Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 139 of 226
Found at i:46373357 original size:27 final size:27
Alignment explanation
Indices: 46373295--46373357 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
46373285 TTCTCAGTGT
* *
46373295 TCACCATACGTACTATTTCTTTAGAGC
1 TCACAATACGTACTATTTCTTTAAAGC
* *
46373322 TCACCATACGTACTA-TTCTCTTAAAGT
1 TCACAATACGTACTATTTCT-TTAAAGC
*
46373349 TTACAATAC
1 TCACAATAC
46373358 CTACCAATCC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 4 0.13
27 27 0.87
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (27 bp):
TCACAATACGTACTATTTCTTTAAAGC
Found at i:46373441 original size:53 final size:53
Alignment explanation
Indices: 46373383--46373684 Score: 277
Period size: 53 Copynumber: 5.7 Consensus size: 53
46373373 AGCTAGTCAC
* *
46373383 ACATATCATTCCTT-CAAGGTTTGCCATACTTACCATTCCTCAGATTTAGCCAT
1 ACATATCATT-CTTCCAAGGTTTGCCATACTTACCATTCCTCAAAGTTAGCCAT
* * ** * * ** *
46373436 ACATATCATTCTTCCAGGGTTTTCTTTATTTACTATTATTAAAAGTTAGCCAT
1 ACATATCATTCTTCCAAGGTTTGCCATACTTACCATTCCTCAAAGTTAGCCAT
* * * * ** **
46373489 ACATATAATTTTTCCAGGGTTTACCATACTTACTGTTCCTCGTAGTTAGCCAT
1 ACATATCATTCTTCCAAGGTTTGCCATACTTACCATTCCTCAAAGTTAGCCAT
** * * *
46373542 ACATATCATTCTTTTAAGGTTTTCCATATTTACCATTCTTCAAAGTTAGCCAT
1 ACATATCATTCTTCCAAGGTTTGCCATACTTACCATTCCTCAAAGTTAGCCAT
* * * *
46373595 ACATATCATTCTTCCAGGGTTTGTCATATTTACCATT-CTCCAAAGTTAGTCAT
1 ACATATCATTCTTCCAAGGTTTGCCATACTTACCATTCCT-CAAAGTTAGCCAT
* * *
46373648 ACATATCATTCTT-CTAGGTTTTGTCATACTTATCATT
1 ACATATCATTCTTCCAAGG-TTTGCCATACTTACCATT
46373685 TTTCTCTTTC
Statistics
Matches: 200, Mismatches: 46, Indels: 6
0.79 0.18 0.02
Matches are distributed among these distances:
52 7 0.04
53 193 0.96
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.42
Consensus pattern (53 bp):
ACATATCATTCTTCCAAGGTTTGCCATACTTACCATTCCTCAAAGTTAGCCAT
Found at i:46373528 original size:106 final size:105
Alignment explanation
Indices: 46373383--46373669 Score: 337
Period size: 106 Copynumber: 2.7 Consensus size: 105
46373373 AGCTAGTCAC
* * *
46373383 ACATATCATTCCTT-CAAGGTTTGCCATACTTACCATTCCTCAGATTTAGCCATACATATCATTC
1 ACATATAATT-CTTCCAGGGTTTGCCATACTTACCATTCCTCAGAGTTAGCCATACATATCATTC
* ** *
46373447 TTCCAGGGTTTTCTTTATTTACTATTATTAAAAGTTAGCCAT
65 TTCTA-GGTTTTCCATATTTACCATTATTAAAAGTTAGCCAT
* * **
46373489 ACATATAATTTTTCCAGGGTTTACCATACTTACTGTTCCTC-GTAGTTAGCCATACATATCATTC
1 ACATATAATTCTTCCAGGGTTTGCCATACTTACCATTCCTCAG-AGTTAGCCATACATATCATTC
* * *
46373553 TTTTAAGGTTTTCCATATTTACCATTCTTCAAAGTTAGCCAT
65 TTCT-AGGTTTTCCATATTTACCATTATTAAAAGTTAGCCAT
* * * * *
46373595 ACATATCATTCTTCCAGGGTTTGTCATATTTACCATT-CTCCAAAGTTAGTCATACATATCATTC
1 ACATATAATTCTTCCAGGGTTTGCCATACTTACCATTCCT-CAGAGTTAGCCATACATATCATTC
46373659 TTCTAGGTTTT
65 TTCTAGGTTTT
46373670 GTCATACTTA
Statistics
Matches: 152, Mismatches: 24, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
105 12 0.08
106 139 0.91
107 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.41
Consensus pattern (105 bp):
ACATATAATTCTTCCAGGGTTTGCCATACTTACCATTCCTCAGAGTTAGCCATACATATCATTCT
TCTAGGTTTTCCATATTTACCATTATTAAAAGTTAGCCAT
Found at i:46373604 original size:26 final size:26
Alignment explanation
Indices: 46373532--46373661 Score: 98
Period size: 26 Copynumber: 4.9 Consensus size: 26
46373522 TGTTCCTCGT
*
46373532 AGTTAGCCATACATATCATTCTTTTAA
1 AGTTAGCCATACATATCATTC-TTCAA
* ** ** *
46373559 GGTTTTCCATATTTACCATTCTTCAA
1 AGTTAGCCATACATATCATTCTTCAA
*
46373585 AGTTAGCCATACATATCATTCTTCCAG
1 AGTTAGCCATACATATCATTCTT-CAA
* * * ** * *
46373612 GGTTTGTCATATTTACCATTCTCCAA
1 AGTTAGCCATACATATCATTCTTCAA
*
46373638 AGTTAGTCATACATATCATTCTTC
1 AGTTAGCCATACATATCATTCTTC
46373662 TAGGTTTTGT
Statistics
Matches: 74, Mismatches: 28, Indels: 3
0.70 0.27 0.03
Matches are distributed among these distances:
26 41 0.55
27 33 0.45
ACGTcount: A:0.28, C:0.22, G:0.09, T:0.41
Consensus pattern (26 bp):
AGTTAGCCATACATATCATTCTTCAA
Found at i:46373631 original size:27 final size:27
Alignment explanation
Indices: 46373566--46373684 Score: 91
Period size: 26 Copynumber: 4.5 Consensus size: 27
46373556 TAAGGTTTTC
* * *
46373566 CATATTTACCATTCTT-CAAAGTTAGC
1 CATACTTATCATTCTTCCAAAGTTAGT
* ** *
46373592 CATACATATCATTCTTCCAGGGTTTGT
1 CATACTTATCATTCTTCCAAAGTTAGT
* *
46373619 CATATTTACCATTC-TCCAAAGTTAGT
1 CATACTTATCATTCTTCCAAAGTTAGT
* * * *
46373645 CATACATATCATTCTT-CTAGGTTTTGT
1 CATACTTATCATTCTTCCAAAG-TTAGT
46373672 CATACTTATCATT
1 CATACTTATCATT
46373685 TTTCTCTTTC
Statistics
Matches: 70, Mismatches: 20, Indels: 5
0.74 0.21 0.05
Matches are distributed among these distances:
26 36 0.51
27 34 0.49
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.42
Consensus pattern (27 bp):
CATACTTATCATTCTTCCAAAGTTAGT
Found at i:46373676 original size:159 final size:159
Alignment explanation
Indices: 46373383--46373679 Score: 407
Period size: 159 Copynumber: 1.9 Consensus size: 159
46373373 AGCTAGTCAC
* *
46373383 ACATATCATTCCTTCAAGGTTTGCCATACTTACCATTCCTCAGATTTAGCCATACATATCATTCT
1 ACATATCATTCCTTCAAGGTTTGCCATACTTACCATTCCTCAAAGTTAGCCATACATATCATTCT
* * * *
46373448 TCCAGGGTTTTCTTTATTTACTATTATTAAAAGTTAGCCATACATATAATTTTTCCAGGGTTTAC
66 TCCAGGGTTTTCTATATTTACCATTATCAAAAGTTAGCCATACATATAATTCTTCCAGGGTTTAC
46373513 CATACTTACTGTTCCTCGTAGTTAGCCAT
131 CATACTTACTGTTCCTCGTAGTTAGCCAT
* * * * *
46373542 ACATATCATTCTTTTAAGGTTTTCCATATTTACCATTCTTCAAAGTTAGCCATACATATCATTCT
1 ACATATCATTCCTTCAAGGTTTGCCATACTTACCATTCCTCAAAGTTAGCCATACATATCATTCT
* * * * * * *
46373607 TCCAGGGTTTGTC-ATATTTACCATTCTCCAAAGTTAGTCATACATATCATTCTTCTAGGTTTTG
66 TCCAGGGTTT-TCTATATTTACCATTATCAAAAGTTAGCCATACATATAATTCTTCCAGGGTTTA
*
46373671 TCATACTTA
130 CCATACTTA
46373680 TCATTTTTCT
Statistics
Matches: 118, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
159 116 0.98
160 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.41
Consensus pattern (159 bp):
ACATATCATTCCTTCAAGGTTTGCCATACTTACCATTCCTCAAAGTTAGCCATACATATCATTCT
TCCAGGGTTTTCTATATTTACCATTATCAAAAGTTAGCCATACATATAATTCTTCCAGGGTTTAC
CATACTTACTGTTCCTCGTAGTTAGCCAT
Found at i:46375414 original size:28 final size:27
Alignment explanation
Indices: 46375332--46375431 Score: 121
Period size: 27 Copynumber: 3.7 Consensus size: 27
46375322 CTATAGATCA
46375332 CCACAAAGGCTT-TCATTTCATAGATTG
1 CCACAAAGGCTTCT-ATTTCATAGATTG
*
46375359 CTACAAAGGCTTCTATTTCATAGATTG
1 CCACAAAGGCTTCTATTTCATAGATTG
* * * *
46375386 CCATAAAGGCTTTTATTTTCACAGGTTG
1 CCACAAAGGCTTCTA-TTTCATAGATTG
*
46375414 CCCCAAAGGCTTCTATTT
1 CCACAAAGGCTTCTATTT
46375432 TCTAGCGTGT
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
27 39 0.63
28 23 0.37
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (27 bp):
CCACAAAGGCTTCTATTTCATAGATTG
Found at i:46375610 original size:50 final size:47
Alignment explanation
Indices: 46375544--46375638 Score: 118
Period size: 47 Copynumber: 2.0 Consensus size: 47
46375534 CTTTAGTTTA
* *
46375544 TTCCATATGATGCCATAACCCTCCAACTATGGTCTTACACGATATGGTCT
1 TTCCATATGATGCCAT-A-CC-CCAACTATGGTATTACACAATATGGTCT
* * *
46375594 TTCCGTATGATTCCATAGCCCAACTATGGTATTACACAATATGGT
1 TTCCATATGATGCCATACCCCAACTATGGTATTACACAATATGGT
46375639 GCCATGGCCA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
47 24 0.60
48 1 0.03
49 1 0.03
50 14 0.35
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (47 bp):
TTCCATATGATGCCATACCCCAACTATGGTATTACACAATATGGTCT
Found at i:46388176 original size:13 final size:13
Alignment explanation
Indices: 46388158--46388183 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
46388148 CATACTTATC
46388158 ATTGGTTAACTCT
1 ATTGGTTAACTCT
46388171 ATTGGTTAACTCT
1 ATTGGTTAACTCT
46388184 GGCTGACTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (13 bp):
ATTGGTTAACTCT
Found at i:46388570 original size:19 final size:20
Alignment explanation
Indices: 46388534--46388573 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
46388524 CAAATGTGTT
*
46388534 AAAATTATTAATTGAAAATA
1 AAAAATATTAATTGAAAATA
*
46388554 AAAAATATTTATT-AAAATA
1 AAAAATATTAATTGAAAATA
46388573 A
1 A
46388574 TAAGAATGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (20 bp):
AAAAATATTAATTGAAAATA
Found at i:46388655 original size:33 final size:35
Alignment explanation
Indices: 46388618--46388713 Score: 87
Period size: 33 Copynumber: 2.8 Consensus size: 35
46388608 ATGGTTATAT
46388618 TTAAATATTTAAAATATAATTTATATATT-C-TAA
1 TTAAATATTTAAAATATAATTTATATATTGCTTAA
* *
46388651 TTAAAT-TTTATAAATAATAA-ATATTTATTGCTTAA
1 TTAAATATTTA-AAAT-ATAATTTATATATTGCTTAA
*
46388686 --AAATATTTAAAATTTATATTTCATATAT
1 TTAAATATTTAAAATATA-ATTT-ATATAT
46388714 AAAAATATTA
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
32 6 0.12
33 26 0.52
34 10 0.20
35 8 0.16
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (35 bp):
TTAAATATTTAAAATATAATTTATATATTGCTTAA
Found at i:46388916 original size:13 final size:13
Alignment explanation
Indices: 46388900--46388950 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
46388890 TAAACCAAAA
46388900 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
* *
46388913 TTTTCCACAGCAC
1 TTTTCAAAAGCAC
*
46388926 ATTTT-AAAAACAC
1 -TTTTCAAAAGCAC
46388939 TTTTCAAAAGCA
1 TTTTCAAAAGCA
46388951 TTGCTAAACT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
12 4 0.13
13 22 0.73
14 4 0.13
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.31
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:46388950 original size:26 final size:27
Alignment explanation
Indices: 46388899--46388950 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
46388889 TTAAACCAAA
* * *
46388899 ATTTTCAAAAGCACTTTTCCACAGCAC
1 ATTTTCAAAAACACTTTTCAAAAGCAC
