGAT
* * * * *
13885 TTTGAAAAATTACCAAAATACCTCTAGAGGGATATCTTCAACGTAGAAGTACCCGATACCTCTAA
66 TCTAAAAAATTACCAAAATGCCTCTAGA-GGATACCTTCGACGTAGAAGTACCCGATACCTCTAA
* *
13950 AGGCCTTAAAAA-GAAAAGCTGAG
130 AGGACTTAAAAAGGAAAAGTTGAG
* * * * * * * *
13973 ATGAACCTACCCTAACTACCCATCTTTGGCATAAAAACGGATCTAGTGACAACCTAGGACTCG-G
1 ATGAACCTATCCTAACTACCCACCTTCGGCATAAAAGCAGACCCAGTGACAACCTAGGACTCGAT
** * * * *
14037 T-TAAAAAAAAACCAAAATGCCTCTAAAAGATATCTTCGATGTAGAAGTACCCGATACCTCTAAA
66 TCTAAAAAATTACCAAAATGCCTCTAGAGGATACCTTCGACGTAGAAGTACCCGATACCTCTAAA
14101 GGACTT-AAAAGGAAAAGTTGAG
131 GGACTTAAAAAGGAAAAGTTGAG
* * *
14123 ATGAACCTATCCTAACTACCCACCTTTGGCATAAAAGCGGACCTAGTGACAACCTAGGACTCGAT
1 ATGAACCTATCCTAACTACCCACCTTCGGCATAAAAGCAGACCCAGTGACAACCTAGGACTCGAT
* * * * *
14188 TCT-AAAAATTATCGAAATGCC-CTTAGGGGATATCTTCGACGTAGAAGTACCTGATACCTCTAA
66 TCTAAAAAATTACCAAAATGCCTC-TAGAGGATACCTTCGACGTAGAAGTACCCGATACCTCTAA
*
14251 AGGACTT-AAAATGAAAAGTTGAG
130 AGGACTTAAAAAGGAAAAGTTGAG
* * * * *
14274 ATGAGCCTACCCTAACTACCCACCTACGGCATAAAAGCAGACCC-GATGACAACTTAGGACT-TA
1 ATGAACCTATCCTAACTACCCACCTTCGGCATAAAAGCAGACCCAG-TGACAACCTAGGACTCGA
* * ** * * * * *
14337 GTTTTGAAAAATTA-TGAAATGCCTTTAGGGGATACCTTTGACGT-GAAAGTATCTCGGTAGCC-
65 -TTCTAAAAAATTACCAAAATGCCTCTAGAGGATACCTTCGACGTAG-AAGTA-CCCGATA-CCT
*
14399 CTAAAGGACTTAAAAAGGATATAGTTGAG
126 CTAAAGGACTTAAAAAGGA-AAAGTTGAG
* * * *
14428 ATGGACCTATCCTAACTACCCACCTTC-GCATAAAAACAGACCC-GCTGACAACCTAAGACTCGG
1 ATGAACCTATCCTAACTACCCACCTTCGGCATAAAAGCAGACCCAG-TGACAACCTAGGACTCGA
** * * *
14491 TTCTAAGAAAATTATTAAAATGCCCCTAGAGGATACCTTCGACGT-GAAAGTATCCTGATACCCC
65 TTCTAA-AAAATTACCAAAATGCCTCTAGAGGATACCTTCGACGTAG-AAGTA-CCCGATACCTC
14555 TAAAGGACTTAAAAAG
127 TAAAGGACTTAAAAAG
14571 ATTATAGGGG
Statistics
Matches: 630, Mismatches: 101, Indels: 40
0.82 0.13 0.05
Matches are distributed among these distances:
149 4 0.01
150 112 0.18
151 178 0.28
152 25 0.04
153 101 0.16
154 43 0.07
155 150 0.24
156 16 0.03
157 1 0.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (153 bp):
ATGAACCTATCCTAACTACCCACCTTCGGCATAAAAGCAGACCCAGTGACAACCTAGGACTCGAT
TCTAAAAAATTACCAAAATGCCTCTAGAGGATACCTTCGACGTAGAAGTACCCGATACCTCTAAA
GGACTTAAAAAGGAAAAGTTGAG
Found at i:14276 original size:301 final size:304
Alignment explanation
Indices: 13579--14571 Score: 938
Period size: 301 Copynumber: 3.2 Consensus size: 304
13569 GTTAAATTTG
* * * * * * * * * * *
13579 AAAAATTATGAAAATGCCCTTAGGTGAGACCTTTGATGTAAAAATACTTGATACCCCTAAAGGAT
1 AAAAATTATCAAAATGCCCTTAGGGGATATCTTCGACGTAGAAGTACCTGATACCTCTAAAGGAC
* * * * * * *
13644 TTAAAAAGGTTTAGAAA-CGGA-ATGAACCTATCCTAAATACCCACTTTCGGCATAAAACCAAAC
