Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008302.1 Hibiscus syriacus cultivar Beakdansim tig00110988_pilon, whole genome shotgun sequence
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: 3402722
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 17
Found at i:352134 original size:33 final size:33
Alignment explanation
Indices: 352088--352181 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
352078 ACACAAATCG
*
352088 CATTGCGACTTTCATTTCGCATTGCGATTTTAT
1 CATTGCGATTTTCATTTCGCATTGCGATTTTAT
* *
352121 CATTGCGATTTTCATTTTGCATTGCGATTTTGT
1 CATTGCGATTTTCATTTCGCATTGCGATTTTAT
*
352154 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CATTGCGATTTTCATTTCGCATTGCGAT
352182 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.16, C:0.19, G:0.18, T:0.47
Consensus pattern (33 bp):
CATTGCGATTTTCATTTCGCATTGCGATTTTAT
Found at i:352188 original size:19 final size:20
Alignment explanation
Indices: 352166--352209 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
352156 TTGCGATTTT
352166 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
* *
352185 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCATTGCGATAGC
352205 CATTT
1 CATTT
352210 TCATGTTGCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:352217 original size:20 final size:20
Alignment explanation
Indices: 352175--352220 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
352165 TCATTTCGCA
*
352175 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCACG
* * *
352195 TTGCGATAGTCATTTTCATG
1 TTGCGATAGCCATTTCCACG
352215 TTGCGA
1 TTGCGA
352221 AAGTAAACTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCACG
Found at i:352725 original size:18 final size:18
Alignment explanation
Indices: 352699--352743 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
352689 GTCGATCAGA
**
352699 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGACGAGG
*
352717 TGATAGCTCTGGACGAGG
1 TGATGGCTCTGGACGAGG
352735 TGATGGCTC
1 TGATGGCTC
352744 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGACGAGG
Found at i:354402 original size:20 final size:21
Alignment explanation
Indices: 354377--354425 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
354367 TCTGAGAGAT
354377 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATTTCGCC
* *
354397 GGAGATGGGGACGGATTTCGTC
1 GGAGAT-GAGACGGATTTCGCC
*
354419 AGAGATG
1 GGAGATG
354426 GGTGAGATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 6 0.25
21 1 0.04
22 17 0.71
ACGTcount: A:0.24, C:0.14, G:0.41, T:0.20
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGCC
Found at i:354411 original size:22 final size:22
Alignment explanation
Indices: 354384--354427 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
354374 GATGGAGATA
*
354384 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
*
354406 GACGGATTTCGTCAGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
354428 TGAGATAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCAGAGATGGG
Found at i:354698 original size:20 final size:20
Alignment explanation
Indices: 354592--354726 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
354582 CGCTTTGAAA
*
354592 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
354613 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
354633 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
354653 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
354674 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
354694 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
354714 ATCGCATTGCGAT
1 ATCGCATTGCGAT
354727 TTTCCCAATT
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.05
20 66 0.69
21 23 0.24
22 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:354698 original size:61 final size:61
Alignment explanation
Indices: 354592--354729 Score: 195
Period size: 61 Copynumber: 2.3 Consensus size: 61
354582 CGCTTTGAAA
* * * *
354592 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
354653 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
354714 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
354730 CCCAATTCGC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:354745 original size:61 final size:61
Alignment explanation
Indices: 354592--354747 Score: 161
Period size: 61 Copynumber: 2.6 Consensus size: 61
354582 CGCTTTGAAA
* ** * * * *
354592 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
* * ** * * * *
354653 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
354714 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
354748 TTACTTATTC
Statistics
Matches: 79, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
61 77 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:355218 original size:21 final size:21
Alignment explanation
Indices: 355145--355219 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
355135 CAGTTTCCAG
* *
355145 ATTCGCAACGCGATTTTGACT-
1 ATTCGCAATGCGATTTT-CCTA
* *
355166 A-TCGCATTGCGATTTTCCAA
1 ATTCGCAATGCGATTTTCCTA
* **
355186 ATTCACGTTGCGATTTTCCTA
1 ATTCGCAATGCGATTTTCCTA
355207 ATTCGCAATGCGA
1 ATTCGCAATGCGA
355220 ATACGTAAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
19 1 0.02
20 14 0.33
21 27 0.64
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (21 bp):
ATTCGCAATGCGATTTTCCTA
Found at i:355251 original size:20 final size:20
Alignment explanation
Indices: 355228--355294 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
355218 GAATACGTAA
* *
355228 ATCGCAACGCGAATCTGACT
1 ATCGCAACGAGATTCTGACT
355248 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
* *
355268 ATCGTAATGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
355288 ATCGCAA
1 ATCGCAA
355295 TACTGAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAACGAGATTCTGACT
Found at i:356168 original size:25 final size:24
Alignment explanation
Indices: 356140--356187 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
356130 TCGAAATTTG
356140 ATCTTGGTCAATACCCGGACTTTTT
1 ATCTTGGTCAATACCCGGA-TTTTT
*
356165 ATCTTGGTCAATACTCGGATTTT
1 ATCTTGGTCAATACCCGGATTTT
356188 GATGATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.42
Consensus pattern (24 bp):
ATCTTGGTCAATACCCGGATTTTT
Found at i:358649 original size:20 final size:20
Alignment explanation
Indices: 358613--358718 Score: 133
Period size: 20 Copynumber: 5.3 Consensus size: 20
358603 CGCGGAAATT
358613 GCAACGC-GAATATGACTATC
1 GCAACGCGGAA-ATGACTATC
* * *
358633 GTAACACAGAAATGACTATC
1 GCAACGCGGAAATGACTATC
*
358653 GCAACGCGGAATTGACTATC
1 GCAACGCGGAAATGACTATC
* *
358673 GCAACTCGGGAATGACTATC
1 GCAACGCGGAAATGACTATC
*
358693 GCAACGCGGGAATGACTATC
1 GCAACGCGGAAATGACTATC
358713 GCAACG
1 GCAACG
358719 AGAGAATCGC
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
20 72 0.96
21 3 0.04
ACGTcount: A:0.34, C:0.25, G:0.24, T:0.18
Consensus pattern (20 bp):
GCAACGCGGAAATGACTATC
Found at i:358725 original size:20 final size:20
Alignment explanation
Indices: 358591--358725 Score: 126
Period size: 20 Copynumber: 7.0 Consensus size: 20
358581 GACATTCATT
358591 TGACTATCGCAACGCG-GAA
1 TGACTATCGCAACGCGAGAA
358610 --A-T-T-GCAACGCGA-ATA
1 TGACTATCGCAACGCGAGA-A
* *
358625 TGACTATCGTAACAC-AGAAA
1 TGACTATCGCAACGCGAG-AA
358645 TGACTATCGCAACGCG-GAA
1 TGACTATCGCAACGCGAGAA
* *
358664 TTGACTATCGCAACTCGGGAA
1 -TGACTATCGCAACGCGAGAA
*
358685 TGACTATCGCAACGCGGGAA
1 TGACTATCGCAACGCGAGAA
*
358705 TGACTATCGCAACGAGAGAA
1 TGACTATCGCAACGCGAGAA
358725 T
1 T
358726 CGCAATGCGA
Statistics
Matches: 96, Mismatches: 8, Indels: 23
0.76 0.06 0.18
Matches are distributed among these distances:
14 9 0.09
15 2 0.02
16 1 0.01
17 2 0.02
18 1 0.01
19 4 0.04
20 73 0.76
21 4 0.04
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.19
Consensus pattern (20 bp):
TGACTATCGCAACGCGAGAA
Found at i:358749 original size:33 final size:34
Alignment explanation
Indices: 358710--358784 Score: 116
Period size: 33 Copynumber: 2.2 Consensus size: 34
358700 GGGAATGACT
*
358710 ATCGCAACGAGAGAATCGCAATGCG-AAATAAAA
1 ATCGCAACGAGAAAATCGCAATGCGAAAATAAAA
* *
358743 ATCGCAACGAGAAAATCGCAATGTGAAAATGAAA
1 ATCGCAACGAGAAAATCGCAATGCGAAAATAAAA
358777 ATCGCAAC
1 ATCGCAAC
358785 ACGAATTTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
33 23 0.61
34 15 0.39
ACGTcount: A:0.48, C:0.19, G:0.20, T:0.13
Consensus pattern (34 bp):
ATCGCAACGAGAAAATCGCAATGCGAAAATAAAA
Found at i:358895 original size:34 final size:33
Alignment explanation
Indices: 358800--358895 Score: 120
Period size: 33 Copynumber: 2.8 Consensus size: 33
358790 TTTAGTTTCG
*
358800 CGTTGCGATTTTCATTTTCGTATTGCGATTCTCT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
** *
358834 CGTTTTGATTTTCATTTTGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
**
358867 CGTTGCGATAGTCATTTCCGCATTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
358896 AGTCTGTTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
33 30 0.58
34 22 0.42
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:359020 original size:14 final size:14
Alignment explanation
Indices: 359001--359037 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
358991 CATCAATTAA
359001 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
359015 ACAAATCATCTTTT
1 ACAAATCAACATTT
359029 ACAAATCAA
1 ACAAATCAA
359038 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:360524 original size:42 final size:42
Alignment explanation
Indices: 360426--360527 Score: 109
Period size: 42 Copynumber: 2.4 Consensus size: 42
360416 TTGGGAGGGA
* * *
360426 CCTCTTCAACGATGACAGTGGCCTCTTGAACGGTGGGAGGAG
1 CCTCTTGAACGATGACAGTGGCCTCTTGAACGATAGGAGGAG
* ** *
360468 ACTCTTGAGGGATGATA-TGGGCCTCTTGAACGATAGG-GGAGG
1 CCTCTTGAACGATGACAGT-GGCCTCTTGAACGATAGGAGGA-G
360510 CCTCTTGAACGATGACAG
1 CCTCTTGAACGATGACAG
360528 GTGAGTCGGG
Statistics
Matches: 46, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
41 4 0.09
42 42 0.91
ACGTcount: A:0.24, C:0.21, G:0.33, T:0.23
Consensus pattern (42 bp):
CCTCTTGAACGATGACAGTGGCCTCTTGAACGATAGGAGGAG
Found at i:361030 original size:20 final size:20
Alignment explanation
Indices: 361007--361055 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
360997 GAAACTTAAA
361007 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
361027 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