46388926 ATTTT-AAAAACACTTTTCAAAAGCA
1 ATTTTCAAAAACACTTTTCAAAAGCA
46388951 TTGCTAAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.40, C:0.23, G:0.06, T:0.31
Consensus pattern (27 bp):
ATTTTCAAAAACACTTTTCAAAAGCAC
Found at i:46393458 original size:26 final size:26
Alignment explanation
Indices: 46393428--46393527 Score: 94
Period size: 26 Copynumber: 3.8 Consensus size: 26
46393418 GGAGGTCCCC
*
46393428 TAAGTTTGAGTCGGTTCGAGGAACCT
1 TAAGTTTGAGTTGGTTCGAGGAACCT
* * *
46393454 CAAGTTTGAGTTGGTTGGA-GATTCCT
1 TAAGTTTGAGTTGGTTCGAGGA-ACCT
* * * * *
46393480 TGAGTTTGAGTGGGTCCAAGGACCCT
1 TAAGTTTGAGTTGGTTCGAGGAACCT
*
46393506 TAAGTTTGAGTTGGTTAGAGGA
1 TAAGTTTGAGTTGGTTCGAGGA
46393528 CCATAAGCGG
Statistics
Matches: 56, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
25 2 0.04
26 52 0.93
27 2 0.04
ACGTcount: A:0.22, C:0.12, G:0.33, T:0.33
Consensus pattern (26 bp):
TAAGTTTGAGTTGGTTCGAGGAACCT
Found at i:46405289 original size:22 final size:22
Alignment explanation
Indices: 46405264--46405321 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
46405254 TAAAAAATCA
46405264 AAAAATTATAAAAAATTATTTT
1 AAAAATTATAAAAAATTATTTT
*
46405286 AAAAATTATTAAAAA-TATTTT
1 AAAAATTATAAAAAATTATTTT
*
46405307 --TAATTA-AAAAAATTA
1 AAAAATTATAAAAAATTA
46405322 ATTAATTGCT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 5 0.16
19 7 0.22
21 6 0.19
22 14 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAAATTATAAAAAATTATTTT
Found at i:46412496 original size:18 final size:16
Alignment explanation
Indices: 46412460--46412506 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
46412450 TTAATTTTTT
*
46412460 AAATATTAAAAATTAA
1 AAATATAAAAAATTAA
46412476 AAATATAAAAAAGTATAA
1 AAATATAAAAAA-T-TAA
46412494 AAATATTAAAAAA
1 AAATA-TAAAAAA
46412507 ATTGTATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 11 0.41
17 1 0.04
18 8 0.30
19 7 0.26
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (16 bp):
AAATATAAAAAATTAA
Found at i:46414114 original size:3 final size:3
Alignment explanation
Indices: 46414108--46414137 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
46414098 GCTCTTTATT
*
46414108 ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
46414138 CATTAAGCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:46415529 original size:3 final size:3
Alignment explanation
Indices: 46415521--46415546 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
46415511 AAATACTTTC
46415521 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
46415547 ATGGATGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:46416127 original size:2 final size:2
Alignment explanation
Indices: 46416114--46416166 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
46416104 AGGAAAACTA
*
46416114 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46416156 AT AT AT AT AT A
1 AT AT AT AT AT A
46416167 AGTTTAGAGT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:46416316 original size:16 final size:15
Alignment explanation
Indices: 46416289--46416327 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
46416279 AATTAGCTAT
*
46416289 TAATTAAAGTGATAG
1 TAATTAATGTGATAG
*
46416304 TATATTAATGTGATAT
1 TA-ATTAATGTGATAG
46416320 TAATTAAT
1 TAATTAAT
46416328 TTATTCACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.44
Consensus pattern (15 bp):
TAATTAATGTGATAG
Found at i:46423895 original size:32 final size:32
Alignment explanation
Indices: 46423838--46423929 Score: 112
Period size: 32 Copynumber: 2.8 Consensus size: 32
46423828 TTGGCCCATA
** * * **
46423838 TGCCCGTGTGGGCCCACACATCCAAATCAGCGT
1 TGCCCGTGT-GGCTTACACACCCAAATCAACCC
*
46423871 TGCCTGTGTGGCTTACACACCCAAATCAACCC
1 TGCCCGTGTGGCTTACACACCCAAATCAACCC
46423903 TGCCCGTGTGGCTTACACACCCAAATC
1 TGCCCGTGTGGCTTACACACCCAAATC
46423930 GGCCTAGGCC
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
32 43 0.84
33 8 0.16
ACGTcount: A:0.23, C:0.37, G:0.20, T:0.21
Consensus pattern (32 bp):
TGCCCGTGTGGCTTACACACCCAAATCAACCC
Found at i:46427764 original size:20 final size:20
Alignment explanation
Indices: 46427739--46427778 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
46427729 TCTTAGTAAC
46427739 ACAATCCAAACTGACTCAAT
1 ACAATCCAAACTGACTCAAT
46427759 ACAATCCAAACTGACTCAAT
1 ACAATCCAAACTGACTCAAT
46427779 GTTCCACAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.30, G:0.05, T:0.20
Consensus pattern (20 bp):
ACAATCCAAACTGACTCAAT
Found at i:46431107 original size:26 final size:26
Alignment explanation
Indices: 46431078--46431131 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
46431068 ATTTCGAACA
46431078 GCCCTTTTTGAAGCTTCAAATAGGTG
1 GCCCTTTTTGAAGCTTCAAATAGGTG
46431104 GCCCTTTTTGAAGCTTCAAATAGGTG
1 GCCCTTTTTGAAGCTTCAAATAGGTG
46431130 GC
1 GC
46431132 TGGCCATTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.33
Consensus pattern (26 bp):
GCCCTTTTTGAAGCTTCAAATAGGTG
Found at i:46433508 original size:19 final size:19
Alignment explanation
Indices: 46433471--46433510 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
46433461 AGCATTTTTA
*
46433471 GCGGCGTTTTTATAAAAGC
1 GCGGCGTTTTTAGAAAAGC
* *
46433490 GCGGCGTTTTTGGAGAAGC
1 GCGGCGTTTTTAGAAAAGC
46433509 GC
1 GC
46433511 CGCTAATGCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.20, C:0.17, G:0.35, T:0.28
Consensus pattern (19 bp):
GCGGCGTTTTTAGAAAAGC
Found at i:46433547 original size:41 final size:41
Alignment explanation
Indices: 46433490--46433677 Score: 290
Period size: 41 Copynumber: 4.6 Consensus size: 41
46433480 TTATAAAAGC
*
46433490 GCGGCGTTTTTGGAGAAGCGCCGCTAATGCT-TAGGGCTTTA
1 GCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCT-GGTCTTTA
46433531 GCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTGGTCTTTA
1 GCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTGGTCTTTA
* *
46433572 GCGGCGTTTTCTGG-GAAGCGCCGGTAATGCTCAGGTCTTTA
1 GCGGCGTTTT-TGGAGAAGCGCCGCTAATGCTCTGGTCTTTA
*
46433613 GCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGTCTTTA
1 GCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTGGTCTTTA
* *
46433654 GCGGCGTTTTTGGAAAAGAGCCGC
1 GCGGCGTTTTTGGAGAAGCGCCGC
46433678 AAAAACATTT
Statistics
Matches: 137, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
40 3 0.02
41 130 0.95
42 4 0.03
ACGTcount: A:0.16, C:0.21, G:0.33, T:0.29
Consensus pattern (41 bp):
GCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTGGTCTTTA
Found at i:46434152 original size:20 final size:20
Alignment explanation
Indices: 46434120--46434171 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
46434110 TGTGATTTAG
*
46434120 GGGTTAAGGGTTAGGGGTTA
1 GGGTTTAGGGTTAGGGGTTA
*
46434140 GGGATTT-GGGTTAGGGTTTA
1 GGG-TTTAGGGTTAGGGGTTA
46434160 GGGTTTAGGGTT
1 GGGTTTAGGGTT
46434172 TAAATTAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 3 0.11
20 23 0.82
21 2 0.07
ACGTcount: A:0.15, C:0.00, G:0.48, T:0.37
Consensus pattern (20 bp):
GGGTTTAGGGTTAGGGGTTA
Found at i:46434169 original size:14 final size:14
Alignment explanation
Indices: 46434115--46434173 Score: 61
Period size: 13 Copynumber: 4.3 Consensus size: 14
46434105 AGGGTTGTGA
*
46434115 TTTAGGGGTTAAGGG
1 TTTA-GGGTTTAGGG
*
46434130 -TTAGGGGTTAGGG
1 TTTAGGGTTTAGGG
46434143 ATTT-GGG-TTAGGG
1 -TTTAGGGTTTAGGG
46434156 TTTAGGGTTTAGGG
1 TTTAGGGTTTAGGG
46434170 TTTA
1 TTTA
46434174 AATTAATTAG
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
12 3 0.08
13 17 0.45
14 16 0.42
15 2 0.05
ACGTcount: A:0.17, C:0.00, G:0.44, T:0.39
Consensus pattern (14 bp):
TTTAGGGTTTAGGG
Found at i:46434172 original size:7 final size:7
Alignment explanation
Indices: 46434115--46434173 Score: 61
Period size: 7 Copynumber: 8.6 Consensus size: 7
46434105 AGGGTTGTGA
46434115 TTTAGGGG
1 TTTA-GGG
*
46434123 TTAAGGG
1 TTTAGGG
46434130 -TTAGGG
1 TTTAGGG
*
46434136 GTTAGGG
1 TTTAGGG
46434143 ATTT-GGG
1 -TTTAGGG
46434150 -TTAGGG
1 TTTAGGG
46434156 TTTAGGG
1 TTTAGGG
46434163 TTTAGGG
1 TTTAGGG
46434170 TTTA
1 TTTA
46434174 AATTAATTAG
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
5 2 0.05
6 8 0.18
7 29 0.66
8 5 0.11
ACGTcount: A:0.17, C:0.00, G:0.44, T:0.39
Consensus pattern (7 bp):
TTTAGGG
Found at i:46434241 original size:7 final size:7
Alignment explanation
Indices: 46434231--46434270 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
46434221 TAGTAGTTAT
46434231 GGGTTTG
1 GGGTTTG
46434238 GGGTTTG
1 GGGTTTG
46434245 GGGTTTG
1 GGGTTTG
46434252 GGGTTTG
1 GGGTTTG
*
46434259 GGGTTAG
1 GGGTTTG
46434266 GGGTT
1 GGGTT
46434271 AAGGGTTAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.03, C:0.00, G:0.57, T:0.40
Consensus pattern (7 bp):
GGGTTTG
Found at i:46434271 original size:7 final size:7
Alignment explanation
Indices: 46434213--46434278 Score: 60
Period size: 7 Copynumber: 9.4 Consensus size: 7
46434203 TAAATAAGGT
46434213 TTAGGGG
1 TTAGGGG
**
46434220 TTAGTAG
1 TTAGGGG
*
46434227 TTATGGG
1 TTAGGGG
*
46434234 TTTGGGG
1 TTAGGGG
*
46434241 TTTGGGG
1 TTAGGGG
*
46434248 TTTGGGG
1 TTAGGGG
*
46434255 TTTGGGG
1 TTAGGGG
46434262 TTAGGGG
1 TTAGGGG
*
46434269 TTAAGGG
1 TTAGGGG
46434276 TTA
1 TTA
46434279 AGAGTTAGTG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.12, C:0.00, G:0.48, T:0.39
Consensus pattern (7 bp):
TTAGGGG
Found at i:46434276 original size:21 final size:21
Alignment explanation
Indices: 46434210--46434277 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
46434200 TATTAAATAA
** *
46434210 GGTTTAGGGGTTAGTAGTTATG
1 GGTTT-GGGGTTAGGGGTTAAG
* **
46434232 GGTTTGGGGTTTGGGGTTTGG
1 GGTTTGGGGTTAGGGGTTAAG
46434253 GGTTTGGGGTTAGGGGTTAAG
1 GGTTTGGGGTTAGGGGTTAAG
46434274 GGTT
1 GGTT
