Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 147 of 190
Found at i:43279912 original size:71 final size:71
Alignment explanation
Indices: 43279824--43280014 Score: 213
Period size: 71 Copynumber: 2.7 Consensus size: 71
43279814 ATTTGATGGC
* * *
43279824 TGAGATCTAACATATGTTGCAGATTCTCAACAGCTTGAGTGAGTATCATCAAATCATTCTTTATC
1 TGAGATCCAACACATGTTGCAGATTCTCAACAGCTTGAGTGAGTAGCATCAAATCATTCTTTATC
*
43279889 GACGGT
66 AACGGT
** * * * *
43279895 TGAGATTTAGCACATGTTGC-GAATTCTCGATAGCTTGAGTGAGTAGCATCGAATCATTCTTTAT
1 TGAGATCCAACACATGTTGCAG-ATTCTCAACAGCTTGAGTGAGTAGCATCAAATCATTCTTTAT
*
43279959 CAATGGT
65 CAACGGT
* * * * * *
43279966 TGAGATCCAACATACGTTGTAGATCCTCAACAACTTGAGTGAGCAGCAT
1 TGAGATCCAACACATGTTGCAGATTCTCAACAGCTTGAGTGAGTAGCAT
43280015 TGAATAAAAC
Statistics
Matches: 98, Mismatches: 20, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
70 1 0.01
71 96 0.98
72 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.32
Consensus pattern (71 bp):
TGAGATCCAACACATGTTGCAGATTCTCAACAGCTTGAGTGAGTAGCATCAAATCATTCTTTATC
AACGGT
Found at i:43280297 original size:2 final size:2
Alignment explanation
Indices: 43280290--43280328 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
43280280 TGGTTTATGA
43280290 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
43280329 AGGATACCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:43282612 original size:23 final size:23
Alignment explanation
Indices: 43282584--43282643 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
43282574 ATAAGTACCA
43282584 CACTGATATGTAGCTGAAGCTAC
1 CACTGATATGTAGCTGAAGCTAC
*
43282607 CACTGATATGTAGCTGTAGCTAC
1 CACTGATATGTAGCTGAAGCTAC
*
43282630 CACTGAAATGTAGC
1 CACTGATATGTAGC
43282644 CGAGACCATC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (23 bp):
CACTGATATGTAGCTGAAGCTAC
Found at i:43282911 original size:18 final size:17
Alignment explanation
Indices: 43282885--43282923 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
43282875 ATTTTCCTTC
43282885 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
43282902 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
43282920 CACA
1 CACA
43282924 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:43284640 original size:42 final size:42
Alignment explanation
Indices: 43284576--43284715 Score: 190
Period size: 42 Copynumber: 3.3 Consensus size: 42
43284566 GATGTGGTTA
* * * * * *
43284576 CGTGTAAGATCATGTCTAGGACATTGGCTTCGTTATGTGATT
1 CGTGTAAGACCATATCTGGGACATTGGCATCGATATGAGATT
* *
43284618 CATGTAAGACCATATCTGGGACATTGACATCGATATGAGATT
1 CGTGTAAGACCATATCTGGGACATTGGCATCGATATGAGATT
* *
43284660 CGTGTAAGACCATGTCTGGGACATTGGCATCGATATGAGAAT
1 CGTGTAAGACCATATCTGGGACATTGGCATCGATATGAGATT
43284702 CGTGTAAGACCATA
1 CGTGTAAGACCATA
43284716 GCTAGCTATT
Statistics
Matches: 85, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 85 1.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (42 bp):
CGTGTAAGACCATATCTGGGACATTGGCATCGATATGAGATT
Found at i:43286636 original size:24 final size:25
Alignment explanation
Indices: 43286604--43286653 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
43286594 TAAGCAAGGC
*
43286604 AAAACAAAA-ACAACAAAAAA-TCAT
1 AAAACAAAAGA-AAAAAAAAAGTCAT
43286628 AAAACAAAAGAAAAAAAAAAGTCAT
1 AAAACAAAAGAAAAAAAAAAGTCAT
43286653 A
1 A
43286654 CAAAGGCATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.76, C:0.12, G:0.04, T:0.08
Consensus pattern (25 bp):
AAAACAAAAGAAAAAAAAAAGTCAT
Found at i:43292600 original size:31 final size:31
Alignment explanation
Indices: 43292508--43292602 Score: 181
Period size: 31 Copynumber: 3.1 Consensus size: 31
43292498 GGCAAATTAC
*
43292508 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
43292539 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
43292570 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
43292601 AA
1 AA
43292603 ATTATCTAAG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:43295564 original size:23 final size:23
Alignment explanation
Indices: 43295520--43295564 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
43295510 TTATCAGTAT
* * *
43295520 CCACCACCACCATGGTACTACCC
1 CCACCACCACCAAGGCAATACCC
*
43295543 CCACCTCCACCAAGGCAATACC
1 CCACCACCACCAAGGCAATACC
43295565 AACACTAGTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.29, C:0.51, G:0.09, T:0.11
Consensus pattern (23 bp):
CCACCACCACCAAGGCAATACCC
Found at i:43298345 original size:26 final size:25
Alignment explanation
Indices: 43298316--43298378 Score: 60
Period size: 26 Copynumber: 2.5 Consensus size: 25
43298306 ATTGCTAATT
43298316 ATTTATTTGATTTTTTAT-TGTTTTAA
1 ATTTATTT-ATTTTTTATAT-TTTTAA
*
43298342 ATTT-TTTAATATTTTTGTATTTTTAA
1 ATTTATTT-AT-TTTTTATATTTTTAA
43298368 A-TTATTTATTT
1 ATTTATTTATTT
43298379 ATGTGACATA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
24 2 0.06
25 9 0.28
26 20 0.62
27 1 0.03
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (25 bp):
ATTTATTTATTTTTTATATTTTTAA
Found at i:43303920 original size:38 final size:38
Alignment explanation
Indices: 43303815--43303920 Score: 142
Period size: 38 Copynumber: 2.8 Consensus size: 38
43303805 ACTATTTTGT
* *
43303815 ATGAGTCATAAAAGTAAGTTTGTTTGTTACGCAAAAGT
1 ATGAGTCATAAAAGTAAGTTTGTTTGTTATGCAAAAGC
* *
43303853 AAGTGTCATAAAAGTAAGTTTGTTTGTTATG-AAAATGC
1 ATGAGTCATAAAAGTAAGTTTGTTTGTTATGCAAAA-GC
* *
43303891 ATGAGTAAAAAAAGTAAGTTTGTTTGTTAT
1 ATGAGTCATAAAAGTAAGTTTGTTTGTTAT
43303921 ATATGTCATA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
37 4 0.07
38 55 0.93
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.37
Consensus pattern (38 bp):
ATGAGTCATAAAAGTAAGTTTGTTTGTTATGCAAAAGC
Found at i:43304319 original size:38 final size:38
Alignment explanation
Indices: 43304276--43304359 Score: 152
Period size: 38 Copynumber: 2.2 Consensus size: 38
43304266 TTCACTATTT
43304276 TGTATGAGTCATAAAAGTAAGTTTGTTTGTTATGTAAAA
1 TGTATGAGTCATAAAAGTAAGTTTGTTTGTTATG-AAAA
43304315 -GTATGAGTCATAAAAGTAAGTTTGTTTGTTATGAAAA
1 TGTATGAGTCATAAAAGTAAGTTTGTTTGTTATGAAAA
43304352 TGTATGAG
1 TGTATGAG
43304360 GAAGTTTGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
37 4 0.09
38 40 0.91
ACGTcount: A:0.36, C:0.02, G:0.23, T:0.39
Consensus pattern (38 bp):
TGTATGAGTCATAAAAGTAAGTTTGTTTGTTATGAAAA
Found at i:43304512 original size:28 final size:28
Alignment explanation
Indices: 43304468--43304526 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
43304458 TTAAAGGTTA
43304468 CAAGACTATCCACGGTTTTCTAGCAGTG
1 CAAGACTATCCACGGTTTTCTAGCAGTG
*
43304496 CAAGACTATCCATGGTTTTCTAGCAGTG
1 CAAGACTATCCACGGTTTTCTAGCAGTG
43304524 CAA
1 CAA
43304527 TAAATCCAGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (28 bp):
CAAGACTATCCACGGTTTTCTAGCAGTG
Found at i:43309634 original size:114 final size:112
Alignment explanation
Indices: 43309413--43309839 Score: 325
Period size: 114 Copynumber: 3.8 Consensus size: 112
43309403 CCAACTCTAT
* * * * * *
43309413 GAATCCTGTAACTAATCCTATGGCTAAAGTTGCATCCCCGGAGCATG-GTGCTACTACCATTCCA
1 GAATCCTGTAACTTATCCCATGGCTAAAGTAGCATCCTCAGAG-ACGAGTG-T--TACCATTCCA
* * * * * * * * *
43309477 GTAGAGACCAACTTAGACCATGTAAAGGATGAAGATTTGTCCAACAACCCCAA
62 GTAAATACGAATTTAGAACATGTAAAAGATAAAGGTTTATCC-A-AACCCCAA
* * * * *
43309530 GAATCTTGTAACTTATCCCAAGGCTGAAGTAGCATCCTCAGAGACAAGTGTTACCATTCCGGTAA
1 GAATCCTGTAACTTATCCCATGGCTAAAGTAGCATCCTCAGAGACGAGTGTTACCATTCCAGTAA
* *
43309595 ATACGAATTTAGAATATGTAAAAGGTAAAGGTTTAT-------CCAA
66 ATACGAATTTAGAACATGTAAAAGATAAAGGTTTATCCAAACCCCAA
* * * * * *
43309635 GAATCCTGTAAGTTATCCCATGGCTAAAGTTGAATCCGCAGAGACGAGTGTTACAATTCCAGTAG
1 GAATCCTGTAACTTATCCCATGGCTAAAGTAGCATCCTCAGAGACGAGTGTTACCATTCCAGTAA
* * * **
43309700 ATACGAATTTAGACCATGTAACAGATAACGGTTTGCCCAATAGCCCCAA
66 ATACGAATTTAGAACATGTAAAAGATAAAGGTTTATCCAA-A-CCCCAA
* * ** *
43309749 GAATCCTGTAACTTCTCCTATGGCTAAAGTTA-CATCCTCAGAGACGAGCATTACCATTCCTGTA
1 GAATCCTGTAACTTATCCCATGGCTAAAG-TAGCATCCTCAGAGACGAGTGTTACCATTCCAGTA
* * *
43309813 GATATGAACTTT-GACCATGTAAAAGAT
65 AATACGAA-TTTAGAACATGTAAAAGAT
43309840 TCCCATGCCA
Statistics
Matches: 246, Mismatches: 52, Indels: 27
0.76 0.16 0.08
Matches are distributed among these distances:
105 87 0.35
114 115 0.47
115 4 0.02
116 2 0.01
117 38 0.15
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (112 bp):
GAATCCTGTAACTTATCCCATGGCTAAAGTAGCATCCTCAGAGACGAGTGTTACCATTCCAGTAA
ATACGAATTTAGAACATGTAAAAGATAAAGGTTTATCCAAACCCCAA
Found at i:43309835 original size:219 final size:221
Alignment explanation
Indices: 43309413--43309837 Score: 495
Period size: 219 Copynumber: 1.9 Consensus size: 221
43309403 CCAACTCTAT
* * * * *
43309413 GAATCCTGTAACTAATCCTATGGCTAAAGTTGCATCCCCGGAGCATGGTGCTACTACCATTCCAG
1 GAATCCTGTAACTAATCCCATGGCTAAAGTTGAATCCCCAGAGCACGGTGCTA-TACAATTCCAG
* *
43309478 TAGAGACCAACTTAGACCATGTAAAGGATGAAGATTTGTCCAACAACCCCAAGAATCTTGTAACT
65 TAGAGACCAACTTAGACCATGTAAAGGATGAAGATTTGCCCAACAACCCCAAGAATCCTGTAACT
* **
43309543 TATCCCAAGGCTGAAGTAGCATCCTCAGAGACAAGTGTTACCATTCCGGTAAATACGAATTTAGA
130 TATCCCAAGGCTAAAGTAGCATCCTCAGAGACAAGCATTACCATTCCGGTAAATACGAATTTAGA
*
43309608 ATATGTAAAAGGTAAAGGTTTATCCAA
195 ACATGTAAAAGGTAAAGGTTTATCCAA
* * *
43309635 GAATCCTGTAAGTTATCCCATGGCTAAAGTTGAATCCGCAGAG-ACGAGTG-T-TACAATTCCAG
1 GAATCCTGTAACTAATCCCATGGCTAAAGTTGAATCCCCAGAGCACG-GTGCTATACAATTCCAG
* * * * * *
43309697 TAGATACGAATTTAGACCATGTAACA-GAT-AACGGTTTGCCCAATAGCCCCAAGAATCCTGTAA
65 TAGAGACCAACTTAGACCATGTAA-AGGATGAA-GATTTGCCCAACAACCCCAAGAATCCTGTAA
* * * * * * *
43309760 CTTCTCCTATGGCTAAAGTTA-CATCCTCAGAGACGAGCATTACCATTCCTGTAGATATGAACTT