66 TTAAAAA-G---A-AAAGCTGAGATGAACCTACCCTAACTACCCACCTACGGCATAAAAACAGAC
* * * ** * * * *
13707 CTGGTGACAACCTAGGACTCCA-T-TCTAAAAAATTACAAAAATGCGC-ATAGAGGATACCTTTG
126 CAGATGACAACCTAGGACT-TAGTGT-TAAAAAAAAAC-AAAATGC-CTCTAAAAGATACCTTCG
* * * *
13769 TCGTGAAAGTATCCCGGTACCTTTAAAGGACTTAAAAAGGATATAGCTGAGATGAACTTATCCTA
187 ACGTGAAAGTATCCCGGTACCTCTAAAGGACTTAAAAAGGATATAGTTGAGATGAACCTATCCTA
* * * *
13834 ACTACCCACCTTCTGCATGAAAGTGGACCCAGTGACAACCTAAGACTCGATTTTG
252 ACTACCCACCTT-TGCATAAAAGCGGA-CCAGTGACAACCTAAGACTCGATTCTA
* * * *
13889 AAAAATTACCAAAAT-ACCTCTAGAGGGATATCTTCAACGTAGAAGTACCCGATACCTCTAAAGG
1 AAAAATTATCAAAATGCCCT-TAG-GGGATATCTTCGACGTAGAAGTACCTGATACCTCTAAAGG
* * ** * *
13953 CCTTAAAAAGAAAAGCTGAGATGAACCTACCCTAACTACCCATCTTTGGCATAAAAACGGATCTA
64 ACTTAAAAAGAAAAGCTGAGATGAACCTACCCTAACTACCCACCTACGGCATAAAAACAGA-CCA
* * *
14018 G-TGACAACCTAGGAC-TCG-GTTAAAAAAAAACCAAAATGCCTCTAAAAGATATCTTCGATGT-
128 GATGACAACCTAGGACTTAGTGTTAAAAAAAAA-CAAAATGCCTCTAAAAGATACCTTCGACGTG
* *
14079 AGAAGTA-CCCGATACCTCTAAAGGACTT-AAAAGGA-AAAGTTGAGATGAACCTATCCTAACTA
192 A-AAGTATCCCGGTACCTCTAAAGGACTTAAAAAGGATATAGTTGAGATGAACCTATCCTAACTA
*
14141 CCCACCTTTGGCATAAAAGCGGACCTAGTGACAACCTAGGACTCGATTCT-
256 CCCACCTTT-GCATAAAAGCGGACC-AGTGACAACCTAAGACTCGATTCTA
*
14191 AAAAATTATCGAAATGCCCTTAGGGGATATCTTCGACGTAGAAGTACCTGATACCTCTAAAGGAC
1 AAAAATTATCAAAATGCCCTTAGGGGATATCTTCGACGTAGAAGTACCTGATACCTCTAAAGGAC
* * * * *
14256 TTAAAATGAAAAGTTGAGATGAGCCTACCCTAACTACCCACCTACGGCATAAAAGCAGACCCGAT
66 TTAAAAAGAAAAGCTGAGATGAACCTACCCTAACTACCCACCTACGGCATAAAAACAGACCAGAT
* * * ** ** * *** *
14321 GACAACTTAGGACTTAGTTTTGAAAAATTATGAAATGCCTTTAGGGGATACCTTTGACGTGAAAG
131 GACAACCTAGGACTTAGTGTTAAAAAAAAACAAAATGCCTCTAAAAGATACCTTCGACGTGAAAG
* *
14386 TATCTCGGTAGCC-CTAAAGGACTTAAAAAGGATATAGTTGAGATGGACCTATCCTAACTACCCA
196 TATCCCGGTA-CCTCTAAAGGACTTAAAAAGGATATAGTTGAGATGAACCTATCCTAACTACCCA
* * * * *
14450 CCTTCGCATAAAAACAGACCCGCTGACAACCTAAGACTCGGTTCTA
260 CCTTTGCATAAAAGCGGACCAG-TGACAACCTAAGACTCGATTCTA
* * * * *
14496 AGAAAATTATTAAAATGCCCCTAGAGGATACCTTCGACGT-GAAAGTATCCTGATACCCCTAAAG
1 A-AAAATTATCAAAATGCCCTTAGGGGATATCTTCGACGTAG-AAGTA-CCTGATACCTCTAAAG
14560 GACTTAAAAAGA
63 GACTTAAAAAGA
14572 TTATAGGGGG
Statistics
Matches: 562, Mismatches: 95, Indels: 55
0.79 0.13 0.08
Matches are distributed among these distances:
300 2 0.00
301 103 0.18
302 47 0.08
303 94 0.17
304 49 0.09
305 56 0.10
306 74 0.13
307 32 0.06
308 47 0.08
309 5 0.01
310 17 0.03
311 36 0.06
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.24
Consensus pattern (304 bp):
AAAAATTATCAAAATGCCCTTAGGGGATATCTTCGACGTAGAAGTACCTGATACCTCTAAAGGAC
