Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 149 of 292
Found at i:44307347 original size:7 final size:7
Alignment explanation
Indices: 44307294--44307569 Score: 104
Period size: 7 Copynumber: 38.4 Consensus size: 7
44307284 CTCCAACCTT
44307294 TAAACCA
1 TAAACCA
44307301 TAAACCA
1 TAAACCA
* *
44307308 TAATCCC
1 TAAACCA
44307315 TAAACCTA
1 TAAACC-A
*
44307323 TAATCCA
1 TAAACCA
*
44307330 TAATCCA
1 TAAACCA
*
44307337 TAAACCT
1 TAAACCA
**
44307344 TAAAATA
1 TAAACCA
*
44307351 TTAACTCA
1 TAAAC-CA
44307359 TAAACCA
1 TAAACCA
*
44307366 TAAACCCC
1 TAAA-CCA
* *
44307374 TGAACCT
1 TAAACCA
*
44307381 TAAACCC
1 TAAACCA
* * *
44307388 CAACCCT
1 TAAACCA
*
44307395 TAAACCC
1 TAAACCA
44307402 TAAACCCA
1 TAAA-CCA
*
44307410 TAATCCA
1 TAAACCA
*
44307417 TAAACCT
1 TAAACCA
**
44307424 TAAAATA
1 TAAACCA
*
44307431 TTAACTCA
1 TAAAC-CA
*
44307439 TAAACTA
1 TAAACCA
*
44307446 TAAACCCC
1 TAAA-CCA
*
44307454 TAAACCT
1 TAAACCA
*
44307461 TAAACCC
1 TAAACCA
* * *
44307468 CAACCCT
1 TAAACCA
*
44307475 TAAACCT
1 TAAACCA
44307482 TAAACCCA
1 TAAA-CCA
*
44307490 TAATCCA
1 TAAACCA
*
44307497 TAAACCT
1 TAAACCA
**
44307504 TAAAATA
1 TAAACCA
*
44307511 TTAACTCA
1 TAAAC-CA
*
44307519 TAAATCA
1 TAAACCA
*
44307526 TAAACCC
1 TAAACCA
*
44307533 TAAATCA
1 TAAACCA
* *
44307540 TATACCC
1 TAAACCA
44307547 TAAACCA
1 TAAACCA
*
44307554 T-AACCC
1 TAAACCA
*
44307560 TAAACTA
1 TAAACCA
44307567 TAA
1 TAA
44307570 TGATAATTAA
Statistics
Matches: 190, Mismatches: 70, Indels: 18
0.68 0.25 0.06
Matches are distributed among these distances:
6 5 0.03
7 146 0.77
8 39 0.21
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24
Consensus pattern (7 bp):
TAAACCA
Found at i:44307411 original size:80 final size:80
Alignment explanation
Indices: 44307327--44307536 Score: 377
Period size: 80 Copynumber: 2.6 Consensus size: 80
44307317 AACCTATAAT
*
44307327 CCATAATCCATAAACCTTAAAATATTAACTCATAAACCATAAACCCCTGAACCTTAAACCCCAAC
1 CCATAATCCATAAACCTTAAAATATTAACTCATAAACCATAAACCCCTAAACCTTAAACCCCAAC
44307392 CCTTAAACCCTAAAC
66 CCTTAAACCCTAAAC
*
44307407 CCATAATCCATAAACCTTAAAATATTAACTCATAAACTATAAACCCCTAAACCTTAAACCCCAAC
1 CCATAATCCATAAACCTTAAAATATTAACTCATAAACCATAAACCCCTAAACCTTAAACCCCAAC
*
44307472 CCTTAAACCTTAAAC
66 CCTTAAACCCTAAAC
*
44307487 CCATAATCCATAAACCTTAAAATATTAACTCATAAATCATAAA-CCCTAAA
1 CCATAATCCATAAACCTTAAAATATTAACTCATAAACCATAAACCCCTAAA
44307537 TCATATACCC
Statistics
Matches: 125, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
79 7 0.06
80 118 0.94
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.23
Consensus pattern (80 bp):
CCATAATCCATAAACCTTAAAATATTAACTCATAAACCATAAACCCCTAAACCTTAAACCCCAAC
CCTTAAACCCTAAAC
Found at i:44307561 original size:13 final size:13
Alignment explanation
Indices: 44307528--44307569 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
44307518 ATAAATCATA
*
44307528 AACCCTAAATCAT
1 AACCCTAAACCAT
44307541 ATACCCTAAACCAT
1 A-ACCCTAAACCAT
*
44307555 AACCCTAAACTAT
1 AACCCTAAACCAT
44307568 AA
1 AA
44307570 TGATAATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 14 0.54
14 12 0.46
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.21
Consensus pattern (13 bp):
AACCCTAAACCAT
Found at i:44308081 original size:155 final size:152
Alignment explanation
Indices: 44307893--44308388 Score: 486
Period size: 155 Copynumber: 3.3 Consensus size: 152
44307883 ACAAAGCACA
* *
44307893 GCTAAAGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCCACTAAGGCTCAATAAA
1 GCTAAAGCTCGATCTATAGCGGCGTTTTCCAAAAAGCGCCGCTAATGCCACTAAGGCTCAACAAA
*
44307958 AAACGATGGCGTGTTGATGAATTAATTTGTGGCGTTTTTTAAAAAACGCCATTAATGCCCTATCT
66 AAACGAT-GCGTGTTGATGAATTATTTTGTGGCGTTTTTTAAAAAA-GCCA-TAATGCCCTATCT
44308023 ATAGTGGCATTTATCATAAAGCGCC
128 ATAGTGGCATTTATCATAAAGCGCC
* *
44308048 GCTAAAGCTCGATCTATAGCGACGTTTTCCAAAAAGCGCCGCTAATGCCACTATGGCTCAACAAA
1 GCTAAAGCTCGATCTATAGCGGCGTTTTCCAAAAAGCGCCGCTAATGCCACTAAGGCTCAACAAA
* * * *
44308113 AAACAACTGCGTGTTGATGAATTATTTTGTGGCATTTTTT-AAAAAG-C---GT-CGC--TC---
66 AAACGA-TGCGTGTTGATGAATTATTTTGTGGCGTTTTTTAAAAAAGCCATAATGCCCTATCTAT
** ** *
44308167 A-T-GC-TCGATCTATAGCG-GCA
130 AGTGGCATTTATC-ATAAAGCGCC
* * * *
44308187 GCTAAAGCTCGATTTATAGCTGTGTTTTCCGAAAAGCGCCGCTAATGCCACTAAGGCTCAACAAA
1 GCTAAAGCTCGATCTATAGCGGCGTTTTCCAAAAAGCGCCGCTAATGCCACTAAGGCTCAACAAA
* * * * *
44308252 AAATGACAGCGTGTTGATGAATTATTTTGCGGCGTTTTTTAAAAAATGCTACTAATG-CTTGATC
66 AAACGA-TGCGTGTTGATGAATTATTTTGTGGCGTTTTTTAAAAAA-GCCA-TAATGCCCT-ATC
* * *
44308316 TATAGCGGCATTTTTCAAAAAGCGCC
127 TATAGTGGCATTTATCATAAAGCGCC
* ** * * * *
44308342 ACTAATTCTCAATCTATAGTGGCGCTTTTCTAAAAA-CACCGCTAATG
1 GCTAAAGCTCGATCTATAGCGGCG-TTTTCCAAAAAGCGCCGCTAATG
44308389 TTTGATCTAT
Statistics
Matches: 272, Mismatches: 48, Indels: 42
0.75 0.13 0.12
Matches are distributed among these distances:
139 100 0.37
140 11 0.04
141 2 0.01
142 1 0.00
145 2 0.01
146 1 0.00
147 2 0.01
148 1 0.00
149 2 0.01
152 2 0.01
153 1 0.00
154 10 0.04
155 127 0.47
156 10 0.04
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.29
Consensus pattern (152 bp):
GCTAAAGCTCGATCTATAGCGGCGTTTTCCAAAAAGCGCCGCTAATGCCACTAAGGCTCAACAAA
AAACGATGCGTGTTGATGAATTATTTTGTGGCGTTTTTTAAAAAAGCCATAATGCCCTATCTATA
GTGGCATTTATCATAAAGCGCC
Found at i:44308310 original size:139 final size:137
Alignment explanation
Indices: 44308048--44308325 Score: 396
Period size: 139 Copynumber: 2.0 Consensus size: 137
44308038 ATAAAGCGCC
*
44308048 GCTAAAGCTCGATCTATAGCGACGTTTTCCAAAAAGCGCCGCTAATGCCACTATGGCTCAACAAA
1 GCTAAAGCTCGATCTATAGCG-CGTTTTCCAAAAAGCGCCGCTAATGCCACTAAGGCTCAACAAA
* * * * *
44308113 AAACAACTGCGTGTTGATGAATTATTTTGTGGCATTTTTT-AAAAAGCGTCGCTCATGCTCGATC
65 AAACGACAGCGTGTTGATGAATTATTTTGTGGCGTTTTTTAAAAAAGC-T-ACTAATGCTCGATC
44308177 TATAGCGGCA
128 TATAGCGGCA
* * *
44308187 GCTAAAGCTCGATTTATAGCTGTGTTTTCCGAAAAGCGCCGCTAATGCCACTAAGGCTCAACAAA
1 GCTAAAGCTCGATCTATAGC-GCGTTTTCCAAAAAGCGCCGCTAATGCCACTAAGGCTCAACAAA
* * *
44308252 AAATGACAGCGTGTTGATGAATTATTTTGCGGCGTTTTTTAAAAAATGCTACTAATGCTTGATCT
65 AAACGACAGCGTGTTGATGAATTATTTTGTGGCGTTTTTTAAAAAA-GCTACTAATGCTCGATCT
44308317 ATAGCGGCA
129 ATAGCGGCA
44308326 TTTTTCAAAA
Statistics
Matches: 124, Mismatches: 12, Indels: 6
0.87 0.08 0.04
Matches are distributed among these distances:
139 115 0.93
140 7 0.06
141 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.29
Consensus pattern (137 bp):
GCTAAAGCTCGATCTATAGCGCGTTTTCCAAAAAGCGCCGCTAATGCCACTAAGGCTCAACAAAA
AACGACAGCGTGTTGATGAATTATTTTGTGGCGTTTTTTAAAAAAGCTACTAATGCTCGATCTAT
AGCGGCA
Found at i:44308346 original size:40 final size:39
Alignment explanation
Indices: 44308280--44308413 Score: 126
Period size: 40 Copynumber: 3.4 Consensus size: 39
44308270 GAATTATTTT
* *
44308280 GCGGCGTTTTTTAAAAA-ATGCTACTAATGCTTGATCTATA
1 GCGGCGTTTTTCAAAAACA--CCACTAATGCTTGATCTATA
* * * **
44308320 GCGGCATTTTTCAAAAAGCGCCACTAATTCTCAATCTATA
1 GCGGCGTTTTTCAAAAA-CACCACTAATGCTTGATCTATA
* * * *
44308360 GTGGCGCTTTTCTAAAAACACCGCTAATGTTTGATCTATA
1 GCGGCGTTTTTC-AAAAACACCACTAATGCTTGATCTATA
44308400 GCGGCGTTTTTCAA
1 GCGGCGTTTTTCAA
44308414 TGCTTGATCT
Statistics
Matches: 73, Mismatches: 18, Indels: 7
0.74 0.18 0.07
Matches are distributed among these distances:
39 2 0.03
40 66 0.90
41 5 0.07
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34
Consensus pattern (39 bp):
GCGGCGTTTTTCAAAAACACCACTAATGCTTGATCTATA
Found at i:44308415 original size:27 final size:27
Alignment explanation
Indices: 44308385--44308437 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
44308375 AAACACCGCT
* *
44308385 AATGTTTGATCTATAGCGGCGTTTTTC
1 AATGCTTGATCTATAGCGGCATTTTTC
*
44308412 AATGCTTGATCTATAGTGGCATTTTT
1 AATGCTTGATCTATAGCGGCATTTTT
44308438 TGTACAAACG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.21, T:0.45
Consensus pattern (27 bp):
AATGCTTGATCTATAGCGGCATTTTTC
Found at i:44311352 original size:23 final size:23
Alignment explanation
Indices: 44311256--44311368 Score: 129
Period size: 23 Copynumber: 4.9 Consensus size: 23
44311246 GAATCTATTA
* *
44311256 GCTACAATATAGTGGTAGCTTTG
1 GCTACAATACAGTGGTAGCTTCG
* *
44311279 GCTAC-ATCTCAGGGGTAGCTTCG
1 GCTACAAT-ACAGTGGTAGCTTCG
*
44311302 GCTACAATACAGTGGTAGCTTTG
1 GCTACAATACAGTGGTAGCTTCG
44311325 GCTACAATACAGTGGTAGCTTCG
1 GCTACAATACAGTGGTAGCTTCG
* ** *
44311348 ACTACGTTACAGTGATAGCTT
1 GCTACAATACAGTGGTAGCTT
44311369 TAGCTATATT
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
22 2 0.03
23 72 0.95
24 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (23 bp):
GCTACAATACAGTGGTAGCTTCG
Found at i:44311380 original size:23 final size:23
Alignment explanation
Indices: 44311253--44311384 Score: 115
Period size: 23 Copynumber: 5.7 Consensus size: 23
44311243 TAAGAATCTA
* *
44311253 TTAGCTACAATATAGTGGTAGCT
1 TTAGCTACATTACAGTGGTAGCT
* *
44311276 TTGGCTACATCT-CAGGGGTAGCT
1 TTAGCTACAT-TACAGTGGTAGCT
** *
44311299 TCGGCTACAATACAGTGGTAGCT
1 TTAGCTACATTACAGTGGTAGCT
* *
44311322 TTGGCTACAATACAGTGGTAGC-
1 TTAGCTACATTACAGTGGTAGCT
* * *
44311344 TTCGACTACGTTACAGTGATAGCT
1 TTAG-CTACATTACAGTGGTAGCT
*
44311368 TTAGCTATATTACAGTG
1 TTAGCTACATTACAGTG
44311385 TGGCACTTTG
Statistics
Matches: 90, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
22 4 0.04
23 82 0.91
24 4 0.04
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (23 bp):
TTAGCTACATTACAGTGGTAGCT
Found at i:44311382 original size:46 final size:46
Alignment explanation
Indices: 44311257--44311384 Score: 159
Period size: 46 Copynumber: 2.8 Consensus size: 46
44311247 AATCTATTAG
* * *
44311257 CTACAATATAGTGGTAGCTTTGGCTACATCT-CAGGGGTAGCTTCGG
1 CTACAATACAGTGGTAGCTTTGGCTACAT-TACAGTGGTAGCTTCGA
*
44311303 CTACAATACAGTGGTAGCTTTGGCTACAATACAGTGGTAGCTTCGA
1 CTACAATACAGTGGTAGCTTTGGCTACATTACAGTGGTAGCTTCGA
** * * *
44311349 CTACGTTACAGTGATAGCTTTAGCTATATTACAGTG
1 CTACAATACAGTGGTAGCTTTGGCTACATTACAGTG
44311385 TGGCACTTTG
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
45 1 0.01
46 70 0.99
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (46 bp):
CTACAATACAGTGGTAGCTTTGGCTACATTACAGTGGTAGCTTCGA
Found at i:44311382 original size:69 final size:69
Alignment explanation
Indices: 44311256--44311384 Score: 152
Period size: 69 Copynumber: 1.9 Consensus size: 69
44311246 GAATCTATTA
* * * * *
44311256 GCTACAATATAGTGGTAGCTTTGGCTACATCTCAGGGGTAGCTTCGGCTACAATACAGTGGTAGC
