Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr12
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: 39383930
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 780790 characters in sequence are not A, C, G, or T
File 15 of 126
Found at i:4323116 original size:120 final size:119
Alignment explanation
Indices: 4322811--4323267 Score: 717
Period size: 120 Copynumber: 3.8 Consensus size: 119
4322801 ATCATATTTA
*
4322811 AACATAATTATAATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTAT-ATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
4322876 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
65 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
*
4322931 AACATAA-T-TATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAAT
1 AACATAATTATATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAAT
* *
4322994 ATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTT
66 ATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
*
4323048 GAA-ATAATTAATATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAACAATTA
1 -AACATAATT-ATATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
* *** * *
4323112 ATATTCTTATATTAAGAGATCTCCAAA-C-TAATATATGATATTGTAAAATATAAATT
64 ATATTCTTATATGAATTTA-CT-CAAATCATAATATATGATACTATAAAATATAAATT
*
4323168 AACATAAATATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTA-TATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
4323233 TATTCTTATATGAATTTACTCAAATCATAATATAT
65 TATTCTTATATGAATTTACTCAAATCATAATATAT
4323268 NNNNNNNNNN
Statistics
Matches: 307, Mismatches: 20, Indels: 20
0.88 0.06 0.06
Matches are distributed among these distances:
117 108 0.35
118 8 0.03
119 7 0.02
120 177 0.58
121 3 0.01
122 4 0.01
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.42
Consensus pattern (119 bp):
AACATAATTATATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAAT
ATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
Found at i:4323206 original size:18 final size:17
Alignment explanation
Indices: 4323185--4323219 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
4323175 ATATTATTAA
*
4323185 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
4323203 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
4323220 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:4328150 original size:12 final size:12
Alignment explanation
Indices: 4328120--4328150 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
4328110 TGTACCCTTT
*
4328120 CACACGACCTAG
1 CACACGGCCTAG
4328132 CACACGGCCTAG
1 CACACGGCCTAG
4328144 CACACGG
1 CACACGG
4328151 GCGTGTGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.42, G:0.23, T:0.06
Consensus pattern (12 bp):
CACACGGCCTAG
Found at i:4336722 original size:23 final size:23
Alignment explanation
Indices: 4336696--4336741 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
4336686 ATATATAAAA
4336696 ATAATTCTTACA-AATTTAAATAT
1 ATAATT-TTACATAATTTAAATAT
* *
4336719 ATAATTTTATATATTTTAAATAT
1 ATAATTTTACATAATTTAAATAT
4336742 TAAAAAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (23 bp):
ATAATTTTACATAATTTAAATAT
Found at i:4340658 original size:56 final size:56
Alignment explanation
Indices: 4340591--4340759 Score: 266
Period size: 56 Copynumber: 3.0 Consensus size: 56
4340581 CGGTAACTAC
* *
4340591 TATTATCGTTATTTCATGGTTATATATGTTAAAGGCGCTATGTTAGAATGTTTGAT
1 TATTATTGTTATTTCATGGTTATATATGTTAAAGACGCTATGTTAGAATGTTTGAT
4340647 TATTATTGTTATTTCATGGTTATATATGTTAAAGACGCTATGTTAGAATGTTTGAT
1 TATTATTGTTATTTCATGGTTATATATGTTAAAGACGCTATGTTAGAATGTTTGAT
* * *
4340703 TATTATTATTATTTTTTCATGGTTATATATGTTAAAGACACTATGTTAGCATGTTTG
1 TATTATTGTTA---TTTCATGGTTATATATGTTAAAGACGCTATGTTAGAATGTTTG
4340760 CTTAAGAACT
Statistics
Matches: 105, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
56 64 0.61
59 41 0.39
ACGTcount: A:0.28, C:0.07, G:0.17, T:0.49
Consensus pattern (56 bp):
TATTATTGTTATTTCATGGTTATATATGTTAAAGACGCTATGTTAGAATGTTTGAT
Found at i:4344403 original size:16 final size:16
Alignment explanation
Indices: 4344382--4344438 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
4344372 TAATGGATAT
4344382 TGGGTTTTAATTTTAA
1 TGGGTTTTAATTTTAA
* *
4344398 TGGGTTTGGACTTTTAA
1 TGGGTTT-TAATTTTAA
*
4344415 -GGGTATTAAATTTTAA
1 TGGGT-TTTAATTTTAA
*
4344431 TGGATTTT
1 TGGGTTTT
4344439 TAAGTTTAGT
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
16 20 0.62
17 12 0.38
ACGTcount: A:0.25, C:0.02, G:0.23, T:0.51
Consensus pattern (16 bp):
TGGGTTTTAATTTTAA
Found at i:4353540 original size:15 final size:16
Alignment explanation
Indices: 4353520--4353550 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
4353510 GAAATTTTAA
4353520 AACCCAAAGT-AACCC
1 AACCCAAAGTCAACCC
4353535 AACCCAAAGTCAACCC
1 AACCCAAAGTCAACCC
4353551 GAAATCAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.45, C:0.42, G:0.06, T:0.06
Consensus pattern (16 bp):
AACCCAAAGTCAACCC
Found at i:4357247 original size:31 final size:31
Alignment explanation
Indices: 4357201--4357261 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
4357191 CTTAAAATTT
* *
4357201 AAACCCCAATGTGAGAATAATTGTCAAGTTC
1 AAACCCCAATATGAGAACAATTGTCAAGTTC
*
4357232 AAACCCCGATATGAGAACAATTGTCAAGTT
1 AAACCCCAATATGAGAACAATTGTCAAGTT
4357262 GAAGGGCTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (31 bp):
AAACCCCAATATGAGAACAATTGTCAAGTTC
Found at i:4358365 original size:15 final size:15
Alignment explanation
Indices: 4358341--4358374 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4358331 AACAATTACG
* *
4358341 ATAATGCGAGTAAAA
1 ATAATACGAGCAAAA
4358356 ATAATACGAGCAAAA
1 ATAATACGAGCAAAA
4358371 ATAA
1 ATAA
4358375 CAAAAAGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.09, G:0.15, T:0.18
Consensus pattern (15 bp):
ATAATACGAGCAAAA
Found at i:4364799 original size:15 final size:15
Alignment explanation
Indices: 4364779--4364810 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4364769 CTGCGACAAA
*
4364779 GACAACGACAACGAC
1 GACAACGACAAAGAC
4364794 GACAACGACAAAGAC
1 GACAACGACAAAGAC
4364809 GA
1 GA
4364811 GCTACTTCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.28, G:0.22, T:0.00
Consensus pattern (15 bp):
GACAACGACAAAGAC
Found at i:4372249 original size:4 final size:4
Alignment explanation
Indices: 4372240--4372264 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
4372230 GAGGGCTAAA
4372240 TCTT TCTT TCTT TCTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT T
4372265 TTATTTAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:4380434 original size:3 final size:3
Alignment explanation
Indices: 4380426--4380453 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
4380416 AATCATAAAA
4380426 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
4380454 GTTTGTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:4383512 original size:576 final size:575
Alignment explanation
Indices: 4382414--4383562 Score: 2244
Period size: 576 Copynumber: 2.0 Consensus size: 575
4382404 TCATCTAGGC
* *
4382414 GAATGCCATTGTCATGTTATGCAGTAAAATCTCCCAAACTTTACATGTCATTTGGGTCACAACAT
1 GAATGCCATTGTCATGTTATGCAATAAAATCTCCCAAACTTTACAAGTCATTTGGGTCACAACAT
4382479 GCAATACAAGTAGGGAAAACACAAAAGGGAGACAAAGAAAATATACCAAGAGAACAACTGCCATA
66 GCAATACAAGTAGGGAAAACACAAAAGGGAGACAAAGAAAATATACCAAGAGAACAACTGCCATA
*
4382544 ACAATATAGGCAAGGAGATATTAACCTGAAAAAGAAAAAAAAATAGCACGAGCTGCATTTACTAG
131 ACAATATAGGCAAGGAGATATTAACCTGAAAAAGAAAAAAAAATAGCACAAGCTGCATTTACTAG
4382609 ATAAAGTTCATCTCGTTAACGATTACCACAGCTGTACATGTCATCAAAATGAGAGAAAAGATGCA
196 ATAAAGTTCATCTCGTTAACGATTACCACAGCTGTACATGTCATCAAAATGAGAGAAAAGATGCA
4382674 ACAAAGAAAATTCTATATAAAATATGTGAAAAGATGTTCATATCATGACATCTTCATAGCTTTCC
261 ACAAAGAAAATTCTATATAAAATATGTGAAAAGATGTTCATATCATGACATCTTCATAGCTTTCC
4382739 ATTCCCTTGAAAGACTATCATATTTATCTCTAAAACTTCTACCCTTTTTGTAAAAAGGGTTCTTT
326 ATTCCCTTGAAAGACTATCATATTTATCTCTAAAACTTCTACCCTTTTTGTAAAAAGGGTTCTTT
4382804 AATTTCTCCATTGTCGAATCGTATATGCTAATTCTTTTATCAAGCATTGTTTCGACAAATCTTTT
391 AATTTCTCCATTGTCGAATCGTATATGCTAATTCTTTTATCAAGCATTGTTTCGACAAATCTTTT
* *
4382869 CACTTCTACTAACCTACCTAAGTTGCAAAGCCCAATGAGTAACTCATTAGCGCTTTCATCGAGCG
456 CACTTCTACTAACCTACCTAAATTGCAAAGCCCAATGAGTAACTCATTAGCGCTTTCATCAAGCG
4382934 TTGAGACATGATTCTCAACCATGTGATTCCACATATTAATTGCCATTTCGGGGGT
521 TTGAGACATGATTCTCAACCATGTGATTCCACATATTAATTGCCATTTCGGGGGT
4382989 GAATGCCATTGTCATGTTATGCAATAAAATCTCCCAAACTTTACAAGTCATTTGGGTCACAACAT
1 GAATGCCATTGTCATGTTATGCAATAAAATCTCCCAAACTTTACAAGTCATTTGGGTCACAACAT
4383054 GCAATACAAGTAGGGAAAACACAAAAGGGAGACAAAGAAAATATACCAAGAGAACAACTGCCATA
66 GCAATACAAGTAGGGAAAACACAAAAGGGAGACAAAGAAAATATACCAAGAGAACAACTGCCATA
4383119 ACAATATAGGCAAGGAGATATTAACCTGAAAAAGAAAAAAAAAATAGCACAAGCTGCATTTACTA
131 ACAATATAGGCAAGGAGATATTAACCTGAAAAAG-AAAAAAAAATAGCACAAGCTGCATTTACTA
4383184 GATAAAGTTCATCTCGTTAACGATTACCACAGCTGTACATGTCATCAAAATGAGAGAAAAGATGC
195 GATAAAGTTCATCTCGTTAACGATTACCACAGCTGTACATGTCATCAAAATGAGAGAAAAGATGC
4383249 AACAAAGAAAATTCTATATAAAATATGTGAAAAGATGTTCATATCATGACATCTTCATAGCTTTC
260 AACAAAGAAAATTCTATATAAAATATGTGAAAAGATGTTCATATCATGACATCTTCATAGCTTTC
4383314 CATTCCCTTGAAAGACTATCATATTTATCTCTAAAACTTCTACCCTTTTTGTAAAAAGGGTTCTT
325 CATTCCCTTGAAAGACTATCATATTTATCTCTAAAACTTCTACCCTTTTTGTAAAAAGGGTTCTT
4383379 TAATTTCTCCATTGTCGAATCGTATATGCTAATTCTTTTATCAAGCATTGTTTCGACAAATCTTT
390 TAATTTCTCCATTGTCGAATCGTATATGCTAATTCTTTTATCAAGCATTGTTTCGACAAATCTTT
4383444 TCACTTCTACTAACCTACCTAAATTGCAAAGCCCAATGAGTAACTCATTAGCGCTTTCATCAAGC
455 TCACTTCTACTAACCTACCTAAATTGCAAAGCCCAATGAGTAACTCATTAGCGCTTTCATCAAGC
4383509 GTTGAGACATGATTCTCAACCATGTGATTCCACATATTAATTGCCATTTCGGGG
520 GTTGAGACATGATTCTCAACCATGTGATTCCACATATTAATTGCCATTTCGGGG
4383563 TCATCGTTCT
Statistics
Matches: 568, Mismatches: 5, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
575 162 0.29
576 406 0.71
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (575 bp):
GAATGCCATTGTCATGTTATGCAATAAAATCTCCCAAACTTTACAAGTCATTTGGGTCACAACAT
GCAATACAAGTAGGGAAAACACAAAAGGGAGACAAAGAAAATATACCAAGAGAACAACTGCCATA
ACAATATAGGCAAGGAGATATTAACCTGAAAAAGAAAAAAAAATAGCACAAGCTGCATTTACTAG
ATAAAGTTCATCTCGTTAACGATTACCACAGCTGTACATGTCATCAAAATGAGAGAAAAGATGCA
ACAAAGAAAATTCTATATAAAATATGTGAAAAGATGTTCATATCATGACATCTTCATAGCTTTCC
