Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 55 of 91
Found at i:19602433 original size:377 final size:376
Alignment explanation
Indices: 19601739--19602443 Score: 1056
Period size: 377 Copynumber: 1.9 Consensus size: 376
19601729 ATATTTTTAG
*
19601739 TATATATATACTTTAAATATAAACATATTTACTTTCTATTTTTTGTTAACATTACAAAATTATAA
1 TATATATATACTTTAAATATAAACATATTTACTTTCTATTTTGTGTTAACATTACAAAATTATAA
* * *
19601804 CTTATAAAATTATTAATTATAATATATATATAACTTTGTTTATATAAACTTATAATATATAAACC
66 CTCATAAAATTATTAATTACAATATATATAT-ACTTTGTTTATATAAACTTATAACATATAAACC
* * * * * *
19601869 TAAAGAGAAGCTGTGACATTAGAATAGTTATAAAACCAAATTATTTTTTTTATTTTATGTAATTA
130 TAAAAAAAAGCTGTAAAATTAGAATAGTTATAAAACCAAATTATTTTTTTTATTTCATATAATTA
* *
19601934 AGGACAAACCCGTATAGTTAATTAAATTAATTCATGAAACTATAATTATTAATTAACTTGTAATG
195 AGGACAAACCCGTATAGTTAATTAAATTAATTAATGAAACTATAATTATTAACTAACTTGTAATG
* * * **
19601999 TCTTTTAATATATACACTTTATATATATTAGATTCATTTCTAAGGAACATAATTACTATTATATA
260 TCTTTTAATATATACACTTTATACACATTAGATTCATTTATAAAAAACATAATTACTATTATATA
19602064 TATATATATATATATATTAAAATACTTTTAATGGCGTGTGTGTGTTTGTGTA
325 TATATATATATATATATTAAAATACTTTTAATGGCGTGTGTGTGTTTGTGTA
*
19602116 TATATATGTACTTTAAATATAAACATATTTACTTTCTATTTTGTGTTAACATTACAAAAATTATA
1 TATATATATACTTTAAATATAAACATATTTACTTTCTATTTTGTGTTAACATTAC-AAAATTATA
*
19602181 ACTCATAAAATTATTAATTACAATATATATAT-CTTTGTTTATATAAACTTATAACATATAAATC
65 ACTCATAAAATTATTAATTACAATATATATATACTTTGTTTATATAAACTTATAACATATAAACC
* * * * * *
19602245 TAAAAAAAAGTTGTAAAATTATAATAGTTTTGAAACCTAGTTATTTTTTTTTAATTTCATATAAT
130 TAAAAAAAAGCTGTAAAATTAGAATAGTTATAAAACCAAATTA-TTTTTTTT-ATTTCATATAAT
* *
19602310 TAAGGATAAACCCAG-ATAGTTAATT-AATTAATTAATGAAACTATAATTATTAACTGACTTGTA
193 TAAGGACAAACCC-GTATAGTTAATTAAATTAATTAATGAAACTATAATTATTAACTAACTTGTA
* * * * *
19602373 ATGTCTTTTAATATATATATTTTATACACATTGGGTTCATTTATAAAAAATATAATTACTATTAT
257 ATGTCTTTTAATATATACACTTTATACACATTAGATTCATTTATAAAAAACATAATTACTATTAT
19602438 ATATAT
322 ATATAT
19602444 TAAAATACTT
Statistics
Matches: 292, Mismatches: 32, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
376 63 0.22
377 157 0.54
378 71 0.24
379 1 0.00
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (376 bp):
TATATATATACTTTAAATATAAACATATTTACTTTCTATTTTGTGTTAACATTACAAAATTATAA
CTCATAAAATTATTAATTACAATATATATATACTTTGTTTATATAAACTTATAACATATAAACCT
AAAAAAAAGCTGTAAAATTAGAATAGTTATAAAACCAAATTATTTTTTTTATTTCATATAATTAA
GGACAAACCCGTATAGTTAATTAAATTAATTAATGAAACTATAATTATTAACTAACTTGTAATGT
CTTTTAATATATACACTTTATACACATTAGATTCATTTATAAAAAACATAATTACTATTATATAT
ATATATATATATATATTAAAATACTTTTAATGGCGTGTGTGTGTTTGTGTA
Found at i:19613488 original size:2 final size:2
Alignment explanation
Indices: 19613469--19613516 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
19613459 TGTTACATAC
* **
19613469 AT AT TT AT AT AT GC AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19613511 AT AT AT
1 AT AT AT
19613517 GTACGTATGT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19615470 original size:60 final size:60
Alignment explanation
Indices: 19615367--19615530 Score: 188
Period size: 60 Copynumber: 2.7 Consensus size: 60
19615357 CACTTACTTG
* * *
19615367 TGGGAACTCCCCACATCACCAAATATGAGTCGGGGCTTCAGGTC-CTTTTTTACCTATTCA
1 TGGGAACTCCCCACACCACCAAATATGAGTCGAGGCTTCAGGTCTC-TTTTTACCTACTCA
* * * * * *
19615427 TGGGAACTCCCTACACCACTAAATATTAGTCGAGGTTTTAGGTCTCTTTTTACCTACTCG
1 TGGGAACTCCCCACACCACCAAATATGAGTCGAGGCTTCAGGTCTCTTTTTACCTACTCA
* * *
19615487 TGGAAACTCCCCACGCCACCAAATATGAATC-AGGGCTTCAGGTC
1 TGGGAACTCCCCACACCACCAAATATGAGTCGA-GGCTTCAGGTC
19615531 CCCCTTTATT
Statistics
Matches: 85, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
59 1 0.01
60 83 0.98
