Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 136 of 235
Found at i:45998728 original size:26 final size:26
Alignment explanation
Indices: 45998698--45998749 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
45998688 GCAAGAGGAG
** *
45998698 ATGGAATCACTTTGCAAAAATAAAAA
1 ATGGAATCACTTCACAAAAACAAAAA
*
45998724 ATGGAATTACTTCACAAAAACAAAAA
1 ATGGAATCACTTCACAAAAACAAAAA
45998750 CTGCATTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.56, C:0.13, G:0.10, T:0.21
Consensus pattern (26 bp):
ATGGAATCACTTCACAAAAACAAAAA
Found at i:46000582 original size:49 final size:48
Alignment explanation
Indices: 46000506--46000613 Score: 135
Period size: 49 Copynumber: 2.2 Consensus size: 48
46000496 GAACTTGTAC
* * * * *
46000506 ATTCAACCATCCGAATGACCCAACAATGATGACTTTTACTGTTTGCAT
1 ATTCTACCATCCCAATGACCCAACAATGATGACTTTGAATATTTGCAT
* *
46000554 ATTCTACCATCCCAAGTGGCCCAACAATGATGGCTTTGAATATTTGCAT
1 ATTCTACCATCCCAA-TGACCCAACAATGATGACTTTGAATATTTGCAT
*
46000603 ATTCTATCATC
1 ATTCTACCATC
46000614 TTGAGCGGCC
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
48 13 0.25
49 38 0.75
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (48 bp):
ATTCTACCATCCCAATGACCCAACAATGATGACTTTGAATATTTGCAT
Found at i:46000629 original size:49 final size:49
Alignment explanation
Indices: 46000524--46000643 Score: 141
Period size: 49 Copynumber: 2.4 Consensus size: 49
46000514 ATCCGAATGA
* * * * *
46000524 CCCAACAATGATGACTTTTACTGTTTGCATATTCTACCATCCCAAGTGG
1 CCCAACAATGATGGCTTTGAATATTTGCATATTCTACCATCCCAAGCGG
* ***
46000573 CCCAACAATGATGGCTTTGAATATTTGCATATTCTATCATCTTGAGCGG
1 CCCAACAATGATGGCTTTGAATATTTGCATATTCTACCATCCCAAGCGG
* *
46000622 CCTAACAATGATGGTTTTGAAT
1 CCCAACAATGATGGCTTTGAAT
46000644 CATTATTTCG
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 60 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.34
Consensus pattern (49 bp):
CCCAACAATGATGGCTTTGAATATTTGCATATTCTACCATCCCAAGCGG
Found at i:46001510 original size:20 final size:20
Alignment explanation
Indices: 46001467--46001506 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
46001457 GGTTAACATT
*
46001467 AGTTAATTATTAATTAGTTA
1 AGTTAATTATTAATTAATTA
46001487 AGTTAATTA-TAATTAATTA
1 AGTTAATTATTAATTAATTA
46001506 A
1 A
46001507 AGTTTAATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (20 bp):
AGTTAATTATTAATTAATTA
Found at i:46029070 original size:43 final size:44
Alignment explanation
Indices: 46028990--46029100 Score: 125
Period size: 43 Copynumber: 2.5 Consensus size: 44
46028980 ATCCTGTCTT
* * * * * *
46028990 CCTGAAGCCTCAGCGAAGCAGATTGAAGTCACTAGTCTTATCTC
1 CCTGAAGCCGCAGTGGAGCAGACTGAAGTCACAAGTCTCATCTC
* * *
46029034 CCTGAAG-TGCAGTGGAGTAGACTGAAGTTACAAGTCTCATCTC
1 CCTGAAGCCGCAGTGGAGCAGACTGAAGTCACAAGTCTCATCTC
*
46029077 CTTGAAGCCGCAGTGGAGCAGACT
1 CCTGAAGCCGCAGTGGAGCAGACT
46029101 AAATGTACAG
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
43 33 0.61
44 21 0.39
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.23
Consensus pattern (44 bp):
CCTGAAGCCGCAGTGGAGCAGACTGAAGTCACAAGTCTCATCTC
Found at i:46029647 original size:68 final size:68
Alignment explanation
Indices: 46029558--46029827 Score: 434
Period size: 68 Copynumber: 4.0 Consensus size: 68
46029548 CAATCAAATA
**
46029558 TCTTCTCCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGTAGATCTCCTTGAAGTTTCAGTGG
1 TCTTCTCCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAACAGATCTCCTTGAAGTTTCAGTGG
46029623 ATC
66 ATC
* * *
46029626 TCTTTTCCCTGAAATGGCGTTGGAGTGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGG
1 TCTTCTCCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAACAGATCTCCTTGAAGTTTCAGTGG
46029691 ATC
66 ATC
* *
46029694 TCTTCTCCCTGATATGGCGTTGGAGCGGCTAAAAGCCACAACAGATCTCCTTGAAGTTTCAGTGA
1 TCTTCTCCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAACAGATCTCCTTGAAGTTTCAGTGG
46029759 ATC
66 ATC
* * * *
46029762 TCTTCTCCCTGAAATGGTGGT-GAGCAGCTAAAAGCCACAACAGATTTCCTTGAAGTTTCAGTGG
1 TCTTCTCCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAACAGATCTCCTTGAAGTTTCAGTGG
46029826 AT
66 AT
46029828 TAATCGAAGC
Statistics
Matches: 188, Mismatches: 14, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
67 42 0.22
68 146 0.78
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.29
Consensus pattern (68 bp):
TCTTCTCCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAACAGATCTCCTTGAAGTTTCAGTGG
ATC
Found at i:46030720 original size:12 final size:13
Alignment explanation
Indices: 46030703--46030753 Score: 54
Period size: 12 Copynumber: 4.1 Consensus size: 13
46030693 AGAGCTTTGT
46030703 TTTATT-TTTTTA
1 TTTATTATTTTTA
46030715 TTTATTATTTTTA
1 TTTATTATTTTTA
* *
46030728 -CTATTATTTATA
1 TTTATTATTTTTA
46030740 -TTATTATTATTTA
1 TTTATTATT-TTTA
46030753 T
1 T
46030754 CATGTATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 23 0.72
13 9 0.28
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTATTATTTTTA
Found at i:46030722 original size:3 final size:3
Alignment explanation
Indices: 46030716--46030787 Score: 51
Period size: 3 Copynumber: 23.3 Consensus size: 3
46030706 ATTTTTTTAT
* * *
46030716 TTA TTA TTT TTA CTA TTA TT- TATA TTA TTA TTA TTTA TCA TGTA TATA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA -TTA TTA T-TA T-TA
46030764 TTA TTA TT- TATA TTA TTA -TA TTA T
1 TTA TTA TTA T-TA TTA TTA TTA TTA T
46030788 ATATGCCCTC
Statistics
Matches: 55, Mismatches: 7, Indels: 14
0.72 0.09 0.18
Matches are distributed among these distances:
2 4 0.07
3 41 0.75
4 10 0.18
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:46030777 original size:12 final size:12
Alignment explanation
Indices: 46030711--46030789 Score: 83
Period size: 12 Copynumber: 6.6 Consensus size: 12
46030701 GTTTTATTTT
46030711 TTTAT-TTATTA
1 TTTATATTATTA
* *
46030722 TTTTTACTATTA
1 TTTATATTATTA
46030734 TTTATATTATTA
1 TTTATATTATTA
*
46030746 -TTAT-TTATCA
1 TTTATATTATTA
46030756 TGTATATATTATTA
1 T-T-TATATTATTA
46030770 TTTATATTATTA
1 TTTATATTATTA
46030782 TATTATAT
1 T-TTATAT
46030790 ATGCCCTCTC
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
10 5 0.09
11 8 0.14
12 27 0.48
13 10 0.18
14 6 0.11
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.65
Consensus pattern (12 bp):
TTTATATTATTA
Found at i:46030790 original size:15 final size:15
Alignment explanation
Indices: 46030716--46030791 Score: 63
Period size: 15 Copynumber: 5.1 Consensus size: 15
46030706 ATTTTTTTAT
*
46030716 TTATTAT-TTTTACTA
1 TTATTATATTATA-TA
46030731 TTATTTATATTAT-TA
1 TTA-TTATATTATATA
46030746 TTATTTATCATGTATATA
1 TTA-TTAT-AT-TATATA
46030764 TTA-T-TATT-TATA
1 TTATTATATTATATA
46030776 TTATTATATTATATA
1 TTATTATATTATATA
46030791 T
1 T
46030792 GCCCTCTCCA
Statistics
Matches: 52, Mismatches: 1, Indels: 16
0.75 0.01 0.23
Matches are distributed among these distances:
12 7 0.13
13 2 0.04
14 6 0.12
15 19 0.37
16 7 0.13
17 6 0.12
18 5 0.10
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (15 bp):
TTATTATATTATATA
Found at i:46033458 original size:5 final size:5
Alignment explanation
Indices: 46033448--46033475 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
46033438 TGGTGTGTTC
46033448 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
46033476 TTCACAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:46035731 original size:26 final size:26
Alignment explanation
Indices: 46035695--46035746 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
46035685 GCAAGAGGAG
*
46035695 ATGGAATCACTTTACAAAAACAAAAA
1 ATGGAATCACTTCACAAAAACAAAAA
46035721 ATGGAATCACTTCACAAAAACAAAAA
1 ATGGAATCACTTCACAAAAACAAAAA
46035747 CTACATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.58, C:0.17, G:0.08, T:0.17
Consensus pattern (26 bp):
ATGGAATCACTTCACAAAAACAAAAA
Found at i:46037448 original size:48 final size:48
Alignment explanation
Indices: 46037385--46037498 Score: 122
Period size: 49 Copynumber: 2.4 Consensus size: 48
46037375 CATGTAGAAC
* * * * * *
46037385 TTGCACATTCAACCATCCG-GATGACCCAACAATGATGATTTTTACTGT
1 TTGCATATTCTACCATCCGAGATG-CCCAACAATGATGACTTTGAATAT
* *
46037433 TTGCATATTCTACCATCCCGAGTTGCCCAACAATGATGGCTTTGAATAT
1 TTGCATATTCTACCAT-CCGAGATGCCCAACAATGATGACTTTGAATAT
*
46037482 TTGCATATTCTATCATC
1 TTGCATATTCTACCATC
46037499 TTAAGCGGCC
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
48 15 0.27
49 37 0.67
50 3 0.05
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (48 bp):
TTGCATATTCTACCATCCGAGATGCCCAACAATGATGACTTTGAATAT
Found at i:46038393 original size:20 final size:20
Alignment explanation
Indices: 46038350--46038389 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
46038340 GGTTAACATT
*
46038350 AGTTAATTATTAATTAGTTA
1 AGTTAATTATTAATTAATTA
46038370 AGTTAATTA-TAATTAATTA
1 AGTTAATTATTAATTAATTA
46038389 A
1 A
46038390 AGTTTAATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (20 bp):
AGTTAATTATTAATTAATTA
Found at i:46044059 original size:45 final size:45
Alignment explanation
Indices: 46043995--46044125 Score: 262
Period size: 45 Copynumber: 2.9 Consensus size: 45
46043985 ATCTTAGCCC
46043995 AATTTCAGATTCTTTTAATCGAATCACATGACGTACCCGATGCCT
1 AATTTCAGATTCTTTTAATCGAATCACATGACGTACCCGATGCCT
46044040 AATTTCAGATTCTTTTAATCGAATCACATGACGTACCCGATGCCT
1 AATTTCAGATTCTTTTAATCGAATCACATGACGTACCCGATGCCT
46044085 AATTTCAGATTCTTTTAATCGAATCACATGACGTACCCGAT
1 AATTTCAGATTCTTTTAATCGAATCACATGACGTACCCGAT
46044126 ATCACGTCAG
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 86 1.00
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.34
Consensus pattern (45 bp):
AATTTCAGATTCTTTTAATCGAATCACATGACGTACCCGATGCCT
Found at i:46046428 original size:19 final size:19
Alignment explanation
Indices: 46046400--46046447 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