ATTCCCTTGAAAGACTATCATATTTATCTCTAAAACTTCTACCCTTTTTGTAAAAAGGGTTCTTT
AATTTCTCCATTGTCGAATCGTATATGCTAATTCTTTTATCAAGCATTGTTTCGACAAATCTTTT
CACTTCTACTAACCTACCTAAATTGCAAAGCCCAATGAGTAACTCATTAGCGCTTTCATCAAGCG
TTGAGACATGATTCTCAACCATGTGATTCCACATATTAATTGCCATTTCGGGGGT
Found at i:4393217 original size:54 final size:54
Alignment explanation
Indices: 4393135--4393246 Score: 197
Period size: 54 Copynumber: 2.1 Consensus size: 54
4393125 GTCCCTGCAC
* *
4393135 GTCAACTATAGGTACACGTGGCACGCCACATGTAACTGTCTAGTTATTCCATCA
1 GTCAACTATAGGTACAAGTGGCACGCCACATGTAACAGTCTAGTTATTCCATCA
*
4393189 GTCAACTATAGGTACAATTGGCACGCCACATGTAACAGTCTAGTTATTCCATCA
1 GTCAACTATAGGTACAAGTGGCACGCCACATGTAACAGTCTAGTTATTCCATCA
4393243 GTCA
1 GTCA
4393247 GGATGAAGTT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (54 bp):
GTCAACTATAGGTACAAGTGGCACGCCACATGTAACAGTCTAGTTATTCCATCA
Found at i:4398526 original size:29 final size:29
Alignment explanation
Indices: 4398483--4398547 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
4398473 TTGGCCTCAC
* * * *
4398483 TTGATTCTTTTTAATAGTATAGGGACTAAA
1 TTGA-TCTATTTAATAATAGAGAGACTAAA
*
4398513 TTGATCTATTTAATAATAGAGAGACTAAT
1 TTGATCTATTTAATAATAGAGAGACTAAA
4398542 TTGATC
1 TTGATC
4398548 AATTCCCTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 26 0.87
30 4 0.13
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (29 bp):
TTGATCTATTTAATAATAGAGAGACTAAA
Found at i:4402859 original size:108 final size:108
Alignment explanation
Indices: 4402670--4402871 Score: 307
Period size: 108 Copynumber: 1.9 Consensus size: 108
4402660 TGGATTAAGA
* * * *
4402670 TTTAAGAGAATATTTGGCTATTTGGTTAAACGAAAAAAATCGGAACCCAGCACATTAGGGCACGT
1 TTTAAAAGAATATTTGGCTATTTGATCAAACGAAAAAAATCGAAACCCAGCACATTAGGGCACGT
* *
4402735 TTCTTCGAATTTCCAAACGCAAAATATTATCTTAACTTGAAAT
66 TTCTTCGAATCTCCAAACGCAAAACATTATCTTAACTTGAAAT
* * *
4402778 TTTAAAAGGATATTTGGCTATTTGATCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
1 TTTAAAAGAATATTTGGCTATTTGATCAAACGAAAAAAATCGAAACCCAGCACATTAGGGCACGT
4402843 TT-TCTCGAATCTCCAAACGCAAAACATTA
66 TTCT-TCGAATCTCCAAACGCAAAACATTA
4402872 CCTTTATTAT
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
107 1 0.01
108 83 0.99
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.28
Consensus pattern (108 bp):
TTTAAAAGAATATTTGGCTATTTGATCAAACGAAAAAAATCGAAACCCAGCACATTAGGGCACGT
TTCTTCGAATCTCCAAACGCAAAACATTATCTTAACTTGAAAT
Found at i:4403568 original size:15 final size:15
Alignment explanation
Indices: 4403542--4403577 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
4403532 AATATAAAGA
4403542 ACATAT-AAATATGT
1 ACATATAAAATATGT
*
4403556 ATATATAAAATATGT
1 ACATATAAAATATGT
4403571 ACATATA
1 ACATATA
4403578 TACGTAGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.36
Consensus pattern (15 bp):
ACATATAAAATATGT
Found at i:4404721 original size:11 final size:11
Alignment explanation
Indices: 4404694--4404732 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
4404684 AGATGAAAAG
*
4404694 AAAAAATCAAA
1 AAAAAAGCAAA
4404705 AGAAAAAGCAAA
1 A-AAAAAGCAAA
*
4404717 AAAAAAGGAAA
1 AAAAAAGCAAA
4404728 AAAAA
1 AAAAA
4404733 GCCCCCCTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.82, C:0.05, G:0.10, T:0.03
Consensus pattern (11 bp):
AAAAAAGCAAA
Found at i:4413438 original size:20 final size:20
Alignment explanation
Indices: 4413399--4413436 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4413389 TATTAGGGCT
4413399 TGAATTAGATAATTAGTTTC
1 TGAATTAGATAATTAGTTTC
*
4413419 TGAATTTGATAATT-GTTT
1 TGAATTAGATAATTAGTTT
4413437 TCATATTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.32, C:0.03, G:0.16, T:0.50
Consensus pattern (20 bp):
TGAATTAGATAATTAGTTTC
Found at i:4428970 original size:31 final size:31
Alignment explanation
Indices: 4428935--4428997 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
4428925 AAAAATTGTT
4428935 ATTGAACTATTCAAAAGTTTTCATTTAAGTC
1 ATTGAACTATTCAAAAGTTTTCATTTAAGTC
** * *
4428966 ATTGAACTATTTGACAGTTTTTATTTAAGTC
1 ATTGAACTATTCAAAAGTTTTCATTTAAGTC
4428997 A
1 A
4428998 CCGGGCCGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (31 bp):
ATTGAACTATTCAAAAGTTTTCATTTAAGTC
Found at i:4433147 original size:24 final size:23
Alignment explanation
Indices: 4433095--4433150 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
4433085 GCCCGGCCCG
*
4433095 ATTTTTAATAAACACAAAAAAAAT
1 ATTTTTAA-AAACAAAAAAAAAAT
*
4433119 A-TTTTAAAAATAAAAATAAAAAT
1 ATTTTTAAAAACAAAAA-AAAAAT
4433142 ATTTTTAAA
1 ATTTTTAAA
4433151 GTATTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 7 0.25
23 13 0.46
24 8 0.29
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (23 bp):
ATTTTTAAAAACAAAAAAAAAAT
Found at i:4440210 original size:24 final size:24
Alignment explanation
Indices: 4440179--4440230 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
4440169 TTCAAAAAAT
*
4440179 AATAAAAAATTCAAAATTCAAAAAA
1 AATAAAAAA-TAAAAATTCAAAAAA
4440204 AAT-AAAAATAAAAAGTTCATAAAAA
1 AATAAAAAATAAAAA-TTCA-AAAAA
4440229 AA
1 AA
4440231 GCATGAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 5 0.21
24 9 0.38
25 10 0.42
ACGTcount: A:0.73, C:0.06, G:0.02, T:0.19
Consensus pattern (24 bp):
AATAAAAAATAAAAATTCAAAAAA
Found at i:4443651 original size:235 final size:236
Alignment explanation
Indices: 4443240--4443690 Score: 645
Period size: 235 Copynumber: 1.9 Consensus size: 236
4443230 CAAGATATTA
*
4443240 AAAAAGGTTAAATTACTAAAGAAGCCCTTAAACTAGTTTTTTAAAAAAATAAGCCTCTAAACTTT
1 AAAAAGGTCAAATTACTAAAGAAGCCCTTAAACTAGTTTTTTAAAAAAATAAGCCTCTAAACTTT
* * *
4443305 TGTTGCAACTCAAATAAACCCTTATGTTTTGATTTGTATTTAAATTAGCTCTTAAATAATGATTT
66 TGTTGCAACTCAAATAAACCCGTATATTTTGATTTGTATTTAAATTAGCCCTTAAATAATGATTT
*
4443370 ATATTAAGAATTTTATTTAAGTTTAAACTAAAGGATAGAGGCTTATTTAGATACAAGTT-AAAGA
131 ATATTAAGAATTTTATTTAAGTATAAACTAAAGGATAGAGGCTTATTTAGATACAAGTTAAAAGA
4443434 TTAAGAGCTTATTTGGTTTTTAAGGGTTTATACAAATCATT
196 TTAAGAGCTTATTTGGTTTTTAAGGGTTTATACAAATCATT
* * * *
4443475 AAAAAGGTCAAATTACTACAGAAGCCCTTAAACTAGTTTTTT-TAAAAATATGCTTCTAAACTTT
1 AAAAAGGTCAAATTACTAAAGAAGCCCTTAAACTAGTTTTTTAAAAAAATAAGCCTCTAAAC-TT
* * * *
4443539 TTTTTGTAACTCAAATAAACCCGTATATTTTGTTTTGTTTTTAAATTAGCCCTTAAATAATGATT
65 TTGTTGCAACTCAAATAAACCCGTATATTTTGATTTGTATTTAAATTAGCCCTTAAATAATGATT
* * ** ** * * *
4443604 TATATTGAGAATTTTATTTAGGTATAAGTTGCAGTATAGATGCTTATTTGGATACAAGTTAAAAA
130 TATATTAAGAATTTTATTTAAGTATAAACTAAAGGATAGAGGCTTATTTAGATACAAGTT---AA
*
4443669 AAGATTAAGAGCTTCTTTGGTT
192 AAGATTAAGAGCTTATTTGGTT
4443691 ACCAATTAAA
Statistics
Matches: 188, Mismatches: 23, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
234 16 0.09
235 150 0.80
239 22 0.12
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (236 bp):
AAAAAGGTCAAATTACTAAAGAAGCCCTTAAACTAGTTTTTTAAAAAAATAAGCCTCTAAACTTT
TGTTGCAACTCAAATAAACCCGTATATTTTGATTTGTATTTAAATTAGCCCTTAAATAATGATTT
ATATTAAGAATTTTATTTAAGTATAAACTAAAGGATAGAGGCTTATTTAGATACAAGTTAAAAGA
TTAAGAGCTTATTTGGTTTTTAAGGGTTTATACAAATCATT
Found at i:4455591 original size:16 final size:16
Alignment explanation
Indices: 4455572--4455613 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
4455562 AAATTAAATA
4455572 AAATTTAAAATAATCC
1 AAATTTAAAATAATCC
* *
4455588 AAATTTATAATAATTC
1 AAATTTAAAATAATCC
*
4455604 GAATTTAAAA
1 AAATTTAAAA
4455614 ATTAAATTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (16 bp):
AAATTTAAAATAATCC
Found at i:4455719 original size:3 final size:3
Alignment explanation
Indices: 4455711--4455739 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4455701 GACAAATACA
4455711 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
4455740 GATGTTAATT
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):
ATT
Found at i:4465842 original size:31 final size:31
Alignment explanation
Indices: 4465804--4465871 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
4465794 AATCGGACTT
*
4465804 TAAAAAAATATT-AACAGTCCAATGACTTAAA
1 TAAAAAAAT-TTGAACAATCCAATGACTTAAA
* **
4465835 TAAAAAAATTTGAATAATTTAATGACTTAAA
1 TAAAAAAATTTGAACAATCCAATGACTTAAA
4465866 TAAAAA
1 TAAAAA
4465872 TTCTCAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.57, C:0.07, G:0.06, T:0.29
Consensus pattern (31 bp):
TAAAAAAATTTGAACAATCCAATGACTTAAA
Found at i:4465882 original size:31 final size:30
Alignment explanation
Indices: 4465824--4465888 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 30
4465814 TTAACAGTCC
*
4465824 AATGACTTAAATAAAAAAATTTGAATAATTT
1 AATGACTTAAAT-AAAAAATTTAAATAATTT
4465855 AATGACTTAAAT-AAAAATTCTCAAATAATTT
1 AATGACTTAAATAAAAAATT-T-AAATAATTT
4465886 AAT
1 AAT
4465889 AATATTTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 7 0.23
30 1 0.03
31 23 0.74
ACGTcount: A:0.54, C:0.06, G:0.05, T:0.35
Consensus pattern (30 bp):
AATGACTTAAATAAAAAATTTAAATAATTT
Found at i:4470123 original size:103 final size:103
Alignment explanation
Indices: 4469965--4470375 Score: 732
Period size: 103 Copynumber: 4.0 Consensus size: 103
4469955 CCAGTGATTC
* * *
4469965 GGGGAATCAGCACTTAGCAACCCCTTTCACATTCAAAGATATGGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
* *
4470030 ACCAATCATTCGGGGAATCAGCACTTAGCAACCCCTTG
66 ACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
4470068 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
4470133 ACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
66 ACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
4470171 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
4470236 ACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
66 ACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
* *
4470274 GGGGAATCAGCACTTAGCAACCCCCTTTATATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
* * *
4470339 ACCATTGAGTCGAGGAATCAGCACTTAGCAACCCCTT
66 ACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTT
4470376 CATATTCCAT
Statistics
Matches: 298, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 298 1.00
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.21
Consensus pattern (103 bp):
GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
ACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
Found at i:4476204 original size:46 final size:44