361047 ATCGCAACG
1 ATCGCAACG
361056 AGAGAATCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:361125 original size:20 final size:20
Alignment explanation
Indices: 361100--361146 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
361090 GATTCTTTCG
361100 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
**
361120 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCAAATTCGCA
361140 TTGCGAT
1 TTGCGAT
361147 TTTGTTGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:361171 original size:53 final size:53
Alignment explanation
Indices: 361062--361179 Score: 141
Period size: 53 Copynumber: 2.2 Consensus size: 53
361052 AACGAGAGAA
* **
361062 TCGCAATGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATAGTCAAAT
1 TCGCATTGCGATAGTCATTTCGCATTGCGATTCTTTCGTTGCGATAGTCAAAT
* ** *
361115 TCGCATTGCGATAGTCATTTTCGCATTGCGATT-TTGTTGTTGCGATTTTC-ATT
1 TCGCATTGCGATAGTCA-TTTCGCATTGCGATTCTT-TCGTTGCGATAGTCAAAT
361168 TCGCATTGCGAT
1 TCGCATTGCGAT
361180 TCTCTCGTTG
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
53 30 0.54
54 26 0.46
ACGTcount: A:0.18, C:0.19, G:0.20, T:0.42
Consensus pattern (53 bp):
TCGCATTGCGATAGTCATTTCGCATTGCGATTCTTTCGTTGCGATAGTCAAAT
Found at i:361175 original size:33 final size:34
Alignment explanation
Indices: 361120--361213 Score: 127
Period size: 33 Copynumber: 2.8 Consensus size: 34
361110 CAAATTCGCA
* * *
361120 TTGCGATAGTCATTTTCGCATTGCGATTTTGTTG
1 TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
**
361154 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
*
361187 TTGCGATAGTCATTTTCGCGTTGCGAT
1 TTGCGATAGTCATTTTCGCATTGCGAT
361214 AGTCATTTTC
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.55
34 23 0.45
ACGTcount: A:0.14, C:0.19, G:0.22, T:0.45
Consensus pattern (34 bp):
TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
Found at i:361176 original size:87 final size:87
Alignment explanation
Indices: 361068--361233 Score: 296
Period size: 87 Copynumber: 1.9 Consensus size: 87
361058 AGAATCGCAA
*
361068 TGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAT
361133 TTTCGCATTGCGATTTTGTTGT
66 TTTCGCATTGCGATTTTGTTGT
** *
361155 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTTCGCGTTGCGATAGTCAT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAT
361220 TTTCGCATTGCGAT
66 TTTCGCATTGCGAT
361234 AGTAAACTAT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 75 1.00
ACGTcount: A:0.16, C:0.20, G:0.21, T:0.43
Consensus pattern (87 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAT
TTTCGCATTGCGATTTTGTTGT
Found at i:361210 original size:20 final size:20
Alignment explanation
Indices: 361185--361236 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
361175 GCGATTCTCT
361185 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
361205 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
361225 CATTGCGATAGT
1 CGTTGCGATAGT
361237 AAACTATTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:363161 original size:20 final size:20
Alignment explanation
Indices: 363103--363172 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
363093 GAAACTTTAA
* **
363103 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCGAAAATGACT
*
363123 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
363143 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
363163 ATCGCAACGC
1 ATCGCAACGC
363173 AAGAATCGCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.41, C:0.26, G:0.17, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:363211 original size:33 final size:33
Alignment explanation
Indices: 363102--363215 Score: 95
Period size: 33 Copynumber: 3.2 Consensus size: 33
363092 TGAAACTTTA
* *
363102 AATCGCAACACGAAAATGAAAATCGCAACACGAAAATG
1 AATCGCAACGCG-AAATGAAAATCGC-A-ACG-ACA-G
* **
363140 ACTATCGCAACGCGAATTTGACTATCGCAACG-CAAG
1 A--ATCGCAACGCGAA-ATGAAAATCGCAACGAC-AG
363176 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
363209 AATCGCA
1 AATCGCA
363216 TTGCGATAGT
Statistics
Matches: 63, Mismatches: 8, Indels: 15
0.73 0.09 0.17
Matches are distributed among these distances:
33 21 0.33
34 14 0.22
36 2 0.03
37 1 0.02
38 4 0.06
39 3 0.05
40 18 0.29
ACGTcount: A:0.44, C:0.25, G:0.18, T:0.13
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:363602 original size:22 final size:22
Alignment explanation
Indices: 363539--363604 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
363529 TGACCGTGAA
*
363539 TGATTTCG-CTGGAGATGGAGAC
1 TGATTTCGTC-GGAGATGGGGAC
*
363561 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
*
363583 TGATTTCGTCGGAGACGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
363605 GGATGTCGCC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
22 38 0.97
23 1 0.03
ACGTcount: A:0.21, C:0.15, G:0.39, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:363823 original size:20 final size:20
Alignment explanation
Indices: 363800--363938 Score: 269
Period size: 20 Copynumber: 7.0 Consensus size: 20
363790 CAATAATTAG
363800 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
363820 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
363840 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
363860 TTTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
363880 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
363900 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
363920 ATTCGCATTGCGATTTACG
1 ATTCGCATTGCGATTTACG
363939 AAAATCGCAA
Statistics
Matches: 117, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 117 1.00
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:364439 original size:34 final size:35
Alignment explanation
Indices: 364372--364438 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 35
364362 AAAATATTTA
* *
364372 TATATTTTCTTTAAAAAATTTAAATTCATAAAAAT
1 TATATTTTCTTTAAAAAATTGAAAATCATAAAAAT
*
364407 TATATTTT-TTTACAAAATTGAAAAT-ATAAAAA
1 TATATTTTCTTTAAAAAATTGAAAATCATAAAAA
364439 AGTTTGATGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 7 0.24
34 14 0.48
35 8 0.28
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (35 bp):
TATATTTTCTTTAAAAAATTGAAAATCATAAAAAT
Found at i:369289 original size:6 final size:6
Alignment explanation
Indices: 369278--369315 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
369268 TATAGATGAC
369278 CAGTGG CAGTGG CAGTGG CAGTGG CAGTGG CAGTGG CA
1 CAGTGG CAGTGG CAGTGG CAGTGG CAGTGG CAGTGG CA
369316 TGCATTGCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.18, C:0.18, G:0.47, T:0.16
Consensus pattern (6 bp):
CAGTGG
Found at i:371664 original size:31 final size:31
Alignment explanation
Indices: 371629--371688 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
371619 GATGGAGTGT
* *
371629 TCATTTTGTTATAAATTGATAATGTTAGTAG
1 TCATTTTATTATAAATCGATAATGTTAGTAG
*
371660 TCATTTTATTATAAATCGATATTGTTAGT
1 TCATTTTATTATAAATCGATAATGTTAGT
371689 GACCTATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.32, C:0.05, G:0.13, T:0.50
Consensus pattern (31 bp):
TCATTTTATTATAAATCGATAATGTTAGTAG
Found at i:371699 original size:31 final size:31
Alignment explanation
Indices: 371630--371701 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
371620 ATGGAGTGTT
* * *
371630 CATTTTGTTATAAATTGATAATGTTAGTAGT
1 CATTTTATTATAAATCGATAATGTTAGTAGA
*
371661 CATTTTATTATAAATCGATATTGTTAGT-GA
1 CATTTTATTATAAATCGATAATGTTAGTAGA
*
371691 CCTATTTATTA
1 CAT-TTTATTA
371702 ATTTTGAAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 3 0.09
31 32 0.91
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.49
Consensus pattern (31 bp):
CATTTTATTATAAATCGATAATGTTAGTAGA
Found at i:374670 original size:33 final size:33
Alignment explanation
Indices: 374622--374694 Score: 94
Period size: 35 Copynumber: 2.2 Consensus size: 33
374612 TTTTCTAATT
* * *
374622 TAAAAAAAAAACAG-AAAATGAAAACTATTTTC
1 TAAAATAAAAACAGAAAAATAAAAAATATTTTC
374654 TGAAAATAAAAACAGAAAAAATAAAAAATATTTTC
1 T-AAAATAAAAACAG-AAAAATAAAAAATATTTTC
374689 TAAAAT
1 TAAAAT
374695 CAAAGACCCT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 1 0.03
33 12 0.34
34 5 0.14
35 17 0.49
ACGTcount: A:0.64, C:0.07, G:0.05, T:0.23
Consensus pattern (33 bp):
TAAAATAAAAACAGAAAAATAAAAAATATTTTC
Found at i:383128 original size:13 final size:13
Alignment explanation
Indices: 383110--383151 Score: 84
Period size: 13 Copynumber: 3.2 Consensus size: 13
383100 TGGATCGAAG
383110 GGATTTAAGAGTA
1 GGATTTAAGAGTA
383123 GGATTTAAGAGTA
1 GGATTTAAGAGTA
383136 GGATTTAAGAGTA
1 GGATTTAAGAGTA
383149 GGA
1 GGA
383152 AGAGTTCATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.33, T:0.29
Consensus pattern (13 bp):
GGATTTAAGAGTA
Found at i:409188 original size:22 final size:21
Alignment explanation
Indices: 409162--409252 Score: 83
Period size: 22 Copynumber: 4.1 Consensus size: 21
409152 TTGGTGCAGA
* *
409162 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCC-TGAAG
* *
409184 GGGAACTGATTCCCTCTTTGAAG
1 GGGAACCGATTCCC-C-CTGAAG
*
409207 GGGAACCGATTTCCCCCTGTAG
1 GGGAACCGA-TTCCCCCTGAAG
*
409229 GGGAACCGATTTCCCCCTGTAG
1 GGGAACCGA-TTCCCCCTGAAG
409251 GG
1 GG
409253 TAATTGATAC
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
22 39 0.66
23 15 0.25
24 5 0.08
ACGTcount: A:0.21, C:0.27, G:0.29, T:0.23
Consensus pattern (21 bp):
GGGAACCGATTCCCCCTGAAG
Found at i:415797 original size:17 final size:16
Alignment explanation
Indices: 415767--415800 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
415757 ATGATGTTGA
415767 TCGGTGATGGCTCGGC
1 TCGGTGATGGCTCGGC
*
415783 TCGGTTGATGTCTCGGC
1 TCGG-TGATGGCTCGGC
415800 T
1 T
415801 TGGCCATGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.06, C:0.24, G:0.38, T:0.32
Consensus pattern (16 bp):
TCGGTGATGGCTCGGC
Found at i:424012 original size:103 final size:103
Alignment explanation
Indices: 423833--424086 Score: 377
Period size: 103 Copynumber: 2.5 Consensus size: 103
423823 GTTGGCATAC
*
423833 AAAAGATGTTTTCTTTGAAATTA-TTGTCTATTTGTTTGTGTAGGATTTAGATGCCATAATTTAC
1 AAAAGATATTTTCTTTGAAA-TAGTTGTCTATTTGTTTGTGTAGGATTTAGATGCCATAATTTAC
423897 CGAAACTCATAGGGAGGCTTCTCGTGTGAAGAAAG-ACTG
65 CGAAACTCATAGGGAGGCTTCTCGTGTGAAGAAAGTA-TG
* * * * **
423936 AAAAGATATTTCCTTTGAAATAGTTGTCTATTTGTTTGTGTAGGATTTAGATGTCGTATTTTATT
1 AAAAGATATTTTCTTTGAAATAGTTGTCTATTTGTTTGTGTAGGATTTAGATGCCATAATTTACC
