Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 145 of 206
Found at i:44370487 original size:40 final size:40
Alignment explanation
Indices: 44370384--44370487 Score: 136
Period size: 40 Copynumber: 2.6 Consensus size: 40
44370374 TATCTACATT
* * * * * *
44370384 ACTGGTGGCTTTTCCACATTATTAGCAGCTTTTCTGTAAC
1 ACTGGTGGCTTGTCCACATTACTGGCAACTTGTCTGCAAC
*
44370424 ACTAGTGGCTTGTCCACATTACTGGCAACTTGTCTGCAAC
1 ACTGGTGGCTTGTCCACATTACTGGCAACTTGTCTGCAAC
*
44370464 ACTGGTGGCCTGTCCACATTACTG
1 ACTGGTGGCTTGTCCACATTACTG
44370488 CAGTTTATCT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.34
Consensus pattern (40 bp):
ACTGGTGGCTTGTCCACATTACTGGCAACTTGTCTGCAAC
Found at i:44380432 original size:20 final size:20
Alignment explanation
Indices: 44380409--44380465 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
44380399 CAGCTTCCCA
* *
44380409 AGCTCATTTCAGCTCCAATC
1 AGCTCATTTAAGCTCAAATC
* * *
44380429 AGCTCACTTGAGCTTAAATC
1 AGCTCATTTAAGCTCAAATC
*
44380449 AGCTCGTTTAAGCTCAA
1 AGCTCATTTAAGCTCAA
44380466 TTTAAATTAT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (20 bp):
AGCTCATTTAAGCTCAAATC
Found at i:44393172 original size:19 final size:19
Alignment explanation
Indices: 44393148--44393198 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
44393138 TTCCATTAGC
44393148 TTAGATTTTTTCTTTAGGT
1 TTAGATTTTTTCTTTAGGT
* *
44393167 TTAGATTCTATCTTTAGGT
1 TTAGATTTTTTCTTTAGGT
*
44393186 TTAGATTTGTTCT
1 TTAGATTTTTTCT
44393199 CTTGTTTTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.18, C:0.08, G:0.16, T:0.59
Consensus pattern (19 bp):
TTAGATTTTTTCTTTAGGT
Found at i:44402205 original size:12 final size:12
Alignment explanation
Indices: 44402190--44402217 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
44402180 TGACAGTAAA
44402190 ATTTAAAAACCT
1 ATTTAAAAACCT
44402202 ATTTAAAAACCT
1 ATTTAAAAACCT
44402214 ATTT
1 ATTT
44402218 CTTTTACTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.39
Consensus pattern (12 bp):
ATTTAAAAACCT
Found at i:44417365 original size:12 final size:12
Alignment explanation
Indices: 44417353--44417392 Score: 66
Period size: 11 Copynumber: 3.5 Consensus size: 12
44417343 TTTCTTCAAT
44417353 TTTCTCTCT-AA
1 TTTCTCTCTAAA
44417364 TTTCTCTC-AAA
1 TTTCTCTCTAAA
44417375 TTTCTCTCTAAA
1 TTTCTCTCTAAA
44417387 TTTCTC
1 TTTCTC
44417393 AAAACTCTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.20, C:0.28, G:0.00, T:0.53
Consensus pattern (12 bp):
TTTCTCTCTAAA
Found at i:44417373 original size:22 final size:23
Alignment explanation
Indices: 44417342--44417392 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
44417332 TTCGTACACT
*
44417342 ATTTCT-TCAATTTTCTCTCT-A
1 ATTTCTCTCAAATTTCTCTCTAA
44417363 ATTTCTCTCAAATTTCTCTCTAA
1 ATTTCTCTCAAATTTCTCTCTAA
44417386 ATTTCTC
1 ATTTCTC
44417393 AAAACTCTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 6 0.22
22 13 0.48
23 8 0.30
ACGTcount: A:0.22, C:0.25, G:0.00, T:0.53
Consensus pattern (23 bp):
ATTTCTCTCAAATTTCTCTCTAA
Found at i:44417585 original size:21 final size:20
Alignment explanation
Indices: 44417559--44417597 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
44417549 TAAGGGTTAA
44417559 TTTTTCAATATTATTTAATAT
1 TTTTTCAAT-TTATTTAATAT
*
44417580 TTTTTCCATTTATTTAAT
1 TTTTTCAATTTATTTAAT
44417598 TTTAATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTTCAATTTATTTAATAT
Found at i:44419176 original size:18 final size:18
Alignment explanation
Indices: 44419153--44419195 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
44419143 TGCTAGGTCC
*
44419153 GTATCCTAGCCCATATAT
1 GTATCCTAACCCATATAT
*
44419171 GTATCCTAACCCTTATAT
1 GTATCCTAACCCATATAT
*
44419189 GTTTCCT
1 GTATCCT
44419196 TTTCCCAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.23, C:0.28, G:0.09, T:0.40
Consensus pattern (18 bp):
GTATCCTAACCCATATAT
Found at i:44419696 original size:93 final size:92
Alignment explanation
Indices: 44419537--44419727 Score: 346
Period size: 93 Copynumber: 2.1 Consensus size: 92
44419527 ATTGATTTTT
* *
44419537 TTAATATATTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAAAAGTTGTTTTTAATA
1 TTAATATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAATAAAAGTTGTTTGTAATA
44419602 TTTTAATAGTAATTTATTTTTTATATTC
66 TTTTAATAGTAATTTA-TTTTTATATTC
44419630 TTAATATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAATAAAAGTTGTTTGTAATA
1 TTAATATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAATAAAAGTTGTTTGTAATA
*
44419695 TTTTAATAGTAATTTATTTTTATATTT
66 TTTTAATAGTAATTTATTTTTATATTC
44419722 TTAATA
1 TTAATA
44419728 AAATAGAAGT
Statistics
Matches: 95, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
92 16 0.17
93 79 0.83
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (92 bp):
TTAATATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAATAAAAGTTGTTTGTAATA
TTTTAATAGTAATTTATTTTTATATTC
Found at i:44423080 original size:127 final size:126
Alignment explanation
Indices: 44422815--44423213 Score: 568
Period size: 126 Copynumber: 3.2 Consensus size: 126
44422805 TAAGGCCAAA
* * *
44422815 CAGGAACTACTGTAGAAAAAGAACATCCACGTGAGAGCCTTTTTCAGTAATTTTGCTGACAGTGC
1 CAGGAACTACTGTAGAAAAAGAGCATCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
* * * *
44422880 AT-TCTACTTGAAGCATTTTTGACACTATTTGTTCAGAACTGTCTTCTTAAAATTATTTTTT
66 ATCT-TGCTTGAAGCATTTTTTACAATATTTGTTCAGAACCGTCTTCTTAAAATTATTTTTT
* * *
44422941 CAGGGACTACTGTAGAAAAAGAGCATCCACGTGGGAGCTTTTTTTAGTAATTTTGCTGACAGTAC
1 CAGGAACTACTGTAGAAAAAGAGCATCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
* *
44423006 ATCTTGCTTGAAGCTTTTTTTTACAATATTTGTTTAGAACCGTCTTCTTAAAATTATTTTTT
66 ATCTTGCTTGAAGC-ATTTTTTACAATATTTGTTCAGAACCGTCTTCTTAAAATTATTTTTT
* * *
44423068 CAGGAACTACTGTAGAAAAAGAGCGTCCACGTAGGAGCTTTTTTCAGTAATTTTGCTGACAGTGT
1 CAGGAACTACTGTAGAAAAAGAGCATCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
* * * *
44423133 ATCTTGCTTGAAGCGTTTTTTACATTATCTT-TTCAGAATCGTCTTCTCAAAATTATTTTTT
66 ATCTTGCTTGAAGCATTTTTTACAATAT-TTGTTCAGAACCGTCTTCTTAAAATTATTTTTT
* *
44423194 CAGAAATTACTGTAGAAAAA
1 CAGGAACTACTGTAGAAAAA
44423214 AAAACAAAAT
Statistics
Matches: 245, Mismatches: 25, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
126 127 0.52
127 118 0.48
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (126 bp):
CAGGAACTACTGTAGAAAAAGAGCATCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
ATCTTGCTTGAAGCATTTTTTACAATATTTGTTCAGAACCGTCTTCTTAAAATTATTTTTT
Found at i:44423343 original size:34 final size:33
Alignment explanation
Indices: 44423263--44423388 Score: 94
Period size: 33 Copynumber: 3.8 Consensus size: 33
44423253 CCAAACACAA
** * *
44423263 ATTTA-TTTTTAAAAAAACTAAACCATAATTTA
1 ATTTATTTTTTAAAAACCCTAAACCCTAATTTT
*
44423295 ATTAATTTTCTTAAAAACCCTAAACCCTAATTTT
1 ATTTATTTT-TTAAAAACCCTAAACCCTAATTTT
* * * * *
44423329 ATTTAGTTATTT-AAAACCCAAAAACCTAGTTTA
1 ATTTA-TTTTTTAAAAACCCTAAACCCTAATTTT
* *
44423362 ATTAATTTTTTTAAAAAACTCTAAACC
1 ATTTA-TTTTTT-AAAAACCCTAAACC
44423389 TACCAAAAAT
Statistics
Matches: 72, Mismatches: 17, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
32 4 0.06
33 29 0.40
34 26 0.36
35 13 0.18
ACGTcount: A:0.44, C:0.15, G:0.02, T:0.40
Consensus pattern (33 bp):
ATTTATTTTTTAAAAACCCTAAACCCTAATTTT
Found at i:44423375 original size:33 final size:33
Alignment explanation
Indices: 44423282--44423377 Score: 102
Period size: 33 Copynumber: 2.8 Consensus size: 33
44423272 TAAAAAAACT
* *
44423282 AAACCATAATTTAATTAATTTTCTTAAAAACCCTA
1 AAACC-TAATTTAATTAATTTT-TTTAAAACCCAA
* * * * *
44423317 AACCCTAATTTTATTTAGTTATTTAAAACCCAA
1 AAACCTAATTTAATTAATTTTTTTAAAACCCAA
*
44423350 AAACCTAGTTTAATTAATTTTTTTAAAA
1 AAACCTAATTTAATTAATTTTTTTAAAA
44423378 AACTCTAAAC
Statistics
Matches: 48, Mismatches: 13, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
33 32 0.67
34 12 0.25
35 4 0.08
ACGTcount: A:0.43, C:0.15, G:0.02, T:0.41
Consensus pattern (33 bp):
AAACCTAATTTAATTAATTTTTTTAAAACCCAA
Found at i:44423390 original size:34 final size:33
Alignment explanation
Indices: 44423268--44423390 Score: 113
Period size: 34 Copynumber: 3.6 Consensus size: 33
44423258 CACAAATTTA
**
44423268 TTTTTAAAAAAACTAAACCATAATTTAATTAATT
1 TTTTTAAAAACCCTAAACC-TAATTTAATTAATT
* * * *
44423302 TTCTTAAAAACCCTAAACCCTAATTTTATTTAGT
1 TTTTTAAAAACCCTAAA-CCTAATTTAATTAATT
* * *
44423336 TATTT-AAAACCCAAAAACCTAGTTTAATTAATT
1 TTTTTAAAAACCC-TAAACCTAATTTAATTAATT
*
44423369 TTTTTAAAAAACTCTAAACCTA
1 TTTTT-AAAAACCCTAAACCTA
44423391 CCAAAAATCC
Statistics
Matches: 69, Mismatches: 16, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
33 23 0.33
34 38 0.55
35 8 0.12
ACGTcount: A:0.44, C:0.15, G:0.02, T:0.39
Consensus pattern (33 bp):
TTTTTAAAAACCCTAAACCTAATTTAATTAATT
Found at i:44425669 original size:13 final size:13
Alignment explanation
Indices: 44425651--44425713 Score: 81
Period size: 13 Copynumber: 4.8 Consensus size: 13
44425641 TTAGCTTCTC
*
44425651 TTTTTCAGAAGTG
1 TTTTTCAAAAGTG
*
44425664 TTTTTCAAAAGTA
1 TTTTTCAAAAGTG
44425677 TTTTTCAAAAGTG
1 TTTTTCAAAAGTG
*
44425690 TTTTTCAAAAATG
1 TTTTTCAAAAGTG
* *
44425703 CTTTTGAAAAG
1 TTTTTCAAAAG
44425714 CCAAAAATTT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 43 1.00
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.44
Consensus pattern (13 bp):
TTTTTCAAAAGTG
Found at i:44427967 original size:13 final size:13
Alignment explanation
Indices: 44427927--44427957 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
44427917 CATGTATATA
44427927 TTCATATAACCAT
1 TTCATATAACCAT
44427940 TTCATATAACCAT
1 TTCATATAACCAT
44427953 TTCAT
1 TTCAT
44427958 TTACACATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (13 bp):
TTCATATAACCAT
Found at i:44431133 original size:41 final size:41
Alignment explanation
Indices: 44431088--44431167 Score: 97
Period size: 41 Copynumber: 2.0 Consensus size: 41
44431078 ATACATCGGT
* * * *
44431088 ACAAATACTACCATGCTCGAAGCCTAATATAATACACCGAC
1 ACAAAGACTACCAGGCACAAAGCCTAATATAATACACCGAC
* * *
44431129 ACAAAGCCTACTAGGCACAAAGCCTGATATAATACACCG
1 ACAAAGACTACCAGGCACAAAGCCTAATATAATACACCG
44431168 GAACGAAGCC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.41, C:0.29, G:0.12, T:0.17
Consensus pattern (41 bp):
ACAAAGACTACCAGGCACAAAGCCTAATATAATACACCGAC
Found at i:44431177 original size:41 final size:41
Alignment explanation
Indices: 44431108--44431272 Score: 160
Period size: 41 Copynumber: 4.1 Consensus size: 41
44431098 CCATGCTCGA
* *
44431108 AGCCTAATATAATACACC-GACACAAAGCCTACTAGGCACAA
1 AGCCTGATATAATACACCGGA-ACAAAGCCTACTAGGCACAG
* * *
44431149 AGCCTGATATAATACACCGGAACGAAGCCGACT-GTACACAG
1 AGCCTGATATAATACACCGGAACAAAGCCTACTAG-GCACAG
** * **
44431190 AGCCTGATATAATACACTAGCACAAAGCCTGTTAGGCACAG
1 AGCCTGATATAATACACCGGAACAAAGCCTACTAGGCACAG
* * *
44431231 AGCCTGA-AT-AT-CACCGGCACAAAGCTTGCTAGGCACAG
1 AGCCTGATATAATACACCGGAACAAAGCCTACTAGGCACAG
44431269 AGCC
1 AGCC
44431273 CAAATATCAC
Statistics
Matches: 104, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
38 27 0.26
39 2 0.02
40 3 0.03
41 69 0.66
42 3 0.03
ACGTcount: A:0.37, C:0.28, G:0.19, T:0.16
Consensus pattern (41 bp):
AGCCTGATATAATACACCGGAACAAAGCCTACTAGGCACAG
Found at i:44436886 original size:41 final size:41
Alignment explanation
Indices: 44436837--44437113 Score: 157
Period size: 41 Copynumber: 7.0 Consensus size: 41
44436827 GGCATACTCG
* *
44436837 AAGCCTGATATAATAC-TCCGGCACAAAGCTTACTAGGCATA
1 AAGCCTGATATAATACAT-CGGCACAAAGCCTACTAGGCACA
* * *
44436878 AAGGCTGATATAATACATCGGCACGAAGCCTGCTAGGCACA
1 AAGCCTGATATAATACATCGGCACAAAGCCTACTAGGCACA
* * * * * *
44436919 AATCCTGATATACTACA-CTGACACGAAGCCTGCTAGACACA
1 AAGCCTGATATAATACATC-GGCACAAAGCCTACTAGGCACA
* * *
44436960 GAGCCTGATATAATACA-CTGGCACAAAACCTGCTAGGCACA
1 AAGCCTGATATAATACATC-GGCACAAAGCCTACTAGGCACA
* * * * * **
44437001 GAGCC-CAAAT-AT-CA-CTGACACAAAGCTTGTTAGGCACA
1 AAGCCTGATATAATACATC-GGCACAAAGCCTACTAGGCACA
* * * *
44437039 GAGCCCGA-AT-AT-CACCAGCACAAAGCCTACTAGGCACA
1 AAGCCTGATATAATACATCGGCACAAAGCCTACTAGGCACA
* * * * *
44437077 GAGCCCGA-AT-AT-CACCGGCATAAAGCCTGCTAGGCAC
1 AAGCCTGATATAATACATCGGCACAAAGCCTACTAGGCAC
44437114 GGAGCTCGAA
Statistics
Matches: 200, Mismatches: 32, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
38 84 0.42
39 4 0.02
40 4 0.02
41 107 0.54
42 1 0.00