Alignment explanation
Indices: 4476152--4476239 Score: 140
Period size: 46 Copynumber: 2.0 Consensus size: 44
4476142 AGAACAGAAA
*
4476152 TGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGGGT
1 TGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAGACAGGGT
*
4476198 TGAGCCATGTAAGTCCATATTATATATGGCATTGGAGACAGG
1 TGAGCCATGTAAGTCCATATTAAATATGGCATTGGAGACAGG
4476240 AATAATTCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
44 19 0.47
46 21 0.52
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (44 bp):
TGAGCCATGTAAGTCCATATTAAATATGGCATTGGAGACAGGGT
Found at i:4476251 original size:44 final size:45
Alignment explanation
Indices: 4476145--4476278 Score: 135
Period size: 46 Copynumber: 3.0 Consensus size: 45
4476135 ACAGGACAGA
* * *
4476145 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATAAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
** * *
4476191 ACAGGGTTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATAAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
** * * *
4476235 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATAAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
4476279 CAGGGTATTG
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
44 35 0.49
45 1 0.01
46 36 0.50
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (45 bp):
ACAGGAATAAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:4480186 original size:103 final size:103
Alignment explanation
Indices: 4480028--4480335 Score: 526
Period size: 103 Copynumber: 3.0 Consensus size: 103
4480018 CCAGTGATTC
* * *
4480028 GGGGAATCAGCACTTAGCAACCCCTTTCACATTCAAAGATATGGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
* *
4480093 ACCAATCATTCGGGGAATCAGCACTTAGCAACCCCTTG
66 ACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
4480131 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
4480196 ACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
66 ACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
* *
4480234 GGGGAATCAGCACTTAGCAACCCCCTTTATATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
* * *
4480299 ACCATTGAGTCGAGGAATCAGCACTTAGCAACCCCTT
66 ACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTT
4480336 CATATTCCAT
Statistics
Matches: 195, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 195 1.00
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.21
Consensus pattern (103 bp):
GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
ACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
Found at i:4485456 original size:35 final size:38
Alignment explanation
Indices: 4485379--4485453 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 38
4485369 ATGTATATAG
4485379 ATATATATAGATATGTATATAAATTATAAAATATAAAAA
1 ATATATATAGATATGTATAT-AATTATAAAATATAAAAA
*
4485418 ATATATATA-AGTATGTATAT-A-TATAAATTATAAAAA
1 ATATATATAGA-TATGTATATAATTATAAAATATAAAAA
4485454 TATGTACGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
36 14 0.41
37 1 0.03
38 1 0.03
39 18 0.53
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.37
Consensus pattern (38 bp):
ATATATATAGATATGTATATAATTATAAAATATAAAAA
Found at i:4485480 original size:23 final size:21
Alignment explanation
Indices: 4485444--4485489 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
4485434 ATATATATAA
*
4485444 ATTATAAAAATATGTACGTAT
1 ATTATAAAAATATGCACGTAT
*
4485465 ATTATAAAAATGTATGCATGTAT
1 ATTATAAAAA--TATGCACGTAT
4485488 AT
1 AT
4485490 ACATAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
23 11 0.52
ACGTcount: A:0.46, C:0.04, G:0.11, T:0.39
Consensus pattern (21 bp):
ATTATAAAAATATGCACGTAT
Found at i:4489188 original size:27 final size:27
Alignment explanation
Indices: 4489146--4489206 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
4489136 GGGCAATAGC
4489146 TTCACATTGGTCGCGTATTGAGGAGGG
1 TTCACATTGGTCGCGTATTGAGGAGGG
*
4489173 TTCACATTGGTTGCGTATTGAGGAGGG
1 TTCACATTGGTCGCGTATTGAGGAGGG
4489200 TT-ACATT
1 TTCACATT
4489207 AAACTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 5 0.15
27 28 0.85
ACGTcount: A:0.20, C:0.13, G:0.33, T:0.34
Consensus pattern (27 bp):
TTCACATTGGTCGCGTATTGAGGAGGG
Found at i:4505811 original size:67 final size:67
Alignment explanation
Indices: 4505703--4505838 Score: 263
Period size: 67 Copynumber: 2.0 Consensus size: 67
4505693 AATCAATGAA
*
4505703 AAAATGTGTCATCAAATTTTGCAATGTCATAGAGAATAGATGTACCTGATACTAGCTCTCCTGAA
1 AAAATGTGTCATCAAATTTTGCAATGTCATAGAGAATAGATGTACCTGAAACTAGCTCTCCTGAA
4505768 GG
66 GG
4505770 AAAATGTGTCATCAAATTTTGCAATGTCATAGAGAATAGATGTACCTGAAACTAGCTCTCCTGAA
1 AAAATGTGTCATCAAATTTTGCAATGTCATAGAGAATAGATGTACCTGAAACTAGCTCTCCTGAA
4505835 GG
66 GG
4505837 AA
1 AA
4505839 GCTTTATTAC
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (67 bp):
AAAATGTGTCATCAAATTTTGCAATGTCATAGAGAATAGATGTACCTGAAACTAGCTCTCCTGAA
GG
Found at i:4534570 original size:438 final size:438
Alignment explanation
Indices: 4533755--4534630 Score: 1752
Period size: 438 Copynumber: 2.0 Consensus size: 438
4533745 CTTGCGAAGA
4533755 TTTCCAATGGGATCACCCCTGCTGAAACAAGGCAATCCACTGTCAAGCATAAGCAACACAGTGTT
1 TTTCCAATGGGATCACCCCTGCTGAAACAAGGCAATCCACTGTCAAGCATAAGCAACACAGTGTT
4533820 GATGATCCCATTCATATGTCGGCGAGCGGCAAGGTATCCCTTCACACACAAGCTGCAAGCATTTG
66 GATGATCCCATTCATATGTCGGCGAGCGGCAAGGTATCCCTTCACACACAAGCTGCAAGCATTTG
4533885 ACAAAGAAAAAACTCACATGACTTGGACAATAAAGATAAAATGAAAGGTATGCAGATAAGATAGA
131 ACAAAGAAAAAACTCACATGACTTGGACAATAAAGATAAAATGAAAGGTATGCAGATAAGATAGA
4533950 AGTATAAAATCGAGCAAAGAAGAAATCACCTTACAAAGTTGTCCCAGGTTTCACTTTTCATAACT
196 AGTATAAAATCGAGCAAAGAAGAAATCACCTTACAAAGTTGTCCCAGGTTTCACTTTTCATAACT
4534015 CCCGATGGGTCTAGTAATTGAGTCATCTCATGGCTCAACTTGAAATGTGCACTCTCGAACCGCAT
261 CCCGATGGGTCTAGTAATTGAGTCATCTCATGGCTCAACTTGAAATGTGCACTCTCGAACCGCAT
4534080 ATTTCCACCAGGTGATGTTTCCAAGATGAAACCAAAATCAATATGAACAAGCCTCCCGACACTGC
326 ATTTCCACCAGGTGATGTTTCCAAGATGAAACCAAAATCAATATGAACAAGCCTCCCGACACTGC
4534145 ATTGACATGCATATCACAGTGGTTGAGTTATATTAAAAATAAATAAAT
391 ATTGACATGCATATCACAGTGGTTGAGTTATATTAAAAATAAATAAAT
4534193 TTTCCAATGGGATCACCCCTGCTGAAACAAGGCAATCCACTGTCAAGCATAAGCAACACAGTGTT
1 TTTCCAATGGGATCACCCCTGCTGAAACAAGGCAATCCACTGTCAAGCATAAGCAACACAGTGTT
4534258 GATGATCCCATTCATATGTCGGCGAGCGGCAAGGTATCCCTTCACACACAAGCTGCAAGCATTTG
66 GATGATCCCATTCATATGTCGGCGAGCGGCAAGGTATCCCTTCACACACAAGCTGCAAGCATTTG
4534323 ACAAAGAAAAAACTCACATGACTTGGACAATAAAGATAAAATGAAAGGTATGCAGATAAGATAGA
131 ACAAAGAAAAAACTCACATGACTTGGACAATAAAGATAAAATGAAAGGTATGCAGATAAGATAGA
4534388 AGTATAAAATCGAGCAAAGAAGAAATCACCTTACAAAGTTGTCCCAGGTTTCACTTTTCATAACT
196 AGTATAAAATCGAGCAAAGAAGAAATCACCTTACAAAGTTGTCCCAGGTTTCACTTTTCATAACT
4534453 CCCGATGGGTCTAGTAATTGAGTCATCTCATGGCTCAACTTGAAATGTGCACTCTCGAACCGCAT
261 CCCGATGGGTCTAGTAATTGAGTCATCTCATGGCTCAACTTGAAATGTGCACTCTCGAACCGCAT
4534518 ATTTCCACCAGGTGATGTTTCCAAGATGAAACCAAAATCAATATGAACAAGCCTCCCGACACTGC
326 ATTTCCACCAGGTGATGTTTCCAAGATGAAACCAAAATCAATATGAACAAGCCTCCCGACACTGC
4534583 ATTGACATGCATATCACAGTGGTTGAGTTATATTAAAAATAAATAAAT
391 ATTGACATGCATATCACAGTGGTTGAGTTATATTAAAAATAAATAAAT
4534631 GTATAAAGTT
Statistics
Matches: 438, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
438 438 1.00
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (438 bp):
TTTCCAATGGGATCACCCCTGCTGAAACAAGGCAATCCACTGTCAAGCATAAGCAACACAGTGTT
GATGATCCCATTCATATGTCGGCGAGCGGCAAGGTATCCCTTCACACACAAGCTGCAAGCATTTG
ACAAAGAAAAAACTCACATGACTTGGACAATAAAGATAAAATGAAAGGTATGCAGATAAGATAGA
AGTATAAAATCGAGCAAAGAAGAAATCACCTTACAAAGTTGTCCCAGGTTTCACTTTTCATAACT
CCCGATGGGTCTAGTAATTGAGTCATCTCATGGCTCAACTTGAAATGTGCACTCTCGAACCGCAT
ATTTCCACCAGGTGATGTTTCCAAGATGAAACCAAAATCAATATGAACAAGCCTCCCGACACTGC
ATTGACATGCATATCACAGTGGTTGAGTTATATTAAAAATAAATAAAT
Found at i:4564535 original size:27 final size:28
Alignment explanation
Indices: 4564475--4564532 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
4564465 AGTAAGTGTG
* *
4564475 AAATTAGAAAATAGAAATATTAGGAATT
1 AAATTAGAAAATAAAAATATTAGGAAAT
*
4564503 AAATTAG-AAATAAAAATATTTAGTAAAT
1 AAATTAGAAAATAAAAATA-TTAGGAAAT
4564531 AA
1 AA
4564533 TTAAATATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.29
Consensus pattern (28 bp):
AAATTAGAAAATAAAAATATTAGGAAAT
Found at i:4567964 original size:13 final size:13
Alignment explanation
Indices: 4567946--4567977 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
4567936 TTTCCAGCAA
4567946 TTATGAATTTATT
1 TTATGAATTTATT
4567959 TTATGAATTTATT
1 TTATGAATTTATT
*
4567972 TGATGA
1 TTATGA
4567978 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:4568152 original size:50 final size:50
Alignment explanation
Indices: 4568072--4568256 Score: 361
Period size: 50 Copynumber: 3.7 Consensus size: 50
4568062 ATTTGGGTAA
*
4568072 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
4568122 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
4568172 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
4568222 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
4568257 TTTGGCATGT
Statistics
Matches: 134, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 134 1.00
ACGTcount: A:0.26, C:0.24, G:0.33, T:0.17
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:4573664 original size:43 final size:43
Alignment explanation
Indices: 4573551--4573678 Score: 177
Period size: 43 Copynumber: 3.0 Consensus size: 43
4573541 ATATCCCAAT
* * * * *
4573551 TTGGCAC-CATAGTGCATCATCGGATAAACTGAAGGAAATATA
1 TTGGCACACATAGTGCATCATCGGACAAGCCGAAGCAATTATA
4573593 TTGGCACACATAGTGCATCATCGGACAAGCCGAAGCAATTATA
1 TTGGCACACATAGTGCATCATCGGACAAGCCGAAGCAATTATA
* * *
4573636 TTGGCACACACAGTGCATCATCGGACAAGCCAAATCAATTATA
1 TTGGCACACATAGTGCATCATCGGACAAGCCGAAGCAATTATA
4573679 CTAGCACATA
Statistics
Matches: 77, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
42 7 0.09
43 70 0.91
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (43 bp):
TTGGCACACATAGTGCATCATCGGACAAGCCGAAGCAATTATA
Found at i:4573699 original size:43 final size:43
Alignment explanation
Indices: 4573596--4573699 Score: 127
Period size: 43 Copynumber: 2.4 Consensus size: 43
4573586 AAATATATTG
* * * * *
4573596 GCACACATAGTGCATCATCGGACAAGCCGAAGCAATTATATTG
1 GCACACACACTGCATCATCGGACAAGCCAAAGCAATTATACTA
* *
