Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1871
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: 379514
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 3
Found at i:160513 original size:60 final size:61
Alignment explanation
Indices: 160404--160518 Score: 178
Period size: 60 Copynumber: 1.9 Consensus size: 61
160394 GGGAAAAAGA
* * * *
160404 GTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAATG
1 GTGCCACAGAGTTGCGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAATG
*
160465 GTGCCACAGAGTTGCGGACTTAAAAGG-AAAAGAGTGCCACGTAGTTGTGGGCTT
1 GTGCCACAGAGTTGCGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
160519 TGCAGAAAAG
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
60 26 0.53
61 23 0.47
ACGTcount: A:0.28, C:0.15, G:0.36, T:0.22
Consensus pattern (61 bp):
GTGCCACAGAGTTGCGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAATG
Found at i:160679 original size:8 final size:8
Alignment explanation
Indices: 160656--160685 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
160646 GATGCAAATA
160656 ATGATGTT
1 ATGATGTT
160664 ATTGATGTT
1 A-TGATGTT
160673 ATGATGTT
1 ATGATGTT
160681 ATGAT
1 ATGAT
160686 TACAGCACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (8 bp):
ATGATGTT
Found at i:161523 original size:16 final size:16
Alignment explanation
Indices: 161504--161558 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
161494 GGTTTTTCCC
161504 TTCTTTTTTTTTTTGT
1 TTCTTTTTTTTTTTGT
*
161520 TTC--TTCTTTTTT-T
1 TTCTTTTTTTTTTTGT
* *
161533 TCCTTTTTTGTTTTGT
1 TTCTTTTTTTTTTTGT
161549 TTCTTTTTTT
1 TTCTTTTTTT
161559 GGAAAAGAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
13 3 0.10
14 8 0.27
15 7 0.23
16 12 0.40
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (16 bp):
TTCTTTTTTTTTTTGT
Found at i:161546 original size:17 final size:17
Alignment explanation
Indices: 161496--161559 Score: 51
Period size: 17 Copynumber: 3.9 Consensus size: 17
161486 TGAAAAGGGG
* *
161496 TTTTTCCCTTCTTT-TT
1 TTTTTTCCTTTTTTGTT
* * *
161512 TTTTTT-GTTTCTTCTT
1 TTTTTTCCTTTTTTGTT
161528 TTTTTTCCTTTTTTGTT
1 TTTTTTCCTTTTTTGTT
* *
161545 TTGTTTCTTTTTTTG
1 TTTTTTCCTTTTTTG
161560 GAAAAGAACA
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
15 4 0.11
16 13 0.35
17 20 0.54
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (17 bp):
TTTTTTCCTTTTTTGTT
Found at i:161825 original size:12 final size:11
Alignment explanation
Indices: 161808--161841 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
161798 TTTTTCTATG
*
161808 TTTTTTTTAGT
1 TTTTTTTTTGT
161819 TTTTTTTTTGT
1 TTTTTTTTTGT
161830 TTTGTTTTTTGT
1 TTT-TTTTTTGT
161842 GTTTACTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 13 0.62
12 8 0.38
ACGTcount: A:0.03, C:0.00, G:0.12, T:0.85
Consensus pattern (11 bp):
TTTTTTTTTGT
Found at i:166464 original size:52 final size:52
Alignment explanation
Indices: 166386--166514 Score: 215
Period size: 52 Copynumber: 2.5 Consensus size: 52
166376 CGAAATATGA
* *
166386 AAATTTGCCTGCATGTATCGATACATT-TAATAGTGTATTGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTCT-ATAGTGTATCGATACATCTGAGC
*
166438 AAATTTGTCTGCATGTATCGATACATTCTATAGTGTATCGATACATCTGAGC
1 AAATTTGCCTGCATGTATCGATACATTCTATAGTGTATCGATACATCTGAGC
166490 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
166515 AAGATTAGTG
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
52 71 0.99
53 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTCTATAGTGTATCGATACATCTGAGC
Found at i:166524 original size:52 final size:52
Alignment explanation
Indices: 166386--166534 Score: 210
Period size: 52 Copynumber: 2.9 Consensus size: 52
166376 CGAAATATGA
* * * *
166386 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATTGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACAATTATTAGTGTATCGATACATCTGAGC
* *
166438 AAATTTGTCTGCATGTATCGATAC-ATTCTATAGTGTATCGATACATCTGAGC
1 AAATTTGCCTGCATGTATCGATACAATTAT-TAGTGTATCGATACATCTGAGC
**
166490 AAATTTGCCTGCATGTATCGATACAAAGATTAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACAATTATTAGTGTATCGATACA
166535 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
51 2 0.02
52 81 0.95
53 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACAATTATTAGTGTATCGATACATCTGAGC
Found at i:166541 original size:13 final size:13
Alignment explanation
Indices: 166523--166547 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
166513 CAAAGATTAG
166523 TGTATCGATACAA
1 TGTATCGATACAA
166536 TGTATCGATACA
1 TGTATCGATACA
166548 TTTTGAGTAA
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:166616 original size:19 final size:19
Alignment explanation
Indices: 166592--166675 Score: 90
Period size: 19 Copynumber: 4.7 Consensus size: 19
166582 TAGCTTACAT
*
166592 TGTATCGATACAACACTTA
1 TGTATCAATACAACACTTA
166611 TGTATCAAT---ACA--T-
1 TGTATCAATACAACACTTA
*
166624 TGTATCAATACAACACTCA
1 TGTATCAATACAACACTTA
*
166643 TGTATCGATACAACACTTTA
1 TGTATCAATACAACAC-TTA
166663 TGTATCAATACAA
1 TGTATCAATACAA
166676 ATCGTTGAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
13 9 0.17
14 1 0.02
16 6 0.11
19 23 0.43
20 14 0.26
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.32
Consensus pattern (19 bp):
TGTATCAATACAACACTTA
Found at i:166628 original size:32 final size:32
Alignment explanation
Indices: 166587--166654 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 32
166577 GGTAGTAGCT
* *
166587 TACATTGTATCGATACAACACTTATGTATCAA
1 TACATTGTATCAATACAACACTCATGTATCAA
*
166619 TACATTGTATCAATACAACACTCATGTATCGA
1 TACATTGTATCAATACAACACTCATGTATCAA
166651 TACA
1 TACA
166655 ACACTTTATG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (32 bp):
TACATTGTATCAATACAACACTCATGTATCAA
Found at i:166629 original size:13 final size:13
Alignment explanation
Indices: 166611--166635 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
166601 ACAACACTTA
166611 TGTATCAATACAT
1 TGTATCAATACAT
166624 TGTATCAATACA
1 TGTATCAATACA
166636 ACACTCATGT
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:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (13 bp):
TGTATCAATACAT
Found at i:171700 original size:13 final size:13
Alignment explanation
Indices: 171682--171708 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
171672 ACATTATGCT
171682 TTGTATCGATACA
1 TTGTATCGATACA
171695 TTGTATCGATACA
1 TTGTATCGATACA
171708 T
1 T
171709 GCACAATTGC
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):
TTGTATCGATACA
Found at i:171797 original size:13 final size:13
Alignment explanation
Indices: 171779--171803 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
171769 CGTGGCACAT
171779 TGTATCGATACAA
1 TGTATCGATACAA
171792 TGTATCGATACA
1 TGTATCGATACA
171804 TGATGAATTG
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:177940 original size:13 final size:13
Alignment explanation
Indices: 177922--177948 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
177912 ACAATGTTCT
177922 TTGTATCGATACA
1 TTGTATCGATACA
177935 TTGTATCGATACA
1 TTGTATCGATACA
177948 T
1 T
177949 GGGTTACTAT
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):
TTGTATCGATACA
Found at i:179453 original size:33 final size:33
Alignment explanation
Indices: 179391--179457 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
179381 CGAGAATTGA
* *
179391 TCACTTCACTTTCGCAGCACATGCGTGAGCACT
1 TCACTTCACTCTCGCAGCACACGCGTGAGCACT
*
179424 TCACTTCACTCTCGCAGCGCACG-GATGAGCACT
1 TCACTTCACTCTCGCAGCACACGCG-TGAGCACT
179457 T
1 T
179458 TAGTGCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 1 0.03
33 29 0.97
ACGTcount: A:0.21, C:0.34, G:0.19, T:0.25
Consensus pattern (33 bp):
TCACTTCACTCTCGCAGCACACGCGTGAGCACT
Found at i:180070 original size:237 final size:237
Alignment explanation
Indices: 179607--180257 Score: 1243
Period size: 237 Copynumber: 2.8 Consensus size: 237
179597 TCTTTCCATA
179607 TTTATAATATGTTATTTGCTTTCTTATCTGTTTTACTTGCCATATTTTTTGTTGTGTATGAAAAA
1 TTTATAATATGTTATTTGCTTTCTTATCTGTTTTACTTGCCATATTTTTTGTTGTGTATGAAAAA
*
179672 CATTTATCTCTCTTAATCTCGTTTTTGCTATAACAAAAAGGGGGAGAA-TTTTTTTAAATAAATT
66 CATTTATCTCTCTTGATCTCGTTTTTGCTATAACAAAAAGGGGGAGAATTTTTTTTAAATAAATT
179736 TTTTATCAAGGGGGAGAAAATTTTTTAAATGAGAGCCTTAATTATTTTAGGAATAGTCGTATTTG
131 TTTTATCAAGGGGGAGAAAATTTTTTAAATGAGAGCCTTAATTATTTTAGGAATAGTCGTATTTG
179801 TTTTGCTTATCTTTGTGAATTTCCTTGTAATTCGACTATATG
196 TTTTGCTTATCTTTGTGAATTTCCTTGTAATTCGACTATATG
*
179843 TTTATAATATGTTATTTGCTTTCTTATCTGTTTTACTTGCCATATTTTTTGTTGTGGATGAAAAA
1 TTTATAATATGTTATTTGCTTTCTTATCTGTTTTACTTGCCATATTTTTTGTTGTGTATGAAAAA
*
179908 CATTTATCTCTCTTGATCTTGTTTTTGCTATAACAAAAAGGGGGAGAATTTTTTTTAAATAAATT
66 CATTTATCTCTCTTGATCTCGTTTTTGCTATAACAAAAAGGGGGAGAATTTTTTTTAAATAAATT
179973 TTTTATCAAGGGGGAGAAAATTTTTTAAATGAGAGCCTTAATTATTTTAGGAATAGTCGTATTTG
131 TTTTATCAAGGGGGAGAAAATTTTTTAAATGAGAGCCTTAATTATTTTAGGAATAGTCGTATTTG
*
180038 TTTTGCTTATCTTTGTGACTTTCCTTGTAATTCGACTATATG
196 TTTTGCTTATCTTTGTGAATTTCCTTGTAATTCGACTATATG
180080 TTTATAATATGTTATTTGCTTTCTTATCTGTTTTACTTGCCATATTTTTTGTTGTGTATGAAAAA