ACGTcount: A:0.35, C:0.28, G:0.19, T:0.17
Consensus pattern (41 bp):
AAGCCTGATATAATACATCGGCACAAAGCCTACTAGGCACA
Found at i:44437035 original size:38 final size:38
Alignment explanation
Indices: 44436903--44437163 Score: 263
Period size: 38 Copynumber: 6.7 Consensus size: 38
44436893 CATCGGCACG
* * * *
44436903 AAGCCTGCTAGGCACAAATCCTGATATACTACACTGACACG
1 AAGCCTGCTAGGCACAGAGCCCGA-ATA-T-CACTGACACA
* * *
44436944 AAGCCTGCTAGACACAGAGCCTGATATAATACACTGGCACA
1 AAGCCTGCTAGGCACAGAGCCCGA-AT-AT-CACTGACACA
* *
44436985 AAACCTGCTAGGCACAGAGCCCAAATATCACTGACACA
1 AAGCCTGCTAGGCACAGAGCCCGAATATCACTGACACA
* * *
44437023 AAGCTTGTTAGGCACAGAGCCCGAATATCAC-CAGCACA
1 AAGCCTGCTAGGCACAGAGCCCGAATATCACTGA-CACA
* * * *
44437061 AAGCCTACTAGGCACAGAGCCCGAATATCACCGGCATA
1 AAGCCTGCTAGGCACAGAGCCCGAATATCACTGACACA
* * **
44437099 AAGCCTGCTAGGCACGGAGCTCGAATATCACCAACACA
1 AAGCCTGCTAGGCACAGAGCCCGAATATCACTGACACA
*
44437137 AAGCCTGCTAGGCACGGAGCCCGAATA
1 AAGCCTGCTAGGCACAGAGCCCGAATA
44437164 ACGTTACGTT
Statistics
Matches: 189, Mismatches: 28, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
37 1 0.01
38 129 0.68
39 2 0.01
40 2 0.01
41 54 0.29
42 1 0.01
ACGTcount: A:0.35, C:0.30, G:0.20, T:0.15
Consensus pattern (38 bp):
AAGCCTGCTAGGCACAGAGCCCGAATATCACTGACACA
Found at i:44437136 original size:114 final size:117
Alignment explanation
Indices: 44436944--44437163 Score: 293
Period size: 114 Copynumber: 1.9 Consensus size: 117
44436934 CACTGACACG
* * *
44436944 AAGCCTGCTAGACACAGAGCCTGATATAATACACTGGCACAAAACCTGCTAGGCACAGAGCCCAA
1 AAGCCTACTAGACACAGAGCCCGATATAATACACCGGCACAAAACCTGCTAGGCACAGAGCCCAA
** * *
44437009 ATATCACTGACACAAAGCTTGTTAGGCACAGAGCCCGAATATCACCAGCACA
66 ATATCACCAACACAAAGCCTGCTAGGCACAGAGCCCGAATATCACCAGCACA
* * * * * *
44437061 AAGCCTACTAGGCACAGAGCCCGA-AT-AT-CACCGGCATAAAGCCTGCTAGGCACGGAGCTCGA
1 AAGCCTACTAGACACAGAGCCCGATATAATACACCGGCACAAAACCTGCTAGGCACAGAGCCCAA
*
44437123 ATATCACCAACACAAAGCCTGCTAGGCACGGAGCCCGAATA
66 ATATCACCAACACAAAGCCTGCTAGGCACAGAGCCCGAATA
44437164 ACGTTACGTT
Statistics
Matches: 89, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
114 64 0.72
115 2 0.02
116 2 0.02
117 21 0.24
ACGTcount: A:0.35, C:0.30, G:0.21, T:0.14
Consensus pattern (117 bp):
AAGCCTACTAGACACAGAGCCCGATATAATACACCGGCACAAAACCTGCTAGGCACAGAGCCCAA
ATATCACCAACACAAAGCCTGCTAGGCACAGAGCCCGAATATCACCAGCACA
Found at i:44443135 original size:147 final size:147
Alignment explanation
Indices: 44442909--44443356 Score: 776
Period size: 147 Copynumber: 3.0 Consensus size: 147
44442899 AGTTTAATAC
**
44442909 AAGGTTGGTTTCTTCTT--ATCTCTATAAGACTTTTTTAAGATTGTCCAAACATTCTTGAAATGA
1 AAGGTTGGTTT-TT-TTGCATCTCTGCAAGACTTTTTTAAGATTGTCCAAA-ATTCTTGAAATGA
44442972 ATCT-CATATACTGAGAAATCATCCATAAATACATCCAAGCCTTCTTCTAACATGTCAGCAAAAA
63 ATCTCCATATACTGAGAAATCATCCATAAATACATCCAAGCCTTCTTCTAACATGTCAGCAAAAA
44443036 TAGCCATCATACATCTCATA
128 TAGCCATCATACATCTCATA
44443056 AAGGTTGGTTTTTTTGCATCTCTGCAAGACTTTTTTAAGATTGTCCAAAATTCTTGAAATGAATC
1 AAGGTTGGTTTTTTTGCATCTCTGCAAGACTTTTTTAAGATTGTCCAAAATTCTTGAAATGAATC
*
44443121 TCCATATACTGAGAAATCATCCGTAAATACATCCAAGCCTTCTTCTAACATGTCAGCAAAAATAG
66 TCCATATACTGAGAAATCATCCATAAATACATCCAAGCCTTCTTCTAACATGTCAGCAAAAATAG
44443186 CCATCATACATCTCATA
131 CCATCATACATCTCATA
44443203 AAGGTTGGTTTTTTTGCATCTCTGCAAGACTTTTTTAAGATTGTCCAAAATTCTTGAAATGAATC
1 AAGGTTGGTTTTTTTGCATCTCTGCAAGACTTTTTTAAGATTGTCCAAAATTCTTGAAATGAATC
*
44443268 TCCATATACTGAGAAATCATCCATAAATACATCCAAGCCTTCTTCTAACATGTCAACAAAAATAG
66 TCCATATACTGAGAAATCATCCATAAATACATCCAAGCCTTCTTCTAACATGTCAGCAAAAATAG
** *
44443333 CTGTTATACATCTCATA
131 CCATCATACATCTCATA
*
44443350 GAGGTTG
1 AAGGTTG
44443357 CTGGGGCATT
Statistics
Matches: 289, Mismatches: 9, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
145 2 0.01
146 19 0.07
147 268 0.93
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (147 bp):
AAGGTTGGTTTTTTTGCATCTCTGCAAGACTTTTTTAAGATTGTCCAAAATTCTTGAAATGAATC
TCCATATACTGAGAAATCATCCATAAATACATCCAAGCCTTCTTCTAACATGTCAGCAAAAATAG
CCATCATACATCTCATA
Found at i:44446972 original size:38 final size:38
Alignment explanation
Indices: 44446930--44447032 Score: 170
Period size: 38 Copynumber: 2.7 Consensus size: 38
44446920 ACTACTATAG
*
44446930 ATATAATATATGTTTTATTATATTAAAAACACAAAAAA
1 ATATAATAAATGTTTTATTATATTAAAAACACAAAAAA
* *
44446968 ATATAATAAAAGTTTTATTATATTAAAAACACAAATAA
1 ATATAATAAATGTTTTATTATATTAAAAACACAAAAAA
*
44447006 ATATAATAAATGTTTTATTGTATTAAA
1 ATATAATAAATGTTTTATTATATTAAA
44447033 TATAATTTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 60 1.00
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (38 bp):
ATATAATAAATGTTTTATTATATTAAAAACACAAAAAA
Found at i:44448054 original size:21 final size:20
Alignment explanation
Indices: 44448028--44448073 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 20
44448018 ATATTTCTCA
44448028 TTTATAAATTTAAATAATTT-T
1 TTTATAAA-TT-AATAATTTAT
*
44448049 TTTATATATTAATAATTTAT
1 TTTATAAATTAATAATTTAT
44448069 TTTAT
1 TTTAT
44448074 CATCTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 8 0.35
20 8 0.35
21 7 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTATAAATTAATAATTTAT
Found at i:44450530 original size:21 final size:21
Alignment explanation
Indices: 44450504--44450562 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
44450494 AACAGCGGTG
*
44450504 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
44450525 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
*
44450546 GCGGTGAGATTGGATAC
1 GCGGTGAGATTAGATAC
44450563 AGCGGTGGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.24, C:0.10, G:0.37, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:44450568 original size:18 final size:19
Alignment explanation
Indices: 44450504--44450569 Score: 71
Period size: 21 Copynumber: 3.3 Consensus size: 19
44450494 AACAGCGGTG
* *
44450504 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTGGATAC--TA
44450525 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTGGATAC--TA
44450546 GCGGTGAGATTGGATAC-A
1 GCGGTGAGATTGGATACTA
44450564 GCGGTG
1 GCGGTG
44450570 GAGTGTGTGT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
18 7 0.16
21 36 0.84
ACGTcount: A:0.23, C:0.11, G:0.39, T:0.27
Consensus pattern (19 bp):
GCGGTGAGATTGGATACTA
Found at i:44450793 original size:15 final size:15
Alignment explanation
Indices: 44450773--44450828 Score: 57
Period size: 15 Copynumber: 4.0 Consensus size: 15
44450763 ATTTACTAAA
*
44450773 ATTATAATATATAAT
1 ATTATAAAATATAAT
44450788 ATTATAAAATAT-A-
1 ATTATAAAATATAAT
*
44450801 ATT-TAAAATA-ATT
1 ATTATAAAATATAAT
*
44450814 ATTATTAAATATAAT
1 ATTATAAAATATAAT
44450829 TTAACAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
12 7 0.21
13 6 0.18
14 7 0.21
15 13 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTATAAAATATAAT
Found at i:44450823 original size:26 final size:25
Alignment explanation
Indices: 44450783--44450961 Score: 85
Period size: 26 Copynumber: 7.3 Consensus size: 25
44450773 ATTATAATAT
*
44450783 ATAATATTATAAAATATAATTTAAA
1 ATAATATTATTAAATATAATTTAAA
44450808 ATAATTATTATTAAATATAATTTAACA
1 ATAA-TATTATTAAATATAATTTAA-A
* *
44450835 AAAATA-TA-T-AATTTAA--TAAA
1 ATAATATTATTAAATATAATTTAAA
** * *
44450855 ATTCTTAGTATTAAATAT--TCTT-AT
1 A-TAATATTATTAAATATAAT-TTAAA
* *
44450879 ATGAAT-TTACTAAAATCATAA--T-AT
1 AT-AATATTA-TTAAAT-ATAATTTAAA
* *
44450903 ATAATACTATAAAATATAATTTAAA
1 ATAATATTATTAAATATAATTTAAA
44450928 ATAATTATTATTAAATATAATTTAACA
1 ATAA-TATTATTAAATATAATTTAA-A
*
44450955 AAAATAT
1 ATAATAT
44450962 ATAATTTAAT
Statistics
Matches: 117, Mismatches: 17, Indels: 39
0.68 0.10 0.23
Matches are distributed among these distances:
20 2 0.02
21 5 0.04
22 6 0.05
23 19 0.16
24 21 0.18
25 14 0.12
26 42 0.36
27 8 0.07
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (25 bp):
ATAATATTATTAAATATAATTTAAA
Found at i:44450841 original size:59 final size:59
Alignment explanation
Indices: 44450778--44450976 Score: 210
Period size: 59 Copynumber: 3.3 Consensus size: 59
44450768 CTAAAATTAT
44450778 AATATATAATATT-ATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAACAAA
1 AATATATAAT-TTAATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAACAAA
* * * * * * ** *
44450837 AATATATAATTTAATAAAATTCTTAGTATT-AAAT-ATTCTTATATGAATTTACTAAAATC-AT
1 AATATATAATTTAATAAAA-T-ATAAT-TTAAAATAATTATTAT-TAAATATAATTTAA-CAAA
*
44450898 AATATATAATACT-ATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAACAAA
1 AATATATAAT-TTAATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAACAAA
44450957 AATATATAATTTAATAAAAT
1 AATATATAATTTAATAAAAT
44450977 TCTTAGTATT
Statistics
Matches: 109, Mismatches: 20, Indels: 22
0.72 0.13 0.15
Matches are distributed among these distances:
58 6 0.06
59 50 0.46
60 16 0.15
61 33 0.30
62 4 0.04
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (59 bp):
AATATATAATTTAATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAACAAA
Found at i:44450889 original size:120 final size:119
Alignment explanation
Indices: 44450756--44451002 Score: 460
Period size: 120 Copynumber: 2.1 Consensus size: 119
44450746 TTTAATAGAA
* *
44450756 TATATGAATTTACTAAAATTATAATATATAATATTATAAAATATAATTTAAAATAATTATTATTA
1 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTA
44450821 AATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTC
66 AATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTC
44450875 TTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATT
1 -TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATT
44450940 AAATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTC
65 AAATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTC
44450995 TA-ATGAAT
1 TATATGAAT
44451003 GTATCAACAA
Statistics
Matches: 125, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
118 6 0.05
119 2 0.02
120 117 0.94
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (119 bp):
TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTA
AATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTC
Found at i:44454038 original size:6 final size:6
Alignment explanation
Indices: 44454027--44454064 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
44454017 TTTGCAACCC
*
44454027 AAGGGG AAGGGG AAAGGG AAGGGG AAGGGG AAAGGGG A
1 AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG -AAGGGG A
44454065 GAAGAAGGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (6 bp):
AAGGGG
Found at i:44454050 original size:18 final size:18
Alignment explanation
Indices: 44454027--44454062 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
44454017 TTTGCAACCC
44454027 AAGGGGAAGGGGAAAGGG
1 AAGGGGAAGGGGAAAGGG
44454045 AAGGGGAAGGGGAAAGGG
1 AAGGGGAAGGGGAAAGGG
44454063 GAGAAGAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (18 bp):
AAGGGGAAGGGGAAAGGG
Found at i:44454071 original size:18 final size:18
Alignment explanation
Indices: 44454032--44454073 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
44454022 AACCCAAGGG
**
44454032 GAAGGGGAAAGGGAAGGG
1 GAAGGGGAAAGGGAAGAA
*
44454050 GAAGGGGAAAGGGGAGAA
1 GAAGGGGAAAGGGAAGAA
44454068 GAAGGG
1 GAAGGG
44454074 TAACCAAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (18 bp):
GAAGGGGAAAGGGAAGAA
Found at i:44457845 original size:16 final size:16
Alignment explanation
Indices: 44457800--44457853 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
44457790 ATTGGTTCGC
*
44457800 TGTAATTGAATAGAGG
1 TGTAATGGAATAGAGG
* *
44457816 CGTAATGAAATAGAGG
1 TGTAATGGAATAGAGG
* *
44457832 TGTAATGGATTAGAGA
1 TGTAATGGAATAGAGG
44457848 TGTAAT
1 TGTAAT
44457854 AGCAAATCAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.39, C:0.02, G:0.30, T:0.30
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:44458087 original size:14 final size:15
Alignment explanation
Indices: 44458044--44458089 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
44458034 TATTAATATC
*
44458044 AATA-ATTATTATTA
1 AATATATTATAATTA
44458058 AATATATTATAATTA
1 AATATATTATAATTA
*
44458073 AA-ATA-TATAATTT
1 AATATATTATAATTA
44458086 AATA
1 AATA
44458090 AAATTCTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 9 0.32
14 8 0.29
15 11 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATATTATAATTA
Found at i:44458137 original size:54 final size:53
Alignment explanation
Indices: 44458079--44458257 Score: 142
