Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 174 of 427
Found at i:48495165 original size:93 final size:93
Alignment explanation
Indices: 48495053--48495223 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
48495043 GCCCATAAGT
*
48495053 GAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAG-TCAGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
48495117 ACGAGTTCGGATGCCTAGTTACATTTCAC
65 ACGAGTTCGGATGCCTAGTTACATTTCAC
**
48495146 GAACTCGGACTCAACTCAACGAGTTTGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTCAGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
48495211 CGAGTTCGGATGC
66 CGAGTTCGGATGC
48495224 TCAACCATCC
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 3 0.04
93 71 0.96
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGTCAGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:48495216 original size:46 final size:46
Alignment explanation
Indices: 48495045--48495216 Score: 183
Period size: 46 Copynumber: 3.7 Consensus size: 46
48495035 TGTAACCCGC
* *
48495045 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAG-TTAGGACATTCGCAT
* *
48495091 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTAGGA---C-A-TTCGCAT
* * * *
48495141 --TTCA-CGAACTCGGACTCAACTCAACGAGTTTGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTAGGACATTCGCAT
48495184 CCATAAGTGAACTCGGACTCAACTCAACGAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTT
48495217 CGGATGCTCA
Statistics
Matches: 104, Mismatches: 12, Indels: 20
0.76 0.09 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 5 0.05
46 56 0.54
47 28 0.27
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.23
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTAGGACATTCGCAT
Found at i:48498342 original size:27 final size:27
Alignment explanation
Indices: 48498312--48498394 Score: 68
Period size: 27 Copynumber: 3.3 Consensus size: 27
48498302 CTAATGGCCG
48498312 ATGTGATGAATGCGAAAATGTATATAT
1 ATGTGATGAATGCGAAAATGTATATAT
* ** ****
48498339 ATGTGAT-AAGGC-CTAATG-GCCGA-
1 ATGTGATGAATGCGAAAATGTATATAT
48498362 -TGTGATGAATGCGAAAATGTATATAT
1 ATGTGATGAATGCGAAAATGTATATAT
48498388 ATGTGAT
1 ATGTGAT
48498395 AAGGCCTAAT
Statistics
Matches: 37, Mismatches: 14, Indels: 10
0.61 0.23 0.16
Matches are distributed among these distances:
22 6 0.16
23 4 0.11
24 5 0.14
25 5 0.14
26 4 0.11
27 13 0.35
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.31
Consensus pattern (27 bp):
ATGTGATGAATGCGAAAATGTATATAT
Found at i:48498534 original size:49 final size:49
Alignment explanation
Indices: 48498133--48498526 Score: 689
Period size: 49 Copynumber: 8.0 Consensus size: 49
48498123 AATATGTATG
*
48498133 ATGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 ATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
* *
48498182 ATGTGTATATATGTGATAAGGCCTAATGCCCGATGTGATGAATGTGAAA
1 ATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
* *
48498231 GTGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 ATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
* *
48498280 GTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGCGAAA
1 ATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
*
48498329 ATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGCGAAA
1 ATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
48498378 ATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 ATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
48498427 ATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 ATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
*
48498476 ATGTATATATATATGTGATAAGGCCTCATGGCCGATGTGATGAATGTGAAA
1 ATG--TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
48498527 GCGTATATCT
Statistics
Matches: 335, Mismatches: 8, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
49 290 0.87
51 45 0.13
ACGTcount: A:0.33, C:0.09, G:0.27, T:0.30
Consensus pattern (49 bp):
ATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
Found at i:48498664 original size:37 final size:36
Alignment explanation
Indices: 48498609--48498695 Score: 147
Period size: 37 Copynumber: 2.3 Consensus size: 36
48498599 AATTTGGAAA
48498609 TATGTTCCGGGTGAGACCCGATGACTACGTGTGGAGAT
1 TATG-TCCGGGT-AGACCCGATGACTACGTGTGGAGAT
48498647 TATGTCCGGGTACGACCCGATGACTACGTGTGGAGAT
1 TATGTCCGGGTA-GACCCGATGACTACGTGTGGAGAT
48498684 TATGTCCGGGTA
1 TATGTCCGGGTA
48498696 AGACTTCGTA
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
36 1 0.02
37 43 0.90
38 4 0.08
ACGTcount: A:0.21, C:0.20, G:0.33, T:0.26
Consensus pattern (36 bp):
TATGTCCGGGTAGACCCGATGACTACGTGTGGAGAT
Found at i:48504279 original size:24 final size:24
Alignment explanation
Indices: 48504011--48504277 Score: 471
Period size: 24 Copynumber: 11.1 Consensus size: 24
48504001 GCAAAGACCA
48504011 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
48504035 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
*
48504059 TATGGCACTATGTGTGCGATTCAC
1 TATGGCACTATGTGTGCGATTTAC
*
48504083 TATGGCACTATGTGTGCGATTCAC
1 TATGGCACTATGTGTGCGATTTAC
*
48504107 TATGGCACTATGTGTGCGATTCAC
1 TATGGCACTATGTGTGCGATTTAC
48504131 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
*
48504155 TATGGCACTATGTGTGCGATTCAC
1 TATGGCACTATGTGTGCGATTTAC
48504179 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
48504203 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
*
48504227 TATGGCACTATGTGTGCGATTTGC
1 TATGGCACTATGTGTGCGATTTAC
* *
48504251 TATAGCACTATGTGTGCGATTTGC
1 TATGGCACTATGTGTGCGATTTAC
48504275 TAT
1 TAT
48504278 AGTCACATTC
Statistics
Matches: 237, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 237 1.00
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (24 bp):
TATGGCACTATGTGTGCGATTTAC
Found at i:48505834 original size:37 final size:37
Alignment explanation
Indices: 48505777--48505879 Score: 179
Period size: 37 Copynumber: 2.8 Consensus size: 37
48505767 CGAATAGTCC
* *
48505777 CCACACGTAGTTATCAGGTCTTACCCGGACAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
*
48505814 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
48505851 CCACACGTAGTCATCGGGTCTTACCCGGA
1 CCACACGTAGTCATCGGGTCTTACCCGGA
48505880 ATATATTTCC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 63 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.23
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
Found at i:48506078 original size:48 final size:48
Alignment explanation
Indices: 48506020--48506549 Score: 916
Period size: 48 Copynumber: 11.0 Consensus size: 48
48506010 ATATACACAC
* * *
48506020 ATCTCCTACATATTTCACATTAGCCATTCGGCTTTACCAAATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
48506068 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
48506116 ATCTCATACATATTTCACACTAGCCATTCGACTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* * *
48506164 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATATAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
48506212 ATCTCATACATATTTCATATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
48506260 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
48506308 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* * *
48506356 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATATAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
48506404 ATCTCATACATATTTCATATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
48506452 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
48506500 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACACATATAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
48506548 AT
1 AT
48506550 ATTTATCTTG
Statistics
Matches: 459, Mismatches: 23, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 459 1.00
ACGTcount: A:0.32, C:0.27, G:0.06, T:0.35
Consensus pattern (48 bp):
ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
Found at i:48515373 original size:43 final size:43
Alignment explanation
Indices: 48515317--48515477 Score: 173
Period size: 43 Copynumber: 3.7 Consensus size: 43
48515307 AATGCCATAG
* * * *
48515317 CCCAGATATGGTCTTACATGTTATCACATATCGATGCCATTGT
1 CCCAGACATGGTCTTACATGTAATCACATATCAATGCCAATGT
* * * * *
48515360 CCCAGATAGGGTCTTACATGGAATCGA-TTAACAATGCCAATGT
1 CCCAGACATGGTCTTACATGTAATC-ACATATCAATGCCAATGT
* *
48515403 CCCAAACATGGTCTTACACGTAATCACA-ATACAATGCCAATGT
1 CCCAGACATGGTCTTACATGTAATCACATAT-CAATGCCAATGT
* *
48515446 GCCAGACATGATCTTACATGTAATCACATATC
1 CCCAGACATGGTCTTACATGTAATCACATATC
48515478 GATAACCTAA
Statistics
Matches: 96, Mismatches: 18, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
42 2 0.02
43 91 0.95
44 3 0.03
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (43 bp):
CCCAGACATGGTCTTACATGTAATCACATATCAATGCCAATGT
Found at i:48516281 original size:30 final size:30
Alignment explanation
Indices: 48516247--48516343 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
48516237 AGCTCACTCC
48516247 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
48516277 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
48516307 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
48516337 TAGCTCA
1 TAGCTCA
48516344 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:48518341 original size:17 final size:16