1 GCTACAATACAGTGGTAGCTTCGACTACATCTCAGGGATAGCTTCAGCTACAATACAGTGGTAGC
44311321 TTTG
66 TTTG
* * * * *
44311325 GCTACAATACAGTGGTAGCTTCGACTACGT-TACAGTGATAGCTTTAGCTATATTACAGTG
1 GCTACAATACAGTGGTAGCTTCGACTACATCT-CAGGGATAGCTTCAGCTACAATACAGTG
44311385 TGGCACTTTG
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
68 1 0.02
69 48 0.98
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.31
Consensus pattern (69 bp):
GCTACAATACAGTGGTAGCTTCGACTACATCTCAGGGATAGCTTCAGCTACAATACAGTGGTAGC
TTTG
Found at i:44311450 original size:25 final size:25
Alignment explanation
Indices: 44311375--44311450 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
44311365 GCTTTAGCTA
44311375 TATTACAGTGTGGCACTTTGTGCCT
1 TATTACAGTGTGGCACTTTGTGCCT
* * * *
44311400 TATT-CCGTGT--TAGC-TT-CGACT
1 TATTACAGTGTGGCA-CTTTGTGCCT
44311421 ATATTACAGTGTGGCACTTTGTGCCT
1 -TATTACAGTGTGGCACTTTGTGCCT
44311447 TATT
1 TATT
44311451 CCGTGTATCC
Statistics
Matches: 36, Mismatches: 8, Indels: 14
0.62 0.14 0.24
Matches are distributed among these distances:
21 3 0.08
22 7 0.19
23 6 0.17
24 6 0.17
25 11 0.31
26 3 0.08
ACGTcount: A:0.17, C:0.20, G:0.21, T:0.42
Consensus pattern (25 bp):
TATTACAGTGTGGCACTTTGTGCCT
Found at i:44311871 original size:36 final size:36
Alignment explanation
Indices: 44311831--44311905 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
44311821 ATGAGATATG
44311831 AAATTAAAGGTCATTGAGTCTATTTTCATAGAAAGA
1 AAATTAAAGGTCATTGAGTCTATTTTCATAGAAAGA
44311867 AAATTAAAGGTCATTGAGTCTATTTTCATAGAAAGA
1 AAATTAAAGGTCATTGAGTCTATTTTCATAGAAAGA
44311903 AAA
1 AAA
44311906 CGGAGTGAGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (36 bp):
AAATTAAAGGTCATTGAGTCTATTTTCATAGAAAGA
Found at i:44313937 original size:12 final size:12
Alignment explanation
Indices: 44313912--44313946 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
44313902 CATAAAATGT
44313912 TAGGAG-TG-GA
1 TAGGAGATGTGA
44313922 TAGGAGATGTGA
1 TAGGAGATGTGA
44313934 TAGGAGATGTGA
1 TAGGAGATGTGA
44313946 T
1 T
44313947 GTAACACCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 6 0.26
11 2 0.09
12 15 0.65
ACGTcount: A:0.31, C:0.00, G:0.43, T:0.26
Consensus pattern (12 bp):
TAGGAGATGTGA
Found at i:44315366 original size:40 final size:40
Alignment explanation
Indices: 44315317--44315524 Score: 249
Period size: 40 Copynumber: 5.2 Consensus size: 40
44315307 TCTTCGGAAT
* * *
44315317 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
* * ** * *
44315356 TTAACCCGGATTTGGTAACTTGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
* *
44315396 TTAGCCCGGATATAA-CAACTCGCACGAATGCCTTCGGGTC
1 TTAGCCCGGATATAATC-ACTAGCACAAATGCCTTCGGGTC
* *
44315436 TTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
* * *
44315476 TTAGCCCGGATATAATCATTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
44315516 TTAGCCCGG
1 TTAGCCCGG
44315525 GTATCATTCA
Statistics
Matches: 145, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
39 3 0.02
40 141 0.97
41 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.25
Consensus pattern (40 bp):
TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
Found at i:44320715 original size:27 final size:27
Alignment explanation
Indices: 44320603--44320862 Score: 221
Period size: 27 Copynumber: 9.7 Consensus size: 27
44320593 TTTAGTTTAC
* * * *
44320603 TAAAATTATTGAGATACCC-CCAATTG
1 TAAAATTACTGAAATACCCTCGATTTG
* * *
44320629 TAAAATTAC-CAAAGTACCC-CCAGTTTA
1 TAAAATTACTGAAA-TACCCTCGA-TTTG
** *
44320656 TAAAATTACTGAAATACTGTTGA-TTG
1 TAAAATTACTGAAATACCCTCGATTTG
* *
44320682 TAAAATTATTGAAATACCCTCGACTTG
1 TAAAATTACTGAAATACCCTCGATTTG
* * *
44320709 TAAAATTAC-CAAAGTA-CCTCCAGTTTA
1 TAAAATTACTGAAA-TACCCTCGA-TTTG
* *
44320736 TAAAATTACCGAAATACCGTCGA-TTG
1 TAAAATTACTGAAATACCCTCGATTTG
44320762 TAAAATTACTGAAATACCCTCGATTTG
1 TAAAATTACTGAAATACCCTCGATTTG
* *
44320789 TAAAATTACCGAAATACCCTC-AGTTTA
1 TAAAATTACTGAAATACCCTCGA-TTTG
* *
44320816 CAAAATTACTGAAATACCCTCAATTTG
1 TAAAATTACTGAAATACCCTCGATTTG
*
44320843 TAAAATTATTGAAATACCCT
1 TAAAATTACTGAAATACCCT
44320863 TATAGGGTAG
Statistics
Matches: 189, Mismatches: 33, Indels: 23
0.77 0.13 0.09
Matches are distributed among these distances:
25 2 0.01
26 69 0.37
27 106 0.56
28 12 0.06
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (27 bp):
TAAAATTACTGAAATACCCTCGATTTG
Found at i:44320721 original size:80 final size:80
Alignment explanation
Indices: 44320603--44320862 Score: 371
Period size: 80 Copynumber: 3.2 Consensus size: 80
44320593 TTTAGTTTAC
* *
44320603 TAAAATTATTGAGATACCC-CCAATTGTAAAATTACCAAAGTACCCCCAGTTTATAAAATTACTG
1 TAAAATTATTGAAATACCCTCGAATTGTAAAATTACCAAAGTACCCCCAGTTTATAAAATTACTG
* *
44320667 AAATACTGTTGATTG
66 AAATACCGTCGATTG
* * *
44320682 TAAAATTATTGAAATACCCTCGACTTGTAAAATTACCAAAGTACCTCCAGTTTATAAAATTACCG
1 TAAAATTATTGAAATACCCTCGAATTGTAAAATTACCAAAGTACCCCCAGTTTATAAAATTACTG
44320747 AAATACCGTCGATTG
66 AAATACCGTCGATTG
* * * *
44320762 TAAAATTACTGAAATACCCTCGATTTGTAAAATTACCGAAA-TACCCTCAGTTTACAAAATTACT
1 TAAAATTATTGAAATACCCTCGAATTGTAAAATTACC-AAAGTACCCCCAGTTTATAAAATTACT
* *
44320826 GAAATACCCTCAATTTG
65 GAAATACCGTCGA-TTG
44320843 TAAAATTATTGAAATACCCT
1 TAAAATTATTGAAATACCCT
44320863 TATAGGGTAG
Statistics
Matches: 162, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
79 18 0.11
80 119 0.73
81 25 0.15
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (80 bp):
TAAAATTATTGAAATACCCTCGAATTGTAAAATTACCAAAGTACCCCCAGTTTATAAAATTACTG
AAATACCGTCGATTG
Found at i:44320876 original size:27 final size:27
Alignment explanation
Indices: 44320853--44321201 Score: 396
Period size: 27 Copynumber: 13.0 Consensus size: 27
44320843 TAAAATTATT
* *
44320853 GAAATACCCTTATAGGGTAGAATTACT
1 GAAATACCCTTGTAGGGTAGAATTACC
* * *
44320880 AAAATACCATTATAGGGTAGAATTACC
1 GAAATACCCTTGTAGGGTAGAATTACC
*
44320907 AAAATACCCTTGTAGGGTAGAATTACC
1 GAAATACCCTTGTAGGGTAGAATTACC
* *
44320934 GAAATACCTTTGTA-GGTAGAAATACC
1 GAAATACCCTTGTAGGGTAGAATTACC
* *
44320960 GAAATACCCCTGTAGGGTAGAATTACT
1 GAAATACCCTTGTAGGGTAGAATTACC
* * * *
44320987 AAAATACCCCTATAGGGTAGAATTATC
1 GAAATACCCTTGTAGGGTAGAATTACC
* **
44321014 GAAATACCCTTGTAGGGTAGAAATATT
1 GAAATACCCTTGTAGGGTAGAATTACC
* *
44321041 GAAATACCTTTGTAGGGTAGAAATACC
1 GAAATACCCTTGTAGGGTAGAATTACC
* * *
44321068 AAAATACCCCTGTAGGGTAGAATTACT
1 GAAATACCCTTGTAGGGTAGAATTACC
* * *
44321095 GAAATACCCCTATAAGGTAGAATTACC
1 GAAATACCCTTGTAGGGTAGAATTACC
*
44321122 GAAATACCCTTGTAAGGTAGAATTACC
1 GAAATACCCTTGTAGGGTAGAATTACC
* * *
44321149 AAAATACCCCTAT-GGGTAGAATTACC
1 GAAATACCCTTGTAGGGTAGAATTACC
* * *
44321175 GAGATACCCTTGTGGGGTAAAATTACC
1 GAAATACCCTTGTAGGGTAGAATTACC
44321202 ATTTTACCCC
Statistics
Matches: 276, Mismatches: 44, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
26 44 0.16
27 232 0.84
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (27 bp):
GAAATACCCTTGTAGGGTAGAATTACC
Found at i:44320877 original size:54 final size:54
Alignment explanation
Indices: 44320736--44321200 Score: 376
Period size: 54 Copynumber: 8.7 Consensus size: 54
44320726 CTCCAGTTTA
* * ** * * **
44320736 TAAAATTACCGAAATACCGTCG-ATTGTAAAATTACTGAAATACCCTCGATTTG
1 TAAAATTACCGAAATACCCTTGTAGGGTAGAATTACTGAAATACCCTCTATGGG
* ** * * **
44320789 TAAAATTACCGAAATACCC-T-CAGTTTACAAAATTACTGAAATACCCTCAATTTG
1 TAAAATTACCGAAATACCCTTGTAGGGT--AGAATTACTGAAATACCCTCTATGGG
** * * *
44320843 TAAAATTATTGAAATACCCTTATAGGGTAGAATTACTAAAATACCAT-TATAGGG
1 TAAAATTACCGAAATACCCTTGTAGGGTAGAATTACTGAAATACCCTCTAT-GGG
* * * * * *
44320897 TAGAATTACCAAAATACCCTTGTAGGGTAGAATTACCGAAATA-CCTTTGTAGG
1 TAAAATTACCGAAATACCCTTGTAGGGTAGAATTACTGAAATACCCTCTATGGG
* *
44320950 TAGAAA-TACCGAAATACCCCTGTAGGGTAGAATTACTAAAATACCC-CTATAGGG
1 TA-AAATTACCGAAATACCCTTGTAGGGTAGAATTACTGAAATACCCTCTAT-GGG
* * * * * *
44321004 TAGAATTATCGAAATACCCTTGTAGGGTAGAAATATTGAAATA-CCTTTGTAGGG
1 TAAAATTACCGAAATACCCTTGTAGGGTAGAATTACTGAAATACCCTCTAT-GGG
* * *
44321058 TAGAAA-TACCAAAATACCCCTGTAGGGTAGAATTACTGAAATACCC-CTATAAGG
1 TA-AAATTACCGAAATACCCTTGTAGGGTAGAATTACTGAAATACCCTCTAT-GGG
* * **
44321112 TAGAATTACCGAAATACCCTTGTAAGGTAGAATTACCAAAATACCC-CTATGGG
1 TAAAATTACCGAAATACCCTTGTAGGGTAGAATTACTGAAATACCCTCTATGGG
* * * *
44321165 TAGAATTACCGAGATACCCTTGTGGGGTAAAATTAC
1 TAAAATTACCGAAATACCCTTGTAGGGTAGAATTAC
44321201 CATTTTACCC
Statistics
Matches: 335, Mismatches: 62, Indels: 30
0.78 0.15 0.07
Matches are distributed among these distances:
52 3 0.01
53 101 0.30
54 223 0.67
55 5 0.01
56 3 0.01
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.28
Consensus pattern (54 bp):
TAAAATTACCGAAATACCCTTGTAGGGTAGAATTACTGAAATACCCTCTATGGG
Found at i:44320904 original size:81 final size:81
Alignment explanation
Indices: 44320853--44321185 Score: 436
Period size: 81 Copynumber: 4.1 Consensus size: 81
44320843 TAAAATTATT
* ** * * *
44320853 GAAATACCCTTATAGGGTAGAATTACTAAAATACCATTATAGGGTAGAATTACCAAAATACCCTT
1 GAAATACCCTTATAGGGTAGAAATACCGAAATACCCTTGTAGGGTAGAATTACCAAAATACCCCT
*
44320918 GTAGGGTAGAATTACC
66 ATAGGGTAGAATTACC
* * * *
44320934 GAAATACCTTTGTA-GGTAGAAATACCGAAATACCCCTGTAGGGTAGAATTACTAAAATACCCCT
1 GAAATACCCTTATAGGGTAGAAATACCGAAATACCCTTGTAGGGTAGAATTACCAAAATACCCCT
*
44320998 ATAGGGTAGAATTATC
66 ATAGGGTAGAATTACC
* ** * *
44321014 GAAATACCCTTGTAGGGTAGAAATATTGAAATACCTTTGTAGGGTAGAAATACCAAAATACCCCT
1 GAAATACCCTTATAGGGTAGAAATACCGAAATACCCTTGTAGGGTAGAATTACCAAAATACCCCT
* *
44321079 GTAGGGTAGAATTACT
66 ATAGGGTAGAATTACC
* * * *
44321095 GAAATACCCCTATAAGGTAGAATTACCGAAATACCCTTGTAAGGTAGAATTACCAAAATACCCCT
1 GAAATACCCTTATAGGGTAGAAATACCGAAATACCCTTGTAGGGTAGAATTACCAAAATACCCCT
44321160 AT-GGGTAGAATTACC
66 ATAGGGTAGAATTACC
*
44321175 GAGATACCCTT
1 GAAATACCCTT
44321186 GTGGGGTAAA
Statistics
Matches: 216, Mismatches: 35, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
80 90 0.42
81 126 0.58
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (81 bp):
GAAATACCCTTATAGGGTAGAAATACCGAAATACCCTTGTAGGGTAGAATTACCAAAATACCCCT
ATAGGGTAGAATTACC
Found at i:44323060 original size:93 final size:93
Alignment explanation
Indices: 44322948--44323119 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
44322938 GCCCATAAGT
* *
44322948 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
44323013 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