Period size: 60 Copynumber: 3.1 Consensus size: 53
44458069 ATTAAAATAT
*
44458079 ATAATTTAATAAAATTCTTAATAAATAATATTCTTATGTGAATTTACTGAAATC
1 ATAATTTAATAAAATTCTTAATAAATAATATTCTTATAT-AATTTACTGAAATC
* * * * * * *
44458133 ATAATATATGATACTATAAAATATAAATTAACATAATTATTATTAAATATAATATAATTAAAATA
1 ATAAT-T-T-A-A-TA-AAATTCTTAA-TAA-ATAA-TATTCTT--ATATAAT-TTACTGAAAT-
*
44458198 T
53 C
44458199 ATAATTTAATAAAATTCTTAATAAATAATATTCTTATATTAATTTACTGAAATC
1 ATAATTTAATAAAATTCTTAATAAATAATATTCTTATA-TAATTTACTGAAATC
44458253 ATAAT
1 ATAAT
44458258 ATATGATACT
Statistics
Matches: 94, Mismatches: 17, Indels: 28
0.68 0.12 0.20
Matches are distributed among these distances:
54 10 0.11
55 11 0.12
56 5 0.05
57 7 0.07
58 5 0.05
59 5 0.05
60 14 0.15
61 5 0.05
62 5 0.05
63 7 0.07
64 4 0.04
65 11 0.12
66 5 0.05
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (53 bp):
ATAATTTAATAAAATTCTTAATAAATAATATTCTTATATAATTTACTGAAATC
Found at i:44458152 original size:61 final size:60
Alignment explanation
Indices: 44458087--44458274 Score: 188
Period size: 61 Copynumber: 3.1 Consensus size: 60
44458077 ATATAATTTA
*
44458087 ATAAAATTCTTAATAAATAATATTCTTATGTGAATTTACTGAAATCATAATATATGATACT
1 ATAAAATTCTTAATAAATAATATTCTTAT-TAAATTTACTGAAATCATAATATATGATACT
* * * * * * * * *
44458148 ATAAAA-TATAAATTAACAT-A-ATTATTATTAAATATAAT-ATAATTAAAATATATAAT-TT
1 ATAAAATTCTTAA-TAA-ATAATATTCTTATTAAATTTACTGA-AATCATAATATATGATACT
*
44458206 AATAAAATTCTTAATAAATAATATTCTTATATTAATTTACTGAAATCATAATATATGATACT
1 -ATAAAATTCTTAATAAATAATATTCTTAT-TAAATTTACTGAAATCATAATATATGATACT
44458268 ATAAAAT
1 ATAAAAT
44458275 ATAAATTAAC
Statistics
Matches: 97, Mismatches: 20, Indels: 20
0.71 0.15 0.15
Matches are distributed among these distances:
58 4 0.04
59 30 0.31
60 22 0.23
61 37 0.38
62 4 0.04
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (60 bp):
ATAAAATTCTTAATAAATAATATTCTTATTAAATTTACTGAAATCATAATATATGATACT
Found at i:44458189 original size:120 final size:120
Alignment explanation
Indices: 44458045--44458335 Score: 555
Period size: 120 Copynumber: 2.4 Consensus size: 120
44458035 ATTAATATCA
44458045 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAATAATAT
1 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAATAATAT
*
44458110 TCTTATGTGAATTTACTGAAATCATAATATATGATACTATAAAATATAAATTAAC
66 TCTTATATGAATTTACTGAAATCATAATATATGATACTATAAAATATAAATTAAC
*
44458165 ATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAAATAATAT
1 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAATAATAT
*
44458230 TCTTATATTAATTTACTGAAATCATAATATATGATACTATAAAATATAAATTAAC
66 TCTTATATGAATTTACTGAAATCATAATATATGATACTATAAAATATAAATTAAC
44458285 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTC
1 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTC
44458336 NNNNNNNNNN
Statistics
Matches: 167, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 167 1.00
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.42
Consensus pattern (120 bp):
ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAATAATAT
TCTTATATGAATTTACTGAAATCATAATATATGATACTATAAAATATAAATTAAC
Found at i:44458200 original size:18 final size:17
Alignment explanation
Indices: 44458179--44458213 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
44458169 TTATTATTAA
44458179 ATATAATATAATTAAAAT
1 ATATAATATAA-TAAAAT
*
44458197 ATATAATTTAATAAAAT
1 ATATAATATAATAAAAT
44458214 TCTTAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATAATATAATAAAAT
Found at i:44458327 original size:14 final size:15
Alignment explanation
Indices: 44458278--44458329 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
44458268 ATAAAATATA
44458278 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
44458293 TATTAAATATATTAT
1 AATTAAATATATTAT
44458308 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
44458321 AATTTAATA
1 AATTAAATA
44458330 AAATTCNNNN
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:44463647 original size:30 final size:30
Alignment explanation
Indices: 44463613--44463675 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
44463603 ACTTATTTTA
44463613 TTGTTAATTTTGTTATTATTTTAAAGATAT
1 TTGTTAATTTTGTTATTATTTTAAAGATAT
* *
44463643 TTGTTAATTTTGTTATTATTTTAGAGGTAT
1 TTGTTAATTTTGTTATTATTTTAAAGATAT
44463673 TTG
1 TTG
44463676 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.00, G:0.14, T:0.60
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGATAT
Found at i:44463779 original size:18 final size:20
Alignment explanation
Indices: 44463758--44463798 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
44463748 GAAATATTTA
*
44463758 TTTTGATGT-TTTTA-ATAT
1 TTTTGATGTATTATATATAT
44463776 TTTTGATGTATTATATATAT
1 TTTTGATGTATTATATATAT
44463796 TTT
1 TTT
44463799 AAAATTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 4 0.20
20 7 0.35
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.66
Consensus pattern (20 bp):
TTTTGATGTATTATATATAT
Found at i:44463829 original size:12 final size:12
Alignment explanation
Indices: 44463799--44463831 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
44463789 TATATATTTT
44463799 AAAATT-ATATA
1 AAAATTAATATA
44463810 AAAA-TAATATA
1 AAAATTAATATA
44463821 AAAATTAATAT
1 AAAATTAATAT
44463832 GGGCAGGCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:44467427 original size:267 final size:267
Alignment explanation
Indices: 44466952--44467484 Score: 1066
Period size: 267 Copynumber: 2.0 Consensus size: 267
44466942 GCAATAAAAG
44466952 ATAAAATTCCTTATGATTGCGTTGCTATGTTTAACCTAAAGCTATTTGTCAAACTCATGCTGATA
1 ATAAAATTCCTTATGATTGCGTTGCTATGTTTAACCTAAAGCTATTTGTCAAACTCATGCTGATA
44467017 TGCAGCTATTCATTATTAAAAGGACTGTTTGAAGCAATATGCACTATGGAAGTTAACATACATTG
66 TGCAGCTATTCATTATTAAAAGGACTGTTTGAAGCAATATGCACTATGGAAGTTAACATACATTG
44467082 ATGAATATAATCATATTAATGATATCATCAACATATTTCTTTTAGGAATGAACTGCAATATTCTA
131 ATGAATATAATCATATTAATGATATCATCAACATATTTCTTTTAGGAATGAACTGCAATATTCTA
44467147 GTTAATGGAGTCAATGATATCATCAATATATTGACATTGTTAATCTCTTGTCAAGATGGAAGACG
196 GTTAATGGAGTCAATGATATCATCAATATATTGACATTGTTAATCTCTTGTCAAGATGGAAGACG
44467212 TTTCATC
261 TTTCATC
44467219 ATAAAATTCCTTATGATTGCGTTGCTATGTTTAACCTAAAGCTATTTGTCAAACTCATGCTGATA
1 ATAAAATTCCTTATGATTGCGTTGCTATGTTTAACCTAAAGCTATTTGTCAAACTCATGCTGATA
44467284 TGCAGCTATTCATTATTAAAAGGACTGTTTGAAGCAATATGCACTATGGAAGTTAACATACATTG
66 TGCAGCTATTCATTATTAAAAGGACTGTTTGAAGCAATATGCACTATGGAAGTTAACATACATTG
44467349 ATGAATATAATCATATTAATGATATCATCAACATATTTCTTTTAGGAATGAACTGCAATATTCTA
131 ATGAATATAATCATATTAATGATATCATCAACATATTTCTTTTAGGAATGAACTGCAATATTCTA
44467414 GTTAATGGAGTCAATGATATCATCAATATATTGACATTGTTAATCTCTTGTCAAGATGGAAGACG
196 GTTAATGGAGTCAATGATATCATCAATATATTGACATTGTTAATCTCTTGTCAAGATGGAAGACG
44467479 TTTCAT
261 TTTCAT
44467485 TTTTCTTGGA
Statistics
Matches: 266, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
267 266 1.00
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (267 bp):
ATAAAATTCCTTATGATTGCGTTGCTATGTTTAACCTAAAGCTATTTGTCAAACTCATGCTGATA
TGCAGCTATTCATTATTAAAAGGACTGTTTGAAGCAATATGCACTATGGAAGTTAACATACATTG
ATGAATATAATCATATTAATGATATCATCAACATATTTCTTTTAGGAATGAACTGCAATATTCTA
GTTAATGGAGTCAATGATATCATCAATATATTGACATTGTTAATCTCTTGTCAAGATGGAAGACG
TTTCATC
Found at i:44473059 original size:48 final size:48
Alignment explanation
Indices: 44472989--44473104 Score: 162
Period size: 48 Copynumber: 2.4 Consensus size: 48
44472979 TTGTGGAACT
* * *
44472989 AAGTGCAGGCCATAATTATGGGCAT-TCATGTGGGCCGTGGTTTAGAGC
1 AAGTGCAGGCCAAAATTTTGGGCATCT-ATGTGGGCCGTGGTTTAGACC
* * *
44473037 AAGTGCAAGCCAGAATTTTGGGCATCTGTGTGGGCCGTGGTTTAGACC
1 AAGTGCAGGCCAAAATTTTGGGCATCTATGTGGGCCGTGGTTTAGACC
44473085 AAGTGCAGGCCAAAATTTTG
1 AAGTGCAGGCCAAAATTTTG
44473105 AATTTGTTAG
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
48 59 0.98
49 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.27
Consensus pattern (48 bp):
AAGTGCAGGCCAAAATTTTGGGCATCTATGTGGGCCGTGGTTTAGACC
Found at i:44476758 original size:11 final size:11
Alignment explanation
Indices: 44476696--44476760 Score: 53
Period size: 12 Copynumber: 5.8 Consensus size: 11
44476686 CTTGTTAACT
*
44476696 TTATTATTATTA
1 TTATCATTA-TA
*
44476708 TTATTATTATTA
1 TTATCATTA-TA
*
44476720 TTATTATTATTA
1 TTATCATTA-TA
44476732 TTATCA-T-TA
1 TTATCATTATA
44476741 TTATCATTATA
1 TTATCATTATA
*
44476752 TTTTCATTA
1 TTATCATTA
44476761 ATAATTATTA
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
9 8 0.16
10 1 0.02
11 11 0.22
12 29 0.59
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (11 bp):
TTATCATTATA
Found at i:44476770 original size:3 final size:3
Alignment explanation
Indices: 44476696--44476750 Score: 92
Period size: 3 Copynumber: 18.3 Consensus size: 3
44476686 CTTGTTAACT
*
44476696 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
44476744 TCA TTA T
1 TTA TTA T
44476751 ATTTTCATTA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:44476854 original size:18 final size:17
Alignment explanation
Indices: 44476833--44476874 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
44476823 TATACATTAC
44476833 ATATATTTTATCTA-ATAT
1 ATATATTTT-T-TATATAT
44476851 ATATAATTTTTTATATAT
1 ATAT-ATTTTTTATATAT
44476869 ATATAT
1 ATATAT
44476875 ATGCATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 4 0.18
18 13 0.59
19 5 0.23
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
ATATATTTTTTATATAT
Found at i:44477398 original size:108 final size:108
Alignment explanation
Indices: 44477203--44477719 Score: 799
Period size: 110 Copynumber: 4.7 Consensus size: 108
44477193 TCAAAAAAGG
*
44477203 AAAATATTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
1 AAAAT-TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
*
44477268 GGTTTCGATTTCTCGTTCGACCAAAT-GACTTAATATTCTTTTCA
65 GGTTTCGATTTCTCGTTCGACCAAATAG-CTTAATATCCTTTTCA
*
44477312 AAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
1 AAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
* * *
44477377 GTTTCAATTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAA
66 GTTTCGATTTCTCGTTCGACCAAATAGCTTAATATCCTTTTCA
* *
44477420 AAAACTTTTCAAAAATAAGACAATGTTTTGCATTTGGAAATTCGAGGAACGTGCCCTAAGGTACT
1 AAAA-TTTTC-AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACT
44477485 GGGTTTCGATTTCTCGTTCGACCAAAT-GACTTAATATCCTTTTCA
64 GGGTTTCGATTTCTCGTTCGACCAAATAG-CTTAATATCCTTTTCA
* *
44477530 AAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTACTG
1 AAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAG-GAACGTGCCCTAAGGTACTG
* *
44477595 GGTGTCGATTTTTCTCGTTCAACCAAATAGC-TAAGTATCCTTTTCA
65 GGTTTCGA--TTTCTCGTTCGACCAAATAGCTTAA-TATCCTTTTCA
* *
44477641 AAAA-TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCTCTAAGGTGCTGG
1 AAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
44477705 GTTTCGATTTCTCGT
66 GTTTCGATTTCTCGT
44477720 CTAACCAAAT
Statistics
Matches: 378, Mismatches: 21, Indels: 20
0.90 0.05 0.05
Matches are distributed among these distances:
107 8 0.02
108 134 0.35
109 65 0.17
110 137 0.36
111 33 0.09
112 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Consensus pattern (108 bp):
AAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
GTTTCGATTTCTCGTTCGACCAAATAGCTTAATATCCTTTTCA
Found at i:44477742 original size:218 final size:215
Alignment explanation
Indices: 44477203--44477719 Score: 845
Period size: 218 Copynumber: 2.4 Consensus size: 215
44477193 TCAAAAAAGG
* *
44477203 AAAATATTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
1 AAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
*
44477268 GGTTTCGATTTCTCGTTCGACCAAATGACTTAATATTCTTTTCAAAAATTTTCAAAATAAGGCAA
66 GGTTTCGATTTCTCGTTCGACCAAATGACTTAATATCCTTTTCAAAAATTTTCAAAATAAGGCAA
* * * *
44477333 TATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCAATTTCTCGTTCGACC
131 TATTTTGCGTTTGGAAATTCGAGAAACATGCCCTAAGGTACTGGGTGTCAATTTCTCGTTCAACC
44477398 AAATAGCTAAATATCCTTTT
196 AAATAGCTAAATATCCTTTT
* *
44477418 AAAAAACTTTTCAAAAATAAGACAATGTTTTGCATTTGGAAATTCGAGGAACGTGCCCTAAGGTA
1 AAAAAA--TTTC-AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTA
44477483 CTGGGTTTCGATTTCTCGTTCGACCAAATGACTTAATATCCTTTTCAAAAATTTTCAAAATAAGG
63 CTGGGTTTCGATTTCTCGTTCGACCAAATGACTTAATATCCTTTTCAAAAATTTTCAAAATAAGG
* *
44477548 CAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTACTGGGTGTCGATTTTTCTCGT