46046390 GTATATATTT
46046400 TAAA-TTTATTTAGG-TAGA
1 TAAATTTTATTT-GGATAGA
46046418 TAAATTTTATTTGGATAGA
1 TAAATTTTATTTGGATAGA
46046437 TAAATTTTATT
1 TAAATTTTATT
46046448 CATATTGTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.21
19 22 0.79
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (19 bp):
TAAATTTTATTTGGATAGA
Found at i:46046516 original size:43 final size:44
Alignment explanation
Indices: 46046461--46046553 Score: 145
Period size: 43 Copynumber: 2.2 Consensus size: 44
46046451 ATTGTAGAAA
*
46046461 TATTTT-TATTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
1 TATTTTCTATTTTATCTTTTAATAGTTTACTAGAATAAGGGAAC
* *
46046504 TATTTTCT-TTTTATGTTTTAATAGTTTATTAGAATAAGGGAAC
1 TATTTTCTATTTTATCTTTTAATAGTTTACTAGAATAAGGGAAC
46046547 TATTTTC
1 TATTTTC
46046554 CCAATTAGGA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
43 45 0.98
44 1 0.02
ACGTcount: A:0.29, C:0.06, G:0.13, T:0.52
Consensus pattern (44 bp):
TATTTTCTATTTTATCTTTTAATAGTTTACTAGAATAAGGGAAC
Found at i:46055735 original size:19 final size:18
Alignment explanation
Indices: 46055706--46055749 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
46055696 GTATATATTT
*
46055706 TAAATTTATTTAG-GTAGA
1 TAAATTTATTT-GCATAGA
46055724 TAAATCTTATTTGCATAGA
1 TAAAT-TTATTTGCATAGA
46055743 TAAATTT
1 TAAATTT
46055750 TATTCATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (18 bp):
TAAATTTATTTGCATAGA
Found at i:46055815 original size:43 final size:43
Alignment explanation
Indices: 46055762--46055859 Score: 144
Period size: 43 Copynumber: 2.3 Consensus size: 43
46055752 TTCATATTCT
*
46055762 AGAAATATTTT-TATTTTATCTTTTAGTAGTTTACTAGAATAAG
1 AGAACTATTTTCT-TTTTATCTTTTAGTAGTTTACTAGAATAAG
* * *
46055805 GGAACTATTTTCTTTTTATGTTTTAGTAGTTTATTAGAATAAG
1 AGAACTATTTTCTTTTTATCTTTTAGTAGTTTACTAGAATAAG
46055848 AGAACTATTTTC
1 AGAACTATTTTC
46055860 CCAATTAGGA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
43 48 0.98
44 1 0.02
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.49
Consensus pattern (43 bp):
AGAACTATTTTCTTTTTATCTTTTAGTAGTTTACTAGAATAAG
Found at i:46060693 original size:17 final size:15
Alignment explanation
Indices: 46060663--46060696 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
46060653 AATCGAGCAA
46060663 AAAGAAAAGAAGAAG
1 AAAGAAAAGAAGAAG
46060678 AAAGAAAACGGAAGAAG
1 AAAGAAAA--GAAGAAG
46060695 AA
1 AA
46060697 GCAATGGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
17 9 0.53
ACGTcount: A:0.71, C:0.03, G:0.26, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAGAAG
Found at i:46064161 original size:29 final size:28
Alignment explanation
Indices: 46064126--46064181 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
46064116 AGTTATACCA
46064126 ATTTGGCTTCGGGCCATGCATATCAGTTG
1 ATTTGGCTTCGGGCCATG-ATATCAGTTG
*
46064155 ATTTGGCTTTGGGCCATGATATCAGTT
1 ATTTGGCTTCGGGCCATGATATCAGTT
46064182 CTTCGGAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 9 0.35
29 17 0.65
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.38
Consensus pattern (28 bp):
ATTTGGCTTCGGGCCATGATATCAGTTG
Found at i:46077065 original size:40 final size:36
Alignment explanation
Indices: 46076962--46077096 Score: 123
Period size: 35 Copynumber: 3.7 Consensus size: 36
46076952 TTTTCCTCAT
* *
46076962 TGAAATACCATACCTACATTTTACAACTCGGTATG-
1 TGAAATACCATACCTACATTTCACAACTCAGTATGA
* * ***
46076997 GGAAATGCCATACCTACATTTTTTAACTCAGTATGAA
1 TGAAATACCATACCTACATTTCACAACTCAGTATG-A
*
46077034 TTTGATAATACCATACCTACATTTCACAACTCAGTGTGGA
1 --TGA-AATACCATACCTACATTTCACAACTCAGTAT-GA
*
46077074 TG--ATAACATACCTACATTTCACA
1 TGAAATACCATACCTACATTTCACA
46077097 CTTTTCCATG
Statistics
Matches: 82, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
35 50 0.61
38 2 0.02
39 2 0.02
40 27 0.33
41 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.32
Consensus pattern (36 bp):
TGAAATACCATACCTACATTTCACAACTCAGTATGA
Found at i:46090449 original size:21 final size:22
Alignment explanation
Indices: 46090412--46090458 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
46090402 TAATTTTCAG
* *
46090412 TTTT-TTTCATGTTCAAGTTTT
1 TTTTATTTCATGTACAAGATTT
46090433 TTTTATTTCAT-TACAAGATTT
1 TTTTATTTCATGTACAAGATTT
*
46090454 CTTTA
1 TTTTA
46090459 CTCCCCATCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.21, C:0.11, G:0.06, T:0.62
Consensus pattern (22 bp):
TTTTATTTCATGTACAAGATTT
Found at i:46091069 original size:34 final size:34
Alignment explanation
Indices: 46091026--46091092 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
46091016 GCATGCTTAG
46091026 CATGAGGATGATCAAAAAGCACCGAGAAACCTAT
1 CATGAGGATGATCAAAAAGCACCGAGAAACCTAT
* *
46091060 CATGAGGATGATCGAAAAGCGCCGAGAAACCTA
1 CATGAGGATGATCAAAAAGCACCGAGAAACCTA
46091093 CCCTACTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.13
Consensus pattern (34 bp):
CATGAGGATGATCAAAAAGCACCGAGAAACCTAT
Found at i:46093294 original size:19 final size:19
Alignment explanation
Indices: 46093266--46093304 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
46093256 AAAGCGAAAG
46093266 AAACGAGAAAA-GGGCCAA
1 AAACGAGAAAATGGGCCAA
46093284 AAACGGAGAAAATGGGCCAA
1 AAAC-GAGAAAATGGGCCAA
46093304 A
1 A
46093305 GTACGAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.21
19 7 0.37
20 8 0.42
ACGTcount: A:0.54, C:0.15, G:0.28, T:0.03
Consensus pattern (19 bp):
AAACGAGAAAATGGGCCAA
Found at i:46099622 original size:16 final size:16
Alignment explanation
Indices: 46099603--46099638 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
46099593 TTTCTTTCTT
* *
46099603 TTTTCTTCTTCTTTGA
1 TTTTCTTCTCCTTCGA
46099619 TTTTCTTCTCCTTCGA
1 TTTTCTTCTCCTTCGA
46099635 TTTT
1 TTTT
46099639 TCGTTTTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.22, G:0.06, T:0.67
Consensus pattern (16 bp):
TTTTCTTCTCCTTCGA
Found at i:46100780 original size:38 final size:39
Alignment explanation
Indices: 46100689--46100782 Score: 109
Period size: 40 Copynumber: 2.4 Consensus size: 39
46100679 CGGTACCTTT
* * * * *
46100689 TGGTGTGCAGGGTTAGATGGGTTGATTATATCCCCATACT
1 TGGTGTGTAGGGTTGGGTGGGTCGATTATATCCCCA-ACA
*
46100729 TGGTGTGTAGGGTTGGGTGGGTCGATTCTATCCCC-ACA
1 TGGTGTGTAGGGTTGGGTGGGTCGATTATATCCCCAACA
*
46100767 TGGTGTGTTGGGTTGG
1 TGGTGTGTAGGGTTGG
46100783 TCAAAGATGG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
38 17 0.36
40 30 0.64
ACGTcount: A:0.14, C:0.14, G:0.37, T:0.35
Consensus pattern (39 bp):
TGGTGTGTAGGGTTGGGTGGGTCGATTATATCCCCAACA
Found at i:46102353 original size:52 final size:52
Alignment explanation
Indices: 46102275--46102375 Score: 193
Period size: 52 Copynumber: 1.9 Consensus size: 52
46102265 ATCAAATTTG
46102275 GAATTGGATCGGGGAAAAGATAAAAGTATTCAACTAATCGACTTGATTCTTT
1 GAATTGGATCGGGGAAAAGATAAAAGTATTCAACTAATCGACTTGATTCTTT
*
46102327 GAATTGGATCGGGGAAAAGATAAAAGTATTCGACTAATCGACTTGATTC
1 GAATTGGATCGGGGAAAAGATAAAAGTATTCAACTAATCGACTTGATTC
46102376 ATTGTTTCCA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.29
Consensus pattern (52 bp):
GAATTGGATCGGGGAAAAGATAAAAGTATTCAACTAATCGACTTGATTCTTT
Found at i:46104966 original size:49 final size:48
Alignment explanation
Indices: 46104911--46105027 Score: 135
Period size: 49 Copynumber: 2.4 Consensus size: 48
46104901 TGGATGACCC
* * * *
46104911 AACAATGATGACTTTTACTGTTTGCATATTCTACCATCCCGAGTGGCCT
1 AACAATGATG-CTTTGAATATTTGCATATTCTACCATCCCGAGCGGCCT
* **
46104960 AACAATGATCGCTTTGAATATTTGCATATTCTATCATCTTGAGCGGCCT
1 AACAATGAT-GCTTTGAATATTTGCATATTCTACCATCCCGAGCGGCCT
*
46105009 AACAATGATGGTTTTGAAT
1 AACAATGAT-GCTTTGAAT
46105028 TATTATATCG
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
49 57 0.98
50 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (48 bp):
AACAATGATGCTTTGAATATTTGCATATTCTACCATCCCGAGCGGCCT
Found at i:46110808 original size:18 final size:18
Alignment explanation
Indices: 46110785--46110819 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
46110775 TTTATTGCTT
46110785 TTCAAAAGCACTTCTGGC
1 TTCAAAAGCACTTCTGGC
46110803 TTCAAAAGCACTTCTGG
1 TTCAAAAGCACTTCTGG
46110820 AAGAAAAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (18 bp):
TTCAAAAGCACTTCTGGC
Found at i:46111330 original size:13 final size:13
Alignment explanation
Indices: 46111314--46111353 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
46111304 TTTAAACCAA
*
46111314 ACTTTTTAAAAGC
1 ACTTTTCAAAAGC
*
46111327 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
46111340 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
46111353 A
1 A
46111354 ATGAAGAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:46111935 original size:21 final size:22
Alignment explanation
Indices: 46111897--46111937 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
46111887 CTCAATTAAA
46111897 ATTTATATGAAATCTAATTTAT
1 ATTTATATGAAATCTAATTTAT
* *
46111919 ATTTAT-TTAAATTTAATTT
1 ATTTATATGAAATCTAATTT
46111938 TCTATGTGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
ATTTATATGAAATCTAATTTAT
Found at i:46120011 original size:13 final size:13
Alignment explanation
Indices: 46119993--46120022 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
46119983 AATACTTTCA
*
46119993 AAAAAAATTTAAT
1 AAAAAAATTAAAT
46120006 AAAAAAATTAAAT
1 AAAAAAATTAAAT
46120019 AAAA
1 AAAA
46120023 TATTGTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAAAAATTAAAT
Found at i:46124660 original size:19 final size:20
Alignment explanation
Indices: 46124632--46124681 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
46124622 ATACATAGGT
*
46124632 TTAA-CTTTAATAAAT-TTA
1 TTAATCTTTAATAAATCTAA
*
46124650 TTAATCTTTAATTAATCTAA
1 TTAATCTTTAATAAATCTAA
*
46124670 TCAATCTTTAAT
1 TTAATCTTTAAT
46124682 TCACTTATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 4 0.15
19 10 0.37
20 13 0.48