44323041 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
44323106 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
44323120 CAAATATCCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:44323115 original size:46 final size:46
Alignment explanation
Indices: 44322940--44323115 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
44322930 TGTAACCCGC
* * *
44322940 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
44322986 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
44323036 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
44323079 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
44323116 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:44325049 original size:29 final size:29
Alignment explanation
Indices: 44325016--44325103 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
44325006 CAAATTATGG
44325016 AAGAAAACCGAATAAAGAAATCCAAGATA
1 AAGAAAACCGAATAAAGAAATCCAAGATA
* *
44325045 GAGAAACCCGAATAAAGAAATCC-AGAATA
1 AAGAAAACCGAATAAAGAAATCCAAG-ATA
* * * *
44325074 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACC-GAATAAAGAAATCCAAGATA
44325104 CGATACTATG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
28 2 0.04
29 30 0.61
30 15 0.31
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (29 bp):
AAGAAAACCGAATAAAGAAATCCAAGATA
Found at i:44325074 original size:15 final size:15
Alignment explanation
Indices: 44325016--44325094 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
44325006 CAAATTATGG
*
44325016 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
44325030 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
44325045 GAGAAA-CCCGAATA
1 AAGAAATCCAGAATA
44325059 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
44325074 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
44325089 AAGAAA
1 AAGAAA
44325095 CCCAAGATAC
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
14 19 0.36
15 34 0.64
ACGTcount: A:0.58, C:0.14, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:44325103 original size:15 final size:15
Alignment explanation
Indices: 44325027--44325103 Score: 77
Period size: 15 Copynumber: 5.2 Consensus size: 15
44325017 AGAAAACCGA
44325027 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* * *
44325042 ATAGAGAAACCCGA-
1 ATAAAGAAATCCAAG
44325056 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
* *
44325070 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
44325086 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
44325101 ATA
1 ATA
44325104 CGATACTATG
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
13 1 0.02
14 10 0.20
15 37 0.76
16 1 0.02
ACGTcount: A:0.56, C:0.16, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:44328133 original size:93 final size:93
Alignment explanation
Indices: 44328021--44328192 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
44328011 GCCCATAAGT
* *
44328021 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
44328086 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
44328114 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
44328179 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
44328193 CAAATATCCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:44328188 original size:46 final size:46
Alignment explanation
Indices: 44328013--44328188 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
44328003 TGTAACCCGC
* * *
44328013 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
44328059 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
44328109 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
44328152 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
44328189 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:44329955 original size:16 final size:17
Alignment explanation
Indices: 44329913--44329970 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
44329903 GATTTATCAT
*
44329913 AGAAATGTATATGTTATA
1 AGAAAAGTATATG-TATA
44329931 A-AAAA--ATATG-ATA
1 AGAAAAGTATATGTATA
44329944 AGAAAAGTATATGTATA
1 AGAAAAGTATATGTATA
* *
44329961 TGAAAGGTAT
1 AGAAAAGTAT
44329971 TACATGATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
13 4 0.12
14 4 0.12
15 5 0.15
16 5 0.15
17 14 0.42
18 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.17, T:0.31
Consensus pattern (17 bp):
AGAAAAGTATATGTATA
Found at i:44331793 original size:29 final size:29
Alignment explanation
Indices: 44331761--44331843 Score: 103
Period size: 29 Copynumber: 2.9 Consensus size: 29
44331751 AAATTCACAT
* * *
44331761 ACCTGTATCTGGCCCATTAGGCCCAAATC
1 ACCTATATATGGCCCATTAGGCCCAAATA
*
44331790 ACCTATATATGGCCCATTAGTCCCAAATA
1 ACCTATATATGGCCCATTAGGCCCAAATA
* * *
44331819 ACATTTATATGGCCCGTTAGGCCCA
1 ACCTATATATGGCCCATTAGGCCCA
44331844 GTCACACTCA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.27
Consensus pattern (29 bp):
ACCTATATATGGCCCATTAGGCCCAAATA
Found at i:44333357 original size:16 final size:16
Alignment explanation
Indices: 44333336--44333368 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
44333326 AAAAATTCTA
44333336 GATTTC-GGAATTTTTG
1 GATTTCAGG-ATTTTTG
44333352 GATTTCAGGATTTTTG
1 GATTTCAGGATTTTTG
44333368 G
1 G
44333369 TGCGTTACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.18, C:0.06, G:0.27, T:0.48
Consensus pattern (16 bp):
GATTTCAGGATTTTTG
Found at i:44338802 original size:40 final size:40
Alignment explanation
Indices: 44338658--44338864 Score: 224
Period size: 40 Copynumber: 5.2 Consensus size: 40
44338648 TGAATGATAC
* *
44338658 CCGGGCTAAGTCCCGAAGGCATTTATGCTA-ATGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTTG-TTATAT
*
44338698 CCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTTG-TTATAT
* *
44338738 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTTGTTATAT
* * *** *
44338778 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTTGTTATAT
* * * * *
44338818 CTGGGTTAAGACCCGAAGGCAATT-TGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTTGTTATAT
44338857 CC-GGCTAA
1 CCGGGCTAA
44338865 ATTCCGAAGA
Statistics
Matches: 145, Mismatches: 20, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
38 5 0.03
39 9 0.06
40 129 0.89
41 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTATGCTAGTTGTTATAT
Found at i:44342423 original size:29 final size:29
Alignment explanation
Indices: 44342366--44342467 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 29
44342356 TACCTATATC
* * *
44342366 TGGCCCATTAAGCCC-AATCATATTTATA
1 TGGCCCATTAGGCCCAAATCACATGTATA
* *
44342394 TGGCCTATTAGGCCCAAATCACCTGTATA
1 TGGCCCATTAGGCCCAAATCACATGTATA
* * *
44342423 TGGCCCATTAGGCTCGAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATGTATA
*
44342452 TGGCCCGTTAGGCCCA
1 TGGCCCATTAGGCCCA
44342468 GTCACATTCA
Statistics
Matches: 60, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
28 13 0.22
29 47 0.78
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.28
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATGTATA
Found at i:44342449 original size:58 final size:57
Alignment explanation
Indices: 44342357--44342467 Score: 150
Period size: 58 Copynumber: 1.9 Consensus size: 57
44342347 AAATTCACAT
* * *
44342357 ACCTATATCTGGCCCATTAAGCCCAATCATATTTATATGGCCTATTAGGCCCAAATC
1 ACCTATATATGGCCCATTAAGCCCAATCACATTTATATGGCCCATTAGGCCCAAATC
* * * *
44342414 ACCTGTATATGGCCCATTAGGCTCGAATCACATTTATATGGCCCGTTAGGCCCA
1 ACCTATATATGGCCCATTAAGC-CCAATCACATTTATATGGCCCATTAGGCCCA
44342468 GTCACATTCA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 19 0.41
58 27 0.59
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (57 bp):
ACCTATATATGGCCCATTAAGCCCAATCACATTTATATGGCCCATTAGGCCCAAATC
Found at i:44342710 original size:8 final size:8
Alignment explanation
Indices: 44342699--44342729 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
44342689 ACTTTCTGCT
*
44342699 TTTCAGCA
1 TTTCGGCA
44342707 TTTCGGCA
1 TTTCGGCA
44342715 TTTCGGCA
1 TTTCGGCA
44342723 TTTCGGC
1 TTTCGGC
44342730 TTTTACTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.13, C:0.26, G:0.23, T:0.39
Consensus pattern (8 bp):
TTTCGGCA
Found at i:44345248 original size:38 final size:38
Alignment explanation
Indices: 44345155--44345250 Score: 106
Period size: 38 Copynumber: 2.5 Consensus size: 38
44345145 GATGGGGGTA
* *
44345155 ATTTGCTCAACACTTCAAAGCTTCAAGATGGTGGCAAG
1 ATTTGCTCAACACTTCAAAGCATCAAGATGGTGGAAAG
* * *
44345193 A-TTCCTTTAACACTTCAAAGCATCAATATGGAT-GAAAG
1 ATTTGC-TCAACACTTCAAAGCATCAAGATGG-TGGAAAG
*
44345231 ATTTGCTCAACATTTCAAAG
1 ATTTGCTCAACACTTCAAAG
44345251 ATTCGAGGAG
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
37 3 0.06
38 40 0.85
39 4 0.09
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (38 bp):
ATTTGCTCAACACTTCAAAGCATCAAGATGGTGGAAAG
Found at i:44346192 original size:31 final size:31
Alignment explanation
Indices: 44346157--44346220 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
44346147 CCTTTTCATG
44346157 TTTCATATTCCATAACACTGGGCCGAAGCCT
1 TTTCATATTCCATAACACTGGGCCGAAGCCT
* **
44346188 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTCCATAACACTGGGCCGAAGCCT
44346219 TT
1 TT
44346221 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCATATTCCATAACACTGGGCCGAAGCCT
Found at i:44346463 original size:24 final size:24
Alignment explanation
Indices: 44346412--44346531 Score: 154
Period size: 24 Copynumber: 5.0 Consensus size: 24
44346402 GCTTTATCAT
*
44346412 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
44346437 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTA
44346461 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
*
44346484 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
44346508 ATAACTGGGCCATAAGCCCCTTTT
1 ATAACTGGGGCATAAG-CCCTTTT
44346532 CACTTCCTCC
Statistics
Matches: 86, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
23 23 0.27
24 44 0.51
25 19 0.22
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:44346491 original size:47 final size:48
Alignment explanation
Indices: 44346412--44346531 Score: 154
Period size: 47 Copynumber: 2.5 Consensus size: 48
44346402 GCTTTATCAT
*
44346412 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCAAAAGCCCTTTCA
* **
44346461 ATAACTGGGGCATAAGCCCTTTT-ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTCA
*