128 CTTATCCCAAGGCTAAAG-TAGCATCCTCAGAGACAAGCATTACCATTCCGGTAAATACGAA-TT
*
43309824 T-GACCATGTAAAAG
191 TAGAACATGTAAAAG
43309838 ATTCCCATGC
Statistics
Matches: 170, Mismatches: 28, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
218 2 0.01
219 119 0.70
220 6 0.04
221 3 0.02
222 40 0.24
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (221 bp):
GAATCCTGTAACTAATCCCATGGCTAAAGTTGAATCCCCAGAGCACGGTGCTATACAATTCCAGT
AGAGACCAACTTAGACCATGTAAAGGATGAAGATTTGCCCAACAACCCCAAGAATCCTGTAACTT
ATCCCAAGGCTAAAGTAGCATCCTCAGAGACAAGCATTACCATTCCGGTAAATACGAATTTAGAA
CATGTAAAAGGTAAAGGTTTATCCAA
Found at i:43314341 original size:14 final size:13
Alignment explanation
Indices: 43314309--43314350 Score: 59
Period size: 14 Copynumber: 3.2 Consensus size: 13
43314299 CTTTTTAAGC
43314309 TTTTCATCAA-TT
1 TTTTCATCAAGTT
*
43314321 CTTTCATCAAGTGT
1 TTTTCATCAAGT-T
43314335 TTTTCATCAAGTT
1 TTTTCATCAAGTT
43314348 TTT
1 TTT
43314351 AAGCAAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 9 0.35
13 5 0.19
14 12 0.46
ACGTcount: A:0.21, C:0.17, G:0.07, T:0.55
Consensus pattern (13 bp):
TTTTCATCAAGTT
Found at i:43314348 original size:12 final size:12
Alignment explanation
Indices: 43314282--43314380 Score: 71
Period size: 12 Copynumber: 8.2 Consensus size: 12
43314272 TTTTTTTATT
*
43314282 AAGTTTTGCATC
1 AAGTTTTTCATC
*
43314294 AAGTTCTTT--TT
1 AAGTT-TTTCATC
*
43314305 AAGCTTTTCATC
1 AAGTTTTTCATC
43314317 AA-TTCTTTCATC
1 AAGTT-TTTCATC
43314329 AAGTGTTTTTCATC
1 AA--GTTTTTCATC
* *
43314343 AAGTTTTTAAGC
1 AAGTTTTTCATC
*
43314355 AAG-TTTCCATC
1 AAGTTTTTCATC
*
43314366 AAGTTTTTAATC
1 AAGTTTTTCATC
43314378 AAG
1 AAG
43314381 CCTTTATCTT
Statistics
Matches: 67, Mismatches: 12, Indels: 16
0.71 0.13 0.17
Matches are distributed among these distances:
10 3 0.04
11 14 0.21
12 37 0.55
13 2 0.03
14 9 0.13
15 2 0.03
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.45
Consensus pattern (12 bp):
AAGTTTTTCATC
Found at i:43314357 original size:26 final size:24
Alignment explanation
Indices: 43314284--43314380 Score: 76
Period size: 23 Copynumber: 4.0 Consensus size: 24
43314274 TTTTTATTAA
*
43314284 GTTTTGCATCAAGTTCTTT--TTAAG
1 GTTTT-CATCAAGTT-TTTAATCAAG
* *
43314308 CTTTTCATCAA-TTCTTTCATCAAG
1 GTTTTCATCAAGTT-TTTAATCAAG
*
43314332 TGTTTTTCATCAAGTTTTTAAGCAA-
1 -G-TTTTCATCAAGTTTTTAATCAAG
*
43314357 GTTTCCATCAAGTTTTTAATCAAG
1 GTTTTCATCAAGTTTTTAATCAAG
43314381 CCTTTATCTT
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
22 6 0.10
23 26 0.43
24 9 0.15
26 17 0.28
27 2 0.03
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.46
Consensus pattern (24 bp):
GTTTTCATCAAGTTTTTAATCAAG
Found at i:43315292 original size:7 final size:7
Alignment explanation
Indices: 43315275--43315308 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
43315265 CAGGTTCCGT
*
43315275 GAACTTG
1 GAACCTG
*
43315282 GAACCTA
1 GAACCTG
43315289 GAACCTG
1 GAACCTG
43315296 GAACCTG
1 GAACCTG
43315303 GAACCT
1 GAACCT
43315309 CGAAAAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.32, C:0.26, G:0.24, T:0.18
Consensus pattern (7 bp):
GAACCTG
Found at i:43318857 original size:24 final size:25
Alignment explanation
Indices: 43318825--43318872 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
43318815 TCATTTCAAT
*
43318825 TTGGTTTTTAAA-TTTTAATGGGTA
1 TTGGGTTTTAAAGTTTTAATGGGTA
43318849 TTGGGTTTTAAAGTTTTAATGGGT
1 TTGGGTTTTAAAGTTTTAATGGGT
43318873 TTTGACTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.23, C:0.00, G:0.25, T:0.52
Consensus pattern (25 bp):
TTGGGTTTTAAAGTTTTAATGGGTA
Found at i:43318882 original size:25 final size:24
Alignment explanation
Indices: 43318830--43318885 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 24
43318820 TCAATTTGGT
**
43318830 TTTTAAATTTTAATGGGTATTGGG
1 TTTTAAATTTTAATGGGTATTGAC
*
43318854 TTTTAAAGTTTTAATGGGTTTTGAC
1 TTTTAAA-TTTTAATGGGTATTGAC
43318879 TTTTAAA
1 TTTTAAA
43318886 AGTATTGTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 7 0.25
25 21 0.75
ACGTcount: A:0.27, C:0.02, G:0.20, T:0.52
Consensus pattern (24 bp):
TTTTAAATTTTAATGGGTATTGAC
Found at i:43332347 original size:3 final size:3
Alignment explanation
Indices: 43332339--43332394 Score: 71
Period size: 3 Copynumber: 19.3 Consensus size: 3
43332329 ATCATTTTAA
* * *
43332339 TAT TAT TAT TAC TAT TA- TAT TA- TAT CAT TAT TAC TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
43332385 TAT TAT TAT T
1 TAT TAT TAT T
43332395 TACTTATTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
2 4 0.09
3 41 0.91
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:43332405 original size:15 final size:13
Alignment explanation
Indices: 43332341--43332412 Score: 58
Period size: 12 Copynumber: 5.3 Consensus size: 13
43332331 CATTTTAATA
*
43332341 TTATTATTACTAT
1 TTATTATTATTAT
43332354 TATATTATATCATTA-
1 T-TATTAT-T-ATTAT
*
43332369 TTACTATTATTA-
1 TTATTATTATTAT
43332381 TTATTATTATTAT
1 TTATTATTATTAT
*
43332394 TTACTTATTTATAAT
1 TTA-TTA-TTATTAT
43332409 TTAT
1 TTAT
43332413 ATACACATGC
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
12 15 0.31
13 5 0.10
14 15 0.31
15 11 0.22
16 3 0.06
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (13 bp):
TTATTATTATTAT
Found at i:43332433 original size:22 final size:22
Alignment explanation
Indices: 43332408--43332460 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
43332398 TTATTTATAA
*
43332408 TTTAT-ATACACATGCATATATT
1 TTTATAATACACATACAT-TATT
*
43332430 TTTATAATATACATACATTATT
1 TTTATAATACACATACATTATT
*
43332452 TTTACAATA
1 TTTATAATA
43332461 TATATATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 17 0.63
23 10 0.37
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (22 bp):
TTTATAATACACATACATTATT
Found at i:43332461 original size:22 final size:23
Alignment explanation
Indices: 43332417--43332472 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
43332407 ATTTATATAC
* *
43332417 ACATGCATATATTTTTATAATAT
1 ACATACATATATTTTTACAATAT
43332440 ACATACAT-TATTTTTACAATAT
1 ACATACATATATTTTTACAATAT
* *
43332462 ATATATATATA
1 ACATACATATA
43332473 CGTATTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 19 0.68
23 9 0.32
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.46
Consensus pattern (23 bp):
ACATACATATATTTTTACAATAT
Found at i:43332660 original size:2 final size:2
Alignment explanation
Indices: 43332653--43332680 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
43332643 ATACATATCC
43332653 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43332681 CAATACACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43338066 original size:18 final size:18
Alignment explanation
Indices: 43338032--43338066 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
43338022 AATTGTTATT
*
43338032 TTTTTCTTATATGTTTTC
1 TTTTTCTTATATCTTTTC
*
43338050 TTTTTCTTATTTCTTTT
1 TTTTTCTTATATCTTTT
43338067 TTCAGATCTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.11, G:0.03, T:0.77
Consensus pattern (18 bp):
TTTTTCTTATATCTTTTC
Found at i:43338765 original size:13 final size:13
Alignment explanation
Indices: 43338747--43338794 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
43338737 TCTTCATTGT
43338747 TTTTGAAAAGTAC
1 TTTTGAAAAGTAC
43338760 TTTTGAAAAGTA-
1 TTTTGAAAAGTAC
* * *
43338772 TTGTGGAGAAGTGC
1 TT-TTGAAAAGTAC
43338786 TTTTGAAAA
1 TTTTGAAAA
43338795 ATTTGAGTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
12 2 0.07
13 24 0.86
14 2 0.07
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.38
Consensus pattern (13 bp):
TTTTGAAAAGTAC
Found at i:43342858 original size:20 final size:21
Alignment explanation
Indices: 43342819--43342881 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 21
43342809 GCTGAACCAA
*
43342819 TATTTTAATCATTTAATTTTAT
1 TATTTTAATCA-TAAATTTTAT
43342841 TATTTTAATCA-AAATTTTAT
1 TATTTTAATCATAAATTTTAT
*
43342861 TAAATTTTTAT-ATAAATTTTA
1 T--ATTTTAATCATAAATTTTA
43342882 ATAATATATG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
20 9 0.25
21 1 0.03
22 26 0.72
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTTTAATCATAAATTTTAT
Found at i:43345218 original size:3 final size:3
Alignment explanation
Indices: 43345210--43345254 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
43345200 AAATAATGGC
43345210 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
43345255 CTAACGTTAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:43346958 original size:31 final size:32
Alignment explanation
Indices: 43346918--43346981 Score: 112
Period size: 31 Copynumber: 2.0 Consensus size: 32
43346908 TTTGAGAAGA
*
43346918 AAAATCTAGTACTCAGATTTTATGTTTTTAGG
1 AAAATCTAGTACTCAGATTTTATGGTTTTAGG
43346950 AAAA-CTAGTACTCAGATTTTATGGTTTTAGG
1 AAAATCTAGTACTCAGATTTTATGGTTTTAGG
43346981 A
1 A
43346982 CAATAAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 27 0.87
32 4 0.13
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (32 bp):
AAAATCTAGTACTCAGATTTTATGGTTTTAGG
Found at i:43350900 original size:60 final size:60
Alignment explanation
Indices: 43350790--43350904 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
43350780 CTGGGTAGTG
* * * * *
43350790 TTTTGGGCCGAATGCAGGCCAGTCTCTTGGGCTTGTTAGTGAGAAAAATAATGGGTAACA
1 TTTTAGGCCAAATGCAGGCAAGTCTCTTGGGCCTGTTAATGAGAAAAATAATGGGTAACA
* * * *
43350850 TTTTAGGCCAAATGTAGGCAAGTCTCTTGGGCCTGTTAATGGGCAGAATAATGGG
1 TTTTAGGCCAAATGCAGGCAAGTCTCTTGGGCCTGTTAATGAGAAAAATAATGGG
43350905 CCGAATAGTG
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.29