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAATCTTTAATAAATCTAA
Found at i:46127714 original size:22 final size:22
Alignment explanation
Indices: 46127689--46127733 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
46127679 ATAATATCTA
*
46127689 TTAATTCATAATTTAA-TTAATT
1 TTAATT-ATAATCTAATTTAATT
*
46127711 TTAATTTTAATCTAATTTAATT
1 TTAATTATAATCTAATTTAATT
46127733 T
1 T
46127734 GGGTTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (22 bp):
TTAATTATAATCTAATTTAATT
Found at i:46127719 original size:16 final size:16
Alignment explanation
Indices: 46127700--46127733 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
46127690 TAATTCATAA
46127700 TTTAAT-TAATTTTAAT
1 TTTAATCTAA-TTTAAT
46127716 TTTAATCTAATTTAAT
1 TTTAATCTAATTTAAT
46127732 TT
1 TT
46127734 GGGTTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTAATCTAATTTAAT
Found at i:46128151 original size:10 final size:10
Alignment explanation
Indices: 46128136--46128160 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
46128126 CACTTTTCTC
46128136 TCTTCATTGT
1 TCTTCATTGT
46128146 TCTTCATTGT
1 TCTTCATTGT
46128156 TCTTC
1 TCTTC
46128161 CCTATTCCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.24, G:0.08, T:0.60
Consensus pattern (10 bp):
TCTTCATTGT
Found at i:46138204 original size:23 final size:22
Alignment explanation
Indices: 46138161--46138218 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
46138151 AAAAGGTATC
* *
46138161 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
46138182 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
46138205 TGCATATCATATCT
1 TACAAATCATATCT
46138219 AAGATTGTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:46138233 original size:18 final size:19
Alignment explanation
Indices: 46138197--46138251 Score: 85
Period size: 18 Copynumber: 2.9 Consensus size: 19
46138187 AATCATATCT
46138197 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
46138216 TCTAAGATTGTA-ATCATA
1 TCTAAGATTGCATATCATA
*
46138234 TTTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
46138252 TGAAGATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
18 16 0.50
19 16 0.50
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:46146155 original size:10 final size:10
Alignment explanation
Indices: 46146142--46146189 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
46146132 TTATTTTCAT
46146142 TTATCTTTAA
1 TTATCTTTAA
*
46146152 TTATCTTAAA
1 TTATCTTTAA
*
46146162 TTATCTTTAT
1 TTATCTTTAA
* * *
46146172 TTATATGTAT
1 TTATCTTTAA
46146182 TTATCTTT
1 TTATCTTT
46146190 TAGAATTTAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.62
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:46146185 original size:20 final size:20
Alignment explanation
Indices: 46146140--46146189 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
46146130 ATTTATTTTC
*
46146140 ATTTATCTTTAATTATCTTA
1 ATTTATCTTTAATTATATTA
* *
46146160 AATTATCTTTATTTATATGT-
1 ATTTATCTTTAATTATAT-TA
46146180 ATTTATCTTT
1 ATTTATCTTT
46146190 TAGAATTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.28, C:0.08, G:0.02, T:0.62
Consensus pattern (20 bp):
ATTTATCTTTAATTATATTA
Found at i:46146954 original size:43 final size:39
Alignment explanation
Indices: 46146887--46146976 Score: 94
Period size: 43 Copynumber: 2.2 Consensus size: 39
46146877 CTCAACTTTT
*
46146887 TTTTATTTCTATTGTTTTTAATTTTCGAAATTCCA-ATCAAAAC
1 TTTTAATTCTATTGTTTTTAATTTT-----TTCCAGATCAAAAC
*
46146930 TTTTAATTCTATT-TTATTTTATTTTTTCCAGATCAAAAC
1 TTTTAATTCTATTGTT-TTTAATTTTTTCCAGATCAAAAC
46146969 TTTTAATT
1 TTTTAATT
46146977 TTTTTCCAGG
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
38 5 0.12
39 16 0.37
42 2 0.05
43 20 0.47
ACGTcount: A:0.29, C:0.12, G:0.03, T:0.56
Consensus pattern (39 bp):
TTTTAATTCTATTGTTTTTAATTTTTTCCAGATCAAAAC
Found at i:46147517 original size:49 final size:49
Alignment explanation
Indices: 46147445--46147543 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
46147435 TAACGCTAGG
46147445 GTTAACAAAAACCCAAATCTAGCATATCAACAAATGGCTCAAACAATTC
1 GTTAACAAAAACCCAAATCTAGCATATCAACAAATGGCTCAAACAATTC
*
46147494 GTTAACGAAAACCCAAATCTAGCATATCAACAAATGGCTCAAACAATTC
1 GTTAACAAAAACCCAAATCTAGCATATCAACAAATGGCTCAAACAATTC
46147543 G
1 G
46147544 GCAACTGGTC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.45, C:0.24, G:0.10, T:0.20
Consensus pattern (49 bp):
GTTAACAAAAACCCAAATCTAGCATATCAACAAATGGCTCAAACAATTC
Found at i:46151367 original size:93 final size:92
Alignment explanation
Indices: 46151207--46151396 Score: 362
Period size: 93 Copynumber: 2.1 Consensus size: 92
46151197 TAAAGAATTA
*
46151207 ATTGTTTAAACGGATTGAAATTGCAATTAATGGACTCAGTACTTAATCAGTGCATGTTTAATTCT
1 ATTGTTTAAACGGATTGAAATTACAATTAATGGACTCAGTACTTAATCAGTGCATGTTTAATTCT
46151272 TCTAAGGTAACTGAAAATTAAATCAGC
66 TCTAAGGTAACTGAAAATTAAATCAGC
46151299 AGTTGTTTAAACGGATTGAAATTACAATTAATGGACTCAGTACTTAATCAGTGCATGTTTAATTC
1 A-TTGTTTAAACGGATTGAAATTACAATTAATGGACTCAGTACTTAATCAGTGCATGTTTAATTC
46151364 TTCTAAGGTAACTGAAAATTAAATCAGC
65 TTCTAAGGTAACTGAAAATTAAATCAGC
46151392 ATTGT
1 ATTGT
46151397 ATTTGGCGAT
Statistics
Matches: 96, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
92 5 0.05
93 91 0.95
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (92 bp):
ATTGTTTAAACGGATTGAAATTACAATTAATGGACTCAGTACTTAATCAGTGCATGTTTAATTCT
TCTAAGGTAACTGAAAATTAAATCAGC
Found at i:46164891 original size:15 final size:14
Alignment explanation
Indices: 46164829--46164896 Score: 64
Period size: 15 Copynumber: 4.6 Consensus size: 14
46164819 CCAATTTTTA
*
46164829 TTTATTTTTCTTAAT
1 TTTATTTTTATT-AT
* *
46164844 TTTAATTTTAATAT
1 TTTATTTTTATTAT
* *
46164858 TTTATTTTATTTTAC
1 TTTATTTT-TATTAT
46164873 TTTATTATTTATTAT
1 TTTATT-TTTATTAT
46164888 TTTATTTTT
1 TTTATTTTT
46164897 GGATGTTAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
14 12 0.29
15 28 0.67
16 2 0.05
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTATTTTTATTAT
Found at i:46167543 original size:97 final size:95
Alignment explanation
Indices: 46167423--46167605 Score: 269
Period size: 97 Copynumber: 1.9 Consensus size: 95
46167413 TTTTTAAGAA
*
46167423 TATGTTGGGCTGAGTAACTGGGGTAAGGTGCTTGGCTGTCATCTCTCCTCGCGTCAAAAAGTTCG
1 TATGTTGGGCTGAGTAACCGGGGTAAGGTGCTTGGCTGTCATCTCT--TCGCGTCAAAAAGTTCG
* *
46167488 ATATGTTCTTAA-AGAAAAATAAAAATTAGGAG
64 ATATATTCCTAAGA-AAAAATAAAAATTAGGAG
** * *
46167520 TATGTTGGGCTGAGTAACCGGGGTGGGGTGCTTGGCTGTTATCTCTTCGCGTCAAAAGGTTCGAT
1 TATGTTGGGCTGAGTAACCGGGGTAAGGTGCTTGGCTGTCATCTCTTCGCGTCAAAAAGTTCGAT
46167585 ATATTCCTAAGAAAAAATAAA
66 ATATTCCTAAGAAAAAATAAA
46167606 TAATAATAAT
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
95 35 0.45
96 1 0.01
97 42 0.54
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (95 bp):
TATGTTGGGCTGAGTAACCGGGGTAAGGTGCTTGGCTGTCATCTCTTCGCGTCAAAAAGTTCGAT
ATATTCCTAAGAAAAAATAAAAATTAGGAG
Found at i:46167643 original size:14 final size:15
Alignment explanation
Indices: 46167599--46167643 Score: 60
Period size: 14 Copynumber: 3.2 Consensus size: 15
46167589 TCCTAAGAAA
46167599 AAAT-AAATAATAAT
1 AAATAAAATAATAAT
*
46167613 -AATTAAATAATAAT
1 AAATAAAATAATAAT
46167627 AAATAAAATAA-AAT
1 AAATAAAATAATAAT
46167641 AAA
1 AAA
46167644 AAGATAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 3 0.11
14 16 0.57
15 9 0.32
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAATAAAATAATAAT
Found at i:46167652 original size:13 final size:14
Alignment explanation
Indices: 46167599--46167653 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 14
46167589 TCCTAAGAAA
46167599 AAAT-AAATAATAAT
1 AAATAAAATAA-AAT
*
46167613 -AATTAAATAATAAT
1 AAATAAAATAA-AAT
46167627 AAATAAAATAAAAT
1 AAATAAAATAAAAT
*
46167641 AAA-AAGATAAAAT
1 AAATAAAATAAAAT
46167654 TTAGGGACTA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
13 12 0.32
14 16 0.43
15 9 0.24
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (14 bp):
AAATAAAATAAAAT
Found at i:46170808 original size:25 final size:25
Alignment explanation
Indices: 46170725--46170804 Score: 85
Period size: 24 Copynumber: 3.3 Consensus size: 25
46170715 TATATAACGA
46170725 GAAGCTCATAAGAGCCA-TAATCGG
1 GAAGCTCATAAGAGCCATTAATCGG
** * *
46170749 GAAGCTCATGGGAGCCAATAA-CCG
1 GAAGCTCATAAGAGCCATTAATCGG
*
46170773 GTAGCTCCA-AAGAGCCATTAATCGG
1 GAAGCT-CATAAGAGCCATTAATCGG
46170798 GAAGCTC
1 GAAGCTC
46170805 CAAATAGCCA
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
24 32 0.73
25 12 0.27
ACGTcount: A:0.34, C:0.24, G:0.26, T:0.16
Consensus pattern (25 bp):
GAAGCTCATAAGAGCCATTAATCGG
Found at i:46170821 original size:25 final size:25
Alignment explanation
Indices: 46170722--46170826 Score: 76
Period size: 24 Copynumber: 4.3 Consensus size: 25
46170712 GGCTATATAA
46170722 CGAGAAGCT-CATAAGAGCCA-TAAT
1 CGAGAAGCTCCA-AAGAGCCATTAAT
* ** * *
46170746 CGGGAAGCT-CATGGGAGCCAATAAC
1 CGAGAAGCTCCA-AAGAGCCATTAAT
*
46170771 CG-GTAGCTCCAAAGAGCCATTAAT
1 CGAGAAGCTCCAAAGAGCCATTAAT
* *
46170795 CGGGAAGCTCCAAATAGCCATGT-AT
1 CGAGAAGCTCCAAAGAGCCAT-TAAT
46170820 CGAGAAG
1 CGAGAAG
46170827 TTCAAGCGAG
Statistics
Matches: 65, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
24 33 0.51
25 31 0.48
26 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.26, T:0.16
Consensus pattern (25 bp):
CGAGAAGCTCCAAAGAGCCATTAAT
Found at i:46170898 original size:25 final size:27
Alignment explanation
Indices: 46170863--46170913 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
46170853 CTGAGATTTA
*
46170863 TTAATTAGG-AAGCTCACAAAAAGCCT
1 TTAATTAGGAAAACTCACAAAAAGCCT
*
46170889 TTAATT-GGAAAACTCACGAAAAGCC
1 TTAATTAGGAAAACTCACAAAAAGCC
46170914 ATATAACGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.22
Consensus pattern (27 bp):
TTAATTAGGAAAACTCACAAAAAGCCT