44346508 ATAACTGGGCCATAAGCCCCTTTT
1 ATAACTGGGGCATAAG-CCCTTTT
44346532 CACTTCCTCC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
47 36 0.56
48 16 0.25
49 12 0.19
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTCA
Found at i:44346606 original size:20 final size:20
Alignment explanation
Indices: 44346581--44346640 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
44346571 TATGATTACC
44346581 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
*
44346601 TCATGTGCATATCATACATT
1 TCATGTGCATATCATACATA
*
44346621 TCATGTGCATATCATCCATA
1 TCATGTGCATATCATACATA
44346641 CCATATTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.37
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:44346611 original size:11 final size:11
Alignment explanation
Indices: 44346581--44346635 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
44346571 TATGATTACC
44346581 TCATGTGCATA
1 TCATGTGCATA
*
44346592 TCA--TACATA
1 TCATGTGCATA
44346601 TCATGTGCATA
1 TCATGTGCATA
* *
44346612 TCA--TACATT
1 TCATGTGCATA
44346621 TCATGTGCATA
1 TCATGTGCATA
44346632 TCAT
1 TCAT
44346636 CCATACCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:44346715 original size:25 final size:25
Alignment explanation
Indices: 44346683--44346730 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
44346673 ATACATAAAC
* * *
44346683 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
44346708 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
44346731 CATGGTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:44354985 original size:27 final size:28
Alignment explanation
Indices: 44354943--44355009 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
44354933 TTTAAAACCC
44354943 TAGGGGT-A-TTCGGTAATTTT-CTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
44354968 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
44354996 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
44355010 TGATCTACGC
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
25 7 0.18
26 1 0.03
27 12 0.31
28 19 0.49
ACGTcount: A:0.18, C:0.10, G:0.27, T:0.45
Consensus pattern (28 bp):
TAGGGGTAATTTCGGTAATTTTGCTCTT
Found at i:44356838 original size:19 final size:18
Alignment explanation
Indices: 44356801--44356844 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
44356791 ATACATACAG
44356801 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
44356818 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
44356837 TACTAATT
1 TAATAATT
44356845 AAATTTCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:44359242 original size:28 final size:28
Alignment explanation
Indices: 44359198--44359265 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
44359188 TTTAAAACCC
44359198 TAGGGGT-A-TTCGGTAATTTTACTCTT
1 TAGGGGTAATTTCGGTAATTTTACTCTT
*
44359224 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTACTCTT
44359252 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
44359266 TGATCTACGC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 7 0.18
27 1 0.03
28 31 0.79
ACGTcount: A:0.19, C:0.10, G:0.26, T:0.44
Consensus pattern (28 bp):
TAGGGGTAATTTCGGTAATTTTACTCTT
Found at i:44361090 original size:19 final size:18
Alignment explanation
Indices: 44361053--44361096 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
44361043 ATACATACAG
44361053 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
44361070 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
44361089 TACTAATT
1 TAATAATT
44361097 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:44361528 original size:31 final size:31
Alignment explanation
Indices: 44361493--44361556 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
44361483 CCTTTTCATG
44361493 TTTCATATTCCATAACACTGGGCCGAAGCCT
1 TTTCATATTCCATAACACTGGGCCGAAGCCT
* **
44361524 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTCCATAACACTGGGCCGAAGCCT
44361555 TT
1 TT
44361557 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCATATTCCATAACACTGGGCCGAAGCCT
Found at i:44361868 original size:25 final size:24
Alignment explanation
Indices: 44361748--44361867 Score: 154
Period size: 24 Copynumber: 5.0 Consensus size: 24
44361738 ACTTTATCAT
*
44361748 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
44361773 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTA
44361797 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
* *
44361820 ATAACTAGGGCATAAGCCCTTTTTG
1 ATAACTGGGGCATAAGCCC-TTTTA
44361845 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
44361868 TCACTTCCTC
Statistics
Matches: 85, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
23 18 0.21
24 37 0.44
25 30 0.35
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:44361943 original size:20 final size:20
Alignment explanation
Indices: 44361918--44361977 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
44361908 TATGATTACC
44361918 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
*
44361938 TCATGTGCATATCATACATT
1 TCATGTGCATATCATACATA
44361958 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
44361978 CCATATTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:44361948 original size:11 final size:11
Alignment explanation
Indices: 44361918--44361972 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
44361908 TATGATTACC
44361918 TCATGTGCATA
1 TCATGTGCATA
*
44361929 TCA--TACATA
1 TCATGTGCATA
44361938 TCATGTGCATA
1 TCATGTGCATA
* *
44361949 TCA--TACATT
1 TCATGTGCATA
44361958 TCATGTGCATA
1 TCATGTGCATA
44361969 TCAT
1 TCAT
44361973 ACATACCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:44362052 original size:25 final size:25
Alignment explanation
Indices: 44362020--44362067 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
44362010 ATACATAAAC
* * *
44362020 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
44362045 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
44362068 CATGGTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:44364448 original size:60 final size:57
Alignment explanation
Indices: 44364375--44364544 Score: 173
Period size: 60 Copynumber: 2.9 Consensus size: 57
44364365 CTTTCAGCTT
*
44364375 TAACTTTTGCTTAAGCCATCCAATGAAGGATGTTCAACTTAATGAG-TATTTTCTCTCAC
1 TAACTTTTGCTTAAACCATCCAATGAAGGATGTTCAACTTAATGAGCT-TTTT-T-TCAC
* * * * * *
44364434 TAACTTTTTTCTTAAACCATCAAATGAAGGATTTTTAGCTTAATGAGCTTTTTTTCCC
1 TAAC-TTTTGCTTAAACCATCCAATGAAGGATGTTCAACTTAATGAGCTTTTTTTCAC
* * * * *
44364492 TAAATTTTGCTTAAACCATCCAATGTAGGAT-TTTAAGGTTAATAAGCTTTTTT
1 TAACTTTTGCTTAAACCATCCAATGAAGGATGTTCAA-CTTAATGAGCTTTTTT
44364545 ATTTTTGCCC
Statistics
Matches: 94, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
56 4 0.04
57 38 0.40
58 6 0.06
59 5 0.05
60 40 0.43
61 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.42
Consensus pattern (57 bp):
TAACTTTTGCTTAAACCATCCAATGAAGGATGTTCAACTTAATGAGCTTTTTTTCAC
Found at i:44364525 original size:57 final size:59
Alignment explanation
Indices: 44364375--44364544 Score: 188
Period size: 57 Copynumber: 2.9 Consensus size: 59
44364365 CTTTCAGCTT
* *
44364375 TAAC-TTTTGCTTAAGCCATCCAATGAAGGATGTTCAA-CTTAATGAG-TATTTTCTCTCAC
1 TAACATTTTGCTTAAACCATCCAATGAAGGAT-TTTAAGCTTAATGAGCT-TTTT-TCTCAC
* * * * *
44364434 TAACTTTTTTCTTAAACCATCAAATGAAGGATTTTTAGCTTAATGAGCTTTTTT-TCCC
1 TAACATTTTGCTTAAACCATCCAATGAAGGATTTTAAGCTTAATGAGCTTTTTTCTCAC
* * *
44364492 TAA-ATTTTGCTTAAACCATCCAATGTAGGATTTTAAGGTTAATAAGCTTTTTT
1 TAACATTTTGCTTAAACCATCCAATGAAGGATTTTAAGCTTAATGAGCTTTTTT
44364545 ATTTTTGCCC
Statistics
Matches: 95, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
57 43 0.45
58 6 0.06
59 8 0.08
60 37 0.39
61 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.42
Consensus pattern (59 bp):
TAACATTTTGCTTAAACCATCCAATGAAGGATTTTAAGCTTAATGAGCTTTTTTCTCAC
Found at i:44366621 original size:18 final size:19
Alignment explanation
Indices: 44366598--44366633 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
44366588 GGCTCAGAAT
*
44366598 CCCACACG-CCCATGTGGA
1 CCCACACGACCCAGGTGGA
44366616 CCCACACGACCCAGGTGG
1 CCCACACGACCCAGGTGG
44366634 TCGATCTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.22, C:0.44, G:0.25, T:0.08
Consensus pattern (19 bp):
CCCACACGACCCAGGTGGA
Found at i:44368010 original size:24 final size:24
Alignment explanation
Indices: 44367982--44368031 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
44367972 AATATTAATT
44367982 ATTTATAAAATTTAATTAGATTAA
1 ATTTATAAAATTTAATTAGATTAA
44368006 ATTTATAAAATTTAATTAGATTAA
1 ATTTATAAAATTTAATTAGATTAA
44368030 AT
1 AT
44368032 AAACTATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (24 bp):
ATTTATAAAATTTAATTAGATTAA
Found at i:44370614 original size:93 final size:93
Alignment explanation
Indices: 44370501--44370672 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
44370491 GCCCATAAGT
* * *
44370501 GAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAATGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAA
*
44370566 TGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
44370594 GAACTCGGACTCAACTCAATGAGTTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAA
1 GAACTCGGACTCAACTCAATGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAA
*
44370659 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
44370673 CAAACATCCT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAATGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:44370668 original size:46 final size:46
Alignment explanation
Indices: 44370493--44370668 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
44370483 TGTAACCCGC
* *
44370493 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGGACATTCGCAT
*
44370539 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGGACATTCGC-A--T
* *** *
44370585 ACATCTCTCGAACTCGGACTCAACTCAATGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAATGAGCTCGGACATTCGCAT
* * *
44370632 CCATAAGTGAACTCGAACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGGA
44370669 TGCCCAAACA
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 68 0.62
47 32 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGGACATTCGCAT
Found at i:44374580 original size:25 final size:26
Alignment explanation
Indices: 44374546--44374594 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