46434278 AAGAGTTAGT
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
21 33 0.87
22 5 0.13
ACGTcount: A:0.10, C:0.00, G:0.50, T:0.40
Consensus pattern (21 bp):
GGTTTGGGGTTAGGGGTTAAG
Found at i:46434884 original size:27 final size:27
Alignment explanation
Indices: 46434852--46434905 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
46434842 TTACATGTTG
46434852 AAATTAATTAAGGGAATGTAAACAAGA
1 AAATTAATTAAGGGAATGTAAACAAGA
46434879 AAATTAATTAAGGGAATGTAAACAAGA
1 AAATTAATTAAGGGAATGTAAACAAGA
46434906 GAAAAGAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.56, C:0.04, G:0.19, T:0.22
Consensus pattern (27 bp):
AAATTAATTAAGGGAATGTAAACAAGA
Found at i:46439330 original size:24 final size:23
Alignment explanation
Indices: 46439302--46439349 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 23
46439292 AATTTAAAAA
46439302 ATAAAACATAATATAATATTT-ATT
1 ATAAAA-ATAA-ATAATATTTGATT
*
46439326 ATAAAAATAAATATTATTTGATT
1 ATAAAAATAAATAATATTTGATT
46439349 A
1 A
46439350 AAATAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 8 0.36
23 8 0.36
24 6 0.27
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
ATAAAAATAAATAATATTTGATT
Found at i:46439421 original size:42 final size:43
Alignment explanation
Indices: 46439398--46439686 Score: 377
Period size: 43 Copynumber: 6.8 Consensus size: 43
46439388 TTGCTAGAAT
* *
46439398 CGTCGCTAAAGGTT-TGTTCTTTAGCGGCGTTTGTGAAAAAAG
1 CGTCGCTAAAGGTTGTGGTCTTTAGCGGCGTTTGTGGAAAAAG
* * *
46439440 CG-CTGCTAAAGGTAGTGGTCTTTAGCGGAGTTTGTGGGAAAAG
1 CGTC-GCTAAAGGTTGTGGTCTTTAGCGGCGTTTGTGGAAAAAG
* *
46439483 CGCCGCTAAAGGTTGTGGTCTTTAGTGGCGTTTGTGGAAAAAG
1 CGTCGCTAAAGGTTGTGGTCTTTAGCGGCGTTTGTGGAAAAAG
* **
46439526 CGTCGCTAAAGGTTGTGGTCTTTAGCGGCG-CTGTGGGGAAAG
1 CGTCGCTAAAGGTTGTGGTCTTTAGCGGCGTTTGTGGAAAAAG
* * *
46439568 CGTTGCTAAAGGTCGTGGTCTTTAGCGGCGTTTGTGGGAAAAG
1 CGTCGCTAAAGGTTGTGGTCTTTAGCGGCGTTTGTGGAAAAAG
* **
46439611 CGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGAAAAAG
1 CGTCGCTAAAGGTTGTGGTCTTTAGCGGCGTTTGTGGAAAAAG
* * *
46439654 CGCCGCTAAAGATCGTGGTCTTTAGCGGCGTTT
1 CGTCGCTAAAGGTTGTGGTCTTTAGCGGCGTTT
46439687 TACGCCGCTA
Statistics
Matches: 219, Mismatches: 24, Indels: 7
0.88 0.10 0.03
Matches are distributed among these distances:
41 1 0.00
42 48 0.22
43 169 0.77
44 1 0.00
ACGTcount: A:0.20, C:0.16, G:0.35, T:0.29
Consensus pattern (43 bp):
CGTCGCTAAAGGTTGTGGTCTTTAGCGGCGTTTGTGGAAAAAG
Found at i:46439603 original size:128 final size:129
Alignment explanation
Indices: 46439362--46439684 Score: 445
Period size: 128 Copynumber: 2.5 Consensus size: 129
46439352 ATAATTTTTT
* * ** * * *
46439362 TAAAGGTTAT-GTTTTTAGTGGCGTTTTTGCTAGAATCGTCGCTAAAGGTT-TGTTCTTTAGCGG
1 TAAAGGTTATGGTCTTTAGTGGCGTTTGTGGAAAAAGCGTCGCTAAAGGTTGTGGTCTTTAGCGG
*
46439425 CGTTTGTGAAAAAAGCGCTGCTAAAGGTAGTGGTCTTTAGCGGAGTTTGTGGGAAAAGCGCCGC
66 CGTCTGTGAAAAAAGCGCTGCTAAAGGTAGTGGTCTTTAGCGGAGTTTGTGGGAAAAGCGCCGC
*
46439489 TAAAGGTTGTGGTCTTTAGTGGCGTTTGTGGAAAAAGCGTCGCTAAAGGTTGTGGTCTTTAGCGG
1 TAAAGGTTATGGTCTTTAGTGGCGTTTGTGGAAAAAGCGTCGCTAAAGGTTGTGGTCTTTAGCGG
*** * * *
46439554 CG-CTGTGGGGAAAGCGTTGCTAAAGGTCGTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
66 CGTCTGTGAAAAAAGCGCTGCTAAAGGTAGTGGTCTTTAGCGGAGTTTGTGGGAAAAGCGCCGC
* * * * *
46439617 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATCGTGGTCTTTAGCGG
1 TAAAGGTTATGGTCTTTAGTGGCGTTTGTGGAAAAAGCGTCGCTAAAGGTTGTGGTCTTTAGCGG
46439682 CGT
66 CGT
46439685 TTTACGCCGC
Statistics
Matches: 172, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
127 9 0.05
128 149 0.87
129 14 0.08
ACGTcount: A:0.21, C:0.15, G:0.34, T:0.31
Consensus pattern (129 bp):
TAAAGGTTATGGTCTTTAGTGGCGTTTGTGGAAAAAGCGTCGCTAAAGGTTGTGGTCTTTAGCGG
CGTCTGTGAAAAAAGCGCTGCTAAAGGTAGTGGTCTTTAGCGGAGTTTGTGGGAAAAGCGCCGC
Found at i:46442017 original size:36 final size:36
Alignment explanation
Indices: 46441971--46442043 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
46441961 GACAAAGTTG
46441971 GTGTGTAGCGGATGAGGGTAGGAACTGATTCTATTT
1 GTGTGTAGCGGATGAGGGTAGGAACTGATTCTATTT
46442007 GTGTGTAGCGGATGAGGGTAGGAACTGATTCTATTT
1 GTGTGTAGCGGATGAGGGTAGGAACTGATTCTATTT
46442043 G
1 G
46442044 ACATTTTGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.22, C:0.08, G:0.37, T:0.33
Consensus pattern (36 bp):
GTGTGTAGCGGATGAGGGTAGGAACTGATTCTATTT
Found at i:46444178 original size:63 final size:63
Alignment explanation
Indices: 46444047--46444191 Score: 157
Period size: 63 Copynumber: 2.3 Consensus size: 63
46444037 GCCACACGAC
* *** *
46444047 TGTGTACCAGGCCATGTAACTCACTGCTTGTGATTTAGGGTCACACAAGCCAGGGGCATGGGCA
1 TGTGT-CCAGGCCATGTAACTCACTGCTTGTGAATTAGGGTCACACAAGCCAGAAACACGGGCA
* * ** * *
46444111 TGTGTCCAGGCTATGTAACTCACTGTTTGTGAATT-GGTGTCACATGAGCCATAAACACGGGCG
1 TGTGTCCAGGCCATGTAACTCACTGCTTGTGAATTAGG-GTCACACAAGCCAGAAACACGGGCA
*
46444174 TGTGTCTAGGCCATGTAA
1 TGTGTCCAGGCCATGTAA
46444192 GAGATATTTT
Statistics
Matches: 67, Mismatches: 13, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
62 2 0.03
63 60 0.90
64 5 0.07
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.27
Consensus pattern (63 bp):
TGTGTCCAGGCCATGTAACTCACTGCTTGTGAATTAGGGTCACACAAGCCAGAAACACGGGCA
Found at i:46444879 original size:22 final size:22
Alignment explanation
Indices: 46444851--46444900 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
46444841 GGGTATGAAA
* *
46444851 TTGCATCTG-ATTTTGATTTGTT
1 TTGCATCTGTA-TCTGATGTGTT
46444873 TTGCATCTGTATCTGATGTGTT
1 TTGCATCTGTATCTGATGTGTT
46444895 TTGCAT
1 TTGCAT
46444901 TTTATCTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 24 0.96
23 1 0.04
ACGTcount: A:0.14, C:0.12, G:0.20, T:0.54
Consensus pattern (22 bp):
TTGCATCTGTATCTGATGTGTT
Found at i:46449259 original size:26 final size:25
Alignment explanation
Indices: 46449199--46449260 Score: 81
Period size: 25 Copynumber: 2.4 Consensus size: 25
46449189 TTTATCGAGG
* *
46449199 TTATTAGTTTATTGATAAAAATATT
1 TTATTAATTTATCGATAAAAATATT
46449224 TTATTAATTTATCGATAAATTAATA-T
1 TTATTAATTTATCGATAAA--AATATT
46449250 TTATTAATTTA
1 TTATTAATTTA
46449261 GAGAATATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
25 17 0.52
26 12 0.36
27 4 0.12
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (25 bp):
TTATTAATTTATCGATAAAAATATT
Found at i:46449382 original size:38 final size:38
Alignment explanation
Indices: 46449337--46449413 Score: 138
Period size: 38 Copynumber: 2.0 Consensus size: 38
46449327 TGAATCAAAG
46449337 TTAATTGGTTCATGTAA-CAAAAAGAAAAAAATAGTTAA
1 TTAATTGGTTCATGTAACCAAAAAG-AAAAAATAGTTAA
46449375 TTAATTGGTTCATGTAACCAAAAAGAAAAAATAGTTAA
1 TTAATTGGTTCATGTAACCAAAAAGAAAAAATAGTTAA
46449413 T
1 T
46449414 GGTTTCAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
38 31 0.82
39 7 0.18
ACGTcount: A:0.51, C:0.06, G:0.13, T:0.30
Consensus pattern (38 bp):
TTAATTGGTTCATGTAACCAAAAAGAAAAAATAGTTAA
Found at i:46451282 original size:17 final size:17
Alignment explanation
Indices: 46451260--46451304 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
46451250 ATTGAAAAAA
46451260 ATTATT-ATTTAATTGAG
1 ATTATTAATTT-ATTGAG
46451277 ATTATTAATTTATTGA-
1 ATTATTAATTTATTGAG
*
46451293 A-TATTCATTTAT
1 ATTATTAATTTAT
46451305 CGAGGTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 10 0.38
16 1 0.04
17 11 0.42
18 4 0.15
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.56
Consensus pattern (17 bp):
ATTATTAATTTATTGAG
Found at i:46451889 original size:19 final size:19
Alignment explanation
Indices: 46451852--46451891 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
46451842 GAATCATTAG
*
46451852 ATTTTTAAAATATATAAAT
1 ATTTTTAAAATATAAAAAT
46451871 ATTTTTAATAATA-AAAAAT
1 ATTTTTAA-AATATAAAAAT
46451890 AT
1 AT
46451892 ATATTTGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTTTAAAATATAAAAAT
Found at i:46456967 original size:2 final size:2
Alignment explanation
Indices: 46456919--46456955 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
46456909 GGAGGGAGGG
46456919 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
46456956 GCATGCATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:46459608 original size:15 final size:15
Alignment explanation
Indices: 46459588--46459616 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
46459578 AGAGAAAAAT
46459588 TATTTTAATTGATAG
1 TATTTTAATTGATAG
46459603 TATTTTAATTGATA
1 TATTTTAATTGATA
46459617 CAGTTACTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (15 bp):
TATTTTAATTGATAG
Found at i:46462601 original size:31 final size:31
Alignment explanation
Indices: 46462566--46462666 Score: 139
Period size: 31 Copynumber: 3.3 Consensus size: 31
46462556 AATCTGGTGA
* * **
46462566 GTGGTTATTTGTGGGACTTAGTCAGATGTGG
1 GTGGTTAATTATGGGACTTAGTGGGATGTGG
* *
46462597 GTGGTAAATTATGGAACTTAGTGGGATGTGG
1 GTGGTTAATTATGGGACTTAGTGGGATGTGG
*
46462628 GTGGTTAATTATGGGACTTAGTGGGATGTGA
1 GTGGTTAATTATGGGACTTAGTGGGATGTGG
46462659 GTGGTTAA
1 GTGGTTAA
46462667 GAAATTATCC
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 61 1.00
ACGTcount: A:0.22, C:0.04, G:0.39, T:0.36
Consensus pattern (31 bp):
GTGGTTAATTATGGGACTTAGTGGGATGTGG
Found at i:46469334 original size:45 final size:45
Alignment explanation
Indices: 46469295--46469425 Score: 176
Period size: 45 Copynumber: 2.9 Consensus size: 45
46469285 ATCATGATGC
46469295 CATAACATCTTTCAACTATGGTCTTACTTGTTTTAATCATATTGT
1 CATAACATCTTTCAACTATGGTCTTACTTGTTTTAATCATATTGT
* *
46469340 CATAGCGA-CTTTCAACTATGGTCTTACTTGTTTTAATCATATTAT
1 CATAAC-ATCTTTCAACTATGGTCTTACTTGTTTTAATCATATTGT
* * *
46469385 CACAACGTCTTTCAACTGTGGTCTTACTCAT-TTTTAATCAT
1 CATAACATCTTTCAACTATGGTCTTACT--TGTTTTAATCAT
46469426 GTTTACGATA