Alignment explanation
Indices: 48518282--48518341 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 16
48518272 GAGACAGCCA
* *
48518282 CCATACATGCATTTAAG
1 CCATTCATGCATTT-AT
48518299 CCATTCATGCATTCTAT
1 CCATTCATGCATT-TAT
*
48518316 -CATCCCATGCATTTGAT
1 CCAT-TCATGCATTT-AT
48518333 CCATTCATG
1 CCATTCATG
48518342 GACTAGCCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 4 0.11
17 27 0.77
18 4 0.11
ACGTcount: A:0.27, C:0.28, G:0.10, T:0.35
Consensus pattern (16 bp):
CCATTCATGCATTTAT
Found at i:48518823 original size:30 final size:30
Alignment explanation
Indices: 48518738--48518834 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
48518728 TAAACTAAAA
* *
48518738 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
48518768 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
*
48518798 TGAGCTAAGGTTTAGCTTGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
48518827 ATGAGCTA
1 -TGAGCTA
48518835 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:48519243 original size:8 final size:8
Alignment explanation
Indices: 48519230--48519256 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
48519220 AAAAGATGAG
48519230 AATGAATT
1 AATGAATT
48519238 AATGAATT
1 AATGAATT
48519246 AATGAATT
1 AATGAATT
48519254 AAT
1 AAT
48519257 TTTGTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (8 bp):
AATGAATT
Found at i:48522388 original size:9 final size:9
Alignment explanation
Indices: 48522374--48522400 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
48522364 GTTATGCACA
48522374 CATTAAATT
1 CATTAAATT
48522383 CATTAAATT
1 CATTAAATT
48522392 CATTAAATT
1 CATTAAATT
48522401 TAACTGACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (9 bp):
CATTAAATT
Found at i:48527737 original size:17 final size:17
Alignment explanation
Indices: 48527704--48527827 Score: 92
Period size: 17 Copynumber: 7.0 Consensus size: 17
48527694 ATACTCACTC
48527704 TCTTTTTCAATTTTCTTT
1 TCTTTTTCAA-TTTCTTT
**
48527722 TCTTGATCAATTTCTTT
1 TCTTTTTCAATTTCTTT
48527739 TCTTTTTCAATTTCACTTT
1 TCTTTTTCAATTT--CTTT
*
48527758 TCTTTTTCACTTTCTTTT
1 TCTTTTTCAATTTC-TTT
* *
48527776 TGCTCTCTTTCACTCTCTTT
1 T-CT-T-TTTCAATTTCTTT
*
48527796 T-TCTTTC-ATTTCTTTT
1 TCTTTTTCAATTTC-TTT
*
48527812 TCTTTTT-AAATTCTTT
1 TCTTTTTCAATTTCTTT
48527828 CTCACTTGCT
Statistics
Matches: 86, Mismatches: 11, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
15 3 0.03
16 11 0.13
17 27 0.31
18 13 0.15
19 18 0.21
20 5 0.06
21 9 0.10
ACGTcount: A:0.11, C:0.21, G:0.02, T:0.66
Consensus pattern (17 bp):
TCTTTTTCAATTTCTTT
Found at i:48527772 original size:36 final size:35
Alignment explanation
Indices: 48527704--48527775 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 35
48527694 ATACTCACTC
*
48527704 TCTTTTTCAATTTTCTTTTCTTGATCAATTTCTTT
1 TCTTTTTCAATTTACTTTTCTTGATCAATTTCTTT
** *
48527739 TCTTTTTCAATTTCACTTTTCTTTTTCACTTTCTTT
1 TCTTTTTCAATTT-ACTTTTCTTGATCAATTTCTTT
48527775 T
1 T
48527776 TGCTCTCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 13 0.41
36 19 0.59
ACGTcount: A:0.12, C:0.19, G:0.01, T:0.67
Consensus pattern (35 bp):
TCTTTTTCAATTTACTTTTCTTGATCAATTTCTTT
Found at i:48527811 original size:15 final size:16
Alignment explanation
Indices: 48527781--48527816 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
48527771 CTTTTTGCTC
48527781 TCTTTCACTCTCTTTT
1 TCTTTCACTCTCTTTT
*
48527797 TCTTTCA-TTTCTTTT
1 TCTTTCACTCTCTTTT
48527812 TCTTT
1 TCTTT
48527817 TTAAATTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.06, C:0.25, G:0.00, T:0.69
Consensus pattern (16 bp):
TCTTTCACTCTCTTTT
Found at i:48528258 original size:63 final size:64
Alignment explanation
Indices: 48528172--48528303 Score: 221
Period size: 63 Copynumber: 2.1 Consensus size: 64
48528162 TCTTGTTGGG
* * * *
48528172 CTCTTGCTTGATGATCGCGCTTTTCTTGGATAGGCTTGATTTTTCGGTTGAGCATGCACTCTAT
1 CTCTTGCTCGATGATCACACTTTTCTTGGATAGGCTTGATTTATCGGTTGAGCATGCACTCTAT
48528236 -TCTTGCTCGATGATCACACTTTTCTTGGATAGGCTTGATTTATCGGTTGAGCATGCACTCTAT
1 CTCTTGCTCGATGATCACACTTTTCTTGGATAGGCTTGATTTATCGGTTGAGCATGCACTCTAT
48528299 CTCTT
1 CTCTT
48528304 TCAAAAAATA
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
63 59 0.94
64 4 0.06
ACGTcount: A:0.16, C:0.21, G:0.21, T:0.42
Consensus pattern (64 bp):
CTCTTGCTCGATGATCACACTTTTCTTGGATAGGCTTGATTTATCGGTTGAGCATGCACTCTAT
Found at i:48531178 original size:27 final size:27
Alignment explanation
Indices: 48531134--48531236 Score: 118
Period size: 27 Copynumber: 3.8 Consensus size: 27
48531124 CAGTAATAAT
* * *
48531134 AATGTAGCATAGCTACCAGAAACAGTG
1 AATGTGGCATAGCCACCAGTAACAGTG
* *
48531161 AATGTGGCAAAGCCACCAGTATCAGT-
1 AATGTGGCATAGCCACCAGTAACAGTG
*
48531187 AATTGTGGCATAGCCACTAGTAACAGTG
1 AA-TGTGGCATAGCCACCAGTAACAGTG
* *
48531215 AATGTGACATAGTCACCAGTAA
1 AATGTGGCATAGCCACCAGTAA
48531237 AGTACTTCCT
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
26 2 0.03
27 59 0.94
28 2 0.03
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.21
Consensus pattern (27 bp):
AATGTGGCATAGCCACCAGTAACAGTG
Found at i:48531379 original size:29 final size:27
Alignment explanation
Indices: 48531346--48531480 Score: 96
Period size: 27 Copynumber: 4.9 Consensus size: 27
48531336 CATACAACAC
48531346 ATAAGGGCATACTCATG-TCATTTTACCCT
1 ATAAGGGCAT--T-ATGATCATTTTACCCT
48531375 ATAAGGGCATTATGATCATTTTACCCT
1 ATAAGGGCATTATGATCATTTTACCCT
* * * * *
48531402 ACAGGGGCATTA-CAGTTATTTTTAGCCT
1 ATAAGGGCATTATGA-TCA-TTTTACCCT
* * * * *
48531430 ACAGGGGCATTACGGTTATTTTACCCT
1 ATAAGGGCATTATGATCATTTTACCCT
*
48531457 AT-AGGGACATTACGATCATTTTAC
1 ATAAGGG-CATTATGATCATTTTAC
48531481 TAATTTCGAG
Statistics
Matches: 89, Mismatches: 12, Indels: 12
0.79 0.11 0.11
Matches are distributed among these distances:
26 7 0.08
27 49 0.55
28 23 0.26
29 10 0.11
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (27 bp):
ATAAGGGCATTATGATCATTTTACCCT
Found at i:48531399 original size:27 final size:27
Alignment explanation
Indices: 48531363--48531480 Score: 114
Period size: 27 Copynumber: 4.3 Consensus size: 27
48531353 CATACTCATG
*
48531363 TCATTTTACCCTATAAGGGCATTATGA
1 TCATTTTACCCTATAAGGGCATTACGA
* *
48531390 TCATTTTACCCTACAGGGGCATTAC-A
1 TCATTTTACCCTATAAGGGCATTACGA
* * * * *
48531416 GTTATTTTTAGCCTACAGGGGCATTACGG
1 -TCA-TTTTACCCTATAAGGGCATTACGA
*
48531445 TTATTTTACCCTAT-AGGGACATTACGA
1 TCATTTTACCCTATAAGGG-CATTACGA
48531472 TCATTTTAC
1 TCATTTTAC
48531481 TAATTTCGAG
Statistics
Matches: 76, Mismatches: 11, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
26 4 0.05
27 48 0.63
28 24 0.32
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.36
Consensus pattern (27 bp):
TCATTTTACCCTATAAGGGCATTACGA
Found at i:48533509 original size:29 final size:29
Alignment explanation
Indices: 48533460--48533519 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
48533450 TGCAGTAGAC
* *
48533460 AATCAATTGTGTTATTTACTTGCACAACT
1 AATCAATTGTGTCATTCACTTGCACAACT
48533489 AATCAATTGTGTCATTCACTTGCACAACT
1 AATCAATTGTGTCATTCACTTGCACAACT
48533518 AA
1 AA
48533520 CTTTCAATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (29 bp):
AATCAATTGTGTCATTCACTTGCACAACT
Found at i:48534653 original size:27 final size:27
Alignment explanation
Indices: 48534623--48534676 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
48534613 AAAATCATCT
48534623 CTTTCAAAAAACCAAAGTTTAGAAAAA
1 CTTTCAAAAAACCAAAGTTTAGAAAAA
** * *
48534650 CTTTTGAAAACCCAAATTTTAGAAAAA
1 CTTTCAAAAAACCAAAGTTTAGAAAAA
48534677 AATTTAGAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.52, C:0.15, G:0.07, T:0.26
Consensus pattern (27 bp):
CTTTCAAAAAACCAAAGTTTAGAAAAA
Found at i:48534687 original size:27 final size:27
Alignment explanation
Indices: 48534629--48534690 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
48534619 ATCTCTTTCA
* * *
48534629 AAAAACCAAAGTTTAGAAAAACTTTTG
1 AAAACCCAAAGTTTAGAAAAAATTTAG
*
48534656 AAAACCCAAATTTTAGAAAAAAATTTAG
1 AAAACCCAAAGTTTAG-AAAAAATTTAG
48534684 -AAACCCA
1 AAAACCCA
48534691 TTCCACAGTC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 21 0.70
28 9 0.30
ACGTcount: A:0.55, C:0.15, G:0.08, T:0.23
Consensus pattern (27 bp):
AAAACCCAAAGTTTAGAAAAAATTTAG
Found at i:48535594 original size:27 final size:27
Alignment explanation
Indices: 48535562--48535625 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
48535552 AGCTACCAAA
48535562 AACAGTGAATATGGCAAAGCCACCAGT
1 AACAGTGAATATGGCAAAGCCACCAGT
* * *
48535589 ATCAGT-AATTGTGGCATAGCCACCAGT
1 AACAGTGAA-TATGGCAAAGCCACCAGT
*
48535616 AACAATGAAT
1 AACAGTGAAT
48535626 GTAACATAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
26 2 0.07
27 26 0.87
28 2 0.07
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (27 bp):
AACAGTGAATATGGCAAAGCCACCAGT
Found at i:48535820 original size:27 final size:27
Alignment explanation
Indices: 48535788--48535958 Score: 252
Period size: 27 Copynumber: 6.3 Consensus size: 27
48535778 CATACTCGTA
*
48535788 TCATTTTACCCTATAGGGGCATTACGG
1 TCATTTTACCCTACAGGGGCATTACGG
48535815 TCATTTTACCCTACAGGGGCATTACGG
1 TCATTTTACCCTACAGGGGCATTACGG
* * *
48535842 TCATTTTATCCTACAGGGGCATTATGA
1 TCATTTTACCCTACAGGGGCATTACGG
* *
48535869 TCATTGTACCCTACAGGGGCAATACGG
1 TCATTTTACCCTACAGGGGCATTACGG
*
48535896 TCATTTTACCCTACAGGGGCAATACGG