1 TTTATAATATGTTATTTGCTTTCTTATCTGTTTTACTTGCCATATTTTTTGTTGTGTATGAAAAA
*
180145 CATTTATCTCTCTTGATCTCGTTTTTGTTATAACAAAAAGGGGGAGAATTTTTTTTAAATAAATT
66 CATTTATCTCTCTTGATCTCGTTTTTGCTATAACAAAAAGGGGGAGAATTTTTTTTAAATAAATT
180210 TTTTATCAAGGGGGAG-AAATTTTTTAAATGAGAGCCTTAATTATTTTA
131 TTTTATCAAGGGGGAGAAAATTTTTTAAATGAGAGCCTTAATTATTTTA
180258 TCAAGGGGGA
Statistics
Matches: 407, Mismatches: 7, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
236 142 0.35
237 265 0.65
ACGTcount: A:0.27, C:0.10, G:0.15, T:0.47
Consensus pattern (237 bp):
TTTATAATATGTTATTTGCTTTCTTATCTGTTTTACTTGCCATATTTTTTGTTGTGTATGAAAAA
CATTTATCTCTCTTGATCTCGTTTTTGCTATAACAAAAAGGGGGAGAATTTTTTTTAAATAAATT
TTTTATCAAGGGGGAGAAAATTTTTTAAATGAGAGCCTTAATTATTTTAGGAATAGTCGTATTTG
TTTTGCTTATCTTTGTGAATTTCCTTGTAATTCGACTATATG
Found at i:180778 original size:19 final size:20
Alignment explanation
Indices: 180754--180806 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
180744 CACATCTAGA
**
180754 TGTATCGATACATGTTC-AT
1 TGTATCGATACATGCACAAT
180773 TGTATCGATACATGCACAAT
1 TGTATCGATACATGCACAAT
180793 TGTATCGATACATG
1 TGTATCGATACATG
180807 AAACTGGCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATGCACAAT
Found at i:180874 original size:13 final size:13
Alignment explanation
Indices: 180856--180880 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
180846 CATGGCACAT
180856 TGTATCGATACAA
1 TGTATCGATACAA
180869 TGTATCGATACA
1 TGTATCGATACA
180881 TTGCTTCAAA
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:182417 original size:19 final size:20
Alignment explanation
Indices: 182376--182423 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
182366 AGTTTCATAA
*
182376 ATCGATACAATTGAGTACGT
1 ATCGATACAATTGAGCACGT
182396 ATCGATACAA-TGAGCATC-T
1 ATCGATACAATTGAGCA-CGT
182415 ATCGATACA
1 ATCGATACA
182424 TTGTATCGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.27
Consensus pattern (20 bp):
ATCGATACAATTGAGCACGT
Found at i:182432 original size:13 final size:13
Alignment explanation
Indices: 182414--182482 Score: 78
Period size: 13 Copynumber: 5.8 Consensus size: 13
182404 AATGAGCATC
182414 TATCGATACATTG
1 TATCGATACATTG
182427 TATCGATACA---
1 TATCGATACATTG
* *
182437 AAGC-ATA-A-TG
1 TATCGATACATTG
182447 TATCGATACATTG
1 TATCGATACATTG
182460 TATCGATACATTG
1 TATCGATACATTG
182473 TATCGATACA
1 TATCGATACA
182483 ATGCATAATG
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
8 1 0.02
9 3 0.06
10 4 0.09
11 3 0.06
12 1 0.02
13 35 0.74
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:185026 original size:13 final size:13
Alignment explanation
Indices: 185008--185032 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
184998 TACCACTATT
185008 TGTATCGATACAA
1 TGTATCGATACAA
185021 TGTATCGATACA
1 TGTATCGATACA
185033 TGAAGAATTG
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:185301 original size:13 final size:13
Alignment explanation
Indices: 185283--185307 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
185273 TACCACTATT
185283 TGTATCGATACAA
1 TGTATCGATACAA
185296 TGTATCGATACA
1 TGTATCGATACA
185308 TGAAGAATTG
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:185386 original size:275 final size:275
Alignment explanation
Indices: 184895--185446 Score: 1059
Period size: 275 Copynumber: 2.0 Consensus size: 275
184885 ATGTATCGAT
184895 ACACATCCAGATGTATCGATACATTATGCTTTGTATCGATGCTTGATCATTGTATCGATATATGC
1 ACACATCCAGATGTATCGATACATTATGCTTTGTATCGATGCTTGATCATTGTATCGATATATGC
*
184960 ACAAATGTATTGATACATGAAACTGGTAGTAGCTACCCTACCACTATTTGTATCGATACAATGTA
66 ACAAATGTATCGATACATGAAACTGGTAGTAGCTACCCTACCACTATTTGTATCGATACAATGTA
* * * *
185025 TCGATACATGAAGAATTGTATCGCTACATTGTCCAAACGGCTATAAATGGCTATACTTTCAAATG
131 TCGATACATGAAGAATTGTATCACAACATTGTCCAAACGGCAATAAATGGCTATAATTTCAAATG
185090 CATGTATCAATACATTATGAATTGTATCGATACATAGTAATAGGAATACATGGAAATAAGCAGCA
196 CATGTATCAATACATTATGAATTGTATCGATACATAGTAATAGGAATACATGGAAATAAGCAGCA
185155 AACAAGACAACAATG
261 AACAAGACAACAATG
185170 ACACATCCAGATGTATCGATACATTATGCTTTGTATCGATGCTTGATCATTGTATCGATATATGC
1 ACACATCCAGATGTATCGATACATTATGCTTTGTATCGATGCTTGATCATTGTATCGATATATGC
185235 ACAAATGTATCGATACATGAAACTGGTAGTAGCTACCCTACCACTATTTGTATCGATACAATGTA
66 ACAAATGTATCGATACATGAAACTGGTAGTAGCTACCCTACCACTATTTGTATCGATACAATGTA
185300 TCGATACATGAAGAATTGTATCACAACATTGTCCAAACGGCAATAAATGGCTATAATTTCAAATG
131 TCGATACATGAAGAATTGTATCACAACATTGTCCAAACGGCAATAAATGGCTATAATTTCAAATG
185365 CATGTATCAATACATTATGAATTGTATCGATACATAGTAATAGGAATACATGGAAATAAGCAGCA
196 CATGTATCAATACATTATGAATTGTATCGATACATAGTAATAGGAATACATGGAAATAAGCAGCA
185430 AACAAGACAACAATG
261 AACAAGACAACAATG
185445 AC
1 AC
185447 TACAAACATA
Statistics
Matches: 272, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
275 272 1.00
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (275 bp):
ACACATCCAGATGTATCGATACATTATGCTTTGTATCGATGCTTGATCATTGTATCGATATATGC
ACAAATGTATCGATACATGAAACTGGTAGTAGCTACCCTACCACTATTTGTATCGATACAATGTA
TCGATACATGAAGAATTGTATCACAACATTGTCCAAACGGCAATAAATGGCTATAATTTCAAATG
CATGTATCAATACATTATGAATTGTATCGATACATAGTAATAGGAATACATGGAAATAAGCAGCA
AACAAGACAACAATG
Found at i:191744 original size:13 final size:13
Alignment explanation
Indices: 191726--191751 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
191716 TACACAAAGT
191726 ATGTATCGATACA
1 ATGTATCGATACA
191739 ATGTATCGATACA
1 ATGTATCGATACA
191752 CAAAAAATTG
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:191751 original size:32 final size:33
Alignment explanation
Indices: 191708--191771 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
191698 TAGCCAAACT
**
191708 TGTATCAATACACAAAGTA-TGTATCGATACAA
1 TGTATCAATACACAAAAAATTGTATCGATACAA
*
191740 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCAATACACAAAAAATTGTATCGATACA
191772 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCAATACACAAAAAATTGTATCGATACAA
Found at i:197223 original size:13 final size:13
Alignment explanation
Indices: 197205--197230 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
197195 CAATTTTTTG
197205 TGTATCGATACAT
1 TGTATCGATACAT
197218 TGTATCGATACAT
1 TGTATCGATACAT
197231 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:199790 original size:13 final size:13
Alignment explanation
Indices: 199772--199810 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
199762 ATAATCACCC
*
199772 TGTATCGATACAG
1 TGTATCGATACAA
199785 TGTATCGATACAA
1 TGTATCGATACAA
199798 TGTATCGATACAA
1 TGTATCGATACAA
199811 AGAGAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:200354 original size:13 final size:13
Alignment explanation
Indices: 200336--200361 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
200326 TACACAAAGT
200336 ATGTATCGATACA
1 ATGTATCGATACA
200349 ATGTATCGATACA
1 ATGTATCGATACA
200362 CAAAAAATTG
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:200359 original size:32 final size:33
Alignment explanation
Indices: 200318--200381 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
200308 TAGCCAAACT
**
200318 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
200350 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
200382 TTGGCTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:200882 original size:34 final size:35
Alignment explanation
Indices: 200819--200885 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
200809 CTAAGTGATT
200819 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
200855 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
200886 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:204084 original size:13 final size:13
Alignment explanation
Indices: 204066--204090 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
204056 TTTTCCAGAT
204066 TGTATCGATACAA
1 TGTATCGATACAA
204079 TGTATCGATACA
1 TGTATCGATACA
204091 TTGCTTCAGT
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:206027 original size:13 final size:13
Alignment explanation
Indices: 206009--206034 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
205999 TACACAAAGT
206009 ATGTATCGATACA
1 ATGTATCGATACA
206022 ATGTATCGATACA
1 ATGTATCGATACA
206035 CAAAAAATTG
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:206032 original size:32 final size:33
Alignment explanation
Indices: 205991--206054 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
205981 TAGCCAAACT
**
205991 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
206023 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
206055 TTGGCTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:206555 original size:34 final size:35
Alignment explanation
Indices: 206492--206558 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
206482 CTAAGTGATT
206492 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
206528 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
206559 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:208773 original size:15 final size:15
Alignment explanation
Indices: 208753--208783 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
208743 ATTTCGTTTG
*
208753 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