128 CAATATTTTGCGTTTGGAAATTCGAG-AAACATGCCCTAAGGTACTGGGTGTC-A-ATTTCTCGT
*
44477613 TCAACCAAATAGCTAAGTATCCTTTT
190 TCAACCAAATAGCTAAATATCCTTTT
* * *
44477639 CAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCTCTAAGGTGCTG
1 AAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
44477704 GGTTTCGATTTCTCGT
66 GGTTTCGATTTCTCGT
44477720 CTAACCAAAT
Statistics
Matches: 279, Mismatches: 17, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
215 5 0.02
217 4 0.01
218 205 0.73
219 27 0.10
220 1 0.00
221 37 0.13
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Consensus pattern (215 bp):
AAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
GGTTTCGATTTCTCGTTCGACCAAATGACTTAATATCCTTTTCAAAAATTTTCAAAATAAGGCAA
TATTTTGCGTTTGGAAATTCGAGAAACATGCCCTAAGGTACTGGGTGTCAATTTCTCGTTCAACC
AAATAGCTAAATATCCTTTT
Found at i:44481051 original size:17 final size:18
Alignment explanation
Indices: 44481029--44481065 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
44481019 TTATTCTTTT
44481029 ATTCTTTCATCCA-AATC
1 ATTCTTTCATCCATAATC
*
44481046 ATTCTTTCATTCATAATC
1 ATTCTTTCATCCATAATC
44481064 AT
1 AT
44481066 ACTGTGCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.30, C:0.24, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTCTTTCATCCATAATC
Found at i:44481812 original size:7 final size:7
Alignment explanation
Indices: 44481797--44481842 Score: 74
Period size: 7 Copynumber: 6.4 Consensus size: 7
44481787 AAAATAGGAG
44481797 AAAAAGA
1 AAAAAGA
*
44481804 AAGAAGA
1 AAAAAGA
44481811 AAAAAGA
1 AAAAAGA
44481818 AAAAAGA
1 AAAAAGA
44481825 AAAAAGAA
1 AAAAAG-A
44481833 AAAAAGA
1 AAAAAGA
44481840 AAA
1 AAA
44481843 GGAAAAAGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
7 29 0.81
8 7 0.19
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:44481847 original size:21 final size:20
Alignment explanation
Indices: 44481795--44481849 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 20
44481785 CAAAAATAGG
*
44481795 AGAAAAAGAAAGAAGAAAAA
1 AGAAAAAGAAAAAAGAAAAA
44481815 AGAAAAAAGAAAAAAGAAAAAA
1 AG-AAAAAGAAAAAAG-AAAAA
*
44481837 AGAAAAGGAAAAA
1 AGAAAAAGAAAAA
44481850 GGAGAGGTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 2 0.06
21 22 0.71
22 7 0.23
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (20 bp):
AGAAAAAGAAAAAAGAAAAA
Found at i:44482703 original size:21 final size:20
Alignment explanation
Indices: 44482678--44482731 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
44482668 ACTTTGAGTA
*
44482678 AAAAAAAAAGAATGAAAGAATG
1 AAAAAAGAA-AATGAAA-AATG
44482700 AAAAAATGAAAATGAAAAATG
1 AAAAAA-GAAAATGAAAAATG
*
44482721 AAAAATGAAAA
1 AAAAAAGAAAA
44482732 ATGGAGAGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 5 0.17
21 9 0.31
22 13 0.45
23 2 0.07
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11
Consensus pattern (20 bp):
AAAAAAGAAAATGAAAAATG
Found at i:44482703 original size:22 final size:21
Alignment explanation
Indices: 44482677--44482734 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
44482667 CACTTTGAGT
*
44482677 AAAAAAAAAAGAATGAAAGAATG
1 AAAAAATAAA-AATGAAA-AATG
*
44482700 AAAAAATGAAAATGAAAAATG
1 AAAAAATAAAAATGAAAAATG
44482721 -AAAAATGAAAAATG
1 AAAAAAT-AAAAATG
44482735 GAGAGGCCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 6 0.19
21 10 0.32
22 7 0.23
23 8 0.26
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (21 bp):
AAAAAATAAAAATGAAAAATG
Found at i:44482718 original size:7 final size:7
Alignment explanation
Indices: 44482688--44482734 Score: 69
Period size: 7 Copynumber: 6.6 Consensus size: 7
44482678 AAAAAAAAAG
44482688 AATGAAA
1 AATGAAA
44482695 GAATGAAAA
1 -AATG-AAA
44482704 AATG-AA
1 AATGAAA
44482710 AATGAAA
1 AATGAAA
44482717 AATGAAA
1 AATGAAA
44482724 AATGAAA
1 AATGAAA
44482731 AATG
1 AATG
44482735 GAGAGGCCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
6 6 0.16
7 20 0.54
8 8 0.22
9 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (7 bp):
AATGAAA
Found at i:44483964 original size:44 final size:43
Alignment explanation
Indices: 44483914--44484316 Score: 126
Period size: 44 Copynumber: 9.2 Consensus size: 43
44483904 AGTTGCAAAC
44483914 CTTGCCTCTCTCGGTTGTAGTGGAGCTGGTTGAAGATAACAGAT
1 CTTGCCTCTCTCGGTTGTAGTGGAGCTGGTTGAAGA-AACAGAT
* * * * * ** * * *
44483958 CTTGCCT-TCCTGCAG-TGACAGCGAAGCAGGTCAAAGACACAAAC
1 CTTGCCTCT-CT-CGGTTG-TAGTGGAGCTGGTTGAAGAAACAGAT
*
44484002 CTTGCCTCTCTCGGTTGT-GATGGAGCTGGTTGAAGACAAAAGAT
1 CTTGCCTCTCTCGGTTGTAG-TGGAGCTGGTTGAAGA-AACAGAT
* * * * * * * * * *
44484046 CTTGCCTTTCTAC-ATTGACAGCGAAGCAGGTCGAAGACACAAAC
1 CTTGCCTCTCT-CGGTTG-TAGTGGAGCTGGTTGAAGAAACAGAT
* *
44484090 CTTGCCTTTCTCGGTTGT-GATGGAGCTGGTTGAAGACAAAAGAT
1 CTTGCCTCTCTCGGTTGTAG-TGGAGCTGGTTGAAGA-AACAGAT
* * * * ** * * *
44484134 CTTGCCT-TCCTGCAG-TGACAGCGAAG-TAGGTCAAAGACACAAAC
1 CTTGCCTCT-CT-CGGTTG-TAGTGGAGCT-GGTTGAAGAAACAGAT
* * *
44484178 CTTGCCTCTCTCGGTTGT-GACGGAGCTAGTTGAAGACAAAAGAT
1 CTTGCCTCTCTCGGTTGTAG-TGGAGCTGGTTGAAGA-AACAGAT
* * * * * * ** * * *
44484222 CTTGCCTTTCT-GCATTGACAGCGAAGCAGGTCAAAGACACAAAC
1 CTTGCCTCTCTCG-GTTG-TAGTGGAGCTGGTTGAAGAAACAGAT
*
44484266 CTTGCCTCTCTCGGTTGT-GATGGAGCTGGTTGAAGACAAAAGAT
1 CTTGCCTCTCTCGGTTGTAG-TGGAGCTGGTTGAAGA-AACAGAT
44484310 CTTGCCT
1 CTTGCCT
44484317 TCCTGCATTA
Statistics
Matches: 244, Mismatches: 86, Indels: 58
0.63 0.22 0.15
Matches are distributed among these distances:
42 4 0.02
43 52 0.21
44 131 0.54
45 54 0.22
46 3 0.01
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (43 bp):
CTTGCCTCTCTCGGTTGTAGTGGAGCTGGTTGAAGAAACAGAT
Found at i:44484388 original size:88 final size:88
Alignment explanation
Indices: 44483909--44484371 Score: 784
Period size: 88 Copynumber: 5.3 Consensus size: 88
44483899 AATGAAGTTG
* * *
44483909 CAAACCTTGCCTCTCTCGGTTGT-AGTGGAGCTGGTTGAAGATAACAGATCTTGCCTTCCTGCAG
1 CAAACCTTGCCTCTCTCGGTTGTGA-TGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCAT
44483973 TGACAGCGAAGCAGGTCAAAGACA
65 TGACAGCGAAGCAGGTCAAAGACA
* *
44483997 CAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTACATT
1 CAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATT
*
44484062 GACAGCGAAGCAGGTCGAAGACA
66 GACAGCGAAGCAGGTCAAAGACA
* *
44484085 CAAACCTTGCCTTTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCAGT
1 CAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATT
*
44484150 GACAGCGAAGTAGGTCAAAGACA
66 GACAGCGAAGCAGGTCAAAGACA
* * *
44484173 CAAACCTTGCCTCTCTCGGTTGTGACGGAGCTAGTTGAAGACAAAAGATCTTGCCTTTCTGCATT
1 CAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATT
44484238 GACAGCGAAGCAGGTCAAAGACA
66 GACAGCGAAGCAGGTCAAAGACA
44484261 CAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATT
1 CAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATT
* *
44484326 AACAGCGAAGCAGGTCGAAGACA
66 GACAGCGAAGCAGGTCAAAGACA
44484349 CAAACCTTGCCTCTCTCGGTTGT
1 CAAACCTTGCCTCTCTCGGTTGT
44484372 AACGGAGTAG
Statistics
Matches: 351, Mismatches: 23, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
88 350 1.00
89 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.25
Consensus pattern (88 bp):
CAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATT
GACAGCGAAGCAGGTCAAAGACA
Found at i:44484693 original size:95 final size:94
Alignment explanation
Indices: 44484566--44484746 Score: 290
Period size: 95 Copynumber: 1.9 Consensus size: 94
44484556 CAAAGAATTT
* * *
44484566 CAGATTTTACCTCCCTGTGATTACAGTGGAGTACATTGAAGCCGAAAATTCTATCTCCCTGATTG
1 CAGATTTTACCTCACTATGACTACAGTGGAGTACATTGAAGCCGAAAATTCTAT-TCCCTGATTG
44484631 GCAGTGGAATAGATTGAAGATTGAAGATGG
65 GCAGTGGAATAGATTGAAGATTGAAGATGG
* * *
44484661 CAGATTTTACCTCACTATGACTATAGTGGAGTACATTGAAGCCGATAATTCTATTCCCTGGTTGG
1 CAGATTTTACCTCACTATGACTACAGTGGAGTACATTGAAGCCGAAAATTCTATTCCCTGATTGG
*
44484726 TAGTGGAATAGATTGAAGATT
66 CAGTGGAATAGATTGAAGATT
44484747 TCAGATCTTA
Statistics
Matches: 79, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
94 30 0.38
95 49 0.62
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.31
Consensus pattern (94 bp):
CAGATTTTACCTCACTATGACTACAGTGGAGTACATTGAAGCCGAAAATTCTATTCCCTGATTGG
CAGTGGAATAGATTGAAGATTGAAGATGG
Found at i:44484887 original size:125 final size:125
Alignment explanation
Indices: 44484648--44484878 Score: 311
Period size: 125 Copynumber: 1.8 Consensus size: 125
44484638 AATAGATTGA
* *
44484648 AGATTGAAGATGGCAGATTTTACCTCACTATGACTATAGTGGAGTACATTGAAGCCGATAATTCT
1 AGATTGAAGAAGGCAGATTTTACCTCACTATGACTACAGTGGAGTACATTGAAGCCGATAATTCT
*** ** * *
44484713 ATTCCCTGGTTGGTAGTGGAATAGATTGAAGATTTCAGATCTTATTTCCCAAAGTGGAAC
66 ATTCCCTGGGCAGTAGTGGAATAGATCAAAGATTGCAGATCTTAGTTCCCAAAGTGGAAC
* * *
44484773 AGATTGAAGAAGGCATATTTTACCTCCCTATGATTACAGTGGAGTACATTGAAGCC-AGTAATTC
1 AGATTGAAGAAGGCAGATTTTACCTCACTATGACTACAGTGGAGTACATTGAAGCCGA-TAATTC
* *
44484837 TATCTCCTTGGGCAGTAGTGTAATAGATCAAAGATTGCAGAT
65 TAT-TCCCTGGGCAGTAGTGGAATAGATCAAAGATTGCAGAT
44484879 TCTGTTCCCC
Statistics
Matches: 91, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
124 1 0.01
125 60 0.66
126 30 0.33
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (125 bp):
AGATTGAAGAAGGCAGATTTTACCTCACTATGACTACAGTGGAGTACATTGAAGCCGATAATTCT
ATTCCCTGGGCAGTAGTGGAATAGATCAAAGATTGCAGATCTTAGTTCCCAAAGTGGAAC
Found at i:44486488 original size:11 final size:11
Alignment explanation
Indices: 44486427--44486490 Score: 53
Period size: 12 Copynumber: 5.8 Consensus size: 11
44486417 CTTGTTAACT
44486427 TTAT-ATTATTA
1 TTATCATTA-TA
*
44486438 TTATTATTATTA
1 TTATCATTA-TA
*
44486450 TTATTATTATTA
1 TTATCATTA-TA
44486462 TTATCA-T-TA
1 TTATCATTATA
44486471 TTATCATTATA
1 TTATCATTATA
*
44486482 TTTTCATTA
1 TTATCATTA
44486491 ATAATTATTA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
9 8 0.17
10 1 0.02
11 15 0.31
12 24 0.50
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATCATTATA
Found at i:44486500 original size:3 final size:3
Alignment explanation
Indices: 44486430--44486480 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
44486420 GTTAACTTTA
* *
44486430 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
44486478 TAT
1 TAT
44486481 ATTTTCATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:44486990 original size:110 final size:108
Alignment explanation
Indices: 44486785--44487250 Score: 604
Period size: 110 Copynumber: 4.3 Consensus size: 108
44486775 GTATTTGTTT
* *
44486785 ATTTCTCGTTCGACCAAATGACTTAATAT-CTTTTCAAAAATTTTCAAAATAAGGCAAT-ATTTG
1 ATTTCTCGTTCGACCAAATGACTAAATATCCTTTTCAAAAATTTTCAAAATAAGGCAATGTTTTG
* *
44486848 CGTTTGAAAATTTGAGGAACGTGCCCTAAGGTACTGGGTTTCA
66 CGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCA
* * * *
44486891 ATTTCTTGTTCGACCAAAT-AGCTAAATATCCTTTTAAAAAACTTTTAAAAAATATGGCAATGTT
1 ATTTCTCGTTCGACCAAATGA-CTAAATATCCTTTTCAAAAA-TTTT-CAAAATAAGGCAATGTT
* * *
44486955 TTGCATTTGGAAATTCGAGGAACGTGCCTTAAGGTACTGGGTTTCG
63 TTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCA
*
44487001 ATTTCTCGTTCGACCAAATGACTTAATATCCTTTTCAAAAATTTTCAAAATAAGGCAATGTTTTG
1 ATTTCTCGTTCGACCAAATGACTAAATATCCTTTTCAAAAATTTTCAAAATAAGGCAATGTTTTG
* * *
44487066 CGTTTGGAAATTCGAGAAAACATGCCCTAAGGTACTGGGTGTCGA
66 CGTTTGGAAATTCGAG-GAACGTGCCCTAAGGTACTGGGTTTC-A
* * *
44487111 GTTTTCTCGTTCAACCAAAT-AGCTAAGTATCCTTTTCAAAAA-TTTCAAAATAAGGCAATGTTT
1 -ATTTCTCGTTCGACCAAATGA-CTAAATATCCTTTTCAAAAATTTTCAAAATAAGGCAATGTTT
* * *
44487174 TGCGTTTGGAAATTCGAGGAACGTGCTCTAAGGTGCTGGGTTTCG
64 TGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCA
*
44487219 ATTTCTCG-TCTAACCAAATTGAC-AAATATCCT
1 ATTTCTCGTTC-GACCAAA-TGACTAAATATCCT
44487251 CTTGAATTTT
Statistics
Matches: 313, Mismatches: 34, Indels: 25
0.84 0.09 0.07
Matches are distributed among these distances:
105 1 0.00
106 27 0.09
107 32 0.10
108 39 0.12
109 60 0.19
110 118 0.38
111 36 0.12
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (108 bp):
ATTTCTCGTTCGACCAAATGACTAAATATCCTTTTCAAAAATTTTCAAAATAAGGCAATGTTTTG
CGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCA
Found at i:44487184 original size:218 final size:215
Alignment explanation
Indices: 44486785--44487227 Score: 667
Period size: 218 Copynumber: 2.0 Consensus size: 215
44486775 GTATTTGTTT
44486785 ATTTCTCGTTCGACCAAATGACTTAATATCTTTTCAAAAATTTTCAAAATAAGGCAATATTTGCG
1 ATTTCTCGTTCGACCAAATGACTTAATATCTTTTCAAAAATTTTCAAAATAAGGCAATATTTGCG