1 TCATTTTACCCTACAGGGGCATTACGG
* **
48535923 TCATTTTACCCTACAGGAGCATTACAA
1 TCATTTTACCCTACAGGGGCATTACGG
48535950 TCATTTTAC
1 TCATTTTAC
48535959 TAATTTGGGG
Statistics
Matches: 130, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 130 1.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (27 bp):
TCATTTTACCCTACAGGGGCATTACGG
Found at i:48541208 original size:25 final size:25
Alignment explanation
Indices: 48541179--48541226 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
48541169 TTATAATATG
* * *
48541179 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
48541204 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
48541227 GTTTATGTAT
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:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:48541295 original size:20 final size:20
Alignment explanation
Indices: 48541270--48541328 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
48541260 TAAATATGGT
48541270 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
* *
48541290 ATGTATGATACGCACATGAT
1 ATGTATGATATGCACATGAA
48541310 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
48541329 GGTAATCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:48541409 original size:23 final size:24
Alignment explanation
Indices: 48541379--48541473 Score: 124
Period size: 24 Copynumber: 4.0 Consensus size: 24
48541369 GAGGAAGTGA
48541379 AAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
48541402 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
48541426 GAAAGGGCTT-TGGCCCCAGTTATT
1 AAAAGGGCTTAT-GCCCCAGTTATT
*
48541450 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
48541474 ATGATAAAGC
Statistics
Matches: 64, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
23 23 0.36
24 30 0.47
25 11 0.17
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:48541447 original size:47 final size:49
Alignment explanation
Indices: 48541380--48541473 Score: 133
Period size: 47 Copynumber: 2.0 Consensus size: 49
48541370 AGGAAGTGAA
*
48541380 AAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTATTG
1 AAAGGGCTTATGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTATTG
48541427 AAAGGGCTT-TGGCCCCAGTTATTAAAAGAGGCTAGGCCTCCAGTTAT
1 AAAGGGCTTAT-GCCCCAGTTATTAAAAGAGGCTAGGCCTCCAGTTAT
48541474 ATGATAAAGC
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
46 1 0.02
47 19 0.45
48 11 0.26
49 11 0.26
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (49 bp):
AAAGGGCTTATGCCCCAGTTATTAAAAGAGGCTAGGCCTCCAGTTATTG
Found at i:48541715 original size:38 final size:38
Alignment explanation
Indices: 48541664--48541826 Score: 232
Period size: 38 Copynumber: 4.4 Consensus size: 38
48541654 CGTTTACAGT
48541664 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
*
48541702 AAAGGCTTCGGCCCAG-----T--AATATGAAATATGA
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
48541733 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
* *
48541771 AAAGGCTTCGGCCCAGTATTATGAAATATGAAATACGA
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
*
48541809 AAAGGGCTACGGCCCAGT
1 AAA-GGCTTCGGCCCAGT
48541827 GCATGATTGA
Statistics
Matches: 112, Mismatches: 5, Indels: 15
0.85 0.04 0.11
Matches are distributed among these distances:
31 29 0.26
33 1 0.01
36 1 0.01
38 68 0.61
39 13 0.12
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (38 bp):
AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
Found at i:48541726 original size:31 final size:31
Alignment explanation
Indices: 48541688--48541803 Score: 142
Period size: 31 Copynumber: 3.5 Consensus size: 31
48541678 AGTATTATGA
48541688 AATATGAAACATGAAAAGGCTTCGGCCCAGT
1 AATATGAAACATGAAAAGGCTTCGGCCCAGT
*
48541719 AATATGAAATATGAAAAGGCTTCGGCCCAGTATTAT
1 AATATGAAACATGAAAAGGCTTCGGCCCAG-----T
48541755 GAAATATGAAACATGAAAAGGCTTCGGCCCAGT
1 --AATATGAAACATGAAAAGGCTTCGGCCCAGT
* *
48541788 ATTATGAAATATGAAA
1 AATATGAAACATGAAA
48541804 TACGAAAAGG
Statistics
Matches: 74, Mismatches: 4, Indels: 14
0.80 0.04 0.15
Matches are distributed among these distances:
31 43 0.58
33 1 0.01
36 1 0.01
38 29 0.39
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.23
Consensus pattern (31 bp):
AATATGAAACATGAAAAGGCTTCGGCCCAGT
Found at i:48541740 original size:69 final size:69
Alignment explanation
Indices: 48541664--48541803 Score: 271
Period size: 69 Copynumber: 2.0 Consensus size: 69
48541654 CGTTTACAGT
48541664 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGAAAAGGCTTCGGCCCAGTAATATGAAAT
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGAAAAGGCTTCGGCCCAGTAATATGAAAT
48541729 ATGA
66 ATGA
*
48541733 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGAAAAGGCTTCGGCCCAGTATTATGAAAT
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGAAAAGGCTTCGGCCCAGTAATATGAAAT
48541798 ATGA
66 ATGA
48541802 AA
1 AA
48541804 TACGAAAAGG
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (69 bp):
AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGAAAAGGCTTCGGCCCAGTAATATGAAAT
ATGA
Found at i:48548233 original size:4 final size:4
Alignment explanation
Indices: 48548224--48548254 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
48548214 CAAAAATGCA
48548224 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGT
1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGT
48548255 ATATGAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.23, G:0.26, T:0.52
Consensus pattern (4 bp):
TGTC
Found at i:48550066 original size:22 final size:24
Alignment explanation
Indices: 48550041--48550095 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
48550031 ATAAGAAGAG
48550041 AAATATTTTAAAAATTACAA-AA-A
1 AAATATTTTAAAAATTA-AAGAATA
* * *
48550064 AATTCTTTTAAAATTTAAAGAATA
1 AAATATTTTAAAAATTAAAGAATA
48550088 AAATATTT
1 AAATATTT
48550096 AATTAAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 2 0.08
23 16 0.64
24 7 0.28
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (24 bp):
AAATATTTTAAAAATTAAAGAATA
Found at i:48550134 original size:21 final size:19
Alignment explanation
Indices: 48550110--48550148 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
48550100 AAAAATTTTA
48550110 AATATATTTCTCTAAAGAAAT
1 AATATATTT-T-TAAAGAAAT
*
48550131 AATATCTTTTTAAAGAAA
1 AATATATTTTTAAAGAAA
48550149 ATATAAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 1 0.06
21 8 0.47
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (19 bp):
AATATATTTTTAAAGAAAT
Found at i:48555466 original size:17 final size:17
Alignment explanation
Indices: 48555444--48555486 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
48555434 AATAGTAAAT
48555444 ATGATATGTGTGCTATA
1 ATGATATGTGTGCTATA
48555461 ATGATATGTGTGCTATA
1 ATGATATGTGTGCTATA
48555478 ATGATATGT
1 ATGATATGT
48555487 ATAAAGTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.30, C:0.05, G:0.23, T:0.42
Consensus pattern (17 bp):
ATGATATGTGTGCTATA
Found at i:48556192 original size:22 final size:22
Alignment explanation
Indices: 48556159--48556226 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
48556149 GGAAAGTTAG
48556159 AAAAAAGAATTATATTCTTTCC
1 AAAAAAGAATTATATTCTTTCC
**
48556181 AAAAAA-ATATTA-A---TTTAG
1 AAAAAAGA-ATTATATTCTTTCC
48556199 AAAAAAGAATTATATTCTTTCC
1 AAAAAAGAATTATATTCTTTCC
48556221 AAAAAA
1 AAAAAA
48556227 TATTAATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
18 13 0.36
19 2 0.06
21 2 0.06
22 19 0.53
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.32
Consensus pattern (22 bp):
AAAAAAGAATTATATTCTTTCC
Found at i:48556225 original size:21 final size:21
Alignment explanation
Indices: 48556160--48556225 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
48556150 GAAAGTTAGA
48556160 AAAAAGAATTATATTCTTTCC
1 AAAAAGAATTATATTCTTTCC
* ***
48556181 AAAAA-AA-TATTAAT-TTAGA
1 AAAAAGAATTA-TATTCTTTCC
48556200 AAAAAGAATTATATTCTTTCC
1 AAAAAGAATTATATTCTTTCC
48556221 AAAAA
1 AAAAA
48556226 ATATTAATTT
Statistics
Matches: 33, Mismatches: 8, Indels: 8
0.67 0.16 0.16
Matches are distributed among these distances:
19 9 0.27
20 10 0.30
21 14 0.42
ACGTcount: A:0.53, C:0.09, G:0.05, T:0.33
Consensus pattern (21 bp):
AAAAAGAATTATATTCTTTCC
Found at i:48556225 original size:39 final size:40
Alignment explanation
Indices: 48556155--48556235 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
48556145 AAATGGAAAG
48556155 TTAGAAAAAAGAATTATATTCTTTCCAAAAAAATATTAAT
1 TTAGAAAAAAGAATTATATTCTTTCCAAAAAAATATTAAT
48556195 TTAGAAAAAAGAATTATATTCTTTCC-AAAAAATATTAAT
1 TTAGAAAAAAGAATTATATTCTTTCCAAAAAAATATTAAT
48556234 TT
1 TT
48556236 TCCATGTCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 15 0.37
40 26 0.63
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (40 bp):
TTAGAAAAAAGAATTATATTCTTTCCAAAAAAATATTAAT
Found at i:48556454 original size:138 final size:137
Alignment explanation
Indices: 48556206--48556628 Score: 681
Period size: 138 Copynumber: 3.1 Consensus size: 137
48556196 TAGAAAAAAG
*
48556206 AATTATATTCTTTCCAAAA-AATATTAATTTTCCATGTCTTTTATATTTTGAGCGAAATTAATTA
1 AATTATATTCTTTCCAAAAGAATATTAATTTT-CATGTCTTTTATATTTTGACCGAAATTAATTA
*
48556270 ATATAACTT-TTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATTAATCAAG
65 ATATAA-TTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAA-