4573639 GCACACACAGTGCATCATCGGACAAGCCAAATCAATTATACTA
1 GCACACACACTGCATCATCGGACAAGCCAAAGCAATTATACTA
* *
4573682 GCACATACACTGTATCAT
1 GCACACACACTGCATCAT
4573700 TGGATGAATC
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 53 1.00
ACGTcount: A:0.37, C:0.26, G:0.16, T:0.21
Consensus pattern (43 bp):
GCACACACACTGCATCATCGGACAAGCCAAAGCAATTATACTA
Found at i:4584895 original size:16 final size:16
Alignment explanation
Indices: 4584874--4584909 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4584864 CCATAAAATG
*
4584874 ATTAAAAATAATAAAA
1 ATTAAAAAAAATAAAA
*
4584890 ATTAAAAAAAATTAAA
1 ATTAAAAAAAATAAAA
4584906 ATTA
1 ATTA
4584910 CATCAACTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
ATTAAAAAAAATAAAA
Found at i:4584949 original size:17 final size:18
Alignment explanation
Indices: 4584921--4584969 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
4584911 ATCAACTTAT
4584921 TAAAACTATAAAAAAT-TA
1 TAAAA-TATAAAAAATCTA
4584939 TAAAATAT-AAAAATCTA
1 TAAAATATAAAAAATCTA
4584956 -ATAAATATAAAAAA
1 TA-AAATATAAAAAA
4584970 AAGTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 7 0.25
17 11 0.39
18 10 0.36
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (18 bp):
TAAAATATAAAAAATCTA
Found at i:4585049 original size:10 final size:10
Alignment explanation
Indices: 4585036--4585105 Score: 58
Period size: 10 Copynumber: 7.4 Consensus size: 10
4585026 TTTAAAAAGA
4585036 ATAAAAAATT
1 ATAAAAAATT
4585046 ATAAAAAA-T
1 ATAAAAAATT
*
4585055 AT-TAAAA-T
1 ATAAAAAATT
* **
4585063 ATTAAAAACG
1 ATAAAAAATT
*
4585073 ATATAAAATT
1 ATAAAAAATT
4585083 AT-AAAAATT
1 ATAAAAAATT
*
4585092 ATAAAAAATC
1 ATAAAAAATT
4585102 ATAA
1 ATAA
4585106 TAATTTGAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
8 7 0.15
9 15 0.31
10 26 0.54
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:4585051 original size:9 final size:9
Alignment explanation
Indices: 4585039--4585098 Score: 59
Period size: 9 Copynumber: 6.6 Consensus size: 9
4585029 AAAAAGAATA
4585039 AAAAATTAT
1 AAAAATTAT
*
4585048 AAAAAATAT
1 AAAAATTAT
*
4585057 TAAAA-TATT
1 AAAAATTA-T
**
4585066 AAAAACGAT
1 AAAAATTAT
4585075 ATAAAATTAT
1 A-AAAATTAT
4585085 AAAAATTAT
1 AAAAATTAT
4585094 AAAAA
1 AAAAA
4585099 ATCATAATAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
8 2 0.05
9 32 0.76
10 8 0.19
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (9 bp):
AAAAATTAT
Found at i:4585052 original size:19 final size:19
Alignment explanation
Indices: 4585028--4585105 Score: 63
Period size: 19 Copynumber: 4.2 Consensus size: 19
4585018 TAGAATTCTT
4585028 TAAAAAGAATAAAAAATTA
1 TAAAAAGAATAAAAAATTA
*
4585047 TAAAAA-ATATTAAAATATTA
1 TAAAAAGA-A-TAAAAAATTA
* *
4585067 -AAAACG-ATATAAAATTA
1 TAAAAAGAATAAAAAATTA
** *
4585084 TAAAAATTATAAAAAATCA
1 TAAAAAGAATAAAAAATTA
4585103 TAA
1 TAA
4585106 TAATTTGAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
17 8 0.17
18 6 0.13
19 23 0.50
20 9 0.20
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.27
Consensus pattern (19 bp):
TAAAAAGAATAAAAAATTA
Found at i:4585058 original size:39 final size:38
Alignment explanation
Indices: 4584999--4585089 Score: 96
Period size: 37 Copynumber: 2.3 Consensus size: 38
4584989 AAACTTATTT
* * *
4584999 AAAATTTTAAAAAATGTATTAGAATTCTTTAAAAA-GAATAA
1 AAAATTATAAAAAA-GTATTA-AAAT-ATTAAAAACG-ATAA
*
4585040 AAAATTATAAAAAA-TATTAAAATATTAAAAACGATAT
1 AAAATTATAAAAAAGTATTAAAATATTAAAAACGATAA
4585077 AAAATTATAAAAA
1 AAAATTATAAAAA
4585090 TTATAAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
37 23 0.51
38 4 0.09
39 5 0.11
41 13 0.29
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (38 bp):
AAAATTATAAAAAAGTATTAAAATATTAAAAACGATAA
Found at i:4585081 original size:37 final size:37
Alignment explanation
Indices: 4585027--4585098 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
4585017 TTAGAATTCT
*
4585027 TTAAAAAGAATAAAAAATTATAAAAAATATTAAAATA
1 TTAAAAAGAATAAAAAATTATAAAAAATATAAAAATA
* *
4585064 TTAAAAACG-ATATAAAATTATAAAAATTATAAAAA
1 TTAAAAA-GAATAAAAAATTATAAAAAATATAAAAA
4585099 ATCATAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 30 0.97
38 1 0.03
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (37 bp):
TTAAAAAGAATAAAAAATTATAAAAAATATAAAAATA
Found at i:4585094 original size:17 final size:17
Alignment explanation
Indices: 4585030--4585097 Score: 66
Period size: 18 Copynumber: 3.8 Consensus size: 17
4585020 GAATTCTTTA
*
4585030 AAAAGAATAAAAAATTAT
1 AAAA-AATATAAAATTAT
4585048 AAAAAATATTAAAA-TATT
1 AAAAAATA-TAAAATTA-T
4585066 AAAAACGATATAAAATTAT
1 AAAAA--ATATAAAATTAT
*
4585085 AAAAATTATAAAA
1 AAAAAATATAAAA
4585098 AATCATAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
17 13 0.30
18 14 0.33
19 11 0.26
20 5 0.12
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.26
Consensus pattern (17 bp):
AAAAAATATAAAATTAT
Found at i:4585931 original size:17 final size:18
Alignment explanation
Indices: 4585895--4585935 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
4585885 ATGTTTTTAA
*
4585895 AAAATATTTAATATATAT
1 AAAATATTTAATAAATAT
4585913 AAAATATTT-ATAAATAT
1 AAAATATTTAATAAATAT
4585930 AAAATA
1 AAAATA
4585936 AATGATGCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAATATTTAATAAATAT
Found at i:4585980 original size:22 final size:21
Alignment explanation
Indices: 4585892--4585982 Score: 57
Period size: 22 Copynumber: 4.2 Consensus size: 21
4585882 TTAATGTTTT
4585892 TAAAAAATAT-T-T-AATATA
1 TAAAAAATATCTATAAATATA
* *
4585910 TATAAAATATTTATAAATATA
1 TAAAAAATATCTATAAATATA
*
4585931 -AAATAAATGATGCTA-AAATTTTAAA
1 TAAA-AAAT-AT-CTATAAA---TATA
4585956 TAAAAAATATCTATAAATTATA
1 TAAAAAATATCTATAAA-TATA
4585978 TAAAA
1 TAAAA
4585983 TACTTATCAA
Statistics
Matches: 57, Mismatches: 5, Indels: 18
0.71 0.06 0.22
Matches are distributed among these distances:
18 9 0.16
19 1 0.02
20 3 0.05
21 10 0.18
22 14 0.25
23 5 0.09
24 5 0.09
25 7 0.12
26 3 0.05
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
TAAAAAATATCTATAAATATA
Found at i:4586851 original size:18 final size:20
Alignment explanation
Indices: 4586811--4586859 Score: 61
Period size: 18 Copynumber: 2.6 Consensus size: 20
4586801 AATAAAGAAA
4586811 ATAAAAATAAA-AAGATGTT
1 ATAAAAATAAATAAGATGTT
4586830 -TAAAAATAAATAA-AT-TT
1 ATAAAAATAAATAAGATGTT
*
4586847 ATAAAAAGAAATA
1 ATAAAAATAAATA
4586860 TTAACCTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 2 0.07
18 23 0.85
19 2 0.07
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (20 bp):
ATAAAAATAAATAAGATGTT
Found at i:4592008 original size:13 final size:13
Alignment explanation
Indices: 4591990--4592046 Score: 60
Period size: 13 Copynumber: 4.1 Consensus size: 13
4591980 CAATTCGGCT
4591990 GAAGGAGAAGAAA
1 GAAGGAGAAGAAA
4592003 GAAGGAGAAGAAA
1 GAAGGAGAAGAAA
**
4592016 GAAAAAGAAAGAAAA
1 GAAGGAG-AAG-AAA
4592031 GGAAAGGAGAAGAAA
1 -G-AAGGAGAAGAAA
4592046 G
1 G
4592047 GAAAGGAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
13 18 0.50
14 4 0.11
15 6 0.17
16 4 0.11
17 4 0.11
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (13 bp):
GAAGGAGAAGAAA
Found at i:4592035 original size:20 final size:21
Alignment explanation
Indices: 4592012--4592094 Score: 82
Period size: 20 Copynumber: 4.0 Consensus size: 21
4592002 AGAAGGAGAA
4592012 GAAA-GAAAAAGAAAGAAAAG
1 GAAAGGAAAAAGAAAGAAAAG
* *
4592032 GAAAGG-AGAAGAAAGGAAAG
1 GAAAGGAAAAAGAAAGAAAAG
**
4592052 GAAATGAGAAAAAG-AAGAGGGAG
1 GAAA-G-GAAAAAGAAAGA-AAAG
4592075 GAAAGGAAAAAGAAAGAAAA
1 GAAAGGAAAAAGAAAGAAAA
4592095 AATAAGGAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
20 20 0.41
21 10 0.20
22 9 0.18
23 10 0.20
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (21 bp):
GAAAGGAAAAAGAAAGAAAAG
Found at i:4592104 original size:11 final size:11
Alignment explanation
Indices: 4592010--4592104 Score: 53
Period size: 10 Copynumber: 9.0 Consensus size: 11
4592000 AAAGAAGGAG
4592010 AAGAAA-GAAA
1 AAGAAAGGAAA
4592020 AAGAAA-GAAA
1 AAGAAAGGAAA
* *
4592030 AGGAAAGG-AG
1 AAGAAAGGAAA
4592040 AAGAAAGG-AA
1 AAGAAAGGAAA
*
4592050 AGGAAATGAGAAA
1 AAGAAA-G-GAAA
*
4592063 AAGAAGAGG--G
1 AAGAA-AGGAAA
*
4592073 AGGAAAGGAAA
1 AAGAAAGGAAA
4592084 AAGAAA-GAAA
1 AAGAAAGGAAA
4592094 AA-ATAAGGAAA
1 AAGA-AAGGAAA
4592105 GGTATTTTTT
Statistics
Matches: 66, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
9 4 0.06
10 41 0.62
11 11 0.17
12 2 0.03
13 7 0.11
14 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (11 bp):
AAGAAAGGAAA
Found at i:4592578 original size:153 final size:154
Alignment explanation
Indices: 4592357--4592862 Score: 759
Period size: 153 Copynumber: 3.3 Consensus size: 154
4592347 TGAAAATAAG
* * * * * *
4592357 AAAAATACGAATAAAGGGCCAAAATAAAGGTTTTTGTAGTAAATTTATATAAAACATACACTAAA
1 AAAAATACGAACAAATGGCCGAAATAAAGGTTTTT-TACTAAATTTATTTAAAACACACACTAAA
* *
4592422 TTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATACGAAAATAATATATT
65 TTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAAGAAAATACGAAAATAGTATATT
4592487 TTTTGAAAGTAATAAAATCCGGGAA
130 TTTTGAAAGTAATAAAATCCGGGAA
*
4592512 AAAAATACGAACAAA-GGCCGAAATAAGGGTTTTTTACTAAATTTATTTAAAACACACACTAAAT
1 AAAAATACGAACAAATGGCCGAAATAAAGGTTTTTTACTAAATTTATTTAAAACACACACTAAAT
* *
4592576 TAATACATTTCAAACATATTGTACTAAAATAATGTAAAATCAGAAAAT-CAGAAAATAGTATATT
66 TAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAAGAAAATAC-GAAAATAGTATATT
***
4592640 TTTTGAAAGTAATAAAATTTTGG-A
130 TTTTGAAAGTAATAAAATCCGGGAA
* * *
4592664 AAAAATACGAACAAATGGCCGAAATAAAGGTTTTTTACTAAATTTATTTAAAAAACACAATTAAT
1 AAAAATACGAACAAATGGCCGAAATAAAGGTTTTTTACTAAATTTATTTAAAACACACACTAAAT
* *
4592729 TAATACATTTCAAACATAATGTACTAAAATAATATAAAATTAGAAAATTA-GAAAATAGTATATT
66 TAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAAGAAAA-TACGAAAATAGTATATT
4592793 TTTTGAAAGTAATAAAATCCGGGAA
130 TTTTGAAAGTAATAAAATCCGGGAA
* * *
4592818 AAAAATATGAGCAAATGGCCGAAATAAGGGTTTTTTACTAAATTT
1 AAAAATACGAACAAATGGCCGAAATAAAGGTTTTTTACTAAATTT
4592863 GTTTTGAAGT
Statistics
Matches: 320, Mismatches: 26, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
152 17 0.05
153 228 0.71
154 61 0.19
155 14 0.04
ACGTcount: A:0.50, C:0.09, G:0.11, T:0.30
Consensus pattern (154 bp):