*
424001 TAAACTCATAGGGAGGCTTCTCGTGTGAAGAAAGTATG
66 GAAACTCATAGGGAGGCTTCTCGTGTGAAGAAAGTATG
* * *
424039 AAAAGATCTTTTCTTTGAAATAGTTGTCTATTTGTTTATGTAGAATTT
1 AAAAGATATTTTCTTTGAAATAGTTGTCTATTTGTTTGTGTAGGATTT
424087 TTTGAGCTTG
Statistics
Matches: 137, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
102 2 0.01
103 134 0.98
104 1 0.01
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (103 bp):
AAAAGATATTTTCTTTGAAATAGTTGTCTATTTGTTTGTGTAGGATTTAGATGCCATAATTTACC
GAAACTCATAGGGAGGCTTCTCGTGTGAAGAAAGTATG
Found at i:441068 original size:20 final size:20
Alignment explanation
Indices: 441043--441134 Score: 65
Period size: 20 Copynumber: 5.0 Consensus size: 20
441033 TTTGTTAGTT
*
441043 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
* *
441063 ATTAGATAAAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTA
* *
441083 ATT--CT---ATTAG--TT-
1 ATTAGATAGAATCAGTTTTA
*
441095 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
*
441115 ATTAGATAGAATCAATTTTA
1 ATTAGATAGAATCAGTTTTA
441135 TTCTGTTGCT
Statistics
Matches: 55, Mismatches: 9, Indels: 16
0.69 0.11 0.20
Matches are distributed among these distances:
12 3 0.05
13 2 0.04
14 1 0.02
15 4 0.07
17 4 0.07
18 1 0.02
19 2 0.04
20 38 0.69
ACGTcount: A:0.37, C:0.05, G:0.14, T:0.43
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:441093 original size:52 final size:51
Alignment explanation
Indices: 441026--441138 Score: 181
Period size: 52 Copynumber: 2.2 Consensus size: 51
441016 TTAACTAGAT
* *
441026 ATTTTATTTTGTTAGTTATTAGATAGGATCAGTTTTAATTAGATAAAATCA
1 ATTTTATTCTATTAGTTATTAGATAGGATCAGTTTTAATTAGATAAAATCA
* *
441077 GTTTTTATTCTATTAGTTATTAGATAGGATCAGTTTTAATTAGATAGAATCA
1 -ATTTTATTCTATTAGTTATTAGATAGGATCAGTTTTAATTAGATAAAATCA
441129 ATTTTATTCT
1 ATTTTATTCT
441139 GTTGCTAATT
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
51 9 0.16
52 47 0.84
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.49
Consensus pattern (51 bp):
ATTTTATTCTATTAGTTATTAGATAGGATCAGTTTTAATTAGATAAAATCA
Found at i:443903 original size:20 final size:20
Alignment explanation
Indices: 443878--443969 Score: 74
Period size: 20 Copynumber: 5.0 Consensus size: 20
443868 ACTGTTAGTT
443878 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGGATCAGTTTTA
* *
443898 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGGATCAGTTTTA
* *
443918 ATT--CT--G-TTAG--TT-
1 ATTAGATAGGATCAGTTTTA
443930 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGGATCAGTTTTA
* *
443950 ATTAGATAGAATTAGTTTTA
1 ATTAGATAGGATCAGTTTTA
443970 TTCTGTTGCT
Statistics
Matches: 55, Mismatches: 9, Indels: 16
0.69 0.11 0.20
Matches are distributed among these distances:
12 3 0.05
13 2 0.04
14 1 0.02
15 3 0.05
16 1 0.02
17 3 0.05
18 1 0.02
19 2 0.04
20 39 0.71
ACGTcount: A:0.34, C:0.04, G:0.17, T:0.45
Consensus pattern (20 bp):
ATTAGATAGGATCAGTTTTA
Found at i:443925 original size:52 final size:51
Alignment explanation
Indices: 443862--443976 Score: 203
Period size: 52 Copynumber: 2.2 Consensus size: 51
443852 TAACTAGATA
*
443862 TTTTATACTGTTAGTTATTAGATAGGATCAGTTTTAATTAGATAGAATCAG
1 TTTTATTCTGTTAGTTATTAGATAGGATCAGTTTTAATTAGATAGAATCAG
*
443913 TTTTTATTCTGTTAGTTATTAGATAGGATCAGTTTTAATTAGATAGAATTAG
1 -TTTTATTCTGTTAGTTATTAGATAGGATCAGTTTTAATTAGATAGAATCAG
443965 TTTTATTCTGTT
1 TTTTATTCTGTT
443977 GCTAATTTTA
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
51 12 0.20
52 49 0.80
ACGTcount: A:0.30, C:0.05, G:0.17, T:0.49
Consensus pattern (51 bp):
TTTTATTCTGTTAGTTATTAGATAGGATCAGTTTTAATTAGATAGAATCAG
Found at i:446296 original size:21 final size:17
Alignment explanation
Indices: 446255--446288 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
446245 CTTTCTTCGC
446255 TTTCCTTCCTTTAATCT
1 TTTCCTTCCTTTAATCT
446272 TTTCCTTCCTTTAATCT
1 TTTCCTTCCTTTAATCT
446289 CTCTTTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.29, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTCCTTCCTTTAATCT
Found at i:454500 original size:134 final size:134
Alignment explanation
Indices: 454260--454528 Score: 538
Period size: 134 Copynumber: 2.0 Consensus size: 134
454250 GGACTGAGAA
454260 CGATATTAGCGTTACCTTGGTAGTAAATGCAGGAGAAAGAGAAGGAAGAATATGGAGAAGACAGT
1 CGATATTAGCGTTACCTTGGTAGTAAATGCAGGAGAAAGAGAAGGAAGAATATGGAGAAGACAGT
454325 CTTGATACGGAGCAAAGCATCCTTGGTAAGACCATGAGCAGCAACCGTGACATCCCTCACCACGC
66 CTTGATACGGAGCAAAGCATCCTTGGTAAGACCATGAGCAGCAACCGTGACATCCCTCACCACGC
454390 TCTC
131 TCTC
454394 CGATATTAGCGTTACCTTGGTAGTAAATGCAGGAGAAAGAGAAGGAAGAATATGGAGAAGACAGT
1 CGATATTAGCGTTACCTTGGTAGTAAATGCAGGAGAAAGAGAAGGAAGAATATGGAGAAGACAGT
454459 CTTGATACGGAGCAAAGCATCCTTGGTAAGACCATGAGCAGCAACCGTGACATCCCTCACCACGC
66 CTTGATACGGAGCAAAGCATCCTTGGTAAGACCATGAGCAGCAACCGTGACATCCCTCACCACGC
454524 TCTC
131 TCTC
454528 C
1 C
454529 AAAGCATCGG
Statistics
Matches: 135, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
134 135 1.00
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.19
Consensus pattern (134 bp):
CGATATTAGCGTTACCTTGGTAGTAAATGCAGGAGAAAGAGAAGGAAGAATATGGAGAAGACAGT
CTTGATACGGAGCAAAGCATCCTTGGTAAGACCATGAGCAGCAACCGTGACATCCCTCACCACGC
TCTC
Found at i:455428 original size:3 final size:3
Alignment explanation
Indices: 455420--455455 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
455410 GAGTTAAAAC
455420 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
455456 ACAATTAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:459407 original size:26 final size:26
Alignment explanation
Indices: 459368--459431 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
459358 ACATTAAAAA
459368 TAAAAA-AA-AATTAGTCAAACATAT
1 TAAAAACAACAATTAGTCAAACATAT
* *
459392 TAAAAACAACAATTAGTCAAATATGT
1 TAAAAACAACAATTAGTCAAACATAT
**
459418 TGTAAACAACAATT
1 TAAAAACAACAATT
459432 TTTTTTTGTC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 6 0.18
25 2 0.06
26 26 0.76
ACGTcount: A:0.56, C:0.11, G:0.06, T:0.27
Consensus pattern (26 bp):
TAAAAACAACAATTAGTCAAACATAT
Found at i:459574 original size:41 final size:44
Alignment explanation
Indices: 459532--459619 Score: 115
Period size: 48 Copynumber: 1.9 Consensus size: 44
459522 ACAAACCCAC
*
459532 TAATTTTGATTTTTAAGTATACTTT-ACTTTCTTCTCAACACTACAA
1 TAATTTTGATTTTTAAGTACA-TTTCACTTTCTTCTCAACAC-AC-A
459578 GGTAATTTTGATTTTTAAGTACATTTCACTTTCTTCTCAACA
1 --TAATTTTGATTTTTAAGTACATTTCACTTTCTTCTCAACA
459620 GTGCATAATC
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
47 3 0.08
48 35 0.92
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (44 bp):
TAATTTTGATTTTTAAGTACATTTCACTTTCTTCTCAACACACA
Found at i:459709 original size:15 final size:15
Alignment explanation
Indices: 459689--459728 Score: 57
Period size: 13 Copynumber: 2.8 Consensus size: 15
459679 CTGATTTTTT
459689 ATTTTATTTTATATA
1 ATTTTATTTTATATA
459704 ATTTTA-TTT-TATA
1 ATTTTATTTTATATA
*
459717 ATTGTATTTTAT
1 ATTTTATTTTAT
459729 TCTATCTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 9 0.41
14 6 0.27
15 7 0.32
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (15 bp):
ATTTTATTTTATATA
Found at i:461151 original size:13 final size:13
Alignment explanation
Indices: 461135--461159 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
461125 ACATTTTTAT
461135 TTTTTTAATATTA
1 TTTTTTAATATTA
461148 TTTTTTAATATT
1 TTTTTTAATATT
461160 TCATATCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTTAATATTA
Found at i:462223 original size:64 final size:63
Alignment explanation
Indices: 462137--462259 Score: 160
Period size: 64 Copynumber: 1.9 Consensus size: 63
462127 GTATCAAACT
* * *
462137 ATGCATCGATGCACCGATGCTTTAATT-GAACATCGAATGCATTTGATGCATCGATGCACATACC
1 ATGCATCAATGCACCGAGGCTTT--TTAAAACATCGAATGCATTTGATGCATCGATGCACATACC
*
462201 ATGCATCAATGCACTC-AGGCTTTTTCAAAACATCGAATGCATTTTATGCATCGATGCAC
1 ATGCATCAATGCAC-CGAGGCTTTTT-AAAACATCGAATGCATTTGATGCATCGATGCAC
462260 TCTTAGTGCA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
62 2 0.04
64 49 0.94
65 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (63 bp):
ATGCATCAATGCACCGAGGCTTTTTAAAACATCGAATGCATTTGATGCATCGATGCACATACC
Found at i:467923 original size:24 final size:24
Alignment explanation
Indices: 467895--467974 Score: 73
Period size: 24 Copynumber: 3.5 Consensus size: 24
467885 CACTTAACAA
467895 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCATCCCTTTGAATG
* *
467919 TGCATCGATTCAT-CATGTTG-A--
1 TGCATCGATGCATCCCT-TTGAATG
*
467940 TGCACCGATGCA-CGCC-TTGAATG
1 TGCATCGATGCATC-CCTTTGAATG
467963 TGCATCGATGCA
1 TGCATCGATGCA
467975 CAAGGTCATG
Statistics
Matches: 44, Mismatches: 6, Indels: 13
0.70 0.10 0.21
Matches are distributed among these distances:
20 3 0.07
21 11 0.25
22 1 0.02
23 14 0.32
24 15 0.34
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.30
Consensus pattern (24 bp):
TGCATCGATGCATCCCTTTGAATG
Found at i:473780 original size:31 final size:30
Alignment explanation
Indices: 473736--473799 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 30
473726 GAAATAAATG
* * *
473736 AAAAATACTTTAATAGAAAACTTTAATAATA
1 AAAAAGACCTTAATAGAAAACTATAATAA-A
473767 AAAAAGACCTTAATAGAAAACTATAATAAA
1 AAAAAGACCTTAATAGAAAACTATAATAAA
473797 AAA
1 AAA
473800 TAAAAAGACA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.25
Consensus pattern (30 bp):
AAAAAGACCTTAATAGAAAACTATAATAAA
Found at i:473828 original size:47 final size:50
Alignment explanation
Indices: 473777--473875 Score: 116
Period size: 49 Copynumber: 2.0 Consensus size: 50
473767 AAAAAGACCT
* * *
473777 TAATAGAAAA-CTATAATAA-AAAATA-AAAAGACATCATTATTACA-TAA
1 TAATA-AAAAGCTATAATAACAAAACAGAAAAAACATAATTATTACATTAA
* *
473824 TAATAAAAAGTTTTAATAACAAAACAGAAAAAACATAATTATTACATTAA
1 TAATAAAAAGCTATAATAACAAAACAGAAAAAACATAATTATTACATTAA
473874 TA
1 TA
473876 TTTTGATGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
46 4 0.09
47 12 0.28
48 5 0.12
49 17 0.40
50 5 0.12
ACGTcount: A:0.61, C:0.08, G:0.04, T:0.27
Consensus pattern (50 bp):
TAATAAAAAGCTATAATAACAAAACAGAAAAAACATAATTATTACATTAA
Found at i:479167 original size:41 final size:44
Alignment explanation
Indices: 479110--479195 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 44
479100 TCTCCTCAAT
* *
479110 CCTGAACTCAAAATTTGG-T-T-AAAATGTAGATAGATGAAACA
1 CCTGAACTCAAAATTTGGTTGTAAAAATCTAGATAGACGAAACA