208768 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
208783 G
1 G
208784 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:210616 original size:21 final size:21
Alignment explanation
Indices: 210587--210631 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
210577 AAGTTTTCAT
*
210587 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
210607 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
210629 TTT
1 TTT
210632 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:212867 original size:13 final size:13
Alignment explanation
Indices: 212849--212874 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
212839 CAATTTTTTG
212849 TGTATCGATACAT
1 TGTATCGATACAT
212862 TGTATCGATACAT
1 TGTATCGATACAT
212875 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:214463 original size:8 final size:8
Alignment explanation
Indices: 214450--214479 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
214440 TTTATTAAAC
214450 TTTGTGAT
1 TTTGTGAT
214458 TTTGTGAT
1 TTTGTGAT
214466 TTTGTGAT
1 TTTGTGAT
214474 TTTGTG
1 TTTGTG
214480 TTGAATGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.10, C:0.00, G:0.27, T:0.63
Consensus pattern (8 bp):
TTTGTGAT
Found at i:214701 original size:13 final size:13
Alignment explanation
Indices: 214683--214720 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
214673 CATTTTTCTT
214683 TGTATCGATACAA
1 TGTATCGATACAA
*
214696 TGTATCGATACAC
1 TGTATCGATACAA
214709 TGTATCGATACA
1 TGTATCGATACA
214721 GGGGAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:214875 original size:20 final size:20
Alignment explanation
Indices: 214832--214877 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
214822 AAATCTTTTG
214832 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
214853 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
214873 CAAAA
1 CAAAA
214878 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:215193 original size:21 final size:20
Alignment explanation
Indices: 215151--215193 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
215141 GGCAGCACCA
* *
215151 CCAGGTCGCAACCGGCATTC
1 CCAGGTCACAACCGGCAGTC
215171 CCAGGTCACAACCGGGCAGTC
1 CCAGGTCACAACC-GGCAGTC
215192 CC
1 CC
215194 CACACTAGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.21, C:0.42, G:0.26, T:0.12
Consensus pattern (20 bp):
CCAGGTCACAACCGGCAGTC
Found at i:220054 original size:13 final size:13
Alignment explanation
Indices: 220036--220061 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
220026 CAATTTTTCG
220036 TGTATCGATACAT
1 TGTATCGATACAT
220049 TGTATCGATACAT
1 TGTATCGATACAT
220062 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:222450 original size:21 final size:21
Alignment explanation
Indices: 222426--222472 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
222416 TTTGATGCTG
222426 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
*
222446 AATTTGAAGTGAAAAACAAGT
1 ATTTTGAAGTGAAAAACAAGT
222467 ATTTTG
1 ATTTTG
222473 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 5 0.22
21 10 0.43
22 8 0.35
ACGTcount: A:0.45, C:0.04, G:0.19, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:222611 original size:13 final size:13
Alignment explanation
Indices: 222593--222618 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
222583 ATAATCACCC
222593 TGTATCGATACAA
1 TGTATCGATACAA
222606 TGTATCGATACAA
1 TGTATCGATACAA
222619 AGAAAAATGT
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):
TGTATCGATACAA
Found at i:224717 original size:15 final size:15
Alignment explanation
Indices: 224697--224727 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
224687 ATTTCGTTTG
*
224697 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
224712 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
224727 G
1 G
224728 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:226560 original size:21 final size:21
Alignment explanation
Indices: 226531--226575 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
226521 AAGTTTTCAT
*
226531 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
226551 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
226573 TTT
1 TTT
226576 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:228808 original size:13 final size:13
Alignment explanation
Indices: 228790--228815 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
228780 CAATTTTTTA
228790 TGTATCGATACAT
1 TGTATCGATACAT
228803 TGTATCGATACAT
1 TGTATCGATACAT
228816 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:230744 original size:13 final size:13
Alignment explanation
Indices: 230726--230755 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
230716 GATACATGGC
230726 ACATTGTATCGAT
1 ACATTGTATCGAT
230739 ACATTGTATCGAT
1 ACATTGTATCGAT
230752 ACAT
1 ACAT
230756 GAAGAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:230746 original size:33 final size:32
Alignment explanation
Indices: 230709--230778 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 32
230699 CTACCACTGT
230709 TTGTATCGATACATG-GCACATTGTATCGATACA
1 TTGTATCGATACATGAG-A-ATTGTATCGATACA
*
230742 TTGTATCGATACATGAAGAATTTTATCGATACA
1 TTGTATCGATACATG-AGAATTGTATCGATACA
230775 TTGT
1 TTGT
230779 CCCAAACGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
33 32 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.37
Consensus pattern (32 bp):
TTGTATCGATACATGAGAATTGTATCGATACA
Found at i:235891 original size:164 final size:166
Alignment explanation
Indices: 235553--235971 Score: 497
Period size: 164 Copynumber: 2.5 Consensus size: 166
235543 TTCCTTATAT
* * * * *
235553 ATTATTGTTTAATCACCATTAAATCAGTTTACAAAAATTCATTCATTTTCATGAGTTTTTTATTT
1 ATTATTATTTAATTAACAGTAAATCAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTTATTT
** **
235618 TTT-TCTTGAAATTTTTCTTTTTCTGAAATGTGTTGTTTTCTACTTCGTATTTATTTTTTGGGGG
66 TTTCT-TTGAAATTTTTCTTTTTCTGAAATACGAAGTTTTCTACTTCGTA--TATTTTTTGGGGG
* *
235682 GGAATTTTCTTGATTTTTAATTTTTAAAATTCATCAAAT
128 GGAATTTTCTTGATTTTTAATTTTTAAAATCCATCAAAG
* * *
235721 ATTATTATTTATTTCACAGTAAATCAGTTTTCAAAGATTCATTCATTTTCATGAGTTTTTTATTT
1 ATTATTATTTAATTAACAGTAAATCAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTTATTT
235786 TTTCTTTGAAATTTTTCTATTTTC-GAAATACGAAGTTTTCTACTTCGTA-ATTTTTT-GGGGGG
66 TTTCTTTGAAATTTTTCT-TTTTCTGAAATACGAAGTTTTCTACTTCGTATATTTTTTGGGGGGG
* * *
235848 ATTTTTCTTGGTTTTTATTTTTTAAAATCCATCAAAG
130 AATTTTCTTGATTTTTAATTTTTAAAATCCATCAAAG
* * * * ** * * ***
235885 ATTATTATTTAATTAATATTAATTCAGTTTTGAAATTTTAATTTATATTT-ATGAGTTTCAGATT
1 ATTATTATTTAATTAACAGTAAATCAGTTTTCAAAAATTCATTCAT-TTTCATGAGTTTTTTATT
*
235949 TTTTCTTTGAAATTCTTCTTTTT
65 TTTTCTTTGAAATTTTTCTTTTT
235972 TTGAGAAACT
Statistics
Matches: 217, Mismatches: 31, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
163 4 0.02
164 103 0.47
165 10 0.05
168 94 0.43
169 6 0.03
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.54
Consensus pattern (166 bp):
ATTATTATTTAATTAACAGTAAATCAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTTATTT
TTTCTTTGAAATTTTTCTTTTTCTGAAATACGAAGTTTTCTACTTCGTATATTTTTTGGGGGGGA
ATTTTCTTGATTTTTAATTTTTAAAATCCATCAAAG
Found at i:236617 original size:23 final size:23
Alignment explanation
Indices: 236571--236618 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
236561 CTAAGCATGA
* *
236571 GGAGAAGAAAAAGAAAAGAGAAG
1 GGAGAAGAAAAAGAAAAAAAAAG
236594 GGAGAA-AGAAAAGAAAAAAAAAG
1 GGAGAAGA-AAAAGAAAAAAAAAG
236617 GG
1 GG
236619 GGGAAGGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 21 0.95
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (23 bp):
GGAGAAGAAAAAGAAAAAAAAAG
Found at i:236867 original size:172 final size:171
Alignment explanation
Indices: 236635--237025 Score: 504
Period size: 173 Copynumber: 2.3 Consensus size: 171
236625 GATGGTAAAG
* * * * ** *
236635 AAGCAATGTTCGGCAGCTTCAGCTACTG-TTTTCGAATCTCCAGCAATAGCAGCTACTAGTTTCG
1 AAGCAATATTC-GCAGCTACAGCTACTGTTTTTGGAA-CTCTAGCAGCAACAGCTACTAGTTT-G
*
236699 A-TTTTGGTGCCAGAAATTAGCAAAGAAAGCGACCCAAA-TAGCAAAGAAGCATGATGAGAAGGA
63 AGTTTTGGTGCCAGAAATTAGCAAAGAAAGCGACCCAAATTAGCAAAGAAGCATGAGGAGAA-GA
236762 GAA-AAAAGAGGAAGAACAA-AGAAAAAGAAAAAAAGATGAAAGTAA
127 -AAGAAAAGAGGAAGAA-AAGAGAAAAAGAAAAAAAGATGAAAGTAA
* * *
236807 AAGCAATATTCAGCAGCTCCAACTACTGTTTTTGGAACTCTAGCAGCAACAGCTACTAGTTTTAG
1 AAGCAATATTC-GCAGCTACAGCTACTGTTTTTGGAACTCTAGCAGCAACAGCTACTAGTTTGAG
* **
236872 TTTTGGTGCTAGAAATTAGCAAAGAAAGCTCCCCAAATTAGCAAAGAAGCATGAGGAGAAGAAAT
65 TTTTGGTGCCAGAAATTAGCAAAGAAAGCGACCCAAATTAGCAAAGAAGCATGAGGAGAAGAAA-
* **
236937 GAAAAGAGGAAGAAAAGAGAAAAAGTAAAATGGATGAAAGTAA
129 GAAAAGAGGAAGAAAAGAGAAAAAGAAAAAAAGATGAAAGTAA
*
236980 ACGCAATATTCGACAGCTACAGCTACTGTTTTTGGAACTCTAGCAG
1 AAGCAATATTCG-CAGCTACAGCTACTGTTTTTGGAACTCTAGCAG
237026 TAAGCAACAT
Statistics
Matches: 192, Mismatches: 20, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
171 3 0.02
172 84 0.44
173 105 0.55
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.20
Consensus pattern (171 bp):
AAGCAATATTCGCAGCTACAGCTACTGTTTTTGGAACTCTAGCAGCAACAGCTACTAGTTTGAGT