Consensus pattern (60 bp):
TTTTAGGCCAAATGCAGGCAAGTCTCTTGGGCCTGTTAATGAGAAAAATAATGGGTAACA
Found at i:43354015 original size:41 final size:41
Alignment explanation
Indices: 43353970--43354074 Score: 140
Period size: 41 Copynumber: 2.6 Consensus size: 41
43353960 ACAAATTCAA
* * *
43353970 CGGCACATAGCCCGCTAAACTTATAGCCTGATTCAGATCAC
1 CGGCACATAGCCTGCTAGACTTATAACCTGATTCAGATCAC
* **
43354011 CGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAGATCAC
1 CGGCACATAGCCTGCTAGACTTATAACCTGATTCAGATCAC
43354052 CGGCA-ATTAGCCTGCTAGACTTA
1 CGGCACA-TAGCCTGCTAGACTTA
43354075 AAGTCTGAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.25
Consensus pattern (41 bp):
CGGCACATAGCCTGCTAGACTTATAACCTGATTCAGATCAC
Found at i:43356466 original size:13 final size:13
Alignment explanation
Indices: 43356448--43356472 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43356438 TAATTTATAT
43356448 GTGTGAAAATTTC
1 GTGTGAAAATTTC
43356461 GTGTGAAAATTT
1 GTGTGAAAATTT
43356473 TATCGTTTGT
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:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:43357730 original size:43 final size:42
Alignment explanation
Indices: 43357633--43357741 Score: 130
Period size: 42 Copynumber: 2.6 Consensus size: 42
43357623 GATTTGAGAT
* *
43357633 TTACGTGTAAGACCATGTCTGGGACATTGACATCGTATATGA
1 TTACGTGTAAGACCCTGTCTGGGACAGTGACATCGTATATGA
* * * *
43357675 TTTCGTGTAAGACCCTGTCTGGGACAGTGGCATCATTATTTGA
1 TTACGTGTAAGACCCTGTCTGGGACAGTGACATC-GTATATGA
*
43357718 TTACATGTAAGACCAC-GTCTGGGA
1 TTACGTGTAAGACC-CTGTCTGGGA
43357742 TGTTGGCATT
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
42 30 0.53
43 26 0.46
44 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (42 bp):
TTACGTGTAAGACCCTGTCTGGGACAGTGACATCGTATATGA
Found at i:43357749 original size:43 final size:43
Alignment explanation
Indices: 43357592--43357750 Score: 130
Period size: 43 Copynumber: 3.7 Consensus size: 43
43357582 TATGTGATAT
* * *
43357592 CGTGTAAGACCACATTTGAGATGTTGGCATCGATT-TGA-GATTTA
1 CGTGTAAGACCACGTCTGGGATGTTGGCATC-ATTAT-ATGA-TTA
* ** * * *
43357636 CGTGTAAGACCATGTCTGGGACATTGACATC-GTATATGATTT
1 CGTGTAAGACCACGTCTGGGATGTTGGCATCATTATATGATTA
* *
43357678 CGTGTAAGACC-CTGTCTGGGACAG-TGGCATCATTATTTGATTA
1 CGTGTAAGACCAC-GTCTGGGA-TGTTGGCATCATTATATGATTA
*
43357721 CATGTAAGACCACGTCTGGGATGTTGGCAT
1 CGTGTAAGACCACGTCTGGGATGTTGGCAT
43357751 TGTATGAGTT
Statistics
Matches: 90, Mismatches: 18, Indels: 15
0.73 0.15 0.12
Matches are distributed among these distances:
42 30 0.33
43 35 0.39
44 25 0.28
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTGGGATGTTGGCATCATTATATGATTA
Found at i:43358585 original size:13 final size:13
Alignment explanation
Indices: 43358567--43358592 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43358557 AGGTGTTTCA
43358567 TGATTGTTTTGGT
1 TGATTGTTTTGGT
43358580 TGATTGTTTTGGT
1 TGATTGTTTTGGT
43358593 ACGGATCCAA
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:0.08, C:0.00, G:0.31, T:0.62
Consensus pattern (13 bp):
TGATTGTTTTGGT
Found at i:43360199 original size:29 final size:29
Alignment explanation
Indices: 43360167--43360233 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
43360157 ACACAAAAAA
43360167 GCCCTTTTTTTAAAAATTTACCGAAATGG
1 GCCCTTTTTTTAAAAATTTACCGAAATGG
** * ** *
43360196 GCCCGGTATTTAATTATTTACCGGAATGG
1 GCCCTTTTTTTAAAAATTTACCGAAATGG
*
43360225 GCCATTTTT
1 GCCCTTTTT
43360234 CGGCAAATCG
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (29 bp):
GCCCTTTTTTTAAAAATTTACCGAAATGG
Found at i:43361902 original size:20 final size:20
Alignment explanation
Indices: 43361865--43361902 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
43361855 TTTATTTTTA
*
43361865 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
43361885 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
43361903 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:43362947 original size:12 final size:12
Alignment explanation
Indices: 43362905--43362950 Score: 53
Period size: 11 Copynumber: 4.0 Consensus size: 12
43362895 AGATTTAAGA
43362905 GAAATTTTGA-AG
1 GAAA-TTTGAGAG
43362917 G-AATTTGAGAG
1 GAAATTTGAGAG
*
43362928 CAAA-TTGAGAG
1 GAAATTTGAGAG
43362939 GAAATTTGAGAG
1 GAAATTTGAGAG
43362951 AGGATTAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
10 5 0.17
11 14 0.48
12 10 0.34
ACGTcount: A:0.41, C:0.02, G:0.30, T:0.26
Consensus pattern (12 bp):
GAAATTTGAGAG
Found at i:43363632 original size:15 final size:15
Alignment explanation
Indices: 43363612--43363640 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
43363602 GTGTGATAAA
43363612 TTAAATAGAATTTTC
1 TTAAATAGAATTTTC
43363627 TTAAATAGAATTTT
1 TTAAATAGAATTTT
43363641 GAATTGTAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.48
Consensus pattern (15 bp):
TTAAATAGAATTTTC
Found at i:43369985 original size:29 final size:29
Alignment explanation
Indices: 43369949--43370009 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
43369939 GTAAATAGTA
43369949 TATAATAAGGAGTTTTCAATCATTGTATT
1 TATAATAAGGAGTTTTCAATCATTGTATT
43369978 TATAATAAGGAGTTTTCAATCATTGTATT
1 TATAATAAGGAGTTTTCAATCATTGTATT
43370007 TAT
1 TAT
43370010 TGTGGACTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.34, C:0.07, G:0.13, T:0.46
Consensus pattern (29 bp):
TATAATAAGGAGTTTTCAATCATTGTATT
Found at i:43372132 original size:10 final size:10
Alignment explanation
Indices: 43372106--43372148 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
43372096 AGAATTATAA
*
43372106 AAAAATCATT
1 AAAAATTATT
43372116 AAAAATTATT
1 AAAAATTATT
43372126 AAAAATTA-T
1 AAAAATTATT
*
43372135 AATAATTATT
1 AAAAATTATT
43372145 AAAA
1 AAAA
43372149 TTAATAAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
9 8 0.28
10 21 0.72
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (10 bp):
AAAAATTATT
Found at i:43372381 original size:16 final size:15
Alignment explanation
Indices: 43372360--43372420 Score: 61
Period size: 15 Copynumber: 3.9 Consensus size: 15
43372350 AAAATTTTAT
43372360 ATAATTTATAAAGAAA
1 ATAATTTATAAA-AAA
43372376 ATAATTTATTAAAAATA
1 ATAATTTA-TAAAAA-A
** *
43372393 A-AAAATAGAAAAAA
1 ATAATTTATAAAAAA
43372407 ATAATTTATAAAAA
1 ATAATTTATAAAAA
43372421 TATTTAGAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
14 2 0.06
15 14 0.39
16 14 0.39
17 6 0.17
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (15 bp):
ATAATTTATAAAAAA
Found at i:43372420 original size:14 final size:16
Alignment explanation
Indices: 43372360--43372418 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
43372350 AAAATTTTAT
43372360 ATAATTTATAAAGAAA
1 ATAATTTATAAAGAAA
43372376 ATAATTTATTAAA-AATA
1 ATAATTTA-TAAAGAA-A
** *
43372393 A-AAAATAGAAA-AAA
1 ATAATTTATAAAGAAA
43372407 ATAATTTATAAA
1 ATAATTTATAAA
43372419 AATATTTAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
14 2 0.06
15 12 0.35
16 14 0.41
17 6 0.18
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
ATAATTTATAAAGAAA
Found at i:43372711 original size:9 final size:9
Alignment explanation
Indices: 43372676--43372728 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
43372666 TTAATTTCTA
43372676 ATAATTTTT
1 ATAATTTTT
*
43372685 ATAAATTTTA
1 AT-AATTTTT
**
43372695 ATTTTTTTT
1 ATAATTTTT
43372704 ATAATTTTT
1 ATAATTTTT
*
43372713 ATGATTTTTT
1 AT-AATTTTT
43372723 ATAATT
1 ATAATT
43372729 CTAGAATTAT
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
9 18 0.53
10 16 0.47
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (9 bp):
ATAATTTTT
Found at i:43372727 original size:19 final size:18
Alignment explanation
Indices: 43372667--43372728 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 18
43372657 GATGTTTAAT
*
43372667 TAATTTCTAATAATTTTTA
1 TAATTT-TAATATTTTTTA
*
43372686 TAAATTTTAATTTTTTTTA
1 T-AATTTTAATATTTTTTA
*
43372705 TAATTTTTATGATTTTTTA
1 TAATTTTAAT-ATTTTTTA
43372724 TAATT
1 TAATT
43372729 CTAGAATTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 8 0.22
19 24 0.65
20 5 0.14
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (18 bp):
TAATTTTAATATTTTTTA
Found at i:43376381 original size:21 final size:21
Alignment explanation
Indices: 43376352--43376392 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
43376342 TATTTTAACT
*
43376352 CAAGGTAATTTTAACTTGACC
1 CAAGATAATTTTAACTTGACC
*
43376373 CAAGATAATTTTGACTTGAC
1 CAAGATAATTTTAACTTGAC
43376393 ATGTGATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (21 bp):
CAAGATAATTTTAACTTGACC
Found at i:43394998 original size:12 final size:13
Alignment explanation
Indices: 43394963--43395004 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
43394953 AAAAGTTTTG
43394963 CTTTCTTTTCCCT
1 CTTTCTTTTCCCT
* *
43394976 ATTTATTTTCCC-
1 CTTTCTTTTCCCT
*
43394988 CTTTCTTTTCCAT
1 CTTTCTTTTCCCT
43395001 CTTT
1 CTTT
43395005 TTCTTTGCAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.07, C:0.31, G:0.00, T:0.62
Consensus pattern (13 bp):
CTTTCTTTTCCCT
Found at i:43395933 original size:17 final size:18
Alignment explanation
Indices: 43395903--43395936 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
43395893 GGTTATTGAT
*
43395903 GTACTATCATTATTACTC
1 GTACTATCAGTATTACTC
43395921 GTACTA-CAGTATTACT
1 GTACTATCAGTATTACT
43395937 GATTGCATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.41
Consensus pattern (18 bp):
GTACTATCAGTATTACTC
Found at i:43396301 original size:91 final size:89
Alignment explanation
Indices: 43396133--43396333 Score: 198