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
45 64 0.84
46 11 0.14
47 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.10, T:0.44
Consensus pattern (45 bp):
CATAACATCTTTCAACTATGGTCTTACTTGTTTTAATCATATTGT
Found at i:46473165 original size:21 final size:21
Alignment explanation
Indices: 46473125--46473168 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
46473115 TGCACTCTTG
* * *
46473125 CTCCTTAGTAGCAAACTCCTA
1 CTCCTTAATAGAAAAATCCTA
46473146 CTCCTTAATAGAAAAATCCTA
1 CTCCTTAATAGAAAAATCCTA
46473167 CT
1 CT
46473169 TTACATAACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.30, G:0.07, T:0.30
Consensus pattern (21 bp):
CTCCTTAATAGAAAAATCCTA
Found at i:46479871 original size:60 final size:60
Alignment explanation
Indices: 46479778--46479995 Score: 319
Period size: 60 Copynumber: 3.6 Consensus size: 60
46479768 TTAGGGTTGC
*
46479778 TCACACAAGTTGGCATTATAATCGGATTGCTCACACAACCTGACATTATAATTGGATTGT
1 TCACACAAGTTGACATTATAATCGGATTGCTCACACAACCTGACATTATAATTGGATTGT
* *
46479838 TCACACAAGTTGACATTATAATCGGATTTCTCACATAACCTGACATTATAATTGGATTGT
1 TCACACAAGTTGACATTATAATCGGATTGCTCACACAACCTGACATTATAATTGGATTGT
* * * * * * *
46479898 TCACATAAGTTGACATTATGATCGGGTTGCTCACACAAGCTGACATTATGATAGGATTGC
1 TCACACAAGTTGACATTATAATCGGATTGCTCACACAACCTGACATTATAATTGGATTGT
* **
46479958 TCACACAAGCTGACATTATAATTAGATTGCTCACACAA
1 TCACACAAGTTGACATTATAATCGGATTGCTCACACAA
46479996 GTTTGCATTA
Statistics
Matches: 140, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 140 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (60 bp):
TCACACAAGTTGACATTATAATCGGATTGCTCACACAACCTGACATTATAATTGGATTGT
Found at i:46479912 original size:90 final size:90
Alignment explanation
Indices: 46479769--46480036 Score: 286
Period size: 90 Copynumber: 3.0 Consensus size: 90
46479759 GGCAGTATTT
* ** * * ** *
46479769 TAGGGTTGCTCACACAAGTTGGCATTATAATCGGATTGCTCACACAACCTGACATTATAATTGGA
1 TAGGATTGCTCACACAACCTGACATTATAATTGGATTGCTCACACAAGTTGACATTATAATCGGA
* *
46479834 TTGTTCACACAAGTTGACATTATAA
66 TTGCTCACACAAGCTGACATTATAA
* * * * * * *
46479859 TCGGATTTCTCACATAACCTGACATTATAATTGGATTGTTCACATAAGTTGACATTATGATCGGG
1 TAGGATTGCTCACACAACCTGACATTATAATTGGATTGCTCACACAAGTTGACATTATAATCGGA
*
46479924 TTGCTCACACAAGCTGACATTATGA
66 TTGCTCACACAAGCTGACATTATAA
* * * ***
46479949 TAGGATTGCTCACACAAGCTGACATTATAATTAGATTGCTCACACAAGTTTG-CATTATGATAAA
1 TAGGATTGCTCACACAACCTGACATTATAATTGGATTGCTCACACAAG-TTGACATTATAATCGG
* *
46480013 ATTGCTCATACAAGCTAACATTAT
65 ATTGCTCACACAAGCTGACATTAT
46480037 CGTCGAGTTA
Statistics
Matches: 146, Mismatches: 31, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
90 143 0.98
91 3 0.02
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (90 bp):
TAGGATTGCTCACACAACCTGACATTATAATTGGATTGCTCACACAAGTTGACATTATAATCGGA
TTGCTCACACAAGCTGACATTATAA
Found at i:46480035 original size:30 final size:30
Alignment explanation
Indices: 46479774--46480036 Score: 213
Period size: 30 Copynumber: 8.8 Consensus size: 30
46479764 TATTTTAGGG
* * * **
46479774 TTGCTCACACAAGTTGGCATTATAATCGGA
1 TTGCTCACACAAGCTGACATTATGATAAGA
* * **
46479804 TTGCTCACACAACCTGACATTATAATTGGA
1 TTGCTCACACAAGCTGACATTATGATAAGA
* * * **
46479834 TTGTTCACACAAGTTGACATTATAATCGGA
1 TTGCTCACACAAGCTGACATTATGATAAGA
* * * * **
46479864 TTTCTCACATAACCTGACATTATAATTGGA
1 TTGCTCACACAAGCTGACATTATGATAAGA
* * * ** *
46479894 TTGTTCACATAAGTTGACATTATGATCGGG
1 TTGCTCACACAAGCTGACATTATGATAAGA
*
46479924 TTGCTCACACAAGCTGACATTATGATAGGA
1 TTGCTCACACAAGCTGACATTATGATAAGA
* *
46479954 TTGCTCACACAAGCTGACATTATAATTAGA
1 TTGCTCACACAAGCTGACATTATGATAAGA
* *
46479984 TTGCTCACACAAGTTTG-CATTATGATAAAA
1 TTGCTCACACAAG-CTGACATTATGATAAGA
* *
46480014 TTGCTCATACAAGCTAACATTAT
1 TTGCTCACACAAGCTGACATTAT
46480037 CGTCGAGTTA
Statistics
Matches: 195, Mismatches: 36, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
29 1 0.01
30 192 0.98
31 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (30 bp):
TTGCTCACACAAGCTGACATTATGATAAGA
Found at i:46483313 original size:35 final size:35
Alignment explanation
Indices: 46483266--46483369 Score: 129
Period size: 35 Copynumber: 3.0 Consensus size: 35
46483256 CTATTGGTCC
*
46483266 TTCAGGGCGACACTATGTAAATGGTATAC-AGATCA
1 TTCAGGACGACACTATGTAAATGGTATACAAG-TCA
* * *
46483301 TTCAGGATGACACTGTGTAAATGGTGTACAAGTCA
1 TTCAGGACGACACTATGTAAATGGTATACAAGTCA
** *
46483336 TTTGGGACGACACTATGTAAATGATATACAAGTC
1 TTCAGGACGACACTATGTAAATGGTATACAAGTC
46483370 CTTCGGGGCA
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
35 56 0.97
36 2 0.03
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (35 bp):
TTCAGGACGACACTATGTAAATGGTATACAAGTCA
Found at i:46487294 original size:3 final size:3
Alignment explanation
Indices: 46487286--46487338 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
46487276 TGTTGCTCCT
46487286 TTC TTC TTC TTC TTC 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
46487334 TTC TT
1 TTC TT
46487339 TTTATTTTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:46496501 original size:22 final size:22
Alignment explanation
Indices: 46496471--46496528 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
46496461 AACACAAGAT
* *
46496471 ATCAAATACAGTTGTAGAACAC
1 ATCAGATACAGATGTAGAACAC
* *
46496493 ATCAGATACAGATGTAGAATAT
1 ATCAGATACAGATGTAGAACAC
46496515 ATCAGATACAGATG
1 ATCAGATACAGATG
46496529 CAAATTCCTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.24
Consensus pattern (22 bp):
ATCAGATACAGATGTAGAACAC
Found at i:46498626 original size:17 final size:18
Alignment explanation
Indices: 46498589--46498646 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
46498579 TAATTGAGAT
*
46498589 AAAATAAATAATTAACAA
1 AAAATAAATAAATAACAA
*
46498607 AAAATAAATAAAT-ACGA
1 AAAATAAATAAATAACAA
* * *
46498624 AAAATAAACAAATGATAA
1 AAAATAAATAAATAACAA
46498642 AAAAT
1 AAAAT
46498647 GATAAACCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
17 15 0.44
18 19 0.56
ACGTcount: A:0.72, C:0.05, G:0.03, T:0.19
Consensus pattern (18 bp):
AAAATAAATAAATAACAA
Found at i:46519978 original size:44 final size:43
Alignment explanation
Indices: 46519930--46520079 Score: 212
Period size: 43 Copynumber: 3.5 Consensus size: 43
46519920 AAAAGGATGG
46519930 GAAGATAATCTTGGGTTGTTGAAAAAAGAATTTAAAAAAAAAGA
1 GAAGATAATCTTGGGTTGTTGAAAAAAGAATTT-AAAAAAAAGA
* * * * *
46519974 GAAGATAATCTTAGGTTGTTGAAAAAAGAACTTAAATAGAGGA
1 GAAGATAATCTTGGGTTGTTGAAAAAAGAATTTAAAAAAAAGA
*
46520017 GAAGATAATCTTGGGTTGTTGAAAAAAGAATTT-AAAAAATGA
1 GAAGATAATCTTGGGTTGTTGAAAAAAGAATTTAAAAAAAAGA
* *
46520059 GAAGAAAAACTTGGGTTGTTG
1 GAAGATAATCTTGGGTTGTTG
46520080 GGTTTACCCT
Statistics
Matches: 94, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
42 25 0.27
43 38 0.40
44 31 0.33
ACGTcount: A:0.47, C:0.03, G:0.23, T:0.27
Consensus pattern (43 bp):
GAAGATAATCTTGGGTTGTTGAAAAAAGAATTTAAAAAAAAGA
Found at i:46524466 original size:33 final size:33
Alignment explanation
Indices: 46524426--46524495 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
46524416 GCATCTATAG
*
46524426 AGAGATAGTCC-ATTGGGACATTAAACACGAAAT
1 AGAGATAG-CCTATTGAGACATTAAACACGAAAT
* * *
46524459 AGAGATAGCCTGTTGAGACATTAAACATGGAAT
1 AGAGATAGCCTATTGAGACATTAAACACGAAAT
46524492 AGAG
1 AGAG
46524496 TAAGTCCGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 2 0.06
33 30 0.94
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.21
Consensus pattern (33 bp):
AGAGATAGCCTATTGAGACATTAAACACGAAAT
Found at i:46531955 original size:20 final size:20
Alignment explanation
Indices: 46531932--46531970 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
46531922 AATATGTTGA
46531932 TAAATCCTTAGAAATATTGG
1 TAAATCCTTAGAAATATTGG
* *
46531952 TAAATCTTTAGATATATTG
1 TAAATCCTTAGAAATATTG
46531971 ATAAGTCATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (20 bp):
TAAATCCTTAGAAATATTGG
Found at i:46532089 original size:20 final size:20
Alignment explanation
Indices: 46532066--46532421 Score: 206
Period size: 20 Copynumber: 17.8 Consensus size: 20
46532056 TTGTAAAATT
46532066 TTAGAAATTTTGGTAAATCG
1 TTAGAAATTTTGGTAAATCG
* *
46532086 TTAGATATTTTGGTGAAA-CA
1 TTAGAAATTTTGGT-AAATCG
* *
46532106 TTAAAAATTTTGGTAAATCA
1 TTAGAAATTTTGGTAAATCG
** * *
46532126 TTAGATGTTTTGGTAAAACC
1 TTAGAAATTTTGGTAAATCG
* * * *
46532146 TTAAAAATTTTGATAATTTG
1 TTAGAAATTTTGGTAAATCG
* * * *
46532166 TTAGACATATCGGTAAATCC
1 TTAGAAATTTTGGTAAATCG
* * *
46532186 TTATAAATTTTGATAAACCG
1 TTAGAAATTTTGGTAAATCG
* *
46532206 TTAGATATATTGGTAAATCG
1 TTAGAAATTTTGGTAAATCG
**
46532226 CCA-AATATTTTGGTAAATTC-
1 TTAGAA-ATTTTGGTAAA-TCG
*
46532246 TTAGAAATATTGGTAAA--G
1 TTAGAAATTTTGGTAAATCG
* * *
46532264 TTTCAAAAATATTAGTAAATCG
1 -TT-AGAAATTTTGGTAAATCG
* * * * *
46532286 ATGGAAATTTTGATATATTG
1 TTAGAAATTTTGGTAAATCG
*
46532306 TTAGATATTTTGGTAAATTC-
1 TTAGAAATTTTGGTAAA-TCG
* * *
46532326 TCAGAAATATTGGTAAATTG
1 TTAGAAATTTTGGTAAATCG
* * *
46532346 TTAG-ATTTATTGGTAAGTCC
1 TTAGAAATT-TTGGTAAATCG
*
46532366 TTAGAAATTTTGGTAAATCA
1 TTAGAAATTTTGGTAAATCG
*
46532386 TTAGATATTTTGGTAAAGTC-
1 TTAGAAATTTTGGTAAA-TCG
*
46532406 ATAGAAATTTTGGTAA
1 TTAGAAATTTTGGTAA
46532422 TTGCTAAGAC
Statistics
Matches: 245, Mismatches: 76, Indels: 30
0.70 0.22 0.09
Matches are distributed among these distances:
19 9 0.04
20 221 0.90
21 14 0.06
22 1 0.00
ACGTcount: A:0.37, C:0.06, G:0.16, T:0.40
Consensus pattern (20 bp):
TTAGAAATTTTGGTAAATCG
Found at i:46532551 original size:20 final size:21
Alignment explanation
Indices: 46532511--46532560 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
46532501 TGTTAGATAT
46532511 ATATTGGT-AAGTTCTTAGAA
1 ATATTGGTAAAGTTCTTAGAA
46532531 ATATTGGTAAAG-TCATT-GAA
1 ATATTGGTAAAGTTC-TTAGAA
*
46532551 ATTTTGGTAA