*
48556334 TTTATATATT
128 TTCATATATT
*
48556344 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTGGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
*
48556409 TATAATTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCGAATT
66 TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATC-AATT
48556474 CATATATT
130 CATATATT
* * * *
48556482 AATTATATTATTTCCAAAAGAAAATTAATTTCCATGTCTTTTATATTTTGACCGAATTTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
*
48556547 TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
66 TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATC-AATT
48556612 CA-ATTATT
130 CATA-TATT
48556620 AATTATATT
1 AATTATATT
48556629 TATGTTCTCT
Statistics
Matches: 268, Mismatches: 13, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
137 3 0.01
138 251 0.94
139 14 0.05
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.46
Consensus pattern (137 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAATTC
ATATATT
Found at i:48558563 original size:30 final size:30
Alignment explanation
Indices: 48558529--48558629 Score: 96
Period size: 30 Copynumber: 3.4 Consensus size: 30
48558519 AGCTCACTCC
*
48558529 TAGCTCATTTTCAACTCACGAGCTAAACCT
1 TAGCTCATTTTCAGCTCACGAGCTAAACCT
** * * * *
48558559 TAGCTCAACTTCAGCTTAGGAGTTTAACCT
1 TAGCTCATTTTCAGCTCACGAGCTAAACCT
* * *
48558589 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTC-ATTTTCAGCTCACGAGCTAAACCT
48558619 TAGCTCATTTT
1 TAGCTCATTTT
48558630 AGTTTAAACT
Statistics
Matches: 53, Mismatches: 17, Indels: 3
0.73 0.23 0.04
Matches are distributed among these distances:
29 4 0.08
30 46 0.87
31 3 0.06
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (30 bp):
TAGCTCATTTTCAGCTCACGAGCTAAACCT
Found at i:48561445 original size:40 final size:40
Alignment explanation
Indices: 48561253--48561438 Score: 236
Period size: 40 Copynumber: 4.7 Consensus size: 40
48561243 TCGAATGATG
* * *
48561253 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
48561293 TCCGGACTAAGAT-CCGAAGGCATTCGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
48561333 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
48561373 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
48561414 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
48561439 AACGAGTAGC
Statistics
Matches: 132, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
39 1 0.01
40 122 0.92
41 9 0.07
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:48561445 original size:80 final size:80
Alignment explanation
Indices: 48561253--48561471 Score: 245
Period size: 80 Copynumber: 2.8 Consensus size: 80
48561243 TCGAATGATG
* * **
48561253 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATATCCGGGTTAAGATCCGAAGGCATT
48561317 CGTGCGAGTTACTAAA
65 CGTGCGAGTTACTAAA
* *
48561333 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAGAT-CCGAAGGCAT
*
48561396 TTGTGCGAGTTACTATAA
64 TCGTGCGAGTTACTA-AA
* **
48561414 -CCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATATCC-GGTTAA-ACTCCGAAGG
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGGGTTAAGA-TCCGAAGG
48561472 TACATGATTC
Statistics
Matches: 119, Mismatches: 12, Indels: 17
0.80 0.08 0.11
Matches are distributed among these distances:
79 17 0.14
80 92 0.77
81 10 0.08
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAGATCCGAAGGCATTC
GTGCGAGTTACTAAA
Found at i:48563889 original size:46 final size:45
Alignment explanation
Indices: 48563836--48564011 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 45
48563826 TATTTGGGCA
48563836 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGTG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAG-G
* * *
48563882 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGAGG
*
48563927 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCG-AGG
* *
48563975 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
48564012 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
43 4 0.04
45 3 0.03
46 67 0.60
47 30 0.27
48 4 0.04
50 4 0.04
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGG
Found at i:48563991 original size:93 final size:93
Alignment explanation
Indices: 48563832--48564003 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
48563822 GGGATATTTG
** *
48563832 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGTGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
48563897 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
48563925 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
48563990 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
48564004 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:48566982 original size:15 final size:15
Alignment explanation
Indices: 48566962--48567030 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
48566952 GTATCTTGGG
48566962 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
48566977 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
48566992 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
48567007 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
48567022 TTTCTTTAT
1 TTTCTTTAT
48567031 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:48567031 original size:30 final size:30
Alignment explanation
Indices: 48566953--48567040 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
48566943 CATAGTATCG
* * * *
48566953 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
48566983 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
48567013 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
48567041 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:48569470 original size:46 final size:46
Alignment explanation
Indices: 48569420--48569595 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
48569410 TATTTGGGCA
48569420 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
48569466 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
48569513 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
48569559 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
48569596 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:48569575 original size:93 final size:93
Alignment explanation
Indices: 48569416--48569587 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
48569406 TGGATATTTG
* *
48569416 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
48569481 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
48569509 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
48569574 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
48569588 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:48573429 original size:33 final size:35
Alignment explanation
Indices: 48573391--48573470 Score: 94
Period size: 33 Copynumber: 2.4 Consensus size: 35
48573381 CCTAAACCCG
*
48573391 TTCAGATAACAGTGATACTGGGCCAGAG-CCCTT-
1 TTCAGATAACAGTGAAACTGGGCCAGAGCCCCTTA
* * **
48573424 TTCAGATTACA-TTAAACTGGGCCTTAGCCCCTTA
1 TTCAGATAACAGTGAAACTGGGCCAGAGCCCCTTA
48573458 TTCAGATAACAGT
1 TTCAGATAACAGT
48573471 ATGGCCCATA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
32 12 0.32
33 15 0.39
34 10 0.26
35 1 0.03
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (35 bp):
TTCAGATAACAGTGAAACTGGGCCAGAGCCCCTTA
Found at i:48575974 original size:21 final size:20
Alignment explanation
Indices: 48575940--48576007 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
48575930 ACATTCTTGT
48575940 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
48575961 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
48575982 AAAGAAAACGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
48576003 AAAGA
1 AAAGA
48576008 GCAGCAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.20
21 27 0.68
22 5 0.12
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.01
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:48575975 original size:6 final size:5
Alignment explanation
Indices: 48575951--48576007 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
48575941 AAGAGAAAAC
*
48575951 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAACGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
48575998 AAAGA AAAGA
1 AAAGA AAAGA
48576008 GCAGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:48575982 original size:15 final size:14
Alignment explanation
Indices: 48575951--48576007 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
48575941 AAGAGAAAAC
48575951 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
48575967 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
48575982 AAAGAAAACGAAATAA
1 AAAGAAAA-G-AAGAA
48575998 AAAGAAAAGA
1 AAAGAAAAGA
48576008 GCAGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:48576122 original size:30 final size:29
Alignment explanation
Indices: 48576088--48576168 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 29
48576078 TTTGGAAAAC
*
48576088 AAAAAGGAAATGAAAAAGAAAATGAGATTG
1 AAAAA-GAAATGAAAAAGAAAATGAGAGTG
***
48576118 AAAAAGAGAATGAAAAAGAGTTTGAGAGTG
1 AAAAAGA-AATGAAAAAGAAAATGAGAGTG
*
48576148 AAAAAGAAGGTGAAAAAGAAA
1 AAAAAGAA-ATGAAAAAGAAA
48576169 TTGAAACAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
29 3 0.07
30 39 0.93