Period size: 91 Copynumber: 2.2 Consensus size: 89
43396123 ACTACAAACA
* * * *
43396133 CTCGTGGTTTATCCACAAATTACTAGCAGCTTTAATCTGCAAACCCTTTGTGTATTCACAACTAC
1 CTCGTAGTTTATCCACAAATTACTAGCAGCTTTAATCTACAAACCCTTTGTGTATTCAAAACCAC
* *
43396198 TTGTAGCATATTAACTTGCAAGCG
66 TGGCAGCATATTAACTTGCAAGCG
*
43396222 CTCGTAGTTTATCCACAACTTA-TACTGACAGCTATT-ATCTACAAA-CCTGTTGTGTATTCAAA
1 CTCGTAGTTTATCCACAAATTACTA--G-CAGCT-TTAATCTACAAACCCT-TTGTGTATTCAAA
** *
43396284 ACCACTGGCAGTGTATTAATCTAT--AA-CA
61 ACCACTGGCAGCATATTAA-CT-TGCAAGCG
*
43396312 CTAGTAGTTTATCCACAAATTA
1 CTCGTAGTTTATCCACAAATTA
43396334 GAGTTACTGT
Statistics
Matches: 93, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
88 2 0.02
89 20 0.22
90 25 0.27
91 41 0.44
92 4 0.04
93 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (89 bp):
CTCGTAGTTTATCCACAAATTACTAGCAGCTTTAATCTACAAACCCTTTGTGTATTCAAAACCAC
TGGCAGCATATTAACTTGCAAGCG
Found at i:43398935 original size:13 final size:14
Alignment explanation
Indices: 43398917--43398945 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
43398907 ATATTACCAT
43398917 ATAAATACTAA-CC
1 ATAAATACTAATCC
43398930 ATAAATACTAATCC
1 ATAAATACTAATCC
43398944 AT
1 AT
43398946 GATTAAAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (14 bp):
ATAAATACTAATCC
Found at i:43399700 original size:41 final size:41
Alignment explanation
Indices: 43399651--43399770 Score: 163
Period size: 41 Copynumber: 2.9 Consensus size: 41
43399641 CCCGATTCGT
*
43399651 TTCACCGGCA-CAAAGCCTGCTAGACATAAAGTCTGAATTAA
1 TTCACCGGCATC-AAGCCTGCTAGACATAAAGTCTGAAATAA
*
43399692 TTGC-CCGGCATCAAGCCTGCTAGACATAAAGTCTAAAATAA
1 TT-CACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAATAA
* * *
43399733 TTCACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAA
1 TTCACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAA
43399771 ATCTCATATA
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
40 1 0.01
41 67 0.96
42 2 0.03
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (41 bp):
TTCACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAATAA
Found at i:43400003 original size:64 final size:63
Alignment explanation
Indices: 43399885--43400092 Score: 298
Period size: 64 Copynumber: 3.3 Consensus size: 63
43399875 GCAAACAAAC
*
43399885 ATTCGAACCACATATGT-AT-AATTTACA-ACATTAAAATTCAGCTCAAAGAA-TTTGTAACCTA
1 ATTCGAACCACATATGTAATAAAATT-CATACATT-AAATTCAGCTC-AAGAACTTTGTAACCTA
43399946 T
63 T
43399947 ATTCGAACCACATATGTAAGTAAAATTCATACATTAAATTCAGCTCAAGAACTTTGTAACCTAT
1 ATTCGAACCACATATGTAA-TAAAATTCATACATTAAATTCAGCTCAAGAACTTTGTAACCTAT
** *
43400011 ATTTAAACCACATATGTATATAAAATTCATACATTAAATACAGCTCAAGAACTTTGTAACCTAT
1 ATTCGAACCACATATGTA-ATAAAATTCATACATTAAATTCAGCTCAAGAACTTTGTAACCTAT
*
43400075 ATTTGAACCACATATGTA
1 ATTCGAACCACATATGTA
43400093 TATNNNNNNN
Statistics
Matches: 135, Mismatches: 5, Indels: 10
0.90 0.03 0.07
Matches are distributed among these distances:
62 17 0.13
63 6 0.04
64 102 0.76
65 10 0.07
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (63 bp):
ATTCGAACCACATATGTAATAAAATTCATACATTAAATTCAGCTCAAGAACTTTGTAACCTAT
Found at i:43404944 original size:38 final size:41
Alignment explanation
Indices: 43404878--43404956 Score: 103
Period size: 40 Copynumber: 2.0 Consensus size: 41
43404868 CTTTTATTAC
43404878 TATAATATATATATTTACTTAAATATTTAGTAA-AATATAT
1 TATAATATATATATTTACTTAAATATTTAGTAATAATATAT
* *
43404918 TATAATATATAT-TTTAACTT-TA-ATTTATTAATAATATAT
1 TATAATATATATATTT-ACTTAAATATTTAGTAATAATATAT
43404957 GCCGCCGCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
38 8 0.23
39 11 0.31
40 16 0.46
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.51
Consensus pattern (41 bp):
TATAATATATATATTTACTTAAATATTTAGTAATAATATAT
Found at i:43406006 original size:26 final size:26
Alignment explanation
Indices: 43405952--43406032 Score: 76
Period size: 26 Copynumber: 3.1 Consensus size: 26
43405942 ATATGTATAC
* *
43405952 ATACATACATACATTATGTTAT-ATAT
1 ATACATACATACATT-TTTTATAATTT
43405978 ATACATACATACATTTTTTATAATTT
1 ATACATACATACATTTTTTATAATTT
* **
43406004 ATATATATGTACATAATTTTT-TAATTT
1 ATACATACATACAT--TTTTTATAATTT
43406031 AT
1 AT
43406033 TTGTACATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
25 5 0.11
26 29 0.62
27 8 0.17
28 5 0.11
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (26 bp):
ATACATACATACATTTTTTATAATTT
Found at i:43406007 original size:30 final size:29
Alignment explanation
Indices: 43405930--43406041 Score: 93
Period size: 30 Copynumber: 3.8 Consensus size: 29
43405920 TGTCCTTTTA
* *
43405930 ATTTTGTTATATATATGTATACATACATAC
1 ATTTT-TTATATTTATATATACATACATAC
*** *
43405960 ATACATTATGTTATATATATACATACATAC
1 ATTTTTTATATT-TATATATACATACATAC
**
43405990 ATTTTTTATAATTTATATATATGTACATA-
1 ATTTTTTAT-ATTTATATATACATACATAC
* *
43406019 ATTTTTTA-ATTTATTTGTACATA
1 ATTTTTTATATTTATATATACATA
43406042 TATATACATA
Statistics
Matches: 64, Mismatches: 16, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
27 11 0.17
29 13 0.20
30 38 0.59
31 2 0.03
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (29 bp):
ATTTTTTATATTTATATATACATACATAC
Found at i:43406344 original size:4 final size:4
Alignment explanation
Indices: 43406335--43406362 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
43406325 TTTTTATAAT
43406335 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
43406363 CGCTTTTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:43407334 original size:18 final size:19
Alignment explanation
Indices: 43407291--43407335 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
43407281 AGAACAATGG
*
43407291 TATAATTGTTTTTTAGTCCC
1 TATAATTATTTTTTAGT-CC
*
43407311 TTTAATTATTTTTTAGT-C
1 TATAATTATTTTTTAGTCC
43407329 TATAATT
1 TATAATT
43407336 CAAATTTTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.24, C:0.09, G:0.07, T:0.60
Consensus pattern (19 bp):
TATAATTATTTTTTAGTCC
Found at i:43416181 original size:19 final size:20
Alignment explanation
Indices: 43416157--43416197 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
43416147 GAATTTAGAC
*
43416157 AAATATTGAATA-AAAATTG
1 AAATATTCAATATAAAATTG
*
43416176 AAATATTCAATATGAAATTG
1 AAATATTCAATATAAAATTG
43416196 AA
1 AA
43416198 TTGTGTTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.56, C:0.02, G:0.10, T:0.32
Consensus pattern (20 bp):
AAATATTCAATATAAAATTG
Found at i:43422082 original size:21 final size:21
Alignment explanation
Indices: 43421995--43422090 Score: 68
Period size: 21 Copynumber: 4.6 Consensus size: 21
43421985 TTTACTCTTG
* *
43421995 AATCGATTGTTTTCCTAATTC
1 AATCGATTGTTTTCTTATTTC
* * *
43422016 AATCAATTGTTCTCTT-TGTTT
1 AATCGATTGTTTTCTTAT-TTC
* * * *
43422037 AATAGATTATTCTCTCATTTC
1 AATCGATTGTTTTCTTATTTC
* *
43422058 AATCGATTGTTTTCTTGTTTT
1 AATCGATTGTTTTCTTATTTC
*
43422079 AATCAATTGTTT
1 AATCGATTGTTT
43422091 CACTATCCTC
Statistics
Matches: 56, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
21 55 0.98
22 1 0.02
ACGTcount: A:0.23, C:0.15, G:0.09, T:0.53
Consensus pattern (21 bp):
AATCGATTGTTTTCTTATTTC
Found at i:43424899 original size:24 final size:24
Alignment explanation
Indices: 43424872--43424918 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
43424862 TTCATGTGAA
*
43424872 AGTAGACTCATTCAGCTT-TAATTT
1 AGTA-ACTCACTCAGCTTCTAATTT
*
43424896 AGTATCTCACTCAGCTTCTAATT
1 AGTAACTCACTCAGCTTCTAATT
43424919 CAATTTCCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (24 bp):
AGTAACTCACTCAGCTTCTAATTT
Found at i:43425723 original size:46 final size:46
Alignment explanation
Indices: 43425645--43425829 Score: 273
Period size: 46 Copynumber: 4.0 Consensus size: 46
43425635 ACATTGCTAT
* *
43425645 AACTCAATATGGTTTTCTTC-ACGAAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCAACG-AAACACCATACCTACTTTTCAC
* *
43425691 AACTCAGTATGGTTTTCTTCAATGAAACACCATACCTACTTTTCAT
1 AACTCAGTATGGTTTTCTTCAACGAAACACCATACCTACTTTTCAC
* *
43425737 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTTAC
1 AACTCAGTATGGTTTTCTTCAACGAAACACCATACCTACTTTTCAC
* * *
43425783 AACTTAGCATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCAACGAAACACCATACCTACTTTTCAC
43425829 A
1 A
43425830 CTTTGCCATG
Statistics
Matches: 127, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
46 125 0.98
47 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.08, T:0.35
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCAACGAAACACCATACCTACTTTTCAC
Found at i:43427108 original size:17 final size:16
Alignment explanation
Indices: 43427061--43427102 Score: 66
Period size: 17 Copynumber: 2.6 Consensus size: 16
43427051 TTTTAAATCG
*
43427061 CAAAAATTCACTAAAT
1 CAAAAATTCACTAATT
43427077 CACAAAATTCACTAATT
1 CA-AAAATTCACTAATT
43427094 CAAAAATTC
1 CAAAAATTC
43427103 TTCTAAATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.26
Consensus pattern (16 bp):
CAAAAATTCACTAATT
Found at i:43438242 original size:22 final size:22
Alignment explanation
Indices: 43438188--43438244 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
43438178 TATTATGATT
**
43438188 AGCTCTCATGGCTAACGTACTA
1 AGCTCTCATGTTTAACGTACTA
*
43438210 AGCTCTCATGTTTCACGTACTA
1 AGCTCTCATGTTTAACGTACTA
43438232 AGCTCTCATGTTT
1 AGCTCTCATGTTT
43438245 GAACAATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.35
Consensus pattern (22 bp):
AGCTCTCATGTTTAACGTACTA
Found at i:43440326 original size:28 final size:25
Alignment explanation
Indices: 43440276--43440326 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 25
43440266 AATACAACTG
43440276 AACTAACTGTAACTACTAATTGATC