1 ATATTGGTAA
46532561 TTGTTAAGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 22 0.81
21 5 0.19
ACGTcount: A:0.36, C:0.04, G:0.20, T:0.40
Consensus pattern (21 bp):
ATATTGGTAAAGTTCTTAGAA
Found at i:46532621 original size:21 final size:21
Alignment explanation
Indices: 46532596--46532649 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
46532586 GAAAATTTGG
* *
46532596 AAATATTAGTAAAATCTTAGA
1 AAATATTGGTAAAATCATAGA
*
46532617 AAATATTGGTAAAATGATAGA
1 AAATATTGGTAAAATCATAGA
46532638 AAAT-TTGGTAAA
1 AAATATTGGTAAA
46532650 TTGTTAGATA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 8 0.27
21 22 0.73
ACGTcount: A:0.52, C:0.02, G:0.15, T:0.31
Consensus pattern (21 bp):
AAATATTGGTAAAATCATAGA
Found at i:46532670 original size:20 final size:20
Alignment explanation
Indices: 46532613--46532670 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
46532603 AGTAAAATCT
*
46532613 TAGAAAATATTGGTAAAATGA
1 TAGAAAAT-TTGGTAAATTGA
*
46532634 TAGAAAATTTGGTAAATTGT
1 TAGAAAATTTGGTAAATTGA
* *
46532654 TAGATATTTTGGTAAAT
1 TAGAAAATTTGGTAAAT
46532671 GTAACACCCC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
20 25 0.76
21 8 0.24
ACGTcount: A:0.43, C:0.00, G:0.19, T:0.38
Consensus pattern (20 bp):
TAGAAAATTTGGTAAATTGA
Found at i:46535021 original size:29 final size:29
Alignment explanation
Indices: 46534979--46535041 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
46534969 CATGCCACAT
* * * *
46534979 GGCCTGGTATACGACTATATGGTTTATAC
1 GGCCTGGCACACGACCATATGGTTTACAC
* *
46535008 GGCCTGGCACACGACCGTGTGGTTTACAC
1 GGCCTGGCACACGACCATATGGTTTACAC
46535037 GGCCT
1 GGCCT
46535042 ACCATATTGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.19, C:0.25, G:0.29, T:0.27
Consensus pattern (29 bp):
GGCCTGGCACACGACCATATGGTTTACAC
Found at i:46537704 original size:20 final size:20
Alignment explanation
Indices: 46537543--46537706 Score: 127
Period size: 20 Copynumber: 8.2 Consensus size: 20
46537533 AGATGTTACA
*
46537543 GTAAATCATTAGAAATTTTG
1 GTAAATCGTTAGAAATTTTG
* ** * *
46537563 GTAAGTTATTAGATATATTG
1 GTAAATCGTTAGAAATTTTG
* *
46537583 GTAAAAT-GATAGAAAATTTG
1 GT-AAATCGTTAGAAATTTTG
46537603 GTAAATCGTTA-AATATTTTG
1 GTAAATCGTTAGAA-ATTTTG
* * *
46537623 GTAAATCCTTAAAAATTTCG
1 GTAAATCGTTAGAAATTTTG
*
46537643 GTAAATCGTTAGATATTTTAG
1 GTAAATCGTTAGAAATTTT-G
* * **
46537664 G-GAATCCTTAGAAATAATG
1 GTAAATCGTTAGAAATTTTG
*
46537683 GTAAATCTTTAGAAATTTTG
1 GTAAATCGTTAGAAATTTTG
46537703 GTAA
1 GTAA
46537707 TTGATAATAT
Statistics
Matches: 111, Mismatches: 27, Indels: 12
0.74 0.18 0.08
Matches are distributed among these distances:
19 8 0.07
20 96 0.86
21 7 0.06
ACGTcount: A:0.39, C:0.05, G:0.17, T:0.38
Consensus pattern (20 bp):
GTAAATCGTTAGAAATTTTG
Found at i:46540726 original size:20 final size:20
Alignment explanation
Indices: 46540703--46540801 Score: 72
Period size: 20 Copynumber: 4.9 Consensus size: 20
46540693 TTTATAAATT
46540703 GTTAGATATTTTGGTAAAAC
1 GTTAGATATTTTGGTAAAAC
* *
46540723 GTTAGAGATATTGGTAAAAC
1 GTTAGATATTTTGGTAAAAC
* * * * * *
46540743 AATAAAAAAATTTGGTAAATC
1 -GTTAGATATTTTGGTAAAAC
* **
46540764 GTTAGATATATTGGTAAATT
1 GTTAGATATTTTGGTAAAAC
* *
46540784 ATTAGATATTTTGATAAA
1 GTTAGATATTTTGGTAAA
46540802 GCCATTGAAC
Statistics
Matches: 59, Mismatches: 19, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
20 46 0.78
21 13 0.22
ACGTcount: A:0.42, C:0.03, G:0.17, T:0.37
Consensus pattern (20 bp):
GTTAGATATTTTGGTAAAAC
Found at i:46540880 original size:20 final size:20
Alignment explanation
Indices: 46540852--46540905 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
46540842 GAAAATTAGG
* *
46540852 AAATATTGGTAAAATTTTAA
1 AAATATTGGTAAAATCTCAA
* *
46540872 AAATTTTGGTAAAATCTCAT
1 AAATATTGGTAAAATCTCAA
46540892 AAATATTGGTAAAA
1 AAATATTGGTAAAA
46540906 CGATAGAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.48, C:0.04, G:0.11, T:0.37
Consensus pattern (20 bp):
AAATATTGGTAAAATCTCAA
Found at i:46540994 original size:41 final size:39
Alignment explanation
Indices: 46540852--46540999 Score: 111
Period size: 40 Copynumber: 3.7 Consensus size: 39
46540842 GAAAATTAGG
** * * *
46540852 AAATATTGGTAAAATTTTA-AAAATTTTGGTAAAATCTCAT
1 AAATATTGGTAAAATGATAGAAATTTTTAGT-AAATC-CTT
* * * *
46540892 AAATATTGGTAAAACGATAGAAA-TTTTGGTAACTCGTT
1 AAATATTGGTAAAATGATAGAAATTTTTAGTAAATCCTT
* * **
46540930 AAATATTTTGATAAATTCTTAGAAATTTTTAGTAAATCCTT
1 AAATA--TTGGTAAAATGATAGAAATTTTTAGTAAATCCTT
46540971 AAATATATCGGTAAAATGATAGAAATTTT
1 AAATAT-T-GGTAAAATGATAGAAATTTT
46541000 GTTATTGTTA
Statistics
Matches: 84, Mismatches: 18, Indels: 11
0.74 0.16 0.10
Matches are distributed among these distances:
38 6 0.07
39 5 0.06
40 37 0.44
41 36 0.43
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (39 bp):
AAATATTGGTAAAATGATAGAAATTTTTAGTAAATCCTT
Found at i:46541090 original size:20 final size:20
Alignment explanation
Indices: 46541039--46541092 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
46541029 GAAAATTTGA
* *
46541039 AAATATTGATAAAATCTTAT
1 AAATATTGGTAAAACCTTAT
* *
46541059 AAATTTTTGGTAAAGCCTTAT
1 AAA-TATTGGTAAAACCTTAT
46541080 AAATATTGGTAAA
1 AAATATTGGTAAA
46541093 CCGATATTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (20 bp):
AAATATTGGTAAAACCTTAT
Found at i:46544207 original size:13 final size:13
Alignment explanation
Indices: 46544164--46544208 Score: 54
Period size: 15 Copynumber: 3.2 Consensus size: 13
46544154 ATATATTTAA
46544164 TATAATTAAATAT
1 TATAATTAAATAT
46544177 TAATTAATTATAACTAT
1 T-A-TAATTA-AA-TAT
46544194 TATAATTAAATAT
1 TATAATTAAATAT
46544207 TA
1 TA
46544209 ATATTAGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 6 0.21
14 3 0.11
15 12 0.43
16 3 0.11
17 4 0.14
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (13 bp):
TATAATTAAATAT
Found at i:46544213 original size:19 final size:20
Alignment explanation
Indices: 46544177--46544219 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
46544167 AATTAAATAT
*
46544177 TAATTAATTATAACTATTA-
1 TAATTAAATATAACTATTAG
46544196 TAATTAAATATTAA-TATTAG
1 TAATTAAATA-TAACTATTAG
46544216 TAAT
1 TAAT
46544220 ATTAAGTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (20 bp):
TAATTAAATATAACTATTAG
Found at i:46547758 original size:20 final size:20
Alignment explanation
Indices: 46547716--46547758 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
46547706 AACTATTTAA
** *
46547716 ATAATATTATTTGAATAGGT
1 ATAATATTAAATGAATAAGT
*
46547736 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAAGT
46547756 ATA
1 ATA
46547759 TGTTTATTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (20 bp):
ATAATATTAAATGAATAAGT
Found at i:46554275 original size:31 final size:31
Alignment explanation
Indices: 46554237--46554298 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
46554227 AGAGAAAGAA
46554237 GAGCTACTCTCCATTGGTGTTGAAGGGATCG
1 GAGCTACTCTCCATTGGTGTTGAAGGGATCG
46554268 GAGCTACTCTCCATTGGTGTTGAAGGGATCG
1 GAGCTACTCTCCATTGGTGTTGAAGGGATCG
46554299 TTTTATACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.19, C:0.19, G:0.32, T:0.29
Consensus pattern (31 bp):
GAGCTACTCTCCATTGGTGTTGAAGGGATCG
Found at i:46557170 original size:19 final size:19
Alignment explanation
Indices: 46557146--46557183 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
46557136 TAATATAACT
46557146 AAATA-TAATTATTACAAAC
1 AAATATTAA-TATTACAAAC
*
46557165 AAATATTAATATTAGAAAC
1 AAATATTAATATTACAAAC
46557184 TTTAAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.32
Consensus pattern (19 bp):
AAATATTAATATTACAAAC
Found at i:46568346 original size:39 final size:39
Alignment explanation
Indices: 46568292--46568371 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
46568282 CAATGCTTGA
46568292 TAGACTATTCTTTTGGCCTCATCTACCTAAGTTACTTCC
1 TAGACTATTCTTTTGGCCTCATCTACCTAAGTTACTTCC
46568331 TAGACTATTCTTTTGGCCTCATCTACCTAAGTTACTTCC
1 TAGACTATTCTTTTGGCCTCATCTACCTAAGTTACTTCC
46568370 TA
1 TA
46568372 AGGTCATCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.21, C:0.28, G:0.10, T:0.41
Consensus pattern (39 bp):
TAGACTATTCTTTTGGCCTCATCTACCTAAGTTACTTCC
Found at i:46571431 original size:20 final size:22
Alignment explanation
Indices: 46571403--46571446 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
46571393 AAACAAAGAG
*
46571403 AAGAGAAA-TAAT-GTAGCAAA
1 AAGAAAAAGTAATAGTAGCAAA
46571423 AAGAAAAATGTAATAGTAGCAAA
1 AAGAAAAA-GTAATAGTAGCAAA
46571446 A
1 A
46571447 GTAAAACTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 7 0.35
22 4 0.20
23 9 0.45
ACGTcount: A:0.61, C:0.05, G:0.18, T:0.16
Consensus pattern (22 bp):
AAGAAAAAGTAATAGTAGCAAA
Found at i:46574823 original size:27 final size:27
Alignment explanation
Indices: 46574807--46574939 Score: 178
Period size: 27 Copynumber: 5.0 Consensus size: 27
46574797 TATAATAGTC
46574807 ATTTTACCCTATGGGGGTATTTCGGTT
1 ATTTTACCCTATGGGGGTATTTCGGTT
*
46574834 ATTTTACCCTATGGAGGTATTTCGGTT
1 ATTTTACCCTATGGGGGTATTTCGGTT
* *
46574861 ATTTTACCCTATGGGGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGGTT
* * *
46574888 ATTTTACCCCAT-AGGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTT
* * *
46574914 ATTCTACCTTATGAGGGTATTTCGGT
1 ATTTTACCCTATGGGGGTATTTCGGT
46574940 GCAGATATAG
Statistics
Matches: 95, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
26 21 0.22
27 74 0.78
ACGTcount: A:0.18, C:0.17, G:0.23, T:0.42
Consensus pattern (27 bp):
ATTTTACCCTATGGGGGTATTTCGGTT
Found at i:46575637 original size:12 final size:12
Alignment explanation
Indices: 46575620--46575661 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
46575610 ATCCCAATAC
46575620 TCTCTCCTCAAA