AAAAATACGAACAAATGGCCGAAATAAAGGTTTTTTACTAAATTTATTTAAAACACACACTAAAT
TAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAAGAAAATACGAAAATAGTATATTT
TTTGAAAGTAATAAAATCCGGGAA
Found at i:4596080 original size:39 final size:40
Alignment explanation
Indices: 4596020--4596120 Score: 113
Period size: 40 Copynumber: 2.6 Consensus size: 40
4596010 CCACTAATCC
** *
4596020 TAATAACTAACACA-A-TAATAA-TAGTTTTTTACTCAAAA
1 TAATAACTAACA-ATAGTAATAATTAGGGTTTTACTAAAAA
4596058 TAAT-ACTAACTAATAGTAATAATTAGGGTTTTACTAAAAA
1 TAATAACTAAC-AATAGTAATAATTAGGGTTTTACTAAAAA
*
4596098 TAATAACTAACAATAAT-ATAATT
1 TAATAACTAACAATAGTAATAATT
4596121 TAAAAACTAA
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
37 7 0.13
38 6 0.11
39 12 0.22
40 23 0.43
41 6 0.11
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.35
Consensus pattern (40 bp):
TAATAACTAACAATAGTAATAATTAGGGTTTTACTAAAAA
Found at i:4596147 original size:23 final size:23
Alignment explanation
Indices: 4596102--4596148 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
4596092 TAAAAATAAT
*
4596102 AACTAACAATAATATAATTTAAA
1 AACTAACAATAATATAATCTAAA
*
4596125 AACTAACAATCATACTAA-CTAAA
1 AACTAACAATAATA-TAATCTAAA
4596148 A
1 A
4596149 TAATAATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.60, C:0.15, G:0.00, T:0.26
Consensus pattern (23 bp):
AACTAACAATAATATAATCTAAA
Found at i:4596439 original size:9 final size:9
Alignment explanation
Indices: 4596425--4596454 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
4596415 CACCACCTTT
*
4596425 TTCTTCTTC
1 TTCTTCTCC
4596434 TTCTTCTCC
1 TTCTTCTCC
4596443 TTCTTCTCC
1 TTCTTCTCC
4596452 TTC
1 TTC
4596455 AGCCGAACTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (9 bp):
TTCTTCTCC
Found at i:4596658 original size:10 final size:10
Alignment explanation
Indices: 4596631--4596674 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
4596621 ATAAAAAAAG
4596631 TTATATTATTT
1 TTATATT-TTT
*
4596642 TGATATTTTT
1 TTATATTTTT
*
4596652 TTTTATTTTT
1 TTATATTTTT
*
4596662 TTATATTATT
1 TTATATTTTT
4596672 TTA
1 TTA
4596675 GTAAAAAAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
10 22 0.79
11 6 0.21
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (10 bp):
TTATATTTTT
Found at i:4598216 original size:42 final size:42
Alignment explanation
Indices: 4598157--4598238 Score: 164
Period size: 42 Copynumber: 2.0 Consensus size: 42
4598147 CAAAGACAGA
4598157 TACAAGAATTGCAGAGGCTTCAAATTCGGGATCAAGAACATC
1 TACAAGAATTGCAGAGGCTTCAAATTCGGGATCAAGAACATC
4598199 TACAAGAATTGCAGAGGCTTCAAATTCGGGATCAAGAACA
1 TACAAGAATTGCAGAGGCTTCAAATTCGGGATCAAGAACA
4598239 GCTCGCTATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.21
Consensus pattern (42 bp):
TACAAGAATTGCAGAGGCTTCAAATTCGGGATCAAGAACATC
Found at i:4603094 original size:21 final size:21
Alignment explanation
Indices: 4603068--4603108 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
4603058 TTTTGTTCAG
4603068 TGTTGTTTACT-TCTATTTTGT
1 TGTTGTTTACTATC-ATTTTGT
4603089 TGTTGTTTACTATCATTTTG
1 TGTTGTTTACTATCATTTTG
4603109 CTATTATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.12, C:0.10, G:0.15, T:0.63
Consensus pattern (21 bp):
TGTTGTTTACTATCATTTTGT
Found at i:4607290 original size:10 final size:10
Alignment explanation
Indices: 4607277--4607302 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
4607267 TAATTCTTAA
4607277 TAATTTAATG
1 TAATTTAATG
4607287 TAATTTAATG
1 TAATTTAATG
4607297 TAATTT
1 TAATTT
4607303 GAGATTTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (10 bp):
TAATTTAATG
Found at i:4609887 original size:51 final size:51
Alignment explanation
Indices: 4609832--4609935 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
4609822 TCAGCTAACG
4609832 CTCCAGTTATGTATGTGCTACCGAATGACTCTTCTGTCCCCCCTGATGGCC
1 CTCCAGTTATGTATGTGCTACCGAATGACTCTTCTGTCCCCCCTGATGGCC
4609883 CTCCAGTTATGTATGTGCTACCGAATGACTCTTCTGTCCCCCCTGATGGCC
1 CTCCAGTTATGTATGTGCTACCGAATGACTCTTCTGTCCCCCCTGATGGCC
4609934 CT
1 CT
4609936 AATACGGTGG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.15, C:0.34, G:0.19, T:0.32
Consensus pattern (51 bp):
CTCCAGTTATGTATGTGCTACCGAATGACTCTTCTGTCCCCCCTGATGGCC
Found at i:4609990 original size:48 final size:48
Alignment explanation
Indices: 4609925--4610078 Score: 245
Period size: 48 Copynumber: 3.2 Consensus size: 48
4609915 TCTGTCCCCC
* * * *
4609925 CTGATGGCCCTAATACGGTGGTTTCTCGTGCTCCTCTTCCTGTCGGTG
1 CTGATGGCCCTACTACGGTGGTTTATCGTGCTCCTCCTCATGTCGGTG
4609973 CTGATGGCCCTACTACGGTGGTTTATCGTGCTCCTCCTCATGTCGGTG
1 CTGATGGCCCTACTACGGTGGTTTATCGTGCTCCTCCTCATGTCGGTG
* * *
4610021 CTGATGGCCCTACTACGTTGGTTTATCGCGCTCTTCCTCATGTCGGTG
1 CTGATGGCCCTACTACGGTGGTTTATCGTGCTCCTCCTCATGTCGGTG
4610069 CTGATGGCCC
1 CTGATGGCCC
4610079 GCATACCTTC
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 99 1.00
ACGTcount: A:0.10, C:0.30, G:0.27, T:0.34
Consensus pattern (48 bp):
CTGATGGCCCTACTACGGTGGTTTATCGTGCTCCTCCTCATGTCGGTG
Found at i:4610105 original size:96 final size:96
Alignment explanation
Indices: 4609925--4610105 Score: 202
Period size: 96 Copynumber: 1.9 Consensus size: 96
4609915 TCTGTCCCCC
* * * * * *
4609925 CTGATGGCCCTAATACGGTGGTTTCTCGTGCTCCTCTTCCTGTCGGTGCTGATGGCCCTACTACG
1 CTGATGGCCCTAATACGGTGGTTTATCGCGCTCCTCCTCATGTCGGTGCTGATGGCCCCACTACC
* * * * *
4609990 GTGGTTTATCGTGCTCCTCCTCATGTCGGTG
66 GTCGTTGATCCTCCCCCTCCTCATGTCGGTG
* * *
4610021 CTGATGGCCCTACTACGTTGGTTTATCGCGCTCTTCCTCATGTCGGTGCTGATGGCCCGCA-TAC
1 CTGATGGCCCTAATACGGTGGTTTATCGCGCTCCTCCTCATGTCGGTGCTGATGGCCC-CACTAC
* *
4610085 CTTCGTTGCTCCTCCCCCTCC
65 CGTCGTTGATCCTCCCCCTCC
4610106 AGCGGCTCGA
Statistics
Matches: 68, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
96 67 0.99
97 1 0.01
ACGTcount: A:0.09, C:0.33, G:0.24, T:0.33
Consensus pattern (96 bp):
CTGATGGCCCTAATACGGTGGTTTATCGCGCTCCTCCTCATGTCGGTGCTGATGGCCCCACTACC
GTCGTTGATCCTCCCCCTCCTCATGTCGGTG
Found at i:4611937 original size:38 final size:39
Alignment explanation
Indices: 4611895--4612015 Score: 110
Period size: 38 Copynumber: 3.1 Consensus size: 39
4611885 ACTAACACAA
* *
4611895 TAACAATAATAATT-GTTTTATACTGAAATAAT-ACTAAC
1 TAACAATAATAATTAGGTTT-TACTAAAATAATAACTAAC
4611933 TAACAATAATAATTAGGGTTTTACTAAAATAATAACTAACC
1 TAACAATAATAATTA-GGTTTTACTAAAATAATAACTAA-C
* * *
4611974 ATAATAATAAT-ATTA-GTTTT-TTAACAATAAT-ACTAAG
1 -TAACAATAATAATTAGGTTTTACTAA-AATAATAACTAAC
4612011 TAACA
1 TAACA
4612016 TCTAAACCCT
Statistics
Matches: 71, Mismatches: 6, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
36 4 0.06
38 22 0.31
39 22 0.31
40 9 0.13
41 5 0.07
42 9 0.13
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.36
Consensus pattern (39 bp):
TAACAATAATAATTAGGTTTTACTAAAATAATAACTAAC
Found at i:4612847 original size:52 final size:52
Alignment explanation
Indices: 4612769--4612870 Score: 195
Period size: 52 Copynumber: 2.0 Consensus size: 52
4612759 TTTGTCAAAG
4612769 GGAGAGATTATTGAAGCAATTTTTGAGTAACACCTGAATTAAGGATAACTGT
1 GGAGAGATTATTGAAGCAATTTTTGAGTAACACCTGAATTAAGGATAACTGT
*
4612821 GGAGAGATTATTGAAGCAATTTTTGAGTAACACCTGCATTAAGGATAACT
1 GGAGAGATTATTGAAGCAATTTTTGAGTAACACCTGAATTAAGGATAACT
4612871 AGTTGTGGCA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (52 bp):
GGAGAGATTATTGAAGCAATTTTTGAGTAACACCTGAATTAAGGATAACTGT
Found at i:4618538 original size:8 final size:8
Alignment explanation
Indices: 4618527--4618565 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
4618517 ATAAAATGAC
4618527 AATAATAT
1 AATAATAT
*
4618535 AATAAAAT
1 AATAATAT
4618543 AATAAATAT
1 AAT-AATAT
4618552 AATAATA-
1 AATAATAT
4618559 AATAATA
1 AATAATA
4618566 ACAATTCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
7 7 0.25
8 14 0.50
9 7 0.25
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (8 bp):
AATAATAT
Found at i:4618561 original size:19 final size:17
Alignment explanation
Indices: 4618530--4618566 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 17
4618520 AAATGACAAT
4618530 AATATAATAAAATAATA
1 AATATAATAAAATAATA
4618547 AATATAATAATAAATAATA
1 AATATAAT-A-AAATAATA
4618566 A
1 A
4618567 CAATTCAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 1 0.06
19 9 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AATATAATAAAATAATA
Found at i:4618616 original size:3 final size:3
Alignment explanation
Indices: 4618527--4618605 Score: 56
Period size: 3 Copynumber: 25.3 Consensus size: 3
4618517 ATAAAATGAC
*
4618527 AAT AAT -AT AAT AA- AAT AAT AA- ATAT AAT AAT AAAT AAT AAC AATT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT -AAT AAT AAT AA-T
* *
4618572 CAATT AAT AAT ACT ATAT AAT AAT GAT AAT AAT A
1 -AA-T AAT AAT AAT A-AT AAT AAT AAT AAT AAT A
4618606 GTGAAATAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
2 5 0.08
3 45 0.73
4 8 0.13
5 4 0.06
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4619039 original size:29 final size:30
Alignment explanation
Indices: 4618990--4619049 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
4618980 ATCTCAAAAC
*
4618990 TATACATAAACTTTGATTTTG-TGCAATTT
1 TATACATAAAATTTGATTTTGATGCAATTT
*
4619019 TATACATGAAAATTTGA-TTTGATTCAATTT
1 TATACAT-AAAATTTGATTTTGATGCAATTT
4619049 T
1 T
4619050 CACAAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.48
Consensus pattern (30 bp):
TATACATAAAATTTGATTTTGATGCAATTT
Found at i:4621464 original size:26 final size:26
Alignment explanation
Indices: 4621435--4621516 Score: 119
Period size: 26 Copynumber: 3.0 Consensus size: 26
4621425 TATGCATTTC
4621435 TATAAAATTACATTTTTATAACTTTT
1 TATAAAATTACATTTTTATAACTTTT
*
4621461 TATAAAACTACATTTTTATAACTTTTT
1 TATAAAATTACATTTTTATAAC-TTTT
*
4621488 ACTATAAAATTACATTTTTATATCTTTT
1 --TATAAAATTACATTTTTATAACTTTT
4621516 T
1 T
4621517 TACGAATTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
26 22 0.44
27 4 0.08
28 4 0.08
29 20 0.40
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.54
Consensus pattern (26 bp):
TATAAAATTACATTTTTATAACTTTT
Found at i:4621503 original size:29 final size:28
Alignment explanation
Indices: 4621431--4621516 Score: 131
Period size: 29 Copynumber: 3.1 Consensus size: 28
4621421 AAATTATGCA
4621431 TTTCTATAAAATTACATTTTTATAAC-T
1 TTTCTATAAAATTACATTTTTATAACTT
*