1 AACTAACTGTAACTACTAATTGATC
*
43440301 AACTAACTATTAACTATTCTAATTGA
1 AACTAACT-GTAACTA--CTAATTGA
43440327 CTTCTGTTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 8 0.36
26 6 0.27
28 8 0.36
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (25 bp):
AACTAACTGTAACTACTAATTGATC
Found at i:43445632 original size:38 final size:33
Alignment explanation
Indices: 43445572--43445649 Score: 93
Period size: 36 Copynumber: 2.2 Consensus size: 33
43445562 ATTTTACATT
*
43445572 AATATTTTATATATTTTATAATTAAATTTAAATAAA
1 AATATTTTATATATTTAATAATTAAA-TT-AA-AAA
*
43445608 AATATTTTTTATAATTTAATTAATTAAATTAAAAA
1 AATATTTTATAT-ATTTAA-TAATTAAATTAAAAA
43445643 AATATTT
1 AATATTT
43445650 GTCCAAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
35 10 0.26
36 13 0.34
37 7 0.18
38 8 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (33 bp):
AATATTTTATATATTTAATAATTAAATTAAAAA
Found at i:43448999 original size:21 final size:21
Alignment explanation
Indices: 43448969--43449012 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
43448959 CGATAGCAGT
*
43448969 AATAAGAC-TTAACAATTTATC
1 AATAAGACTTTAAC-ATTAATC
*
43448990 AATAATACTTTAACATTAATC
1 AATAAGACTTTAACATTAATC
43449011 AA
1 AA
43449013 GTTTAATAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.50, C:0.14, G:0.02, T:0.34
Consensus pattern (21 bp):
AATAAGACTTTAACATTAATC
Found at i:43452034 original size:19 final size:18
Alignment explanation
Indices: 43451992--43452068 Score: 70
Period size: 19 Copynumber: 4.1 Consensus size: 18
43451982 ATTACAAAAT
43451992 AATTCAAAATAATTTTCAAA
1 AATTCAAAATAATTTT--AA
*
43452012 AATTTAAAATAAATTTTAA
1 AATTCAAAAT-AATTTTAA
43452031 AATTCAAAAT-ATTTATAAA
1 AATTCAAAATAATTT-T-AA
43452050 AATT-ATAAA-AATTTTAA
1 AATTCA-AAATAATTTTAA
43452067 AA
1 AA
43452069 AATTAAAAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
17 8 0.16
18 3 0.06
19 24 0.48
20 9 0.18
21 6 0.12
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTCAAAATAATTTTAA
Found at i:43452039 original size:27 final size:27
Alignment explanation
Indices: 43452006--43452059 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
43451996 CAAAATAATT
*
43452006 TTCAAAA-ATTTAAAATAAATTTTAAAA
1 TTCAAAATATTTAAAA-AAATTATAAAA
*
43452033 TTCAAAATATTTATAAAAATTATAAAA
1 TTCAAAATATTTAAAAAAATTATAAAA
43452060 ATTTTAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 17 0.71
28 7 0.29
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (27 bp):
TTCAAAATATTTAAAAAAATTATAAAA
Found at i:43452069 original size:19 final size:20
Alignment explanation
Indices: 43452036--43452077 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
43452026 TTTAAAATTC
43452036 AAAATATTTATAAAAATTATA
1 AAAATATTTATAAAAATTA-A
43452057 AAAAT-TTTA-AAAAATTAA
1 AAAATATTTATAAAAATTAA
43452075 AAA
1 AAA
43452078 TATAAAGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.19
19 8 0.38
20 4 0.19
21 5 0.24
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAATATTTATAAAAATTAA
Found at i:43452071 original size:38 final size:39
Alignment explanation
Indices: 43451978--43452080 Score: 106
Period size: 38 Copynumber: 2.6 Consensus size: 39
43451968 CTCTCTCAAC
**
43451978 AAAAATTACAAAATAATTCAAAATAATTTTCAAAAATTTAA
1 AAAAATTTTAAAA-AATTCAAAAT-ATTTTCAAAAATTTAA
*
43452019 AATAAATTTT--AAAATTCAAAATATTTAT-AAAAA-TTAT
1 AA-AAATTTTAAAAAATTCAAAATATTT-TCAAAAATTTAA
*
43452056 AAAAATTTTAAAAAATTAAAAATAT
1 AAAAATTTTAAAAAATTCAAAATAT
43452081 AAAGAATGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
36 7 0.13
37 5 0.09
38 22 0.41
39 11 0.20
40 2 0.04
41 2 0.04
42 5 0.09
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (39 bp):
AAAAATTTTAAAAAATTCAAAATATTTTCAAAAATTTAA
Found at i:43452083 original size:8 final size:9
Alignment explanation
Indices: 43452043--43452083 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
43452033 TTCAAAATAT
43452043 TTATAAAAA
1 TTATAAAAA
43452052 TTATAAAAA
1 TTATAAAAA
*
43452061 TTTTAAAAA
1 TTATAAAAA
*
43452070 AT-TAAAAA
1 TTATAAAAA
43452078 -TATAAA
1 TTATAAA
43452084 GAATGTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
7 1 0.03
8 10 0.34
9 18 0.62
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
TTATAAAAA
Found at i:43452092 original size:26 final size:26
Alignment explanation
Indices: 43452046--43452098 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
43452036 AAAATATTTA
*
43452046 TAAAAATTATAAAAATTTTAAAAAAT
1 TAAAAATTATAAAAATGTTAAAAAAT
43452072 TAAAAA-TATAAAGAATGTTAAAAAAT
1 TAAAAATTATAAA-AATGTTAAAAAAT
43452098 T
1 T
43452099 TAGAATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (26 bp):
TAAAAATTATAAAAATGTTAAAAAAT
Found at i:43455284 original size:34 final size:34
Alignment explanation
Indices: 43455239--43455338 Score: 127
Period size: 34 Copynumber: 3.1 Consensus size: 34
43455229 AAACAAATTC
*
43455239 TCTCAATTTCCTTCAAAAATTCTCTCAATTTCCT
1 TCTCAATTTCCTTCCAAAATTCTCTCAATTTCCT
* *
43455273 TTTCAATTTCCTTCCAAAATTCTCTCAA---AC-
1 TCTCAATTTCCTTCCAAAATTCTCTCAATTTCCT
* *
43455303 TCTCAAATTCCTTCCAAAATCCTCTCAATTTCCT
1 TCTCAATTTCCTTCCAAAATTCTCTCAATTTCCT
43455337 TC
1 TC
43455339 AAAAAATCTC
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
30 25 0.45
31 1 0.02
33 1 0.02
34 28 0.51
ACGTcount: A:0.27, C:0.32, G:0.00, T:0.41
Consensus pattern (34 bp):
TCTCAATTTCCTTCCAAAATTCTCTCAATTTCCT
Found at i:43455329 original size:22 final size:22
Alignment explanation
Indices: 43455302--43455343 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
43455292 TTCTCTCAAA
*
43455302 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCAAAAATC
*
43455324 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCAAAAA
43455344 ATCTCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCAAAAATC
Found at i:43455409 original size:27 final size:27
Alignment explanation
Indices: 43455378--43455437 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
43455368 TTTTTCCATT
43455378 AAATTTCAT-TTTTTTAAGAAAATTTTA
1 AAATTTCATATTTTTTAA-AAAATTTTA
* ** *
43455405 CAATTTTTTATTTTTTAAATAATTTTA
1 AAATTTCATATTTTTTAAAAAATTTTA
43455432 AAATTT
1 AAATTT
43455438 TTAATATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 19 0.70
28 8 0.30
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (27 bp):
AAATTTCATATTTTTTAAAAAATTTTA
Found at i:43455438 original size:27 final size:28
Alignment explanation
Indices: 43455387--43455439 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
43455377 TAAATTTCAT
*
43455387 TTTTTTAAGAAAATTTTACAATTTTTTA
1 TTTTTTAAGAAAATTTTAAAATTTTTTA
*
43455415 TTTTTTAA-ATAATTTTAAAATTTTT
1 TTTTTTAAGAAAATTTTAAAATTTTT
43455440 AATATTTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (28 bp):
TTTTTTAAGAAAATTTTAAAATTTTTTA
Found at i:43455447 original size:27 final size:28
Alignment explanation
Indices: 43455389--43455447 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
43455379 AATTTCATTT
* * *
43455389 TTTTAAGAAAATTTTACAATTTTTTATT
1 TTTTAAGAAAATTTTAAAATTTTTAATA
*
43455417 TTTTAA-ATAATTTTAAAATTTTTAATA
1 TTTTAAGAAAATTTTAAAATTTTTAATA
43455444 TTTT
1 TTTT
43455448 CAACCATGGC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 21 0.78
28 6 0.22
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (28 bp):
TTTTAAGAAAATTTTAAAATTTTTAATA
Found at i:43456355 original size:21 final size:19
Alignment explanation
Indices: 43456325--43456364 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
43456315 GTAACGAGGT
43456325 AAATTTTATATTACATTTTG
1 AAATTTTATA-TACATTTTG
*
43456345 AAATTGTTATATAGATTTTG
1 AAATT-TTATATACATTTTG
43456365 TAAGAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.53
Consensus pattern (19 bp):
AAATTTTATATACATTTTG
Found at i:43457750 original size:28 final size:28
Alignment explanation
Indices: 43457710--43457812 Score: 144
Period size: 28 Copynumber: 3.9 Consensus size: 28
43457700 TTTTGACATT
*
43457710 ATTTGATTAAAAACCCTAACCTAACTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
43457738 ATTTAATTAAAAACCCTAA-C---C-TA
1 ATTTAATTAAAAACCCTAACCTAACTTA
*
43457761 ATTTAATTAAAAACCCAAACCTAACTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
*
43457789 ATTGAATTAAAAACCCTAACCTAA
1 ATTTAATTAAAAACCCTAACCTAA
43457813 TTGAATTAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 10
0.82 0.05 0.12
Matches are distributed among these distances:
23 20 0.30
24 2 0.03
27 2 0.03
28 42 0.64
ACGTcount: A:0.48, C:0.21, G:0.02, T:0.29
Consensus pattern (28 bp):
ATTTAATTAAAAACCCTAACCTAACTTA
Found at i:43457755 original size:23 final size:23
Alignment explanation
Indices: 43457715--43458466 Score: 739
Period size: 23 Copynumber: 33.7 Consensus size: 23
43457705 ACATTATTTG
43457715 ATTAAAAACCCTAACCTAACTTAATTTA
1 ATTAAAAACCCTAACCTAAC-----TTA
*
43457743 ATTAAAAACCCTAACCTAATTTA
1 ATTAAAAACCCTAACCTAACTTA
*
43457766 ATTAAAAACCCAAACCTAACTTAATTGA
1 ATTAAAAACCCTAACCTAAC----TT-A
43457794 ATTAAAAACCCTAACCTAA-TTGA
1 ATTAAAAACCCTAACCTAACTT-A
43457817 ATTAAAAA-CCTAA--T---TTA
1 ATTAAAAACCCTAACCTAACTTA
43457834 ATTAAAAACCCTAACCTAACTTA
1 ATTAAAAACCCTAACCTAACTTA
43457857 ATGT-AAAACCCTAACCTAACTTA
1 AT-TAAAAACCCTAACCTAACTTA
* *
43457880 ACTT-AAAA-CCTAACTTAATTTA
1 A-TTAAAAACCCTAACCTAACTTA
**
43457902 ATTAAAAACCCTAAATTAACTTA
1 ATTAAAAACCCTAACCTAACTTA
43457925 ATTAAAAACCCTAACCTAACTTA
1 ATTAAAAACCCTAACCTAACTTA
43457948 ATTAAAAACCCTAACCTAACTTA
1 ATTAAAAACCCTAACCTAACTTA
43457971 ATGT-AAAACCCTAACCTAA-TTGA
1 AT-TAAAAACCCTAACCTAACTT-A
43457994 ATTAAAAA-CCTAA--T---TTA
1 ATTAAAAACCCTAACCTAACTTA
*
43458011 AATAAAAACCCTAACCTAACTTA