**
479151 CCTGAACTCGGAATTTGGTTGTAAAAATCTAGATAGACGAAACA
1 CCTGAACTCAAAATTTGGTTGTAAAAATCTAGATAGACGAAACA
479195 C
1 C
479196 TATTGAAGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
41 16 0.42
42 1 0.03
43 1 0.03
44 20 0.53
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.26
Consensus pattern (44 bp):
CCTGAACTCAAAATTTGGTTGTAAAAATCTAGATAGACGAAACA
Found at i:484038 original size:20 final size:19
Alignment explanation
Indices: 484015--484059 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
484005 GATATACCAT
484015 GTAAAAATATGATAAAACCG
1 GTAAAAA-ATGATAAAACCG
*
484035 GTAACAAAATTATAAAACCG
1 GTAA-AAAATGATAAAACCG
484055 GTAAA
1 GTAAA
484060 CGTTACCAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 19 0.83
21 3 0.13
ACGTcount: A:0.56, C:0.11, G:0.13, T:0.20
Consensus pattern (19 bp):
GTAAAAAATGATAAAACCG
Found at i:484202 original size:168 final size:176
Alignment explanation
Indices: 483816--484250 Score: 502
Period size: 168 Copynumber: 2.5 Consensus size: 176
483806 TAAAAATGAG
* * **
483816 TCGATCCAAAACG--ATAACAGGT-AAACTATGACAAAACCGGT-ATGAAATGAT-AAACCGGTA
1 TCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATAAAACCGGTA
* * * *
483876 AAGCGCTACTG-GATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTCGTGAATTT
66 AA-CGATACCGAGAT--ATTGAAA--GT-GATACTTTAATATAAGGATCGACACTTCGTGAATTT
* *
483940 AAAAGAGAAACAGTTTTAAATCCTATAAAGTGTCGATACTTTTAAAAAATGTA
125 AAAAGAGAAACAGTTTTAAAGCC-ATAAAGTGTCGATACTTTTAAAAAATATA
* * *
483993 TCGATCCAAAACGATATACCATGTAAAAATATGATAAAACCGGTAACAAAATTATAAAACCGGTA
1 TCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATAAAACCGGTA
*
484058 AACGTTACC-AGATATTGAAAGTGATACTTT-ATATAAGGATCGACACTT-GTGAATTTAAAAGA
66 AACGATACCGAGATATTGAAAGTGATACTTTAATATAAGGATCGACACTTCGTGAATTTAAAAGA
* ** *
484120 G-AAGAGTTTTAGCGCC-TAATGTGTCGATAC-TTTAAAAAA-ATA
131 GAAACAGTTTTAAAGCCATAAAGTGTCGATACTTTTAAAAAATATA
* *
484162 TCGATCCACAACGAT-TAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATAAAACCGGTA
1 TCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATAAAACCGGTA
* *
484226 AATGATACCGGATATATTGAAAGTG
66 AACGATACC-GAGATATTGAAAGTG
484251 TCGATACTTT
Statistics
Matches: 225, Mismatches: 25, Indels: 23
0.82 0.09 0.08
Matches are distributed among these distances:
168 52 0.23
169 16 0.07
170 22 0.10
171 13 0.06
173 11 0.05
174 15 0.07
175 18 0.08
176 7 0.03
177 15 0.07
179 13 0.06
180 17 0.08
181 15 0.07
182 11 0.05
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (176 bp):
TCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATAAAACCGGTA
AACGATACCGAGATATTGAAAGTGATACTTTAATATAAGGATCGACACTTCGTGAATTTAAAAGA
GAAACAGTTTTAAAGCCATAAAGTGTCGATACTTTTAAAAAATATA
Found at i:486403 original size:21 final size:21
Alignment explanation
Indices: 486379--486436 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
486369 TCAAGAGTTG
*
486379 AAGAGAAACTTGATAGAGTCA
1 AAGAGAAACTTGAGAGAGTCA
*
486400 AAGAGAAACTTGAGAGAGTCG
1 AAGAGAAACTTGAGAGAGTCA
* *
486421 AAGATACACTTGAGAG
1 AAGAGAAACTTGAGAG
486437 GCATAAGGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.45, C:0.10, G:0.28, T:0.17
Consensus pattern (21 bp):
AAGAGAAACTTGAGAGAGTCA
Found at i:486533 original size:33 final size:34
Alignment explanation
Indices: 486470--486536 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
486460 AAATAGATGG
*
486470 AGTGGTGAAAGAAGTAGAGGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGGTGTTAAGGGGTGA
*
486504 AGTGGTGAAAGAAGTTG-GGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGGTGTTAAGGGGTGA
486537 TATTAAGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 15 0.48
34 16 0.52
ACGTcount: A:0.28, C:0.00, G:0.49, T:0.22
Consensus pattern (34 bp):
AGTGGTGAAAGAAGTAGAGGGTGTTAAGGGGTGA
Found at i:488320 original size:18 final size:19
Alignment explanation
Indices: 488281--488328 Score: 80
Period size: 18 Copynumber: 2.6 Consensus size: 19
488271 AAATGTAGGT
488281 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
488300 TAATTTTGTATACGA-TTA
1 TAATTTTGTATAAGATTTA
488318 TAATTTTGTAT
1 TAATTTTGTAT
488329 GTGAATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 14 0.50
19 14 0.50
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.54
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:488337 original size:18 final size:18
Alignment explanation
Indices: 488281--488340 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
488271 AAATGTAGGT
* *
488281 TAATTTTGTATAAGATTTA
1 TAATTTTGTATACGA-ATA
*
488300 TAATTTTGTATACGATTA
1 TAATTTTGTATACGAATA
**
488318 TAATTTTGTATGTGAATA
1 TAATTTTGTATACGAATA
488336 TAATT
1 TAATT
488341 ATGAATGAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
18 23 0.62
19 14 0.38
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.52
Consensus pattern (18 bp):
TAATTTTGTATACGAATA
Found at i:489152 original size:200 final size:199
Alignment explanation
Indices: 488453--489220 Score: 1305
Period size: 200 Copynumber: 3.9 Consensus size: 199
488443 GGCAAACAGG
*
488453 GTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACC
1 GTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACA
488518 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATG
* **
488583 TAATATGTAATTTTTCAATCTAATTGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATAGGTAA-TTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAAT
488648 AATGT
195 AATGT
* *
488653 ATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACC
1 GTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACA
488718 ATAAAGTGTCGATCCATATATAAAAAGTGTCGAT-CCATAAACATCGAAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATG
* *
488782 TAATATGTAA-TTTCAATCTAACC-GTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATA
131 TAATAGGTAATTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATA
488845 ATGT
196 ATGT
* *
488849 GTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTACAGAATGAATGGAAAACAGGGTGCAACA
1 GTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACA
* *
488914 ATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCATAAACATCGAAACCCATAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATG
*
488979 TAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGTTTTTATGAGAGAATATGTCTAAAT
131 TAATAGGTAA-TTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAAT
489044 AATGT
195 AATGT
* ** *
489049 GTCGACACTTTTTTTAGTTTGTGTCGATATTTTTATTCTAGAATGAATGGCAAACAGGGTGCAAC
1 GTCGACAC-TTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAAC
*
489114 AATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAT-AACATCGAAA-CCATAAGTATAAT
65 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAAT
489176 GTAATAGGTAATTTTCAATCTAACCGGTACAAGTATACCGGTTTT
130 GTAATAGGTAATTTTCAATCTAACCGGTACAAGTATACCGGTTTT
489221 GAGAAAATTG
Statistics
Matches: 542, Mismatches: 21, Indels: 13
0.94 0.04 0.02
Matches are distributed among these distances:
196 137 0.25
197 82 0.15
198 24 0.04
199 63 0.12
200 164 0.30
201 72 0.13
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (199 bp):
GTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACA
ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATG
TAATAGGTAATTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATA
ATGT
Found at i:489194 original size:396 final size:397
Alignment explanation
Indices: 488453--489220 Score: 1328
Period size: 396 Copynumber: 1.9 Consensus size: 397
488443 GGCAAACAGG
* * *
488453 GTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACC
1 GTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTACAGAATGAATGGAAAACAGGGTGCAACA
*
488518 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCATAAACATCGAAACCCAAAAGTATAATG
* **
488583 TAATATGTAATTTTTCAATCTAATTGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAAT
*
488648 AATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTG
196 AATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTAGTCCAGAATGAATGGCAAACAGGGTG
*
488713 CAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCATAAACATCGAAACCCAAAAGTAT
261 CAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCATAAACATCGAAACCCAAAAGTAT
*
488778 AATGTAATATGTAATTTCAATCTAACC-GTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAA
326 AATGTAATAGGTAATTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAA
488842 ATAATGT
391 ATAATGT
488849 GTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTACAGAATGAATGGAAAACAGGGTGCAACA
1 GTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTACAGAATGAATGGAAAACAGGGTGCAACA
*
488914 ATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCATAAACATCGAAACCCATAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCATAAACATCGAAACCCAAAAGTATAATG
*
488979 TAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGTTTTTATGAGAGAATATGTCTAAAT
131 TAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAAT
* * * *
489044 AATGTGTCGACACTTTTTTTAGTTTGTGTCGATATTTTTATTCTAGAATGAATGGCAAACAGGGT
196 AATGTATCGACAC-TTTTGTAGTTTGTGTCGATATTTTTAGTCCAGAATGAATGGCAAACAGGGT
*
489109 GCAACAATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAT-AACATCGAAA-CCATAAGT
260 GCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGAT-CCATAAACATCGAAACCCAAAAGT
489171 ATAATGTAATAGGTAATTTTCAATCTAACCGGTACAAGTATACCGGTTTT
324 ATAATGTAATAGGTAA-TTTCAATCTAACCGGTACAAGTATACCGGTTTT
489221 GAGAAAATTG
Statistics
Matches: 351, Mismatches: 17, Indels: 7
0.94 0.05 0.02
Matches are distributed among these distances:
395 22 0.06
396 233 0.66
397 96 0.27
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (397 bp):
GTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTACAGAATGAATGGAAAACAGGGTGCAACA
ATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCATAAACATCGAAACCCAAAAGTATAATG
TAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAAT
AATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTAGTCCAGAATGAATGGCAAACAGGGTG
CAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCATAAACATCGAAACCCAAAAGTAT
AATGTAATAGGTAATTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAA
ATAATGT
Found at i:490744 original size:6 final size:6
Alignment explanation
Indices: 490733--490784 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
490723 CAAGCGGTCA
* * * * * *
490733 ATGAAG ATGAAG CTGACG ATGAAG ATGACG ATGATG ATGATG ATGATG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