* * * * * *
44486850 TTTGAAAATTTGAGGAACGTGCCCTAAGGTACTGGGTTTCAATTTCTTGTTCGACCAAATAGCTA
66 TTTGAAAATTCGAGAAACATGCCCTAAGGTACTGGGTGTCAATTTCTCGTTCAACCAAATAGCTA
*
44486915 AATATCCTTTTAAAAAACTTTTAAAAAATATGGCAATGTTTTGCATTTGGAAATTCGAGGAACGT
131 AATATCCTTTTAAAAAAC-TTTAAAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGGAACGT
44486980 GC-CTTAAGGTACTGGGTTTCG
195 GCTC-TAAGGTACTGGGTTTCG
*
44487001 ATTTCTCGTTCGACCAAATGACTTAATATCCTTTTCAAAAATTTTCAAAATAAGGCAATGTTTTG
1 ATTTCTCGTTCGACCAAATGACTTAATAT-CTTTTCAAAAATTTTCAAAATAAGGCAAT-ATTTG
* *
44487066 CGTTTGGAAATTCGAGAAAACATGCCCTAAGGTACTGGGTGTCGAGTTTTCTCGTTCAACCAAAT
64 CGTTTGAAAATTCGAG-AAACATGCCCTAAGGTACTGGGTGTC-A-ATTTCTCGTTCAACCAAAT
* * * *
44487131 AGCTAAGTATCCTTTTCAAAAA-TTT-CAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGA
126 AGCTAAATATCCTTTTAAAAAACTTTAAAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGGA
*
44487194 ACGTGCTCTAAGGTGCTGGGTTTCG
191 ACGTGCTCTAAGGTACTGGGTTTCG
44487219 ATTTCTCGT
1 ATTTCTCGT
44487228 CTAACCAAAT
Statistics
Matches: 206, Mismatches: 15, Indels: 10
0.89 0.06 0.04
Matches are distributed among these distances:
216 29 0.14
217 29 0.14
218 84 0.41
219 27 0.13
220 1 0.00
221 36 0.17
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (215 bp):
ATTTCTCGTTCGACCAAATGACTTAATATCTTTTCAAAAATTTTCAAAATAAGGCAATATTTGCG
TTTGAAAATTCGAGAAACATGCCCTAAGGTACTGGGTGTCAATTTCTCGTTCAACCAAATAGCTA
AATATCCTTTTAAAAAACTTTAAAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGGAACGTG
CTCTAAGGTACTGGGTTTCG
Found at i:44488639 original size:21 final size:21
Alignment explanation
Indices: 44488615--44488669 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
44488605 TCATTTTCTG
44488615 CCACTTCCTTGCTAGTCTGTT
1 CCACTTCCTTGCTAGTCTGTT
* *
44488636 CCACTTCCTTACTAGTTTGTT
1 CCACTTCCTTGCTAGTCTGTT
* *
44488657 -AAGTTCCTTGCTA
1 CCACTTCCTTGCTA
44488670 CAAATCTCCG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 10 0.34
21 19 0.66
ACGTcount: A:0.15, C:0.29, G:0.13, T:0.44
Consensus pattern (21 bp):
CCACTTCCTTGCTAGTCTGTT
Found at i:44493784 original size:16 final size:16
Alignment explanation
Indices: 44493753--44493794 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
44493743 TAATAATAAC
44493753 TAATATATAA-ATATAT
1 TAAT-TATAATATATAT
*
44493769 TTATTATAATATATAT
1 TAATTATAATATATAT
44493785 TAATTATAAT
1 TAATTATAAT
44493795 CAACTTTGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 5 0.22
16 18 0.78
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TAATTATAATATATAT
Found at i:44495925 original size:3 final size:3
Alignment explanation
Indices: 44495912--44495985 Score: 139
Period size: 3 Copynumber: 24.7 Consensus size: 3
44495902 CAGGGAAGTT
*
44495912 GAA GCA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
44495960 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
44495986 TCCCATAGAG
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.65, C:0.01, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:44497274 original size:5 final size:5
Alignment explanation
Indices: 44497264--44497327 Score: 71
Period size: 5 Copynumber: 13.0 Consensus size: 5
44497254 GAAAAAAAAG
*
44497264 AAGAA AAGAA AAGACA AAG-A AAGAA AAAAA AAGAA AAGAA AAG-A AA-AA
1 AAGAA AAGAA AAGA-A AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA
*
44497312 AAGAA GAAGAA GAGAA
1 AAGAA -AAGAA AAGAA
44497328 GAGCATATGT
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
4 10 0.20
5 32 0.63
6 9 0.18
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:44497289 original size:20 final size:19
Alignment explanation
Indices: 44497255--44497329 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 19
44497245 AATGCTCGTG
*
44497255 AAAA-AAAAG-AAGAAAAG
1 AAAAGAAAAGAAAGAAAAA
44497272 AAAAGACAAAGAAAGAAAAA
1 AAAAGA-AAAGAAAGAAAAA
44497292 AAAAGAAAAGAAAAGAAAAA
1 AAAAGAAAAG-AAAGAAAAA
44497312 AAGAAGAAGAAGAGAAGA
1 AA-AAGAA-AAGA-AAGA
44497330 GCATATGTAC
Statistics
Matches: 50, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
17 4 0.08
18 1 0.02
19 8 0.16
20 24 0.48
21 6 0.12
22 7 0.14
ACGTcount: A:0.79, C:0.01, G:0.20, T:0.00
Consensus pattern (19 bp):
AAAAGAAAAGAAAGAAAAA
Found at i:44497298 original size:30 final size:29
Alignment explanation
Indices: 44497256--44497316 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 29
44497246 ATGCTCGTGA
44497256 AAAAAAAGAAGAAAAGAAAAGACAAAGAAAG
1 AAAAAAAGAAGAAAAGAAAAGA-AAA-AAAG
44497287 AAAAAAA-AAGAAAAGAAAAGAAAAAAAG
1 AAAAAAAGAAGAAAAGAAAAGAAAAAAAG
44497315 AA
1 AA
44497317 GAAGAAGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
28 6 0.20
29 3 0.10
30 14 0.47
31 7 0.23
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (29 bp):
AAAAAAAGAAGAAAAGAAAAGAAAAAAAG
Found at i:44497306 original size:24 final size:24
Alignment explanation
Indices: 44497256--44497327 Score: 83
Period size: 24 Copynumber: 2.9 Consensus size: 24
44497246 ATGCTCGTGA
44497256 AAAAAAAGAAGAAAAGAAAAGACAAAG
1 AAAAAAAG-A-AAAAGAAAAGA-AAAG
44497283 AAAGAAAA-AAAAAGAAAAGAAAAG
1 AAA-AAAAGAAAAAGAAAAGAAAAG
* *
44497307 AAAAAAAGAAGAAGAAGAGAA
1 AAAAAAAGAAAAAGAAAAGAA
44497328 GAGCATATGT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
23 4 0.10
24 18 0.44
25 11 0.27
26 1 0.02
27 3 0.07
28 4 0.10
ACGTcount: A:0.79, C:0.01, G:0.19, T:0.00
Consensus pattern (24 bp):
AAAAAAAGAAAAAGAAAAGAAAAG
Found at i:44497319 original size:35 final size:33
Alignment explanation
Indices: 44497255--44497319 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 33
44497245 AATGCTCGTG
*
44497255 AAAAAAAAGAAGAAAAGAAAAGACAAAGAAAGA
1 AAAAAAAAGAAGAAAAGAAAAGAAAAAGAAAGA
44497288 AAAAAAAAGAAAAGAAAAGAAAA-AAAGAAGAA
1 AAAAAAAAG--AAGAAAAGAAAAGAAA-AAGAA
44497320 GAAGAGAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 9 0.32
34 2 0.07
35 17 0.61
ACGTcount: A:0.82, C:0.02, G:0.17, T:0.00
Consensus pattern (33 bp):
AAAAAAAAGAAGAAAAGAAAAGAAAAAGAAAGA
Found at i:44497327 original size:19 final size:18
Alignment explanation
Indices: 44497255--44497327 Score: 78
Period size: 19 Copynumber: 3.9 Consensus size: 18
44497245 AATGCTCGTG
44497255 AAAA-AAAAGAAGA-AAA
1 AAAAGAAAAGAAGAGAAA
*
44497271 GAAAAGACAAAGAAAGAAAAA
1 -AAAAGA-AAAG-AAGAGAAA
*
44497292 AAAAGAAAAGAAAAGAAA
1 AAAAGAAAAGAAGAGAAA
44497310 AAAAGAAGAAGAAGAGAA
1 AAAAGAA-AAGAAGAGAA
44497328 GAGCATATGT
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
17 4 0.08
18 14 0.29
19 17 0.35
20 10 0.21
21 3 0.06
ACGTcount: A:0.79, C:0.01, G:0.19, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAGAAGAGAAA
Found at i:44498917 original size:20 final size:18
Alignment explanation
Indices: 44498881--44498920 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 18
44498871 ACTTGAGATG
44498881 TTAATATGTTTAATTTAA
1 TTAATATGTTTAATTTAA
44498899 TTAATATGGTTTAAATTTAA
1 TTAATAT-GTTT-AATTTAA
44498919 TT
1 TT
44498921 CATGTTAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.35
19 4 0.20
20 9 0.45
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (18 bp):
TTAATATGTTTAATTTAA
Found at i:44500686 original size:31 final size:31
Alignment explanation
Indices: 44500645--44501189 Score: 699
Period size: 31 Copynumber: 17.7 Consensus size: 31
44500635 ATCCAATGCT
* *
44500645 CAAATC-AATTCGGCAATATATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
*
44500675 CGAATCAAATTCGGCAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* * *
44500706 CAAATC-AATTTGGCAATGAATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
44500736 CAAATCAAATTCGGCAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* *
44500767 CAAATCAAATTCGACAATGTATATCTATAGA
1 CAAATCAAATTCGGCAATGTATATCTATATA
*
44500798 CAAATC-AATTCGGCAATGTATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* * *
44500828 CAAATCAAATTCGACAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
**
44500859 CAAATCAAATTTAGCAATGTATAT-TAATATA
1 CAAATCAAATTCGGCAATGTATATCT-ATATA
*
44500890 CAAATCAAATTCAGCAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
*
44500921 CAAATCAAATTCGGCAATGTATATTTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* *
44500952 CAAATC-AATTCGGCAATATATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* * *
44500982 GAAATCAAATTTGACAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* * * *
44501013 CAAATCAAATTTGACAATGTATATCTACAAA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* * **
44501044 CAATTCTAATTCAACAATGTATATCTATA-A
1 CAAATCAAATTCGGCAATGTATATCTATATA
* * *
44501074 GCAATTCAACTTCGGCAATGTATATCTATAAA
1 -CAAATCAAATTCGGCAATGTATATCTATATA
* *
44501106 CAAATCAATTTCGGCAATGTATATCTATAAA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* *
44501137 CAAATCAAATTCGCCAATGTATATCTTTATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
44501168 CAAATC-AATTCGGCAATGTATA
1 CAAATCAAATTCGGCAATGTATA
44501190 AAACATATAC
Statistics
Matches: 455, Mismatches: 52, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
30 101 0.22
31 352 0.77
32 2 0.00
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.32
Consensus pattern (31 bp):
CAAATCAAATTCGGCAATGTATATCTATATA
Found at i:44500749 original size:92 final size:92
Alignment explanation
Indices: 44500645--44501189 Score: 702
Period size: 92 Copynumber: 5.9 Consensus size: 92
44500635 ATCCAATGCT
* * *
44500645 CAAATC-AATTCGGCAATATATATCCATATACGAATCAAATTCGGCAATGTATATCTATATACAA
1 CAAATCAAATTCGGCAATGTATATCTATATACAAATCAAATTCGGCAATGTATATCTATATACAA
* * *
44500709 ATCAATTTGGCAATGAATATCCATATA
66 ATCAATTCGGCAATGTATATCTATATA
* *
44500736 CAAATCAAATTCGGCAATGTATATCTATATACAAATCAAATTCGACAATGTATATCTATAGACAA
1 CAAATCAAATTCGGCAATGTATATCTATATACAAATCAAATTCGGCAATGTATATCTATATACAA
*
44500801 ATCAATTCGGCAATGTATATCCATATA
66 ATCAATTCGGCAATGTATATCTATATA
* * * **
44500828 CAAATCAAATTCGACAATGTATAACCATATACAAATCAAATTTAGCAATGTATAT-TAATATACA
1 CAAATCAAATTCGGCAATGTATATCTATATACAAATCAAATTCGGCAATGTATATCT-ATATACA
*
44500892 AATCAAATTCAGCAATGTATATCTATATA
65 AATC-AATTCGGCAATGTATATCTATATA
* * * *
44500921 CAAATCAAATTCGGCAATGTATATTTATATACAAATC-AATTCGGCAATATATATCCATATAGAA
1 CAAATCAAATTCGGCAATGTATATCTATATACAAATCAAATTCGGCAATGTATATCTATATACAA
* *
44500985 ATCAAATTTGACAATGTATATCTATATA
66 ATC-AATTCGGCAATGTATATCTATATA
* * * * * * **
44501013 CAAATCAAATTTGACAATGTATATCTACAAACAATTCTAATTCAACAATGTATATCTATA-AGCA
1 CAAATCAAATTCGGCAATGTATATCTATATACAAATCAAATTCGGCAATGTATATCTATATA-CA
* *
44501077 ATTCAACTTCGGCAATGTATATCTATAAA
65 AATCAA-TTCGGCAATGTATATCTATATA
* * * *
44501106 CAAATCAATTTCGGCAATGTATATCTATAAACAAATCAAATTCGCCAATGTATATCTTTATACAA
1 CAAATCAAATTCGGCAATGTATATCTATATACAAATCAAATTCGGCAATGTATATCTATATACAA
44501171 ATCAATTCGGCAATGTATA
66 ATCAATTCGGCAATGTATA
44501190 AAACATATAC
Statistics
Matches: 393, Mismatches: 53, Indels: 15
0.85 0.11 0.03
Matches are distributed among these distances:
91 7 0.02
92 231 0.59
93 154 0.39
94 1 0.00
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.32
Consensus pattern (92 bp):
CAAATCAAATTCGGCAATGTATATCTATATACAAATCAAATTCGGCAATGTATATCTATATACAA
ATCAATTCGGCAATGTATATCTATATA
Found at i:44500939 original size:154 final size:153
Alignment explanation
Indices: 44500645--44501189 Score: 763
Period size: 154 Copynumber: 3.5 Consensus size: 153
44500635 ATCCAATGCT
* *
44500645 CAAATCAATTCGGCAATATATATCCATATACGAATCAAATTCGGCAATGTATATCTATATACAAA
1 CAAATCAATTCGGCAATATATATCCATATACAAATCAAATTCGACAATGTATATCTATATACAAA
* ** *
44500710 TCAATTTGGCAATGAATATCCATATACAAATCAAATTCGGCAATGTATATCTATATACAAATCAA
66 TCAATTTGGCAATGTATATTAATATACAAATCAAATTCAGCAATGTATATCTATATACAAATCAA
* *
44500775 ATTCGACAATGTATATCTATAGA
131 ATTCGGCAATGTATATCTATAAA
* * *
44500798 CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGACAATGTATAACCATATACAAA
1 CAAATCAATTCGGCAATATATATCCATATACAAATCAAATTCGACAATGTATATCTATATACAAA
*
44500863 TCAAATTTAGCAATGTATATTAATATACAAATCAAATTCAGCAATGTATATCTATATACAAATCA
66 TC-AATTTGGCAATGTATATTAATATACAAATCAAATTCAGCAATGTATATCTATATACAAATCA
* *
44500928 AATTCGGCAATGTATATTTATATA
130 AATTCGGCAATGTATATCTATAAA
* *
44500952 CAAATCAATTCGGCAATATATATCCATATAGAAATCAAATTTGACAATGTATATCTATATACAAA
1 CAAATCAATTCGGCAATATATATCCATATACAAATCAAATTCGACAATGTATATCTATATACAAA
* * * * *
44501017 TCAAATTTGACAATGTATATCTACA-A-ACAATTCTAATTCAACAATGTATATCTATA-AGCAAT
66 TC-AATTTGGCAATGTATAT-TA-ATATACAAATCAAATTCAGCAATGTATATCTATATA-CAAA
*