44374536 TTCTAAGCAA
* *
44374546 AATAATAAGA-AAATAGATAAAAATG
1 AATAAGAAGATAAAGAGATAAAAATG
44374571 AATAAGAAGATAAAGAGATAAAAA
1 AATAAGAAGATAAAGAGATAAAAA
44374595 AATAGAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.16
Consensus pattern (26 bp):
AATAAGAAGATAAAGAGATAAAAATG
Found at i:44374603 original size:25 final size:23
Alignment explanation
Indices: 44374544--44374603 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 23
44374534 GTTTCTAAGC
* *
44374544 AAAATAATAAGAAAATAGATAAA
1 AAAATAAGAAGAAAAGAGATAAA
44374567 AATGAATAAGAAGATAAAGAGATAAA
1 AA--AATAAGAAGA-AAAGAGATAAA
44374593 AAAATAGAGAA
1 AAAATA-AGAA
44374604 ACAACCGACA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
23 2 0.06
24 4 0.13
25 13 0.42
26 12 0.39
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (23 bp):
AAAATAAGAAGAAAAGAGATAAA
Found at i:44374666 original size:7 final size:7
Alignment explanation
Indices: 44374654--44374732 Score: 56
Period size: 7 Copynumber: 11.3 Consensus size: 7
44374644 AAAATAAAAT
44374654 AAAACAA
1 AAAACAA
44374661 AAAACAAA
1 AAAAC-AA
44374669 AAAACTAAA
1 AAAAC--AA
*
44374678 AAAACTA
1 AAAACAA
44374685 AAAAC--
1 AAAACAA
*
44374690 AAAACTA
1 AAAACAA
44374697 AAAACAA
1 AAAACAA
*
44374704 AAAATAA
1 AAAACAA
*
44374711 AAGAC-A
1 AAAACAA
**
44374717 AAAGTAA
1 AAAACAA
44374724 AAAACAA
1 AAAACAA
44374731 AA
1 AA
44374733 GTAAAAGTAA
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
5 5 0.09
6 3 0.05
7 34 0.60
8 7 0.12
9 8 0.14
ACGTcount: A:0.80, C:0.11, G:0.03, T:0.06
Consensus pattern (7 bp):
AAAACAA
Found at i:44374678 original size:9 final size:9
Alignment explanation
Indices: 44374659--44374688 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
44374649 AAAATAAAAC
44374659 AAAAAAC-A
1 AAAAAACTA
44374667 AAAAAACTA
1 AAAAAACTA
44374676 AAAAAACTA
1 AAAAAACTA
44374685 AAAA
1 AAAA
44374689 CAAAACTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.83, C:0.10, G:0.00, T:0.07
Consensus pattern (9 bp):
AAAAAACTA
Found at i:44374700 original size:13 final size:13
Alignment explanation
Indices: 44374649--44374738 Score: 66
Period size: 13 Copynumber: 7.2 Consensus size: 13
44374639 AAAATAAAAT
*
44374649 AAAATAAAAC-AA
1 AAAACAAAACTAA
44374661 AAAACAAAA--AA
1 AAAACAAAACTAA
44374672 ACTAAA-AAAACT-A
1 A--AAACAAAACTAA
44374685 AAAACAAAACT-A
1 AAAACAAAACTAA
*
44374697 AAAACAAAAAATAA
1 AAAAC-AAAACTAA
* *
44374711 AAGACAAAAGTAA
1 AAAACAAAACTAA
*
44374724 AAAACAAAAGTAA
1 AAAACAAAACTAA
44374737 AA
1 AA
44374739 GTAAAAGTAA
Statistics
Matches: 66, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
11 6 0.09
12 24 0.36
13 31 0.47
14 5 0.08
ACGTcount: A:0.79, C:0.10, G:0.03, T:0.08
Consensus pattern (13 bp):
AAAACAAAACTAA
Found at i:44374712 original size:6 final size:6
Alignment explanation
Indices: 44374639--44374814 Score: 64
Period size: 6 Copynumber: 29.3 Consensus size: 6
44374629 AGTGCATAAT
* *
44374639 AAAAT- AAAAT- AAAATA AAACA-A AAAACA AAAA-A ACTAAA-A AAACTA
1 AAAATA AAAATA AAAATA AAA-ATA AAAATA AAAATA A--AAATA AAAATA
* * * * *
44374685 AAAACA AAACTA AAAACAA AAAATA AAAGACA AAAGTA AAAA-A CAAAAGTA
1 AAAATA AAAATA AAAA-TA AAAATA AAA-ATA AAAATA AAAATA -AAAA-TA
* * * * * * *
44374736 AAAGTA AAAGTA AAAGTA AAAGTG AAAGTA AAATTA AAAATTA AAAAT-
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAA-TA AAAATA
* *
44374784 -AAAT- AAAATA TAAATA AAATATA AAACTA AA
1 AAAATA AAAATA AAAATA AAA-ATA AAAATA AA
44374815 TTAAATGACT
Statistics
Matches: 136, Mismatches: 20, Indels: 29
0.74 0.11 0.16
Matches are distributed among these distances:
4 4 0.03
5 20 0.15
6 80 0.59
7 31 0.23
8 1 0.01
ACGTcount: A:0.74, C:0.06, G:0.05, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:44374719 original size:20 final size:20
Alignment explanation
Indices: 44374654--44374733 Score: 56
Period size: 20 Copynumber: 3.9 Consensus size: 20
44374644 AAAATAAAAT
*
44374654 AAAACAAAAAACAAAAAAACTAAA
1 AAAACAAAAAAC-AAAAGAC---A
*
44374678 AAAACTAAAAAC-AAA-ACTA
1 AAAACAAAAAACAAAAGAC-A
*
44374697 AAAACAAAAAATAAAAGACA
1 AAAACAAAAAACAAAAGACA
**
44374717 AAAGTAAAAAACAAAAG
1 AAAACAAAAAACAAAAG
44374734 TAAAAGTAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
19 11 0.23
20 18 0.38
21 4 0.09
22 3 0.06
24 11 0.23
ACGTcount: A:0.79, C:0.11, G:0.04, T:0.06
Consensus pattern (20 bp):
AAAACAAAAAACAAAAGACA
Found at i:44374738 original size:12 final size:12
Alignment explanation
Indices: 44374678--44374750 Score: 74
Period size: 12 Copynumber: 5.8 Consensus size: 12
44374668 AAAAACTAAA
*
44374678 AAAACTAAAAAC
1 AAAAGTAAAAAC
*
44374690 AAAACTAAAAAC
1 AAAAGTAAAAAC
*
44374702 AAAAAATAAAAGAC
1 -AAAAGTAAAA-AC
44374716 AAAAGTAAAAAAC
1 AAAAGT-AAAAAC
**
44374729 AAAAGTAAAAGT
1 AAAAGTAAAAAC
44374741 AAAAGTAAAA
1 AAAAGTAAAA
44374751 GTAAAAGTGA
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
12 26 0.48
13 22 0.41
14 6 0.11
ACGTcount: A:0.75, C:0.08, G:0.07, T:0.10
Consensus pattern (12 bp):
AAAAGTAAAAAC
Found at i:44374751 original size:12 final size:12
Alignment explanation
Indices: 44374729--44374774 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
44374719 AGTAAAAAAC
44374729 AAAAGTAAAAGT
1 AAAAGTAAAAGT
44374741 AAAAGTAAAAGT
1 AAAAGTAAAAGT
*
44374753 AAAAGTGAAAGT
1 AAAAGTAAAAGT
*
44374765 AAAATTAAAA
1 AAAAGTAAAA
44374775 ATTAAAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.67, C:0.00, G:0.15, T:0.17
Consensus pattern (12 bp):
AAAAGTAAAAGT
Found at i:44374757 original size:18 final size:18
Alignment explanation
Indices: 44374729--44374774 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
44374719 AGTAAAAAAC
44374729 AAAAGTAAAAGTAAAAGT
1 AAAAGTAAAAGTAAAAGT
*
44374747 AAAAGTAAAAGTGAAAGT
1 AAAAGTAAAAGTAAAAGT
*
44374765 AAAATTAAAA
1 AAAAGTAAAA
44374775 ATTAAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.67, C:0.00, G:0.15, T:0.17
Consensus pattern (18 bp):
AAAAGTAAAAGTAAAAGT
Found at i:44374796 original size:11 final size:11
Alignment explanation
Indices: 44374777--44374808 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
44374767 AATTAAAAAT
44374777 TAAAA-ATAAA
1 TAAAATATAAA
44374787 TAAAATATAAA
1 TAAAATATAAA
44374798 TAAAATATAAA
1 TAAAATATAAA
44374809 ACTAAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.24
11 16 0.76
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (11 bp):
TAAAATATAAA
Found at i:44377115 original size:29 final size:29
Alignment explanation
Indices: 44377083--44377401 Score: 293
Period size: 29 Copynumber: 11.0 Consensus size: 29
44377073 TTGATTGTCG
*
44377083 ACTATGAAAAGGGATGGTAACGACCATCA
1 ACTATGAAAAGGGATGGTGACGACCATCA
* * *
44377112 ACTATGAAAAGGGTTGGTGATGACCATTGA
1 ACTATGAAAAGGGATGGTGACGACCA-TCA
* * ** * * *
44377142 A-TATGAAACGGGATAGTTTCAACTATCG
1 ACTATGAAAAGGGATGGTGACGACCATCA
44377170 ACTATGAAAAGGGATGGTGACGACCATCA
1 ACTATGAAAAGGGATGGTGACGACCATCA
* *
44377199 AATATGAAAAGGGATGGTGACAACCATCGA
1 ACTATGAAAAGGGATGGTGACGACCATC-A
* * ** * *
44377229 A-TATGAAAAGAGATAGTTTCGACTATCG
1 ACTATGAAAAGGGATGGTGACGACCATCA
* *
44377257 ACTGTGAAAAGGGATGGTGATGACCATCA
1 ACTATGAAAAGGGATGGTGACGACCATCA
* * *
44377286 ACTATGAAAAGGGATGGTGACAAACATCG
1 ACTATGAAAAGGGATGGTGACGACCATCA
* * ** *
44377315 ATTAATGAAAAGGGATGATTTCAACCATCGA
1 ACT-ATGAAAAGGGATGGTGACGACCATC-A
*
44377346 A-TATAAAAAGGGATGGTGACGACCATCA
1 ACTATGAAAAGGGATGGTGACGACCATCA
* *
44377374 AATATGAAAAGGGATGGTTACGACCATC
1 ACTATGAAAAGGGATGGTGACGACCATC
44377402 GTTTAGCACA
Statistics
Matches: 227, Mismatches: 56, Indels: 14
0.76 0.19 0.05
Matches are distributed among these distances:
28 5 0.02
29 194 0.85
30 27 0.12
31 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.22
Consensus pattern (29 bp):
ACTATGAAAAGGGATGGTGACGACCATCA
Found at i:44377210 original size:87 final size:87
Alignment explanation
Indices: 44377080--44377402 Score: 450
Period size: 87 Copynumber: 3.7 Consensus size: 87
44377070 GCTTTGATTG
* * * ** *
44377080 TCGACTATGAAAAGGGATGGTAACGACCATCAACTATGAAAAGGGTTGGTGATGACCATTGAATA
1 TCGACTATGAAAAGGGATGGTGACGACCATCAAATATGAAAAGGGATGGTGACAACCATCGAATA
*
44377145 TGAAACGGGATAGTTTCAACTA
66 TGAAAAGGGATAGTTTCAACTA
44377167 TCGACTATGAAAAGGGATGGTGACGACCATCAAATATGAAAAGGGATGGTGACAACCATCGAATA
1 TCGACTATGAAAAGGGATGGTGACGACCATCAAATATGAAAAGGGATGGTGACAACCATCGAATA
* *
44377232 TGAAAAGAGATAGTTTCGACTA
66 TGAAAAGGGATAGTTTCAACTA
* * * * *
44377254 TCGACTGTGAAAAGGGATGGTGATGACCATCAACTATGAAAAGGGATGGTGACAAACATCGATTA
1 TCGACTATGAAAAGGGATGGTGACGACCATCAAATATGAAAAGGGATGGTGACAACCATCGAAT-
*
44377319 ATGAAAAGGGAT-GATTTCAACCA
65 ATGAAAAGGGATAG-TTTCAACTA
* * * *
44377342 TCGAATATAAAAAGGGATGGTGACGACCATCAAATATGAAAAGGGATGGTTACGACCATCG
1 TCGACTATGAAAAGGGATGGTGACGACCATCAAATATGAAAAGGGATGGTGACAACCATCG
44377403 TTTAGCACAC
Statistics
Matches: 209, Mismatches: 25, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
87 138 0.66
88 71 0.34
ACGTcount: A:0.39, C:0.14, G:0.26, T:0.22
Consensus pattern (87 bp):
TCGACTATGAAAAGGGATGGTGACGACCATCAAATATGAAAAGGGATGGTGACAACCATCGAATA
TGAAAAGGGATAGTTTCAACTA
Found at i:44377402 original size:58 final size:58
Alignment explanation
Indices: 44377080--44377402 Score: 326
Period size: 58 Copynumber: 5.6 Consensus size: 58
44377070 GCTTTGATTG
* * * * *
44377080 TCGACTATGAAAAGGGATGGTAACGACCATC-AACTATGAAAAGGGTTGGTGATGACCA
1 TCGAATATGAAAAGGGATGGTTACAACCATCGAA-TATGAAAAGGGATGGTGACGACCA
* * * * * *
44377138 TTGAATATGAAACGGGATAGTTTCAACTATCGACTATGAAAAGGGATGGTGACGACCA
1 TCGAATATGAAAAGGGATGGTTACAACCATCGAATATGAAAAGGGATGGTGACGACCA
* * * * ** *
44377196 TCAAATATGAAAAGGGATGGTGACAACCATCGAATATGAAAAGAGATAGTTTCGACTA
1 TCGAATATGAAAAGGGATGGTTACAACCATCGAATATGAAAAGGGATGGTGACGACCA
* * * ** * *
44377254 TCGACTGTGAAAAGGGATGGTGATGACCATC-AACTATGAAAAGGGATGGTGACAAACA
1 TCGAATATGAAAAGGGATGGTTACAACCATCGAA-TATGAAAAGGGATGGTGACGACCA
* * * *
44377312 TCGATTAATGAAAAGGGATGATTTCAACCATCGAATATAAAAAGGGATGGTGACGACCA
1 TCGAAT-ATGAAAAGGGATGGTTACAACCATCGAATATGAAAAGGGATGGTGACGACCA
* *
44377371 TCAAATATGAAAAGGGATGGTTACGACCATCG
1 TCGAATATGAAAAGGGATGGTTACAACCATCG
44377403 TTTAGCACAC
Statistics
Matches: 210, Mismatches: 51, Indels: 8
0.78 0.19 0.03
Matches are distributed among these distances:
57 2 0.01
58 161 0.77
59 45 0.21
60 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.26, T:0.22