Found at i:46179263 original size:20 final size:19
Alignment explanation
Indices: 46179241--46179294 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
46179231 CTTTTACTAT
*
46179241 TTTTGGTTTTTTT-TTATTC
1 TTTTGGTTTTTTTATT-TTA
46179260 TTTT-GTTTGTTTTATTTTA
1 TTTTGGTTT-TTTTATTTTA
46179279 GTTTTGGTTTTTTTAT
1 -TTTTGGTTTTTTTAT
46179295 GGGCCCAGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 4 0.13
19 10 0.33
20 12 0.40
21 4 0.13
ACGTcount: A:0.07, C:0.02, G:0.13, T:0.78
Consensus pattern (19 bp):
TTTTGGTTTTTTTATTTTA
Found at i:46180956 original size:26 final size:24
Alignment explanation
Indices: 46180894--46180955 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
46180884 TCACTATTCT
46180894 AAATATTAAAAAATTTATAATTATA
1 AAATA-TAAAAAATTTATAATTATA
* *
46180919 AAATATTAAAAATTTATAAAATTATG
1 AAATATAAAAAATTTAT--AATTATA
46180945 AAAT-TAAAAAA
1 AAATATAAAAAA
46180956 ACTTAACTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 11 0.34
25 11 0.34
26 10 0.31
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (24 bp):
AAATATAAAAAATTTATAATTATA
Found at i:46181018 original size:21 final size:22
Alignment explanation
Indices: 46180980--46181038 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
46180970 TTATTAAATT
46180980 AAAT-TAAATTATAAAAACT-ATA
1 AAATATAAA-TAT-AAAACTAATA
46181002 AAATATAAATATAAAACTAATA
1 AAATATAAATATAAAACTAATA
*
46181024 ATATATAAA-ATAAAA
1 AAATATAAATATAAAA
46181039 AAAAGTAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
21 12 0.35
22 18 0.53
23 4 0.12
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (22 bp):
AAATATAAATATAAAACTAATA
Found at i:46182190 original size:56 final size:56
Alignment explanation
Indices: 46182128--46182239 Score: 197
Period size: 56 Copynumber: 2.0 Consensus size: 56
46182118 AGTAAATATG
* * *
46182128 TCTGCAACTTGTTTATTGGTTCGTACTTTTTGCAGCTCAATATCTTGAGATAACAC
1 TCTGCAACTTGTTCATCGGTTCGTACTTTTTGCAACTCAATATCTTGAGATAACAC
46182184 TCTGCAACTTGTTCATCGGTTCGTACTTTTTGCAACTCAATATCTTGAGATAACAC
1 TCTGCAACTTGTTCATCGGTTCGTACTTTTTGCAACTCAATATCTTGAGATAACAC
46182240 ATTTTCTTGA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.39
Consensus pattern (56 bp):
TCTGCAACTTGTTCATCGGTTCGTACTTTTTGCAACTCAATATCTTGAGATAACAC
Found at i:46188834 original size:10 final size:10
Alignment explanation
Indices: 46188819--46188846 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
46188809 GCGTGATAGA
46188819 ATTAAAATAT
1 ATTAAAATAT
46188829 ATTAAAATAT
1 ATTAAAATAT
46188839 ATTAAAAT
1 ATTAAAAT
46188847 TAAACTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:46190868 original size:19 final size:18
Alignment explanation
Indices: 46190826--46190864 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
46190816 TCCTTATAAT
**
46190826 AAATTTATTTATTTTTGG
1 AAATTTATTTATTTTTAA
*
46190844 AAATTTTTTTATTTTTAA
1 AAATTTATTTATTTTTAA
46190862 AAA
1 AAA
46190865 ATTTGTTGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (18 bp):
AAATTTATTTATTTTTAA
Found at i:46200994 original size:14 final size:14
Alignment explanation
Indices: 46200975--46201002 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
46200965 AGATATGTTC
46200975 GGTGATGGAAATAA
1 GGTGATGGAAATAA
46200989 GGTGATGGAAATAA
1 GGTGATGGAAATAA
46201003 AAGCTTGGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.36, T:0.21
Consensus pattern (14 bp):
GGTGATGGAAATAA
Found at i:46201778 original size:30 final size:31
Alignment explanation
Indices: 46201723--46201809 Score: 140
Period size: 30 Copynumber: 2.8 Consensus size: 31
46201713 TGAAACATAG
46201723 GAGTGATCAAATTATAAATTTATTAATAATT
1 GAGTGATCAAATTATAAATTTATTAATAATT
* *
46201754 GAGTGATTAAATTATAAA-TTATTAATTATT
1 GAGTGATCAAATTATAAATTTATTAATAATT
*
46201784 GAGGGATCAAATTATAAATTTATTAA
1 GAGTGATCAAATTATAAATTTATTAA
46201810 CCCATCTAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 27 0.53
31 24 0.47
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.41
Consensus pattern (31 bp):
GAGTGATCAAATTATAAATTTATTAATAATT
Found at i:46204671 original size:34 final size:33
Alignment explanation
Indices: 46204623--46204686 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
46204613 TTTAAATTAC
*
46204623 AAAAATAATAAA-TTTAAAAGTATAAAAATAACA
1 AAAAATAATAAATTTTAAAAATA-AAAAATAACA
*
46204656 AAAAAGTACTAAATTTTAAAAATAAAAAATA
1 AAAAA-TAATAAATTTTAAAAATAAAAAATA
46204687 TTTTTAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 5 0.19
34 13 0.48
35 9 0.33
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (33 bp):
AAAAATAATAAATTTTAAAAATAAAAAATAACA
Found at i:46207047 original size:56 final size:56
Alignment explanation
Indices: 46206984--46207119 Score: 227
Period size: 56 Copynumber: 2.4 Consensus size: 56
46206974 ACCATGGCAT
46206984 CGATATATGTGTGCGAGTAAGACCACGTTTAATAAGTTGGCAACGATATGTGATTC
1 CGATATATGTGTGCGAGTAAGACCACGTTTAATAAGTTGGCAACGATATGTGATTC
** * * *
46207040 CGATATATGTGTATGAGTAAGACCACGTTTAATACGTTGGCATCTATATGTGATTC
1 CGATATATGTGTGCGAGTAAGACCACGTTTAATAAGTTGGCAACGATATGTGATTC
46207096 CGATATATGTGTGCGAGTAAGACC
1 CGATATATGTGTGCGAGTAAGACC
46207120 TTGTCTGGGA
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 73 1.00
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (56 bp):
CGATATATGTGTGCGAGTAAGACCACGTTTAATAAGTTGGCAACGATATGTGATTC
Found at i:46207359 original size:16 final size:16
Alignment explanation
Indices: 46207335--46207365 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
46207325 TGGTTATTTA
*
46207335 ATATTTGATGCAAATT
1 ATATATGATGCAAATT
46207351 ATATATGATGCAAAT
1 ATATATGATGCAAAT
46207366 GAAAATATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (16 bp):
ATATATGATGCAAATT
Found at i:46210837 original size:11 final size:11
Alignment explanation
Indices: 46210821--46210849 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
46210811 GTAATGTTAA
46210821 AATATATACAT
1 AATATATACAT
46210832 AATATATACAT
1 AATATATACAT
46210843 -ATATATA
1 AATATATA
46210850 AAAAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (11 bp):
AATATATACAT
Found at i:46212395 original size:5 final size:5
Alignment explanation
Indices: 46212385--46212422 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
46212375 TTATGAGTAG
*
46212385 GAAAA GAAAA GAAAA GAAAA AAAAA G-AAA G-AAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
46212423 TCTATTCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 8 0.27
5 22 0.73
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:46213711 original size:75 final size:75
Alignment explanation
Indices: 46213533--46213751 Score: 277
Period size: 75 Copynumber: 3.0 Consensus size: 75
46213523 CTCTTTAAAA
* * *
46213533 CTCAGCGTGTCTTGAGGCTCAACTCACCTCTTGCAATATGAGTTGA-ATTCTTGAAAAGCAGAAA
1 CTCAGCGTGACTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTTGAAAAGCAGAAA
46213597 TTGAAAATAC
66 TTGAAAATAC
* * * * *
46213607 CTCAACGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGATGAA-CAGAA
1 CTCAGCGTGACTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTTGA-AAAGCAGAA
46213671 ATT-AAAATTAC
65 ATTGAAAA-TAC
* * *
46213682 CTCAGTGTGACTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTCTTTAAAA-CATAAA
1 CTCAGCGTGACTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTTGAAAAGCAGAAA
*
46213745 TTAAAAA
66 TTGAAAA
46213752 ACAAAAATTG
Statistics
Matches: 126, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
73 9 0.07
74 56 0.44
75 59 0.47
76 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.30
Consensus pattern (75 bp):
CTCAGCGTGACTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTTGAAAAGCAGAAA
TTGAAAATAC
Found at i:46213867 original size:73 final size:72
Alignment explanation
Indices: 46213745--46213904 Score: 223
Period size: 73 Copynumber: 2.2 Consensus size: 72
46213735 AAAACATAAA
* * *
46213745 TTAAAAAACAAAAATTGAACATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCT-AGCAATATG
1 TTAAAAAACAGAAATTGAAAATACCTCAGCATGCCCCGAGGCTCAACTCACCTCTCA-CAATATG
46213809 AGTCGATTT
65 AGTCGA-TT
* * *
46213818 TTGAAAAACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCACAATATGA
1 TTAAAAAACAGAAATTGAAAATACCTCAGCATGCCCCGAGGCTCAACTCACCTCTCACAATATGA
*
46213883 GTTGATT
66 GTCGATT
*
46213890 TTAAAAAATAGAAAT
1 TTAAAAAACAGAAAT
46213905 AAAAATATCA
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
72 15 0.19
73 61 0.79
74 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (72 bp):
TTAAAAAACAGAAATTGAAAATACCTCAGCATGCCCCGAGGCTCAACTCACCTCTCACAATATGA
GTCGATT
Found at i:46213888 original size:160 final size:161
Alignment explanation
Indices: 46213594--46213890 Score: 454
Period size: 160 Copynumber: 1.8 Consensus size: 161
46213584 TGAAAAGCAG
* * *
46213594 AAATTGAAAATACCTCAACGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
1 AAATTGAAAATACCTCAACGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTCGA-TTTTT
** ** * *
46213659 TGATGAACAGAAATTAAAATTACCTCAGTGTGACTTGAGGCTCAACTCACCTCTCGCAATATGAG
65 TGAAAAACAGAAATTAAAATTACCTCAGCATGACCTGAGGCTCAACTCACCTCTCACAATATGAG
46213724 TTGATTTCTTTAAAACATAAATTAAAAAACAA
130 TTGATTTCTTTAAAACATAAATTAAAAAACAA
* *
46213756 AAATTGAACATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTCGA-TTTTT
1 AAATTGAAAATACCTCAACGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTCGATTTTTT
*
46213820 GAAAAACAGAAATTGAAAA-TACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCACAATATGAG
66 GAAAAACAGAAATT-AAAATTACCTCAGCATGACCTGAGGCTCAACTCACCTCTCACAATATGAG
46213884 TTGATTT
130 TTGATTT
46213891 TAAAAAATAG
Statistics
Matches: 122, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
160 64 0.52
161 4 0.03
162 54 0.44
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (161 bp):
AAATTGAAAATACCTCAACGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTCGATTTTTT
GAAAAACAGAAATTAAAATTACCTCAGCATGACCTGAGGCTCAACTCACCTCTCACAATATGAGT
TGATTTCTTTAAAACATAAATTAAAAAACAA
Found at i:46235317 original size:49 final size:47
Alignment explanation
Indices: 46235024--46235338 Score: 163
Period size: 47 Copynumber: 6.7 Consensus size: 47
46235014 TTTCTTGTGT
* *
46235024 GCCAGTGTAAGACATGTCTGGGACATGCATCGACCACATTAT-AAG-T-
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGACCTC--TATGAGGATA
* * * * * *
46235070 GTCAGTTTAATACCATGTCTAGGACATGACATC-AGC-GTA-GA-GATGA
1 GCCAGTGTAAGA-CATGTCTGGGACATG-CATCGACCTCTATGAGGAT-A
* * * * * *
46235116 GTGCCAGTGTAAGACGTGTCTGAGACATGCATCGGCCTCGACGATGATA
1 --GCCAGTGTAAGACATGTCTGGGACATGCATCGACCTCTATGAGGATA
* * *
46235165 GCCAGTGTAAGACATGTCTGGGACTTGCATCG---GCTAAGAGTTG-T-
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGACCTCTATGAG--GATA
* * * * * * *
46235209 GCTAGTGTAAGACATGTCCGGAACATGCATCAGCACGTATAT-ACGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATC-G-ACCTCTATGAGGATA
* *
46235257 GCTAGTATAAGACCATGTCTGGGACATGGCATCGACCTCTATGAGGATA
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGACCTCTATGAGGATA
46235306 GCCAGTGTAAGACCATGTCT-GGACATGGCATCG
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCG
46235339 GCAACTTATC
Statistics
Matches: 204, Mismatches: 41, Indels: 46
0.70 0.14 0.16
Matches are distributed among these distances:
43 1 0.00
44 35 0.17
45 2 0.01
46 15 0.07
47 58 0.28
48 45 0.22
49 40 0.20
50 8 0.04
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (47 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGACCTCTATGAGGATA
Found at i:46237239 original size:29 final size:28
Alignment explanation
Indices: 46237203--46237283 Score: 80
Period size: 27 Copynumber: 2.9 Consensus size: 28
46237193 CACACCCGGA
46237203 ATAATATAAATCCTCCATAACACACCAGT
1 ATAATAT-AATCCTCCATAACACACCAGT
* *
46237232 ATAATAT-AGCCTCTCA-AACACACTAGT
1 ATAATATAATCCTC-CATAACACACCAGT
*
46237259 A-AAT-TATATCCTCCCTAACACACCA
1 ATAATATA-ATCCTCCATAACACACCA
46237284 ATAAGGCATT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
25 1 0.02
26 4 0.09
27 29 0.67
28 2 0.05
29 7 0.16
ACGTcount: A:0.42, C:0.30, G:0.04, T:0.25
Consensus pattern (28 bp):
ATAATATAATCCTCCATAACACACCAGT
Found at i:46237812 original size:17 final size:18
Alignment explanation
Indices: 46237782--46237815 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
46237772 AATTTTTATT
*
46237782 CAATTTATTCCCTAATTC
1 CAATTTAATCCCTAATTC
46237800 CAATTTAAT-CCTAATT
1 CAATTTAATCCCTAATT
46237816 AACTCTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (18 bp):
CAATTTAATCCCTAATTC
Found at i:46238251 original size:17 final size:17
Alignment explanation
Indices: 46238229--46238261 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
46238219 GTTTTCGTTT
46238229 TGTTC-TCTGTTCTTTTC
1 TGTTCTTCT-TTCTTTTC
46238246 TGTTCTTCTTTCTTTT
1 TGTTCTTCTTTCTTTT
46238262 ATTTTCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.00, C:0.21, G:0.09, T:0.70
Consensus pattern (17 bp):
TGTTCTTCTTTCTTTTC
Found at i:46242854 original size:57 final size:57
Alignment explanation
Indices: 46242784--46242896 Score: 208
Period size: 57 Copynumber: 2.0 Consensus size: 57
46242774 AAGGGGATCC
*
46242784 ATAGATCGAGTTAATGCAACCCTAGGGTGTTAATTAGAGAAATGTCTCAATTATTCT
1 ATAGATCGAGTTAATGCAACCCTAGGGTGTTAATTAGAGAAAGGTCTCAATTATTCT
*
46242841 ATAGATTGAGTTAATGCAACCCTAGGGTGTTAATTAGAGAAAGGTCTCAATTATTC
1 ATAGATCGAGTTAATGCAACCCTAGGGTGTTAATTAGAGAAAGGTCTCAATTATTC
46242897 AATCTAGGGA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (57 bp):
ATAGATCGAGTTAATGCAACCCTAGGGTGTTAATTAGAGAAAGGTCTCAATTATTCT
Found at i:46244699 original size:13 final size:13
Alignment explanation
Indices: 46244660--46244723 Score: 67
Period size: 13 Copynumber: 4.9 Consensus size: 13
46244650 AGTTCTTCAT
46244660 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
46244673 TGC-TGTGAAAAAG
1 TGCTTTTG-AAAAG
*
46244686 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
* *
46244699 TACTTTTGAGAAG
1 TGCTTTTGAAAAG
*
46244712 TGCTTTGGAAAA
1 TGCTTTTGAAAA
46244724 ATTTAAGTGT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
12 3 0.07
13 36 0.86
14 3 0.07
ACGTcount: A:0.31, C:0.08, G:0.27, T:0.34
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:46259078 original size:11 final size:10
Alignment explanation
Indices: 46259052--46259085 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
46259042 GGAGAGCACC
*
46259052 AAGAGTCAAA
1 AAGAGCCAAA
46259062 AAGAGCCAAA
1 AAGAGCCAAA
46259072 AACGAGCCAAA
1 AA-GAGCCAAA
46259083 AAG
1 AAG
46259086 GGACAAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.59, C:0.18, G:0.21, T:0.03
Consensus pattern (10 bp):
AAGAGCCAAA
Found at i:46259517 original size:18 final size:17
Alignment explanation
Indices: 46259494--46259528 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
46259484 CCCTTCAAGG
46259494 GTTTTGGATTTTCTTTAT
1 GTTTTGGATTTT-TTTAT
*
46259512 GTTTTGTATTTTTTTAT
1 GTTTTGGATTTTTTTAT
46259529 TCTTCTGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.11, C:0.03, G:0.14, T:0.71
Consensus pattern (17 bp):
GTTTTGGATTTTTTTAT
Found at i:46263170 original size:162 final size:166
Alignment explanation
Indices: 46262804--46263287 Score: 518
Period size: 162 Copynumber: 2.9 Consensus size: 166
46262794 GTTACACTTG
* * * *
46262804 TATTGCGGTTAATTACCCCTAAAATTAGTTATATGACACATCTTAATCTCCGTAC-ATTACTTCA
1 TATTGCGGTTAATTACCCCTGAAGTTAGTTGTATGACACATCTTAGTCTCCGTACAATTACTTCA
* * * *
46262868 TGGTCATTTCTTTAGCCCACCATGCTTTTTTGCACTACACCCTGTACTAGAACCTGACTTACATG
66 TGGTCATTTGTTTAGCCCACCATGCCTTTTTGCACGACACCCTGTACTAGAACCAGACTTACATG
* *
46262933 TCAACAATTAGGACTAGTACAGGAATAATGGGCATGTCTT
131 TCAACAATTAGAACTAATACAGG----ATGGGCATGTCTT
** * * * ** *
46262973 TATTATGGTTGATCACCCCTGAAGTTAGTTGTATGACACATCTCAGTCTTTGTACAACTACTTCA
1 TATTGCGGTTAATTACCCCTGAAGTTAGTTGTATGACACATCTTAGTCTCCGTACAATTACTTCA
* * ** * *
46263038 TGGTCATTTGTTTAGCCCA-CATTCCTTTTTGCGCGACATTCTGTACTGGAATCAGACTTACATG
66 TGGTCATTTGTTTAGCCCACCATGCCTTTTTGCACGACACCCTGTACTAGAACCAGACTTACATG
* *
46263102 TCGATAATTAGAAC-AATACA-G-TGGGCATGTCTT
131 TCAACAATTAGAACTAATACAGGATGGGCATGTCTT
* *
46263135 TATTGCAGTTAATTACCCCTGAAGTTAGTTGTATGACACATCTTAGTCTCCGTACAATTGCTTCA
1 TATTGCGGTTAATTACCCCTGAAGTTAGTTGTATGACACATCTTAGTCTCCGTACAATTACTTCA
** * ** *
46263200 TGGTCATTTGTTTAGCCTGCAATG-CTTTTCTATACGACA-CCTCGTAC-AGAA-CTGAACTTAC
66 TGGTCATTTGTTTAGCCCACCATGCCTTTT-TGCACGACACCCT-GTACTAGAACCAG-ACTTAC
* *
46263261 ATGTCGACAATTAGGACTAATACAGGA
128 ATGTCAACAATTAGAACTAATACAGGA
46263288 ATAGTACGAA
Statistics
Matches: 259, Mismatches: 48, Indels: 20
0.79 0.15 0.06
Matches are distributed among these distances:
161 2 0.01
162 115 0.44
163 18 0.07
164 1 0.00
167 1 0.00
168 5 0.02
169 91 0.35
170 26 0.10
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (166 bp):
TATTGCGGTTAATTACCCCTGAAGTTAGTTGTATGACACATCTTAGTCTCCGTACAATTACTTCA
TGGTCATTTGTTTAGCCCACCATGCCTTTTTGCACGACACCCTGTACTAGAACCAGACTTACATG
TCAACAATTAGAACTAATACAGGATGGGCATGTCTT
Found at i:46267221 original size:75 final size:75
Alignment explanation
Indices: 46267098--46267247 Score: 264
Period size: 75 Copynumber: 2.0 Consensus size: 75
46267088 CTCTGAGAAG
**
46267098 CGCTTATTTATAGTCTAAGCTCGACTTACCTTTTTATTGAATGGTTATGGTGGTTCGAGGAGATT
1 CGCTTATTTATAGTCTAAGCTCGACTTACCTTTCCATTGAATGGTTATGGTGGTTCGAGGAGATT
*
46267163 ATCCTCCTCA
66 ATACTCCTCA
*
46267173 CGCTTATTTATAGTCTAAGCTTGACTTACCTTTCCATTGAATGGTTATGGTGGTTCGAGGAGATT
1 CGCTTATTTATAGTCTAAGCTCGACTTACCTTTCCATTGAATGGTTATGGTGGTTCGAGGAGATT
46267238 ATACTCCTCA
66 ATACTCCTCA
46267248 TTCCTNTCTC
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (75 bp):
CGCTTATTTATAGTCTAAGCTCGACTTACCTTTCCATTGAATGGTTATGGTGGTTCGAGGAGATT
ATACTCCTCA
Found at i:46277723 original size:40 final size:41
Alignment explanation
Indices: 46277663--46277756 Score: 163
Period size: 40 Copynumber: 2.3 Consensus size: 41
46277653 GGCTATTTGG
*
46277663 AAAAATACATACTGGTTCCACTTGACACAGTGGCGACAGCCA
1 AAAAATATATA-TGGTTCCACTTGACACAGTGGCGACAGCCA
46277705 AAAAATATATAT-GTTCCACTTGACACAGTGGCGACAGCCA
1 AAAAATATATATGGTTCCACTTGACACAGTGGCGACAGCCA
46277745 AAAAATATATAT
1 AAAAATATATAT
46277757 TTTTAAAAAG
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 40 0.78
41 1 0.02
42 10 0.20
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.22
Consensus pattern (41 bp):
AAAAATATATATGGTTCCACTTGACACAGTGGCGACAGCCA
Found at i:46279905 original size:31 final size:31
Alignment explanation
Indices: 46279867--46279984 Score: 202
Period size: 31 Copynumber: 3.8 Consensus size: 31
46279857 ACAAATGACA
46279867 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
46279898 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
46279929 AGTGAAAAATGGTAGC-TCTGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTC-GGCTACCTGATC
*
46279960 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
46279985 AAGTGACAAG
Statistics
Matches: 82, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
30 2 0.02
31 78 0.95
32 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:46280159 original size:42 final size:42
Alignment explanation
Indices: 46280084--46280210 Score: 168
Period size: 42 Copynumber: 3.0 Consensus size: 42
46280074 GCATCAGTGA
*
46280084 GATATGTGATT-CGTGTAAGACCATAGCTGGGCTATGGCATC
1 GATATGTGATTACGTGTAAGACCATAGCTAGGCTATGGCATC
46280125 GATATGTGATTACGTGTAAGACCATAGCTAGGCTATGGCATC
1 GATATGTGATTACGTGTAAGACCATAGCTAGGCTATGGCATC
* ** * * *
46280167 AATATGTGAAGATGTGTAAGACCATAG-TTGAACTATGGCATC
1 GATATGTGATTACGTGTAAGACCATAGCTAG-GCTATGGCATC
46280209 GA
1 GA
46280211 GAAAACGAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
41 13 0.17
42 63 0.83
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (42 bp):