61 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (60 bp):
TGGGAACTCCCCACACCACCAAATATGAGTCGAGGCTTCAGGTCTCTTTTTACCTACTCA
Found at i:19616443 original size:74 final size:73
Alignment explanation
Indices: 19616347--19616525 Score: 207
Period size: 74 Copynumber: 2.4 Consensus size: 73
19616337 GACTTAGTTG
* * * * * *
19616347 ACTAAGAAATATTGTTAGTCAACTAAGAGCTCACTGCTAGAGACTTCAGTTACAAGACAGAGAAA
1 ACTAAGAAA-AATGTTAGTCAACTAAGAGCACACTGCCAAAGAATTCAATTACAAGACAGAGAAA
19616412 ACTTAATCC
65 ACTTAATCC
* * * *
19616421 ACTAA-AAAGCATGGTTAGTCAACTAAGAACACATTGCCAAAGAATTCAATTACAAGACAGAGAC
1 ACTAAGAAA-AAT-GTTAGTCAACTAAGAGCACACTGCCAAAGAATTCAATTACAAGACAGAGAA
* *
19616485 GACTTAATCG
64 AACTTAATCC
*
19616495 ACTAAGAAAAATGTAAGTCAACTAAGAGCAC
1 ACTAAGAAAAATGTTAGTCAACTAAGAGCAC
19616526 TCTGTCTGAA
Statistics
Matches: 87, Mismatches: 16, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
73 21 0.24
74 63 0.72
75 3 0.03
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.21
Consensus pattern (73 bp):
ACTAAGAAAAATGTTAGTCAACTAAGAGCACACTGCCAAAGAATTCAATTACAAGACAGAGAAAA
CTTAATCC
Found at i:19621084 original size:3 final size:3
Alignment explanation
Indices: 19621076--19621100 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
19621066 CTTGAGCATA
19621076 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
19621101 TAATAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:19632522 original size:74 final size:73
Alignment explanation
Indices: 19632400--19632600 Score: 233
Period size: 74 Copynumber: 2.7 Consensus size: 73
19632390 AGTAAAGCAT
* * * * * * *
19632400 ATTACAAAATAGAGAAGACTTAGTCGACTAAGAAATATTGTTAGTCAACTAA-AAGCTCACTGTT
1 ATTACAAGACAGAGAAGACTTAATCGACTAAGAAGTA-TGTTAGTCAACTAAGAA-CACAATGCT
19632464 AGAGACTTCA
64 AGAGACTTCA
* *
19632474 GTTACAAGACAGAGAAAACTTAATCGACTAAGAAGTATGGTTAGTCAACTAAGAACACAATGCTA
1 ATTACAAGACAGAGAAGACTTAATCGACTAAGAAGTAT-GTTAGTCAACTAAGAACACAATGCTA
*
19632539 GAGATTTCA
65 GAGACTTCA
* * * * *
19632548 ATTACAAGACAAAGACGATTTAATCGACTACGAAGAATGTTAGTCAACTAAGA
1 ATTACAAGACAGAGAAGACTTAATCGACTAAGAAGTATGTTAGTCAACTAAGA
19632601 GCACTCTGTT
Statistics
Matches: 108, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
73 16 0.15
74 90 0.83
75 2 0.02
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.24
Consensus pattern (73 bp):
ATTACAAGACAGAGAAGACTTAATCGACTAAGAAGTATGTTAGTCAACTAAGAACACAATGCTAG
AGACTTCA
Found at i:19634780 original size:2 final size:2
Alignment explanation
Indices: 19634723--19634761 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
19634713 NNNNNNNNNN
*
19634723 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19634762 CCATGTATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19636157 original size:13 final size:13
Alignment explanation
Indices: 19636129--19636167 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
19636119 TTAAATTTTG
*
19636129 GTTAATTAGTTTTA
1 GTTAATTA-ATTTA
19636143 GTTAATTAATTTA
1 GTTAATTAATTTA
*
19636156 GTTATTTAATTT
1 GTTAATTAATTT
19636168 TGATTATTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 15 0.65
14 8 0.35
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (13 bp):
GTTAATTAATTTA
Found at i:19636578 original size:72 final size:72
Alignment explanation
Indices: 19636461--19636617 Score: 287
Period size: 72 Copynumber: 2.2 Consensus size: 72
19636451 ATTTTGGCCA
19636461 AAGGTCGACTATACAAGGTCTTTAGTCAACTATAGCTAAGAAAAGGAAGCCATAGTCAACTACCA
1 AAGGTCGACTATACAAGGTCTTTAGTCAACTATAGCTAAGAAAAGGAAGCCATAGTCAACTACCA
19636526 AGGCTAC
66 AGGCTAC
* * *
19636533 AAGGTCGATTATATAAGGTCTTTAGTCAACTATAGCTAAGAAAAGGAAGCCATAGTCGACTACCA