44501079 TCAACTTCGGCAATGTATATCTATAAA
127 TCAAATTCGGCAATGTATATCTATAAA
* * * * *
44501106 CAAATCAATTTCGGCAATGTATATCTATAAACAAATCAAATTCGCCAATGTATATCTTTATACAA
1 CAAATCAA-TTCGGCAATATATATCCATATACAAATCAAATTCGACAATGTATATCTATATACAA
*
44501171 ATCAATTCGGCAATGTATA
65 ATCAATTTGGCAATGTATA
44501190 AAACATATAC
Statistics
Matches: 351, Mismatches: 36, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
153 63 0.18
154 232 0.66
155 55 0.16
156 1 0.00
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.32
Consensus pattern (153 bp):
CAAATCAATTCGGCAATATATATCCATATACAAATCAAATTCGACAATGTATATCTATATACAAA
TCAATTTGGCAATGTATATTAATATACAAATCAAATTCAGCAATGTATATCTATATACAAATCAA
ATTCGGCAATGTATATCTATAAA
Found at i:44508226 original size:20 final size:20
Alignment explanation
Indices: 44508203--44508243 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
44508193 ACCAAATTAG
44508203 ATCACTTTTAATTTGGGCTA
1 ATCACTTTTAATTTGGGCTA
44508223 ATCACTTTTAATTTGGGCTA
1 ATCACTTTTAATTTGGGCTA
44508243 A
1 A
44508244 CATTTTATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATCACTTTTAATTTGGGCTA
Found at i:44514263 original size:39 final size:38
Alignment explanation
Indices: 44514200--44514668 Score: 499
Period size: 39 Copynumber: 12.1 Consensus size: 38
44514190 TAGAAATACA
*
44514200 GTGATTGTTCGGGCTATGTGCCTAGCAGGCTGTGTGTCG
1 GTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTG-CG
* * * * * * *
44514239 ATGATTATTCAGGTTTTGTACCTAGCAAGCTGGGTGCG
1 GTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCG
* * * *
44514277 AATGATTATTCGGGTTATGAGCCTAGCAGGTTGTGTGCGG
1 -GTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGC-G
* * ***
44514317 GTGATTATTCGGTCTATGTGCCTAGCAGGATGCACGCAG
1 GTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGC-G
* * *
44514356 GTGATTATTCGGGCTGTGTGCCTAGCAGGTTGAGTGCCG
1 GTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTG-CG
** *
44514395 GTGATTATTAAGGCTATGTGCCTAGCAGGCTGTGTGCCA
1 GTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTG-CG
*
44514434 GTGATTATTCGGGCTATGTGCCTAGCAGGGTGTGTGCCG
1 GTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTG-CG
* **
44514473 ATGATTATTCAAGCTATGTGCCTAGCAGGCTGTGTGCTG
1 GTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGC-G
**
44514512 GTGATTATTCAAGCTATGTGCCTAGCAGGCTGTGTGCTG
1 GTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGC-G
*
44514551 GTGATTATTCGGGCTTTGTGCCTAGCAGGCTGTGTGCCG
1 GTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTG-CG
* * *
44514590 GTGATTATTCGGGTTATGTGCCTAGCAAGTTGTGTGCCG
1 GTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTG-CG
* * * *
44514629 ATGATTATTCGGGCTATATGCCTAGCAAGTTGTGT-CG
1 GTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCG
44514666 GTG
1 GTG
44514669 TATTGAAAAT
Statistics
Matches: 369, Mismatches: 56, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
37 4 0.01
38 3 0.01
39 359 0.97
40 3 0.01
ACGTcount: A:0.17, C:0.17, G:0.33, T:0.33
Consensus pattern (38 bp):
GTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCG
Found at i:44517762 original size:31 final size:32
Alignment explanation
Indices: 44517724--44517785 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
44517714 GGCCCATTTT
44517724 TATTTTAAAAAT-TTTAAAAAATTAAAAAAAG
1 TATTTTAAAAATCTTTAAAAAATTAAAAAAAG
* *
44517755 TATTTTAAAAATCTTTTAAAATTTAAAAAAA
1 TATTTTAAAAATCTTTAAAAAATTAAAAAAA
44517786 ATTAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 12 0.43
32 16 0.57
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (32 bp):
TATTTTAAAAATCTTTAAAAAATTAAAAAAAG
Found at i:44517784 original size:41 final size:41
Alignment explanation
Indices: 44517724--44517906 Score: 268
Period size: 42 Copynumber: 4.5 Consensus size: 41
44517714 GGCCCATTTT
*
44517724 TATTTTAAAAATTTTAAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATTTAAAAAAATTAAAAAAAGTATTTTAAAAA
*
44517766 TCTTTTAAAATTTAAAAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTT-AAAAAAATTAAAAAAAGTATTTTAAAAA
44517808 TATTTTAAAA-TTAAAAAAATTAAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTTAAAAAAATT-AAAAAAAGTATTTTAAAAA
* *
44517849 TATTTTAAAATTAAAAAAAATT--AAAAAGTA-TGTAAAAA
1 TATTTTAAAATTTAAAAAAATTAAAAAAAGTATTTTAAAAA
44517887 TATTTTAAAA-TTAAAAAAAT
1 TATTTTAAAATTTAAAAAAAT
44517907 AAATATATTA
Statistics
Matches: 132, Mismatches: 6, Indels: 11
0.89 0.04 0.07
Matches are distributed among these distances:
37 9 0.07
38 17 0.13
39 8 0.06
40 9 0.07
41 38 0.29
42 51 0.39
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.36
Consensus pattern (41 bp):
TATTTTAAAATTTAAAAAAATTAAAAAAAGTATTTTAAAAA
Found at i:44517806 original size:12 final size:11
Alignment explanation
Indices: 44517724--44517858 Score: 67
Period size: 11 Copynumber: 12.9 Consensus size: 11
44517714 GGCCCATTTT
44517724 TATTTT-AAAA
1 TATTTTAAAAA
44517734 -ATTTTAAAAA
1 TATTTTAAAAA
**
44517744 -ATTAAAAAAA
1 TATTTTAAAAA
44517754 GTATTTTAAAAA
1 -TATTTTAAAAA
*
44517766 TCTTTT--AAA
1 TATTTTAAAAA
*
44517775 -ATTTAAAAAA
1 TATTTTAAAAA
* **
44517785 AATTAAAAAAA
1 TATTTTAAAAA
44517796 GTATTTTAAAAA
1 -TATTTTAAAAA
44517808 TATTTT--AAA
1 TATTTTAAAAA
44517817 -A--TTAAAAA
1 TATTTTAAAAA
* **
44517825 AATTAAAAAAAA
1 TATT-TTAAAAA
44517837 GTATTTTAAAAA
1 -TATTTTAAAAA
44517849 TATTTTAAAA
1 TATTTTAAAA
44517859 TTAAAAAAAA
Statistics
Matches: 95, Mismatches: 16, Indels: 27
0.69 0.12 0.20
Matches are distributed among these distances:
6 2 0.02
8 7 0.07
9 12 0.13
10 15 0.16
11 30 0.32
12 26 0.27
13 3 0.03
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:44520721 original size:299 final size:299
Alignment explanation
Indices: 44520176--44521054 Score: 1251
Period size: 299 Copynumber: 2.9 Consensus size: 299
44520166 ATCTGGTCTA
* * * *
44520176 TAACTCCGAGAAAGAAAGATTCAATCT-GAGGGATTGTTGACAGATTGACGAAAACGAAACATTT
1 TAACTCCGAGAAAGAAAGATTCAATCTGGA-TGATTGTTGACAGATTGATGAAATCGGAACATTT
* * * *
44520240 TATTCTAATCAGAACATACTATACCCTTGAGAGATTAGCAGAACTATATGGGTCTGAGATTGTGA
65 TATTCCAATCAGAACAGACTACACCCTTGAGAGATTAGCAGAACTATATGTGTCTGAGATTGTGA
* * * *
44520305 GATTACACGGAG-TTCTGACATCTATTATTTCGAATCGAGATCTGAAATTTACATCGAGATTTTA
130 GATTACACGGAGTTTC-AACATCTATTATTTCGGATCGAGATCTGAGATTTACATCGAGATTTTG
* * *
44520369 TAGCAAACTTCATGAGGCTTTAGGCACTAAGCTTAATTTCAGCACCACGATTCATCCTCAGACTG
194 GAACAAACTTCATGAGGCTTTAGGCACTAAGCTTAATTTCAGCACCGCGATTCATCCTCAGACTG
* * * *
44520434 ACCGGTAATCAAAACGAGTGATTTCGTATCTGGTTTACCTG
259 ACGGGCAATCAGAACGAGTGATTTCATATCTGGTTTACCTG
* * *
44520475 TAACTCTGAGAAAGAAAGATTCAATCTGGATGATTGTTGATAGATTGATGAAATCGGCACATTTT
1 TAACTCCGAGAAAGAAAGATTCAATCTGGATGATTGTTGACAGATTGATGAAATCGGAACATTTT
* * **
44520540 ATTCCAATTAGAACAGACTACAACCTTGAGAGATTAATAGAACTATATGTGTCTGAGATTGTGAG
66 ATTCCAATCAGAACAGACTACACCCTTGAGAGATTAGCAGAACTATATGTGTCTGAGATTGTGAG
* *
44520605 ATTACACGAAGTTTCAACATCTATTATTTCGGATCGAGATCTGAGATTTACATTGAGATTTTGGA
131 ATTACACGGAGTTTCAACATCTATTATTTCGGATCGAGATCTGAGATTTACATCGAGATTTTGGA
* * *
44520670 ACAAAATTCATGAGGCTTTACGCACTAAGCTTAATTTCAGCACCGCGATTCATCTTCAGACTGAC
196 ACAAACTTCATGAGGCTTTAGGCACTAAGCTTAATTTCAGCACCGCGATTCATCCTCAGACTGAC
*
44520735 GGGCAATCAGAACGAGTGATTTCATATTTGGTTTACCTG
261 GGGCAATCAGAACGAGTGATTTCATATCTGGTTTACCTG
* * *
44520774 TAACTCCGAGAAATAAAGACTGAATCTGGATGATTGTTGACAGATTGATGAAATCGGAACATTTT
1 TAACTCCGAGAAAGAAAGATTCAATCTGGATGATTGTTGACAGATTGATGAAATCGGAACATTTT
* * *
44520839 ACTCCAATCAGAATAGACTACACCCTTGAGAGATTAGCAAAACTATATGTGTCTGAGATTGTGAG
66 ATTCCAATCAGAACAGACTACACCCTTGAGAGATTAGCAGAACTATATGTGTCTGAGATTGTGAG
* * * * * ** *
44520904 ATTACACGGAGTTCCAGCATTTATTATTTTGGATTGAGATCCAAGATCTACATCGAGATTTTGGA
131 ATTACACGGAGTTTCAACATCTATTATTTCGGATCGAGATCTGAGATTTACATCGAGATTTTGGA
* * * * *
44520969 GA-AAACTTCACGAGGCTTTAGGCACTAAGCTTAATTTCAACACTGCGTTTCATCCTCAGATTGA
196 -ACAAACTTCATGAGGCTTTAGGCACTAAGCTTAATTTCAGCACCGCGATTCATCCTCAGACTGA
44521033 CGGGCAATCAGAACGAGTGATT
260 CGGGCAATCAGAACGAGTGATT
44521055 CAAATTTTGG
Statistics
Matches: 514, Mismatches: 63, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
299 508 0.99
300 6 0.01
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (299 bp):
TAACTCCGAGAAAGAAAGATTCAATCTGGATGATTGTTGACAGATTGATGAAATCGGAACATTTT
ATTCCAATCAGAACAGACTACACCCTTGAGAGATTAGCAGAACTATATGTGTCTGAGATTGTGAG
ATTACACGGAGTTTCAACATCTATTATTTCGGATCGAGATCTGAGATTTACATCGAGATTTTGGA
ACAAACTTCATGAGGCTTTAGGCACTAAGCTTAATTTCAGCACCGCGATTCATCCTCAGACTGAC
GGGCAATCAGAACGAGTGATTTCATATCTGGTTTACCTG
Found at i:44523064 original size:23 final size:23
Alignment explanation
Indices: 44523034--44523078 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
44523024 TGTGCCTAGC
44523034 GGGCTGTGTGC-GGATGATTATTT
1 GGGCTGTGTGCTGG-TGATTATTT
44523057 GGGCTGTGTGCTGGTGATTATT
1 GGGCTGTGTGCTGGTGATTATT
44523079 CAGGCTACGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 19 0.90
24 2 0.10
ACGTcount: A:0.11, C:0.09, G:0.40, T:0.40
Consensus pattern (23 bp):
GGGCTGTGTGCTGGTGATTATTT
Found at i:44523084 original size:23 final size:23
Alignment explanation
Indices: 44523035--44523084 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
44523025 GTGCCTAGCG
**
44523035 GGCTGTGTGCGGATGATTATTTG
1 GGCTGTGTGCGGATGATTATTCA
44523058 GGCTGTGTGCTGG-TGATTATTCA
1 GGCTGTGTGC-GGATGATTATTCA
44523081 GGCT
1 GGCT
44523085 ACGTTCCTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 22 0.92
24 2 0.08
ACGTcount: A:0.12, C:0.12, G:0.38, T:0.38
Consensus pattern (23 bp):
GGCTGTGTGCGGATGATTATTCA
Found at i:44523124 original size:39 final size:40
Alignment explanation
Indices: 44523065--44523332 Score: 201
Period size: 39 Copynumber: 6.9 Consensus size: 40
44523055 TTGGGCTGTG
* * * *
44523065 TGCT-GGTGATTATTCAGGCTACGTTCCTAGCAAGCTGCA
1 TGCTAGGTGATTATTCGGGCTATGTGCCTAGCAGGCTGCA
* *
44523104 TG-TAGGTGATTATTCGGGCTATGTGCCTAGCCGGCTGCT
1 TGCTAGGTGATTATTCGGGCTATGTGCCTAGCAGGCTGCA
* * * **
44523143 TGC-CGATGATTATTCGGGCTATATGCCTAGCAGGCTGTG
1 TGCTAGGTGATTATTCGGGCTATGTGCCTAGCAGGCTGCA
* * *
44523182 TGCTA-GTGAATATTCGGGCTATGTGCCTAGCTGGCTGTA
1 TGCTAGGTGATTATTCGGGCTATGTGCCTAGCAGGCTGCA
* ** ** * **
44523221 TGCT-GGTGATTATTCAGGCTATGTATCTTCCAGACTGTG
1 TGCTAGGTGATTATTCGGGCTATGTGCCTAGCAGGCTGCA
* * * *
44523260 TGC-CGGTAATTATTCGGGCTATGTGCCTAGTAGTCTG--
1 TGCTAGGTGATTATTCGGGCTATGTGCCTAGCAGGCTGCA
* * * *
44523297 TGTTTCGATGATTATTCGGGCTATATGCCTAGCAGG
1 TG-CTAGGTGATTATTCGGGCTATGTGCCTAGCAGG
44523333 ATGTGTGCCG
Statistics
Matches: 181, Mismatches: 41, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
37 2 0.01
38 1 0.01
39 178 0.98
ACGTcount: A:0.18, C:0.19, G:0.29, T:0.34
Consensus pattern (40 bp):
TGCTAGGTGATTATTCGGGCTATGTGCCTAGCAGGCTGCA
Found at i:44523196 original size:78 final size:78
Alignment explanation
Indices: 44523109--44523341 Score: 254
Period size: 78 Copynumber: 3.0 Consensus size: 78
44523099 CTGCATGTAG
* *
44523109 GTGATTATTCGGGCTATGTGCCTAGCCGGCTGCT-TGCCGATGATTATTCGGGCTATATGCCTAG
1 GTGAATATTCGGGCTATGTGCCTAGCAGGCTG-TATGCCGATGATTATTCGGGCTATATGCCTAG
*
44523173 CAGGCTGTGTGCTA
65 CAGGCTGTGTGCCA
* * * * * ** **
44523187 GTGAATATTCGGGCTATGTGCCTAGCTGGCTGTATGCTGGTGATTATTCAGGCTATGTATCTTCC
1 GTGAATATTCGGGCTATGTGCCTAGCAGGCTGTATGCCGATGATTATTCGGGCTATATGCCTAGC
* *
44523252 AGACTGTGTGCCG
66 AGGCTGTGTGCCA
* * * **
44523265 GT-AATTATTCGGGCTATGTGCCTAGTAGTCTGTGTTTCGATGATTATTCGGGCTATATGCCTAG
1 GTGAA-TATTCGGGCTATGTGCCTAGCAGGCTGTATGCCGATGATTATTCGGGCTATATGCCTAG
*
44523329 CAGGATGTGTGCC
65 CAGGCTGTGTGCC
44523342 GGTGTATGAA
Statistics
Matches: 124, Mismatches: 29, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
77 3 0.02
78 121 0.98
ACGTcount: A:0.17, C:0.19, G:0.30, T:0.34
Consensus pattern (78 bp):
GTGAATATTCGGGCTATGTGCCTAGCAGGCTGTATGCCGATGATTATTCGGGCTATATGCCTAGC
AGGCTGTGTGCCA
Found at i:44523264 original size:117 final size:117
Alignment explanation
Indices: 44523058--44523330 Score: 293
Period size: 117 Copynumber: 2.3 Consensus size: 117
44523048 TGATTATTTG
* * * * *
44523058 GGCTGTGTGCTGGTGATTATTCAGGCTACGTTCCTAGCAAGCTGCATGTAGGTGATTATTCGGGC
1 GGCTGTGTGCTAGTGATTATTCGGGCTATGTGCCTAGCAAGCTGCATGTAGGTGATTATTCAGGC
* * *
44523123 TATGTGCCTAGCCGGCTGCTTGCCGATGATTATTCGGGCTATATGCCTAGCA
66 TATGTACCTAGCCGACTGCTTGCCGATAATTATTCGGGCTATATGCCTAGCA
* ** *
44523175 GGCTGTGTGCTAGTGAATATTCGGGCTATGTGCCTAGCTGGCTGTATGCT-GGTGATTATTCAGG