4621458 TTT-TATAAAACTACATTTTTATAACTT
1 TTTCTATAAAATTACATTTTTATAACTT
*
4621485 TTTACTATAAAATTACATTTTTATATCTT
1 TTT-CTATAAAATTACATTTTTATAACTT
4621514 TTT
1 TTT
4621517 TACGAATTAT
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
26 21 0.40
27 7 0.13
29 25 0.47
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (28 bp):
TTTCTATAAAATTACATTTTTATAACTT
Found at i:4624529 original size:29 final size:29
Alignment explanation
Indices: 4624498--4624554 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
4624488 TAAGTAAATA
4624498 AAAAGAAAAAGA-AACAAAA-GAAGAACAG
1 AAAAGAAAAAGAGAACAAAACGAA-AACAG
*
4624526 AAAAGAAACAGAGAACAAAACGAAAACAG
1 AAAAGAAAAAGAGAACAAAACGAAAACAG
4624555 GGGAAGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 11 0.42
29 12 0.46
30 3 0.12
ACGTcount: A:0.72, C:0.11, G:0.18, T:0.00
Consensus pattern (29 bp):
AAAAGAAAAAGAGAACAAAACGAAAACAG
Found at i:4624550 original size:22 final size:22
Alignment explanation
Indices: 4624504--4624551 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
4624494 AATAAAAAGA
*
4624504 AAAAGAAACAAAAGAAGAACAG
1 AAAAGAAACAAAACAAGAACAG
4624526 AAAAGAAACAGAGAACAA-AAC-G
1 AAAAGAAACA-A-AACAAGAACAG
4624548 AAAA
1 AAAA
4624552 CAGGGGAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 15 0.65
23 4 0.17
24 4 0.17
ACGTcount: A:0.73, C:0.10, G:0.17, T:0.00
Consensus pattern (22 bp):
AAAAGAAACAAAACAAGAACAG
Found at i:4625232 original size:24 final size:23
Alignment explanation
Indices: 4625205--4625251 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
4625195 TAATCATGAG
4625205 ACATTT-AAAGTAAGGTAAGTAATA
1 ACATTTGAAAGTAA-GTAAG-AATA
*
4625229 ACATTTGAAATTAAGTAAGAATA
1 ACATTTGAAAGTAAGTAAGAATA
4625252 TGTGTGAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 11 0.52
25 6 0.29
ACGTcount: A:0.51, C:0.04, G:0.15, T:0.30
Consensus pattern (23 bp):
ACATTTGAAAGTAAGTAAGAATA
Found at i:4625724 original size:12 final size:12
Alignment explanation
Indices: 4625707--4625732 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4625697 AGAAAGAATG
4625707 TATGAATTAAAT
1 TATGAATTAAAT
4625719 TATGAATTAAAT
1 TATGAATTAAAT
4625731 TA
1 TA
4625733 GTATATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (12 bp):
TATGAATTAAAT
Found at i:4627763 original size:24 final size:25
Alignment explanation
Indices: 4627711--4627757 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
4627701 TGGCTCTCGT
**
4627711 GAGCTTCCCGTTATATAGTTCTTGC
1 GAGCTTCCCGTTATATAACTCTTGC
4627736 GAGCTTCCCGTTAT-TAACTCTT
1 GAGCTTCCCGTTATATAACTCTT
4627758 CGGAGCATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.40
Consensus pattern (25 bp):
GAGCTTCCCGTTATATAACTCTTGC
Found at i:4627861 original size:26 final size:26
Alignment explanation
Indices: 4627832--4627960 Score: 111
Period size: 26 Copynumber: 5.0 Consensus size: 26
4627822 CCTGATATAT
4627832 GGCTCTTCGTGAGCTTTCCGATTAAA
1 GGCTCTTCGTGAGCTTTCCGATTAAA
* *
4627858 GGCTCTTTGTGAGC-TTCTCGATTAAT
1 GGCTCTTCGTGAGCTTTC-CGATTAAA
* ** *
4627884 GGCTCTCCAAG-GCTTTTCGATTAAA
1 GGCTCTTCGTGAGCTTTCCGATTAAA
* * * *
4627909 TGCTCTTTCATGAGCTTCCCGATTAAT
1 GGCTC-TTCGTGAGCTTTCCGATTAAA
* *
4627936 GGCTCTTCG-AAGCTTCCCGATTAAA
1 GGCTCTTCGTGAGCTTTCCGATTAAA
4627961 TTCTCTTTCA
Statistics
Matches: 81, Mismatches: 18, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
25 30 0.37
26 36 0.44
27 15 0.19
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.36
Consensus pattern (26 bp):
GGCTCTTCGTGAGCTTTCCGATTAAA
Found at i:4627886 original size:52 final size:52
Alignment explanation
Indices: 4627830--4628002 Score: 206
Period size: 52 Copynumber: 3.3 Consensus size: 52
4627820 ATCCTGATAT
* * *
4627830 ATGGCTCTTCGTGAGCTTTCCGATTAAAGGCTCTTT-GTGAGCTTCTCGATTA
1 ATGGCTCTTCG-GAGCTTTCCGATTAAATGCTCTTTCATGAGCTTCCCGATTA
** *
4627882 ATGGCTC-TCCAAGGCTTTTCGATTAAATGCTCTTTCATGAGCTTCCCGATTA
1 ATGGCTCTTCGGA-GCTTTCCGATTAAATGCTCTTTCATGAGCTTCCCGATTA
* * * *
4627934 ATGGCTCTTCGAAGCTTCCCGATTAAATTCTCTTTCATGAACTTCCCGATTA
1 ATGGCTCTTCGGAGCTTTCCGATTAAATGCTCTTTCATGAGCTTCCCGATTA
* *
4627986 ATGGCTATCCGGAGCTT
1 ATGGCTCTTCGGAGCTT
4628003 CTAAATATTG
Statistics
Matches: 104, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
50 1 0.01
51 22 0.21
52 77 0.74
53 4 0.04
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.36
Consensus pattern (52 bp):
ATGGCTCTTCGGAGCTTTCCGATTAAATGCTCTTTCATGAGCTTCCCGATTA
Found at i:4627955 original size:25 final size:25
Alignment explanation
Indices: 4627830--4627991 Score: 100
Period size: 26 Copynumber: 6.2 Consensus size: 25
4627820 ATCCTGATAT
* *
4627830 ATGGCTCTTCGTGAGCTTTCCGATTA
1 ATGGCTCTTCG-AAGCTTCCCGATTA
* * * *
4627856 AAGGCTCTTTGTGAGCTTCTCGATTA
1 ATGGCTCTTCG-AAGCTTCCCGATTA
* **
4627882 ATGGCTC-TCCAAGGCTTTTCGATTAA
1 ATGGCTCTTCGAA-GCTTCCCGATT-A
4627908 AT-GCTCTTTC-ATGAGCTTCCCGATTA
1 ATGGCTC-TTCGA--AGCTTCCCGATTA
4627934 ATGGCTCTTCGAAGCTTCCCGATTAA
1 ATGGCTCTTCGAAGCTTCCCGATT-A
*
4627960 AT-TCTCTTTCATGAA-CTTCCCGATTA
1 ATGGCTC-TTC--GAAGCTTCCCGATTA
4627986 ATGGCT
1 ATGGCT
4627992 ATCCGGAGCT
Statistics
Matches: 110, Mismatches: 13, Indels: 25
0.74 0.09 0.17
Matches are distributed among these distances:
24 1 0.01
25 30 0.27
26 47 0.43
27 28 0.25
28 4 0.04
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.37
Consensus pattern (25 bp):
ATGGCTCTTCGAAGCTTCCCGATTA
Found at i:4637356 original size:17 final size:17
Alignment explanation
Indices: 4637334--4637367 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4637324 AATTATGTAT
4637334 ATTTTAGATGTTATATA
1 ATTTTAGATGTTATATA
*
4637351 ATTTTAGATTTTATATA
1 ATTTTAGATGTTATATA
4637368 GTCAAAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (17 bp):
ATTTTAGATGTTATATA
Found at i:4637688 original size:23 final size:25
Alignment explanation
Indices: 4637658--4637708 Score: 70
Period size: 23 Copynumber: 2.1 Consensus size: 25
4637648 AAAAAATGAA
4637658 AATGAAAAT-GAAAATC-CAAAAAT
1 AATGAAAATAGAAAATCTCAAAAAT
*
4637681 AATGAAAATAAGAGAATCTCAAAAAT
1 AATGAAAAT-AGAAAATCTCAAAAAT
4637707 AA
1 AA
4637709 AAAAAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 9 0.38
25 6 0.25
26 9 0.38
ACGTcount: A:0.65, C:0.08, G:0.10, T:0.18
Consensus pattern (25 bp):
AATGAAAATAGAAAATCTCAAAAAT
Found at i:4643687 original size:10 final size:11
Alignment explanation
Indices: 4643669--4643695 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
4643659 AAAAGAGAAT
4643669 GGAAAAAAAAA
1 GGAAAAAAAAA
4643680 GGAAAAAAAAA
1 GGAAAAAAAAA
4643691 GGAAA
1 GGAAA
4643696 GTTAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (11 bp):
GGAAAAAAAAA
Found at i:4644797 original size:7 final size:7
Alignment explanation
Indices: 4644785--4644818 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
4644775 AATAAATATA
4644785 TATTTTT
1 TATTTTT
4644792 TA-TTTT
1 TATTTTT
4644798 TATTTTT
1 TATTTTT
4644805 TATTTTT
1 TATTTTT
*
4644812 TAATTTT
1 TATTTTT
4644819 AAAATACTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (7 bp):
TATTTTT
Found at i:4644801 original size:13 final size:13
Alignment explanation
Indices: 4644785--4644811 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4644775 AATAAATATA
4644785 TATTTTTTATTTT
1 TATTTTTTATTTT
4644798 TATTTTTTATTTT
1 TATTTTTTATTTT
4644811 T
1 T
4644812 TAATTTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TATTTTTTATTTT
Found at i:4645157 original size:42 final size:42
Alignment explanation
Indices: 4645109--4645194 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
4645099 AGAGGGAAGA
4645109 TAGTTTACAGCTATAGCTATGATGATATAATTAAGCAATTAT
1 TAGTTTACAGCTATAGCTATGATGATATAATTAAGCAATTAT
*
4645151 TAGTTTACAGCTATGGCTATGATGATATAATTAAGCAATTAT
1 TAGTTTACAGCTATAGCTATGATGATATAATTAAGCAATTAT
4645193 TA
1 TA
4645195 CACTTTGAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.38
Consensus pattern (42 bp):
TAGTTTACAGCTATAGCTATGATGATATAATTAAGCAATTAT
Found at i:4646342 original size:41 final size:41
Alignment explanation
Indices: 4646291--4646373 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
4646281 GCCACTCCCA
*
4646291 TGGCGATTTTATACCTTGTATCCCGTGTCAACAAGCATGGC
1 TGGCGATTTTATACCATGTATCCCGTGTCAACAAGCATGGC
4646332 TGGCGATTTTATACCATGTATCCCGTGTCAACAAGCATGGC
1 TGGCGATTTTATACCATGTATCCCGTGTCAACAAGCATGGC
4646373 T
1 T
4646374 CTCTATGTAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (41 bp):
TGGCGATTTTATACCATGTATCCCGTGTCAACAAGCATGGC
Found at i:4650255 original size:3 final size:3
Alignment explanation
Indices: 4650247--4650310 Score: 56
Period size: 3 Copynumber: 21.0 Consensus size: 3
4650237 ATTATTTAGT
* * * * * *
4650247 TTA TTA TTA TTA TTA TTA GTG TTA GTG TTA TTA TCA TTA TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
4650295 TTA TTAA CTA TTA TTA
1 TTA TT-A TTA TTA TTA
4650311 ATTTTATTTT
Statistics
Matches: 46, Mismatches: 14, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
3 44 0.96
4 2 0.04
ACGTcount: A:0.31, C:0.05, G:0.06, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:4651122 original size:108 final size:110
Alignment explanation
Indices: 4650929--4651239 Score: 428
Period size: 112 Copynumber: 2.8 Consensus size: 110
4650919 TTTCTAATTG
* *
4650929 AGGCAATATTTAGCGTTTGGAAATTCGAGAAAACGTGTGCCCTAAGGTGCTGGGTGTCGATTTTT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAAC--GTGCCCTAAGGTGCTGGGTGTCGATTTTT
* * * *
4650994 CTCGTTCAACAAAATAGCTAAATATCC-TTT-CAAAATTTTAAAATA
64 CTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAAAATTCAAAATA
* * * *
4651039 AGGCAATGTTTTGCGTTTGAAAATTCGAGGAAACATGCCCTAAGGTGTTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCT
* *
4651104 CGTTCAACCAAATGGCTAAATATCCTTTTAAAAAAAATTCGAAATA
66 CGTTCAACCAAATAGCTAAATATCCTTTT-AAAAAAATTCAAAATA
*
4651150 AGGCAATGTTTTGCATTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTC
1 AGGCAATGTTTTGCGTTT-GGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTC
* * *
4651215 TCATTTAACCAAATAGCAAAATATC
65 TCGTTCAACCAAATAGCTAAATATC
4651240 ATCTTGAATT
Statistics
Matches: 176, Mismatches: 21, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
108 52 0.30
109 3 0.02
110 30 0.17
111 28 0.16
112 63 0.36
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (110 bp):
AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCT
CGTTCAACCAAATAGCTAAATATCCTTTTAAAAAAATTCAAAATA
Found at i:4652937 original size:40 final size:40
Alignment explanation
Indices: 4652882--4652962 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
4652872 ATTTTCATTG
* *
4652882 CGGAGTGTACTGTTGTCAAAGTTTCCAAAATTAAAATATA
1 CGGAGTGTACGGTTGTCAAAGTTGCCAAAATTAAAATATA
4652922 CGGAGTGTACGGTTGTCAAAGTTGCCAAAATTAAAATATA
1 CGGAGTGTACGGTTGTCAAAGTTGCCAAAATTAAAATATA
4652962 C
1 C
4652963 TTGAAAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.30
Consensus pattern (40 bp):
CGGAGTGTACGGTTGTCAAAGTTGCCAAAATTAAAATATA
Found at i:4661776 original size:24 final size:24
Alignment explanation
Indices: 4661739--4661786 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
4661729 CTTAGTACAG
*
4661739 TTTTAGAGAGTTCTATCTACATTT
1 TTTTAGAGAGTTCTATCTAAATTT
4661763 TTTTAGAGTA-TTCTATCTAAATTT
1 TTTTAGAG-AGTTCTATCTAAATTT
4661787 AGAAATACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 21 0.95
25 1 0.05
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.52
Consensus pattern (24 bp):
TTTTAGAGAGTTCTATCTAAATTT
Found at i:4668892 original size:31 final size:29
Alignment explanation
Indices: 4668822--4668895 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
4668812 GGCTCAGGTT
* *
4668822 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTCAAATGTA
* **
4668851 ACGTTTTAGTCACTTATGTTATCACGTTGTA
1 ACATTTTAGTCACTTATGTT-TCA-AATGTA
4668882 ACATTTTAGTCACT
1 ACATTTTAGTCACT
4668896 GAGCCGTTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 19 0.51
30 2 0.05
31 16 0.43
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.46
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTCAAATGTA
Found at i:4671263 original size:19 final size:21
Alignment explanation
Indices: 4671229--4671267 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
4671219 TACATTATTT
4671229 TTTTAAATTATTATCAATATG
1 TTTTAAATTATTATCAATATG
4671250 TTTT-AATT-TTATCAATAT
1 TTTTAAATTATTATCAATAT
4671268 TACTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
20 4 0.22
21 4 0.22
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (21 bp):
TTTTAAATTATTATCAATATG
Found at i:4675570 original size:2 final size:2
Alignment explanation
Indices: 4675558--4675589 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
4675548 GTGAGCATAA
4675558 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT A
4675590 GACAGACATG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4679217 original size:16 final size:16
Alignment explanation
Indices: 4679198--4679249 Score: 58
Period size: 15 Copynumber: 3.4 Consensus size: 16
4679188 TTATATTATA
4679198 AAAATATTATTAAATT
1 AAAATATTATTAAATT
4679214 AAAATATTA-TAAATT
1 AAAATATTATTAAATT
4679229 ---ATATTAATTAAAATT
1 AAAATATT-ATT-AAATT
4679244 AAAATA
1 AAAATA
4679250 ATATATTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
12 5 0.17
13 1 0.03
14 1 0.03
15 11 0.37
16 9 0.30
18 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAAATATTATTAAATT
Found at i:4679233 original size:25 final size:26
Alignment explanation
Indices: 4679190--4679242 Score: 74
Period size: 24 Copynumber: 2.1 Consensus size: 26
4679180 TTCTTGATTT
4679190 ATATTATAAAAATATTATTAAATTAAA
1 ATATTATAAAAATATTATT-AATTAAA
*
4679217 ATATTAT-AAATTA-TATTAATTAAA
1 ATATTATAAAAATATTATTAATTAAA
4679241 AT
1 AT
4679243 TAAAATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 9 0.36
25 4 0.16
26 5 0.20
27 7 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
ATATTATAAAAATATTATTAATTAAA
Found at i:4679245 original size:30 final size:27
Alignment explanation
Indices: 4679190--4679254 Score: 85
Period size: 30 Copynumber: 2.3 Consensus size: 27
4679180 TTCTTGATTT
4679190 ATATTATAAAAATATTATTAAATTAAA
1 ATATTATAAAAATATTATTAAATTAAA
*
4679217 ATATTATAAATTATATTAATTAAAATTAAA
1 ATATTATAAA-AATATT-ATT-AAATTAAA
*
4679247 ATAATATA
1 ATATTATA
4679255 TTATAGGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 10 0.30
28 5 0.15
29 3 0.09
30 15 0.45
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
ATATTATAAAAATATTATTAAATTAAA
Found at i:4679394 original size:3 final size:3
Alignment explanation
Indices: 4679386--4679432 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
4679376 GTGAATAAAA
* *
4679386 TAT TAT TA- TAT AAT TAT TAT AAT ATAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT
4679431 TA
1 TA
4679433 ACTAATGCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 34 0.89
4 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:4679422 original size:19 final size:22
Alignment explanation
Indices: 4679384--4679432 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 22
4679374 TTGTGAATAA
4679384 AATATTATTATATAATTATTAT
1 AATATTATTATATAATTATTAT
4679406 AATA-TATTAT-T-ATTATTAT
1 AATATTATTATATAATTATTAT
4679425 --TATTATTA
1 AATATTATTA
4679433 ACTAATGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 2 0.08
18 5 0.19
19 8 0.31
20 1 0.04
21 6 0.23
22 4 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
AATATTATTATATAATTATTAT
Found at i:4680170 original size:23 final size:22
Alignment explanation
Indices: 4680143--4680226 Score: 86
Period size: 21 Copynumber: 4.0 Consensus size: 22
4680133 GGCCTTGCCG
* *
4680143 ATCAGGCACTTTATGTGTCGTAT
1 ATCAGGCACCTCATGTGTCGT-T
*
4680166 ATCAGGCACCTCGTGTGTCG-T
1 ATCAGGCACCTCATGTGTCGTT
*
4680187 ATCAGGCACCTCGTG-GTCGTT
1 ATCAGGCACCTCATGTGTCGTT
*
4680208 -TCAGGCA-CTTATGTGTCGT
1 ATCAGGCACCTCATGTGTCGT
4680227 ATACTGATCA
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
19 4 0.07
20 16 0.30
21 17 0.31
23 17 0.31
ACGTcount: A:0.17, C:0.24, G:0.26, T:0.33
Consensus pattern (22 bp):
ATCAGGCACCTCATGTGTCGTT
Found at i:4680211 original size:20 final size:21
Alignment explanation
Indices: 4680156--4680228 Score: 87
Period size: 20 Copynumber: 3.5 Consensus size: 21
4680146 AGGCACTTTA
4680156 TGTGTCGTATATCAGGCACCTCG
1 TGTGTCG--TATCAGGCACCTCG
4680179 TGTGTCGTATCAGGCACCTCG
1 TGTGTCGTATCAGGCACCTCG
* **
4680200 TG-GTCGTTTCAGGCA-CTTA
1 TGTGTCGTATCAGGCACCTCG
4680219 TGTGTCGTAT
1 TGTGTCGTAT
4680229 ACTGATCAGG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
19 4 0.09
20 18 0.40
21 16 0.36
23 7 0.16
ACGTcount: A:0.15, C:0.23, G:0.27, T:0.34
Consensus pattern (21 bp):
TGTGTCGTATCAGGCACCTCG
Found at i:4681331 original size:12 final size:13
Alignment explanation
Indices: 4681310--4681341 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
4681300 TATCATATAT
4681310 ATAT-ATAGATAG
1 ATATGATAGATAG
4681322 ATA-GATAGATAG
1 ATATGATAGATAG
4681334 ATATGATA
1 ATATGATA
4681342 TGACCTACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 14 0.78
13 4 0.22
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (13 bp):
ATATGATAGATAG
Found at i:4687178 original size:5 final size:5
Alignment explanation
Indices: 4687163--4687204 Score: 77
Period size: 5 Copynumber: 8.6 Consensus size: 5
4687153 CATAAATCAG
4687163 TAATA -AATA TAATA TAATA TAATA TAATA TAATA TAATA TAA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAA
4687205 AACAAAATTC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 4 0.11
5 32 0.89
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
TAATA
Found at i:4687881 original size:27 final size:27
Alignment explanation
Indices: 4687860--4687934 Score: 125
Period size: 27 Copynumber: 2.8 Consensus size: 27
4687850 CGCCAACGGG
*
4687860 ATTGGCGGCACCAAAGGTGCCAAAGCC
1 ATTGGCGGCACCAATGGTGCCAAAGCC
4687887 ATTGGCGGCACCAATGGTGCCAATA-CC
1 ATTGGCGGCACCAATGGTGCCAA-AGCC
4687914 ATTGGCGGCACCAATGGTGCC
1 ATTGGCGGCACCAATGGTGCC
4687935 GTATTGATTG
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
27 45 0.98
28 1 0.02
ACGTcount: A:0.25, C:0.29, G:0.29, T:0.16
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAAAGCC
Found at i:4688123 original size:19 final size:21
Alignment explanation
Indices: 4688085--4688123 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
4688075 AATAATTGAT
*
4688085 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
4688106 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
4688124 TTGTTTTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:4688196 original size:3 final size:3
Alignment explanation
Indices: 4688190--4688230 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
4688180 ATTATTATTA
4688190 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
4688231 AGTATTAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:4689045 original size:18 final size:18
Alignment explanation
Indices: 4689022--4689059 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
4689012 GGTTGGTGGT
4689022 GAAGAAGAAGGTGCTGGC
1 GAAGAAGAAGGTGCTGGC
4689040 GAAGAAGAAGGTGCTGGC
1 GAAGAAGAAGGTGCTGGC
4689058 GA
1 GA
4689060 TCATTGGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.45, T:0.11
Consensus pattern (18 bp):
GAAGAAGAAGGTGCTGGC
Found at i:4699171 original size:19 final size:19
Alignment explanation
Indices: 4699149--4699211 Score: 62
Period size: 16 Copynumber: 3.4 Consensus size: 19
4699139 TAATAGTCTT
4699149 AATAATTTTTAATTTTTAA
1 AATAATTTTTAATTTTTAA
*
4699168 AATAATTTTTATAAATTTTT-G
1 AATAA-TTTT-T-AATTTTTAA
4699189 AAT-A-TTTTAATTTTTAA
1 AATAATTTTTAATTTTTAA
4699206 AA-AATT
1 AATAATT
4699212 AATTGATAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
16 7 0.19
17 4 0.11
18 4 0.11
19 5 0.14
20 5 0.14
21 4 0.11
22 7 0.19
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
AATAATTTTTAATTTTTAA
Found at i:4699171 original size:28 final size:28
Alignment explanation
Indices: 4699122--4699198 Score: 68
Period size: 28 Copynumber: 2.6 Consensus size: 28
4699112 ATATTTTTTT
*
4699122 ATAATTTTTATACTTTTT--AATAGTCTTA
1 ATAATTTTTA-A-TTTTTAAAATAATCTTA
* *
4699150 ATAATTTTTAATTTTTAAAATAATTTTT
1 ATAATTTTTAATTTTTAAAATAATCTTA
4699178 ATAAATTTTTGAATATTTTAA
1 AT-AATTTTT-AAT-TTTTAA
4699199 TTTTTAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
26 5 0.12
27 1 0.02
28 19 0.46
29 7 0.17
30 3 0.07
31 6 0.15
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (28 bp):
ATAATTTTTAATTTTTAAAATAATCTTA