ACGTcount: A:0.62, C:0.00, G:0.26, T:0.12
Consensus pattern (29 bp):
AAAAAGAAATGAAAAAGAAAATGAGAGTG
Found at i:48578794 original size:13 final size:13
Alignment explanation
Indices: 48578776--48578800 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48578766 GTATTGATCA
48578776 TGTGTTCACACCT
1 TGTGTTCACACCT
48578789 TGTGTTCACACC
1 TGTGTTCACACC
48578801 ATGATGACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:48581305 original size:33 final size:35
Alignment explanation
Indices: 48581267--48581346 Score: 94
Period size: 33 Copynumber: 2.4 Consensus size: 35
48581257 CCTAAACCCG
*
48581267 TTCAGATAACAGTGATACTGGGCCAGAG-CCCTT-
1 TTCAGATAACAGTGAAACTGGGCCAGAGCCCCTTA
* * **
48581300 TTCAGATTACA-TTAAACTGGGCCTTAGCCCCTTA
1 TTCAGATAACAGTGAAACTGGGCCAGAGCCCCTTA
48581334 TTCAGATAACAGT
1 TTCAGATAACAGT
48581347 ATGGCCCATA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
32 12 0.32
33 15 0.39
34 10 0.26
35 1 0.03
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (35 bp):
TTCAGATAACAGTGAAACTGGGCCAGAGCCCCTTA
Found at i:48583280 original size:80 final size:80
Alignment explanation
Indices: 48583196--48583344 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
48583186 TATGGTAACC
* * * *
48583196 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
48583260 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
48583276 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
48583341 CCGG
66 CCGG
48583345 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:48583286 original size:40 final size:38
Alignment explanation
Indices: 48583237--48583344 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
48583227 ATCACGATTT
*
48583237 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
48583277 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
48583317 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
48583345 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:48592502 original size:33 final size:34
Alignment explanation
Indices: 48592464--48592543 Score: 85
Period size: 33 Copynumber: 2.4 Consensus size: 34
48592454 CCTAAACCCG
* *
48592464 TTCAGATAACAGTGATACTGGGCC-AGAGCCCTT-
1 TTCAGATAACAGTGAAACTGGGCCTA-ACCCCTTA
* *
48592497 TTCAGATTACA-TTAAACTGGGCCTTAACCCCTTA
1 TTCAGATAACAGTGAAACTGGGCC-TAACCCCTTA
48592531 TTCAGATAACAGT
1 TTCAGATAACAGT
48592544 ATGGCCCATA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
32 10 0.26
33 16 0.42
34 11 0.29
35 1 0.03
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (34 bp):
TTCAGATAACAGTGAAACTGGGCCTAACCCCTTA
Found at i:48599749 original size:46 final size:46
Alignment explanation
Indices: 48599696--48599911 Score: 233
Period size: 46 Copynumber: 4.6 Consensus size: 46
48599686 TGTGTGGGCT
48599696 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACGA-TATGAGAGCC
* * * *
48599742 AGTGTAAGACCATGTCTGGGACATGGCATCAG-CATTGAGATGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCA-CGATATGAGAGCC
* *
48599790 AGTGTAAGACATGTC-GGGACATGCATCGGCCACGAGACGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACGATATG-AGAGCC
* * * * *
48599835 AGTGTAAGACATGTCTGGGACATGCATCAGCTACGAAATGATAGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACGATATGAGAGCC
*
48599881 AATGTAAGACCATGTCTGGGACATGGCATCG
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCG
48599912 ACTTGAGATA
Statistics
Matches: 145, Mismatches: 15, Indels: 18
0.81 0.08 0.10
Matches are distributed among these distances:
45 30 0.21
46 50 0.34
47 36 0.25
48 28 0.19
49 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.29, T:0.21
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCACGATATGAGAGCC
Found at i:48599902 original size:93 final size:94
Alignment explanation
Indices: 48599693--48599911 Score: 272
Period size: 93 Copynumber: 2.3 Consensus size: 94
48599683 ATGTGTGTGG
* * *
48599693 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATGTC
1 GCTAATGTAAGACATGTCTGGGACATGCATCGGCCACATGACGAGAGCCAGTGTAAGACCATGTC
* *
48599758 TGGGACATGGCATCAGCATTGAGATGAGA
66 TGGGACATGGCATCAGCATCGAAATGAGA
*
48599787 GCTAGTGTAAGACATGTC-GGGACATGCATCGGCCACGA-GACGTA-AGCCAGTGTAAGA-CATG
1 GCTAATGTAAGACATGTCTGGGACATGCATCGGCCAC-ATGACG-AGAGCCAGTGTAAGACCATG
*
48599848 TCTGGGACAT-GCATCAGC-TACGAAATGATA
64 TCTGGGACATGGCATCAGCAT-CGAAATGAGA
48599878 G-TCAATGTAAGACCATGTCTGGGACATGGCATCG
1 GCT-AATGTAAGA-CATGTCTGGGACAT-GCATCG
48599912 ACTTGAGATA
Statistics
Matches: 112, Mismatches: 6, Indels: 14
0.85 0.05 0.11
Matches are distributed among these distances:
90 2 0.02
91 24 0.21
92 20 0.18
93 40 0.36
94 26 0.23
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.21
Consensus pattern (94 bp):
GCTAATGTAAGACATGTCTGGGACATGCATCGGCCACATGACGAGAGCCAGTGTAAGACCATGTC
TGGGACATGGCATCAGCATCGAAATGAGA
Found at i:48599932 original size:93 final size:92
Alignment explanation
Indices: 48599693--48599957 Score: 238
Period size: 93 Copynumber: 2.8 Consensus size: 92
48599683 ATGTGTGTGG
* * **
48599693 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-A-TTATGAGAGCCAGTGTAAGACCATG
1 GCTAATGTAAGACATGTC-GGGACATGCATCGGACACGAGACAT--GAGCCAGTGTAAGA-CATG
* *
48599756 TCTGGGACATGGCATCAGCATTGAGATGAGA
62 TCTGGGACATGGCATCAGCATCGAAATGAGA
* * * *
48599787 GCTAGTGTAAGACATGTCGGGACATGCATCGGCCACGAGACGTAAGCCAGTGTAAGACATGTCTG
1 GCTAATGTAAGACATGTCGGGACATGCATCGGACACGAGACATGAGCCAGTGTAAGACATGTCTG
*
48599852 GGACAT-GCATCAGC-TACGAAATGATA
66 GGACATGGCATCAGCAT-CGAAATGAGA
** * * *
48599878 G-TCAATGTAAGACCATGTCTGGGACATGGCATC-GACTTGAGATATGAGCTAGTGTAAGACCGT
1 GCT-AATGTAAGA-CATGTC-GGGACAT-GCATCGGACACGAGACATGAGCCAGTGTAAGA-CAT
48599941 GT-TAGGGACATGGCATC
61 GTCT-GGGACATGGCATC
48599958 GGTACCTTAC
Statistics
Matches: 145, Mismatches: 16, Indels: 19
0.81 0.09 0.11
Matches are distributed among these distances:
90 2 0.01
91 24 0.17
92 20 0.14
93 58 0.40
94 35 0.24
95 6 0.04
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.22
Consensus pattern (92 bp):
GCTAATGTAAGACATGTCGGGACATGCATCGGACACGAGACATGAGCCAGTGTAAGACATGTCTG
GGACATGGCATCAGCATCGAAATGAGA
Found at i:48599938 original size:47 final size:45
Alignment explanation
Indices: 48599693--48599937 Score: 182
Period size: 47 Copynumber: 5.3 Consensus size: 45
48599683 ATGTGTGTGG
* *
48599693 GCTAGTGTAAGACATGTCTGGGACATGCATCGGC-C-ACATTATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGACTCGAGA-TAT--GA
* *
48599739 GCCAGTGTAAGACCATGTCTGGGACATGGCATC-AGCATTGAGATGA-GA
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGA-C-TCGAGAT-ATGA
* * ** *
48599787 GCTAGTGTAAGACATGTC-GGGACATGCATCGGCCACGAGACGTAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATC-GACTCGAGATATGA
* *
48599832 GCCAGTGTAAGACATGTCTGGGACATGCATC-AGCTACGAAATGAT-A
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGA-CT-CGAGAT-ATGA
* *
48599878 G-TCAATGTAAGACCATGTCTGGGACATGGCATCGACTTGAGATATGA
1 GCT-AGTGTAAGA-CATGTCTGGGACAT-GCATCGACTCGAGATATGA
48599925 GCTAGTGTAAGAC
1 GCTAGTGTAAGAC
48599938 CGTGTTAGGG
Statistics
Matches: 157, Mismatches: 22, Indels: 40
0.72 0.10 0.18
Matches are distributed among these distances:
45 28 0.18
46 48 0.31
47 49 0.31
48 27 0.17
49 1 0.01
50 1 0.01
51 3 0.02
ACGTcount: A:0.30, C:0.19, G:0.29, T:0.22
Consensus pattern (45 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGACTCGAGATATGA
Found at i:48607036 original size:46 final size:46
Alignment explanation
Indices: 48606986--48607158 Score: 187
Period size: 46 Copynumber: 3.7 Consensus size: 46
48606976 TGGTTGAGCA
48606986 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
48607032 TCCGAACTCGTTGAGTTGAGTCCGAG----CTTGTGAAATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCGAA-T--G
*
48607077 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
48607125 -CCTGAGCTCGTTGAGTTGAGTCTGAGTTCACTTA
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTA
48607159 GGGGCGGGTT
Statistics
Matches: 106, Mismatches: 9, Indels: 24
0.76 0.06 0.17
Matches are distributed among these distances:
42 7 0.07
43 4 0.04
45 3 0.03
46 55 0.52
47 26 0.25
48 1 0.01
50 3 0.03
51 7 0.07
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:48612778 original size:20 final size:20
Alignment explanation
Indices: 48612753--48612798 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
48612743 TAGAAAATGA
48612753 TTTCTGGAA-ATTGATTTACT
1 TTTCTGGAAGA-TGATTTACT
48612773 TTTCT-GAAGATGATTTACT
1 TTTCTGGAAGATGATTTACT
48612792 TTTCTGG
1 TTTCTGG
48612799 TGTTTAGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.22, C:0.11, G:0.17, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAGATGATTTACT
Found at i:48618468 original size:22 final size:22
Alignment explanation
Indices: 48618427--48618468 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
48618417 AATCAATTTC
*
48618427 ATACTCAATTTCATATCAAAGA
1 ATACTCAATTTCATAACAAAGA
48618449 ATAC-CAATTTCATGAACAAA
1 ATACTCAATTTCAT-AACAAA
48618469 TATCCTACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.48, C:0.19, G:0.05, T:0.29
Consensus pattern (22 bp):
ATACTCAATTTCATAACAAAGA
Found at i:48619296 original size:42 final size:42
Alignment explanation
Indices: 48619244--48619329 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 42
48619234 GCACTATCCT
*