490781 ATGA
1 ATGA
490785 TGATCCAAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.38, C:0.06, G:0.33, T:0.23
Consensus pattern (6 bp):
ATGAAG
Found at i:490755 original size:12 final size:12
Alignment explanation
Indices: 490733--490784 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
490723 CAAGCGGTCA
*
490733 ATGAAGATGAAG
1 ATGACGATGAAG
*
490745 CTGACGATGAAG
1 ATGACGATGAAG
*
490757 ATGACGATGATG
1 ATGACGATGAAG
* *
490769 ATGATGATGATG
1 ATGACGATGAAG
490781 ATGA
1 ATGA
490785 TGATCCAAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.38, C:0.06, G:0.33, T:0.23
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:490770 original size:3 final size:3
Alignment explanation
Indices: 490750--490788 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
490740 TGAAGCTGAC
* *
490750 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
490789 CCAAACAAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.36, C:0.03, G:0.33, T:0.28
Consensus pattern (3 bp):
GAT
Found at i:492404 original size:182 final size:183
Alignment explanation
Indices: 491969--492715 Score: 1203
Period size: 183 Copynumber: 4.1 Consensus size: 183
491959 CAAAGTTTTC
* * *
491969 ACAC-TTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACATTTT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
* * * *
492033 CAAAAAATGTCG--ATTGAAAAAACATCGGAACCTAGAATTATAATGTAATAGATAATTTTGTAA
66 CAAAAAGTGTCGACATT---TACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAA
* * *
492096 TATAACCGGTATAAATATACCGGTTTTATGAGTAAATAGGTATACAACCTATATCA
128 TATAACCGGTATAAATATACCGGTTTTATGAGCAAATAGGTCTACAACCTATATCG
*
492152 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGAAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
* * *
492217 CAAAAAGTATCGACATTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTATAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
*
492282 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAA-CTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCAAATAGGTCTACAACCTATATCG
492334 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
*
492399 CAAAAAGTGT---CATTTACACATCGGAA-CCAGAATTATAA-GTAATATATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
*
492459 AACCGGTATAAATATACCGGTTTTATGAGCAAATAGGTTTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCAAATAGGTCTACAACCTATATCG
*
492512 ACACTTTTTAATATTGTGTCGGTATTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
*
492577 CAAAAAGTGTCGACATTTACACATCGGAACCCTGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
*
492642 AACCGGTATAAATATACCGG-TTT-T-AGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCAAATAGGTCTACAACCTATATCG
492692 ACACTTTTTAATATTGTGTCGGTA
1 ACACTTTTTAATATTGTGTCGGTA
492716 ATTTTAAGTA
Statistics
Matches: 528, Mismatches: 27, Indels: 21
0.92 0.05 0.04
Matches are distributed among these distances:
177 62 0.12
178 93 0.18
179 16 0.03
180 48 0.09
181 17 0.03
182 94 0.18
183 129 0.24
184 66 0.12
186 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (183 bp):
ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAATATACCGGTTTTATGAGCAAATAGGTCTACAACCTATATCG
Found at i:492496 original size:360 final size:362
Alignment explanation
Indices: 491969--492715 Score: 1265
Period size: 360 Copynumber: 2.1 Consensus size: 362
491959 CAAAGTTTTC
*
491969 ACAC-TTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACATTTT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACATTGT
492033 CAAAAAATGTCGATTGAAAAAACATCGGAACCTAGAATTATAATGTAATAGATAATTTTGTAATA
66 CAAAAAATGTCGATT--AAAAACATCGGAACCTAGAATTATAATGTAATAGATAATTTTGTAATA
*
492098 TAACCGGTATAAATATACCGGTTTTATGAGTAAATAGGTATACAACCTATATCAACACTTTTTAA
129 TAACCGGTATAAATATACCGGTTTTATGAGCAAATAGGTATACAACCTATATCAACACTTTTTAA
492163 TATTGTGTCGGTACTTTATGTCCAGATTGAAAGAAAAATGTGTCGATACCTTGTCAAAAAGTATC
194 TATTGTGTCGGTACTTTATGTCCAGATTGAAAGAAAAATGTGTCGATACCTTGTCAAAAAGTATC
492228 GACATTTACACATCGGAACCCAT-AATTATAATGTAATAGATAATTTTATAATATAACCGGTATA
259 GACATTTACACATCGGAACCC-TGAATTATAATGTAATAGATAATTTTATAATATAACCGGTATA
492292 AATATACCGGTTTTATGAGCGAATAGGTCTACAA-CTATATCG
323 AATATACCGG-TTT-T-AGCGAATAGGTCTACAACCTATATCG
* *
492334 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACATTGT
* * * *
492399 CAAAAAGTGTC-ATT-TACACATCGGAACC-AGAATTATAA-GTAATATATAATTTTGTAATATA
66 CAAAAAATGTCGATTAAAAACATCGGAACCTAGAATTATAATGTAATAGATAATTTTGTAATATA
* *
492460 ACCGGTATAAATATACCGGTTTTATGAGCAAATAGGTTTACAACCTATATCGACACTTTTTAATA
131 ACCGGTATAAATATACCGGTTTTATGAGCAAATAGGTATACAACCTATATCAACACTTTTTAATA
* * *
492525 TTGTGTCGGTATTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGA
196 TTGTGTCGGTACTTTATGTCCAGATTGAAAGAAAAATGTGTCGATACCTTGTCAAAAAGTATCGA
*
492590 CATTTACACATCGGAACCCTGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAAT
261 CATTTACACATCGGAACCCTGAATTATAATGTAATAGATAATTTTATAATATAACCGGTATAAAT
492655 ATACCGGTTTTAGCGAATAGGTCTACAACCTATATCG
326 ATACCGGTTTTAGCGAATAGGTCTACAACCTATATCG
492692 ACACTTTTTAATATTGTGTCGGTA
1 ACACTTTTTAATATTGTGTCGGTA
492716 ATTTTAAGTA
Statistics
Matches: 365, Mismatches: 14, Indels: 13
0.93 0.04 0.03
Matches are distributed among these distances:
357 17 0.05
358 33 0.09
359 4 0.01
360 215 0.59
361 10 0.03
362 12 0.03
365 7 0.02
366 67 0.18
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (362 bp):
ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACATTGT
CAAAAAATGTCGATTAAAAACATCGGAACCTAGAATTATAATGTAATAGATAATTTTGTAATATA
ACCGGTATAAATATACCGGTTTTATGAGCAAATAGGTATACAACCTATATCAACACTTTTTAATA
TTGTGTCGGTACTTTATGTCCAGATTGAAAGAAAAATGTGTCGATACCTTGTCAAAAAGTATCGA
CATTTACACATCGGAACCCTGAATTATAATGTAATAGATAATTTTATAATATAACCGGTATAAAT
ATACCGGTTTTAGCGAATAGGTCTACAACCTATATCG
Found at i:495174 original size:25 final size:25
Alignment explanation
Indices: 495146--495210 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
495136 TTATCATTAA
*
495146 ATTTAGGTATGTACAATAACTATAT
1 ATTTAGGTATGTACAATAACTACAT
495171 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
495196 ATTTAGGTATGTACA
1 ATTTAGGTATGTACA
495211 TCTTTTGAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.38
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:495530 original size:21 final size:21
Alignment explanation
Indices: 495488--495530 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
495478 ATTACATAAC
*
495488 TTTAAAAAAGTATCGATCCTT
1 TTTAAAAAAGTATCGAACCTT
*
495509 TTTATAAAAGTAT-GAACACTT
1 TTTAAAAAAGTATCGAAC-CTT
495530 T
1 T
495531 CATATAATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.40
Consensus pattern (21 bp):
TTTAAAAAAGTATCGAACCTT
Found at i:495558 original size:84 final size:85
Alignment explanation
Indices: 495470--495638 Score: 322
Period size: 84 Copynumber: 2.0 Consensus size: 85
495460 AAAAAAAATT
495470 GAAACATAATTACATAACTTTAAAAAAGTATCGATCCTTTTTATAAAAGTATGAACACTTTC-AT
1 GAAACATAATTACATAACTTTAAAAAAGTATCGATCCTTTTTATAAAAGTATGAACACTTTCAAT
495534 ATAATAGGTAAAAAATGATG
66 ATAATAGGTAAAAAATGATG
495554 GAAACATAATTACATAACTTTAAAAAAGTATCGATCCTTTTTATAAAAGTATGAACACTTTCAAT
1 GAAACATAATTACATAACTTTAAAAAAGTATCGATCCTTTTTATAAAAGTATGAACACTTTCAAT
*
495619 ATAATAGGTAAAATATGATG
66 ATAATAGGTAAAAAATGATG
495639 TAATAGGTAG
Statistics
Matches: 83, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
84 62 0.75
85 21 0.25
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.33
Consensus pattern (85 bp):
GAAACATAATTACATAACTTTAAAAAAGTATCGATCCTTTTTATAAAAGTATGAACACTTTCAAT
ATAATAGGTAAAAAATGATG
Found at i:495614 original size:21 final size:21
Alignment explanation
Indices: 495572--495614 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
495562 ATTACATAAC
*
495572 TTTAAAAAAGTATCGATCCTT
1 TTTAAAAAAGTATCGAACCTT
*
495593 TTTATAAAAGTAT-GAACACTT
1 TTTAAAAAAGTATCGAAC-CTT
495614 T
1 T
495615 CAATATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.40
Consensus pattern (21 bp):
TTTAAAAAAGTATCGAACCTT
Found at i:495657 original size:23 final size:21
Alignment explanation
Indices: 495631--495691 Score: 79
Period size: 23 Copynumber: 2.8 Consensus size: 21
495621 AATAGGTAAA
495631 ATATGATGTAATAGGTAGCACTT
1 ATAT-ATGTAATAGGTAGC-CTT
*
495654 ATATAATGTAATAGGTAGCGTT
1 ATAT-ATGTAATAGGTAGCCTT
495676 ATA-ATGTAATAGGTAG
1 ATATATGTAATAGGTAG
495692 TGCTTTATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 13 0.36
22 5 0.14
23 18 0.50
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.34
Consensus pattern (21 bp):
ATATATGTAATAGGTAGCCTT
Found at i:495680 original size:20 final size:22
Alignment explanation
Indices: 495631--495691 Score: 81
Period size: 20 Copynumber: 2.8 Consensus size: 22
495621 AATAGGTAAA
* *
495631 ATATGATGTAATAGGTAGCACTT
1 ATATAATGTAATAGGTAG-ACGT
495654 ATATAATGTAATAGGTAG-CGT
1 ATATAATGTAATAGGTAGACGT
495675 -TATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
495692 TGCTTTATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 17 0.47
21 2 0.06
23 17 0.47
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.34
Consensus pattern (22 bp):
ATATAATGTAATAGGTAGACGT
Found at i:496141 original size:21 final size:21
Alignment explanation
Indices: 496116--496186 Score: 97
Period size: 21 Copynumber: 3.3 Consensus size: 21
496106 GTAAAATGTG
496116 ATGTAATAGGTAGCGCTTATA
1 ATGTAATAGGTAGCGCTTATA
*
496137 ATGTAATAGGTAGCGTTTATATA
1 ATGTAATAGGTAGCG-CT-TATA
*
496160 ATGTAATAGGTAGTGCTTATA
1 ATGTAATAGGTAGCGCTTATA
*
496181 TTGTAA
1 ATGTAA
496187 AGTATCTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
21 24 0.55
22 2 0.05
23 18 0.41
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.38
Consensus pattern (21 bp):
ATGTAATAGGTAGCGCTTATA
Found at i:496163 original size:23 final size:22
Alignment explanation
Indices: 496116--496181 Score: 89
Period size: 23 Copynumber: 3.0 Consensus size: 22
496106 GTAAAATGTG
*
496116 ATGTAATAGGTAGCGCT-TATA
1 ATGTAATAGGTAGCGTTATATA
496137 ATGTAATAGGTAGCGTTTATATA
1 ATGTAATAGGTAGCG-TTATATA
*
496160 ATGTAATAGGTAGTGCTTATAT
1 ATGTAATAGGTAGCG-TTATAT
496182 TGTAAAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 15 0.38
22 1 0.03
23 24 0.60
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.38
Consensus pattern (22 bp):
ATGTAATAGGTAGCGTTATATA
Found at i:500142 original size:21 final size:21
Alignment explanation