Consensus pattern (58 bp):
TCGAATATGAAAAGGGATGGTTACAACCATCGAATATGAAAAGGGATGGTGACGACCA
Found at i:44385424 original size:31 final size:31
Alignment explanation
Indices: 44385386--44385445 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
44385376 TATTTGGGTA
44385386 TAGCTAGTCTAATCATTTTGAGTATGACACG
1 TAGCTAGTCTAATCATTTTGAGTATGACACG
44385417 TAGCTAGTCTAATCATTTTGAGTATGACA
1 TAGCTAGTCTAATCATTTTGAGTATGACA
44385446 TGTATAGGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (31 bp):
TAGCTAGTCTAATCATTTTGAGTATGACACG
Found at i:44394476 original size:21 final size:20
Alignment explanation
Indices: 44394443--44394482 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
44394433 ATAAATTTAA
44394443 AAAGAAAAAGAGAGTGAGAG
1 AAAGAAAAAGAGAGTGAGAG
*
44394463 AAAGAAAAATGAGATTGAGA
1 AAAGAAAAA-GAGAGTGAGA
44394483 TTGAAAAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.60, C:0.00, G:0.30, T:0.10
Consensus pattern (20 bp):
AAAGAAAAAGAGAGTGAGAG
Found at i:44396932 original size:28 final size:27
Alignment explanation
Indices: 44396899--44396979 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 27
44396889 TTAGAATACT
44396899 TTAGTTTACTAAAATTACCGAAATACCC
1 TTAGTTT-CTAAAATTACCGAAATACCC
* * *
44396927 TTAGTTTGTAAAAATACTGAAATACCC
1 TTAGTTTCTAAAATTACCGAAATACCC
* * *
44396954 -TCGATTTTTAAATTTACCGAAATACC
1 TTAG-TTTCTAAAATTACCGAAATACC
44396980 TTCGACTTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
26 2 0.05
27 35 0.80
28 7 0.16
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.35
Consensus pattern (27 bp):
TTAGTTTCTAAAATTACCGAAATACCC
Found at i:44396938 original size:27 final size:28
Alignment explanation
Indices: 44396908--44397007 Score: 100
Period size: 27 Copynumber: 3.7 Consensus size: 28
44396898 TTTAGTTTAC
44396908 TAAAATTACCGAAATACCCTTAG-TTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
* * * *
44396935 TAAAAATACTGAAATACCC-TCGATTTT
1 TAAAATTACCGAAATACCCTTAGATTTG
* * *
44396962 TAAATTTACCGAAATA-CCTTCGACTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
44396989 TAAAATTACC-AAAGTACCC
1 TAAAATTACCGAAA-TACCC
44397008 CCGATTTACA
Statistics
Matches: 59, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
26 7 0.12
27 50 0.85
28 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (28 bp):
TAAAATTACCGAAATACCCTTAGATTTG
Found at i:44397007 original size:54 final size:54
Alignment explanation
Indices: 44396908--44397014 Score: 128
Period size: 54 Copynumber: 2.0 Consensus size: 54
44396898 TTTAGTTTAC
* * *
44396908 TAAAATTACCGAAATACCCTTAGTTTGTAAAAATACTGAAATACCCTCGATTTT
1 TAAAATTACCGAAATACCCTTAGCTTGTAAAAATACTCAAATACCCCCGATTTT
* * *
44396962 TAAATTTACCGAAATA-CCTTCGACTTGTAAAATTAC-CAAAGTACCCCCGATTT
1 TAAAATTACCGAAATACCCTTAG-CTTGTAAAAATACTCAAA-TACCCCCGATTT
44397015 ACAGAATTAC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
53 8 0.18
54 37 0.82
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.32
Consensus pattern (54 bp):
TAAAATTACCGAAATACCCTTAGCTTGTAAAAATACTCAAATACCCCCGATTTT
Found at i:44397033 original size:27 final size:27
Alignment explanation
Indices: 44397010--44397294 Score: 290
Period size: 27 Copynumber: 10.6 Consensus size: 27
44397000 AAGTACCCCC
*
44397010 GATTTACAGAATTACTGTTTTACCCCT
1 GATTTACAGAATTACTGTTTTACCCTT
* * * *
44397037 AATTTACATAATTACCGTTTTACCCCT
1 GATTTACAGAATTACTGTTTTACCCTT
* * *
44397064 AATTTACATAATTA-TCGTTTTACCCTC
1 GATTTACAGAATTACT-GTTTTACCCTT
* * *
44397091 GACTTACAGAATTACCGTTTTACCCCT
1 GATTTACAGAATTACTGTTTTACCCTT
* * *
44397118 AATTTACATAATTA-TCGTTTTACCCCT
1 GATTTACAGAATTACT-GTTTTACCCTT
* *
44397145 GATTTACATAATTA-TCGTTTTACCCTC
1 GATTTACAGAATTACT-GTTTTACCCTT
* * *
44397172 GACTTACAGAATTACCGTTTTACCCTC
1 GATTTACAGAATTACTGTTTTACCCTT
* *
44397199 GATTTACTGAATTACT-ATTTACCCTT
1 GATTTACAGAATTACTGTTTTACCCTT
*
44397225 GATTTATAGAATTACTGTTTTACCCTT
1 GATTTACAGAATTACTGTTTTACCCTT
*
44397252 GATTTACAGAATTACTGTTTTACCCTC
1 GATTTACAGAATTACTGTTTTACCCTT
* *
44397279 GATTTATAAAATTACT
1 GATTTACAGAATTACT
44397295 AAAATACCCT
Statistics
Matches: 219, Mismatches: 34, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
26 22 0.10
27 197 0.90
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (27 bp):
GATTTACAGAATTACTGTTTTACCCTT
Found at i:44397077 original size:81 final size:81
Alignment explanation
Indices: 44397003--44397276 Score: 360
Period size: 81 Copynumber: 3.4 Consensus size: 81
44396993 ATTACCAAAG
* * *
44397003 TACCCCCGATTTACAGAATTACTGTTTTACCCCTAATTTACATAATTACCGTTTTACCCCTAATT
1 TACCCTCGACTTACAGAATTACCGTTTTACCCCTAATTTACATAATTACCGTTTTACCCCTAATT
44397068 TACATAATTATCGTTT
66 TACATAATTATCGTTT
* *
44397084 TACCCTCGACTTACAGAATTACCGTTTTACCCCTAATTTACATAATTATCGTTTTACCCCTGATT
1 TACCCTCGACTTACAGAATTACCGTTTTACCCCTAATTTACATAATTACCGTTTTACCCCTAATT
44397149 TACATAATTATCGTTT
66 TACATAATTATCGTTT
* * *
44397165 TACCCTCGACTTACAGAATTACCGTTTTA-CCCTCGATTTAC-TGAATTA-C-TATTTACCCTTG
1 TACCCTCGACTTACAGAATTACCGTTTTACCCCT-AATTTACAT-AATTACCGT-TTTACCCCTA
* *
44397226 ATTTATAGAATTA-CTGTTT
63 ATTTACATAATTATC-GTTT
* * *
44397245 TACCCTTGATTTACAGAATTACTGTTTTACCC
1 TACCCTCGACTTACAGAATTACCGTTTTACCC
44397277 TCGATTTATA
Statistics
Matches: 176, Mismatches: 12, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
79 2 0.01
80 56 0.32
81 118 0.67
ACGTcount: A:0.27, C:0.24, G:0.08, T:0.41
Consensus pattern (81 bp):
TACCCTCGACTTACAGAATTACCGTTTTACCCCTAATTTACATAATTACCGTTTTACCCCTAATT
TACATAATTATCGTTT
Found at i:44397302 original size:27 final size:27
Alignment explanation
Indices: 44397272--44397492 Score: 187
Period size: 27 Copynumber: 8.1 Consensus size: 27
44397262 ATTACTGTTT
* *
44397272 TACCCTCGATTTATAAAATTACTAAAA
1 TACCCTTGATTTATAAAATTACCAAAA
* *
44397299 TACCCTTGGTTTGTAAAATTACCAAAA
1 TACCCTTGATTTATAAAATTACCAAAA
* *
44397326 TACCCCT-AGTTTGTAAAATTACCAAAA
1 TACCCTTGA-TTTATAAAATTACCAAAA
* * * *
44397353 TACCCTTGGTTTGTGAAATTACCGAAA
1 TACCCTTGATTTATAAAATTACCAAAA
*
44397380 TACCCTTAATTT-TAAAATTACCAAAA
1 TACCCTTGATTTATAAAATTACCAAAA
* * * *
44397406 TACCCCTGATTTACAAAGTTACAAAAA
1 TACCCTTGATTTATAAAATTACCAAAA
* *
44397433 TACCCTTGACTTTCTAAAAATTA-TAGAAA
1 TACCCTTGA-TTTAT-AAAATTACCA-AAA
* * * **
44397462 TACCATTGGTTTACAAAATTACTGAAA
1 TACCCTTGATTTATAAAATTACCAAAA
44397489 TACC
1 TACC
44397493 TTTGGTTTGT
Statistics
Matches: 158, Mismatches: 29, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
26 22 0.14
27 112 0.71
28 8 0.05
29 16 0.10
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.32
Consensus pattern (27 bp):
TACCCTTGATTTATAAAATTACCAAAA
Found at i:44397347 original size:81 final size:80
Alignment explanation
Indices: 44397272--44397438 Score: 203
Period size: 80 Copynumber: 2.1 Consensus size: 80
44397262 ATTACTGTTT
* **
44397272 TACCCTCGATTTATAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCCTAGTT
1 TACCCTCGATTTATAAAATTACCAAAATACCCTTAATTT-TAAAATTACCAAAATACCCCTAGTT
44397337 TGTAAAATTACCAAAA
65 TGTAAAATTACCAAAA
* * * * * *
44397353 TACCCTTGGTTTGTGAAATTACCGAAATACCCTTAATTTTAAAATTACCAAAATACCCCT-GATT
1 TACCCTCGATTTATAAAATTACCAAAATACCCTTAATTTTAAAATTACCAAAATACCCCTAGTTT
*
44397417 -TACAAAGTTACAAAAA
66 GTA-AAA-TTACCAAAA
44397433 TACCCT
1 TACCCT
44397439 TGACTTTCTA
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
78 2 0.03
79 6 0.08
80 35 0.47
81 31 0.42
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.32
Consensus pattern (80 bp):
TACCCTCGATTTATAAAATTACCAAAATACCCTTAATTTTAAAATTACCAAAATACCCCTAGTTT
GTAAAATTACCAAAA
Found at i:44397497 original size:27 final size:27
Alignment explanation
Indices: 44397449--44397500 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
44397439 TGACTTTCTA
44397449 AAAATTATAGAAATACCATTGGTTTAC
1 AAAATTATAGAAATACCATTGGTTTAC
*
44397476 AAAATTACT-GAAATACCTTTGGTTT
1 AAAATTA-TAGAAATACCATTGGTTT
44397501 GTTGATTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (27 bp):
AAAATTATAGAAATACCATTGGTTTAC
Found at i:44397618 original size:27 final size:27
Alignment explanation
Indices: 44397554--44397618 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
44397544 ACCCCTAAAA
*
44397554 GGTAAAAAGACCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAG
* *
44397581 GGTAAAGTGACCGTAATA-CCCCTGTAT
1 GGTAAAATGACCGTAA-AGCCCCTGTAG
44397608 GGTAAAATGAC
1 GGTAAAATGAC
44397619 GAATATGCCC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 32 0.97
28 1 0.03
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (27 bp):
GGTAAAATGACCGTAAAGCCCCTGTAG
Found at i:44398809 original size:25 final size:24
Alignment explanation
Indices: 44398776--44398823 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
44398766 TTATAACATG
* * *
44398776 AAAATGACCGTTTTGCCCCTAGGT
1 AAAATGACCATTATACCCCTAGGT
44398800 AAAAGTGACCATTATACCCCTAGG
1 AAAA-TGACCATTATACCCCTAGG
44398824 GTTTATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (24 bp):
AAAATGACCATTATACCCCTAGGT
Found at i:44398876 original size:9 final size:9
Alignment explanation
Indices: 44398862--44398918 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
44398852 TTTAATAAAC
44398862 ATGATATGT
1 ATGATATGT
*
44398871 ATGATATGCAC
1 ATGATATG--T
*
44398882 ATGACATGT
1 ATGATATGT
*
44398891 ATGATATGCAC
1 ATGATATG--T
44398902 ATGATATGT
1 ATGATATGT
44398911 ATGATATG
1 ATGATATG
44398919 CACATGAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:44398885 original size:20 final size:20
Alignment explanation
Indices: 44398860--44398930 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
44398850 ATTTTAATAA
44398860 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
44398880 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
44398900 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
44398920 ACATGAGATGT
1 ACATGATATGT
44398931 TCATAAATGC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:44398907 original size:11 final size:11
Alignment explanation
Indices: 44398871--44398925 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
44398861 CATGATATGT
44398871 ATGATATGCAC
1 ATGATATGCAC
* *
44398882 ATGACATG--T
1 ATGATATGCAC
44398891 ATGATATGCAC
1 ATGATATGCAC
*
44398902 ATGATATG--T
1 ATGATATGCAC
44398911 ATGATATGCAC
1 ATGATATGCAC
44398922 ATGA
1 ATGA
44398926 GATGTTCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:44399003 original size:24 final size:24