TTAAAAAGAAAAGCTGAGATGAACCTACCCTAACTACCCACCTACGGCATAAAAACAGACCAGAT
GACAACCTAGGACTTAGTGTTAAAAAAAAACAAAATGCCTCTAAAAGATACCTTCGACGTGAAAG
TATCCCGGTACCTCTAAAGGACTTAAAAAGGATATAGTTGAGATGAACCTATCCTAACTACCCAC
CTTTGCATAAAAGCGGACCAGTGACAACCTAAGACTCGATTCTA
Found at i:17891 original size:20 final size:20
Alignment explanation
Indices: 17868--17920 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
17858 ACAATTCAAA
17868 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
17888 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
17908 GTATCGATACATG
1 GTATCGATACATG
17921 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:18008 original size:13 final size:13
Alignment explanation
Indices: 17990--18015 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17980 TACACAAAAT
17990 ATGTATCGATACA
1 ATGTATCGATACA
18003 ATGTATCGATACA
1 ATGTATCGATACA
18016 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:18013 original size:32 final size:34
Alignment explanation
Indices: 17972--18036 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 34
17962 TAGCCAAACT
*
17972 TGTATCGATACAC-AAAATA-TGTATCGATACAA
1 TGTATCGATACACAAAAAAATTGTATCGATACAA
18004 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAAATTGTATCGATACA
18037 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 13 0.43
33 5 0.17
34 12 0.40
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (34 bp):
TGTATCGATACACAAAAAAATTGTATCGATACAA
Found at i:21115 original size:13 final size:13
Alignment explanation
Indices: 21099--21135 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
21089 AATCCCCCTA
* *
21099 TATCGATATAGTG
1 TATCGATACAATG
21112 TATCGATACAATG
1 TATCGATACAATG
21125 TATCGATACAA
1 TATCGATACAA
21136 AGAATGATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:27340 original size:13 final size:13
Alignment explanation
Indices: 27322--27346 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27312 CATTTTATGG
27322 TGTATCGATACAA
1 TGTATCGATACAA
27335 TGTATCGATACA
1 TGTATCGATACA
27347 TACTTTGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:27362 original size:32 final size:33
Alignment explanation
Indices: 27299--27366 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
27289 CGTTACAAGC
*
27299 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATCTTATGGTGTATCGATA
27332 CAATGTATCGATACATACTT-T-GTGTATCGATA
1 CAATGTATCGATACAT-CTTATGGTGTATCGATA
27364 CAA
1 CAA
27367 GTTTGGCTAC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 14 0.42
33 17 0.52
34 2 0.06
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (33 bp):
CAATGTATCGATACATCTTATGGTGTATCGATA
Done.