TTTGGTGCCAGAAATTAGCAAAGAAAGCGACCCAAATTAGCAAAGAAGCATGAGGAGAAGAAAGA
AAAGAGGAAGAAAAGAGAAAAAGAAAAAAAGATGAAAGTAA
Found at i:238153 original size:13 final size:13
Alignment explanation
Indices: 238135--238161 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
238125 ACATCATGCT
238135 TTGTATCGATACA
1 TTGTATCGATACA
238148 TTGTATCGATACA
1 TTGTATCGATACA
238161 T
1 T
238162 GTTCATTGTA
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):
TTGTATCGATACA
Found at i:238247 original size:13 final size:13
Alignment explanation
Indices: 238226--238255 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
238216 CGATATATGG
*
238226 TACATTGTATCGA
1 TACAATGTATCGA
238239 TACAATGTATCGA
1 TACAATGTATCGA
238252 TACA
1 TACA
238256 TGATGAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
TACAATGTATCGA
Found at i:238253 original size:33 final size:33
Alignment explanation
Indices: 238211--238275 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
238201 TACCACTGTT
* *
238211 TGTATCGATATATGGT-ACATTGTATCGATACAA
1 TGTATCGATACATGATGA-ATTGTATCGATACAA
*
238244 TGTATCGATACATGATGAATTGTATTGATACA
1 TGTATCGATACATGATGAATTGTATCGATACA
238276 TTGCATCTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (33 bp):
TGTATCGATACATGATGAATTGTATCGATACAA
Found at i:239620 original size:142 final size:142
Alignment explanation
Indices: 239431--239712 Score: 501
Period size: 142 Copynumber: 2.0 Consensus size: 142
239421 ATTAAAGGGA
* * *
239431 CAAAATGGTCTCTTCCCATTTTAAATTACCCATTTGGGTTATTTTGGTCATTTTAGAGATATTTA
1 CAAAATGGTCTCTTCCCATTTTAAATTACCAATTTAGGTTATTTTGGTCATTTAAGAGATATTTA
*
239496 TAGCATTTTAGGTCCTTTTGAGGTCAATAGAAAATTTTAAAAAATAAAAGGGCATAACTGTAATT
66 TAGCATTTTAGGTCCTTTTGAGGTCAAAAGAAAATTTTAAAAAATAAAAGGGCATAACTGTAATT
239561 TTAACTTTTAGG
131 TTAACTTTTAGG
*
239573 CAAAATGGTCTCTTCCCATTTTAAATTGCCAATTTAGGTTATTTTGGTCATTTAAGAGATATTTA
1 CAAAATGGTCTCTTCCCATTTTAAATTACCAATTTAGGTTATTTTGGTCATTTAAGAGATATTTA
* *
239638 TAGCATTTTAGGTCCTTTTGAGGTCAAAAGAAAATTTTAAAAAGTAAAAGGGCATAACTGTGATT
66 TAGCATTTTAGGTCCTTTTGAGGTCAAAAGAAAATTTTAAAAAATAAAAGGGCATAACTGTAATT
239703 TTAACTTTTA
131 TTAACTTTTA
239713 AAGTTAAAAT
Statistics
Matches: 133, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
142 133 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.40
Consensus pattern (142 bp):
CAAAATGGTCTCTTCCCATTTTAAATTACCAATTTAGGTTATTTTGGTCATTTAAGAGATATTTA
TAGCATTTTAGGTCCTTTTGAGGTCAAAAGAAAATTTTAAAAAATAAAAGGGCATAACTGTAATT
TTAACTTTTAGG
Found at i:241346 original size:5 final size:5
Alignment explanation
Indices: 241332--241365 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
241322 AAACTAGTTT
*
241332 ATAAA GTAAA ATAAA ATAAA ATAAA ATAAA ATAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAA
241366 TCCAAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:241590 original size:9 final size:9
Alignment explanation
Indices: 241576--241602 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
241566 ATATTAGATG
241576 AATTTTAAA
1 AATTTTAAA
241585 AATTTTAAA
1 AATTTTAAA
241594 AATTTTAAA
1 AATTTTAAA
241603 CTGAGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
AATTTTAAA
Found at i:245486 original size:89 final size:88
Alignment explanation
Indices: 245275--245547 Score: 293
Period size: 88 Copynumber: 3.1 Consensus size: 88
245265 GGGAATAGAG
* **
245275 TTTCCCAAGGATAAAATTATGCAAAAGAAAATTTTAATTTTTTGTTAGAATTGGGTTGGAA-TAT
1 TTTCCCAAGGATAAAATTATGCAAAAGAAAATTTGAATTTTTTGTTAGAACAGGGTT-GAAGTAT
* *
245339 CCTTCA-AAGGAATAGGGATGGAG-
65 CCCTCAGAA-AAATAGGGATGGAGT
* * * * * *
245362 TTTCCTTAAGAATAAAATTTTGCAGAAGAAAATTTGAATTTTTTGTTAGAACGGGGTTAAAGTAT
1 TTTCC-CAAGGATAAAATTATGCAAAAGAAAATTTGAATTTTTTGTTAGAACAGGGTTGAAGTAT
245427 CTCCTCAGAAAAATAGGGATGGAGT
65 C-CCTCAGAAAAATAGGGATGGAGT
* * ** *
245452 TTTCCCAAGGACAAAATTATACAAAAGATTATTTGAA-TTTTTATTAGAACAGGGTTGAAGTATC
1 TTTCCCAAGGATAAAATTATGCAAAAGAAAATTTGAATTTTTTGTTAGAACAGGGTTGAAGTAT-
* * *
245516 CCCTCGGAATAGTAGGGATGGAGT
65 CCCTCAGAAAAATAGGGATGGAGT
*
245540 TTCCCCAA
1 TTTCCCAA
245548 AATCAAAAAT
Statistics
Matches: 155, Mismatches: 25, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
87 7 0.05
88 99 0.64
89 42 0.27
90 7 0.05
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (88 bp):
TTTCCCAAGGATAAAATTATGCAAAAGAAAATTTGAATTTTTTGTTAGAACAGGGTTGAAGTATC
CCTCAGAAAAATAGGGATGGAGT
Found at i:245555 original size:88 final size:90
Alignment explanation
Indices: 245247--245555 Score: 262
Period size: 88 Copynumber: 3.5 Consensus size: 90
245237 TGGGGTTTGG
* * * *
245247 GTATCCCTTCA-AAAGAAT-GGGAATAGAGTTT-CCCAAGGAT-AAAATTATGCAAAAGAAAATT
1 GTATCCCCTCAGAAA-AATAGGG-ATGGAGTTTCCCCAAGAATCAAAATTATACAAAAGAAAATT
* * ** *
245308 TTAATTTTTTGTTAGAATTGGGTTGGAA
64 TGAATTTTTTATTAGAACAGGGTT-AAA
* * ** * * *
245336 -TAT-CCTTCA-AAGGAATAGGGATGGAGTTTCCTTAAGAAT-AAAATTTTGCAGAAGAAAATTT
1 GTATCCCCTCAGAA-AAATAGGGATGGAGTTTCCCCAAGAATCAAAATTATACAAAAGAAAATTT
* *
245397 GAATTTTTTGTTAGAACGGGGTTAAA
65 GAATTTTTTATTAGAACAGGGTTAAA
* * * **
245423 GTATCTCCTCAGAAAAATAGGGATGGAGTTTTCCCAAGGA-CAAAATTATACAAAAGATTATTTG
1 GTATCCCCTCAGAAAAATAGGGATGGAGTTTCCCCAAGAATCAAAATTATACAAAAGAAAATTTG
*
245487 AA-TTTTTATTAGAACAGGGTTGAA
66 AATTTTTTATTAGAACAGGGTTAAA
* * *
245511 GTATCCCCTCGGAATAGTAGGGATGGAGTTTCCCCAA-AATCAAAA
1 GTATCCCCTCAGAAAAATAGGGATGGAGTTTCCCCAAGAATCAAAA
245556 ATTTTTAATG
Statistics
Matches: 180, Mismatches: 32, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
87 22 0.12
88 111 0.62
89 45 0.25
90 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (90 bp):
GTATCCCCTCAGAAAAATAGGGATGGAGTTTCCCCAAGAATCAAAATTATACAAAAGAAAATTTG
AATTTTTTATTAGAACAGGGTTAAA
Found at i:246067 original size:17 final size:17
Alignment explanation
Indices: 246045--246079 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
246035 TTTAAAAACT
246045 TTGGAAAAATCATTTGA
1 TTGGAAAAATCATTTGA
246062 TTGGAAAAATCATTTGA
1 TTGGAAAAATCATTTGA
246079 T
1 T
246080 GGGCCAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.37
Consensus pattern (17 bp):
TTGGAAAAATCATTTGA
Found at i:247602 original size:19 final size:20
Alignment explanation
Indices: 247560--247611 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
247550 AAGCCCAGAA
*
247560 GTATCGATACATATTGCTTT
1 GTATCGATACATATTGCATT
*
247580 GTATCGATACATGTT-CATT
1 GTATCGATACATATTGCATT
247599 GTATCGATACATA
1 GTATCGATACATA
247612 AAGAATTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
GTATCGATACATATTGCATT
Found at i:249294 original size:3 final size:3
Alignment explanation
Indices: 249279--249316 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
249269 AACCATCAAA
*
249279 GAT GAT GAA GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
249317 AGTTAACTCG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.37, C:0.00, G:0.34, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:253609 original size:13 final size:13
Alignment explanation
Indices: 253588--253623 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
253578 AGGATCTTTG
*
253588 TATCAATACATTA
1 TATCGATACATTA
*
253601 TATCGATACATTG
1 TATCGATACATTA
253614 TATCGATACA
1 TATCGATACA
253624 AGGGCACTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (13 bp):
TATCGATACATTA
Found at i:255543 original size:22 final size:21
Alignment explanation
Indices: 255507--255565 Score: 88
Period size: 21 Copynumber: 2.9 Consensus size: 21
255497 AACAAAAAGA
255507 GGGAG-AAA-TTTTATTAAGGG
1 GGGAGAAAATTTTTATTAA-GG
255527 GGGAGAAAATTTTTATTAAGG
1 GGGAGAAAATTTTTATTAAGG
255548 GGGAGAAAATTTTT-TTAA
1 GGGAGAAAATTTTTATTAA
255566 TTAAAAAAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.24
21 19 0.51
22 9 0.24
ACGTcount: A:0.37, C:0.00, G:0.29, T:0.34
Consensus pattern (21 bp):
GGGAGAAAATTTTTATTAAGG
Found at i:256213 original size:72 final size:72
Alignment explanation
Indices: 256115--256271 Score: 269
Period size: 72 Copynumber: 2.2 Consensus size: 72
256105 ATAGGTATTT
*
256115 GTATCGATACATAGAAGGTTGGCTTAAGCTACAAAGGTCAAAACCCTAGAAAATATCGATACAAG
1 GTATCGATACATAGAAGGTTGACTTAAGCTACAAAGGTCAAAACCCTAGAAAATATCGATACAAG
256180 CCCAGAA
66 CCCAGAA
* * *
256187 GTATCGATACATAGAAGGTTGACTTAAGCTACAAAGGTCAAAACCCTGGAAAGTATTGATACAAG
1 GTATCGATACATAGAAGGTTGACTTAAGCTACAAAGGTCAAAACCCTAGAAAATATCGATACAAG
*
256252 CCGAGAA
66 CCCAGAA
256259 GTATCGATACATA
1 GTATCGATACATA
256272 TTGCTTTGTA
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 80 1.00
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.21
Consensus pattern (72 bp):
GTATCGATACATAGAAGGTTGACTTAAGCTACAAAGGTCAAAACCCTAGAAAATATCGATACAAG
CCCAGAA
Found at i:258059 original size:33 final size:33
Alignment explanation
Indices: 258022--258088 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
258012 TTCAATGATT
258022 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
258055 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
258088 T
1 T
258089 TCAAGCTACT
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:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:258060 original size:13 final size:13