48619244 AGACAGGGTCTTACAC-AATATCATATACGATGCCAATGTCCC
1 AGACAGGGTCTTACACAAATATCAAAT-CGATGCCAATGTCCC
* *
48619286 AGACATGGTCTTACACGTAAATCTCAAATCGATGCCAATGTCCC
1 AGACAGGGTCTTACAC--AAATATCAAATCGATGCCAATGTCCC
48619330 GGAGGTGGTC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 15 0.39
44 15 0.39
45 8 0.21
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (42 bp):
AGACAGGGTCTTACACAAATATCAAATCGATGCCAATGTCCC
Found at i:48621192 original size:6 final size:7
Alignment explanation
Indices: 48621163--48621191 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
48621153 TATTCCCAAG
48621163 TTATTTT
1 TTATTTT
48621170 TTATTTT
1 TTATTTT
48621177 TTATTTT
1 TTATTTT
48621184 TTATTTT
1 TTATTTT
48621191 T
1 T
48621192 ACATATGATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTATTTT
Found at i:48622043 original size:127 final size:127
Alignment explanation
Indices: 48621817--48622133 Score: 467
Period size: 127 Copynumber: 2.5 Consensus size: 127
48621807 GAAAATTCCT
** * *
48621817 TAAAACGAAGGCAATGTTTGATGTTTGGAAATTCAGGG-ATCGTGCTCTATCGTGCTGGGTTTCG
1 TAAAAC-AAGGCAATGTTCAATGTTTGGAAATTCGGGGAATCGTGCCCTATCGTGCTGGGTTTCG
* *
48621881 ACTTCCTGTTTGTTCAAAATAATCAAATATTCCTTTAGAATTTCACTCGTGTTTT-TCACATTC
65 ACTTCCGGTTTGTTCAAAATAATCAAATATTCCTTTAGAATTTCACTCGTGTTTTAT-AAATTC
*
48621944 TAAAACAAGGCAATGTTCAATGTTTGGAAATTCGGGGAATCGTGCCCTATCGTGTTGGGTTTCGA
1 TAAAACAAGGCAATGTTCAATGTTTGGAAATTCGGGGAATCGTGCCCTATCGTGCTGGGTTTCGA
* * **
48622009 TTTTCGGTTTGTTCAAAATAATTGAATATTCCTTTAGAATTTCACTCGTGTTTTATAAATTC
66 CTTCCGGTTTGTTCAAAATAATCAAATATTCCTTTAGAATTTCACTCGTGTTTTATAAATTC
* * * *
48622071 TAAAGCAAGGCAATGTTCAATGTTTGGAAATTCGAGGAATCGTGCCCTACCGTGCTGAGTTTC
1 TAAAACAAGGCAATGTTCAATGTTTGGAAATTCGGGGAATCGTGCCCTATCGTGCTGGGTTTC
48622134 AGTTTTTTGT
Statistics
Matches: 172, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
126 28 0.16
127 143 0.83
128 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (127 bp):
TAAAACAAGGCAATGTTCAATGTTTGGAAATTCGGGGAATCGTGCCCTATCGTGCTGGGTTTCGA
CTTCCGGTTTGTTCAAAATAATCAAATATTCCTTTAGAATTTCACTCGTGTTTTATAAATTC
Found at i:48635341 original size:26 final size:26
Alignment explanation
Indices: 48635312--48635368 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
48635302 TCAGTCTGAA
*
48635312 AGAACTCCCAAGTGACTCGTTCTTTT
1 AGAACTCCCAAGTGACTCGTTCTTTC
48635338 AGAACTCCCAAGTGACTCGTTCTTTC
1 AGAACTCCCAAGTGACTCGTTCTTTC
48635364 AGAAC
1 AGAAC
48635369 CACTGATATC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (26 bp):
AGAACTCCCAAGTGACTCGTTCTTTC
Found at i:48637542 original size:40 final size:40
Alignment explanation
Indices: 48637483--48637690 Score: 209
Period size: 40 Copynumber: 5.2 Consensus size: 40
48637473 CAATTGAATG
* * * *
48637483 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * ** *
48637523 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
48637563 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
48637603 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * **
48637643 CTATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
48637683 ATATCCGG
1 ATATCCGG
48637691 TTGTATTCGA
Statistics
Matches: 140, Mismatches: 28, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 140 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
Found at i:48637621 original size:80 final size:80
Alignment explanation
Indices: 48637484--48637690 Score: 247
Period size: 80 Copynumber: 2.6 Consensus size: 80
48637474 AATTGAATGA
* * ** * * *
48637484 TATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATATCCGGGTTAAGACCCGAAGGCAA
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAA
*
48637549 TTGTGCTAG-CG-AC
66 TTGTGCAAGTCGTAC
* * *
48637562 TACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGC
1 T--ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGC
* *
48637627 ATTTGTGCAAGTCGTTC
64 AATTGTGCAAGTCGTAC
* *
48637644 TATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGG
48637691 TTGTATTCGA
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
78 1 0.01
80 104 0.95
81 2 0.02
82 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (80 bp):
TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAA
TTGTGCAAGTCGTAC
Found at i:48642012 original size:13 final size:13
Alignment explanation
Indices: 48641994--48642018 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48641984 ACAAATGATA
48641994 AAATTTTCACACG
1 AAATTTTCACACG
48642007 AAATTTTCACAC
1 AAATTTTCACAC
48642019 ATACATATCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:48644791 original size:12 final size:14
Alignment explanation
Indices: 48644756--48644791 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 14
48644746 TATACAAGTT
48644756 TGAAAAAAAAATTC
1 TGAAAAAAAAATTC
48644770 TG-AAAAAAAA-TC
1 TGAAAAAAAAATTC
48644782 -GAAAAAAAAA
1 TGAAAAAAAAA
48644792 ATGATTTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 1 0.05
12 10 0.48
13 8 0.38
14 2 0.10
ACGTcount: A:0.72, C:0.06, G:0.08, T:0.14
Consensus pattern (14 bp):
TGAAAAAAAAATTC
Found at i:48658184 original size:25 final size:25
Alignment explanation
Indices: 48658156--48658250 Score: 163
Period size: 25 Copynumber: 3.8 Consensus size: 25
48658146 CTCTTTTAAT
* *
48658156 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGGTA
*
48658181 AACTGGGGCAAATCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGGTA
48658206 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGGTA
48658231 AACTGGGGCAAAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
48658251 AGCACTTCCT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 66 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.26
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGGTA
Found at i:48658186 original size:50 final size:50
Alignment explanation
Indices: 48658143--48658250 Score: 148
Period size: 50 Copynumber: 2.2 Consensus size: 50
48658133 CTGGAGGCCT
*
48658143 AGCCTCTTTT-AAT-AACTGGGGCAAAGCCCTTTTTGATAAACTGGGGCAA
1 AGCC-CTTTTCAATAAACTGGGGCAAAGCCCTTTTCGATAAACTGGGGCAA
* ** *
48658192 ATCCCTTTTCGGTAAACTGGGGCAAAGCCCTTTTCGGTAAACTGGGGCAA
1 AGCCCTTTTCAATAAACTGGGGCAAAGCCCTTTTCGATAAACTGGGGCAA
48658242 AGCCCTTTT
1 AGCCCTTTT
48658251 AGCACTTCCT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
48 5 0.10
49 4 0.08
50 42 0.82
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (50 bp):
AGCCCTTTTCAATAAACTGGGGCAAAGCCCTTTTCGATAAACTGGGGCAA
Found at i:48658513 original size:27 final size:27
Alignment explanation
Indices: 48658456--48658515 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
48658446 GGGCAAAATG
* *
48658456 GTAATTTTACCCCACAAGGGTATCTCG
1 GTAATTCTACCCCACAAGGGTATCTCA
* * * *
48658483 GTAATTCTACCCTACAGGGGTATTTTA
1 GTAATTCTACCCCACAAGGGTATCTCA
48658510 GTAATT
1 GTAATT
48658516 TTTTAAATCG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (27 bp):
GTAATTCTACCCCACAAGGGTATCTCA
Found at i:48658530 original size:27 final size:26
Alignment explanation
Indices: 48658500--48658712 Score: 167
Period size: 27 Copynumber: 7.9 Consensus size: 26
48658490 TACCCTACAG
**
48658500 GGGTATTTTAGTAATTTTTTAAATCGA
1 GGGTATTTTAGTAATTTTACAAA-CGA
*** * * *
48658527 GGGTAAAATAATAATTCTGTA-AAATGG
1 GGGTATTTTAGTAATT-T-TACAAACGA
* * *
48658554 GGGTACTTTGGTAATTTTACAAGTCGA
1 GGGTATTTTAGTAATTTTACAA-ACGA
* *
48658581 GGGTATTTTAGTAATTTCACAAACCA
1 GGGTATTTTAGTAATTTTACAAACGA
* *
48658607 GGGGTATTTTGGTAATTTTACAAACTA
1 -GGGTATTTTAGTAATTTTACAAACGA
* *
48658634 GGGGTATTTTGGTAATTTTACAAACTA
1 -GGGTATTTTAGTAATTTTACAAACGA
* * *
48658661 GTGGTATTTTGGTAATTTTATAAACCAA
1 G-GGTATTTTAGTAATTTTACAAA-CGA
48658689 GGGTATTTTAGTAATTTTACAAAC
1 GGGTATTTTAGTAATTTTACAAAC
48658713 CAAGGGTAAT
Statistics
Matches: 152, Mismatches: 27, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
25 2 0.01
26 7 0.05
27 135 0.89
28 7 0.05
29 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.39
Consensus pattern (26 bp):
GGGTATTTTAGTAATTTTACAAACGA
Found at i:48658713 original size:27 final size:27
Alignment explanation
Indices: 48658554--48658729 Score: 219
Period size: 27 Copynumber: 6.5 Consensus size: 27
48658544 TGTAAAATGG
* ** *
48658554 GGGTACTTTGGTAATTTTACAAGTCGA
1 GGGTATTTTGGTAATTTTACAAACCAA
* * *
48658581 GGGTATTTTAGTAATTTCACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAA
* *
48658608 GGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACCAA
*
48658635 GGGTATTTTGGTAATTTTACAAA-CTA
1 GGGTATTTTGGTAATTTTACAAACCAA
*
48658661 GTGGTATTTTGGTAATTTTATAAACCAA
1 G-GGTATTTTGGTAATTTTACAAACCAA
*
48658689 GGGTATTTTAGTAATTTTACAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
*
48658716 GGGTAATTTGGTAA
1 GGGTATTTTGGTAA
48658730 ACTAAAGTAT
Statistics
Matches: 128, Mismatches: 19, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
26 1 0.01
27 124 0.97
28 3 0.02
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACCAA
Found at i:48661602 original size:2 final size:2
Alignment explanation
Indices: 48661595--48661626 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
48661585 TTACACATAC
48661595 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48661627 TGTATATTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48665049 original size:20 final size:20
Alignment explanation