Indices: 500092--500143 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
500082 TTCTAACTAC
500092 CGCATTGCGATTTCCCAAATT
1 CGCATTGCGATTTCCCAAATT
* * *
500113 CGCGTTGCGATTTTCCTAATT
1 CGCATTGCGATTTCCCAAATT
*
500134 CGCAATGCGA
1 CGCATTGCGA
500144 ATACGTAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (21 bp):
CGCATTGCGATTTCCCAAATT
Found at i:500158 original size:20 final size:21
Alignment explanation
Indices: 500133--500230 Score: 101
Period size: 21 Copynumber: 4.8 Consensus size: 21
500123 TTTTCCTAAT
*
500133 TCGCAATGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
* **
500153 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATTACGAAAA
* **
500174 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATTACGAAAA
*
500195 TCGCAATGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
*
500215 TCGCAATGCGATTTAC
1 TCGCAATGCGAATTAC
500231 ATAGCGCTAT
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
20 27 0.40
21 40 0.60
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:500176 original size:21 final size:21
Alignment explanation
Indices: 500150--500207 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
500140 GCGAATACGT
500150 AAATCGCAACGCGAATTTGGA
1 AAATCGCAACGCGAATTTGGA
500171 AAATCGCAACGCGAATTTGGA
1 AAATCGCAACGCGAATTTGGA
*
500192 AAATCGCAATGCGAAT
1 AAATCGCAACGCGAAT
500208 ACGTAAATCG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.19
Consensus pattern (21 bp):
AAATCGCAACGCGAATTTGGA
Found at i:500824 original size:19 final size:20
Alignment explanation
Indices: 500785--500832 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
500775 CAACGAGTGA
500785 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
500805 ATCGCAATGCG-AATTGACT
1 ATCGCAACGCGAAAATGACT
500824 ATCGCAACG
1 ATCGCAACG
500833 AGAGAATCGC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:500901 original size:20 final size:18
Alignment explanation
Indices: 500885--500921 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
500875 CGTTGCGGTA
500885 GTCATTTTCGTGTTGCGAT
1 GTCA-TTTCGTGTTGCGAT
*
500904 TTCATTTCGTGTTGCGAT
1 GTCATTTCGTGTTGCGAT
500922 TTAAAGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.11, C:0.16, G:0.24, T:0.49
Consensus pattern (18 bp):
GTCATTTCGTGTTGCGAT
Found at i:502803 original size:20 final size:20
Alignment explanation
Indices: 502778--502921 Score: 201
Period size: 20 Copynumber: 7.5 Consensus size: 20
502768 AGAATAGTTT
502778 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
502798 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
502818 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
502834 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
502852 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
502872 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
502892 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
*
502912 CCTATCGCAA
1 ACTATCGCAA
502922 CGAAAGAATC
Statistics
Matches: 112, Mismatches: 6, Indels: 12
0.86 0.05 0.09
Matches are distributed among these distances:
14 7 0.06
16 4 0.04
17 4 0.04
18 4 0.04
20 93 0.83
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.19
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:502976 original size:20 final size:20
Alignment explanation
Indices: 502946--503000 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
502936 TGCGAAATGA
502946 AAATT-GCATTGCGATAGTC
1 AAATTCGCATTGCGATAGTC
502965 AAATTCGCATTGCGATAGTC
1 AAATTCGCATTGCGATAGTC
** *
502985 ATTTTCGCGTTGCGAT
1 AAATTCGCATTGCGAT
503001 TTTGTTGTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 5 0.16
20 27 0.84
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (20 bp):
AAATTCGCATTGCGATAGTC
Found at i:503054 original size:33 final size:33
Alignment explanation
Indices: 502974--503055 Score: 101
Period size: 33 Copynumber: 2.5 Consensus size: 33
502964 CAAATTCGCA
* * * *
502974 TTGCGATAGTCATTTTCGCGTTGCGATTTTGTTG
1 TTGCGATAGTCA-TTTCGCATTGCGATTCTCTCG
**
503008 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCATTGCGATTCTCTCG
503041 TTGCGATAGTCATTT
1 TTGCGATAGTCATTT
503056 GCAGATTCTA
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
33 30 0.75
34 10 0.25
ACGTcount: A:0.13, C:0.18, G:0.22, T:0.46
Consensus pattern (33 bp):
TTGCGATAGTCATTTCGCATTGCGATTCTCTCG
Found at i:505012 original size:14 final size:14
Alignment explanation
Indices: 504993--505026 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
504983 TGTTTAATTT
504993 ATTTGTAAAAGATG
1 ATTTGTAAAAGATG
* *
505007 ATTTGTAAATGTTG
1 ATTTGTAAAAGATG
505021 ATTTGT
1 ATTTGT
505027 TTAATTGATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTGTAAAAGATG
Found at i:505218 original size:33 final size:33
Alignment explanation
Indices: 505161--505256 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
505151 GCAACTTTCG
505161 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
* *
505195 CGTTGCGATTTTCATTTCGCATTGTGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
** *
505228 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
505257 AGTCAATTCC
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 32 0.58
34 23 0.42
ACGTcount: A:0.14, C:0.23, G:0.21, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:505253 original size:20 final size:20
Alignment explanation
Indices: 505228--505335 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
505218 GTGATTCTCT
505228 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
505248 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
* * *
505268 CATTGTGATAGTCATTTCTG
1 CGTTGCGATAGTCATTTCCG
*
505288 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
505308 CGTT--G-T-G--ATTTCCG
1 CGTTGCGATAGTCATTTCCG
505322 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
505336 AATGAATGTC
Statistics
Matches: 70, Mismatches: 10, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
13 2 0.03
14 8 0.11
16 2 0.03
17 2 0.03
18 2 0.03
20 52 0.74
21 2 0.03
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:507631 original size:23 final size:23
Alignment explanation
Indices: 507582--507631 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
507572 ATTCGAGTAT
** *
507582 TGACCAAGATCAAATCCGGGTAT
1 TGACCAAGATCAAATCCGAATAC
**
507605 TGACCAAGATCAAATTTGAATAC
1 TGACCAAGATCAAATCCGAATAC
507628 TGAC
1 TGAC
507632 TGTACTCACA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (23 bp):
TGACCAAGATCAAATCCGAATAC
Found at i:508330 original size:60 final size:60
Alignment explanation
Indices: 508237--508357 Score: 242
Period size: 60 Copynumber: 2.0 Consensus size: 60
508227 AACTAAAACC
508237 TGTTGCTGGATGGGGAAGGATGTCGTTGGATATAGGAACGGATGTCGCCGGAGAGAGTGA
1 TGTTGCTGGATGGGGAAGGATGTCGTTGGATATAGGAACGGATGTCGCCGGAGAGAGTGA
508297 TGTTGCTGGATGGGGAAGGATGTCGTTGGATATAGGAACGGATGTCGCCGGAGAGAGTGA
1 TGTTGCTGGATGGGGAAGGATGTCGTTGGATATAGGAACGGATGTCGCCGGAGAGAGTGA
508357 T
1 T
508358 AGATGGAGAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.23, C:0.10, G:0.43, T:0.24
Consensus pattern (60 bp):
TGTTGCTGGATGGGGAAGGATGTCGTTGGATATAGGAACGGATGTCGCCGGAGAGAGTGA
Found at i:508534 original size:20 final size:20
Alignment explanation
Indices: 508511--508767 Score: 194
Period size: 20 Copynumber: 12.8 Consensus size: 20
508501 TTGCGATAGT
* *
508511 CAGAATCTCGTTGCGATTTA
1 CAGAATCGCATTGCGATTTA
*
508531 CAGATTCGCATTGCGATTTA
1 CAGAATCGCATTGCGATTTA
* *
508551 C-GTATTCGTATTGCGATTTA
1 CAG-AATCGCATTGCGATTTA
*
508571 C-GTAATCGCATTACGATTTA
1 CAG-AATCGCATTGCGATTTA
*
508591 C-GTATTCGCATTGCGATTTA
1 CAG-AATCGCATTGCGATTTA
*
508611 C-GTAATCGCATTACGATTTA
1 CAG-AATCGCATTGCGATTTA
*
508631 C-GTATTCGCATTGCGATTTA
1 CAG-AATCGCATTGCGATTTA
*
508651 C-GTAATCGCATTACGATTTA
1 CAG-AATCGCATTGCGATTTA
*
508671 C-GTATTCGCATTGCGATTTA
1 CAG-AATCGCATTGCGATTTA
508691 C-GTAATCGCATTGCGATTTA
1 CAG-AATCGCATTGCGATTTA
* *
508711 C-GTAATCGTATTGCGATTTTC
1 CAG-AATCGCATTGCGA-TTTA
*
508732 CA-AATTCGCGTTGCGATTTA
1 CAGAA-TCGCATTGCGATTTA
*
508752 C-GTATTCGCATTGCGA
1 CAG-AATCGCATTGCGA
508768 ATTAGGAAAA
Statistics
Matches: 206, Mismatches: 25, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
19 1 0.00
20 191 0.93
21 14 0.07
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
CAGAATCGCATTGCGATTTA
Found at i:508565 original size:40 final size:40
Alignment explanation
Indices: 508521--508767 Score: 370
Period size: 40 Copynumber: 6.2 Consensus size: 40
508511 CAGAATCTCG
* * *
508521 TTGCGATTTACAG-ATTCGCATTGCGATTTACGTATTCGTA
1 TTGCGATTTAC-GTAATCGCATTACGATTTACGTATTCGCA
508561 TTGCGATTTACGTAATCGCATTACGATTTACGTATTCGCA
1 TTGCGATTTACGTAATCGCATTACGATTTACGTATTCGCA
508601 TTGCGATTTACGTAATCGCATTACGATTTACGTATTCGCA
1 TTGCGATTTACGTAATCGCATTACGATTTACGTATTCGCA
508641 TTGCGATTTACGTAATCGCATTACGATTTACGTATTCGCA
1 TTGCGATTTACGTAATCGCATTACGATTTACGTATTCGCA
* * *
508681 TTGCGATTTACGTAATCGCATTGCGATTTACGTAATCGTA
1 TTGCGATTTACGTAATCGCATTACGATTTACGTATTCGCA
* ** * *
508721 TTGCGATTTTCCAAATTCGCGTTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTAA-TCGCATTACGATTTACGTATTCGCA
508762 TTGCGA
1 TTGCGA
508768 ATTAGGAAAA
Statistics
Matches: 193, Mismatches: 12, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
39 1 0.01
40 164 0.85
41 28 0.15
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (40 bp):
TTGCGATTTACGTAATCGCATTACGATTTACGTATTCGCA
Found at i:508588 original size:60 final size:60
Alignment explanation
Indices: 508521--508767 Score: 343
Period size: 60 Copynumber: 4.1 Consensus size: 60
508511 CAGAATCTCG
* *
508521 TTGCGATTTACAG-ATTCGCATTGCGATTTACGTATTCGTATTGCGATTTACGTAATCGCA
1 TTGCGATTTAC-GTAATCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCA
* * * * *
508581 TTACGATTTACGTATTCGCATTGCGATTTACGTAATCGCATTACGATTTACGTATTCGCA
1 TTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCA
*
508641 TTGCGATTTACGTAATCGCATTACGATTTACGTATTCGCATTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCA
* * ** * *
508701 TTGCGATTTACGTAATCGTATTGCGATTTTCCAAATTCGCGTTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTAATCGCATTGCGA-TTTACGTATTCGCATTGCGATTTACGTAATCGCA
508762 TTGCGA
1 TTGCGA
508768 ATTAGGAAAA
Statistics
Matches: 167, Mismatches: 18, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
59 1 0.01
60 131 0.78
61 35 0.21
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (60 bp):
TTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCA
Found at i:508788 original size:21 final size:21
Alignment explanation
Indices: 508764--508809 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
508754 TATTCGCATT
508764 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
508785 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
508806 GCGA
1 GCGA
508810 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:510353 original size:20 final size:20
Alignment explanation
Indices: 510328--510382 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
510318 TTTCTAGGTA
510328 GGTGCATCGATGCATTAAGG
1 GGTGCATCGATGCATTAAGG
510348 GGTGCATCGATGCATTAAGG
1 GGTGCATCGATGCATTAAGG
510368 GGTGCATCGATGCAT
1 GGTGCATCGATGCAT
510383 GGATATTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.24, C:0.16, G:0.35, T:0.25
Consensus pattern (20 bp):
GGTGCATCGATGCATTAAGG
Found at i:511154 original size:31 final size:31
Alignment explanation
Indices: 511116--511217 Score: 177
Period size: 31 Copynumber: 3.3 Consensus size: 31
511106 AGGGTCGAGG
511116 GTTTACCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGATATATGGACT
*
511147 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGATATATGGACT
*
511178 GTTTACCTATGTTCTTCGGAATATATGGACT
1 GTTTACCTATGTTCTTCGGGATATATGGACT
*
511209 GATTACCTA
1 GTTTACCTA
511218 GGTTTTTTGG
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 67 1.00
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGATATATGGACT
Found at i:511182 original size:62 final size:62
Alignment explanation
Indices: 511116--511240 Score: 187
Period size: 62 Copynumber: 2.0 Consensus size: 62
511106 AGGGTCGAGG
* * * *
511116 GTTTACCTATGTTCTTCGGGATATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAATATATGGACTGATTACCTAGGTTCTTCGGAACATATGGACT
* * *
511178 GTTTACCTATGTTCTTCGGAATATATGGACTGATTACCTAGGTTTTTTGGAACCTATGGACT
1 GTTTACCTATGTTCTTCGGAATATATGGACTGATTACCTAGGTTCTTCGGAACATATGGACT
511240 G
1 G
511241 GTCCTTCGGG
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (62 bp):
GTTTACCTATGTTCTTCGGAATATATGGACTGATTACCTAGGTTCTTCGGAACATATGGACT
Found at i:511236 original size:31 final size:31
Alignment explanation
Indices: 511116--511240 Score: 169
Period size: 31 Copynumber: 4.0 Consensus size: 31
511106 AGGGTCGAGG
* *
511116 GTTTACCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
511147 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
511178 GTTTACCTATGTTCTTCGGAATATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* * * * *
511209 GATTACCTAGGTTTTTTGGAACCTATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
511240 G
1 G
511241 GTCCTTCGGG
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 85 1.00
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:511902 original size:21 final size:21
Alignment explanation
Indices: 511876--511916 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
511866 GAAATTTTGG
511876 TGCATCGATGCACTGTAGCAA
1 TGCATCGATGCACTGTAGCAA
511897 TGCATCGATGCACTGTAGCA
1 TGCATCGATGCACTGTAGCA
511917 CTGTTCACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (21 bp):
TGCATCGATGCACTGTAGCAA
Found at i:511977 original size:22 final size:22
Alignment explanation
Indices: 511916--511968 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
511906 GCACTGTAGC
511916 ACTGTTCACGGTATTGTTCATT
1 ACTGTTCACGGTATTGTTCATT
511938 ACTGTTCACGGTATTGTTCATT
1 ACTGTTCACGGTATTGTTCATT
511960 ACTGTTCAC
1 ACTGTTCAC
511969 AGCACTGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.19, C:0.21, G:0.17, T:0.43
Consensus pattern (22 bp):
ACTGTTCACGGTATTGTTCATT
Found at i:515077 original size:315 final size:310
Alignment explanation
Indices: 514512--515137 Score: 1175
Period size: 315 Copynumber: 2.0 Consensus size: 310
514502 GACCTTGTGG
514512 TATTTCCTAGAATAAAAATATTGTTTTTCTCTTGTTTCCTGTGTCAGACTGTGAGAAAGAGATAT
1 TATTTCCTAGAATAAAAATATTGTTTTTCTCTTGTTTCCTGTGTCAGACTGTGAGAAAGAGATAT
514577 GAAATGTGACAACAGTTTCCATAAAAGAAGCTTCATATATATCTTGTGTGTGTACTGTTTAATGA
66 GAAATGTGACAACAGTTTCCATAAAAGAAGCTTCATATATATCTTGTGTGTGTACTGTTTAATGA
514642 GTGACTGACTAGTTTGATATTATTGCATATGGGGGTTTTGGGTGTGCCATGTCATTATGATGTTG
131 GTGACTGACTAGTTTGATATTATTGCATATGGGGGTTTTGGGTGTGCCATGTCATTATGATGTTG
514707 TCATCATACAAATAAATGCCAACTCTAAGCCTTTTGATATGTAAAGAACTAAGTTTCTTTTTAAA
196 TCATCATACAAATAAATGCCAACTCTAAGCCTTTTGATATGTAAAGAACTAAGTTTCTTTTTAAA
514772 ATTTATTCATGTTCTTTATTTATAATGTGAATA-G-GTGCACGCGTGGAT
261 ATTTATTCATGTTCTTTATTTATAATGTGAATAGGTGTGCACGCGTGGAT
514820 TATTTCCTAGAATAAAAATATTGTTTTTCTCTTGTTTCCTGTGTCAGACTGTGAGAAAGAGATAT
1 TATTTCCTAGAATAAAAATATTGTTTTTCTCTTGTTTCCTGTGTCAGACTGTGAGAAAGAGATAT
514885 GAAATGTGACAACAGTTTCCATAAAAGAAGCTTCATCTAATATATCTTGTGTGTGGTACTGTTTA
66 GAAATGTGACAACAGTTTCCATAAAAGAAGCTTCA--T-ATATATCTTGTGTGT-GTACTG-TT-
514950 ATAATGAGTGACTGACTAGTTTGATATTATTGCATATGGGGGTTTTGGGTGTGCCATGTCATTAT
125 -TAATGAGTGACTGACTAGTTTGATATTATTGCATATGGGGGTTTTGGGTGTGCCATGTCATTAT
515015 GATGTTGTCATCATACAAATAAATGCCAACTCTAAGCCTTTTGATATGTAAAGAACTAAGTTTCT
189 GATGTTGTCATCATACAAATAAATGCCAACTCTAAGCCTTTTGATATGTAAAGAACTAAGTTTCT
515080 TTTTAAAATTTATTCATGTTCTTTATTTATAATGTGAATAGGTGTGCACGCGTGGAT
254 TTTTAAAATTTATTCATGTTCTTTATTTATAATGTGAATAGGTGTGCACGCGTGGAT
515137 T
1 T
515138 TGCGCGCACA
Statistics
Matches: 309, Mismatches: 0, Indels: 9
0.97 0.00 0.03
Matches are distributed among these distances:
308 100 0.32
310 1 0.00
311 15 0.05
312 6 0.02
313 2 0.01
315 169 0.55
316 1 0.00
317 15 0.05
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.39
Consensus pattern (310 bp):
TATTTCCTAGAATAAAAATATTGTTTTTCTCTTGTTTCCTGTGTCAGACTGTGAGAAAGAGATAT
GAAATGTGACAACAGTTTCCATAAAAGAAGCTTCATATATATCTTGTGTGTGTACTGTTTAATGA
GTGACTGACTAGTTTGATATTATTGCATATGGGGGTTTTGGGTGTGCCATGTCATTATGATGTTG
TCATCATACAAATAAATGCCAACTCTAAGCCTTTTGATATGTAAAGAACTAAGTTTCTTTTTAAA
ATTTATTCATGTTCTTTATTTATAATGTGAATAGGTGTGCACGCGTGGAT
Found at i:523500 original size:16 final size:17
Alignment explanation
Indices: 523469--523501 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
523459 ACTGATTCGA
*
523469 GAATTGATGCGTTGGTG
1 GAATTGAAGCGTTGGTG
523486 GAATTGAAG-GTTGGTG
1 GAATTGAAGCGTTGGTG
523502 ACAACTTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.21, C:0.03, G:0.42, T:0.33
Consensus pattern (17 bp):
GAATTGAAGCGTTGGTG
Found at i:528342 original size:41 final size:41
Alignment explanation
Indices: 528294--528372 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
528284 TTGGAAGACG
*
528294 GGGATTTTCCGCAACAGGTGCTGGATAGTTCTTGTTGTTTA
1 GGGATTTTCCGCAACAGGTGCTGGATAATTCTTGTTGTTTA
528335 GGGATTTTCCGCAACAGGTGCTGGATAATTCTTGTTGT
1 GGGATTTTCCGCAACAGGTGCTGGATAATTCTTGTTGT
528373 ATAGCTTACT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.18, C:0.15, G:0.29, T:0.38
Consensus pattern (41 bp):
GGGATTTTCCGCAACAGGTGCTGGATAATTCTTGTTGTTTA
Found at i:532681 original size:31 final size:32
Alignment explanation
Indices: 532646--532711 Score: 116
Period size: 31 Copynumber: 2.1 Consensus size: 32
532636 GTAACTATTG
532646 GGGGACCATATTGCAAACGGACTAAAAGTT-A
1 GGGGACCATATTGCAAACGGACTAAAAGTTGA
*
532677 GGGGACCATATTGCAAATGGACTAAAAGTTGA
1 GGGGACCATATTGCAAACGGACTAAAAGTTGA
532709 GGG
1 GGG
532712 ACTGTATTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 29 0.88
32 4 0.12
ACGTcount: A:0.36, C:0.14, G:0.30, T:0.20
Consensus pattern (32 bp):
GGGGACCATATTGCAAACGGACTAAAAGTTGA
Found at i:535045 original size:2 final size:2
Alignment explanation
Indices: 535038--535063 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
535028 TTATAAAATA
535038 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
535064 TCGAATCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:543660 original size:50 final size:50
Alignment explanation
Indices: 543604--543705 Score: 159
Period size: 50 Copynumber: 2.0 Consensus size: 50
543594 TACCATAAAT
* * * *
543604 ATGAAATTAAAATTCTGGTCCAACTTGCCAAACACAATAATTCATAATGA
1 ATGAAATTAAAACTCTGGTCCAACTTGCCAAACACAAGAATCCAGAATGA
*
543654 ATGAAATTAAAACTCTGGTCCAGCTTGCCAAACACAAGAATCCAGAATGA
1 ATGAAATTAAAACTCTGGTCCAACTTGCCAAACACAAGAATCCAGAATGA
543704 AT
1 AT
543706 TAGTTTCAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.25
Consensus pattern (50 bp):
ATGAAATTAAAACTCTGGTCCAACTTGCCAAACACAAGAATCCAGAATGA
Found at i:545144 original size:3 final size:3
Alignment explanation
Indices: 545138--545166 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
545128 CATTTGCTTA
545138 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
545167 AATAATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:545766 original size:24 final size:25
Alignment explanation
Indices: 545722--545773 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
545712 TAATGAAAAA
*
545722 CAAATAGACGAAGCAAGACAGAAAG
1 CAAATAGACGAAGCAAAACAGAAAG
*
545747 CAAA-AGACGAA-CACAAACAGACAG
1 CAAATAGACGAAGCA-AAACAGAAAG
545771 CAA
1 CAA
545774 CCACCCACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 2 0.08
24 18 0.75
25 4 0.17
ACGTcount: A:0.58, C:0.21, G:0.19, T:0.02
Consensus pattern (25 bp):
CAAATAGACGAAGCAAAACAGAAAG
Found at i:557087 original size:112 final size:113
Alignment explanation
Indices: 556830--557369 Score: 781
Period size: 112 Copynumber: 4.8 Consensus size: 113
556820 TGACAGGAAT
*
556830 TTCAACCTTTTGCCTGAATTCATCACTTGATGGATTAACTTTTCCAGAGGAAGTTCATAATGAGA
1 TTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAACTTTTCCAGAGGAAGTTCATAATGAGA
* *
556895 AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
66 AGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTG
* * * *
556943 TTTAACCTTTTG-CTCGAATTCATCACTTGATGGATCCACATTTCCAGAGAAAGTTCATAATGAG
1 TTCAACCTTTTGCCT-GAATTCATCACTTGATGGATCAACTTTTCCAGAGGAAGTTCATAATGAG
*
557007 AAGAACTTATCTGAAG-AGGAAGAAGAAATTCATAATGAGAAGAATTTG
65 AAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTG
* *
557055 TTCAACCTTTTGCCTGAATTCATTACTTGATGGATTAACTTTTCCAGAGGAAGTTCATAATGAGA
1 TTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAACTTTTCCAGAGGAAGTTCATAATGAGA
* *
557120 AGAACTCATTTGAAGAAGG-AGAAGAAGTTCATAATGAGAAGAATTTG
66 AGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTG
* * ** * *
557167 TTTAACTTTTTGTTTGAATTCATCA-TTCGATGGATCAACTTTTCCAGA-TAAGCTCATAATGAG
1 TTCAACCTTTTGCCTGAATTCATCACTT-GATGGATCAACTTTTCCAGAGGAAGTTCATAATGAG