1 TCTCTCCTCAAA
46575632 TCTCTCCT-AATA
1 TCTCTCCTCAA-A
* *
46575644 TCCCTCCTCAAT
1 TCTCTCCTCAAA
46575656 TCTCTC
1 TCTCTC
46575662 TATGACCAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
11 2 0.08
12 21 0.84
13 2 0.08
ACGTcount: A:0.19, C:0.43, G:0.00, T:0.38
Consensus pattern (12 bp):
TCTCTCCTCAAA
Found at i:46575829 original size:24 final size:24
Alignment explanation
Indices: 46575797--46575845 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
46575787 ACTTGACCAC
46575797 AGGCTCTTTTTGTGATATAAAACA
1 AGGCTCTTTTTGTGATATAAAACA
46575821 AGGCTCTTTTTGTGATATAAAACA
1 AGGCTCTTTTTGTGATATAAAACA
46575845 A
1 A
46575846 ACACTATTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (24 bp):
AGGCTCTTTTTGTGATATAAAACA
Found at i:46576506 original size:18 final size:17
Alignment explanation
Indices: 46576474--46576523 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 17
46576464 GAACACAGAT
*
46576474 GAAAA-AAAACTGAAAA
1 GAAAAGAAAACCGAAAA
*
46576490 GAAATATAAAACCGAAAA
1 GAAA-AGAAAACCGAAAA
46576508 GAAAAGAAAACC-AAAA
1 GAAAAGAAAACCGAAAA
46576524 ACTAAATTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 8 0.27
17 8 0.27
18 14 0.47
ACGTcount: A:0.72, C:0.10, G:0.12, T:0.06
Consensus pattern (17 bp):
GAAAAGAAAACCGAAAA
Found at i:46581225 original size:28 final size:28
Alignment explanation
Indices: 46581185--46581344 Score: 176
Period size: 28 Copynumber: 5.7 Consensus size: 28
46581175 TAACAAAACT
* *
46581185 GTGTGGGCCTTAGCCCAATACAGTAACA
1 GTGTGGGCTTTAGCCCAATACAGTATCA
*
46581213 GTGTGGGCCTTAGCCCAATACAGTATCA
1 GTGTGGGCTTTAGCCCAATACAGTATCA
* * * * *
46581241 GTGTGAGCGTTAGCCTAACACGGTATCA
1 GTGTGGGCTTTAGCCCAATACAGTATCA
* * * *
46581269 ATGTGGGCTTTAGCCCAAAATAATATCA
1 GTGTGGGCTTTAGCCCAATACAGTATCA
* * *
46581297 GTGTGGGCTTTAGCCCAAAATAGTATAA
1 GTGTGGGCTTTAGCCCAATACAGTATCA
*
46581325 GTGTGGGCTTTAGCCTAATA
1 GTGTGGGCTTTAGCCCAATA
46581345 TAATAATAGT
Statistics
Matches: 113, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 113 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (28 bp):
GTGTGGGCTTTAGCCCAATACAGTATCA
Found at i:46581286 original size:84 final size:84
Alignment explanation
Indices: 46581186--46581342 Score: 215
Period size: 84 Copynumber: 1.9 Consensus size: 84
46581176 AACAAAACTG
* * * *
46581186 TGTGGGCCTTAGCCCAATACAGTAACAGTGTGGGCCTTAGCCCAATACAGTATCAGTGTGAGCGT
1 TGTGGGCCTTAGCCCAAAACAATAACAGTGTGGGCCTTAGCCCAAAACAGTATAAGTGTGAGCGT
46581251 TAGCCTAACACGGTATCAA
66 TAGCCTAACACGGTATCAA
* * * * * * *
46581270 TGTGGGCTTTAGCCCAAAATAATATCAGTGTGGGCTTTAGCCCAAAATAGTATAAGTGTGGGCTT
1 TGTGGGCCTTAGCCCAAAACAATAACAGTGTGGGCCTTAGCCCAAAACAGTATAAGTGTGAGCGT
46581335 TAGCCTAA
66 TAGCCTAA
46581343 TATAATAATA
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
84 62 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (84 bp):
TGTGGGCCTTAGCCCAAAACAATAACAGTGTGGGCCTTAGCCCAAAACAGTATAAGTGTGAGCGT
TAGCCTAACACGGTATCAA
Found at i:46581845 original size:26 final size:27
Alignment explanation
Indices: 46581732--46581864 Score: 171
Period size: 27 Copynumber: 5.0 Consensus size: 27
46581722 GGGTATACCA
* *
46581732 GTCATTTTACCCCATGGGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* * * *
46581759 ATCATTCTACCCTATGGGGGTATTTCA
1 GTCATTTTACCCTATGAGGGTATTTCG
*
46581786 GTCATTTTACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGAGGGTATTTCG
46581813 GTCATTTTACCCTATGAGGGTATTT-G
1 GTCATTTTACCCTATGAGGGTATTTCG
*
46581839 GTCATTTTACCCT-TCGGGGGTATTTC
1 GTCATTTTACCCTAT-GAGGGTATTTC
46581865 AGTCCAGATA
Statistics
Matches: 94, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
25 1 0.01
26 23 0.24
27 70 0.74
ACGTcount: A:0.17, C:0.20, G:0.23, T:0.41
Consensus pattern (27 bp):
GTCATTTTACCCTATGAGGGTATTTCG
Found at i:46582847 original size:23 final size:23
Alignment explanation
Indices: 46582817--46582864 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
46582807 TTTAAGAGTA
46582817 AAACTAAAAATTATGCAAAAGCC
1 AAACTAAAAATTATGCAAAAGCC
46582840 AAACTAAAAATTATGCAAAAGCC
1 AAACTAAAAATTATGCAAAAGCC
46582863 AA
1 AA
46582865 GACTGGAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.58, C:0.17, G:0.08, T:0.17
Consensus pattern (23 bp):
AAACTAAAAATTATGCAAAAGCC
Found at i:46585080 original size:38 final size:38
Alignment explanation
Indices: 46585029--46585221 Score: 217
Period size: 38 Copynumber: 5.1 Consensus size: 38
46585019 GGACTTGTAT
** *
46585029 TGTTATTCGGGCTTTGTGCTTAGCAGGCTTAGTGCCAG
1 TGTTATTTAGGCTTTGTGCTTAGTAGGCTTAGTGCCAG
* * *
46585067 TATTATTTAGGCTTTGTGCCTAGTAGGCTTAGTGCCGG
1 TGTTATTTAGGCTTTGTGCTTAGTAGGCTTAGTGCCAG
* * * * *
46585105 TGTTATTAAGGCTGTGTGCCTAGTAGGCTTCGTGCCGG
1 TGTTATTTAGGCTTTGTGCTTAGTAGGCTTAGTGCCAG
* *
46585143 TGTTATTCAGGCATTGTGCTTAGTAGGCATT-GTGCCAG
1 TGTTATTTAGGCTTTGTGCTTAGTAGGC-TTAGTGCCAG
* ** *
46585181 TGTTATTTAAGCTTTGTGCTTAACAGGCTTAGTGCCGG
1 TGTTATTTAGGCTTTGTGCTTAGTAGGCTTAGTGCCAG
46585219 TGT
1 TGT
46585222 ATTAAAAAGT
Statistics
Matches: 132, Mismatches: 21, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
37 2 0.02
38 128 0.97
39 2 0.02
ACGTcount: A:0.16, C:0.17, G:0.30, T:0.38
Consensus pattern (38 bp):
TGTTATTTAGGCTTTGTGCTTAGTAGGCTTAGTGCCAG
Found at i:46595609 original size:40 final size:40
Alignment explanation
Indices: 46595532--46595609 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
46595522 TTATCCTAGA
* * *
46595532 AAAAAAGAATTTAAAAAGAGGAGAATATAAGCTTGGGTTG
1 AAAAAAGAATTTAAAAAGAGGAGAAGATAAACATGGGTTG
*
46595572 AAAAAAGACTTTAAAAAGAGGAGAAGATAAACATGGGT
1 AAAAAAGAATTTAAAAAGAGGAGAAGATAAACATGGGT
46595610 AGTTGGATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.53, C:0.04, G:0.24, T:0.19
Consensus pattern (40 bp):
AAAAAAGAATTTAAAAAGAGGAGAAGATAAACATGGGTTG
Found at i:46601841 original size:37 final size:37
Alignment explanation
Indices: 46601799--46601873 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
46601789 AGTAATAAAG
46601799 TAAGTAAAAGAGTTATTGTCTCCACAGGGACTGTGTA
1 TAAGTAAAAGAGTTATTGTCTCCACAGGGACTGTGTA
46601836 TAAGTAAAAGAGTTATTGTCTCCACAGGGACTGTGTA
1 TAAGTAAAAGAGTTATTGTCTCCACAGGGACTGTGTA
46601873 T
1 T
46601874 GTTAATCAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (37 bp):
TAAGTAAAAGAGTTATTGTCTCCACAGGGACTGTGTA
Found at i:46607165 original size:30 final size:29
Alignment explanation
Indices: 46607131--46607194 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 29
46607121 TTAGTAAAGG
46607131 TAAAATTACACTTTAGTCCCCTT-AAAATTA
1 TAAAATTACA-TTTAGT-CCCTTAAAAATTA
* *
46607161 TAAAAATTTCATTTAGTCCTTTAAAAATTA
1 T-AAAATTACATTTAGTCCCTTAAAAATTA
46607191 TAAA
1 TAAA
46607195 GATATAGACT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
29 7 0.23
30 15 0.50
31 8 0.27
ACGTcount: A:0.44, C:0.14, G:0.03, T:0.39
Consensus pattern (29 bp):
TAAAATTACATTTAGTCCCTTAAAAATTA
Found at i:46609252 original size:38 final size:38
Alignment explanation
Indices: 46609208--46609297 Score: 99
Period size: 38 Copynumber: 2.4 Consensus size: 38
46609198 CCAGTTTTAG
** *
46609208 CTCTTATGAGCAAAATAATTTGTTATCAGATGGAATAA
1 CTCTTATGAGCAAAATAACATGTTATCAGATGAAATAA
* * * **
46609246 CTCTTATGGGTAAACTGGCATGTTATCAGATGAAATAA
1 CTCTTATGAGCAAAATAACATGTTATCAGATGAAATAA
*
46609284 CCCTTATGAGCAAA
1 CTCTTATGAGCAAA
46609298 TTGGCATGTT
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (38 bp):
CTCTTATGAGCAAAATAACATGTTATCAGATGAAATAA
Found at i:46609303 original size:38 final size:38
Alignment explanation
Indices: 46609228--46609308 Score: 117
Period size: 38 Copynumber: 2.1 Consensus size: 38
46609218 CAAAATAATT
* * * *
46609228 TGTTATCAGATGGAATAACTCTTATGGGTAAACTGGCA
1 TGTTATCAGATGAAATAACCCTTATGAGCAAACTGGCA
*
46609266 TGTTATCAGATGAAATAACCCTTATGAGCAAATTGGCA
1 TGTTATCAGATGAAATAACCCTTATGAGCAAACTGGCA
46609304 TGTTA
1 TGTTA
46609309 CAGTTGGTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (38 bp):
TGTTATCAGATGAAATAACCCTTATGAGCAAACTGGCA
Found at i:46612385 original size:17 final size:16
Alignment explanation
Indices: 46612363--46612394 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
46612353 AAGTCATAGT
46612363 TATGGGTATCAGAAATA
1 TATGGGTATCA-AAATA
46612380 TATGGGTATCAAAAT
1 TATGGGTATCAAAAT
46612395 CTTGGATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.31
Consensus pattern (16 bp):
TATGGGTATCAAAATA
Found at i:46628979 original size:51 final size:50
Alignment explanation
Indices: 46628907--46629104 Score: 218
Period size: 51 Copynumber: 3.9 Consensus size: 50
46628897 ATCAGTGATG
* *
46628907 TCCGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCA
1 TCCGGTACACATAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCA
** * * * * *
46628958 TCCAATACACGTAATAGCCTGCACATAGTACTACACACGTGATCGAAACTA
1 TCCGGTACACATAGTAGCCTGCACATAGTACTACACACGTGA-CCATACCA
* * * * * *
46629009 TCCGGTACGCATAGTAGCCTGCACATATTACTACACATGCGGCC-TATCA
1 TCCGGTACACATAGTAGCCTGCACATAGTACTACACACGTGACCATACCA
*
46629058 TTCCGGTACACATAGTAGCCTGCAAATAGTACTACACACGTGACCAT
1 -TCCGGTACACATAGTAGCCTGCACATAGTACTACACACGTGACCAT
46629105 CAATTTCACT
Statistics
Matches: 116, Mismatches: 28, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
49 2 0.02
50 39 0.34
51 73 0.63
52 2 0.02
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (50 bp):
TCCGGTACACATAGTAGCCTGCACATAGTACTACACACGTGACCATACCA
Found at i:46629124 original size:101 final size:99
Alignment explanation
Indices: 46628915--46629100 Score: 239
Period size: 101 Copynumber: 1.8 Consensus size: 99
46628905 TGTCCGGTTC
* *
46628915 ACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCAATACACGTAATAGCCTGC
1 ACATAGTAGCCTGCACATAGTACTACACATGCGACCA-TACCATCCAATACACATAATAGCCTGC
* *
46628980 ACATAGTACTACACACGTGATCGAAACTATCCGGT