1 AAGGTCGACTATACAAGGTCTTTAGTCAACTATAGCTAAGAAAAGGAAGCCATAGTCAACTACCA
19636598 AGGCTAC
66 AGGCTAC
19636605 AAGGTCGACTATA
1 AAGGTCGACTATA
19636618 GAGCTACAGA
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 81 1.00
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.22
Consensus pattern (72 bp):
AAGGTCGACTATACAAGGTCTTTAGTCAACTATAGCTAAGAAAAGGAAGCCATAGTCAACTACCA
AGGCTAC
Found at i:19639536 original size:31 final size:30
Alignment explanation
Indices: 19639498--19639579 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 30
19639488 CACTATTGTT
*
19639498 GGTTATACCTCCACGTAAAAGATAGTGCT-AA
1 GGTTATACCTCCACGTAAAAG-TAATG-TAAA
* **
19639529 GGTTATACCTCCTCAAAAAAGTAATGTAAA
1 GGTTATACCTCCACGTAAAAGTAATGTAAA
* *
19639559 GGTTATACCTCTAAGTAAAAG
1 GGTTATACCTCCACGTAAAAG
19639580 GTAGAGAGGT
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
29 1 0.02
30 22 0.54
31 18 0.44
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (30 bp):
GGTTATACCTCCACGTAAAAGTAATGTAAA
Found at i:19639644 original size:37 final size:36
Alignment explanation
Indices: 19639594--19639712 Score: 142
Period size: 37 Copynumber: 3.4 Consensus size: 36
19639584 AGAGGTTACA
*
19639594 CTTGATCTTTAAAAGGCATTTGGTTGTAGCGGTTGTG
1 CTTGATCCTTAAAAGGCATTTGGTTGTA-CGGTTGTG
*
19639631 CTTGATCCTTAAAAGGCA-TTGGTTGT-C----ATG
1 CTTGATCCTTAAAAGGCATTTGGTTGTACGGTTGTG
*
19639661 CTTGATCCTTAAAAGGCATTTGGTTGTAAAGGTTGTG
1 CTTGATCCTTAAAAGGCATTTGGTTGT-ACGGTTGTG
*
19639698 CTTGATCCTAAAAAG
1 CTTGATCCTTAAAAG
19639713 ACAGTGATTT
Statistics
Matches: 70, Mismatches: 5, Indels: 14
0.79 0.06 0.16
Matches are distributed among these distances:
30 20 0.29
31 8 0.11
34 1 0.01
36 8 0.11
37 33 0.47
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.37
Consensus pattern (36 bp):
CTTGATCCTTAAAAGGCATTTGGTTGTACGGTTGTG
Found at i:19639664 original size:30 final size:31
Alignment explanation
Indices: 19639629--19639687 Score: 111
Period size: 30 Copynumber: 1.9 Consensus size: 31
19639619 GTAGCGGTTG
19639629 TGCTTGATCCTTAAAAGGCA-TTGGTTGTCA
1 TGCTTGATCCTTAAAAGGCATTTGGTTGTCA
19639659 TGCTTGATCCTTAAAAGGCATTTGGTTGT
1 TGCTTGATCCTTAAAAGGCATTTGGTTGT
19639688 AAAGGTTGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 20 0.71
31 8 0.29
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (31 bp):
TGCTTGATCCTTAAAAGGCATTTGGTTGTCA
Found at i:19647422 original size:2 final size:2
Alignment explanation
Indices: 19647415--19647477 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
19647405 ACTACTTTGA
19647415 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19647457 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
19647478 ATGCATGAGA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19662645 original size:34 final size:34
Alignment explanation
Indices: 19662605--19662744 Score: 147
Period size: 34 Copynumber: 4.1 Consensus size: 34
19662595 CGCATAGCGC
* ***
19662605 TTTTCATGGGAGTAAGTGGAACCCTTACAATGCT
1 TTTTCATGGGAGCAAGCACAACCCTTACAATGCT
**
19662639 TTTTCATGGGAGCAAGCACAACTTTTACAATGCT
1 TTTTCATGGGAGCAAGCACAACCCTTACAATGCT
**
19662673 TTTTCATGGGAGCAAGCACAACTTTTACAATGCCT
1 TTTTCATGGGAGCAAGCACAACCCTTACAATG-CT
* * * * *
19662708 TTTGC-CGGGAGTAAGCACAACCCATACAATGGT
1 TTTTCATGGGAGCAAGCACAACCCTTACAATGCT
19662741 TTTT
1 TTTT
19662745 AACAAGCTCA
Statistics
Matches: 91, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
33 4 0.04
34 81 0.89
35 6 0.07
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (34 bp):
TTTTCATGGGAGCAAGCACAACCCTTACAATGCT
Found at i:19670747 original size:42 final size:42
Alignment explanation
Indices: 19670680--19670798 Score: 112
Period size: 42 Copynumber: 2.8 Consensus size: 42