1 GGCTGTGTGCTAGTGATTATTCGGGCTATGTGCCTAGCAAGCTGCATG-TAGGTGATTATTCAGG
* * * * *
44523239 CTATGTATCT-TCCAGACTG-TGTGCCGGTAATTATTCGGGCTATGTGCCTAGTA
65 CTATGTACCTAGCC-GACTGCT-TGCCGATAATTATTCGGGCTATATGCCTAGCA
* * * *
44523292 GTCTGTGT-TTCGATGATTATTCGGGCTATATGCCTAGCA
1 GGCTGTGTGCTAG-TGATTATTCGGGCTATGTGCCTAGCA
44523331 GGATGTGTGC
Statistics
Matches: 129, Mismatches: 23, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
116 5 0.04
117 123 0.95
118 1 0.01
ACGTcount: A:0.17, C:0.19, G:0.29, T:0.34
Consensus pattern (117 bp):
GGCTGTGTGCTAGTGATTATTCGGGCTATGTGCCTAGCAAGCTGCATGTAGGTGATTATTCAGGC
TATGTACCTAGCCGACTGCTTGCCGATAATTATTCGGGCTATATGCCTAGCA
Found at i:44527901 original size:299 final size:299
Alignment explanation
Indices: 44527363--44527957 Score: 937
Period size: 299 Copynumber: 2.0 Consensus size: 299
44527353 ATGGATTTCG
* *
44527363 TATCTGGTTTACCTATAACTCCGACAAAGAAAGATTCAATCTGGGTGATTTTTGACAGATTGACG
1 TATCTGGTTTACCTATAACTCCGACAAAGAAAGATTCAATCTGGGTGATTGTTGACAAATTGACG
*
44527428 AAATCGGCACATTTTATTCCAATTAGAACAGACTACACCCTTGAGAGATTAGCAGAATTATATGT
66 AAATCGGCACATTTTATTCCAATTAGAACAGACTACACCCTTGAGAGATTAGCAGAACTATATGT
* * * *
44527493 ATCTTAGATTGTGAGATTACATGGAGTTCCGACATCTATTATTTTGAATTGAGATCTGATATTTA
131 ATCTTAGATTGTGAGATTACACGGAGTTCCGACATCTATTATTTTGAATCGAGATCCGAGATTTA
* * **
44527558 CATCGAGATTTTGGAGCAAACTTAATGAGGCTTTAAGCACTAAGCTTAATTTCAGTACTGCATTT
196 CATCAAGATTTTGGAGCAAACTTAACGAGGCTTTAAGCACTAAGCTTAATTTCAACACTGCATTT
*
44527623 CATCCTCAGACTGACGGGCAATCAGAATGAATGATTTTT
261 CATCCTCAGACTGACGGGCAATCAGAACGAATGATTTTT
* * *
44527662 TATCTGGTTTACTTGTAACTCCGAGAAAGAAAGATTCAATAC-GGGTGATTGTTGACAAATTGAC
1 TATCTGGTTTACCTATAACTCCGACAAAGAAAGATTCAAT-CTGGGTGATTGTTGACAAATTGAC
* *
44527726 -AAAGTCGGCACATTTTATTCCAATTAGAATATACTACACCCTTGAGAGATTAGCAGAACTATAT
65 GAAA-TCGGCACATTTTATTCCAATTAGAACAGACTACACCCTTGAGAGATTAGCAGAACTATAT
* *
44527790 GTGT-TTGAGATTGTGAGATTACACGGAGTTTCGACATCTATTATTTT-AGATCGAGATCCGAGA
129 GTATCTT-AGATTGTGAGATTACACGGAGTTCCGACATCTATTATTTTGA-ATCGAGATCCGAGA
*
44527853 TTTACATCAAGATTTTGGAGCAAACTTTACGAGGCTTTAAGCACTAAGCTTAATTTCAACACTGC
192 TTTACATCAAGATTTTGGAGCAAACTTAACGAGGCTTTAAGCACTAAGCTTAATTTCAACACTGC
*
44527918 ATTTCATCCTCAGACTGACGGGCAATCAGAACGAGTGATT
257 ATTTCATCCTCAGACTGACGGGCAATCAGAACGAATGATT
44527958 CTGTAACAGC
Statistics
Matches: 271, Mismatches: 21, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
298 6 0.02
299 264 0.97
300 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (299 bp):
TATCTGGTTTACCTATAACTCCGACAAAGAAAGATTCAATCTGGGTGATTGTTGACAAATTGACG
AAATCGGCACATTTTATTCCAATTAGAACAGACTACACCCTTGAGAGATTAGCAGAACTATATGT
ATCTTAGATTGTGAGATTACACGGAGTTCCGACATCTATTATTTTGAATCGAGATCCGAGATTTA
CATCAAGATTTTGGAGCAAACTTAACGAGGCTTTAAGCACTAAGCTTAATTTCAACACTGCATTT
CATCCTCAGACTGACGGGCAATCAGAACGAATGATTTTT
Found at i:44529191 original size:50 final size:50
Alignment explanation
Indices: 44529132--44529418 Score: 323
Period size: 50 Copynumber: 5.8 Consensus size: 50
44529122 GGCAGTGAGT
* * *
44529132 GTGCCAGTGTAAGACCATGTCTGGTACATGGCATCGGCACAGACCGAGGA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACAGAGGA
* *
44529182 GTGCTAGTGTAAGACCATGTCTAGGACATGGTATCGGCACAGACAGAGGA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACAGAGGA
* * * **
44529232 GAGTTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACCGATAA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACAGAGGA
* * *
44529282 GTGCTAGTGTAAGACCTTGTCTGGGACATGGCATTGGCACGGACAGATGAGA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACAGA-G-GA
* * *** *
44529334 GT-C-AGTGTAAGACCATGTTTGGGACATGGCATCAG--C-TTTAGATGA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACAGAGGA
* * *
44529379 GTGCCAGTGTAAGACCATATCCGGGACATGGCATCGGCAC
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC
44529419 CGATATACGA
Statistics
Matches: 199, Mismatches: 32, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
45 4 0.02
46 1 0.01
47 31 0.16
48 1 0.01
49 1 0.01
50 157 0.79
51 1 0.01
52 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.21
Consensus pattern (50 bp):
GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACAGAGGA
Found at i:44529285 original size:100 final size:100
Alignment explanation
Indices: 44529136--44529366 Score: 363
Period size: 100 Copynumber: 2.3 Consensus size: 100
44529126 GTGAGTGTGC
* *
44529136 CAGTGTAAGACCATGTCTGGTACATGGCATCGGCACAGACCGAGGAGTGCTAGTGTAAGACCATG
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACCGAGAAGTGCTAGTGTAAGACCATG
*
44529201 TCTAGGACATGGTATCGGCACAGACAGAGGAGAGT
66 TCTAGGACATGGCATCGGCACAGACAGAGGAGAGT
* * *
44529236 TAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACCGATAAGTGCTAGTGTAAGACCTTG
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACCGAGAAGTGCTAGTGTAAGACCATG
* * * *
44529301 TCTGGGACATGGCATTGGCACGGACAGATGAGAGT
66 TCTAGGACATGGCATCGGCACAGACAGAGGAGAGT
*
44529336 CAGTGTAAGACCATGTTTGGGACATGGCATC
1 CAGTGTAAGACCATGTCTGGGACATGGCATC
44529367 AGCTTTAGAT
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
100 119 1.00
ACGTcount: A:0.28, C:0.19, G:0.32, T:0.21
Consensus pattern (100 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACCGAGAAGTGCTAGTGTAAGACCATG
TCTAGGACATGGCATCGGCACAGACAGAGGAGAGT
Found at i:44535350 original size:38 final size:38
Alignment explanation
Indices: 44535282--44535434 Score: 202
Period size: 38 Copynumber: 4.1 Consensus size: 38
44535272 ACCTTTATTG
*
44535282 CACCGACTA-TAAGCCTGCTAGGCACTAAGCTTAAATAA
1 CACCGAC-ACTAAGCCTGCTAGGCACTAAGCTTGAATAA
* * * * *
44535320 TAGCGACACTAAGCCTACTAGACACAAAGCTTGAATAA
1 CACCGACACTAAGCCTGCTAGGCACTAAGCTTGAATAA
* *
44535358 CACCAACACAAAGCCTGCTAGGCACTAAGCTTGAATAA
1 CACCGACACTAAGCCTGCTAGGCACTAAGCTTGAATAA
*
44535396 CACCGACACTAAACCT-CTAGGCACTAAGCTTGAATAA
1 CACCGACACTAAGCCTGCTAGGCACTAAGCTTGAATAA
44535433 CA
1 CA
44535435 GTACGATTCA
Statistics
Matches: 98, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
37 24 0.24
38 74 0.76
ACGTcount: A:0.39, C:0.27, G:0.15, T:0.18
Consensus pattern (38 bp):
CACCGACACTAAGCCTGCTAGGCACTAAGCTTGAATAA
Found at i:44548989 original size:3 final size:3
Alignment explanation
Indices: 44548981--44549011 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
44548971 TCCATTTTCC
*
44548981 TCT TCT TCT TCT TAT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
44549012 TTCAATTCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:44553618 original size:13 final size:13
Alignment explanation
Indices: 44553600--44553655 Score: 73
Period size: 13 Copynumber: 4.5 Consensus size: 13
44553590 AATTTTGAAT
44553600 TATTTAGTGATAA
1 TATTTAGTGATAA
* *
44553613 TATTTAATGACAA
1 TATTTAGTGATAA
44553626 TATTTAG-GAT--
1 TATTTAGTGATAA
44553636 TATTTAGTGATAA
1 TATTTAGTGATAA
44553649 TATTTAG
1 TATTTAG
44553656 GAAAAAATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
10 7 0.19
11 3 0.08
12 2 0.06
13 24 0.67
ACGTcount: A:0.38, C:0.02, G:0.14, T:0.46
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:44553639 original size:23 final size:23
Alignment explanation
Indices: 44553613--44553657 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
44553603 TTAGTGATAA
44553613 TATTTAATGACAATATTTAGGAT
1 TATTTAATGACAATATTTAGGAT
* *
44553636 TATTTAGTGATAATATTTAGGA
1 TATTTAATGACAATATTTAGGA
44553658 AAAAATTAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.02, G:0.16, T:0.44
Consensus pattern (23 bp):
TATTTAATGACAATATTTAGGAT
Found at i:44557058 original size:81 final size:81
Alignment explanation
Indices: 44556883--44557119 Score: 237
Period size: 81 Copynumber: 2.9 Consensus size: 81
44556873 CATCTTGGCT
* * * * * *
44556883 GACTACCCCGTGTTTACTGTCCCAGC-GAACTACCCCGTGTTTACTATCCCAATGGACTAACCTG
1 GACTAACCTGTGTTTACTGTCCCAGCAG-ACTAACCCGTGTTTAATATCCCGATGGACTAACCCG
* *
44556947 TGTTTAATGTCCTAATA
65 TGTTTACTGTCCCAATA
* * * *
44556964 GTCTAA-TTCGTGTTTACTGTCCCAGCAGACTAACCCATGTTTAATGTCCCGATGGACTAACCCG
1 GACTAACCT-GTGTTTACTGTCCCAGCAGACTAACCCGTGTTTAATATCCCGATGGACTAACCCG
** *
44557028 TGTTTACTGTCCCGGTG
65 TGTTTACTGTCCCAATA
** * ***
44557045 GACTAACCTGTGTTTACTGT-CTTGCTAGACTAATCCGTGTTTAATATCCCGACAAACTAACCCG
1 GACTAACCTGTGTTTACTGTCCCAGC-AGACTAACCCGTGTTTAATATCCCGATGGACTAACCCG
44557109 TGTTTACTGTC
65 TGTTTACTGTC
44557120 TCGACAGACT
Statistics
Matches: 127, Mismatches: 25, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
80 3 0.02
81 122 0.96
82 2 0.02
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.32
Consensus pattern (81 bp):
GACTAACCTGTGTTTACTGTCCCAGCAGACTAACCCGTGTTTAATATCCCGATGGACTAACCCGT
GTTTACTGTCCCAATA
Found at i:44557124 original size:27 final size:27
Alignment explanation
Indices: 44556883--44557130 Score: 171
Period size: 27 Copynumber: 9.2 Consensus size: 27
44556873 CATCTTGGCT
*
44556883 GACTACCCCGTGTTTACTGTCCC-AGC-
1 GACTAACCCGTGTTTACTGTCCCGA-CA
* * * **
44556909 GAACTACCCCGTGTTTACTATCCCAATG
1 G-ACTAACCCGTGTTTACTGTCCCGACA
* * ** *
44556937 GACTAACCTGTGTTTAATGTCCTAATA
1 GACTAACCCGTGTTTACTGTCCCGACA
* **
44556964 GTCTAATTCGTGTTTACTGTCCC-AGCA
1 GACTAACCCGTGTTTACTGTCCCGA-CA
* * **
44556991 GACTAACCCATGTTTAATGTCCCGATG
1 GACTAACCCGTGTTTACTGTCCCGACA
***
44557018 GACTAACCCGTGTTTACTGTCCCGGTG
1 GACTAACCCGTGTTTACTGTCCCGACA
* **
44557045 GACTAACCTGTGTTTACTGTCTTG-CTA
1 GACTAACCCGTGTTTACTGTCCCGAC-A
* * *
44557072 GACTAATCCGTGTTTAATATCCCGACA
1 GACTAACCCGTGTTTACTGTCCCGACA
* *
44557099 AACTAACCCGTGTTTACTGTCTCGACA
1 GACTAACCCGTGTTTACTGTCCCGACA
44557126 GACTA
1 GACTA
44557131 TACTGGTTGC
Statistics
Matches: 173, Mismatches: 42, Indels: 13
0.76 0.18 0.06
Matches are distributed among these distances:
26 2 0.01
27 167 0.97
28 4 0.02
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (27 bp):
GACTAACCCGTGTTTACTGTCCCGACA
Found at i:44560362 original size:4 final size:4
Alignment explanation
Indices: 44560353--44560386 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
44560343 ACCATGTCTC
44560353 TCTT TCTT TCTT TCTT TCTT TCTT TCTT T-TT TCT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCT
44560387 GAATGGAGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:44566214 original size:37 final size:39
Alignment explanation
Indices: 44566119--44566215 Score: 99
Period size: 40 Copynumber: 2.5 Consensus size: 39
44566109 ACACACCAGT
**
44566119 TTGGCACCTAGTGCCTCATCAGATAATTCGAAGTAGTAAA
1 TTGGCACCTAGTGCCTCATCAGATAAACCGAAG-AGTAAA
* * * * *
44566159 TTGACACCCAATGTCTCATCAGCTAAACCG-A-AGTAAA
1 TTGGCACCTAGTGCCTCATCAGATAAACCGAAGAGTAAA
*
44566196 TTGGCACCTAGTACCTCATC
1 TTGGCACCTAGTGCCTCATC
44566216 GAATATATTC
Statistics
Matches: 45, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
37 21 0.47
39 1 0.02
40 23 0.51
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (39 bp):
TTGGCACCTAGTGCCTCATCAGATAAACCGAAGAGTAAA
Found at i:44567211 original size:31 final size:31
Alignment explanation
Indices: 44567176--44567237 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
44567166 CTTTTCTTTC
*
44567176 CTTTCTGTTTCTTTCTT-TTTATTCATTTGTT
1 CTTTCTATTTCTTT-TTCTTTATTCATTTGTT
* *
44567207 CTTTCTATTTCTTTTTCTTTCTTTATTTGTT
1 CTTTCTATTTCTTTTTCTTTATTCATTTGTT
44567238 TTATTATATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 2 0.07
31 25 0.93
ACGTcount: A:0.06, C:0.16, G:0.05, T:0.73
Consensus pattern (31 bp):
CTTTCTATTTCTTTTTCTTTATTCATTTGTT
Found at i:44567298 original size:13 final size:13
Alignment explanation
Indices: 44567276--44567308 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
44567266 ATATTTAATC
*
44567276 ATTAAGAATATAT
1 ATTAATAATATAT
44567289 ATTAATAATATAT
1 ATTAATAATATAT
44567302 A-TAATAA
1 ATTAATAA
44567309 ATTTATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (13 bp):
ATTAATAATATAT
Found at i:44569300 original size:3 final size:3
Alignment explanation
Indices: 44569292--44569414 Score: 210
Period size: 3 Copynumber: 40.7 Consensus size: 3
44569282 GTTTTGCTAT
*
44569292 TTC TTC TTC TTC TTC TTC TTC TTC TTA TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
44569340 TTC TTC TTC TTC TTT TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
44569388 TTC TTC TTC TTTC TTC TTC CTC TTC TT
1 TTC TTC TTC -TTC TTC TTC TTC TTC TT
44569415 TTTACACTTT
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
3 110 0.97
4 3 0.03
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:44574462 original size:12 final size:12