Alignment explanation
Indices: 258042--258066 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
258032 CATAAAATGT
258042 TGTATCGATACAA
1 TGTATCGATACAA
258055 TGTATCGATACA
1 TGTATCGATACA
258067 TATTTTTTTG
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:258218 original size:52 final size:52
Alignment explanation
Indices: 258162--258290 Score: 204
Period size: 52 Copynumber: 2.5 Consensus size: 52
258152 CACTGATCTT
* *
258162 TGTATCGATACATGTAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* * **
258214 TGTATCGATACATGCAGGCGAATTTGCCTAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
258266 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
258291 TCATATTTCG
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:272083 original size:1 final size:1
Alignment explanation
Indices: 272077--272165 Score: 70
Period size: 1 Copynumber: 89.0 Consensus size: 1
272067 TGTCCTCCAC
* * * * * * * * *
272077 AAAAAAAAAACAAAACAAAACAAAACAAAAAGAAACAAAACAAAAAAAACAAAAAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
272142 GAAAAAAAACAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAA
272166 GGGTCCGGAT
Statistics
Matches: 64, Mismatches: 24, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 64 1.00
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:272096 original size:10 final size:10
Alignment explanation
Indices: 272078--272163 Score: 92
Period size: 10 Copynumber: 8.9 Consensus size: 10
272068 GTCCTCCACA
*
272078 AAAAAAAAAC
1 AAAACAAAAC
272088 AAAACAAAAC
1 AAAACAAAAC
272098 AAAACAAAA-
1 AAAACAAAAC
272107 AGAAACAAAAC
1 A-AAACAAAAC
272118 AAAA-AAAAC
1 AAAACAAAAC
*
272127 AAAAAAAAAC
1 AAAACAAAAC
*
272137 AAAA-AGAAAA
1 AAAACA-AAAC
272147 AAAAC-AAAC
1 AAAACAAAAC
272156 AAAA-AAAA
1 AAAACAAAA
272164 AAGGGTCCGG
Statistics
Matches: 67, Mismatches: 3, Indels: 13
0.81 0.04 0.16
Matches are distributed among these distances:
9 21 0.31
10 45 0.67
11 1 0.01
ACGTcount: A:0.86, C:0.12, G:0.02, T:0.00
Consensus pattern (10 bp):
AAAACAAAAC
Found at i:272136 original size:34 final size:34
Alignment explanation
Indices: 272077--272165 Score: 128
Period size: 34 Copynumber: 2.7 Consensus size: 34
272067 TGTCCTCCAC
* *
272077 AAAAAAA-AAACAAAACAAAACAAAACAAAAAGA
1 AAAAAAACAAAAAAAACAAAAAAAAACAAAAAGA
*
272110 AACAAAACAAAAAAAACAAAAAAAAACAAAAAGA
1 AAAAAAACAAAAAAAACAAAAAAAAACAAAAAGA
*
272144 AAAAAAACAAACAAAA-AAAAAA
1 AAAAAAACAAAAAAAACAAAAAA
272166 GGGTCCGGAT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
33 12 0.24
34 38 0.76
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (34 bp):
AAAAAAACAAAAAAAACAAAAAAAAACAAAAAGA
Found at i:272164 original size:15 final size:15
Alignment explanation
Indices: 272075--272165 Score: 98
Period size: 15 Copynumber: 6.1 Consensus size: 15
272065 GGTGTCCTCC
*
272075 ACAAAAAAAAAACAAA
1 ACAAACAAAAAA-AAA
*
272091 ACAAAACAAAACAAAA
1 AC-AAACAAAAAAAAA
* *
272107 AGAAACAAAACAAAA
1 ACAAACAAAAAAAAA
272122 A-AAAC-AAAAAAAA
1 ACAAACAAAAAAAAA
272135 ACAAA-AAGAAAAAAA
1 ACAAACAA-AAAAAAA
272150 ACAAACAAAAAAAAA
1 ACAAACAAAAAAAAA
272165 A
1 A
272166 GGGTCCGGAT
Statistics
Matches: 66, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
13 8 0.12
14 8 0.12
15 34 0.52
16 8 0.12
17 8 0.12
ACGTcount: A:0.86, C:0.12, G:0.02, T:0.00
Consensus pattern (15 bp):
ACAAACAAAAAAAAA
Found at i:273584 original size:29 final size:29
Alignment explanation
Indices: 273551--273834 Score: 180
Period size: 30 Copynumber: 9.4 Consensus size: 29
273541 TTCAAAAGTT
*
273551 CACAAGTTAGTGGCATCTTTTTCAAAGCC
1 CACAAGTCAGTGGCATCTTTTTCAAAGCC
* *
273580 CACAAGTCAGTGGCATTTTTTTTCAAAAGCT
1 CACAAGTCAGTGGCA-TCTTTTTC-AAAGCC
* *
273611 CACAAGTCAGTGGCAAC--CTTCAAAGCC
1 CACAAGTCAGTGGCATCTTTTTCAAAGCC
* * * *
273638 CACAAATCAGTGGCACCCTTTTCCGAAGCC
1 CACAAGTCAGTGGCA-TCTTTTTCAAAGCC
* * *
273668 CACAAGTCGGTGGCATCTTTTCCAAAGTC
1 CACAAGTCAGTGGCATCTTTTTCAAAGCC
* * * *
273697 CACAACTCCGTGGCACTCTTTTTCTTTTGTAAGCT
1 CACAAGTCAGTGGCA-TCTTTTTC-----AAAGCC
* * *
273732 CACAACTCTA-TAGCACTCTTTTTCTTTTTAAGCC
1 CACAAGTC-AGTGGCA-TCTTTTTC----AAAGCC
* *
273766 CACAAGTTAGTGGCATCCTTTTCAAAAGCC
1 CACAAGTCAGTGGCATCTTTTTC-AAAGCC
* * *
273796 CACAAGTCAGTGGCAAC-CTTTAAAAGCC
1 CACAAGTCAGTGGCATCTTTTTCAAAGCC
273824 CACAAGTCAGT
1 CACAAGTCAGT
273835 AGCAACCTTC
Statistics
Matches: 205, Mismatches: 37, Indels: 27
0.76 0.14 0.10
Matches are distributed among these distances:
27 19 0.09
28 21 0.10
29 41 0.20
30 54 0.26
31 20 0.10
33 8 0.04
34 18 0.09
35 24 0.12
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (29 bp):
CACAAGTCAGTGGCATCTTTTTCAAAGCC
Found at i:273787 original size:34 final size:36
Alignment explanation
Indices: 273696--273788 Score: 106
Period size: 35 Copynumber: 2.7 Consensus size: 36
273686 TTTCCAAAGT
*
273696 CCACAACTC-CGTGGCACTCTTTTTCTTTTGTAAGC
1 CCACAACTCTAGTGGCACTCTTTTTCTTTTGTAAGC
* *
273731 TCACAACTCTA-TAGCACTCTTTTTCTTTT-TAAGC
1 CCACAACTCTAGTGGCACTCTTTTTCTTTTGTAAGC
* *
273765 CCACAAGT-TAGTGGCA-TCCTTTTC
1 CCACAACTCTAGTGGCACTCTTTTTC
273789 AAAAGCCCAC
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
33 9 0.18
34 15 0.31
35 25 0.51
ACGTcount: A:0.20, C:0.29, G:0.12, T:0.39
Consensus pattern (36 bp):
CCACAACTCTAGTGGCACTCTTTTTCTTTTGTAAGC
Found at i:273795 original size:30 final size:29
Alignment explanation
Indices: 273761--273884 Score: 139
Period size: 28 Copynumber: 4.3 Consensus size: 29
273751 TTTTCTTTTT
* *
273761 AAGCCCACAAGTTAGTGGCATCCTTTTCAA
1 AAGCCCACAAGTCAGTGGCAACC-TTTCAA
273791 AAGCCCACAAGTCAGTGGCAACCTTT-AA
1 AAGCCCACAAGTCAGTGGCAACCTTTCAA
*
273819 AAGCCCACAAGTCAGTAGCAACC-TTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTTCAA
* * *
273847 AAGCACACAAGT-TGAT-GCAAACCTCTCAA
1 AAGCCCACAAGTCAG-TGGC-AACCTTTCAA
273876 AAGCCCACA
1 AAGCCCACA
273885 CAAGTTGGTG
Statistics
Matches: 83, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
27 5 0.06
28 42 0.51
29 15 0.18
30 21 0.25
ACGTcount: A:0.37, C:0.30, G:0.15, T:0.18
Consensus pattern (29 bp):
AAGCCCACAAGTCAGTGGCAACCTTTCAA
Found at i:274062 original size:43 final size:43
Alignment explanation
Indices: 273904--274089 Score: 138
Period size: 43 Copynumber: 4.1 Consensus size: 43
273894 GGCGTCTCCT
* * * *
273904 TTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTGCC
1 TTTAAGTCCAATATAGCTGACCTTGAATCAACACATTGGCA-----CC
* * * * * *
273952 TTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCCCCTTC
1 TTTAAGTCCAATATAGCTGACCTTGAATCAACACATTGG-CAC--C
* * *
273998 ATATTTAAGTCCAATGTAGCTGATCTTGAATCAGCACATTGGCACC
1 ---TTTAAGTCCAATATAGCTGACCTTGAATCAACACATTGGCACC
* *
274044 TTTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCACC
1 TTTAAGTCCAATATAGCTGACCTTGAATCAACACATTGGCACC
274087 TTT
1 TTT
274090 TTCATCTTTA
Statistics
Matches: 116, Mismatches: 16, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
43 41 0.35
44 1 0.01
46 2 0.02
48 38 0.33
49 34 0.29
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.32
Consensus pattern (43 bp):
TTTAAGTCCAATATAGCTGACCTTGAATCAACACATTGGCACC
Found at i:274121 original size:52 final size:52
Alignment explanation
Indices: 274043--274204 Score: 182
Period size: 52 Copynumber: 3.1 Consensus size: 52
274033 ACATTGGCAC
274043 CTTTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCACCTTTTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCACCTTTTTCAT
* * * * *
274095 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCA-CC-TTTT-TCAT
* * * * * * *
274150 CTTTAAGCCCAATATCGTTGGTCGTGAATCAACATATTGGCATCTTTATCA-
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCACCTTTTTCAT
274201 CTTT
1 CTTT
274205 TCTCATCTTC
Statistics
Matches: 90, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
51 4 0.04
52 40 0.44
53 5 0.06
54 5 0.06
55 36 0.40
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (52 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCACCTTTTTCAT
Found at i:274132 original size:95 final size:93
Alignment explanation
Indices: 273904--274142 Score: 282
Period size: 95 Copynumber: 2.5 Consensus size: 93
273894 GGCGTCTCCT
* * * * * *
273904 TTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTGCCTTTAAGTCCAATATCGC
1 TTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATT-G-A-CAT-CCTTTAAGTCCAATATAGC
*
273969 TGGCCTTAAATCAGCATATTGGCCCCTTCATA
62 TGGCCTTAAATCAACATATTGGCCCCTTCATA
* *
274001 TTTAAGTCCAATGTAGCTGATCTTGAATCAGCACATTGGCA-CCTTTAAGTCCAATATAGCTGGC
1 TTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGACATCCTTTAAGTCCAATATAGCTGGC
* * *
274065 CTTGAATCAACATATTGGCACCTTTTTCATC
66 CTTAAATCAACATATTGGC-CC--CTTCATA
* *
274096 TTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTT
1 TTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGACATCCTTT
274143 TTCTCATCTT
Statistics
Matches: 122, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
92 39 0.32
93 2 0.02
94 1 0.01
95 42 0.34
96 6 0.05
97 32 0.26
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.33
Consensus pattern (93 bp):
TTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGACATCCTTTAAGTCCAATATAGCTGGC
CTTAAATCAACATATTGGCCCCTTCATA
Found at i:275044 original size:33 final size:33
Alignment explanation
Indices: 275007--275073 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
274997 TTCAATGATT
275007 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
275040 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
275073 T
1 T
275074 TCAAGCTACT
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:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:275045 original size:13 final size:13
Alignment explanation
Indices: 275027--275051 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
275017 CATAAAATGT
275027 TGTATCGATACAA
1 TGTATCGATACAA
275040 TGTATCGATACA
1 TGTATCGATACA
275052 TATTTTTTTG
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:275132 original size:13 final size:13
Alignment explanation
Indices: 275114--275139 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
275104 ATCACTTAAA
275114 TGTATCGATACAT
1 TGTATCGATACAT
275127 TGTATCGATACAT
1 TGTATCGATACAT
275140 GTAGGCAAAT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:275205 original size:52 final size:52
Alignment explanation
Indices: 275127--275255 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
275117 ATCGATACAT
* *
275127 TGTATCGATACATGTAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
275179 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
275231 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
275256 TCATATTTTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:278512 original size:23 final size:21
Alignment explanation
Indices: 278465--278520 Score: 69
Period size: 23 Copynumber: 2.6 Consensus size: 21
278455 GTCAAAACTA
278465 TGTATCGATACA-TCATAATT
1 TGTATCGATACATTCATAATT
* *
278485 GGTATCAATACATCTCATGAATT
1 TGTATCGATACAT-TCAT-AATT
278508 TGTATCGATACAT
1 TGTATCGATACAT
278521 AAGCTTGTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 10 0.34
22 4 0.14
23 15 0.52
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCATAATT
Found at i:281548 original size:110 final size:110
Alignment explanation
Indices: 281355--281684 Score: 579
Period size: 110 Copynumber: 3.0 Consensus size: 110
281345 ATTTTCAATA
* * * * *
281355 CTCCTATATCTTAGCTTCATTTGAACATAAATTGAAAAGTTTGGACATTGTCAGTAGTCATTGGG
1 CTCCTATGTCTTAGCTTCATGTGAACATAAATTGAAAAGTTTGGGCATTGTTAGCAGTCATTGGG
* *
281420 CAGTTTGCAGGAAGATGATCTCGATTTTTGTTATATGAATTTAAT
66 CAGTTTGCAGGAAGATGATCTTGATTCTTGTTATATGAATTTAAT
* *
281465 CTCCTATGTGTTAGCTTCATGTGAGCATAAATTGAAAAGTTTGGGCATTGTTAGCAGTCATTGGG
1 CTCCTATGTCTTAGCTTCATGTGAACATAAATTGAAAAGTTTGGGCATTGTTAGCAGTCATTGGG
281530 CAGTTTGCAGGAAGATGATCTTGATTCTTGTTATATGAATTTAAT
66 CAGTTTGCAGGAAGATGATCTTGATTCTTGTTATATGAATTTAAT
281575 CTCCTATGTCTTAGCTTCATGTGAACATAAATTGAAAAGTTTGGGCATTGTTAGCAGTCATTGGG
1 CTCCTATGTCTTAGCTTCATGTGAACATAAATTGAAAAGTTTGGGCATTGTTAGCAGTCATTGGG
281640 CAGTTTGCAGGAAGATGATCTTGATTCTTGTTATATGAATTTAAT
66 CAGTTTGCAGGAAGATGATCTTGATTCTTGTTATATGAATTTAAT
281685 TGTTTATTAC
Statistics
Matches: 209, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
110 209 1.00
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (110 bp):
CTCCTATGTCTTAGCTTCATGTGAACATAAATTGAAAAGTTTGGGCATTGTTAGCAGTCATTGGG
CAGTTTGCAGGAAGATGATCTTGATTCTTGTTATATGAATTTAAT
Found at i:283643 original size:7 final size:7
Alignment explanation
Indices: 283631--283655 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
283621 AATTGCCGAG
283631 TTCACAC
1 TTCACAC
283638 TTCACAC
1 TTCACAC
283645 TTCACAC
1 TTCACAC
283652 TTCA
1 TTCA
283656 TTGAAAGGGA
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:0.28, C:0.40, G:0.00, T:0.32
Consensus pattern (7 bp):
TTCACAC
Found at i:285816 original size:35 final size:35
Alignment explanation
Indices: 285770--285838 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
285760 ATACATGTAA
*
285770 GATAACAAAAGGAAAGAATGTCTAAATAAAACTAT
1 GATAACAAAAGGAAAGAATGTCCAAATAAAACTAT
285805 GATAACAAAAGGAAAGAATGTCCAAATAAAACTA
1 GATAACAAAAGGAAAGAATGTCCAAATAAAACTA
285839 CGTTGTCATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.58, C:0.10, G:0.14, T:0.17
Consensus pattern (35 bp):
GATAACAAAAGGAAAGAATGTCCAAATAAAACTAT
Found at i:286925 original size:3 final size:3
Alignment explanation
Indices: 286917--286947 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
286907 TTCAAATCCT
*
286917 TTA TTA TTA TTA GTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
286948 CTATAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:289262 original size:9 final size:9
Alignment explanation
Indices: 289248--289277 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
289238 AGGTTCAACT
289248 AAAAAAAGA
1 AAAAAAAGA
289257 AAAAAAAGA
1 AAAAAAAGA
289266 AAAAATAAGA
1 AAAAA-AAGA
289276 AA
1 AA
289278 GTGTAGATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 14 0.70
10 6 0.30
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:289625 original size:19 final size:19
Alignment explanation
Indices: 289601--289650 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
289591 AAACAGTAAC
289601 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
289620 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
289639 TGTATCGATACA
1 TGTATCGATACA
289651 ATGTATCGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:289705 original size:20 final size:20
Alignment explanation
Indices: 289680--289732 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 20
289670 CTGCCAAGGA
*
289680 AATGTATCGATACATTATTC
1 AATGTATCGATACATTATAC
289700 AATGTATCGAT--A-TATAC
1 AATGTATCGATACATTATAC
*
289717 ATTGTATCGATACATT
1 AATGTATCGATACATT
289733 GATCTTTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 14 0.50
18 1 0.04
19 1 0.04
20 12 0.43
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (20 bp):
AATGTATCGATACATTATAC
Found at i:290764 original size:21 final size:21
Alignment explanation
Indices: 290738--290813 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
290728 CTGCTAAGAA
*
290738 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
290759 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
290779 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
290800 ATGTATCGATACAT
1 ATGTATCGATACAT
290814 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:290784 original size:20 final size:20
Alignment explanation
Indices: 290759--290831 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
290749 CATCTTTTTT
290759 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
290779 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
290800 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
290820 ATGTATCGATAC
1 ATGTATCGATAC
290832 TTTAAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:290795 original size:41 final size:41
Alignment explanation
Indices: 290738--290831 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
290728 CTGCTAAGAA
*
290738 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
290779 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
290820 ATGTATCGATAC
1 ATGTATCGATAC
290832 TTTAAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:293276 original size:13 final size:13
Alignment explanation
Indices: 293258--293295 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
293248 ATAATCACCC
293258 TGTATCGATACAG
1 TGTATCGATACAG
*
293271 TGTATCGATACAT
1 TGTATCGATACAG
293284 TGTATCGATACA
1 TGTATCGATACA
293296 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:293309 original size:20 final size:20
Alignment explanation
Indices: 293284--293360 Score: 73
Period size: 20 Copynumber: 3.6 Consensus size: 20
293274 ATCGATACAT
293284 TGTATCGATACAAAGAAAAA
1 TGTATCGATACAAAGAAAAA
* *
293304 TGTATCGATACATAGAATTTCCAGA
1 TGTATCGATACAAAGAA-----AAA
* *
293329 TGTATCGATACACAGAAACA
1 TGTATCGATACAAAGAAAAA
293349 TGTATCGATACA
1 TGTATCGATACA
293361 TTTTGGACAT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
20 30 0.62
25 18 0.38
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.26
Consensus pattern (20 bp):
TGTATCGATACAAAGAAAAA
Found at i:295404 original size:16 final size:15
Alignment explanation
Indices: 295375--295405 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
295365 ATTTCGTTTG
295375 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
*
295390 GAGCTTCCTCAATTT
1 GAGCTTCCTCATTTT
295405 G
1 G
295406 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.26, G:0.16, T:0.42
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:298698 original size:13 final size:13
Alignment explanation
Indices: 298680--298705 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
298670 CAATTTTTTG
298680 TGTATCGATACAT
1 TGTATCGATACAT
298693 TGTATCGATACAT
1 TGTATCGATACAT
298706 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:298770 original size:21 final size:21
Alignment explanation
Indices: 298744--298819 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
298734 CTGCCAAGAA
*