19670670 TATGCAACGA
* * * * *
19670680 CTTATGTGCACTCCTACTTGTACATAGCCGGGTTAGCAAAGG
1 CTTATGCGCACTCCCACTCGCACATAGCCGGGTCAGCAAAGG
* * *
19670722 CTTTTGCGCACTCCCACTCGCACATAGCTGGGTCAGCAATGG
1 CTTATGCGCACTCCCACTCGCACATAGCCGGGTCAGCAAAGG
* *** * *
19670764 CTTATGCACACTTTTACTTGCACATAGCCAGGTCA
1 CTTATGCGCACTCCCACTCGCACATAGCCGGGTCA
19670799 ATATCATTAC
Statistics
Matches: 61, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.28
Consensus pattern (42 bp):
CTTATGCGCACTCCCACTCGCACATAGCCGGGTCAGCAAAGG
Found at i:19674704 original size:42 final size:42
Alignment explanation
Indices: 19674637--19674755 Score: 112
Period size: 42 Copynumber: 2.8 Consensus size: 42
19674627 TATGCAACGA
* * * * *
19674637 CTTATGTGCACTCCTACTTGTACATAGCCGGGTTAGCAAAGG
1 CTTATGCGCACTCCCACTCGCACATAGCCGGGTCAGCAAAGG
* * *
19674679 CTTTTGCGCACTCCCACTCGCACATAGCTGGGTCAGCAATGG
1 CTTATGCGCACTCCCACTCGCACATAGCCGGGTCAGCAAAGG
* *** * *
19674721 CTTATGCACACTTTTACTTGCACATAGCCAGGTCA
1 CTTATGCGCACTCCCACTCGCACATAGCCGGGTCA
19674756 ATATCATTAC
Statistics
Matches: 61, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.28
Consensus pattern (42 bp):
CTTATGCGCACTCCCACTCGCACATAGCCGGGTCAGCAAAGG
Found at i:19679390 original size:14 final size:15
Alignment explanation
Indices: 19679362--19679392 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
19679352 ATGAAATTAA
19679362 AACAAACATTAAATT
1 AACAAACATTAAATT
19679377 AACAAACA-TAAATT
1 AACAAACATTAAATT
19679391 AA
1 AA
19679393 ATATCTTGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.65, C:0.13, G:0.00, T:0.23
Consensus pattern (15 bp):
AACAAACATTAAATT
Found at i:19694597 original size:29 final size:29
Alignment explanation
Indices: 19694555--19694613 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
19694545 AGAGGAGAAT
*
19694555 TGAGAAAAAAACTTTTGGTTTATTTCTCA
1 TGAGAAAAAAACTTTTGGTTCATTTCTCA
* *
19694584 TGAGAGAAGAACTTTTGGTTCATTTCTCA
1 TGAGAAAAAAACTTTTGGTTCATTTCTCA
19694613 T
1 T
19694614 TATTTTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.41
Consensus pattern (29 bp):
TGAGAAAAAAACTTTTGGTTCATTTCTCA
Found at i:19711792 original size:25 final size:25
Alignment explanation
Indices: 19711764--19711815 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
19711754 TTCCTATTTG
*
19711764 CACTTATATTGACAACTTCAGGAGT
1 CACTTATATTAACAACTTCAGGAGT
* *
19711789 CACTTGTATTAACAACTTCAGGTGT
1 CACTTATATTAACAACTTCAGGAGT
19711814 CA
1 CA
19711816 AAAATTCAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (25 bp):
CACTTATATTAACAACTTCAGGAGT
Found at i:19713200 original size:12 final size:12
Alignment explanation
Indices: 19713174--19713216 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
19713164 AGAAACATAT
* *
19713174 ATTGAGAAAATA
1 ATTGAGAGAAGA
19713186 ATTGAGAGAAGA
1 ATTGAGAGAAGA
* *
19713198 ATTTAGAGGAGA
1 ATTGAGAGAAGA
19713210 ATTGAGA
1 ATTGAGA
19713217 AAAAAGTTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.49, C:0.00, G:0.28, T:0.23
Consensus pattern (12 bp):
ATTGAGAGAAGA
Found at i:19717205 original size:21 final size:21
Alignment explanation
Indices: 19717179--19717231 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
19717169 GTTCATGCAG
19717179 TTCATGACAAAGACTGATACA
1 TTCATGACAAAGACTGATACA
* *
19717200 TTCATGATAAAGACTGATGCA
1 TTCATGACAAAGACTGATACA
*
19717221 TTCATAACAAA
1 TTCATGACAAA
19717232 AATCGATGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.26
Consensus pattern (21 bp):
TTCATGACAAAGACTGATACA
Found at i:19717260 original size:21 final size:20
Alignment explanation
Indices: 19717173--19717261 Score: 70
Period size: 21 Copynumber: 4.2 Consensus size: 20
19717163 AAATATGTTC
*