GATATGTGATTACGTGTAAGACCATAGCTAGGCTATGGCATC
Found at i:46281236 original size:6 final size:6
Alignment explanation
Indices: 46281225--46281251 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
46281215 ACTTAGTAAC
46281225 AAAAAG AAAAAG AAAAAG AAAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAA
46281252 GAGTAAACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:46281602 original size:18 final size:19
Alignment explanation
Indices: 46281581--46281621 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
46281571 TAAAAATTCT
*
46281581 GAAATTTATAT-TTTTTTA
1 GAAAATTATATATTTTTTA
46281599 GAAAATTATATATTTTTTA
1 GAAAATTATATATTTTTTA
46281618 -AAAA
1 GAAAA
46281622 AATTAAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (19 bp):
GAAAATTATATATTTTTTA
Found at i:46281612 original size:20 final size:20
Alignment explanation
Indices: 46281582--46281626 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
46281572 AAAAATTCTG
* *
46281582 AAATT-TATATTTTTTTAGA
1 AAATTATATATTTTTTAAAA
46281601 AAATTATATATTTTTTAAAA
1 AAATTATATATTTTTTAAAA
46281621 AAATTA
1 AAATTA
46281627 AAGTATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
AAATTATATATTTTTTAAAA
Found at i:46283080 original size:18 final size:16
Alignment explanation
Indices: 46283032--46283083 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
46283022 TTATATTCTT
* * *
46283032 TATAAATTTAAAATTC
1 TATAAAATTAAAAATA
*
46283048 TAAAAAATTAAAAATA
1 TATAAAATTAAAAATA
46283064 TATAAAATCTAATAAATA
1 TATAAAAT-TAA-AAATA
46283082 TA
1 TA
46283084 ATATTTGACT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
16 19 0.66
17 3 0.10
18 7 0.24
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (16 bp):
TATAAAATTAAAAATA
Found at i:46285144 original size:13 final size:14
Alignment explanation
Indices: 46285117--46285150 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
46285107 AACTATCGAA
46285117 GTTTAAAAGCATTT
1 GTTTAAAAGCATTT
46285131 GTTTAAAA-CATTT
1 GTTTAAAAGCATTT
46285144 GCTTTAA
1 G-TTTAA
46285151 CTTTGGGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (14 bp):
GTTTAAAAGCATTT
Found at i:46286870 original size:39 final size:39
Alignment explanation
Indices: 46286811--46286950 Score: 217
Period size: 39 Copynumber: 3.6 Consensus size: 39
46286801 ATCGTGATCT
** *
46286811 GAAGCCCGAAATCTAGCTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
46286850 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
* *
46286889 GAAGCCCGGAGGCTAACTGAAGCATATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
* *
46286928 AAAGCCTGAAGGCTAACTGAAGC
1 GAAGCCCGAAGGCTAACTGAAGC
46286951 TCATTAGAGC
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 93 1.00
ACGTcount: A:0.38, C:0.22, G:0.26, T:0.14
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
Found at i:46290092 original size:12 final size:12
Alignment explanation
Indices: 46290069--46290100 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
46290059 GAATGCATTA
46290069 AAAGTG-TTGAG
1 AAAGTGATTGAG
46290080 AAAGTGATTGAG
1 AAAGTGATTGAG
46290092 AAAGT-ATTG
1 AAAGTGATTG
46290101 TTAACAAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.28
Consensus pattern (12 bp):
AAAGTGATTGAG
Found at i:46291609 original size:25 final size:25
Alignment explanation
Indices: 46291575--46291624 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
46291565 ATCAGGGACT
46291575 CAATTGAGTGAAATAAAACTCTAAA
1 CAATTGAGTGAAATAAAACTCTAAA
46291600 CAATTGAGTGAAATAAAACTCTAAA
1 CAATTGAGTGAAATAAAACTCTAAA
46291625 AATAGTTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (25 bp):
CAATTGAGTGAAATAAAACTCTAAA
Found at i:46294441 original size:30 final size:29
Alignment explanation
Indices: 46294402--46294460 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 29
46294392 AACACTCTTC
*
46294402 TTCAGCAAATTGATGAACAAAAACTGAAAA
1 TTCAACAAATTGATGAACAAAAACT-AAAA
46294432 TTCAACAAATTGATGAACAAAAACTAAAA
1 TTCAACAAATTGATGAACAAAAACTAAAA
46294461 CTTGTTTCAG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 4 0.14
30 24 0.86
ACGTcount: A:0.56, C:0.14, G:0.10, T:0.20
Consensus pattern (29 bp):
TTCAACAAATTGATGAACAAAAACTAAAA
Found at i:46297802 original size:31 final size:31
Alignment explanation
Indices: 46297734--46297804 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
46297724 TAAATTTACA
* * *
46297734 TAAAAAAAATTAAAAATTATTGTTTCATATT
1 TAAAAAAATTTAAAAATTATTATATCATATT
*
46297765 TAAAAAAATTTAAAAATTATATATAT-ATTTT
1 TAAAAAAATTTAAAAATTAT-TATATCATATT
*
46297796 TTAAAAAAT
1 TAAAAAAAT
46297805 AATAACTCTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 31 0.91
32 3 0.09
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (31 bp):
TAAAAAAATTTAAAAATTATTATATCATATT
Found at i:46298295 original size:5 final size:5
Alignment explanation
Indices: 46298285--46298311 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
46298275 AAAATTTGTG
46298285 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
46298312 TCACAAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:46302436 original size:14 final size:15
Alignment explanation
Indices: 46302417--46302473 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 15
46302407 AATCTTTAAG
46302417 GATATG-CAATCTTA
1 GATATGACAATCTTA
46302431 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
46302448 GATATGATATGCAATCTTA
1 GATATG--A--CAATCTTA
46302467 GATATGA
1 GATATGA
46302474 TATGCAATCT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
14 6 0.16
17 18 0.47
19 14 0.37
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.35
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:46302458 original size:36 final size:38
Alignment explanation
Indices: 46302417--46302495 Score: 126
Period size: 36 Copynumber: 2.1 Consensus size: 38
46302407 AATCTTTAAG
46302417 GATATGCAATCTTAGATATGATA-CAATCTT-AGATAT
1 GATATGCAATCTTAGATATGATAGCAATCTTAAGATAT
46302453 GATATGCAATCTTAGATATGATATGCAATCTTGAAGATAT
1 GATATGCAATCTTAGATATGATA-GCAATCTT-AAGATAT
46302493 GAT
1 GAT
46302496 CTTGTAATCT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
36 23 0.59
38 7 0.18
40 9 0.23
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (38 bp):
GATATGCAATCTTAGATATGATAGCAATCTTAAGATAT
Found at i:46302464 original size:19 final size:19
Alignment explanation
Indices: 46302417--46302495 Score: 126
Period size: 19 Copynumber: 4.2 Consensus size: 19
46302407 AATCTTTAAG
46302417 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
46302436 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
46302453 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
46302472 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
46302493 GAT
1 GAT
46302496 CTTGTAATCT
Statistics
Matches: 56, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.30
19 30 0.54
21 9 0.16
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:46305595 original size:12 final size:12
Alignment explanation
Indices: 46305578--46305602 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
46305568 TAAAGTTATC
46305578 AAAAAGAGAAAG
1 AAAAAGAGAAAG
46305590 AAAAAGAGAAAG
1 AAAAAGAGAAAG
46305602 A
1 A
46305603 GAGAGAAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AAAAAGAGAAAG
Found at i:46307104 original size:158 final size:158
Alignment explanation
Indices: 46306816--46307131 Score: 632
Period size: 158 Copynumber: 2.0 Consensus size: 158
46306806 TACTCTTTAT
46306816 ACTTACGTTGGGGCAAACACCTTCAATTCCAGTTGTTTTAAAGGTTCCAGCCATCATCCTTGGAA
1 ACTTACGTTGGGGCAAACACCTTCAATTCCAGTTGTTTTAAAGGTTCCAGCCATCATCCTTGGAA
46306881 TGGGTGCATTGTTTGGCTCTCCTGAGCAATCTGATGTACCGTCAATAGCTGTGATGGTTAGCTCC
66 TGGGTGCATTGTTTGGCTCTCCTGAGCAATCTGATGTACCGTCAATAGCTGTGATGGTTAGCTCC
46306946 AGGCGTTGGCCATTGATTTCCAGGGGCA
131 AGGCGTTGGCCATTGATTTCCAGGGGCA
46306974 ACTTACGTTGGGGCAAACACCTTCAATTCCAGTTGTTTTAAAGGTTCCAGCCATCATCCTTGGAA
1 ACTTACGTTGGGGCAAACACCTTCAATTCCAGTTGTTTTAAAGGTTCCAGCCATCATCCTTGGAA
46307039 TGGGTGCATTGTTTGGCTCTCCTGAGCAATCTGATGTACCGTCAATAGCTGTGATGGTTAGCTCC
66 TGGGTGCATTGTTTGGCTCTCCTGAGCAATCTGATGTACCGTCAATAGCTGTGATGGTTAGCTCC
46307104 AGGCGTTGGCCATTGATTTCCAGGGGCA
131 AGGCGTTGGCCATTGATTTCCAGGGGCA
46307132 TCAGGTCATA
Statistics
Matches: 158, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
158 158 1.00
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (158 bp):
ACTTACGTTGGGGCAAACACCTTCAATTCCAGTTGTTTTAAAGGTTCCAGCCATCATCCTTGGAA
TGGGTGCATTGTTTGGCTCTCCTGAGCAATCTGATGTACCGTCAATAGCTGTGATGGTTAGCTCC
AGGCGTTGGCCATTGATTTCCAGGGGCA
Found at i:46308322 original size:18 final size:18
Alignment explanation
Indices: 46308301--46308341 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
46308291 ACAAAAAAGG
*
46308301 AAAAA-AAAGAAAAAAAT
1 AAAAATAAAAAAAAAAAT
*
46308318 AAAAATAAAAATAAAAAT
1 AAAAATAAAAAAAAAAAT
46308336 AAAAAT
1 AAAAAT
46308342 GAGAAAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.85, C:0.00, G:0.02, T:0.12
Consensus pattern (18 bp):
AAAAATAAAAAAAAAAAT
Found at i:46309487 original size:175 final size:175
Alignment explanation
Indices: 46309196--46309564 Score: 578
Period size: 175 Copynumber: 2.1 Consensus size: 175
46309186 CAAAGAAACA
*
46309196 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACACTCCTGTGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCAAAGATAGCAGATCTGACACTCCTGTGCTT
* *
46309261 ACAGCGAAGCTGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATT
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
* * * * * *
46309326 TCAGCA-TGGCATCCCTTTGTTTTTACGGAACAAGTTGAAGATAGC
131 GCAG-ATTGGCATCCCTGTATTTATACGGAACAAATCGAAGATAGC
* *
46309371 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCAAAGATAGCAGATCTGATATTCCTGTGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCAAAGATAGCAGATCTGACACTCCTGTGCTT