298744 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
298765 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
298785 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
298806 ATGTATCGATACAT
1 ATGTATCGATACAT
298820 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:298790 original size:20 final size:20
Alignment explanation
Indices: 298765--298837 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
298755 CATCTTTTTT
298765 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
298785 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
298806 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
298826 ATGTATCGATAC
1 ATGTATCGATAC
298838 TTTAAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:298801 original size:41 final size:41
Alignment explanation
Indices: 298744--298837 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
298734 CTGCCAAGAA
*
298744 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
298785 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
298826 ATGTATCGATAC
1 ATGTATCGATAC
298838 TTTAAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:303945 original size:27 final size:27
Alignment explanation
Indices: 303915--303970 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
303905 CGGGAATACT
* *
303915 CCCTATTCCTCCGAGGGGATACTCTAA
1 CCCTATTCCTCCGAGGAGATACTCCAA
303942 CCCTATTCCTCCGAGGAGATACTCCAA
1 CCCTATTCCTCCGAGGAGATACTCCAA
303969 CC
1 CC
303971 TCACTTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.23, C:0.38, G:0.16, T:0.23
Consensus pattern (27 bp):
CCCTATTCCTCCGAGGAGATACTCCAA
Found at i:316031 original size:18 final size:18
Alignment explanation
Indices: 316004--316043 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
315994 TCTGTGCCAC
*
316004 TTGATTTCTTACGATTAG
1 TTGATCTCTTACGATTAG
316022 TTGATCTCTTACGATTAG
1 TTGATCTCTTACGATTAG
316040 TTGA
1 TTGA
316044 ACAAGAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.47
Consensus pattern (18 bp):
TTGATCTCTTACGATTAG
Found at i:319421 original size:19 final size:18
Alignment explanation
Indices: 319395--319486 Score: 80
Period size: 19 Copynumber: 4.8 Consensus size: 18
319385 ATTTGTACAA
*
319395 AAAAAAAACAAAAAAACT
1 AAAAAAAACAAAAAAACC
319413 AAGAAAAAACAAAAAAACC
1 AA-AAAAAACAAAAAAACC
319432 AAAAAAAAAAAACAAAAGAAACC
1 ----AAAAAAAACAAAA-AAACC
*
319455 AAAAACACAA-AAAAAACCC
1 AAAAA-A-AACAAAAAAACC
319474 AAAAAAAA-AAAAA
1 AAAAAAAACAAAAA
319487 CAAACAAAAC
Statistics
Matches: 64, Mismatches: 2, Indels: 17
0.77 0.02 0.20
Matches are distributed among these distances:
17 7 0.11
18 3 0.05
19 29 0.45
20 5 0.08
21 2 0.03
22 11 0.17
23 7 0.11
ACGTcount: A:0.83, C:0.14, G:0.02, T:0.01
Consensus pattern (18 bp):
AAAAAAAACAAAAAAACC
Found at i:319469 original size:42 final size:42
Alignment explanation
Indices: 319393--319496 Score: 133
Period size: 43 Copynumber: 2.5 Consensus size: 42
319383 TTATTTGTAC
*
319393 AAAAAAAAAACAAAAAAACTAAGAAAAAACAAAAAAACC-AA
1 AAAAAAAAAACAAAAAAACCAAGAAAAAACAAAAAAACCAAA
*
319434 AAAAAAAAAACAAAAGAAACCAA-AAACACAA-AAAAAACCCAAA
1 AAAAAAAAAACAAAA-AAACCAAGAAA-A-AACAAAAAAACCAAA
319477 AAAAAAAAAACAAACAAAAC
1 AAAAAAAAAACAAA-AAAAC
319497 AGAAGGGTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
41 18 0.32
42 15 0.27
43 22 0.39
44 1 0.02
ACGTcount: A:0.82, C:0.15, G:0.02, T:0.01
Consensus pattern (42 bp):
AAAAAAAAAACAAAAAAACCAAGAAAAAACAAAAAAACCAAA
Found at i:320823 original size:29 final size:28
Alignment explanation
Indices: 320790--321434 Score: 785
Period size: 28 Copynumber: 22.7 Consensus size: 28
320780 CAATACGACC
* *
320790 CTTTTTAAAGCCCACAAGTCATTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* * *
320818 CTTTTTTAAAGCCCATAAGTCAATGGCAT
1 C-TTTTCAAAGCCCACAAGTCAGTGGCAT
*
320847 CCTTTTAAAAG-CCACAAGTCAGTGGCAT
1 -CTTTTCAAAGCCCACAAGTCAGTGGCAT
*
320875 CTTTTCAAAGCCCACAAGTCAGTAGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* *
320903 CCTTTCAAAGCCCACAAGTTAGTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
*
320931 CCTTTCAAAGCCCACAAGTCAGTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* *
320959 CCTTTCAAAGCCCACAAGTCAGCGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
*
320987 CCTTTCGAAAGCCCACAAGTCAGTGGCAT
1 CTTTTC-AAAGCCCACAAGTCAGTGGCAT
* *
321016 CCTTTCAAAGCCCACCAGTCAGTGGCATT
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-T
* *
321045 TTTTTTAAAGCCCACAAGTCAGTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* *
321073 CTTTTAAAAGCCCACGAGTCAGTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
*
321101 CCTTTCAAAAGCCCACAAGTCAGTGGCAT
1 CTTTTC-AAAGCCCACAAGTCAGTGGCAT
321130 CTTTTCAAAGCCCACAAGTCAGTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* *
321158 CTTTTTAAAGCTCACAAGTCAGTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* *
321186 CCTTTTTAAAGCCCACAAGTTAGTGGCAT
1 -CTTTTCAAAGCCCACAAGTCAGTGGCAT
*
321215 CTTTTCAATAGCCCACGAGTCAGTGGCAT
1 CTTTTCAA-AGCCCACAAGTCAGTGGCAT
* *
321244 CCTTTCAAAAGCCCATAAGTCAGTGGCAT
1 CTTTTC-AAAGCCCACAAGTCAGTGGCAT
* *
321273 CCTTTCAAAGCCCACAAGTTAGTGGCA-
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* *
321300 CCTTTCAAAGCCCACAAGTCAATGGCA-
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
*
321327 CTTTTCAAAAGCCAACAAGTCAGTGGCA-
1 CTTTTC-AAAGCCCACAAGTCAGTGGCAT
* * ** * *
321355 CCTTTCAAAAGCCAACAAGTCAACGACAC
1 CTTTTC-AAAGCCCACAAGTCAGTGGCAT
*
321384 CTTTTCAAAGCCCACAAGTCAGTGGCAACC
1 CTTTTCAAAGCCCACAAGTCAGTGGC-A-T
321414 CTTTTCAAAGCTCACACAAGT
1 CTTTTCAAAGC-C-CACAAGT
321435 TGGTGGCACC
Statistics
Matches: 551, Mismatches: 51, Indels: 26
0.88 0.08 0.04
Matches are distributed among these distances:
27 39 0.07
28 300 0.54
29 189 0.34
30 15 0.03
31 1 0.00
32 7 0.01
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (28 bp):
CTTTTCAAAGCCCACAAGTCAGTGGCAT
Found at i:320873 original size:57 final size:57
Alignment explanation
Indices: 320789--321434 Score: 812
Period size: 57 Copynumber: 11.4 Consensus size: 57
320779 TCAATACGAC
* * * * *
320789 CCTTTTTAAAGCCCACAAGTCATTGGCATCTTTTTTAAAGCCCATAAGTCAATGGCAT
1 CCTTTTCAAAGCCCACAAGTCAGTGGCATC-TTTTCAAAGCCCACAAGTCAGTGGCAT
* *
320847 CCTTTTAAAAG-CCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTAGCAT
1 CCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCAT
* *
320903 CC-TTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCAT
1 CCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCAT
* *
320959 CC-TTTCAAAGCCCACAAGTCAGCGGCATCCTTTCGAAAGCCCACAAGTCAGTGGCAT
1 CCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTC-AAAGCCCACAAGTCAGTGGCAT
* * *
321016 CC-TTTCAAAGCCCACCAGTCAGTGGCATTTTTTTTAAAGCCCACAAGTCAGTGGCAT
1 CCTTTTCAAAGCCCACAAGTCAGTGGCA-TCTTTTCAAAGCCCACAAGTCAGTGGCAT
* * *
321073 -CTTTTAAAAGCCCACGAGTCAGTGGCATCCTTTCAAAAGCCCACAAGTCAGTGGCAT
1 CCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTC-AAAGCCCACAAGTCAGTGGCAT
* *
321130 -CTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTTAAAGCTCACAAGTCAGTGGCAT
1 CCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCAT
* * *
321186 CCTTTTTAAAGCCCACAAGTTAGTGGCATCTTTTCAATAGCCCACGAGTCAGTGGCAT
1 CCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAA-AGCCCACAAGTCAGTGGCAT
* * *
321244 CC-TTTCAAAAGCCCATAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCA-
1 CCTTTTC-AAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCAT
* *
321300 CC-TTTCAAAGCCCACAAGTCAATGGCA-CTTTTCAAAAGCCAACAAGTCAGTGGCA-
1 CCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTC-AAAGCCCACAAGTCAGTGGCAT
* ** * * *
321355 CC-TTTCAAAAGCCAACAAGTCAACGACACCTTTTCAAAGCCCACAAGTCAGTGGCAAC
1 CCTTTTC-AAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGC-AT
321413 CCTTTTCAAAGCTCACACAAGT
1 CCTTTTCAAAGC-C-CACAAGT
321435 TGGTGGCACC
Statistics
Matches: 524, Mismatches: 48, Indels: 30
0.87 0.08 0.05
Matches are distributed among these distances:
54 5 0.01
55 51 0.10
56 168 0.32
57 221 0.42
58 68 0.13
59 5 0.01
60 6 0.01
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (57 bp):
CCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCAT
Found at i:321453 original size:31 final size:30
Alignment explanation
Indices: 321388--321475 Score: 97
Period size: 31 Copynumber: 2.9 Consensus size: 30
321378 CGACACCTTT
** **
321388 TCAAAGCC-CACAAGTCAGTGGCAACCCTTT
1 TCAAAGCCACACAAGTTGGTGGC-ACCCTAG
321418 TCAAAGCTCACACAAGTTGGTGGCACCCTAG
1 TCAAAGC-CACACAAGTTGGTGGCACCCTAG
*
321449 TCAAAGACCACACAAATTGGTGGCACC
1 TCAAAG-CCACACAAGTTGGTGGCACC
321476 TATGTCCGAG
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
30 7 0.14
31 30 0.60
32 13 0.26
ACGTcount: A:0.32, C:0.31, G:0.19, T:0.18
Consensus pattern (30 bp):
TCAAAGCCACACAAGTTGGTGGCACCCTAG
Found at i:323258 original size:12 final size:12
Alignment explanation
Indices: 323241--323273 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
323231 TTACACCATG
323241 ATTATTTTTATT
1 ATTATTTTTATT
*
323253 ATTATTGTTATT
1 ATTATTTTTATT
323265 ATTATTTTT
1 ATTATTTTT
323274 TTCTCAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (12 bp):
ATTATTTTTATT