Indices: 48665024--48665061 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
48665014 GTTTATTCGC
*
48665024 GATTTTCAATATTTTGTAAA
1 GATTTTCAAAATTTTGTAAA
*
48665044 GATTTTTAAAATTTTGTA
1 GATTTTCAAAATTTTGTA
48665062 TTTGGATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.53
Consensus pattern (20 bp):
GATTTTCAAAATTTTGTAAA
Found at i:48673931 original size:20 final size:20
Alignment explanation
Indices: 48673908--48673978 Score: 99
Period size: 20 Copynumber: 3.5 Consensus size: 20
48673898 AATGAGCTGA
48673908 AACGAGCTAAAATCAAGCTC
1 AACGAGCTAAAATCAAGCTC
48673928 AACGAGCTAAAATCAAGCTC
1 AACGAGCTAAAATCAAGCTC
* *
48673948 AACAAGCTGAAA-CAAGCTC
1 AACGAGCTAAAATCAAGCTC
*
48673967 AAGTGAGCTAAA
1 AA-CGAGCTAAA
48673979 TGGAGCTTGG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
19 9 0.20
20 36 0.80
ACGTcount: A:0.46, C:0.23, G:0.17, T:0.14
Consensus pattern (20 bp):
AACGAGCTAAAATCAAGCTC
Found at i:48675501 original size:19 final size:19
Alignment explanation
Indices: 48675477--48675516 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
48675467 AGCTCCCATG
48675477 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
* *
48675496 TAGCTCGAGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
48675515 TA
1 TA
48675517 TCAGCTCACG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.35, G:0.15, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:48683258 original size:19 final size:19
Alignment explanation
Indices: 48683234--48683273 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
48683224 AGCTCCCATG
*
48683234 TAGCTCCACACCAGTTCAT
1 TAGCTCCACACCAGCTCAT
* *
48683253 TAGCTCGAGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
48683272 TA
1 TA
48683274 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.25
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:48683770 original size:14 final size:14
Alignment explanation
Indices: 48683751--48683795 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
48683741 AACTCATCTT
*
48683751 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
48683765 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
48683778 AATTTAATTTAATG
1 AGTTTAATTTAATG
48683792 AGTT
1 AGTT
48683796 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:48684808 original size:29 final size:29
Alignment explanation
Indices: 48684775--48684834 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
48684765 ATAACCAAAC
*
48684775 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
48684804 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
48684833 CT
1 CT
48684835 TTGAATCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:48684827 original size:15 final size:15
Alignment explanation
Indices: 48684781--48684828 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
48684771 AAACCTACAA
*
48684781 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
48684796 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
48684810 AAACTTCATATCCAT
1 AAACTTCATATCCAT
48684825 AAAC
1 AAAC
48684829 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:48686115 original size:13 final size:13
Alignment explanation
Indices: 48686086--48686125 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
48686076 AACTGAACAA
*
48686086 TTTGTTCATATCCC
1 TTTGTTCCTA-CCC
48686100 TTTGTTCCTACCC
1 TTTGTTCCTACCC
48686113 TTTCGTTCCTACC
1 TTT-GTTCCTACC
48686126 ATTCCGTTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 6 0.25
14 18 0.75
ACGTcount: A:0.10, C:0.35, G:0.07, T:0.47
Consensus pattern (13 bp):
TTTGTTCCTACCC
Found at i:48686736 original size:6 final size:6
Alignment explanation
Indices: 48686714--48686788 Score: 66
Period size: 6 Copynumber: 12.3 Consensus size: 6
48686704 TATAGGCTTC
*
48686714 ATTCTG ATTCT- AGTTCTG ATTCTG ATTCTG -TCACCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG A-TTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG
* *
48686763 ATTCTA ATTTTG ATTCT- AGTTCTG AT
1 ATTCTG ATTCTG ATTCTG A-TTCTG AT
48686789 AATGTTTCTT
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
5 3 0.05
6 47 0.84
7 5 0.09
8 1 0.02
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:48695581 original size:27 final size:26
Alignment explanation
Indices: 48695523--48695585 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 26
48695513 ACAGCTGAAT
*
48695523 TTTAATATGTCTTAGTTCATACATGT
1 TTTAATATGTCTTAGTTCATACATGA
* * *
48695549 TGTTAATTTGTCTTAGTTTATTGCATGA
1 T-TTAATATGTCTTAGTTCA-TACATGA
48695577 TTTAA-ATGT
1 TTTAATATGT
48695586 GTCTTTGAGC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
26 4 0.13
27 20 0.67
28 6 0.20
ACGTcount: A:0.25, C:0.08, G:0.14, T:0.52
Consensus pattern (26 bp):
TTTAATATGTCTTAGTTCATACATGA
Found at i:48695672 original size:18 final size:20
Alignment explanation
Indices: 48695634--48695675 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
48695624 GTATAACTGA
*
48695634 ATTTATTGTGTCTCAATTTG
1 ATTTAATGTGTCTCAATTTG
48695654 ATTTAATGTGT-TC-ATTTG
1 ATTTAATGTGTCTCAATTTG
48695672 ATTT
1 ATTT
48695676 GTGCAGTAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 2 0.10
20 10 0.48
ACGTcount: A:0.21, C:0.07, G:0.14, T:0.57
Consensus pattern (20 bp):
ATTTAATGTGTCTCAATTTG
Found at i:48700234 original size:24 final size:24
Alignment explanation
Indices: 48700207--48700278 Score: 117
Period size: 24 Copynumber: 3.0 Consensus size: 24
48700197 TAAAAAAAAA
*
48700207 AACCAGCAGCTCATTAAATTCGTC
1 AACCAGCAGCTCATTAAATCCGTC
* *
48700231 AACCAACAGCTCATTAAATCCATC
1 AACCAGCAGCTCATTAAATCCGTC
48700255 AACCAGCAGCTCATTAAATCCGTC
1 AACCAGCAGCTCATTAAATCCGTC
48700279 CAGGCATGCT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.36, C:0.32, G:0.10, T:0.22
Consensus pattern (24 bp):
AACCAGCAGCTCATTAAATCCGTC
Found at i:48703879 original size:46 final size:46
Alignment explanation
Indices: 48703812--48703986 Score: 192
Period size: 46 Copynumber: 3.8 Consensus size: 46
48703802 AACCCGCCCC
* * *
48703812 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTAGCATCCA
* * *
48703858 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAG-TTACA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATG-TTAGCATCCA
* * * ** *
48703904 TTTCA-CGAACTCGGACTCAACTCAACGAGTTCGAACATTTGCATCCA
1 --TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTAGCATCCA
*
48703951 TAAGTGAACTCGGACTCAACTCAACGAGTTCAGATG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATG
48703987 CTCAACCATC
Statistics
Matches: 103, Mismatches: 21, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
45 2 0.02
46 66 0.64
47 33 0.32
48 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTAGCATCCA
Found at i:48703924 original size:93 final size:93
Alignment explanation
Indices: 48703817--48703987 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
48703807 GCCCCTAAGT
****
48703817 GAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
48703882 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCAGATGCCTAGTTACATTTCAC
* *
48703910 GAACTCGGACTCAACTCAACGAGTTCGAACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
48703975 CGAGTTCAGATGC
66 CGAGTTCAGATGC
48703988 TCAACCATCC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCAGATGCCTAGTTACATTTCAC
Found at i:48704439 original size:30 final size:29
Alignment explanation
Indices: 48704405--48704463 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
48704395 ATTTAATACG
*
48704405 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTT-GAAAAATTACAATTTTGCCCCTA
* *
48704435 AACTTTGCATAATTACAATTTTGCCCCTA
1 AACTTTGAAAAATTACAATTTTGCCCCTA
48704464 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 20 0.77
30 6 0.23
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.36
Consensus pattern (29 bp):
AACTTTGAAAAATTACAATTTTGCCCCTA
Found at i:48709516 original size:19 final size:18
Alignment explanation
Indices: 48709469--48709516 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
48709459 GAATTAACAC
*
48709469 ATAATTAATTAAAATATA
1 ATAATTAATAAAAATATA
*
48709487 ACT-ATTCATAAAAATCATA
1 A-TAATTAATAAAAAT-ATA
48709506 ATAATTAATAA
1 ATAATTAATAA
48709517 TTAAATAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (18 bp):
ATAATTAATAAAAATATA
Found at i:48709743 original size:10 final size:10
Alignment explanation
Indices: 48709730--48709764 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
48709720 AAGCTCGGTT
48709730 GAGCTCAAAC
1 GAGCTCAAAC
*
48709740 GAGCTGAAAC
1 GAGCTCAAAC
*
48709750 GAGCTCAAAT
1 GAGCTCAAAC
48709760 GAGCT
1 GAGCT
48709765 GAGTTGAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.37, C:0.23, G:0.26, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:48709773 original size:20 final size:20
Alignment explanation
Indices: 48709727--48709774 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
48709717 AGTAAGCTCG
48709727 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
*** *
48709747 AACGAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
48709767 GTTGAGCT
1 GTTGAGCT
48709775 GGACAGAGCT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:48716249 original size:10 final size:10
Alignment explanation
Indices: 48716234--48716260 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