1 ATTAAAAACCCTAACCTAACTTA
43458034 ATGT-AAAACCCTAACCTAACTTA
1 AT-TAAAAACCCTAACCTAACTTA
43458057 ACTT---AA----AACCTAACTTA
1 A-TTAAAAACCCTAACCTAACTTA
43458074 ATTAAAAACCCTAACCTAACTTA
1 ATTAAAAACCCTAACCTAACTTA
43458097 ATTAAAAACCCTAACCTAACTTA
1 ATTAAAAACCCTAACCTAACTTA
43458120 ATGT-AAAACCCTAACCTAA-TTGA
1 AT-TAAAAACCCTAACCTAACTT-A
43458143 ATTAAAAA-CCTAA--T---TTA
1 ATTAAAAACCCTAACCTAACTTA
*
43458160 AATAAAAACCCTAACCTAACTTA
1 ATTAAAAACCCTAACCTAACTTA
43458183 ATGT-AAAACCCTAACCTAACTTA
1 AT-TAAAAACCCTAACCTAACTTA
43458206 ACTT---AA----AACCTAACTTA
1 A-TTAAAAACCCTAACCTAACTTA
43458223 ATTAAAAACCCTAACCTAACTTA
1 ATTAAAAACCCTAACCTAACTTA
43458246 ATTAAAAACCCTAACCTAACTTA
1 ATTAAAAACCCTAACCTAACTTA
43458269 ATGT-AAAACCCTAACCTAA-TTGA
1 AT-TAAAAACCCTAACCTAACTT-A
43458292 ATTAAAAA-CCTAA--T---TTA
1 ATTAAAAACCCTAACCTAACTTA
43458309 ATTAAAAACCCTAACCTAACTTA
1 ATTAAAAACCCTAACCTAACTTA
* *
43458332 ACTT-AAAA-CCTAACTTAATTTA
1 A-TTAAAAACCCTAACCTAACTTA
43458354 ATTAAAAACCCTAACCTAACTTAATTTA
1 ATTAAAAACCCTAACCTAAC-----TTA
*
43458382 ATTAAAAACCCTAAGCTAACTTA
1 ATTAAAAACCCTAACCTAACTTA
*
43458405 ATTTAAAACCCT-ACCTTAACTTA
1 ATTAAAAACCCTAACC-TAACTTA
43458428 ATTAAAAACCCTAACCTAACTTA
1 ATTAAAAACCCTAACCTAACTTA
43458451 ATGT-AAAACCCTAACC
1 AT-TAAAAACCCTAACC
43458467 CTAAGCTAAT
Statistics
Matches: 631, Mismatches: 22, Indels: 147
0.79 0.03 0.18
Matches are distributed among these distances:
16 4 0.01
17 58 0.09
18 28 0.04
19 4 0.01
20 8 0.01
21 8 0.01
22 65 0.10
23 379 0.60
24 15 0.02
27 2 0.00
28 60 0.10
ACGTcount: A:0.47, C:0.23, G:0.02, T:0.28
Consensus pattern (23 bp):
ATTAAAAACCCTAACCTAACTTA
Found at i:43457847 original size:18 final size:17
Alignment explanation
Indices: 43457806--43457843 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
43457796 TAAAAACCCT
43457806 AACCTAATTGAATTAAA
1 AACCTAATTGAATTAAA
*
43457823 AACCTAATTTAATTAAA
1 AACCTAATTGAATTAAA
43457840 AACC
1 AACC
43457844 CTAACCTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.53, C:0.16, G:0.03, T:0.29
Consensus pattern (17 bp):
AACCTAATTGAATTAAA
Found at i:43457870 original size:63 final size:62
Alignment explanation
Indices: 43457755--43458466 Score: 585
Period size: 63 Copynumber: 10.8 Consensus size: 62
43457745 TAAAAACCCT
*
43457755 AACCTAATTTAATTAAAAACCCAAACCTAACTTAATTGAATTAAAAACCCTAACCTAA-TTGAAT
1 AACCTAATTTAATTAAAAACCCTAACCTAAC----TT-AATT-AAAACCCTAACCTAACTT-AAT
43457819 TAAA
59 TAAA
43457823 AACCTAATTTAATTAAAAACCCTAACCTAACTTAATGTAAAACCCTAACCTAACTTAACTTAAAA
1 AACCTAATTTAATTAAAAACCCTAACCTAACTTAAT-TAAAACCCTAACCTAACTTAA-TT-AAA
* **
43457888 CCTAACTTAATTTAATTAAAAACCCTAAATTAACTTAATTAAAAACCCTAACCTAACTTAATTAA
1 ---AACCTAATTTAATTAAAAACCCTAACCTAACTTAATT-AAAACCCTAACCTAACTTAATTAA
43457953 A
62 A
* ** *
43457954 AACCCTAACCTAACTTAATGT-AAAACCCTAACCTAA-TTGAATTAAAAACCTAATTTAA-ATAA
1 AA-CCTAA--T---TTAAT-TAAAAACCCTAACCTAACTT-AATTAAAACCCTAACCTAACTTAA
43458016 --AAA
58 TTAAA
* *
43458019 CCCTAACCTAACTTAATGT-AAAACCCTAACCTAACTTAACTTAAAA-CCTAACTTAA-TTAA--
1 ----AACCTAATTTAAT-TAAAAACCCTAACCTAACTTAA-TTAAAACCCTAACCTAACTTAATT
43458079 AAA
60 AAA
*
43458082 CCCTAACCTAACTTAATTAAAAACCCTAACCTAACTTAATGTAAAACCCTAACCTAA-TTGAATT
1 ----AACCTAATTTAATTAAAAACCCTAACCTAACTTAAT-TAAAACCCTAACCTAACTT-AATT
43458146 AAA
60 AAA
*
43458149 AACCTAATTTAAATAAAAACCCTAACCTAACTTAATGTAAAACCCTAACCTAACTTAACTT-AA
1 AACCTAATTTAATTAAAAACCCTAACCTAACTTAAT-TAAAACCCTAACCTAACTTAA-TTAAA
*
43458212 AACCTAACTTAATTAAAAACCCTAACCTAACTTAATTAAAAACCCTAACCTAACTTAATGTAAA
1 AACCTAATTTAATTAAAAACCCTAACCTAACTTAATT-AAAACCCTAACCTAACTTAAT-TAAA
* ** *
43458276 ACCCTAACCTAATTGAATTAAA----AACCTAATTTAATTAAAAACCCTAACCTAACTTAACTTA
1 AACCTAATTTAATT-AA--AAACCCTAACCTAACTTAATT-AAAACCCTAACCTAACTTAA-TT-
43458337 AAA
60 AAA
* *
43458340 CCTAACTTAATTTAATTAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAAGCTAACTTA
1 ---AACCTAATTTAATTAAAAACCCTAACCTAAC-----TTAATT-AAAACCCTAACCTAACTTA
43458405 ATTTAAA
57 A-TTAAA
*
43458412 ACCCTACCTTAACTTAATTAAAAACCCTAACCTAACTTAATGTAAAACCCTAACC
1 A----ACC-TAATTTAATTAAAAACCCTAACCTAACTTAAT-TAAAACCCTAACC
43458467 CTAAGCTAAT
Statistics
Matches: 556, Mismatches: 32, Indels: 111
0.80 0.05 0.16
Matches are distributed among these distances:
62 4 0.01
63 248 0.45
64 55 0.10
65 10 0.02
66 6 0.01
67 22 0.04
68 109 0.20
69 41 0.07
70 2 0.00
72 3 0.01
73 30 0.05
74 26 0.05
ACGTcount: A:0.47, C:0.23, G:0.02, T:0.28
Consensus pattern (62 bp):
AACCTAATTTAATTAAAAACCCTAACCTAACTTAATTAAAACCCTAACCTAACTTAATTAAA
Found at i:43457891 original size:17 final size:17
Alignment explanation
Indices: 43457869--43457902 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
43457859 GTAAAACCCT
43457869 AACCTAACTTAACTTAA
1 AACCTAACTTAACTTAA
*
43457886 AACCTAACTTAATTTAA
1 AACCTAACTTAACTTAA
43457903 TTAAAAACCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (17 bp):
AACCTAACTTAACTTAA
Found at i:43458005 original size:17 final size:17
Alignment explanation
Indices: 43457983--43458020 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
43457973 GTAAAACCCT
*
43457983 AACCTAATTGAATTAAA
1 AACCTAATTGAAATAAA
*
43458000 AACCTAATTTAAATAAA
1 AACCTAATTGAAATAAA
43458017 AACC
1 AACC
43458021 CTAACCTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.55, C:0.16, G:0.03, T:0.26
Consensus pattern (17 bp):
AACCTAATTGAAATAAA
Found at i:43458068 original size:17 final size:17
Alignment explanation
Indices: 43458046--43458097 Score: 70
Period size: 17 Copynumber: 3.0 Consensus size: 17
43458036 GTAAAACCCT
43458046 AACCTAACTTAACTTAA
1 AACCTAACTTAACTTAA
43458063 AACCTAACTTAA-TTAAA
1 AACCTAACTTAACTT-AA
*
43458080 AACCCTAACCTAACTTAA
1 AA-CCTAACTTAACTTAA
43458098 TTAAAAACCC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
16 2 0.06
17 16 0.52
18 11 0.35
19 2 0.06
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (17 bp):
AACCTAACTTAACTTAA
Found at i:43458120 original size:149 final size:148
Alignment explanation
Indices: 43457755--43458464 Score: 852
Period size: 149 Copynumber: 4.6 Consensus size: 148
43457745 TAAAAACCCT
* *
43457755 AACCTAATTTAATTAAAAACCCAAACCTAACTTAATTGAATTAAAAACCCTAACCTAA-TTGAAT
1 AACCTAACTTAATTAAAAACCCTAACCTAAC----TT-AATTAAAAACCCTAACCTAACTT-AAT
* ** * *
43457819 -TAAAAACCTAATTTAATT-AA--AAACCCTAACCTAACTT-AATGTAAAACCCTAACCTAACTT
60 GTAAAACCCTAACCTAATTGAATTAAA----AACCTAATTTAAAT-AAAAACCCTAACCTAACTT
* *
43457879 AACTTAAAACCTAACTTAATTTAATTAAA
120 AACTTAAAACCTAACCTAACTTAATTAAA
43457908 AACCCTAAATTAACTTAATTAAAAACCCTAACCTAACTTAATTAAAAACCCTAACCTAACTTAAT
1 AA-CC-----TAACTTAATTAAAAACCCTAACCTAACTTAATTAAAAACCCTAACCTAACTTAAT
43457973 GTAAAACCCTAACCTAATTGAATTAAAAACCTAATTTAAATAAAAACCCTAACCTAACTTAA-TG
60 GTAAAACCCTAACCTAATTGAATTAAAAACCTAATTTAAATAAAAACCCTAACCTAACTTAACT-
43458037 TAAAACCCTAACCTAACTTAACTT-AA
124 TAAAA-CCTAACCTAACTTAA-TTAAA
43458063 AACCTAACTTAATTAAAAACCCTAACCTAACTTAATTAAAAACCCTAACCTAACTTAATGTAAAA
1 AACCTAACTTAATTAAAAACCCTAACCTAACTTAATTAAAAACCCTAACCTAACTTAATGTAAAA
43458128 CCCTAACCTAATTGAATTAAAAACCTAATTTAAATAAAAACCCTAACCTAACTTAA-TGTAAAAC
66 CCCTAACCTAATTGAATTAAAAACCTAATTTAAATAAAAACCCTAACCTAACTTAACT-TAAAA-
43458192 CCTAACCTAACTTAACTT-AA
129 CCTAACCTAACTTAA-TTAAA
43458212 AACCTAACTTAATTAAAAACCCTAACCTAACTTAATTAAAAACCCTAACCTAACTTAATGTAAAA
1 AACCTAACTTAATTAAAAACCCTAACCTAACTTAATTAAAAACCCTAACCTAACTTAATGTAAAA
*
43458277 CCCTAACCTAATTGAATTAAAAACCTAATTTAATTAAAAACCCTAACCTAACTTAACTTAAAACC
66 CCCTAACCTAATTGAATTAAAAACCTAATTTAAATAAAAACCCTAACCTAACTTAACTTAAAACC
* *
43458342 TAACTTAATTTAATTAAAAA
131 TAACCTAACTTAATT--AAA
* *
43458362 CCCTAACCTAACTTAATTTAATTAAAAACCCTAAGCTAACTTAATTTAAAACCCT-ACCTTAACT
1 ----AACCTAAC-----TTAATTAAAAACCCTAACCTAACTTAATTAAAAACCCTAACC-TAACT
*
43458426 TAAT-TAAAAACCCTAACCTAACTT-AATGTAAAACCCTAA
56 TAATGT-AAAACCCTAACCTAA-TTGAAT-TAAAAACCTAA
43458465 CCCTAAGCTA
Statistics
Matches: 510, Mismatches: 15, Indels: 57
0.88 0.03 0.10
Matches are distributed among these distances:
147 2 0.00
148 13 0.03
149 270 0.53
150 3 0.01
153 3 0.01
154 69 0.14
155 39 0.08
156 4 0.01
158 7 0.01
159 88 0.17
160 12 0.02
ACGTcount: A:0.47, C:0.23, G:0.02, T:0.28
Consensus pattern (148 bp):
AACCTAACTTAATTAAAAACCCTAACCTAACTTAATTAAAAACCCTAACCTAACTTAATGTAAAA
CCCTAACCTAATTGAATTAAAAACCTAATTTAAATAAAAACCCTAACCTAACTTAACTTAAAACC
TAACCTAACTTAATTAAA
Found at i:43458154 original size:17 final size:17
Alignment explanation
Indices: 43458132--43458169 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
43458122 GTAAAACCCT
*
43458132 AACCTAATTGAATTAAA
1 AACCTAATTGAAATAAA
*
43458149 AACCTAATTTAAATAAA
1 AACCTAATTGAAATAAA
43458166 AACC
1 AACC
43458170 CTAACCTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.55, C:0.16, G:0.03, T:0.26
Consensus pattern (17 bp):
AACCTAATTGAAATAAA
Found at i:43458217 original size:17 final size:17
Alignment explanation
Indices: 43458195--43458246 Score: 70
Period size: 17 Copynumber: 3.0 Consensus size: 17
43458185 GTAAAACCCT
43458195 AACCTAACTTAACTTAA
1 AACCTAACTTAACTTAA
43458212 AACCTAACTTAA-TTAAA
1 AACCTAACTTAACTT-AA
*
43458229 AACCCTAACCTAACTTAA
1 AA-CCTAACTTAACTTAA
43458247 TTAAAAACCC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
16 2 0.06
17 16 0.52
18 11 0.35
19 2 0.06
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (17 bp):
AACCTAACTTAACTTAA
Found at i:43458303 original size:17 final size:17
Alignment explanation
Indices: 43458281--43458318 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
43458271 GTAAAACCCT
43458281 AACCTAATTGAATTAAA
1 AACCTAATTGAATTAAA
*