46309436 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
*
46309501 GCAGATTTGGCATCCCTGTATTTATAGGGAACAAATCGAAGATAGC
131 GCAGA-TTGGCATCCCTGTATTTATACGGAACAAATCGAAGATAGC
* * *
46309547 AGATCTGACATTCCTGTG
1 AGATTTGGCATCCCTGTG
46309565 CTTACAGCAA
Statistics
Matches: 177, Mismatches: 15, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
174 1 0.01
175 128 0.72
176 48 0.27
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (175 bp):
AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCAAAGATAGCAGATCTGACACTCCTGTGCTT
ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
GCAGATTGGCATCCCTGTATTTATACGGAACAAATCGAAGATAGC
Found at i:46309646 original size:44 final size:44
Alignment explanation
Indices: 46309196--46309646 Score: 330
Period size: 44 Copynumber: 10.3 Consensus size: 44
46309186 CAAAGAAACA
*
46309196 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
* * * * * * **
46309240 AGATCTGACA-CTCCTGTGCTTACAGCGAAGC-TGATCGAAGATTTC
1 AGATTTGGCATC-CCTGTGTTTATAGGGAA-CAAG-TCGAAGATAGC
* **
46309285 AGCA--TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATTTC
1 AG-ATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
* * * *
46309328 AGCA--TGGCATCCCTTTGTTTTTACGGAACAAGTTGAAGATAGC
1 AG-ATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
* *
46309371 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCAAAGATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
* ** * * * * **
46309415 AGATCTGATATTCCTGTGCTTACAGCGAAGC-AGATCGAAGATTTC
1 AGATTTGGCATCCCTGTGTTTATAGGGAA-CAAG-TCGAAGATAGC
*
46309460 AGCA--TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGC
1 AG-ATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
* *
46309503 AGATTTGGCATCCCTGTATTTATAGGGAACAAATCGAAGATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
* * * * * ** ***
46309547 AGATCTGACATTCCTGTGCTTACAGCAAAGC-AGATCGAAGATTTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAA-CAAG-TCGAAGATAGC
** * **
46309592 A-ACATGGCATCCATGTGTTTATAGGGAACAAGTTAAAGATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
46309635 AGATTTGGCATC
1 AGATTTGGCATC
46309647 ATTGTGCTTA
Statistics
Matches: 312, Mismatches: 77, Indels: 36
0.73 0.18 0.08
Matches are distributed among these distances:
42 2 0.01
43 71 0.23
44 203 0.65
45 34 0.11
46 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.28
Consensus pattern (44 bp):
AGATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
Found at i:46309657 original size:88 final size:87
Alignment explanation
Indices: 46309508--46309674 Score: 212
Period size: 88 Copynumber: 1.9 Consensus size: 87
46309498 ATAGCAGATT
* *
46309508 TGGCATCCCTGTATTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTTAC-AG
1 TGGCATCCATGTATTTATAGGGAACAAATCAAAGATAGCAGATCTGACATTCCTGTGCTTACAAG
*
46309572 CAAAGCAGATCGAAGATTTTAACA
66 -AAA-CAAATCGAAGATTTTAACA
* * * * * *
46309596 TGGCATCCATGTGTTTATAGGGAACAAGTTAAAGATAGCAGATTTGGCA-TCATTGTGCTTACAA
1 TGGCATCCATGTATTTATAGGGAACAAATCAAAGATAGCAGATCTGACATTC-CTGTGCTTACAA
46309660 GAAACAAATCGAAGA
65 GAAACAAATCGAAGA
46309675 CATAGCTGAT
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
87 12 0.18
88 54 0.79
89 2 0.03
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (87 bp):
TGGCATCCATGTATTTATAGGGAACAAATCAAAGATAGCAGATCTGACATTCCTGTGCTTACAAG
AAACAAATCGAAGATTTTAACA
Found at i:46309666 original size:132 final size:132
Alignment explanation
Indices: 46309201--46309674 Score: 562
Period size: 132 Copynumber: 3.6 Consensus size: 132
46309191 AAACAAGATT
* * * * * *
46309201 TGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACA-CTCCTGTGCTTACAG
1 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATC-CCTGTGTTTATAG
* ** ** * * * * ** *
46309265 CGAAGCTGATCGAAGATTTCAG--CATGGCATCCCTGTGTTTATAGGGAA-CA-AGTTGAAGATT
65 GGAA-CAAATCGAAGATAGCAGATC-TGACATTCCTGTGCTTACAGCAAAGCAGA-TCGAAGATT
46309326 TCAGCA
127 TCAGCA
* * *
46309332 TGGCATCCCTTTGTTTTTACGGAACAAGTTGAAGATAGCAGATTTGGCATCCCTGTGTTTATAGG
1 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATCCCTGTGTTTATAGG
* * *
46309397 GAACAAATCAAAGATAGCAGATCTGATATTCCTGTGCTTACAGCGAAGCAGATCGAAGATTTCAG
66 GAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTTACAGCAAAGCAGATCGAAGATTTCAG
46309462 CA
131 CA
*
46309464 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATCCCTGTATTTATAGG
1 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATCCCTGTGTTTATAGG
* *
46309529 GAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTTACAGCAAAGCAGATCGAAGATTTTAA
66 GAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTTACAGCAAAGCAGATCGAAGATTTCAG
46309594 CA
131 CA
* * ** * * *
46309596 TGGCATCCATGTGTTTATAGGGAACAAGTTAAAGATAGCAGATTTGGCATCATTGTGCTTACAAG
1 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATCCCTGTGTTTATAGG
*
46309661 AAACAAATCGAAGA
66 GAACAAATCGAAGA
46309675 CATAGCTGAT
Statistics
Matches: 298, Mismatches: 40, Indels: 9
0.86 0.12 0.03
Matches are distributed among these distances:
130 12 0.04
131 74 0.25
132 211 0.71
133 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (132 bp):
TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATCCCTGTGTTTATAGG
GAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTTACAGCAAAGCAGATCGAAGATTTCAG
CA
Found at i:46309989 original size:206 final size:206
Alignment explanation
Indices: 46309636--46310377 Score: 1306
Period size: 206 Copynumber: 3.6 Consensus size: 206
46309626 AAAGATAGCA
* * * *
46309636 GATTTGGCATCATTGTGCTTACAAGAAACAAATCGAAGACATAGCTGATTTGGCTTTCACG-GTT
1 GATTTGGCATCCTTGTGCTTACAAGGAACAAATAGAAGACATAGCTGATTTGGCTTTCACGTGCT
*
46309700 TACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGG
66 TACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGG
* * ** * *
46309765 CGTCTCCATATTCGACGGAGAGCAGACACAAAGCAGATTTGGCCTTCATATGTTTATACTGAAGC
131 CGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGTTTATACTGAAGA
*
46309830 AGATCCAAGGT
196 AGATCCAAGAT
*
46309841 GATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGCT
1 GATTTGGCATCCTTGTGCTTACAAGGAACAAATAGAAGACATAGCTGATTTGGCTTTCACGTGCT
46309906 TACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGG
66 TACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGG
46309971 CGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGTTTATACTGAAGA
131 CGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGTTTATACTGAAGA
46310036 AGATCCAAGAT
196 AGATCCAAGAT
*
46310047 GATTTGGCATTCTTGTGCTTACAAGGAACAAATAGAAGACATAGCTGATTTGGCTTTCACGTGCT
1 GATTTGGCATCCTTGTGCTTACAAGGAACAAATAGAAGACATAGCTGATTTGGCTTTCACGTGCT
46310112 TACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGG
66 TACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGG
* *
46310177 GGTCTCCACATTCGACGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGTTTATACTGAAGA
131 CGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGTTTATACTGAAGA
46310242 AGATCCAAGAT
196 AGATCCAAGAT
*
46310253 GATTTGGCATTCTTGTGCTTACAAGGAACAAATAGAAGACATAGCTGATTTGGCTTTCACGTGCT
1 GATTTGGCATCCTTGTGCTTACAAGGAACAAATAGAAGACATAGCTGATTTGGCTTTCACGTGCT
* *
46310318 TACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAAAACAGATCGAAG
66 TACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAG
46310378 ATAACAGATT
Statistics
Matches: 519, Mismatches: 17, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
205 59 0.11
206 460 0.89
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (206 bp):
GATTTGGCATCCTTGTGCTTACAAGGAACAAATAGAAGACATAGCTGATTTGGCTTTCACGTGCT
TACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGG
CGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGTTTATACTGAAGA
AGATCCAAGAT
Found at i:46310789 original size:19 final size:19
Alignment explanation
Indices: 46310765--46310862 Score: 164
Period size: 19 Copynumber: 5.2 Consensus size: 19
46310755 AATCTTTAAG
46310765 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
46310784 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
46310803 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
46310820 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
46310839 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
46310860 GAT
1 GAT
46310863 CTTGTAATCT
Statistics
Matches: 75, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
17 17 0.23
19 49 0.65
21 9 0.12
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:46310795 original size:36 final size:35
Alignment explanation
Indices: 46310755--46310862 Score: 112
Period size: 36 Copynumber: 2.9 Consensus size: 35
46310745 ATGGAAATAT
46310755 AATCTTTAAGGATATGCAATCTTAGATATGATATGC
1 AATCTTTAA-GATATGCAATCTTAGATATGATATGC
46310791 AATC-TT-AGATATGATACAATCTTAGATATGATATGC
1 AATCTTTAAGATATG---CAATCTTAGATATGATATGC
*
46310827 AATCTTAGATATGATATGCAATCTTGAAGATATGAT
1 AATCTT---TAAGATATGCAATCTT--AGATATGAT
46310863 CTTGTAATCT
Statistics
Matches: 61, Mismatches: 1, Indels: 16
0.78 0.01 0.21
Matches are distributed among these distances:
33 6 0.10
34 1 0.02
35 2 0.03
36 28 0.46
37 1 0.02
38 7 0.11
40 10 0.16
41 6 0.10
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (35 bp):
AATCTTTAAGATATGCAATCTTAGATATGATATGC
Found at i:46315300 original size:29 final size:28
Alignment explanation
Indices: 46315268--46315322 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
46315258 GAGTTTTGTT
46315268 TTTTAATAA-AATAATAAATTATTAATATG
1 TTTTAATAATAA-AATAAATTA-TAATATG
* *
46315297 TTTTTATAATAAAATAATTTATAATA
1 TTTTAATAATAAAATAAATTATAATA
46315323 CATCTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 5 0.22
29 16 0.70
30 2 0.09
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (28 bp):
TTTTAATAATAAAATAAATTATAATATG
Found at i:46318098 original size:5 final size:5
Alignment explanation