48716224 TAAGTTGAAG
48716234 TTGAGCTGAT
1 TTGAGCTGAT
48716244 TTGAGCTGAT
1 TTGAGCTGAT
48716254 TTGAGCT
1 TTGAGCT
48716261 TGAAGGAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.30, T:0.41
Consensus pattern (10 bp):
TTGAGCTGAT
Found at i:48716620 original size:13 final size:13
Alignment explanation
Indices: 48716602--48716626 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48716592 TGGTCATCAT
48716602 GGTGTGAACACAA
1 GGTGTGAACACAA
48716615 GGTGTGAACACA
1 GGTGTGAACACA
48716627 TGATCAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:48717195 original size:30 final size:30
Alignment explanation
Indices: 48717110--48717206 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
48717100 TAAACTAAAA
* * * *
48717110 TGAGCTAAGCTTTAGTTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCATGAGCTGAAGT
* * * * *
48717140 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCATGAGCTGAAGT
*
48717170 TGAGCTAAGGTTTAGCTCATGAGCTGAA-T
1 TGAGCTAAGATTTAGCTCATGAGCTGAAGT
48717199 ATGAGCTA
1 -TGAGCTA
48717207 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCATGAGCTGAAGT
Found at i:48721088 original size:21 final size:20
Alignment explanation
Indices: 48721052--48721099 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
48721042 ATCAGCTCAC
*
48721052 TTGAGCTTGTTTTAGCTCGT
1 TTGAGCTTGATTTAGCTCGT
48721072 TTGAGCTTGAATTTAGCTCGT
1 TTGAGCTTG-ATTTAGCTCGT
*
48721093 TTCAGCT
1 TTGAGCT
48721100 CATTCCTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.15, C:0.17, G:0.23, T:0.46
Consensus pattern (20 bp):
TTGAGCTTGATTTAGCTCGT
Found at i:48721343 original size:13 final size:13
Alignment explanation
Indices: 48721325--48721349 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48721315 AATAGTTGCG
48721325 TGTTATTTAATTA
1 TGTTATTTAATTA
48721338 TGTTATTTAATT
1 TGTTATTTAATT
48721350 TTGTAGGTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:48723554 original size:19 final size:19
Alignment explanation
Indices: 48723523--48723560 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
48723513 AATGAAATCG
48723523 AGAGAAGAAACAAAGGAAAA
1 AGAGAAGAAACAAA-GAAAA
48723543 AGAGAA-AAACAAAGAAAA
1 AGAGAAGAAACAAAGAAAA
48723561 GAAAATGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 7 0.39
20 6 0.33
ACGTcount: A:0.74, C:0.05, G:0.21, T:0.00
Consensus pattern (19 bp):
AGAGAAGAAACAAAGAAAA
Found at i:48725777 original size:10 final size:10
Alignment explanation
Indices: 48725764--48725809 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
48725754 AGCTCACTTG
48725764 AGCTCGTTTT
1 AGCTCGTTTT
*
48725774 AGCTCGTTTG
1 AGCTCGTTTT
*
48725784 AGCTCGAATTT
1 AGCTCG-TTTT
*
48725795 AGCTCGTTTC
1 AGCTCGTTTT
48725805 AGCTC
1 AGCTC
48725810 ATTCCTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 22 0.73
11 8 0.27
ACGTcount: A:0.15, C:0.24, G:0.22, T:0.39
Consensus pattern (10 bp):
AGCTCGTTTT
Found at i:48725797 original size:21 final size:20
Alignment explanation
Indices: 48725761--48725809 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
48725751 ATCAGCTCAC
*
48725761 TTGAGCTCGTTTTAGCTCGT
1 TTGAGCTCGATTTAGCTCGT
48725781 TTGAGCTCGAATTTAGCTCGT
1 TTGAGCTCG-ATTTAGCTCGT
*
48725802 TTCAGCTC
1 TTGAGCTC
48725810 ATTCCTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.41
Consensus pattern (20 bp):
TTGAGCTCGATTTAGCTCGT
Found at i:48728409 original size:11 final size:12
Alignment explanation
Indices: 48728377--48728407 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
48728367 TTGAGAGAAC
48728377 TTGAAAAAGCCT
1 TTGAAAAAGCCT
48728389 TTGAAAAAGCCT
1 TTGAAAAAGCCT
48728401 TTGAAAA
1 TTGAAAA
48728408 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:48728418 original size:12 final size:12
Alignment explanation
Indices: 48728410--48728434 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
48728400 TTTGAAAAGC
48728410 AAAAAGAAAATG
1 AAAAAGAAAATG
48728422 AAAAAGAAAATG
1 AAAAAGAAAATG
48728434 A
1 A
48728435 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:48728431 original size:18 final size:18
Alignment explanation
Indices: 48728404--48728459 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
48728394 AAAGCCTTTG
*
48728404 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAATGAAAATGA
* *
48728423 AAAAGAAAATGAGATTGA
1 AAAAGAAAATGAAAATGA
*
48728441 AAAAGAGAATGAAAA-GA
1 AAAAGAAAATGAAAATGA
48728458 AA
1 AA
48728460 TTTGAGGGTG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
17 4 0.13
18 22 0.71
19 5 0.16
ACGTcount: A:0.70, C:0.02, G:0.20, T:0.09
Consensus pattern (18 bp):
AAAAGAAAATGAAAATGA
Found at i:48728444 original size:30 final size:31
Alignment explanation
Indices: 48728410--48728491 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
48728400 TTTGAAAAGC
*
48728410 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
48728440 AAAAAGAGAATG-AAAAGAAATTTGAGGGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
48728470 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
48728492 TGAAACAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 8 0.18
30 27 0.61
31 9 0.20
ACGTcount: A:0.63, C:0.00, G:0.23, T:0.13
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:48734129 original size:13 final size:13
Alignment explanation
Indices: 48734111--48734135 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48734101 TAACCTACAA
48734111 AATTAAATAACAT
1 AATTAAATAACAT
48734124 AATTAAATAACA
1 AATTAAATAACA
48734136 CACAACTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (13 bp):
AATTAAATAACAT
Found at i:48734393 original size:10 final size:10
Alignment explanation
Indices: 48734360--48734408 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
48734350 AAAAAGGAAT
*
48734360 GAGCTGAAAC
1 GAGCTCAAAC
48734370 GAGCT-AAATTC
1 GAGCTCAAA--C
48734381 GAGCTCAAAC
1 GAGCTCAAAC
*
48734391 GAGCTAAAAC
1 GAGCTCAAAC
48734401 GAGCTCAA
1 GAGCTCAA
48734409 GTGAGCTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 3 0.09
10 22 0.65
11 6 0.18
12 3 0.09
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:48734415 original size:20 final size:21
Alignment explanation
Indices: 48734360--48734408 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
48734350 AAAAAGGAAT
* *
48734360 GAGCTGAAACGAGCTAAATTC
1 GAGCTCAAACGAGCTAAATAC
48734381 GAGCTCAAACGAGCTAAA-AC
1 GAGCTCAAACGAGCTAAATAC
48734401 GAGCTCAA
1 GAGCTCAA
48734409 GTGAGCTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.14
Consensus pattern (21 bp):
GAGCTCAAACGAGCTAAATAC
Found at i:48736534 original size:30 final size:29
Alignment explanation
Indices: 48736479--48736542 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
48736469 TTTTTCAATT
* *
48736479 TCTTTTTCACTCTCAAATTTCTTTTCGTTC
1 TCTTTTTCAATCTCAAATCTCTTTTC-TTC
*
48736509 TCTTTTTCAATCTC-AATCTCATTTTCTTT
1 TCTTTTTCAATCTCAAATCTC-TTTTCTTC
48736538 TCTTT
1 TCTTT
48736543 GTTTTTCTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 12 0.40
30 18 0.60
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (29 bp):
TCTTTTTCAATCTCAAATCTCTTTTCTTC
Found at i:48736558 original size:18 final size:19
Alignment explanation
Indices: 48736535--48736571 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
48736525 TCTCATTTTC
48736535 TTTTCTTTGTTT-TTCTCT
1 TTTTCTTTGTTTCTTCTCT
48736553 TTTTCTTTGTTTCTTCTCT
1 TTTTCTTTGTTTCTTCTCT
48736572 CGATTTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.00, C:0.19, G:0.05, T:0.76
Consensus pattern (19 bp):
TTTTCTTTGTTTCTTCTCT
Found at i:48738750 original size:13 final size:13
Alignment explanation
Indices: 48738732--48738756 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48738722 TAACCTACAA
48738732 AATTAAATAACAT
1 AATTAAATAACAT
48738745 AATTAAATAACA
1 AATTAAATAACA
48738757 CACAACTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (13 bp):
AATTAAATAACAT
Found at i:48739014 original size:10 final size:10
Alignment explanation
Indices: 48738981--48739029 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
48738971 AAAAAGGAAT
*
48738981 GAGCTGAAAC
1 GAGCTCAAAC
48738991 GAGCT-AAATTC
1 GAGCTCAAA--C
48739002 GAGCTCAAAC
1 GAGCTCAAAC
*
48739012 GAGCTAAAAC
1 GAGCTCAAAC
48739022 GAGCTCAA
1 GAGCTCAA
48739030 GTGAGCTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 3 0.09
10 22 0.65
11 6 0.18
12 3 0.09
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:48739036 original size:20 final size:21
Alignment explanation
Indices: 48738981--48739029 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
48738971 AAAAAGGAAT
* *
48738981 GAGCTGAAACGAGCTAAATTC
1 GAGCTCAAACGAGCTAAATAC
48739002 GAGCTCAAACGAGCTAAA-AC
1 GAGCTCAAACGAGCTAAATAC
48739022 GAGCTCAA
1 GAGCTCAA
48739030 GTGAGCTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.14
Consensus pattern (21 bp):
GAGCTCAAACGAGCTAAATAC
Found at i:48739462 original size:17 final size:17
Alignment explanation
Indices: 48739442--48739479 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
48739432 CATTTTTTCC
*
48739442 TTTCTTTT-TTTTTCATT
1 TTTCTTTTATTTCTC-TT
48739459 TTTCTTTTATTTCTCTT
1 TTTCTTTTATTTCTCTT
48739476 TTTC
1 TTTC
48739480 AATCTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTCTTTTATTTCTCTT
Done.