Found at i:4699717 original size:26 final size:26
Alignment explanation
Indices: 4699661--4699730 Score: 74
Period size: 26 Copynumber: 2.8 Consensus size: 26
4699651 TAACATGAAA
4699661 ATTTATTTTTCATTTATTTTATCTCT
1 ATTTATTTTTCATTTATTTTATCTCT
* * * *
4699687 CTTTATTTTTC-TTTCTTATTCTCTTT
1 ATTTATTTTTCATTTATT-TTATCTCT
4699713 ATTTATTTTT--TTTATTTT
1 ATTTATTTTTCATTTATTTT
4699731 TTTTGAAGCT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
24 2 0.05
25 10 0.27
26 25 0.68
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.74
Consensus pattern (26 bp):
ATTTATTTTTCATTTATTTTATCTCT
Found at i:4699727 original size:22 final size:22
Alignment explanation
Indices: 4699672--4699728 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
4699662 TTTATTTTTC
*
4699672 ATTTATTTTATCTCTCTTTATTT
1 ATTTTTTTTAT-TCTCTTTATTT
*
4699695 -TTCTTTCTTATTCTCTTTATTT
1 ATT-TTTTTTATTCTCTTTATTT
4699717 ATTTTTTTTATT
1 ATTTTTTTTATT
4699729 TTTTTTGAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 21 0.72
23 8 0.28
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.74
Consensus pattern (22 bp):
ATTTTTTTTATTCTCTTTATTT
Found at i:4704633 original size:2 final size:2
Alignment explanation
Indices: 4704628--4704654 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4704618 TATATATATA
4704628 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
4704655 AACTCTGGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:4704867 original size:7 final size:7
Alignment explanation
Indices: 4704855--4704892 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
4704845 TTGATGATCA
4704855 ATTGAAT
1 ATTGAAT
4704862 ATTGAAT
1 ATTGAAT
4704869 ATTGAAT
1 ATTGAAT
4704876 ATTGAAT
1 ATTGAAT
4704883 ATTGAAT
1 ATTGAAT
4704890 ATT
1 ATT
4704893 AAGTAATGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (7 bp):
ATTGAAT
Found at i:4705231 original size:43 final size:43
Alignment explanation
Indices: 4705177--4705424 Score: 300
Period size: 43 Copynumber: 5.8 Consensus size: 43
4705167 AAAACCGGCT
*
4705177 TTTAGCGGCGCTTTTCCCACAAACGCTGCTAAAGACCAAGACC
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGACC
* * *
4705220 TTTAGCAGCGCTTTTACCACAAACGCCGTTAAAGACTC-AGACC
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAC-CAAGACC
*
4705263 TTTAGCGGCGCTTTTCCTACAAACGCCGCTAAAGACCAAGACC
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGACC
* * *
4705306 TTTAGCGGCGCTTTTCCTACAAATGCCGCTAAAGACCACGACC
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGACC
* * ** * * *
4705349 TTTAGTGGCACTTTTATCACAAACGCCGCTATAGATCATGACC
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGACC
* * ** *
4705392 TTTAGCGGCACTTCTAGCAAAAACGCCGCTAAA
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAA
4705425 AACATAATCT
Statistics
Matches: 179, Mismatches: 24, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
42 1 0.01
43 177 0.99
44 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (43 bp):
TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGACC
Found at i:4705416 original size:129 final size:129
Alignment explanation
Indices: 4705177--4705424 Score: 338
Period size: 129 Copynumber: 1.9 Consensus size: 129
4705167 AAAACCGGCT
* *
4705177 TTTAGCGGCGCTTTTCCCACAAACGCTGCTAAAGACCAAGACCTTTAGCAGCGCTTTTACCACAA
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGACCTTTAGCAGCACTTTTACCACAA
* * * *
4705242 ACGCCGTTAAAGACTCAGACCTTTAGCGGCGCTTTTCCTACAAACGCCGCTAAAGACCAAGACC
66 ACGCCGCTAAAGACTCAGACCTTTAGCGGCACTTTACCTAAAAACGCCGCTAAAGACCAAGACC
* * * ** *
4705306 TTTAGCGGCGCTTTTCCTACAAATGCCGCTAAAGACCACGACCTTTAGTGGCACTTTTATCACAA
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGACCTTTAGCAGCACTTTTACCACAA
* *
4705371 ACGCCGCTATAGA-TCATGACCTTTAGCGGCACTTCTAGC-AAAAACGCCGCTAAA
66 ACGCCGCTAAAGACTCA-GACCTTTAGCGGCACTT-TACCTAAAAACGCCGCTAAA
4705425 AACATAATCT
Statistics
Matches: 103, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
128 3 0.03
129 98 0.95
130 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (129 bp):
TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGACCTTTAGCAGCACTTTTACCACAA
ACGCCGCTAAAGACTCAGACCTTTAGCGGCACTTTACCTAAAAACGCCGCTAAAGACCAAGACC
Found at i:4708017 original size:20 final size:19
Alignment explanation
Indices: 4707981--4708032 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
4707971 TTTTAAATAA
4707981 ATAAT-TTTTGAAAAATTA-
1 ATAATATTTT-AAAAATTAG
4707999 AGTAATATTTTAAAGAATTAG
1 A-TAATATTTTAAA-AATTAG
4708020 ATAA-ATTTTAAAA
1 ATAATATTTTAAAA
4708033 TTTTTATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
18 2 0.07
19 15 0.50
20 12 0.40
21 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (19 bp):
ATAATATTTTAAAAATTAG
Found at i:4708961 original size:29 final size:29
Alignment explanation
Indices: 4708893--4708971 Score: 72
Period size: 29 Copynumber: 2.7 Consensus size: 29
4708883 TAGTTAATCT
* *
4708893 AAACCATAAACCATAAA-CCTAAACTCTA
1 AAACCCTAAACCATAAACCCTAAACACTA
*
4708921 AAACCCTAAAACCATAAACCCTTAACAC-A
1 AAACCCT-AAACCATAAACCCTAAACACTA
* **
4708950 TAACCTCTAAACTTTAAACCCT
1 AAACC-CTAAACCATAAACCCT
4708972 CAATATTGAT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
28 6 0.14
29 27 0.64
30 9 0.21
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.20
Consensus pattern (29 bp):
AAACCCTAAACCATAAACCCTAAACACTA
Found at i:4709518 original size:796 final size:796
Alignment explanation
Indices: 4708175--4709767 Score: 3186
Period size: 796 Copynumber: 2.0 Consensus size: 796
4708165 TTGAATTAAT
4708175 TCAATATTGATTAATTATCATTATGATTTAAATTAGGGGTTAAGGGTTAGGGGTTTCAGGGGGAA
1 TCAATATTGATTAATTATCATTATGATTTAAATTAGGGGTTAAGGGTTAGGGGTTTCAGGGGGAA
4708240 AAGTTAGGTCTTTTCTTTAAAAGTATATAAATATTATAAAAATAAAAGTTTAAAATATTTTTTAA
66 AAGTTAGGTCTTTTCTTTAAAAGTATATAAATATTATAAAAATAAAAGTTTAAAATATTTTTTAA
4708305 ATTTTAAAAAAAATTTAAAATCTTTTAAAATTCATTTTAAAATTTTAAATCACGAAAAATATAAA
131 ATTTTAAAAAAAATTTAAAATCTTTTAAAATTCATTTTAAAATTTTAAATCACGAAAAATATAAA
4708370 ACCTTTCAAAATTTAGAAAAATATATGTTATTTACCCTTTAAATGATAATTAGAAATGTTCACTA
196 ACCTTTCAAAATTTAGAAAAATATATGTTATTTACCCTTTAAATGATAATTAGAAATGTTCACTA
4708435 CCCATACAACCCACCTAGTCCAAAATATGGTTAGGCTTAGATTTATATTTTTCATTGTTTTTAAA
261 CCCATACAACCCACCTAGTCCAAAATATGGTTAGGCTTAGATTTATATTTTTCATTGTTTTTAAA
4708500 CAATGAAATGGGTGATTCGGGTAAAACGAGCTTGAAGTTGGAAAAGTATTTAAAATTGGGCATTG
326 CAATGAAATGGGTGATTCGGGTAAAACGAGCTTGAAGTTGGAAAAGTATTTAAAATTGGGCATTG
4708565 GCACAGCTTGGTCTGGCTTGGCCCACTAATTAATTCAATATTTTAAAACCTTTGCAAAGTTTAAT
391 GCACAGCTTGGTCTGGCTTGGCCCACTAATTAATTCAATATTTTAAAACCTTTGCAAAGTTTAAT
4708630 CTATATATTCAATCAATTCTTATTTGATCACGGCGGGGGCAAGGCAAAACACGCAAAAAATTGAA
456 CTATATATTCAATCAATTCTTATTTGATCACGGCGGGGGCAAGGCAAAACACGCAAAAAATTGAA
4708695 CTGGATAAAAAAAACTGAACCGAGCACTAAAAATACGGAACCGGGATGGGATAAGGTGGGGATAT
521 CTGGATAAAAAAAACTGAACCGAGCACTAAAAATACGGAACCGGGATGGGATAAGGTGGGGATAT
4708760 CCTTGGATATAGCTTATATCGATTTTGAAGAACTAAATCTTCACACGATTTTGAAGAACCATATT
586 CCTTGGATATAGCTTATATCGATTTTGAAGAACTAAATCTTCACACGATTTTGAAGAACCATATT
4708825 AATATTATCTCTTTTACAATTATATAAGAAATTAATTAATATATAAATTAGAAAACAATAGTTAA
651 AATATTATCTCTTTTACAATTATATAAGAAATTAATTAATATATAAATTAGAAAACAATAGTTAA
4708890 TCTAAACCATAAACCATAAACCTAAACTCTAAAACCCTAAAACCATAAACCCTTAACACATAACC
716 TCTAAACCATAAACCATAAACCTAAACTCTAAAACCCTAAAACCATAAACCCTTAACACATAACC
4708955 TCTAAACTTTAAACCC
781 TCTAAACTTTAAACCC
4708971 TCAATATTGATTAATTATCATTATGATTTAAATTAGGGGTTAAGGGTTAGGGGTTTCAGGGGGAA
1 TCAATATTGATTAATTATCATTATGATTTAAATTAGGGGTTAAGGGTTAGGGGTTTCAGGGGGAA
4709036 AAGTTAGGTCTTTTCTTTAAAAGTATATAAATATTATAAAAATAAAAGTTTAAAATATTTTTTAA
66 AAGTTAGGTCTTTTCTTTAAAAGTATATAAATATTATAAAAATAAAAGTTTAAAATATTTTTTAA
4709101 ATTTTAAAAAAAATTTAAAATCTTTTAAAATTCATTTTAAAATTTTAAATCACGAAAAATATAAA
131 ATTTTAAAAAAAATTTAAAATCTTTTAAAATTCATTTTAAAATTTTAAATCACGAAAAATATAAA
4709166 ACCTTTCAAAATTTAGAAAAATATATGTTATTTACCCTTTAAATGATAATTAGAAATGTTCACTA
196 ACCTTTCAAAATTTAGAAAAATATATGTTATTTACCCTTTAAATGATAATTAGAAATGTTCACTA
4709231 CCCATACAACCCACCTAGTCCAAAATATGGTTAGGCTTAGATTTATATTTTTCATTGTTTTTAAA
261 CCCATACAACCCACCTAGTCCAAAATATGGTTAGGCTTAGATTTATATTTTTCATTGTTTTTAAA
4709296 CAATGAAATGGGTGATTCGGGTAAAACGAGCTTGAAGTTGGAAAAGTATTTAAAATTGGGCATTG
326 CAATGAAATGGGTGATTCGGGTAAAACGAGCTTGAAGTTGGAAAAGTATTTAAAATTGGGCATTG
4709361 GCACAGCTTGGTCTGGCTTGGCCCACTAATTAATTCAATATTTTAAAACCTTTGCAAAGTTTAAT
391 GCACAGCTTGGTCTGGCTTGGCCCACTAATTAATTCAATATTTTAAAACCTTTGCAAAGTTTAAT
4709426 CTATATATTCAATCAATTCTTATTTGATCACGGCGGGGGCAAGGCAAAACACGCAAAAAATTGAA
456 CTATATATTCAATCAATTCTTATTTGATCACGGCGGGGGCAAGGCAAAACACGCAAAAAATTGAA
4709491 CTGGATAAAAAAAACTGAACCGAGCACTAAAAATACGGAACCGGGATGGGATAAGGTGGGGATAT
521 CTGGATAAAAAAAACTGAACCGAGCACTAAAAATACGGAACCGGGATGGGATAAGGTGGGGATAT
4709556 CCTTGGATATAGCTTATATCGATTTTGAAGAACTAAATCTTCACACGATTTTGAAGAACCATATT
586 CCTTGGATATAGCTTATATCGATTTTGAAGAACTAAATCTTCACACGATTTTGAAGAACCATATT
4709621 AATATTATCTCTTTTACAATTATATAAGAAATTAATTAATATATAAATTAGAAAACAATAGTTAA
651 AATATTATCTCTTTTACAATTATATAAGAAATTAATTAATATATAAATTAGAAAACAATAGTTAA
4709686 TCTAAACCATAAACCATAAACCTAAACTCTAAAACCCTAAAACCATAAACCCTTAACACATAACC
716 TCTAAACCATAAACCATAAACCTAAACTCTAAAACCCTAAAACCATAAACCCTTAACACATAACC
4709751 TCTAAACTTTAAACCC
781 TCTAAACTTTAAACCC
4709767 T
1 T
4709768 AACCTTTAAA
Statistics
Matches: 797, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
796 797 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (796 bp):
TCAATATTGATTAATTATCATTATGATTTAAATTAGGGGTTAAGGGTTAGGGGTTTCAGGGGGAA
AAGTTAGGTCTTTTCTTTAAAAGTATATAAATATTATAAAAATAAAAGTTTAAAATATTTTTTAA
ATTTTAAAAAAAATTTAAAATCTTTTAAAATTCATTTTAAAATTTTAAATCACGAAAAATATAAA
ACCTTTCAAAATTTAGAAAAATATATGTTATTTACCCTTTAAATGATAATTAGAAATGTTCACTA
CCCATACAACCCACCTAGTCCAAAATATGGTTAGGCTTAGATTTATATTTTTCATTGTTTTTAAA
CAATGAAATGGGTGATTCGGGTAAAACGAGCTTGAAGTTGGAAAAGTATTTAAAATTGGGCATTG
GCACAGCTTGGTCTGGCTTGGCCCACTAATTAATTCAATATTTTAAAACCTTTGCAAAGTTTAAT
CTATATATTCAATCAATTCTTATTTGATCACGGCGGGGGCAAGGCAAAACACGCAAAAAATTGAA
CTGGATAAAAAAAACTGAACCGAGCACTAAAAATACGGAACCGGGATGGGATAAGGTGGGGATAT
CCTTGGATATAGCTTATATCGATTTTGAAGAACTAAATCTTCACACGATTTTGAAGAACCATATT
AATATTATCTCTTTTACAATTATATAAGAAATTAATTAATATATAAATTAGAAAACAATAGTTAA
TCTAAACCATAAACCATAAACCTAAACTCTAAAACCCTAAAACCATAAACCCTTAACACATAACC
TCTAAACTTTAAACCC
Done.