19717173 ATGCAGTTCATGACAAAGACTG
1 ATGCA-TTCATGA-TAAGACTG
*
19717195 ATACATTCATGATAAAGACTG
1 ATGCATTCATGAT-AAGACTG
* * * *
19717216 ATGCATTCATAACAAAAATCG
1 ATGCATTCATGATAAGACT-G
*
19717237 ATGCATTTATGATAAGGACTG
1 ATGCATTCATGATAA-GACTG
19717258 ATGC
1 ATGC
19717262 CTCCATTCAA
Statistics
Matches: 52, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
20 4 0.08
21 42 0.81
22 6 0.12
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (20 bp):
ATGCATTCATGATAAGACTG
Found at i:19719084 original size:84 final size:84
Alignment explanation
Indices: 19718938--19719119 Score: 292
Period size: 84 Copynumber: 2.2 Consensus size: 84
19718928 GCCAACAATT
* * *
19718938 GGTAGCCCACTACCCACTACCCTCCATTGGGTTGCCGACATTGGGCAGCCCACTAACCAAACCCA
1 GGTAGCCCACTACCAACTACCCTCCATTGGGTTGCCAACATTGGGCAGCCCACTAACAAAACCCA
*
19719003 ATCCCCCCCTTTTTATTTG
66 ATCCCCCCATTTTTATTTG
* * *
19719022 GGTAGCCCACTACCAACTACCTTCCATTGGGTTGCCAACATTGGGTAGCCCACTAACAAAACCTA
1 GGTAGCCCACTACCAACTACCCTCCATTGGGTTGCCAACATTGGGCAGCCCACTAACAAAACCCA
19719087 ATCCCCCCATTTTTATTTG
66 ATCCCCCCATTTTTATTTG
*
19719106 GGCAGCCCACTACC
1 GGTAGCCCACTACC
19719120 CCGTAAACCC
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
84 90 1.00
ACGTcount: A:0.24, C:0.37, G:0.15, T:0.24
Consensus pattern (84 bp):
GGTAGCCCACTACCAACTACCCTCCATTGGGTTGCCAACATTGGGCAGCCCACTAACAAAACCCA
ATCCCCCCATTTTTATTTG
Found at i:19720680 original size:3 final size:3
Alignment explanation
Indices: 19720672--19720703 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
19720662 ACTTTATCTC
*
19720672 TAG TAG TAG TAG TAG TAG TAA TAG TAG TAG TA
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TA
19720704 ACTATATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.28, T:0.34
Consensus pattern (3 bp):
TAG
Found at i:19722116 original size:21 final size:21
Alignment explanation
Indices: 19722091--19722149 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
19722081 TTTGCTAATA
19722091 TATTAGTTTTAATTATTAGTT
1 TATTAGTTTTAATTATTAGTT
* **
19722112 TATTAGTTTCAATT-TTTCTT
1 TATTAGTTTTAATTATTAGTT
*
19722132 T-TTAATTTTAATTATTAG
1 TATTAGTTTTAATTATTAG
19722150 ATAAATTAAG
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 10 0.33
20 7 0.23
21 13 0.43
ACGTcount: A:0.27, C:0.03, G:0.07, T:0.63
Consensus pattern (21 bp):
TATTAGTTTTAATTATTAGTT
Found at i:19724947 original size:92 final size:92
Alignment explanation
Indices: 19724837--19725028 Score: 278
Period size: 92 Copynumber: 2.1 Consensus size: 92
19724827 ATATTAGAGC
* * *
19724837 AAATCTATCAACAGATGATGAAAATCTATCGATAGATTTTACCTAGAAAGATTTTTAAAGGGATT
1 AAATCTATCAACAAATGATAAAAATCTATCGATAGATTTTACCTAGAAAGATTTTTAAAAGGATT
* * *
19724902 TTGATGA-ACTATTATCGATAGATTTCA
66 TTGATGACA-AAGTATCAATAGATTTCA
* * * *
19724929 AAATCTATCAATAAATGATAAAAATCTATGGATAGATTTTACCTAGTAAGCTTTTTAAAAGGATT
1 AAATCTATCAACAAATGATAAAAATCTATCGATAGATTTTACCTAGAAAGATTTTTAAAAGGATT
19724994 TTGATGACAAAGTATCAATAGATTTCA
66 TTGATGACAAAGTATCAATAGATTTCA
19725021 AAATCTAT
1 AAATCTAT
19725029 TGATACTTTA
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
92 88 0.99
93 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (92 bp):
AAATCTATCAACAAATGATAAAAATCTATCGATAGATTTTACCTAGAAAGATTTTTAAAAGGATT
TTGATGACAAAGTATCAATAGATTTCA
Found at i:19731701 original size:35 final size:35
Alignment explanation
Indices: 19731653--19731721 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
19731643 GTATGAATGT
* *
19731653 TGATTATATCCCATCGTGGGGGTAAGAATACCATA
1 TGATTATAGCCCATCGTGAGGGTAAGAATACCATA
*
19731688 TGATTATAGCCCATTGTGAGGGTAAGAATACCAT
1 TGATTATAGCCCATCGTGAGGGTAAGAATACCAT
19731722 TTAATAAAGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (35 bp):