557230 AAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTG
65 AAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTG
* ** * *
557279 TCCAAACCTTTTGTTTGAACTCATCA-TTCGATGGATCAACTTTTCCAGA-GAGGTTCATAATGA
1 TTC-AACCTTTTGCCTGAATTCATCACTT-GATGGATCAACTTTTCCAGAGGAAGTTCATAATGA
557342 GAAGAACTCATCTGAAGAAGG-AGAAGAA
64 GAAGAACTCATCTGAAGAAGGAAGAAGAA
557370 TTTGTTCAAC
Statistics
Matches: 387, Mismatches: 34, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
111 34 0.09
112 202 0.52
113 151 0.39
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.30
Consensus pattern (113 bp):
TTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAACTTTTCCAGAGGAAGTTCATAATGAGA
AGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTG
Found at i:557664 original size:3 final size:3
Alignment explanation
Indices: 557656--557703 Score: 73
Period size: 3 Copynumber: 16.7 Consensus size: 3
557646 CATTTGCTTA
*
557656 TAT TAT TAT TAT TAT TAT TAT TA- TGT TA- TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
557702 TA
1 TA
557704 AATAATAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 3 0.07
3 38 0.93
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:559513 original size:17 final size:18
Alignment explanation
Indices: 559491--559525 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
559481 TAAATAAAAA
559491 ATAAATAT-TTTTAATAT
1 ATAAATATGTTTTAATAT
*
559508 ATAAATATGTTTTTATAT
1 ATAAATATGTTTTAATAT
559526 TATTTTCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
ATAAATATGTTTTAATAT
Found at i:559672 original size:11 final size:13
Alignment explanation
Indices: 559635--559674 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 13
559625 TGTTTAATAA
559635 AATATA-TATATT
1 AATATATTATATT
*
559647 AATATATTATCTT
1 AATATATTATATT
559660 AA-A-ATTATATT
1 AATATATTATATT
559671 AATA
1 AATA
559675 AACTTAACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 8 0.33
13 7 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
AATATATTATATT
Found at i:559959 original size:77 final size:77
Alignment explanation
Indices: 559866--560020 Score: 283
Period size: 77 Copynumber: 2.0 Consensus size: 77
559856 TCAGTTTATC
*
559866 TTTTAACTGATGTTTTTCTAAAAACTCTTTTAAAAGATAATTTTTAGGTATTCGACCTACCTAAT
1 TTTTAACTGATGTTTTTCTAAAAACTCTTTTAAAAGATAATTTTTAGGTATTCGACCTACATAAT
559931 CCAAAAGGTCGA
66 CCAAAAGGTCGA
* *
559943 TTTTAACTGATGTTTTTCTAAAAACTCTTTTAAAAGATAATTTTTAGGTATTCTACCTACATGAT
1 TTTTAACTGATGTTTTTCTAAAAACTCTTTTAAAAGATAATTTTTAGGTATTCGACCTACATAAT
560008 CCAAAAGGTCGA
66 CCAAAAGGTCGA
560020 T
1 T
560021 GGCGACTCCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 75 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.40
Consensus pattern (77 bp):
TTTTAACTGATGTTTTTCTAAAAACTCTTTTAAAAGATAATTTTTAGGTATTCGACCTACATAAT
CCAAAAGGTCGA
Found at i:562957 original size:33 final size:33
Alignment explanation
Indices: 562920--563051 Score: 210
Period size: 33 Copynumber: 4.0 Consensus size: 33
562910 ATTTGGCAAG
562920 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
562953 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
** * *
562986 TTGGAAGTTTCATCTCGGTTGGTGACCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
*
563019 TTGGAAAATTCATCTTTGGTAGGTGGCCAACTT
1 TTGGAAAATTCATC-TTGGTTGGTGGCCAACTT
563052 TGCACATGGG
Statistics
Matches: 89, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
33 74 0.83
34 15 0.17
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.36
Consensus pattern (33 bp):
TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
Found at i:563442 original size:23 final size:22
Alignment explanation
Indices: 563415--563481 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 22
563405 AACTCAAGAC
563415 TCAAGCTCGATTTTGAGCTCGAT
1 TCAAGCTCGA-TTTGAGCTCGAT
*
563438 TCAAGCTCGACTTTGAGCTCAAT
1 TCAAGCTCGA-TTTGAGCTCGAT
*
563461 TTAAGCTC-ATTTGAAGCTCGA
1 TCAAGCTCGATTTG-AGCTCGA
563482 AACGGGTTAG
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
21 4 0.10
22 7 0.18
23 28 0.72
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.33
Consensus pattern (22 bp):
TCAAGCTCGATTTGAGCTCGAT
Found at i:563446 original size:11 final size:12
Alignment explanation
Indices: 563415--563481 Score: 52
Period size: 11 Copynumber: 5.8 Consensus size: 12
563405 AACTCAAGAC
563415 TCAAGCTCGATT
1 TCAAGCTCGATT
**
563427 TTGAGCTCGA-T
1 TCAAGCTCGATT
563438 TCAAGCTCGACTT
1 TCAAGCTCGA-TT
* *
563451 T-GAGCTCAATT
1 TCAAGCTCGATT
563462 T-AAGCTC-ATT
1 TCAAGCTCGATT
*
563472 TGAAGCTCGA
1 TCAAGCTCGA
563482 AACGGGTTAG
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
10 4 0.09
11 23 0.52
12 15 0.34
13 2 0.05
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.33
Consensus pattern (12 bp):
TCAAGCTCGATT
Found at i:569868 original size:34 final size:33
Alignment explanation
Indices: 569783--569878 Score: 147
Period size: 33 Copynumber: 2.9 Consensus size: 33
569773 ATTTGGCAAG
*
569783 TTGGAAAATTCATCTTGGTTGATGGCCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
*
569816 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
* *
569849 TTGGAAAATTCATCTTTGGTAGGTAGCCAA
1 TTGGAAAATTCATC-TTGGTTGGTGGCCAA
569879 TTTGCACATG
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 44 0.77
34 13 0.23
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (33 bp):
TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
Found at i:573052 original size:3 final size:3
Alignment explanation
Indices: 573044--573108 Score: 78
Period size: 3 Copynumber: 21.3 Consensus size: 3
573034 CATTTAAATT
* * *
573044 TTA TTA TTA TTA TTA TTA -AA TTTA TTA TTA CTAA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA -TTA TTA TTA TTA TTA
573090 TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA T
573109 ATATATATAT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 1 0.02
3 49 0.92
4 3 0.06
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:575107 original size:20 final size:21
Alignment explanation
Indices: 575084--575134 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
575074 AGAAATTAAA
575084 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
*
575104 AATTC-TTTCTTTCAAATTTTT
1 AATTCATTTATTT-AAATTTTT
575125 -ATT-ATTTATT
1 AATTCATTTATT
575135 ATTTTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 6 0.23
20 13 0.50
21 7 0.27
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:579799 original size:20 final size:23
Alignment explanation
Indices: 579774--579824 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
579764 ATCCAGCAAG
*
579774 AAAAAAGAGG-AA-AAA-AGAAA
1 AAAAAAAAGGAAAGAAATAGAAA
579794 AAAAAAAAGGAAAGAAATAGAAA
1 AAAAAAAAGGAAAGAAATAGAAA
579817 AAAAAAAA
1 AAAAAAAA
579825 TTAAATCAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 9 0.33
21 2 0.07
22 3 0.11
23 13 0.48
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (23 bp):
AAAAAAAAGGAAAGAAATAGAAA
Found at i:583181 original size:45 final size:45
Alignment explanation
Indices: 583131--583220 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
583121 AGCAATATGA
*
583131 ATATTTGAGTATTTTTGGGGGCTCATCTCAACAAGAAGTAATGTT
1 ATATTTGAGTATTTTTGGAGGCTCATCTCAACAAGAAGTAATGTT
583176 ATATTTGAGTATTTTTGGAGGCTCATCTCAACAAGAAGTAATGTT
1 ATATTTGAGTATTTTTGGAGGCTCATCTCAACAAGAAGTAATGTT
583221 GAACACACTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (45 bp):
ATATTTGAGTATTTTTGGAGGCTCATCTCAACAAGAAGTAATGTT
Found at i:583371 original size:75 final size:75
Alignment explanation
Indices: 583248--583861 Score: 1149
Period size: 75 Copynumber: 8.2 Consensus size: 75
583238 CTGTATCAGC
583248 CAATATTGGGGCATTTTAGAGCTCACTTCAGACAGATCCATGTGGTGTATTTTGAAGACTCATAT
1 CAATATTGGGGCATTTTAGAGCTCACTTCAGACAGATCCATGTGGTGTATTTTGAAGACTCATAT
583313 TAACAAGAAG
66 TAACAAGAAG
*
583323 CAATATTGGGTCATTTTAGAGCTCACTTCAGACAGATCCATGTGGTGTATTTTGAAGACTCATAT
1 CAATATTGGGGCATTTTAGAGCTCACTTCAGACAGATCCATGTGGTGTATTTTGAAGACTCATAT
583388 TAACAAGAAG
66 TAACAAGAAG
*
583398 CAAT-TTGGGTCATTTTAGAGCTCACTTCAGACAGATCCATGTGGTGTATTTTGAAGACTCATAT
1 CAATATTGGGGCATTTTAGAGCTCACTTCAGACAGATCCATGTGGTGTATTTTGAAGACTCATAT
583462 TAACAAGAAG
66 TAACAAGAAG
*
583472 CAATATTGGGGCATTTTAGAGCTCACTTCAGATAGATCCATGTGGTGTATTTTGAAGACTCATAT
1 CAATATTGGGGCATTTTAGAGCTCACTTCAGACAGATCCATGTGGTGTATTTTGAAGACTCATAT
583537 TAACAAGAAG
66 TAACAAGAAG
*
583547 CAATATTGGGTCATTTTAGAGCTCACTTCAGACAGATCCATGTGGTGTATTTTGAAGACTCATAT
1 CAATATTGGGGCATTTTAGAGCTCACTTCAGACAGATCCATGTGGTGTATTTTGAAGACTCATAT
583612 TAACAAGAAG
66 TAACAAGAAG
*
583622 CAATATTGGGTCATTTTAGAGCTCACTTCAGACAGATCCATGTGGTGTATTTTGAAGACTCATAT
1 CAATATTGGGGCATTTTAGAGCTCACTTCAGACAGATCCATGTGGTGTATTTTGAAGACTCATAT
583687 TAACAAGAAG
66 TAACAAGAAG
*
583697 CAATATTGGGGCATTTTAGAGCTCACTTCAGATAGATCCATGTGGTGTATTTTGAAGACTCATAT
1 CAATATTGGGGCATTTTAGAGCTCACTTCAGACAGATCCATGTGGTGTATTTTGAAGACTCATAT
583762 TAACAAGAAG
66 TAACAAGAAG
*
583772 CAATATTGGGGCATTTTAGAGCTCACTTCAGATAGATCCATGTGGTGTATTTTGAAGACTCATAT
1 CAATATTGGGGCATTTTAGAGCTCACTTCAGACAGATCCATGTGGTGTATTTTGAAGACTCATAT
583837 TAACAAGAAG
66 TAACAAGAAG
583847 CAAATATTGGGGCAT
1 C-AATATTGGGGCAT
583862 GCTGAAAACC
Statistics
Matches: 530, Mismatches: 7, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
74 74 0.14
75 443 0.84
76 13 0.02
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (75 bp):
CAATATTGGGGCATTTTAGAGCTCACTTCAGACAGATCCATGTGGTGTATTTTGAAGACTCATAT
TAACAAGAAG
Found at i:584006 original size:74 final size:74
Alignment explanation
Indices: 583854--584016 Score: 195
Period size: 74 Copynumber: 2.2 Consensus size: 74
583844 AAGCAAATAT
* * *
583854 TGGGGCATGCTGAAAACCCTTTTCAAACAGAATCAGAAATGTTGAAATATTCTGAATATTTATCA
1 TGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAACATTTATCA
583919 GCAAAATGC
66 GCAAAATGC
* * ** *
583928 TGGGGCATGCTGAAAACCCATTTCAATCAGAATCAGAACTGTTGATGCATTTTGAACACTTGTAT
1 TGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAACA-TT-TAT
* *
583993 TAGC-CAATG-
64 CAGCAAAATGC
584002 TGGGGGCATGCTGAA
1 T-GGGGCATGCTGAA
584017 GGCCTATATC
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
74 51 0.67
75 19 0.25
76 6 0.08
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.28
Consensus pattern (74 bp):
TGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAACATTTATCA
GCAAAATGC
Done.