Indices: 46318083--46318111 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
46318073 ATATTCTAAT
46318083 TTTTA -TTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
46318112 GTGTAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:46319468 original size:14 final size:14
Alignment explanation
Indices: 46319434--46319471 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
46319424 TTTTAATTTT
*
46319434 TGTTTAATTTTAAA
1 TGTTTATTTTTAAA
*
46319448 T-TTTATTTTTCAA
1 TGTTTATTTTTAAA
46319461 TGTTTATTTTT
1 TGTTTATTTTT
46319472 TTGTATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68
Consensus pattern (14 bp):
TGTTTATTTTTAAA
Found at i:46321979 original size:41 final size:41
Alignment explanation
Indices: 46321933--46322014 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
46321923 GCTGTGTATG
* * *
46321933 ACACACGGTCGTATGACAACCCATGTCTCAGGCCGTGTGTA
1 ACACACAGTCGTATGACAACCCATGTCCCAGGCCATGTGTA
* * *
46321974 ACACACAGTTGTGTGACAACCCATTTCCCAGGCCATGTGTA
1 ACACACAGTCGTATGACAACCCATGTCCCAGGCCATGTGTA
46322015 CCTTAAAAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (41 bp):
ACACACAGTCGTATGACAACCCATGTCCCAGGCCATGTGTA
Found at i:46324827 original size:18 final size:20
Alignment explanation
Indices: 46324804--46324840 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
46324794 TTTATACATA
46324804 TGAA-TTTTAAAT-ATTTTT
1 TGAATTTTTAAATAATTTTT
46324822 TGAATTTTTAAATAATTTT
1 TGAATTTTTAAATAATTTT
46324841 CTATAGGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 8 0.47
20 5 0.29
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
TGAATTTTTAAATAATTTTT
Found at i:46325888 original size:20 final size:20
Alignment explanation
Indices: 46325865--46325914 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
46325855 AAATCCAAAT
46325865 TAAAATACTAAAATTCAAGA
1 TAAAATACTAAAATTCAAGA
* *
46325885 TAAAAT-CTTGAAATTCAGGA
1 TAAAATAC-TAAAATTCAAGA
46325905 TAAGAATACT
1 TAA-AATACT
46325915 GATGTGGCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 1 0.04
20 19 0.76
21 4 0.16
22 1 0.04
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.28
Consensus pattern (20 bp):
TAAAATACTAAAATTCAAGA
Found at i:46327860 original size:28 final size:28
Alignment explanation
Indices: 46327827--46327882 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
46327817 AAAGCACAAA
46327827 AGCTTAATAAAGTCAAATTAACAAAAAC
1 AGCTTAATAAAGTCAAATTAACAAAAAC
46327855 AGCTTAATAAAGTCAAATTAACAAAAAC
1 AGCTTAATAAAGTCAAATTAACAAAAAC
46327883 TATAAAGTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.57, C:0.14, G:0.07, T:0.21
Consensus pattern (28 bp):
AGCTTAATAAAGTCAAATTAACAAAAAC
Found at i:46333950 original size:27 final size:26
Alignment explanation
Indices: 46333888--46333980 Score: 114
Period size: 27 Copynumber: 3.5 Consensus size: 26
46333878 AGCATGGCTG
* * *
46333888 CCAGAACAGACAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
46333914 CCAGATACAGATAATCATGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
46333942 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
*
46333969 CCAGATCAGATA
1 CCAGAACAGATA
46333981 NNNNNNNNNN
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
26 5 0.09
27 37 0.64
28 16 0.28
ACGTcount: A:0.40, C:0.24, G:0.23, T:0.14
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:46335472 original size:26 final size:26
Alignment explanation
Indices: 46335311--46335464 Score: 299
Period size: 26 Copynumber: 5.9 Consensus size: 26
46335301 CATGAAATTC
*
46335311 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCCA
46335337 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCCA
46335363 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCCA
46335389 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCCA
46335415 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCCA
46335441 TTATCATGGAACATTTACCTAACC
1 TTATCATGGAACATTTACCTAACC
46335465 TTTTATCAAT
Statistics
Matches: 127, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
26 127 1.00
ACGTcount: A:0.35, C:0.27, G:0.07, T:0.31
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCCA
Found at i:46344000 original size:18 final size:17
Alignment explanation
Indices: 46343942--46344002 Score: 51
Period size: 16 Copynumber: 3.7 Consensus size: 17
46343932 ACATTTTACT
*
46343942 TTATATATTATT-TATT
1 TTATATATTATTATATA
46343958 TTACTATA-T-TTATATA
1 TTA-TATATTATTATATA
46343974 TGTA-A-ATTATTATATA
1 T-TATATATTATTATATA
46343990 TTATTATATTATT
1 TTA-TATATTATT
46344003 TTTTATTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
14 1 0.03
15 6 0.17
16 16 0.44
17 7 0.19
18 6 0.17
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (17 bp):
TTATATATTATTATATA
Found at i:46349355 original size:19 final size:20
Alignment explanation
Indices: 46349331--46349368 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
46349321 GAAACTACAT
46349331 TATTTT-CTAAACCAGAAGC
1 TATTTTACTAAACCAGAAGC
*
46349350 TATTTTACTAAACTAGAAG
1 TATTTTACTAAACCAGAAG
46349369 AGAATAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (20 bp):
TATTTTACTAAACCAGAAGC
Found at i:46352429 original size:17 final size:17
Alignment explanation
Indices: 46352370--46352429 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
46352360 TAATAAATTT
46352370 AAAATATAATATATAATAA
1 AAAATATAAT-TAT-ATAA
46352389 AAAATAT-ATT-TAT-A
1 AAAATATAATTATATAA
*
46352403 AGAATAATAATTATATAA
1 AAAAT-ATAATTATATAA
46352421 AAAATATAA
1 AAAATATAA
46352430 AATATATTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 5 0.14
15 4 0.11
16 4 0.11
17 8 0.23
18 7 0.20
19 7 0.20
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
AAAATATAATTATATAA
Found at i:46352970 original size:35 final size:35
Alignment explanation
Indices: 46352912--46353029 Score: 209
Period size: 35 Copynumber: 3.3 Consensus size: 35
46352902 AATCATATCT
46352912 TCTAAGATTGTATATCATATCTAAGATTGCAATCATA
1 TCTAAGATTG--TATCATATCTAAGATTGCAATCATA
46352949 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
1 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
46352984 TCTAAGATTGTATCATATCTAAGATTGCATATCATA
1 TCTAAGATTGTATCATATCTAAGATTGCA-ATCATA
46353020 TCTAAGATTG
1 TCTAAGATTG
46353030 CTTATCATTG
Statistics
Matches: 80, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
35 54 0.68
36 16 0.20
37 10 0.12
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (35 bp):
TCTAAGATTGTATCATATCTAAGATTGCAATCATA
Found at i:46353030 original size:19 final size:19
Alignment explanation
Indices: 46352912--46353037 Score: 192
Period size: 19 Copynumber: 6.9 Consensus size: 19
46352902 AATCATATCT
*
46352912 TCTAAGATTGTATATCATA
1 TCTAAGATTGCATATCATA
46352931 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
46352949 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
46352966 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
46352984 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
46353001 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
46353020 TCTAAGATTGCTTATCAT
1 TCTAAGATTGCATATCAT
46353038 TGAAGATTAT
Statistics
Matches: 99, Mismatches: 2, Indels: 12
0.88 0.02 0.11
Matches are distributed among these distances:
17 32 0.32
18 32 0.32
19 35 0.35
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:46353045 original size:17 final size:19
Alignment explanation
Indices: 46352915--46353045 Score: 134
Period size: 17 Copynumber: 7.3 Consensus size: 19
46352905 CATATCTTCT
* *
46352915 AAGATTGTATATCATATCT
1 AAGATTGCATATCATATCG
*
46352934 AAGATTGCA-ATCATATCT
1 AAGATTGCATATCATATCG
*
46352952 AAGATTG--TATCATATCT
1 AAGATTGCATATCATATCG
*
46352969 AAGATTGCA-ATCATATCT
1 AAGATTGCATATCATATCG
*
46352987 AAGATTG--TATCATATCT
1 AAGATTGCATATCATATCG
*
46353004 AAGATTGCATATCATATCT
1 AAGATTGCATATCATATCG
*
46353023 AAGATTGCTTATCAT-T-G
1 AAGATTGCATATCATATCG
46353040 AAGATT
1 AAGATT
46353046 ATATTTCCAT
Statistics
Matches: 103, Mismatches: 3, Indels: 14
0.86 0.03 0.12
Matches are distributed among these distances:
17 38 0.37
18 33 0.32
19 32 0.31
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (19 bp):
AAGATTGCATATCATATCG
Found at i:46354046 original size:83 final size:83
Alignment explanation
Indices: 46353907--46354376 Score: 841
Period size: 83 Copynumber: 5.7 Consensus size: 83
46353897 AGAGTCAAAT
*
46353907 TGTTTGAGAACATCTGAGAGTCTAATCTGCTATGTCCTCGATTTGTTCCTTGTAAGCACAAGGAC
1 TGTTTGAGAACATCCGAGAGTCTAATCTGCTATGTCCTCGATTTGTTCCTTGTAAGCACAAGGAC
46353972 GCCAAACCATCTTGAGTC
66 GCCAAACCATCTTGAGTC
* * * *
46353990 TGTTTGAGAACATCCGAGAGTCTAATCTGCTATGTCGTCGATTTGTTCATTGTAAGCACAAGAAT
1 TGTTTGAGAACATCCGAGAGTCTAATCTGCTATGTCCTCGATTTGTTCCTTGTAAGCACAAGGAC
46354055 GCCAAACCATCTTGAGTC
66 GCCAAACCATCTTGAGTC
*
46354073 TGTTTGAGAACATCTGAGAGTCTAATCTGCTATGTCCTCGATTTGTTCCTTGTAAGCACAAGGAC
1 TGTTTGAGAACATCCGAGAGTCTAATCTGCTATGTCCTCGATTTGTTCCTTGTAAGCACAAGGAC
46354138 GCCAAACCATCTTGAGTC
66 GCCAAACCATCTTGAGTC
* * *
46354156 TGTTTGAGAACATCCGAGAGTCTAATCTGCTATGTCGTCGATTTGTTCATTGTAAGCACAAGGAT
1 TGTTTGAGAACATCCGAGAGTCTAATCTGCTATGTCCTCGATTTGTTCCTTGTAAGCACAAGGAC
46354221 GCCAAACCATCTTGAGTC
66 GCCAAACCATCTTGAGTC
*
46354239 TGTTTGAGAACATCTGAGAGTCTAATCTGCTATGTCCTCGATTTGTTCCTTGTAAGCACAAGGAC
1 TGTTTGAGAACATCCGAGAGTCTAATCTGCTATGTCCTCGATTTGTTCCTTGTAAGCACAAGGAC
46354304 GCCAAACCATCTTGAGTC
66 GCCAAACCATCTTGAGTC
*
46354322 AGTTTGAGAACATCCGAGAGTCTAATCTGCTATGTCCTCGATTTGTTCCTTGTAA
1 TGTTTGAGAACATCCGAGAGTCTAATCTGCTATGTCCTCGATTTGTTCCTTGTAA
46354377 TCTTGAGTCT
Statistics
Matches: 367, Mismatches: 20, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 367 1.00
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.32
Consensus pattern (83 bp):
TGTTTGAGAACATCCGAGAGTCTAATCTGCTATGTCCTCGATTTGTTCCTTGTAAGCACAAGGAC
GCCAAACCATCTTGAGTC
Done.