65 AAATAGTACTACACACGTGATCCAAACTATCCGGT
* * * ** *
46629015 ACGCATAGTAGCCTGCACATATTACTACACATGCGGCC-TATCATTCCGGTACACATAGTAGCCT
1 A--CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCA-TCCAATACACATAATAGCCT
46629079 GCAAATAGTACTACACACGTGA
63 GCAAATAGTACTACACACGTGA
46629101 CCATCAATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
100 5 0.07
101 37 0.50
102 32 0.43
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (99 bp):
ACATAGTAGCCTGCACATAGTACTACACATGCGACCATACCATCCAATACACATAATAGCCTGCA
AATAGTACTACACACGTGATCCAAACTATCCGGT
Found at i:46642728 original size:39 final size:38
Alignment explanation
Indices: 46642660--46642865 Score: 225
Period size: 39 Copynumber: 5.3 Consensus size: 38
46642650 TATATAATTA
* * * * * *
46642660 TACCCTGGTTGCACTTACATACCCATGTTGTACTTCAA
1 TACCCTGATCGCACTTACGTGCCCCTGTTGTACTTCAG
* * *
46642698 TAGCCCTGATCGCACTTATGTGCTCCTGTTGTACTTCGG
1 TA-CCCTGATCGCACTTACGTGCCCCTGTTGTACTTCAG
* *
46642737 TACCCTGATCACACTTA-GTGCTCCTGTTGTACTTCAG
1 TACCCTGATCGCACTTACGTGCCCCTGTTGTACTTCAG
**
46642774 TACCCCTGATCGCACTTACGTGCCCCTGTTGTACTTTGG
1 TA-CCCTGATCGCACTTACGTGCCCCTGTTGTACTTCAG
* * *
46642813 TACCCCTGATCGCACTTACATGCCCCTGCTATACTTCAG
1 TA-CCCTGATCGCACTTACGTGCCCCTGTTGTACTTCAG
46642852 TACACCTGATCGCA
1 TAC-CCTGATCGCA
46642866 TTTTTATGCC
Statistics
Matches: 144, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
37 21 0.15
38 31 0.22
39 92 0.64
ACGTcount: A:0.18, C:0.32, G:0.17, T:0.33
Consensus pattern (38 bp):
TACCCTGATCGCACTTACGTGCCCCTGTTGTACTTCAG
Found at i:46642781 original size:19 final size:18
Alignment explanation
Indices: 46642749--46642820 Score: 54
Period size: 19 Copynumber: 3.8 Consensus size: 18
46642739 CCCTGATCAC
* *
46642749 ACTTAGTGCTCCTGTTGT
1 ACTTAGTACCCCTGTTGT
* *
46642767 ACTTCAGTACCCCTGATCGC
1 ACTT-AGTACCCCTG-TTGT
*
46642787 ACTTACGTGCCCCTGTTGT
1 ACTTA-GTACCCCTGTTGT
*
46642806 ACTTTGGTACCCCTG
1 AC-TTAGTACCCCTG
46642821 ATCGCACTTA
Statistics
Matches: 41, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
18 4 0.10
19 21 0.51
20 16 0.39
ACGTcount: A:0.14, C:0.32, G:0.19, T:0.35
Consensus pattern (18 bp):
ACTTAGTACCCCTGTTGT
Found at i:46642781 original size:76 final size:78
Alignment explanation
Indices: 46642671--46642865 Score: 259
Period size: 76 Copynumber: 2.5 Consensus size: 78
46642661 ACCCTGGTTG
* * * * * *
46642671 CACTTACATACCCATGTTGTACTTCAATAGCCCTGATCGCACTTATGTGCTCCTGTTGTACTTCG
1 CACTTACATGCCCCTGTTGTACTTCAGTACCCCTGATCGCACTTACGTGCCCCTGTTGTACTTCG
46642736 GTA-CCCTGATCA
66 GTACCCCTGATCA
* * *
46642748 CACTTA-GTGCTCCTGTTGTACTTCAGTACCCCTGATCGCACTTACGTGCCCCTGTTGTACTTTG
1 CACTTACATGCCCCTGTTGTACTTCAGTACCCCTGATCGCACTTACGTGCCCCTGTTGTACTTCG
*
46642812 GTACCCCTGATCG
66 GTACCCCTGATCA
* * *
46642825 CACTTACATGCCCCTGCTATACTTCAGTACACCTGATCGCA
1 CACTTACATGCCCCTGTTGTACTTCAGTACCCCTGATCGCA
46642866 TTTTTATGCC
Statistics
Matches: 101, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
76 52 0.51
77 20 0.20
78 29 0.29
ACGTcount: A:0.19, C:0.32, G:0.16, T:0.32
Consensus pattern (78 bp):
CACTTACATGCCCCTGTTGTACTTCAGTACCCCTGATCGCACTTACGTGCCCCTGTTGTACTTCG
GTACCCCTGATCA
Found at i:46642799 original size:20 final size:20
Alignment explanation
Indices: 46642776--46642840 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
46642766 TACTTCAGTA
46642776 CCCCTGATCGCACTTACGTG
1 CCCCTGATCGCACTTACGTG
* * ** *
46642796 CCCCTG-TTGTACTTTGGTA
1 CCCCTGATCGCACTTACGTG
*
46642815 CCCCTGATCGCACTTACATG
1 CCCCTGATCGCACTTACGTG
46642835 CCCCTG
1 CCCCTG
46642841 CTATACTTCA
Statistics
Matches: 33, Mismatches: 11, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
19 14 0.42
20 19 0.58
ACGTcount: A:0.14, C:0.38, G:0.18, T:0.29
Consensus pattern (20 bp):
CCCCTGATCGCACTTACGTG
Found at i:46648555 original size:27 final size:27
Alignment explanation
Indices: 46648127--46648544 Score: 525
Period size: 27 Copynumber: 15.6 Consensus size: 27
46648117 AAACCCAAAA
* * *
46648127 ATAGGGTAAAATGATCGAAATACCCCT
1 ATAGGGTAGAATGACCGAAATACCCCC
* *
46648154 AAAGGGTAGAATGACCTAAATA-CCCC
1 ATAGGGTAGAATGACCGAAATACCCCC
*
46648180 ATAAGGTAGAATGACCGAAATACCCCC
1 ATAGGGTAGAATGACCGAAATACCCCC
*
46648207 ATAGGGTAGAATGATCGAAATACCCCC
1 ATAGGGTAGAATGACCGAAATACCCCC
*
46648234 ATAGGGTAGAATGACCGAAATACCCTC
1 ATAGGGTAGAATGACCGAAATACCCCC
* *
46648261 GTAGGGTAGAATAACCGAAATACCCCC
1 ATAGGGTAGAATGACCGAAATACCCCC
* *
46648288 GTAGGGTAGAATGACCGAAATACCCCT
1 ATAGGGTAGAATGACCGAAATACCCCC
*
46648315 ATAGGGTAGAATGATCGAAATACCCCC
1 ATAGGGTAGAATGACCGAAATACCCCC
* * *
46648342 ATAGGGTAAAATGACTGAAATACCCCT
1 ATAGGGTAGAATGACCGAAATACCCCC
* *
46648369 ATAGGGTAAAATGACCGAAATA-CTCC
1 ATAGGGTAGAATGACCGAAATACCCCC
* * *
46648395 ATAGAGTAGAATGATCGAAATACCCCT
1 ATAGGGTAGAATGACCGAAATACCCCC
* *
46648422 ATAGGGTAAAATGACCGAGATACCCCC
1 ATAGGGTAGAATGACCGAAATACCCCC
* * * *
46648449 ATAAGGTAAAATGACTGAAATACCCCT
1 ATAGGGTAGAATGACCGAAATACCCCC
* *
46648476 ATTGGGTAGAATGATCGAAATACCCCC
1 ATAGGGTAGAATGACCGAAATACCCCC
* * *
46648503 ATAGGGTAAAATTACCAAAATACCCCC
1 ATAGGGTAGAATGACCGAAATACCCCC
*
46648530 ATAGGGTAAAATGAC
1 ATAGGGTAGAATGAC
46648545 TGTTATACCC
Statistics
Matches: 336, Mismatches: 53, Indels: 4
0.85 0.13 0.01
Matches are distributed among these distances:
26 43 0.13
27 293 0.87
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (27 bp):
ATAGGGTAGAATGACCGAAATACCCCC
Found at i:46661280 original size:44 final size:44
Alignment explanation
Indices: 46661230--46661318 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 44
46661220 AGCTCCAATG
46661230 ATCTTAAAAACATAAAATTTACAAGAAACAAGCTAGAAAAACAT
1 ATCTTAAAAACATAAAATTTACAAGAAACAAGCTAGAAAAACAT
* * * * * *
46661274 ATCTTAAAAATATAAAATTTATAATAAACAGGCTGGCAAAACAT
1 ATCTTAAAAACATAAAATTTACAAGAAACAAGCTAGAAAAACAT
46661318 A
1 A
46661319 CCATGCATAC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.56, C:0.12, G:0.08, T:0.24
Consensus pattern (44 bp):
ATCTTAAAAACATAAAATTTACAAGAAACAAGCTAGAAAAACAT
Found at i:46672827 original size:43 final size:43
Alignment explanation
Indices: 46672681--46672946 Score: 376
Period size: 42 Copynumber: 6.3 Consensus size: 43
46672671 TTTTAGAAAT
* *
46672681 AAACGCTGCTATAGATCATGACCTTTAGCGGCGC-TTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
46672723 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTT-ACAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
*
46672765 AAACGCCGCTATAGCTCAAGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
46672808 AAACGCCGCTATAGATCAAGACCTTTAGCGGCCCTTTT-ACAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
46672850 AAATGCCGCTATAGCTCAAGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * * *
46672893 AAACGCCGCTATAGATCATGACTTTTAGCAGTGCTTCTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
*
46672936 AAACGCTGCTA
1 AAACGCCGCTA
46672947 AAAGTGCCAT
Statistics
Matches: 200, Mismatches: 21, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
42 109 0.55
43 91 0.46
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:46672831 original size:85 final size:85
Alignment explanation
Indices: 46672681--46672921 Score: 403
Period size: 85 Copynumber: 2.8 Consensus size: 85
46672671 TTTTAGAAAT
* * * *
46672681 AAACGCTGCTATAGATCATGACCTTTAGCGGCGC-TTTCCCACAAACGCCGCTATAGATCAGGAC
1 AAACGCCGCTATAGCTCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGAC
*
46672745 CTTTAGCGGCGCTTTTACAC
66 CTTTAGCGGCCCTTTTACAC
46672765 AAACGCCGCTATAGCTCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGAC
1 AAACGCCGCTATAGCTCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGAC
46672830 CTTTAGCGGCCCTTTTACAC
66 CTTTAGCGGCCCTTTTACAC
* *
46672850 AAATGCCGCTATAGCTCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCATGAC
1 AAACGCCGCTATAGCTCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGAC
*
46672915 TTTTAGC
66 CTTTAGC
46672922 AGTGCTTCTC
Statistics
Matches: 148, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
84 31 0.21
85 117 0.79
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.25
Consensus pattern (85 bp):
AAACGCCGCTATAGCTCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGAC
CTTTAGCGGCCCTTTTACAC
Found at i:46675509 original size:32 final size:33
Alignment explanation
Indices: 46675436--46675508 Score: 137
Period size: 33 Copynumber: 2.2 Consensus size: 33
46675426 TTTGGCCCCC
*
46675436 TCAAAAAATGGAAAAAAAGTATACTTAATCCTT
1 TCAAAAAATGGAAAAAAAGAATACTTAATCCTT
46675469 TCAAAAAATGGAAAAAAAGAATACTTAATCCTT
1 TCAAAAAATGGAAAAAAAGAATACTTAATCCTT
46675502 TCAAAAA
1 TCAAAAA
46675509 TTATAAAATC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.55, C:0.12, G:0.08, T:0.25
Consensus pattern (33 bp):
TCAAAAAATGGAAAAAAAGAATACTTAATCCTT
Found at i:46677455 original size:28 final size:27
Alignment explanation
Indices: 46677424--46677520 Score: 74
Period size: 28 Copynumber: 3.5 Consensus size: 27
46677414 CAGACCCTTG
46677424 AAACCCTAAATCCCTAACTCTTAACCCT
1 AAACCCTAAATCCCTAAC-CTTAACCCT
** *
46677452 AAACTCCT-AGCCCCTAACCATAACCCCT
1 AAAC-CCTAAATCCCTAACCTTAA-CCCT
* *
46677480 AAACCTTAAATCCC-AACCCTTAATCC-
1 AAACCCTAAATCCCTAA-CCTTAACCCT
46677506 AGAATCCCTAAATCC
1 A-AA-CCCTAAATCC
46677521 ATATATAATC
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
26 1 0.02
27 12 0.22
28 38 0.70
29 3 0.06
ACGTcount: A:0.36, C:0.40, G:0.02, T:0.22
Consensus pattern (27 bp):
AAACCCTAAATCCCTAACCTTAACCCT
Found at i:46677804 original size:29 final size:28
Alignment explanation
Indices: 46677767--46677869 Score: 100
Period size: 29 Copynumber: 3.6 Consensus size: 28
46677757 ACCTATGAAT
46677767 CCCTAAACCCTAAATCTCTAACTCTTAAC
1 CCCTAAACCCTAAATC-CTAACTCTTAAC
**
46677796 CCCTAAACCCTTAACCCCTAA-TCCTTAAC