43458298 AACCTAATTTAATTAAA
1 AACCTAATTGAATTAAA
43458315 AACC
1 AACC
43458319 CTAACCTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.53, C:0.16, G:0.03, T:0.29
Consensus pattern (17 bp):
AACCTAATTGAATTAAA
Found at i:43458343 original size:17 final size:17
Alignment explanation
Indices: 43458321--43458354 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
43458311 TAAAAACCCT
43458321 AACCTAACTTAACTTAA
1 AACCTAACTTAACTTAA
*
43458338 AACCTAACTTAATTTAA
1 AACCTAACTTAACTTAA
43458355 TTAAAAACCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (17 bp):
AACCTAACTTAACTTAA
Found at i:43458370 original size:28 final size:28
Alignment explanation
Indices: 43458338--43458410 Score: 137
Period size: 28 Copynumber: 2.6 Consensus size: 28
43458328 CTTAACTTAA
43458338 AACCTAACTTAATTTAATTAAAAACCCT
1 AACCTAACTTAATTTAATTAAAAACCCT
43458366 AACCTAACTTAATTTAATTAAAAACCCT
1 AACCTAACTTAATTTAATTAAAAACCCT
*
43458394 AAGCTAACTTAATTTAA
1 AACCTAACTTAATTTAA
43458411 AACCCTACCT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.33
Consensus pattern (28 bp):
AACCTAACTTAATTTAATTAAAAACCCT
Found at i:43458445 original size:28 final size:28
Alignment explanation
Indices: 43458338--43458451 Score: 131
Period size: 28 Copynumber: 4.4 Consensus size: 28
43458328 CTTAACTTAA
*
43458338 AACCTAACTTAATTTAATTAAAAACCCT
1 AACCTAACTTAACTTAATTAAAAACCCT
*
43458366 AACCTAACTTAATTTAATTAAAAACCCT
1 AACCTAACTTAACTTAATTAAAAACCCT
*
43458394 AAGCTAACTTAA--T--TT-AAAACCCT
1 AACCTAACTTAACTTAATTAAAAACCCT
43458417 -A-C---CTTAACTTAATTAAAAACCCT
1 AACCTAACTTAACTTAATTAAAAACCCT
43458440 AACCTAACTTAA
1 AACCTAACTTAA
43458452 TGTAAAACCC
Statistics
Matches: 75, Mismatches: 1, Indels: 20
0.78 0.01 0.21
Matches are distributed among these distances:
18 5 0.07
20 1 0.01
21 1 0.01
22 3 0.04
23 16 0.21
24 3 0.04
25 1 0.01
26 1 0.01
28 44 0.59
ACGTcount: A:0.46, C:0.23, G:0.01, T:0.31
Consensus pattern (28 bp):
AACCTAACTTAACTTAATTAAAAACCCT
Found at i:43458467 original size:29 final size:29
Alignment explanation
Indices: 43458433--43458507 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
43458423 ACTTAATTAA
*
43458433 AAACCCTAACCTAACTTAATGTAAAACCCT
1 AAACCCTAACCTAA-TTAATCTAAAACCCT
* * * *
43458463 -AACCCTAAGCTAATAAACCCTAAATCCCT
1 AAACCCTAACCTAATTAA-TCTAAAACCCT
43458492 AAACCCTAACCTAATT
1 AAACCCTAACCTAATT
43458508 TAATTAATGT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
28 3 0.08
29 20 0.56
30 13 0.36
ACGTcount: A:0.43, C:0.32, G:0.03, T:0.23
Consensus pattern (29 bp):
AAACCCTAACCTAATTAATCTAAAACCCT
Found at i:43461952 original size:125 final size:124
Alignment explanation
Indices: 43461730--43461996 Score: 333
Period size: 125 Copynumber: 2.1 Consensus size: 124
43461720 CCACGAGGGC
* * *
43461730 GCGATTTGACACTATTTGCTCAGAAACGTAAAAGAAATTTATTTCCTACATGACCAATTGTAGCG
1 GCGATTTGACACTATTTGCTCAGAAACGTAAAAGAAAATTATTTCCTACATGACCAACTGTACCG
* * *
43461795 AAATTGCGTCCACGAGGGCGCGATTTCACAATTT-TTGCCCAATATAGCATCTTTGTATCA
66 AAATCGCGTCCACGAGGCCACGATTTCACAATTTCTT-CCCAA-ATAGCATCTTTGTATCA
* * *
43461855 GCGATTTTATACTATTTGCTCAGAAAACGTCAAAA-AAAATTATTTCTTACATGACC-ACTGTAC
1 GCGATTTGACACTATTTGCTCAG-AAACGT-AAAAGAAAATTATTTCCTACATGACCAACTGTAC
* * * **
43461918 CGAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
64 CGAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCCCAAATAGCATCTTTGTATCA
**
43461979 GCGATTTCCCACTATTTG
1 GCGATTTGACACTATTTG
43461997 ACCAGATACG
Statistics
Matches: 122, Mismatches: 17, Indels: 7
0.84 0.12 0.05
Matches are distributed among these distances:
124 28 0.23
125 63 0.52
126 27 0.22
127 4 0.03
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (124 bp):
GCGATTTGACACTATTTGCTCAGAAACGTAAAAGAAAATTATTTCCTACATGACCAACTGTACCG
AAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCCCAAATAGCATCTTTGTATCA
Found at i:43462620 original size:16 final size:17
Alignment explanation
Indices: 43462583--43462621 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
43462573 TTATCTATAA
*
43462583 AAAAATAAACTCAGTAG
1 AAAAATAAACTCAATAG
*
43462600 AAAAATGAACTCAATAG
1 AAAAATAAACTCAATAG
43462617 AAAAA
1 AAAAA
43462622 CTTCTCATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.64, C:0.10, G:0.10, T:0.15
Consensus pattern (17 bp):
AAAAATAAACTCAATAG
Found at i:43469297 original size:42 final size:42
Alignment explanation
Indices: 43469251--43469384 Score: 119
Period size: 42 Copynumber: 3.2 Consensus size: 42
43469241 TAGCTCTCAC
* *
43469251 GAGCTTCTGTTTAACTCATATGAGTTTTCGTTCAGCTCTATT
1 GAGCTTCTGTTTAACCCATATGAGTTTCCGTTCAGCTCTATT
* * * *
43469293 GAGCTTCTGTTTAACCCTTATGGGTTTCCGTTTAGCTCT-TAC
1 GAGCTTCTGTTTAACCCATATGAGTTTCCGTTCAGCTCTAT-T
* * * * * * *
43469335 AAGCTTCCGTTCAACCCTTATGGGTTTCTGTTTAGCTCTCA-T
1 GAGCTTCTGTTTAACCCATATGAGTTTCCGTTCAGCTCT-ATT
43469377 GAGCTTCT
1 GAGCTTCT
43469385 ATTCAGCCTT
Statistics
Matches: 76, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
41 1 0.01
42 75 0.99
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.43
Consensus pattern (42 bp):
GAGCTTCTGTTTAACCCATATGAGTTTCCGTTCAGCTCTATT
Found at i:43469333 original size:21 final size:21
Alignment explanation
Indices: 43469309--43469373 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 21
43469299 CTGTTTAACC
43469309 CTTATGGGTTTCCGTTTAGCT
1 CTTATGGGTTTCCGTTTAGCT
*** * * * *
43469330 CTTACAAGCTTCCGTTCAACC
1 CTTATGGGTTTCCGTTTAGCT
*
43469351 CTTATGGGTTTCTGTTTAGCT
1 CTTATGGGTTTCCGTTTAGCT
43469372 CT
1 CT
43469374 CATGAGCTTC
Statistics
Matches: 29, Mismatches: 15, Indels: 0
0.66 0.34 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.43
Consensus pattern (21 bp):
CTTATGGGTTTCCGTTTAGCT
Found at i:43470878 original size:11 final size:11
Alignment explanation
Indices: 43470847--43470883 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
43470837 TTTTAATCAT
43470847 ATATATATATT-
1 ATATATAT-TTA
43470858 ATATATATTTA
1 ATATATATTTA
43470869 ATATATATTTA
1 ATATATATTTA
43470880 ATAT
1 ATAT
43470884 GGACCAGGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 2 0.08
11 23 0.92
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
ATATATATTTA
Found at i:43478835 original size:15 final size:15
Alignment explanation
Indices: 43478794--43478836 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
43478784 AATAGACAAT
*
43478794 AAAAGTAAGAGAAAGG
1 AAAAGAAAG-GAAAGG
*
43478810 AAAGGAAAGGAAAGG
1 AAAAGAAAGGAAAGG
*
43478825 AAAAGAGAGGAA
1 AAAAGAAAGGAA
43478837 GCTTGTAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.63, C:0.00, G:0.35, T:0.02
Consensus pattern (15 bp):
AAAAGAAAGGAAAGG
Found at i:43482016 original size:13 final size:13
Alignment explanation
Indices: 43481998--43482022 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43481988 ATTAGAAGAT
43481998 AAAAAATATTTTC
1 AAAAAATATTTTC
43482011 AAAAAATATTTT
1 AAAAAATATTTT
43482023 TATTTAATTC
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:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAAAATATTTTC
Found at i:43485637 original size:59 final size:58
Alignment explanation
Indices: 43485516--43485646 Score: 142
Period size: 59 Copynumber: 2.2 Consensus size: 58
43485506 ATGTTGAAAT
** * *
43485516 AATTGTCAAGTTCAAGATTAACTTGGACAAAAAAAAACTCAGGCCCTAATGTAAGAAT
1 AATTGTCAAGTTCAAGACAAACTTGGACAAAAAAAAACTCAAGCCCTAATGTAAGAAC
* *
43485574 AATTGTCAAGTTCAATGACAAACTTGGACCATAAAAAAA-TCAAGCTCC-AATTTGAA-AAC
1 AATTGTCAAGTTCAA-GACAAACTTGGA-CAAAAAAAAACTCAAGC-CCTAATGT-AAGAAC
*
43485633 AATTGTCAAATTCA
1 AATTGTCAAGTTCA
43485647 GACTCTAAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
58 15 0.24
59 34 0.55
60 13 0.21
ACGTcount: A:0.45, C:0.17, G:0.13, T:0.25
Consensus pattern (58 bp):
AATTGTCAAGTTCAAGACAAACTTGGACAAAAAAAAACTCAAGCCCTAATGTAAGAAC
Found at i:43490454 original size:33 final size:33
Alignment explanation
Indices: 43490417--43490486 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
43490407 TTGTTTCAAA
*
43490417 AAAATACAATAAATTATTTCAAATTTTAGAAAC
1 AAAATACAATAAATTATTTCAAATTTCAGAAAC
* *
43490450 AAAATACAGTAAATTATTTTAAATTTCAGAAAC
1 AAAATACAATAAATTATTTCAAATTTCAGAAAC
43490483 AAAA
1 AAAA
43490487 CACGGTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.56, C:0.09, G:0.04, T:0.31
Consensus pattern (33 bp):
AAAATACAATAAATTATTTCAAATTTCAGAAAC
Found at i:43490495 original size:33 final size:33
Alignment explanation
Indices: 43490417--43490496 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
43490407 TTGTTTCAAA
* * *
43490417 AAAATACAATAAATTATTTCAAATTTTAGAAAC
1 AAAACACAGTAAATTATTTCAAATTTCAGAAAC
* *
43490450 AAAATACAGTAAATTATTTTAAATTTCAGAAAC
1 AAAACACAGTAAATTATTTCAAATTTCAGAAAC
*
43490483 AAAACACGGTAAAT
1 AAAACACAGTAAAT
43490497 ATCTAATAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.54, C:0.10, G:0.06, T:0.30
Consensus pattern (33 bp):
AAAACACAGTAAATTATTTCAAATTTCAGAAAC
Found at i:43490508 original size:33 final size:33
Alignment explanation
Indices: 43490417--43490509 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 33
43490407 TTGTTTCAAA
* * * * *
43490417 AAAATACAATAAATTATTTCAAATTTTAGAAAC
1 AAAACACAGTAAATTATCTAAAATTTCAGAAAC
* * *
43490450 AAAATACAGTAAATTATTTTAAATTTCAGAAAC
1 AAAACACAGTAAATTATCTAAAATTTCAGAAAC
*
43490483 AAAACACGGTAAA-TATCTAATAATTTC
1 AAAACACAGTAAATTATCTAA-AATTTC
43490510 TCATAATTTA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
32 5 0.10
33 47 0.90
ACGTcount: A:0.52, C:0.11, G:0.05, T:0.32
Consensus pattern (33 bp):
AAAACACAGTAAATTATCTAAAATTTCAGAAAC
Found at i:43491721 original size:60 final size:60