TGATTATAGCCCATCGTGAGGGTAAGAATACCATA
Found at i:19733734 original size:71 final size:71
Alignment explanation
Indices: 19733641--19733774 Score: 187
Period size: 71 Copynumber: 1.9 Consensus size: 71
19733631 GGGCCAATCT
* * * * * *
19733641 TTTTGGTTCCAGAAGCTATTCTAAGTGTTTTGTCTTGTAGAGATTGACCCTTTAACACTTGGGGC
1 TTTTGGTTCCAAAAACTATTCTAAGTGTTATATCTTGTAGAGATCGACCCTTGAACACTTGGGGC
19733706 TGATCC
66 TGATCC
* * *
19733712 TTTTGGTTCTAAAAACTATTCTAAGTGTTATATCTTGTAGAGATCGACGCTTGAACCCTTGGG
1 TTTTGGTTCCAAAAACTATTCTAAGTGTTATATCTTGTAGAGATCGACCCTTGAACACTTGGG
19733775 AGTCAATCCT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
71 54 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (71 bp):
TTTTGGTTCCAAAAACTATTCTAAGTGTTATATCTTGTAGAGATCGACCCTTGAACACTTGGGGC
TGATCC
Found at i:19738645 original size:16 final size:15
Alignment explanation
Indices: 19738626--19738668 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
19738616 TTATTTATTT
19738626 TTAGTTATTTTTATAA
1 TTAGTTATTTTTA-AA
*
19738642 TTAGTTTATTTTTAAG
1 TTAG-TTATTTTTAAA
*
19738658 TGAGTTATTTT
1 TTAGTTATTTT
19738669 AATTTTATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.29
16 8 0.33
17 9 0.38
ACGTcount: A:0.26, C:0.00, G:0.12, T:0.63
Consensus pattern (15 bp):
TTAGTTATTTTTAAA
Found at i:19739716 original size:9 final size:9
Alignment explanation
Indices: 19739702--19739740 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
19739692 ATACGATTAA
*
19739702 TAACACGTT
1 TAACACGAT
19739711 TAACACGAT
1 TAACACGAT
* *
19739720 TAACATGTT
1 TAACACGAT
19739729 TAACACGAT
1 TAACACGAT
19739738 TAA
1 TAA
19739741 ATAAAAATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (9 bp):
TAACACGAT
Found at i:19739729 original size:18 final size:18
Alignment explanation
Indices: 19739702--19739740 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
19739692 ATACGATTAA
19739702 TAACACGTTTAACACGAT
1 TAACACGTTTAACACGAT
*
19739720 TAACATGTTTAACACGAT
1 TAACACGTTTAACACGAT
19739738 TAA
1 TAA
19739741 ATAAAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (18 bp):
TAACACGTTTAACACGAT
Found at i:19739886 original size:25 final size:24
Alignment explanation
Indices: 19739826--19739889 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 24
19739816 AAAAAATATC
*
19739826 AAATATAATAAAATTTAATACAAAT
1 AAATAT-ATAAAATTCAATACAAAT
*
19739851 AACATATATAAAATTCAATATCATAT
1 AA-ATATATAAAATTCAATA-CAAAT
19739877 -AATATGATAAAAT
1 AAATAT-ATAAAAT
19739890 ATATCATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
24 4 0.12
25 22 0.65
26 8 0.24
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATATATAAAATTCAATACAAAT
Found at i:19741695 original size:22 final size:22
Alignment explanation
Indices: 19741651--19741695 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
19741641 TTCTCGTTGT
*
19741651 AGCGAGAATCCATTTTAGTTGC
1 AGCGAGAATCCATTTTAGCTGC
* * *
19741673 AGCGAGAATTCTTTTTTGCTGC
1 AGCGAGAATCCATTTTAGCTGC
19741695 A
1 A
19741696 TTGAGAAACA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (22 bp):
AGCGAGAATCCATTTTAGCTGC
Found at i:19743368 original size:40 final size:39
Alignment explanation
Indices: 19743324--19743402 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 39
19743314 TGTTGCAATA
19743324 AAAAATCAATTTGCAAGAAAATGAGAAATTCTCAAGATT
1 AAAAATCAATTTGCAAGAAAATGAGAAATTCTCAAGATT
*
19743363 NAAAAATCAATTTGCAAGAAAATGGGAAATTCTCAAGATT
1 -AAAAATCAATTTGCAAGAAAATGAGAAATTCTCAAGATT
19743403 CATCATGCCA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.25
Consensus pattern (39 bp):
AAAAATCAATTTGCAAGAAAATGAGAAATTCTCAAGATT
Found at i:19743603 original size:38 final size:39