Alignment explanation
Indices: 44574445--44574470 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
44574435 CTGATGTACA
44574445 TAAGACGACATT
1 TAAGACGACATT
44574457 TAAGACGACATT
1 TAAGACGACATT
44574469 TA
1 TA
44574471 GGACTCGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (12 bp):
TAAGACGACATT
Found at i:44575600 original size:33 final size:33
Alignment explanation
Indices: 44575554--44575623 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
44575544 ATTTTAACCT
44575554 GAAT-AGCGAAGGGGTGCTCTATTTCCGTGGGA
1 GAATCAGCGAAGGGGTGCTCTATTTCCGTGGGA
44575586 GAATCAGCGAAGGGGTGCTCTATTTCCGTGGGA
1 GAATCAGCGAAGGGGTGCTCTATTTCCGTGGGA
44575619 GAATC
1 GAATC
44575624 TGTGTACCGA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 4 0.11
33 33 0.89
ACGTcount: A:0.23, C:0.17, G:0.36, T:0.24
Consensus pattern (33 bp):
GAATCAGCGAAGGGGTGCTCTATTTCCGTGGGA
Found at i:44581182 original size:16 final size:16
Alignment explanation
Indices: 44581161--44581228 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
44581151 TTTGGTTCGC
44581161 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
44581177 TGTATTGGATTAAAGG
1 TGTATTGGATTAGAGG
44581193 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
44581209 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
44581225 TGTA
1 TGTA
44581229 ATAGCAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.26, C:0.00, G:0.35, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:44581485 original size:18 final size:17
Alignment explanation
Indices: 44581464--44581498 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
44581454 TTATTATTAA
*
44581464 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
44581482 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
44581499 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:44581552 original size:157 final size:157
Alignment explanation
Indices: 44581351--44581667 Score: 589
Period size: 157 Copynumber: 2.0 Consensus size: 157
44581341 TAGAATACCC
*
44581351 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* * *
44581416 TTATCAATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
44581481 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
*
44581508 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
44581573 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
44581638 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
44581665 TTA
1 TTA
44581668 ATATTCTTAT
Statistics
Matches: 155, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 155 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (157 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:44581638 original size:16 final size:16
Alignment explanation
Indices: 44581601--44581642 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
44581591 TTAATCATAT
*
44581601 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
44581617 TT-AAATATATTATAA
1 TTAAAATATATTATAA
44581632 TTAAAATATAT
1 TTAAAATATAT
44581643 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:44581649 original size:14 final size:15
Alignment explanation
Indices: 44581610--44581651 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
44581600 TTTAAACATA
*
44581610 ATTATTATTAAATAT
1 ATTATAATTAAATAT
44581625 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
44581639 A-TATAATTTAATA
1 ATTATAATTAAATA
44581652 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:44581664 original size:82 final size:82
Alignment explanation
Indices: 44581421--44581670 Score: 215
Period size: 76 Copynumber: 3.1 Consensus size: 82
44581411 TATTATTATC
* *
44581421 AATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATAT
1 AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATAT
44581486 AATTTAATAAAATTCTT
66 AATTTAATAAAATTCTT
* * * *
44581503 AATAATTAGCAGA-AATTT-GT--T-TTGGT-AA-ATTATTATTGTT--AT-TGTTAT--TTAAA
1 AATAA-TA--A-ATAATTTAATCATATT--TAAACATAATTATTATTAAATATATTATAATTAAA
* * * * *
44581556 TTTTAATAAGATTATTAATA-TC--
60 ATAT-ATAA-TTTAATAAAATTCTT
44581578 AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATAT
1 AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATAT
44581643 AATTTAATAAAATTCTT
66 AATTTAATAAAATTCTT
*
44581660 AATAATTAATA
1 AATAATAAATA
44581671 TTCTTATATG
Statistics
Matches: 124, Mismatches: 21, Indels: 46
0.65 0.11 0.24
Matches are distributed among these distances:
71 1 0.01
72 6 0.05
73 1 0.01
74 3 0.02
75 8 0.06
76 19 0.15
77 6 0.05
78 13 0.10
79 14 0.11
80 6 0.05
81 19 0.15
82 18 0.15
83 3 0.02
84 1 0.01
85 5 0.04
86 1 0.01
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (82 bp):
AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATAT
AATTTAATAAAATTCTT
Found at i:44581751 original size:157 final size:154
Alignment explanation
Indices: 44581406--44581752 Score: 342
Period size: 157 Copynumber: 2.2 Consensus size: 154
44581396 AAATTTTAAT
* *
44581406 AAGATTATTATTATCAATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATT
1 AAGATAATTAATAT-AATAAT-AATATTTTAATCATATTTAAACATAATTATTATTAAATATATT
* * * * * ** *
44581471 TTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAGAAATTTGTTTTGGTAAATTAT
64 ATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAACACAAATATGATTTACTAAATTAA
* * * * * * * *
44581536 TATTGTTATTGTTATTTAAATTTTAAT
129 TATTGATACTATAAATGAAAATTT-AG
* *
44581563 AAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATT
1 AAGATAATTAATAT-AATAAT-AATATTTTAATCATATTTAAACATAATTATTATTAAATATATT
* **
44581628 ATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAA
64 ATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAACA--CAAATATG-ATTTACT-AAA
44581693 TCATAATATATGATACTATAAATGAAAATTT-G
125 T--TAATAT-TGATACTATAAATGAAAATTTAG
*
44581725 AA-ATAATTAATAT-ATCAT-ATATTTTAAT
1 AAGATAATTAATATAATAATAATATTTTAAT
44581753 TAAAATATAT
Statistics
Matches: 159, Mismatches: 24, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
157 112 0.70
159 8 0.05
160 4 0.03
161 14 0.09
162 2 0.01
163 5 0.03
164 14 0.09
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (154 bp):
AAGATAATTAATATAATAATAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTAT
AATTAAAATATATAATTTAATAAAATTCTTAATAATTAACACAAATATGATTTACTAAATTAATA
TTGATACTATAAATGAAAATTTAG
Found at i:44581863 original size:24 final size:25
Alignment explanation
Indices: 44581817--44581864 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
44581807 TATGAATTTG
44581817 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
44581843 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
44581865 AATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:44581868 original size:92 final size:92
Alignment explanation
Indices: 44581772--44581981 Score: 232
Period size: 92 Copynumber: 2.3 Consensus size: 92
44581762 TGATTTAATA
* * *
44581772 AAATTT-AAAATAATT-ATAACTAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TA
1 AAATTTCAAAA-AATTCATAA-TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTA
*
44581834 ATTATTACATATAATTTAATAATTAATATT
64 A-TATTAAATATAATTTAATAATTAATATT
* * * * *
44581864 AAATTTCATAAAATTCTTGATAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAAT
1 AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
* *
44581929 ATTAAATATAATTTAAT-AGTGATA-T
66 ATTAAATATAATTTAATAATTAATATT
* *
44581954 ATAATTTCATAAAATTCTTAATAATAAA
1 A-AATTTCAAAAAATTCATAATAATAAA
44581982 ATGTTCTTCT
Statistics
Matches: 102, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
90 2 0.02
91 30 0.29
92 62 0.61
93 8 0.08
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (92 bp):
AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
ATTAAATATAATTTAATAATTAATATT
Found at i:44581989 original size:92 final size:92
Alignment explanation
Indices: 44581807--44582000 Score: 268
Period size: 92 Copynumber: 2.1 Consensus size: 92
44581797 AATTATATTT
* * * *
44581807 TATGAATTTGTATAATTTAAAATAATAATTATTACATATAATTTAATAATTAATATTAAATTTCA
1 TATGAATTTATACAATTTAAAATAATAATTATTAAATATAATTTAATAATGAATATTAAATTTCA
* *
44581872 TAAAATTCTTGATAATAAATTTTCTTA
66 TAAAATTCTTAATAATAAATGTTCTTA
*
44581899 TATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTTAATAGTG-ATA-TATAATTT
1 TATGAATTTATACAATTTAAAATAA-TAATTATTAAATATAATTTAATAATGAATATTA-AATTT
*
44581961 CATAAAATTCTTAATAATAAAATGTTCTTC
64 CATAAAATTCTTAATAAT-AAATGTTCTTA
44581991 TATGAATTTA
1 TATGAATTTA
44582001 CTAAAATCAA
Statistics
Matches: 91, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
90 2 0.02
91 25 0.27
92 61 0.67
93 3 0.03
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (92 bp):
TATGAATTTATACAATTTAAAATAATAATTATTAAATATAATTTAATAATGAATATTAAATTTCA
TAAAATTCTTAATAATAAATGTTCTTA
Found at i:44590113 original size:16 final size:15
Alignment explanation
Indices: 44590101--44590164 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 15
44590091 CCCTTTTTCT
44590101 TTTCTTTCCTTTTTG
1 TTTCTTTCCTTTTTG
44590116 TTTCTTT-CTTTTT-
1 TTTCTTTCCTTTTTG
* *
44590129 TTTCATT--TTTTTC
1 TTTCTTTCCTTTTTG
* *
44590142 TTTCTATTTCTTTTTA
1 TTTCT-TTCCTTTTTG
44590158 TTTCTTT
1 TTTCTTT
44590165 ATTTGTTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
12 5 0.12
13 10 0.24
14 8 0.19
15 9 0.21
16 10 0.24
ACGTcount: A:0.05, C:0.16, G:0.02, T:0.78
Consensus pattern (15 bp):
TTTCTTTCCTTTTTG
Found at i:44590122 original size:10 final size:9
Alignment explanation
Indices: 44590120--44590164 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
44590110 TTTTTGTTTC
44590120 TTTCTTTTT
1 TTTCTTTTT
*
44590129 TTTCATTTT
1 TTTCTTTTT
*
44590138 TTTCTTTCTA
1 TTTCTTT-TT
44590148 TTTCTTTTT
1 TTTCTTTTT
44590157 ATTTCTTT
1 -TTTCTTT
44590165 ATTTGTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
9 15 0.50
10 15 0.50
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:44590132 original size:24 final size:22
Alignment explanation
Indices: 44590096--44590160 Score: 67
Period size: 24 Copynumber: 2.8 Consensus size: 22
44590086 CCTTCCCCTT
* *
44590096 TTTCTTTTCTTTCCTTTTTGTTTC
1 TTTCTTTT-TTTTCATTTT-TTTC
44590120 TTTCTTTTTTTTCATTTTTTTC
1 TTTCTTTTTTTTCATTTTTTTC
*
44590142 TTTCTATTTCTTTTTATTT
1 TTTCT-TTT-TTTTCATTT
44590161 CTTTATTTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 9 0.25
23 11 0.31
24 16 0.44
ACGTcount: A:0.05, C:0.15, G:0.02, T:0.78
Consensus pattern (22 bp):
TTTCTTTTTTTTCATTTTTTTC
Found at i:44590155 original size:42 final size:42
Alignment explanation
Indices: 44590094--44590173 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
44590084 TTCCTTCCCC
* * *
44590094 TTTTTCTTTTCTTTCCTTTTTGTTTCTTTCTTTTTTTTCATT
1 TTTTTCTTTTCTTTCCTTTTTATTTCTTTATTTGTTTTCATT
*
44590136 TTTTTC-TTTCTATTTCTTTTTATTTCTTTATTTGTTTT
1 TTTTTCTTTTCT-TTCCTTTTTATTTCTTTATTTGTTTT
44590174 ATTATATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 5 0.15
42 28 0.85
ACGTcount: A:0.05, C:0.14, G:0.03, T:0.79
Consensus pattern (42 bp):
TTTTTCTTTTCTTTCCTTTTTATTTCTTTATTTGTTTTCATT
Found at i:44590702 original size:4 final size:4
Alignment explanation
Indices: 44590685--44590721 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
44590675 TCTTTCCATC
* *
44590685 TTCT TTCC TTCT TTCT TTCT TTCT TTCC TTCT TTCT T
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT T
44590722 GCATTATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (4 bp):
TTCT
Found at i:44590702 original size:12 final size:12
Alignment explanation
Indices: 44590673--44590721 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
44590663 AAACGTGCAT
*
44590673 TTTCTTTCCATC
1 TTTCTTTCCTTC
44590685 -TTCTTTCCTTC
1 TTTCTTTCCTTC
*
44590696 TTTCTTTCTTTC
1 TTTCTTTCCTTC
* *
44590708 TTTCCTTCTTTC
1 TTTCTTTCCTTC
44590720 TT
1 TT
44590722 GCATTATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
11 10 0.30
12 23 0.70
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTCTTTCCTTC
Found at i:44594222 original size:21 final size:20
Alignment explanation
Indices: 44594181--44594222 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
44594171 TTAAATTGAG
*
44594181 AAATGTGTAAATTCTGTAGT
1 AAATGTGTAAATTCTGAAGT
*
44594201 AAATGTGTGAAATTGTGAAGT
1 AAATGTGT-AAATTCTGAAGT
44594222 A
1 A
44594223 TATGGGCTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (20 bp):
AAATGTGTAAATTCTGAAGT
Done.