Found at i:324540 original size:79 final size:79
Alignment explanation
Indices: 324441--324626 Score: 194
Period size: 79 Copynumber: 2.4 Consensus size: 79
324431 TGTCCCCTTG
* * * * * * **
324441 AAAATGACGGGGCTGAAGTATCCCCGGTTGTGAGAAATCGATGA-TTAGGAAAAAAAATTGGGAT
1 AAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTTAGGAAAAAAAACCGGGAT
*
324505 TGGAGTATCCCCTCA
65 TAGAGTATCCCCTCA
* * * * * *
324520 AAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTT
1 AAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGGAAAAAAAACCGGGATT
324585 AGAGTATCCCCTCA
66 AGAGTATCCCCTCA
* **
324599 GAGGTAACGGGGTTGGAGTATCCCCGAT
1 AAAATAACGGGGTTGGAGTATCCCCGAT
324627 GAAATAACGA
Statistics
Matches: 87, Mismatches: 19, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
78 1 0.01
79 86 0.99
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.24
Consensus pattern (79 bp):
AAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGGAAAAAAAACCGGGATT
AGAGTATCCCCTCA
Found at i:324618 original size:28 final size:28
Alignment explanation
Indices: 324578--324649 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
324568 GGAATAAAGC
* **
324578 CGGGGTTAGAGTATCCCCTCA-GAGGTAA
1 CGGGGTTGGAGTATCCCC-CATGAAATAA
*
324606 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCCATGAAATAA
*
324634 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
324650 TCGATTGTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
27 1 0.03
28 37 0.97
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCCATGAAATAA
Found at i:324698 original size:53 final size:52
Alignment explanation
Indices: 324637--324812 Score: 212
Period size: 52 Copynumber: 3.4 Consensus size: 52
324627 GAAATAACGA
* * *
324637 GGTTGGAGTATCCTCGATTGTGAAAAAATTGGTGTTTTTGGAAATAAAATTGG
1 GGTTGGAGTATCCCCGATTGTGAAAAAATTGGTG-TTTTAGAAATAAAATCGG
* * * *
324690 AGTTGGAGTATCCCCGA-T-TAAAGGAAAATTGGTGTTTCAAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAA--AAAATTGGTGTTTTAGAAATAAAATCGG
* * *
324742 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAAATTGGTGTTTTAGAAATAAAATCGG
*
324794 GGTTGAAGTATCCCCGATT
1 GGTTGGAGTATCCCCGATT
324813 ATGAGAAATC
Statistics
Matches: 104, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
51 3 0.03
52 73 0.70
53 26 0.25
54 2 0.02
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.31
Consensus pattern (52 bp):
GGTTGGAGTATCCCCGATTGTGAAAAAATTGGTGTTTTAGAAATAAAATCGG
Found at i:324855 original size:51 final size:52
Alignment explanation
Indices: 324731--324859 Score: 147
Period size: 52 Copynumber: 2.5 Consensus size: 52
324721 GTGTTTCAAA
* * * * *
324731 AATAAAATCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGC
1 AATAAAAGCGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATATTTTAGC
* * *
324783 AATAAAATCGGGGTTGAAGTATCCCCGATTAT-GAGAAATCAATATTTTAAG-
1 AATAAAAGCGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATATTTT-AGC
324834 AAT-AAAGCAGGGGTTGGAGTATCCCC
1 AATAAAAGC-GGGGTTGGAGTATCCCC
324860 TCGGAAATAA
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
50 4 0.06
51 31 0.46
52 32 0.48
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (52 bp):
AATAAAAGCGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATATTTTAGC
Found at i:324960 original size:55 final size:51
Alignment explanation
Indices: 324901--325025 Score: 153
Period size: 51 Copynumber: 2.4 Consensus size: 51
324891 GATTAACGGG
* *
324901 GTTGGAGTATCCCTGATTGT-GAAAAATTTGTGTTTTTTTTAAAAATAAAATCGGA
1 GTTGGAGTATCCCTGATTATAG-AAAATTAGTG----TTTTAAAAATAAAATCGGA
*
324956 GTTGGAGTATCCCCGATTATAGAAAATTAGTGTTTTAAAAATAAAATCGGA
1 GTTGGAGTATCCCTGATTATAGAAAATTAGTGTTTTAAAAATAAAATCGGA
* *
325007 GATGGAATATCCCTGATTA
1 GTTGGAGTATCCCTGATTA
325026 CGGAGAATTG
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
51 35 0.56
55 27 0.43
56 1 0.02
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (51 bp):
GTTGGAGTATCCCTGATTATAGAAAATTAGTGTTTTAAAAATAAAATCGGA
Found at i:324998 original size:264 final size:264
Alignment explanation
Indices: 324527--325024 Score: 723
Period size: 264 Copynumber: 1.9 Consensus size: 264
324517 TCAAAAATAA
* ** *
324527 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTAGAGTAT
1 CGGGGTTGAAGTATCCCCAATTATGAGAAATCAATATTTTAAGAATAAAGCAGGGGTTAGAGTAT
** *
324592 CCCCTCAGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTG
66 CCCCTCAGAAATAACGGGGCTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTG
** * *
324657 TGAAAAAATTGGTGTTTTTGGAAATAAAATTGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGG
131 TGAAAAAATTGGTGTTTTTAAAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTAG
* * *
324722 TGTTTCAAAAATAAAATCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATA
196 TGTTTCAAAAATAAAATCGGAGATGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATA
324787 AAAT
261 AAAT
* *
324791 CGGGGTTGAAGTATCCCCGATTATGAGAAATCAATATTTTAAGAATAAAGCAGGGGTTGGAGTAT
1 CGGGGTTGAAGTATCCCCAATTATGAGAAATCAATATTTTAAGAATAAAGCAGGGGTTAGAGTAT
* * * *
324856 CCCCTCGGAAATAACGGGGCTGGAGTATCCCTGATG-ATTAACGGGGTTGGAGTATCC-CTGATT
66 CCCCTCAGAAATAACGGGGCTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTC-GATT
* * *
324919 GTGAAAAATTTGTGTTTTTTTTAAAAATAAAATCGGAGTTGGAGTATCCCCGATTATA-GAAAAT
130 GTGAAAAAATTG-G-TGTTTTTAAAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAAT
* *
324983 TAGTGTTTTAAAAATAAAATCGGAGATGGAATATCCCTGATT
193 TAGTGTTTCAAAAATAAAATCGGAGATGGAATATCCCCGATT
325025 ACGGAGAATT
Statistics
Matches: 206, Mismatches: 25, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
262 1 0.00
263 34 0.17
264 133 0.65
265 38 0.18
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (264 bp):
CGGGGTTGAAGTATCCCCAATTATGAGAAATCAATATTTTAAGAATAAAGCAGGGGTTAGAGTAT
CCCCTCAGAAATAACGGGGCTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTG
TGAAAAAATTGGTGTTTTTAAAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTAG
TGTTTCAAAAATAAAATCGGAGATGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATA
AAAT
Found at i:327410 original size:33 final size:33
Alignment explanation
Indices: 327372--327438 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
327362 AAAATTTCCA
***
327372 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
327405 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
327438 A
1 A
327439 TTTCCTTGGC
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:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:327411 original size:13 final size:13
Alignment explanation
Indices: 327393--327418 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
327383 ACAAAGATCC
327393 ATGTATCGATACA
1 ATGTATCGATACA
327406 ATGTATCGATACA
1 ATGTATCGATACA
327419 CAGAAAAATG
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:327482 original size:19 final size:19
Alignment explanation
Indices: 327458--327512 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
327448 CAATAGCTAA
*
327458 TTATGTATCGATACAATAC
1 TTATGTATCGATACAAAAC
327477 TTATGTATCGATACAAAAC
1 TTATGTATCGATACAAAAC
327496 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
327513 TTGTTGAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (19 bp):
TTATGTATCGATACAAAAC
Found at i:327601 original size:21 final size:21
Alignment explanation
Indices: 327575--327614 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
327565 GGAATGTATC
327575 ACAAATGTATCGATACATTCT
1 ACAAATGTATCGATACATTCT
327596 ACAAATGTATCGATACATT
1 ACAAATGTATCGATACATT
327615 TGAATTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (21 bp):
ACAAATGTATCGATACATTCT
Found at i:328455 original size:55 final size:55
Alignment explanation
Indices: 328371--328889 Score: 526
Period size: 55 Copynumber: 9.3 Consensus size: 55
328361 ATAAAGCGTA
* * *
328371 TCCTGCTCTTTGAGGACT-AAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGCG
*
328426 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
*
328481 TCCTGCTCTTT---GA--GG---ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
328528 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTCGAAAGGGG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * * *
328583 TCCTGCTCTTTGGGGACTGAAAAATGCCACCAACTTGTGTGGGCTTCGAAAGGGG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * * *
328638 TCCTGCTCTTTGGGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAACA
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GCG
** * *
328699 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGCG
** *
328758 T-CTCGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAATGCG
1 TCCT-GCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGCG
** * *
328817 TCCCACTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
328872 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
328890 AAAAAGCGGA
Statistics
Matches: 411, Mismatches: 28, Indels: 50
0.84 0.06 0.10
Matches are distributed among these distances:
47 40 0.10
48 2 0.00
50 4 0.01
52 4 0.01
54 5 0.01
55 202 0.49
56 8 0.02
58 2 0.00
59 69 0.17
60 49 0.12
61 20 0.05
64 6 0.01
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
Done.