Alignment explanation
Indices: 19743526--19743621 Score: 104
Period size: 38 Copynumber: 2.5 Consensus size: 39
19743516 ACCCAGCTCA
** *
19743526 TGTGCATCCCCCCACATTGTGCACATAGTCAGAGTCATCG
1 TGTGCATCCCCCCACATCATG-ACATAGTCAGAGCCATCG
* *
19743566 TGTGCATCCCCCCACATCATG-CATAGTTAGTGCCATCG
1 TGTGCATCCCCCCACATCATGACATAGTCAGAGCCATCG
* **
19743604 TGTACATCCTGCCACATC
1 TGTGCATCCCCCCACATC
19743622 GTGAACACGG
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
38 29 0.60
40 19 0.40
ACGTcount: A:0.22, C:0.34, G:0.18, T:0.26
Consensus pattern (39 bp):
TGTGCATCCCCCCACATCATGACATAGTCAGAGCCATCG
Found at i:19745374 original size:21 final size:21
Alignment explanation
Indices: 19745350--19745392 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
19745340 AGGAAGAAGA
*
19745350 AGAAGAAGCTACTGGAAAATG
1 AGAAAAAGCTACTGGAAAATG
**
19745371 AGAAAAAGCTGTTGGAAAATG
1 AGAAAAAGCTACTGGAAAATG
19745392 A
1 A
19745393 TATTTATAGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.07, G:0.28, T:0.16
Consensus pattern (21 bp):
AGAAAAAGCTACTGGAAAATG
Found at i:19755114 original size:65 final size:65
Alignment explanation
Indices: 19754992--19755115 Score: 160
Period size: 65 Copynumber: 1.9 Consensus size: 65
19754982 ATATCATTCG
* ** *
19754992 GTGCCATCACCACGTGTGGAATGTTACATCACACCATTTGGAAACGCTATCATACATTTTACTAA
1 GTGCCATCACCACGTGTGGAATGTCACATCACACCATTTGGAAACGCTAGAAAACATTTTACTAA
* * * *
19755057 GTGCCATCATCACGTGTGGAATGTCGCCTCACACC-TTGTGGAAATGCTAGAAAACATTT
1 GTGCCATCACCACGTGTGGAATGTCACATCACACCATT-TGGAAACGCTAGAAAACATTT
19755116 ACATACAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
64 2 0.04
65 48 0.96
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (65 bp):
GTGCCATCACCACGTGTGGAATGTCACATCACACCATTTGGAAACGCTAGAAAACATTTTACTAA
Found at i:19758988 original size:42 final size:42
Alignment explanation
Indices: 19758900--19759004 Score: 111
Period size: 42 Copynumber: 2.5 Consensus size: 42
19758890 TCTCCCATCG
* * * * * *
19758900 TCATCAGCTCATGTGCACTTCCCATTACCACATGGCTGGGTCA
1 TCATCGGCTTATGTGCAC-TCCCATTACCACATAGCCGAGTAA
* * *
19758943 TCATCGGGTTATGTGCACTCCCATTAGCATATAGCCGAGTAA
1 TCATCGGCTTATGTGCACTCCCATTACCACATAGCCGAGTAA
*
19758985 TCATCGGCTTATGTACACTC
1 TCATCGGCTTATGTGCACTC
19759005 TTATTCACAC
Statistics
Matches: 51, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
42 36 0.71
43 15 0.29
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.30
Consensus pattern (42 bp):
TCATCGGCTTATGTGCACTCCCATTACCACATAGCCGAGTAA
Found at i:19759074 original size:42 final size:42
Alignment explanation
Indices: 19758984--19759067 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
19758974 TAGCCGAGTA
* * * * **
19758984 ATCATCGGCTTATGTACACTCTTATTCACACATAGTTGGGTC
1 ATCATCAGCTTATGTACACCCCTACTCACACATAACTGGGTC
*
19759026 ATCATCAGCTTATGTACACCCCTACTCTCACATAACTGGGTC
1 ATCATCAGCTTATGTACACCCCTACTCACACATAACTGGGTC
19759068 CACATCAACA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.32
Consensus pattern (42 bp):
ATCATCAGCTTATGTACACCCCTACTCACACATAACTGGGTC
Found at i:19763131 original size:27 final size:27
Alignment explanation
Indices: 19763101--19763156 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
19763091 TTTTGAAAAG
19763101 AATAAATGAAAACATTTCTTGAGGGAA
1 AATAAATGAAAACATTTCTTGAGGGAA
19763128 AATAAATGAAAACATTTCTTGAGGGAA
1 AATAAATGAAAACATTTCTTGAGGGAA
19763155 AA
1 AA
19763157 CAAAAGAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.25
Consensus pattern (27 bp):
AATAAATGAAAACATTTCTTGAGGGAA
Found at i:19765180 original size:40 final size:38
Alignment explanation
Indices: 19765125--19765222 Score: 108
Period size: 38 Copynumber: 2.5 Consensus size: 38