1 CCCTAAACCC-TAAATCCTAACT-CTTAAC
* * * *
46677825 CCCTAAACCTTAAATCCCAACCCTTAAA
1 CCCTAAACCCTAAATCCTAACTCTTAAC
* *
46677853 CCATAATCCCTAAATCC
1 CCCTAAACCCTAAATCC
46677870 GTACTCCTTA
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
28 27 0.45
29 29 0.48
30 4 0.07
ACGTcount: A:0.35, C:0.41, G:0.00, T:0.24
Consensus pattern (28 bp):
CCCTAAACCCTAAATCCTAACTCTTAAC
Found at i:46677823 original size:14 final size:14
Alignment explanation
Indices: 46677790--46677837 Score: 78
Period size: 14 Copynumber: 3.4 Consensus size: 14
46677780 ATCTCTAACT
46677790 CTTAACCCCTAAACC
1 CTTAACCCCTAAA-C
*
46677805 CTTAACCCCTAATC
1 CTTAACCCCTAAAC
46677819 CTTAACCCCTAAAC
1 CTTAACCCCTAAAC
46677833 CTTAA
1 CTTAA
46677838 ATCCCAACCC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
14 19 0.61
15 12 0.39
ACGTcount: A:0.33, C:0.42, G:0.00, T:0.25
Consensus pattern (14 bp):
CTTAACCCCTAAAC
Found at i:46677825 original size:21 final size:20
Alignment explanation
Indices: 46677801--46677862 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
46677791 TTAACCCCTA
* * *
46677801 AACCCTTAACCCCTAATCCTT
1 AACCCTTAAACCATAATCC-C
* *
46677822 AACCCCTAAACCTTAAATCCC
1 AACCCTTAAACCAT-AATCCC
46677843 AACCCTTAAACCATAATCCC
1 AACCCTTAAACCATAATCCC
46677863 TAAATCCGTA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
20 6 0.18
21 23 0.68
22 5 0.15
ACGTcount: A:0.35, C:0.42, G:0.00, T:0.23
Consensus pattern (20 bp):
AACCCTTAAACCATAATCCC
Found at i:46678287 original size:41 final size:41
Alignment explanation
Indices: 46678242--46678332 Score: 155
Period size: 41 Copynumber: 2.2 Consensus size: 41
46678232 GCGCTTTATA
*
46678242 TAGCGGCGCTTTTTCAAAAACGCCGCTAAAAACCTGAGCAT
1 TAGCGGCGCTTTTTCAAAAACGCCACTAAAAACCTGAGCAT
**
46678283 TAGCGGCGCTTTTTCAAAAACGCCACTAAAGCCCTGAGCAT
1 TAGCGGCGCTTTTTCAAAAACGCCACTAAAAACCTGAGCAT
46678324 TAGCGGCGC
1 TAGCGGCGC
46678333 CCGAAAGGTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.21
Consensus pattern (41 bp):
TAGCGGCGCTTTTTCAAAAACGCCACTAAAAACCTGAGCAT
Found at i:46678417 original size:39 final size:40
Alignment explanation
Indices: 46678368--46678503 Score: 148
Period size: 40 Copynumber: 3.4 Consensus size: 40
46678358 TCGGATTTGG
* ** *
46678368 TTTTTTGCGGCGTTTTTCAAAAAACGCATCTAATGCTC-A
1 TTTTTAGCGGCGTTTTTCAAAAAACGCCGCTAATACTCAA
* *
46678407 TTTTTAGCGGCGTTTTTCAAAAAACACCGCTAATACTCGA
1 TTTTTAGCGGCGTTTTTCAAAAAACGCCGCTAATACTCAA
* * * * *
46678447 TCTTTAGTGGCGATTTCCATAAAACGCCGCTAATACTCAA
1 TTTTTAGCGGCGTTTTTCAAAAAACGCCGCTAATACTCAA
* *
46678487 TTTTTACCGGTGTTTTT
1 TTTTTAGCGGCGTTTTT
46678504 TGTCCAAACG
Statistics
Matches: 78, Mismatches: 18, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
39 33 0.42
40 45 0.58
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTTCAAAAAACGCCGCTAATACTCAA
Found at i:46687457 original size:20 final size:21
Alignment explanation
Indices: 46687434--46687472 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
46687424 TAATAATTTA
*
46687434 TAATTAATTTA-ATTAATCCT
1 TAATTAATTAATATTAATCCT
46687454 TAATTAATTAATATTAATC
1 TAATTAATTAATATTAATC
46687473 ACCTTTAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.49
Consensus pattern (21 bp):
TAATTAATTAATATTAATCCT
Found at i:46693465 original size:41 final size:41
Alignment explanation
Indices: 46693420--46693600 Score: 240
Period size: 41 Copynumber: 4.4 Consensus size: 41
46693410 TATATGATTT
* * *
46693420 GCACTAAGTGTGCGGAATTAAATAATGATGTTGAATAATGA
1 GCACTAAGTGTGCGAAACTAAATAATGATGTTGAATAACGA
* *
46693461 GCACTAAGTGTGCGAAACTAAGTAATGATGTTGGATAACGA
1 GCACTAAGTGTGCGAAACTAAATAATGATGTTGAATAACGA
* * *
46693502 GCACTAAGTGTGCGAAACTAAGTAATGATGATGGATAACGA
1 GCACTAAGTGTGCGAAACTAAATAATGATGTTGAATAACGA
* * *
46693543 GCACTAAGTGTGCGAAACCAAA-AGATAATGTT-AATAACGG
1 GCACTAAGTGTGCGAAACTAAATA-ATGATGTTGAATAACGA
46693583 GCACTAAGTGTGCGAAAC
1 GCACTAAGTGTGCGAAAC
46693601 CGGGATCAAT
Statistics
Matches: 127, Mismatches: 12, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
40 25 0.20
41 102 0.80
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.23
Consensus pattern (41 bp):
GCACTAAGTGTGCGAAACTAAATAATGATGTTGAATAACGA
Found at i:46694642 original size:22 final size:21
Alignment explanation
Indices: 46694600--46694642 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
46694590 TTAATATATT
*
46694600 AATAAATAAATTATTATAGTA
1 AATAAATAAATTATTAAAGTA
46694621 AATATAATAATATT-TTAAAGTA
1 AATA-AATAA-ATTATTAAAGTA
46694643 TGACATCTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 4 0.21
22 12 0.63
23 3 0.16
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (21 bp):
AATAAATAAATTATTAAAGTA
Found at i:46695870 original size:26 final size:26
Alignment explanation
Indices: 46695834--46695885 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
46695824 AAAATTAACG
46695834 CTAATTAAACTGAAATATTGAATGTT
1 CTAATTAAACTGAAATATTGAATGTT
46695860 CTAATTAAACTGAAATATTGAATGTT
1 CTAATTAAACTGAAATATTGAATGTT
46695886 TTCGTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (26 bp):
CTAATTAAACTGAAATATTGAATGTT
Found at i:46701906 original size:25 final size:26
Alignment explanation
Indices: 46701856--46701906 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
46701846 AAAATTAATG
*
46701856 CTAATTAAACTAAATTATTGATTGTT
1 CTAATTAAACTAAATTATTGAATGTT
46701882 CTAATTAAA-TGAAA-TATTGAATGTT
1 CTAATTAAACT-AAATTATTGAATGTT
46701907 TTCTTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (26 bp):
CTAATTAAACTAAATTATTGAATGTT
Found at i:46704004 original size:26 final size:26
Alignment explanation
Indices: 46703974--46704025 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
46703964 AAAAATAATG
* *
46703974 CTAATAAAACTGATATATTGAATGTT
1 CTAATAAAACTGAAACATTGAATGTT
*
46704000 CTAATTAAACTGAAACATTGAATGTT
1 CTAATAAAACTGAAACATTGAATGTT
46704026 TTATTTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.37
Consensus pattern (26 bp):
CTAATAAAACTGAAACATTGAATGTT
Found at i:46705856 original size:26 final size:26
Alignment explanation
Indices: 46705826--46705877 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
46705816 AAAAATAATG
*
46705826 CTAATAAAACTGAAATATTGAATGTT
1 CTAATAAAACTGAAACATTGAATGTT
*
46705852 CTAATTAAACTGAAACATTGAATGTT
1 CTAATAAAACTGAAACATTGAATGTT
46705878 TTATTTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.35
Consensus pattern (26 bp):
CTAATAAAACTGAAACATTGAATGTT
Found at i:46707709 original size:26 final size:26
Alignment explanation
Indices: 46707679--46707730 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
46707669 AAAAATAATG
*
46707679 CTAATAAAACTGAAATATTGAATGTT
1 CTAATAAAACTGAAACATTGAATGTT
*
46707705 CTAATTAAACTGAAACATTGAATGTT
1 CTAATAAAACTGAAACATTGAATGTT
46707731 TTATTTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.35
Consensus pattern (26 bp):
CTAATAAAACTGAAACATTGAATGTT
Found at i:46709561 original size:26 final size:26
Alignment explanation
Indices: 46709531--46709582 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
46709521 AAAAATAATG
*
46709531 CTAATAAAACTGAAATATTGAATGTT
1 CTAATAAAACTGAAACATTGAATGTT
*
46709557 CTAATTAAACTGAAACATTGAATGTT
1 CTAATAAAACTGAAACATTGAATGTT
46709583 TTATTTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.35
Consensus pattern (26 bp):
CTAATAAAACTGAAACATTGAATGTT
Found at i:46711490 original size:26 final size:26
Alignment explanation
Indices: 46711460--46711511 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
46711450 AAAATTAATG
46711460 CTAATTAAACTAAAATATTGAATGTT
1 CTAATTAAACTAAAATATTGAATGTT
*
46711486 CTAATTAAACTGAAATATTGAATGTT
1 CTAATTAAACTAAAATATTGAATGTT
46711512 TTCTTTTATT
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:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (26 bp):
CTAATTAAACTAAAATATTGAATGTT
Found at i:46720553 original size:3 final size:3
Alignment explanation
Indices: 46720545--46720586 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
46720535 TAATTCCCAC
46720545 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
46720587 AACTATTACT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:46720597 original size:6 final size:6
Alignment explanation
Indices: 46720548--46720614 Score: 53
Period size: 6 Copynumber: 11.2 Consensus size: 6
46720538 TTCCCACTAA
* * * * * * * *
46720548 TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA TAAAAC TATTAC
1 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC
*
46720596 TAATAC TAATAT TAATAC T
1 TAATAC TAATAC TAATAC T
46720615 TACCTCGCAT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 54 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (6 bp):
TAATAC
Found at i:46721614 original size:14 final size:17
Alignment explanation
Indices: 46721595--46721632 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
46721585 ATTTATTTCT
46721595 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
46721609 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
46721626 TAATATA
1 TAATATA
46721633 CTTTATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.38
15 1 0.05
16 4 0.19
17 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:46721649 original size:20 final size:19
Alignment explanation
Indices: 46721622--46721672 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
46721612 TATAATTAAT
46721622 TTAATAATATACTT-TATAA
1 TTAATAATATA-TTATATAA
46721641 TTAATTAATATATTATATAAA
1 TTAA-TAATATATTATAT-AA
*
46721662 TAAATAATATA
1 TTAATAATATA
46721673 AATATCTAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 6 0.21
20 17 0.61
21 5 0.18
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
TTAATAATATATTATATAA
Done.