Alignment explanation
Indices: 43491628--43491746 Score: 202
Period size: 60 Copynumber: 2.0 Consensus size: 60
43491618 ATACTAAACT
* * * *
43491628 AAACACAACAATTTATAACTTAATCCTAAATTACTAATAACTTAATTTTAAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
43491688 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
43491747 TAAAAAGCAA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (60 bp):
AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
Found at i:43491819 original size:7 final size:7
Alignment explanation
Indices: 43491809--43491834 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
43491799 ACTAAACATA
43491809 AATAATT
1 AATAATT
43491816 AATAATT
1 AATAATT
43491823 AATAATT
1 AATAATT
43491830 AATAA
1 AATAA
43491835 CAAAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
AATAATT
Found at i:43492398 original size:37 final size:37
Alignment explanation
Indices: 43492357--43492427 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
43492347 TAAAAATTTG
*
43492357 ATTCGTGCCTGTTAGATAGGCGCGATTAAAAAAACGT
1 ATTCGTGCCTGTTAAATAGGCGCGATTAAAAAAACGT
43492394 ATTCGTGCCTGTTAAATAGGCGCGATTAAAAAAA
1 ATTCGTGCCTGTTAAATAGGCGCGATTAAAAAAA
43492428 TATACTATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (37 bp):
ATTCGTGCCTGTTAAATAGGCGCGATTAAAAAAACGT
Found at i:43494874 original size:22 final size:22
Alignment explanation
Indices: 43494846--43494889 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
43494836 TGTTACATCT
43494846 ATACATTACCATTCAACCAAAA
1 ATACATTACCATTCAACCAAAA
*
43494868 ATACATTACCGTTCAACCAAAA
1 ATACATTACCATTCAACCAAAA
43494890 CCACATTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.48, C:0.27, G:0.02, T:0.23
Consensus pattern (22 bp):
ATACATTACCATTCAACCAAAA
Found at i:43494895 original size:22 final size:22
Alignment explanation
Indices: 43494848--43494896 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
43494838 TTACATCTAT
*
43494848 ACATTACCATTCAACCAAAAAT
1 ACATTACCATTCAACCAAAAAC
* *
43494870 ACATTACCGTTCAACCAAAACC
1 ACATTACCATTCAACCAAAAAC
43494892 ACATT
1 ACATT
43494897 TGTTGTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.45, C:0.31, G:0.02, T:0.22
Consensus pattern (22 bp):
ACATTACCATTCAACCAAAAAC
Found at i:43499560 original size:17 final size:19
Alignment explanation
Indices: 43499538--43499573 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
43499528 ATATTATTAG
43499538 GAAAAT-ATTTT-AATTTT
1 GAAAATAATTTTAAATTTT
43499555 GAAAATAATTTTAAATTTT
1 GAAAATAATTTTAAATTTT
43499574 TTTAATACGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 5 0.29
19 6 0.35
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (19 bp):
GAAAATAATTTTAAATTTT
Found at i:43499883 original size:21 final size:19
Alignment explanation
Indices: 43499859--43499904 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
43499849 TTAATGGTTT
43499859 ATAATTAATTTCTGATGAAAA
1 ATAATTAATTT-T-ATGAAAA
*
43499880 ATAA-TAATTTTTTGAAAA
1 ATAATTAATTTTATGAAAA
43499898 ATAATTA
1 ATAATTA
43499905 TTGAGTGCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 10 0.43
19 3 0.13
20 6 0.26
21 4 0.17
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (19 bp):
ATAATTAATTTTATGAAAA
Found at i:43501701 original size:3 final size:3
Alignment explanation
Indices: 43501693--43501738 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
43501683 ATTCATTTAC
43501693 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
43501739 TCTTTTCCTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:43518959 original size:17 final size:17
Alignment explanation
Indices: 43518937--43518972 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
43518927 ATTTAACTCA
43518937 TTTATTTTTAAAGTATT
1 TTTATTTTTAAAGTATT
43518954 TTTATTTTTAAAGTATT
1 TTTATTTTTAAAGTATT
43518971 TT
1 TT
43518973 AAATTTTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTATTTTTAAAGTATT
Found at i:43518979 original size:17 final size:17
Alignment explanation
Indices: 43518942--43518979 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
43518932 ACTCATTTAT
* *
43518942 TTTTAAAGTATTTTTAT
1 TTTTAAAGTATTTTAAA
43518959 TTTTAAAGTATTTTAAA
1 TTTTAAAGTATTTTAAA
43518976 TTTT
1 TTTT
43518980 GTTATTTGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (17 bp):
TTTTAAAGTATTTTAAA
Found at i:43519084 original size:6 final size:6
Alignment explanation
Indices: 43519073--43519109 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
43519063 ATTAACCACG
43519073 TCATTA TCATTA TCATTA TCATTA TCATTA TCATTA T
1 TCATTA TCATTA TCATTA TCATTA TCATTA TCATTA T
43519110 TATCATCTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.51
Consensus pattern (6 bp):
TCATTA
Found at i:43525215 original size:88 final size:89
Alignment explanation
Indices: 43525056--43525548 Score: 359
Period size: 94 Copynumber: 5.4 Consensus size: 89
43525046 TTGTAGTTAT
* * * * * *
43525056 AAATCCCATACCCCTAAAGTTGCAGTGGGTCAGATTAATTTTACCATAGTAAATCTTATCTCTAT
1 AAATCCTATACCCCTGAAGTTGCAGTAGGTC-G---AA-TGTACCATAGCAAATCTTATCTCTCT
*
43525121 GAAGTTGTAGTGGAGCAGATTGAAGCTAC
61 GAAGTTGCAGTGGAGCAGATTGAAGCTAC
* * ** *
43525150 AAATCCTATACCCCTG-AGTTGTAGTAGGTCGGATGTACCATAGTGAATCTTATCTCTCTAAAGT
1 AAATCCTATACCCCTGAAGTTGCAGTAGGTCGAATGTACCATAGCAAATCTTATCTCTCTGAAGT
* *
43525214 TGCGGTGAAGCAGATTGAAGCTAC
66 TGCAGTGGAGCAGATTGAAGCTAC
* * * * * *
43525238 AAATCTTA-ACCCCTGAAGTTGTAATGGGCCAGGTTGAATCTACCATAGCAAATCTTATCTCCCT
1 AAATCCTATACCCCTGAAGTTG-CA---G-TAGGTCGAATGTACCATAGCAAATCTTATCTCTCT
* *
43525302 GAAGTTGCAGTGGAGCAAATTGAAGCTAT
61 GAAGTTGCAGTGGAGCAGATTGAAGCTAC
* * * * * * *
43525331 AAATCCTATACCTCTGAAGTTGCAGTGGGTCAAATTGAAACAAATGACGAATCTTATCTC-CTTG
1 AAATCCTATACCCCTGAAGTTGCAGTAGGTCGAA-TGTACCATA-G-CAAATCTTATCTCTC-TG
** *
43525395 AAGTTATAGTGGAGCAAGA-TAAAGCTAC
62 AAGTTGCAGTGGAGC-AGATTGAAGCTAC
* * * * * *
43525423 AAATCCTATACCTCTGAAGTTGCAGTGGGTCAAAATGAAACTACAAATGACGAATCTTATCTC-C
1 AAATCCTATACCCCTGAAGTTGCAGTAGGTC-GAATG-TAC--CATA-G-CAAATCTTATCTCTC
* * * *
43525487 TGAAATTACAGTAGAGCAAGA-TGAAACTAC
60 TGAAGTTGCAGTGGAGC-AGATTGAAGCTAC
*
43525517 AAATCCTATACCCCTGAAGTTGCAGTGGGTCG
1 AAATCCTATACCCCTGAAGTTGCAGTAGGTCG
43525549 GATTGAAACT
Statistics
Matches: 332, Mismatches: 51, Indels: 33
0.80 0.12 0.08
Matches are distributed among these distances:
87 7 0.02
88 60 0.18
89 7 0.02
90 6 0.02
91 2 0.01
92 69 0.21
93 79 0.24
94 81 0.24
95 21 0.06
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (89 bp):
AAATCCTATACCCCTGAAGTTGCAGTAGGTCGAATGTACCATAGCAAATCTTATCTCTCTGAAGT
TGCAGTGGAGCAGATTGAAGCTAC
Found at i:43525467 original size:44 final size:43
Alignment explanation
Indices: 43525300--43525545 Score: 165
Period size: 44 Copynumber: 5.4 Consensus size: 43
43525290 TCTTATCTCC
* * *
43525300 CTGAAGTTGCAGTGGAGCAAATTGAAGCTATAAATCCTATACCT
1 CTGAAGTTGCAGTGG-GCAAAATGAAACTACAAATCCTATACCT
* * * *
43525344 CTGAAGTTGCAGTGGGTCAAATTGAAACAAATGACGAATCTTATCTCCT
1 CTGAAGTTGCAGTGGG-CAAAATGAAAC---T-ACAAATCCTAT-ACCT
** *
43525393 -TGAAGTTATAGTGGAGCAAGAT-AAAGCTACAAATCCTATACCT
1 CTGAAGTTGCAGTGG-GCAAAATGAAA-CTACAAATCCTATACCT
*
43525436 CTGAAGTTGCAGTGGGTCAAAATGAAACTACAAATGACGAATCT-TATCT
1 CTGAAGTTGCAGTGGG-CAAAATGAAACTACAAAT--C----CTATACCT
* * * * *
43525485 CCTGAAATTACAGTAGAGCAAGATGAAACTACAAATCCTATACCC
1 -CTGAAGTTGCAGT-GGGCAAAATGAAACTACAAATCCTATACCT
43525530 CTGAAGTTGCAGTGGG
1 CTGAAGTTGCAGTGGG
43525546 TCGGATTGAA
Statistics
Matches: 157, Mismatches: 25, Indels: 41
0.70 0.11 0.18
Matches are distributed among these distances:
43 7 0.04
44 72 0.46
45 7 0.04
46 1 0.01
47 4 0.03
48 26 0.17
49 8 0.05
50 30 0.19
51 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (43 bp):
CTGAAGTTGCAGTGGGCAAAATGAAACTACAAATCCTATACCT
Found at i:43525544 original size:94 final size:94
Alignment explanation
Indices: 43525288--43525578 Score: 405
Period size: 92 Copynumber: 3.1 Consensus size: 94
43525278 TACCATAGCA
* * *
43525288 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAA-ATTGAAGCTATAAATCCTATACCTCTGAAGTT
1 AATCTTATCT-CCTGAAGTTACAGTGGAGCAAGA-TGAAACTACAAATCCTATACCTCTGAAGTT
43525352 GCAGTGGGTCAAATTG-AA--ACAAATGACG
64 GCAGTGGGTCAAATTGAAACTACAAATGACG
*
43525380 AATCTTATCTCCTTGAAGTTATAGTGGAGCAAGAT-AAAGCTACAAATCCTATACCTCTGAAGTT
1 AATCTTATCTCC-TGAAGTTACAGTGGAGCAAGATGAAA-CTACAAATCCTATACCTCTGAAGTT
*
43525444 GCAGTGGGTCAAAATGAAACTACAAATGACG
64 GCAGTGGGTCAAATTGAAACTACAAATGACG
* * *
43525475 AATCTTATCTCCTGAAATTACAGTAGAGCAAGATGAAACTACAAATCCTATACCCCTGAAGTTGC
1 AATCTTATCTCCTGAAGTTACAGTGGAGCAAGATGAAACTACAAATCCTATACCTCTGAAGTTGC
** *
43525540 AGTGGGTCGGATTGAAACTAC-AATGATG
66 AGTGGGTCAAATTGAAACTACAAATGACG
43525568 AATCTTATCTC
1 AATCTTATCTC
43525579 TTTCAACTCT
Statistics
Matches: 179, Mismatches: 13, Indels: 13
0.87 0.06 0.06
Matches are distributed among these distances:
91 4 0.02
92 67 0.37
93 20 0.11
94 63 0.35
95 25 0.14
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (94 bp):
AATCTTATCTCCTGAAGTTACAGTGGAGCAAGATGAAACTACAAATCCTATACCTCTGAAGTTGC
AGTGGGTCAAATTGAAACTACAAATGACG
Found at i:43529878 original size:23 final size:23
Alignment explanation
Indices: 43529852--43529927 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
43529842 ATAAGTGCCA
43529852 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
43529875 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
43529898 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
43529921 CACTGAT
1 CACTGAT
43529928 CAATAACACA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Done.