Alignment explanation
Indices: 44398976--44399191 Score: 334
Period size: 23 Copynumber: 9.2 Consensus size: 24
44398966 GAGGAAGTGC
44398976 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
44399000 AAAA-GGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
44399023 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
44399046 -AAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
*
44399069 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
44399093 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
44399117 AAAA-GGCTTATGCCCCAGTGATC
1 AAAAGGGCTTATGCCCCAGTTATT
*
44399140 AAAAGGGCTTACGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
44399164 -AAAGGTCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
44399187 AAAAG
1 AAAAG
44399192 AGGCAAGGCC
Statistics
Matches: 178, Mismatches: 10, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
22 3 0.02
23 101 0.57
24 74 0.42
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:44399125 original size:47 final size:47
Alignment explanation
Indices: 44398976--44399191 Score: 312
Period size: 47 Copynumber: 4.6 Consensus size: 47
44398966 GAGGAAGTGC
*
44398976 AAAAGGGCTTATGCCCCAGTTATTAAAA-GGCTTATGCCCCAGTTATT
1 AAAA-GGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
* * *
44399023 AAAGGGCTTATGCCCCAGTTAT-TAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
44399069 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
1 AAAA-GGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
* *
44399117 AAAAGGCTTATGCCCCAGTGATCAAAAGGGCTTACGCCCCAGTTATT
1 AAAAGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
* *
44399164 -AAAGGTCTTTTGCCCCAGTTATTAAAAG
1 AAAAGG-CTTATGCCCCAGTTATCAAAAG
44399192 AGGCAAGGCC
Statistics
Matches: 154, Mismatches: 11, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
45 3 0.02
46 44 0.29
47 81 0.53
48 26 0.17
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (47 bp):
AAAAGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
Found at i:44399394 original size:42 final size:42
Alignment explanation
Indices: 44399331--44399422 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
44399321 TAGTCTCCCC
* **
44399331 AAATGGGTTTGCATACATTCATTGGTATT-TCATGTGATATTG
1 AAATGGGCTTGCATACATTCATTGACATTAT-ATGTGATATTG
* *
44399373 AAATGGGCTTGCATTCTTTCATTGACATTATATGTGATATTG
1 AAATGGGCTTGCATACATTCATTGACATTATATGTGATATTG
44399415 AAATGGGC
1 AAATGGGC
44399423 CTATGGGCCA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 43 0.98
43 1 0.02
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.40
Consensus pattern (42 bp):
AAATGGGCTTGCATACATTCATTGACATTATATGTGATATTG
Found at i:44400900 original size:3 final size:3
Alignment explanation
Indices: 44400892--44400954 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
44400882 ACTACCAGCC
44400892 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
44400940 ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT
44400955 TTCTTTTAGC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:44401778 original size:21 final size:20
Alignment explanation
Indices: 44401726--44401784 Score: 68
Period size: 18 Copynumber: 3.0 Consensus size: 20
44401716 ATAAAAAAAT
* *
44401726 GAAAGAAAAAGAAATTGA-A
1 GAAAGAAAAAGAGAGTGAGA
44401745 -AAAGAAAAAGAGAGTGAGA
1 GAAAGAAAAAGAGAGTGAGA
*
44401764 GAAAGAAAAACGAGATTGAGA
1 GAAAGAAAAA-GAGAGTGAGA
44401785 TTGAAAAAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 15 0.44
19 1 0.03
20 9 0.26
21 9 0.26
ACGTcount: A:0.63, C:0.02, G:0.27, T:0.08
Consensus pattern (20 bp):
GAAAGAAAAAGAGAGTGAGA
Found at i:44403558 original size:31 final size:31
Alignment explanation
Indices: 44403493--44403561 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 31
44403483 AACTTAATTT
*
44403493 CAGCTCAACGAGCTCAATCTTGGATTTTGCC
1 CAGCTCAACGAGCTCAATCTTGGATTATGCC
* *
44403524 CAGCTCAATGGAGCTCAAT-TTGGCTTGATG-C
1 CAGCTCAA-CGAGCTCAATCTTGGATT-ATGCC
44403555 CAGCTCA
1 CAGCTCA
44403562 TTGAGTTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 22 0.67
32 11 0.33
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.28
Consensus pattern (31 bp):
CAGCTCAACGAGCTCAATCTTGGATTATGCC
Found at i:44409604 original size:20 final size:20
Alignment explanation
Indices: 44409579--44409617 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
44409569 AAAATTTCAA
44409579 TTATTTCAC-ACATTTACAAC
1 TTATTTCACAAC-TTTACAAC
*
44409599 TTATTTTACAACTTTACAA
1 TTATTTCACAACTTTACAA
44409618 AATTGCCCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.44
Consensus pattern (20 bp):
TTATTTCACAACTTTACAAC
Found at i:44414152 original size:16 final size:16
Alignment explanation
Indices: 44414131--44414162 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
44414121 AATTGAGTTG
*
44414131 AGAAAATTATTTAATT
1 AGAAAATTAATTAATT
44414147 AGAAAATTAATTAATT
1 AGAAAATTAATTAATT
44414163 TAAATTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (16 bp):
AGAAAATTAATTAATT
Found at i:44421129 original size:46 final size:46
Alignment explanation
Indices: 44421079--44421254 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
44421069 TATTTGGGCA
44421079 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
44421125 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
44421172 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
44421218 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
44421255 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:44421234 original size:93 final size:93
Alignment explanation
Indices: 44421075--44421246 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
44421065 TGGATATTTG
* *
44421075 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
44421140 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
44421168 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
44421233 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
44421247 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:44424222 original size:15 final size:15
Alignment explanation
Indices: 44424202--44424270 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
44424192 GTATCTTGGG
44424202 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
44424217 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
44424232 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
44424247 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
44424262 TTTCTTTAT
1 TTTCTTTAT
44424271 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:44424271 original size:30 final size:30
Alignment explanation
Indices: 44424193--44424280 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
44424183 CATAGTATCG
* * * *
44424193 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
44424223 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
44424253 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
44424281 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:44426718 original size:46 final size:46
Alignment explanation
Indices: 44426665--44426840 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
44426655 TATTTGGGCA
44426665 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
44426711 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
44426758 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
44426804 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
44426841 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:44426820 original size:93 final size:93
Alignment explanation
Indices: 44426661--44426832 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
44426651 GGGATATTTG
* *
44426661 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
44426726 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
44426754 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
44426819 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
44426833 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:44429135 original size:13 final size:12
Alignment explanation
Indices: 44429099--44429137 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
44429089 GGTTTTCTCC
*
44429099 AAAATGAAAATG
1 AAAATGAAAATA
44429111 AAAATGAGAAATA
1 AAAATGA-AAATA
44429124 AAACATGAAAATA
1 AAA-ATGAAAATA
44429137 A
1 A
44429138 CCTAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 7 0.29
13 13 0.54
14 4 0.17
ACGTcount: A:0.69, C:0.03, G:0.13, T:0.15
Consensus pattern (12 bp):
AAAATGAAAATA
Found at i:44437728 original size:144 final size:144
Alignment explanation
Indices: 44437468--44437802 Score: 460
Period size: 144 Copynumber: 2.3 Consensus size: 144
44437458 CGGAGGTCTT
* * *
44437468 GCACCC-AAGGTGCCAATATCATGGCCCGAAGCCAAATCAATGAAG-GTCACCCTTGAAGTGATA
1 GCACCCGAA-GTGCTAATATCATGGCCCGAAGCCAAATCAATGAAGCTTCACCC-TAAAGTGATA
* * * *
44437531 ATATTATGGCCCAAAGCCAAATCAATGAAGCTCGCACCCGAAGTGCTAATATCATGGCCCAAACC
64 ATATCATGGCCCAAAGCCAAATCAATGAAGCTCACACCCAAAGTGCCAATATCATGGCCCAAACC
*
44437596 CAAATAAATGAATCTC
129 CAAATAAATGAAGCTC
* *
44437612 GCACCCGAAGTGCTAATATCATGGCTCGAAGCCAAATCAATGAAGCTTGCACCC-AAAGTGCTAA
1 GCACCCGAAGTGCTAATATCATGGCCCGAAGCCAAATCAATGAAGCTT-CACCCTAAAGTGATAA
* * * **
44437676 TATCATGGCCCGAAGCCAAATCAATGAAGTTCATACCCAAAGTGCCAATATCATGGCCCAAATTC
65 TATCATGGCCCAAAGCCAAATCAATGAAGCTCACACCCAAAGTGCCAATATCATGGCCCAAACCC
44437741 AAATAAATGAAGCTC
130 AAATAAATGAAGCTC
* * *
44437756 GCACCTGAAGTGCTAATATCATAGCCCGAAGCCTAATCAATGAAGCT
1 GCACCCGAAGTGCTAATATCATGGCCCGAAGCCAAATCAATGAAGCT
44437803 CCTAATGACA
Statistics
Matches: 169, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
144 161 0.95
145 3 0.02
146 5 0.03
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (144 bp):
GCACCCGAAGTGCTAATATCATGGCCCGAAGCCAAATCAATGAAGCTTCACCCTAAAGTGATAAT
ATCATGGCCCAAAGCCAAATCAATGAAGCTCACACCCAAAGTGCCAATATCATGGCCCAAACCCA
AATAAATGAAGCTC
Found at i:44437803 original size:48 final size:48
Alignment explanation
Indices: 44437468--44437803 Score: 408
Period size: 48 Copynumber: 7.0 Consensus size: 48
44437458 CGGAGGTCTT
* *
44437468 GCACCC-AAGGTGCCAATATCATGGCCCGAAGCCAAATCAATGAAGGT-
1 GCACCCGAA-GTGCTAATATCATGGCCCGAAGCCAAATCAATGAAGCTC
* * *
44437515 -CACCCTTGAAGTGATAATATTATGGCCCAAAGCCAAATCAATGAAGCTC
1 GCACCC--GAAGTGCTAATATCATGGCCCGAAGCCAAATCAATGAAGCTC
* * * *
44437564 GCACCCGAAGTGCTAATATCATGGCCCAAACCCAAATAAATGAATCTC
1 GCACCCGAAGTGCTAATATCATGGCCCGAAGCCAAATCAATGAAGCTC
* *
44437612 GCACCCGAAGTGCTAATATCATGGCTCGAAGCCAAATCAATGAAGCTT
1 GCACCCGAAGTGCTAATATCATGGCCCGAAGCCAAATCAATGAAGCTC
* *
44437660 GCACCCAAAGTGCTAATATCATGGCCCGAAGCCAAATCAATGAAGTTC
1 GCACCCGAAGTGCTAATATCATGGCCCGAAGCCAAATCAATGAAGCTC
** * * * ** *
44437708 ATACCCAAAGTGCCAATATCATGGCCCAAATTCAAATAAATGAAGCTC
1 GCACCCGAAGTGCTAATATCATGGCCCGAAGCCAAATCAATGAAGCTC
* * *
44437756 GCACCTGAAGTGCTAATATCATAGCCCGAAGCCTAATCAATGAAGCTC
1 GCACCCGAAGTGCTAATATCATGGCCCGAAGCCAAATCAATGAAGCTC
44437804 CTAATGACAT
Statistics
Matches: 245, Mismatches: 39, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
46 5 0.02
48 233 0.95
49 2 0.01
50 5 0.02
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (48 bp):
GCACCCGAAGTGCTAATATCATGGCCCGAAGCCAAATCAATGAAGCTC
Found at i:44441261 original size:22 final size:22
Alignment explanation
Indices: 44441236--44441292 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
44441226 AAACAGGGTT
44441236 ACACGCCCATGTGGACACAAGG
1 ACACGCCCATGTGGACACAAGG
*
44441258 ACACTCCCATGTGGACACAAGG
1 ACACGCCCATGTGGACACAAGG
44441280 ACACGCCCATGTG
1 ACACGCCCATGTG
44441293 CCTTCGACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.30, C:0.33, G:0.25, T:0.12
Consensus pattern (22 bp):
ACACGCCCATGTGGACACAAGG
Found at i:44443114 original size:29 final size:29
Alignment explanation
Indices: 44443075--44443151 Score: 118
Period size: 29 Copynumber: 2.7 Consensus size: 29
44443065 AATCATATTC
*
44443075 ATATGGCCCATTAGGCCCAAACCACCTGT
1 ATATGGCCCATTAGGCCCAAACCACATGT
* *
44443104 ATATGGCCCATTAGGCCCAAATCACATTT
1 ATATGGCCCATTAGGCCCAAACCACATGT
*
44443133 ATATGGCCCGTTAGGCCCA
1 ATATGGCCCATTAGGCCCA
44443152 GTCACATTCA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.23
Consensus pattern (29 bp):
ATATGGCCCATTAGGCCCAAACCACATGT
Found at i:44443116 original size:57 final size:58
Alignment explanation
Indices: 44443041--44443151 Score: 152
Period size: 58 Copynumber: 1.9 Consensus size: 58
44443031 AAATTCACAT
* * *
44443041 ACCTGTATCTGGTACATTAAGCCC-AATCATATTCATATGGCCCATTAGGCCCAAACC
1 ACCTGTATATGGCACATTAAGCCCAAATCACATTCATATGGCCCATTAGGCCCAAACC
* * * *
44443098 ACCTGTATATGGCCCATTAGGCCCAAATCACATTTATATGGCCCGTTAGGCCCA
1 ACCTGTATATGGCACATTAAGCCCAAATCACATTCATATGGCCCATTAGGCCCA
44443152 GTCACATTCA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 20 0.43
58 26 0.57
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (58 bp):
ACCTGTATATGGCACATTAAGCCCAAATCACATTCATATGGCCCATTAGGCCCAAACC
Found at i:44443396 original size:16 final size:16
Alignment explanation
Indices: 44443375--44443442 Score: 102
Period size: 16 Copynumber: 4.3 Consensus size: 16
44443365 ATAGCTAGAC
*
44443375 TTTTGGCTTTTCGGCA
1 TTTTGGCATTTCGGCA
44443391 TTTTGGCATTTCGGCA
1 TTTTGGCATTTCGGCA
*
44443407 TTTTGGCTTTTCGGCA
1 TTTTGGCATTTCGGCA
*
44443423 TTTCGGCATTTCGGC-
1 TTTTGGCATTTCGGCA
44443438 TTTTG
1 TTTTG
44443443 CCGGTTCATA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
15 4 0.09
16 43 0.91
ACGTcount: A:0.07, C:0.19, G:0.25, T:0.49
Consensus pattern (16 bp):
TTTTGGCATTTCGGCA
Found at i:44443400 original size:8 final size:8
Alignment explanation
Indices: 44443375--44443442 Score: 70
Period size: 8 Copynumber: 8.6 Consensus size: 8
44443365 ATAGCTAGAC
44443375 TTTTGGC-
1 TTTTGGCA
44443382 TTTTCGGCA
1 TTTT-GGCA
44443391 TTTTGGCA
1 TTTTGGCA
*
44443399 TTTCGGCA
1 TTTTGGCA
44443407 TTTTGGC-
1 TTTTGGCA
44443414 TTTTCGGCA
1 TTTT-GGCA
*
44443423 TTTCGGCA
1 TTTTGGCA
*
44443431 TTTCGGC-
1 TTTTGGCA
44443438 TTTTG
1 TTTTG
44443443 CCGGTTCATA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
7 12 0.23
8 34 0.64
9 7 0.13
ACGTcount: A:0.07, C:0.19, G:0.25, T:0.49
Consensus pattern (8 bp):
TTTTGGCA
Found at i:44443416 original size:32 final size:31
Alignment explanation
Indices: 44443374--44443442 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 31
44443364 CATAGCTAGA
*
44443374 CTTTTGGCTTTTCGGCATTTTGGCATTTCGG
1 CTTTTGGCTTTTCGGCATTTCGGCATTTCGG
44443405 CATTTTGGCTTTTCGGCATTTCGGCATTTCGG
1 C-TTTTGGCTTTTCGGCATTTCGGCATTTCGG
44443437 CTTTTG
1 CTTTTG
44443443 CCGGTTCATA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 6 0.17
32 30 0.83
ACGTcount: A:0.07, C:0.20, G:0.25, T:0.48
Consensus pattern (31 bp):
CTTTTGGCTTTTCGGCATTTCGGCATTTCGG
Found at i:44443422 original size:24 final size:24
Alignment explanation
Indices: 44443383--44443441 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
44443373 ACTTTTGGCT
44443383 TTTCGGCATTTT-GGCATTTCGGCA
1 TTTCGGC-TTTTCGGCATTTCGGCA
*
44443407 TTTTGGCTTTTCGGCATTTCGGCA
1 TTTCGGCTTTTCGGCATTTCGGCA
44443431 TTTCGGCTTTT
1 TTTCGGCTTTT
44443442 GCCGGTTCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 4 0.12
24 28 0.88
ACGTcount: A:0.08, C:0.20, G:0.24, T:0.47
Consensus pattern (24 bp):
TTTCGGCTTTTCGGCATTTCGGCA
Found at i:44444675 original size:16 final size:16
Alignment explanation
Indices: 44444650--44444682 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
44444640 AAAAATTTAA
*
44444650 GATTTTGAGATTTTTG
1 GATTTCGAGATTTTTG
44444666 GATTTCGAGATTTTTG
1 GATTTCGAGATTTTTG
44444682 G
1 G
44444683 GGCTTTACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.03, G:0.27, T:0.52
Consensus pattern (16 bp):
GATTTCGAGATTTTTG
Found at i:44454045 original size:34 final size:29
Alignment explanation
Indices: 44453942--44454031 Score: 119
Period size: 29 Copynumber: 3.1 Consensus size: 29
44453932 GCACATTAAA
*
44453942 CCAAATCATATTCATATGGCCCATTAGGC
1 CCAAATCATATTTATATGGCCCATTAGGC
***
44453971 CC-AATCCGCTTGTATATGGCCCATTAGGC
1 CCAAATCATATT-TATATGGCCCATTAGGC
*
44454000 CCAAATCATATTTATATGGCCCGTTAGGC
1 CCAAATCATATTTATATGGCCCATTAGGC
44454029 CCA
1 CCA
44454032 GTGAAATTCA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
28 6 0.12
29 39 0.76
30 6 0.12
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.28
Consensus pattern (29 bp):
CCAAATCATATTTATATGGCCCATTAGGC
Found at i:44454268 original size:8 final size:8
Alignment explanation
Indices: 44454255--44454313 Score: 50
Period size: 8 Copynumber: 7.4 Consensus size: 8
44454245 GTAGCCAGAC
44454255 TTTCGGCT
1 TTTCGGCT
44454263 TTTCGGCAT
1 TTTCGGC-T
*
44454272 TTT-GACAT
1 TTTCGGC-T
44454280 TTT-GGCT
1 TTTCGGCT
* *
44454287 TTTCGACA
1 TTTCGGCT
*
44454295 TTTCGGCA
1 TTTCGGCT
44454303 TTTCGGCT
1 TTTCGGCT
44454311 TTT
1 TTT
44454314 GCCGATTCAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
7 4 0.09
8 35 0.81
9 4 0.09
ACGTcount: A:0.10, C:0.20, G:0.20, T:0.49
Consensus pattern (8 bp):
TTTCGGCT
Found at i:44454291 original size:24 final size:24
Alignment explanation
Indices: 44454255--44454313 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
44454245 GTAGCCAGAC
* *
44454255 TTTCGGCTTTTCGGCATTTTGACA
1 TTTCGGCTTTTCGACATTTCGACA
* *
44454279 TTTTGGCTTTTCGACATTTCGGCA
1 TTTCGGCTTTTCGACATTTCGACA
44454303 TTTCGGCTTTT
1 TTTCGGCTTTT
44454314 GCCGATTCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.10, C:0.20, G:0.20, T:0.49
Consensus pattern (24 bp):
TTTCGGCTTTTCGACATTTCGACA
Found at i:44454296 original size:16 final size:16
Alignment explanation
Indices: 44454263--44454307 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
44454253 ACTTTCGGCT
44454263 TTTCGGCATTTT-GACA
1 TTTCGGC-TTTTCGACA
*
44454279 TTTTGGCTTTTCGACA
1 TTTCGGCTTTTCGACA
*
44454295 TTTCGGCATTTCG
1 TTTCGGCTTTTCG
44454308 GCTTTTGCCG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 4 0.16
16 21 0.84
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.47
Consensus pattern (16 bp):
TTTCGGCTTTTCGACA
Found at i:44455543 original size:16 final size:16
Alignment explanation
Indices: 44455522--44455553 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
44455512 AAAATTTAAT
44455522 ATTTCGAGATTTTTGG
1 ATTTCGAGATTTTTGG
44455538 ATTTCGAGATTTTTGG
1 ATTTCGAGATTTTTGG
44455554 GGCGTTACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.25, T:0.50
Consensus pattern (16 bp):
ATTTCGAGATTTTTGG
Found at i:44456756 original size:25 final size:25
Alignment explanation
Indices: 44456728--44456776 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
44456718 CCAGAGGACC
*
44456728 AATCACATAACTCATGATAATGATT
1 AATCACATAACTCATCATAATGATT
* * *
44456753 AATCATATAATTCTTCATAATGAT
1 AATCACATAACTCATCATAATGAT
44456777 AATAATAAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (25 bp):
AATCACATAACTCATCATAATGATT
Found at i:44460693 original size:17 final size:18
Alignment explanation
Indices: 44460668--44460701 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
44460658 AAAACACAAA
*
44460668 GTAACAATCA-CAAAAAT
1 GTAAAAATCATCAAAAAT
44460685 GTAAAAATCATCAAAAA
1 GTAAAAATCATCAAAAA
44460702 CGGATCAAAA
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:0.62, C:0.15, G:0.06, T:0.18
Consensus pattern (18 bp):
GTAAAAATCATCAAAAAT
Found at i:44467639 original size:19 final size:18
Alignment explanation
Indices: 44467615--44467655 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
44467605 AACAATAAAC
44467615 AAATCCCAAATTAAAGTAA
1 AAAT-CCAAATTAAAGTAA
* *
44467634 AAATCCATATTACAGTAA
1 AAATCCAAATTAAAGTAA
44467652 AAAT
1 AAAT
44467656 ACCCCAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.56, C:0.15, G:0.05, T:0.24
Consensus pattern (18 bp):
AAATCCAAATTAAAGTAA
Found at i:44476189 original size:23 final size:22
Alignment explanation
Indices: 44476163--44476207 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
44476153 ACCCCATGCA
44476163 ATGCAACATAACAT-TATACATGG
1 ATGCAACAT-ACATATA-ACATGG
44476186 ATGCAACATACATATAACATGG
1 ATGCAACATACATATAACATGG
44476208 CATTCTCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.24
Consensus pattern (22 bp):
ATGCAACATACATATAACATGG
Found at i:44476205 original size:22 final size:23
Alignment explanation
Indices: 44476163--44476207 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
44476153 ACCCCATGCA
44476163 ATGCAACATAACATTATACATGG
1 ATGCAACATAACATTATACATGG
44476186 ATGCAACAT-ACA-TATAACATGG
1 ATGCAACATAACATTAT-ACATGG
44476208 CATTCTCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 3 0.14
22 9 0.43
23 9 0.43
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.24
Consensus pattern (23 bp):
ATGCAACATAACATTATACATGG
Done.