19765115 GCTCATGTAT
* *
19765125 ATCCCTCCACATCGTGCACATAGCAG-GCACCATCACGTGC
1 ATCCCCCCACATCGTGCACA-AGCAGTG--CCATCACGTAC
* * * *
19765165 ATCCCCCCACATCGTGCATAATCAGTGCTATCAGGTAC
1 ATCCCCCCACATCGTGCACAAGCAGTGCCATCACGTAC
19765203 ATCCCCCCACATCGTGCACA
1 ATCCCCCCACATCGTGCACA
19765223 CGGGCACTAT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
38 27 0.54
39 4 0.08
40 19 0.38
ACGTcount: A:0.26, C:0.40, G:0.15, T:0.19
Consensus pattern (38 bp):
ATCCCCCCACATCGTGCACAAGCAGTGCCATCACGTAC
Found at i:19767531 original size:33 final size:35
Alignment explanation
Indices: 19767449--19767535 Score: 97
Period size: 33 Copynumber: 2.5 Consensus size: 35
19767439 ATGAAAAATA
**
19767449 CTTTTCAAGGCTCAAGCATAACCTTTACAACAATGC
1 CTTTTCAAGGAGCAAGCATAACC-TTACAACAATGC
* * * *
19767485 CTTTACAAAGAGCAAGCATAACC-T-CTACGATGC
1 CTTTTCAAGGAGCAAGCATAACCTTACAACAATGC
19767518 CTTTTCAAGGAGCAAGCA
1 CTTTTCAAGGAGCAAGCA
19767536 CAATCTCTCT
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
33 23 0.53
34 1 0.02
36 19 0.44
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.24
Consensus pattern (35 bp):
CTTTTCAAGGAGCAAGCATAACCTTACAACAATGC
Found at i:19769394 original size:21 final size:21
Alignment explanation
Indices: 19769368--19769407 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19769358 TGGAATGAAA
*
19769368 GAACAAGTGTCAATACTTGTG
1 GAACAAGTATCAATACTTGTG
*
19769389 GAACAAGTATCGATACTTG
1 GAACAAGTATCAATACTTG
19769408 AAACCTAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.28
Consensus pattern (21 bp):
GAACAAGTATCAATACTTGTG
Found at i:19769661 original size:17 final size:16
Alignment explanation
Indices: 19769629--19769665 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
19769619 TAAACATATG
19769629 AAAATTAAAAAAAACT
1 AAAATTAAAAAAAACT
*
19769645 AAAATTAAACTAAAACT
1 AAAATTAAA-AAAAACT
19769662 AAAA
1 AAAA
19769666 AAAAGAACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.19
Consensus pattern (16 bp):
AAAATTAAAAAAAACT
Found at i:19775994 original size:2 final size:2
Alignment explanation
Indices: 19775987--19776073 Score: 156
Period size: 2 Copynumber: 42.5 Consensus size: 2
19775977 AGAATTCATG
19775987 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA NTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
19776030 TA CTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19776073 T
1 T
19776074 GTATGTATGG
Statistics
Matches: 83, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 79 0.95
3 4 0.05
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:19776255 original size:33 final size:33
Alignment explanation
Indices: 19776173--19776278 Score: 104
Period size: 33 Copynumber: 3.1 Consensus size: 33
19776163 TCAACTCAAT
** * * *
19776173 TCATGTGCACTTTCACACCGGACATAGCTAATAA
1 TCATGTGCACTCCCACACCGCACATGGCAAAT-A
* * *
19776207 CCTCATGTGCGCTCCCACACTGTACATGGCAAATA
1 --TCATGTGCACTCCCACACCGCACATGGCAAATA
*
19776242 TCATGTGCACTCCCACACCGCACATGGCATATA
1 TCATGTGCACTCCCACACCGCACATGGCAAATA
19776275 TCAT
1 TCAT
19776279 CAGTGTGTGC
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
33 33 0.56
35 1 0.02
36 25 0.42
ACGTcount: A:0.28, C:0.32, G:0.15, T:0.25
Consensus pattern (33 bp):
TCATGTGCACTCCCACACCGCACATGGCAAATA
Found at i:19786770 original size:2 final size:2
Alignment explanation
Indices: 19786758--19786791 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
19786748 ACCGTATACC
* *
19786758 AT AT AT GT AT AT AT AT AT AT AT AC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19786792 CAATCATCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:19786891 original size:42 final size:42
Alignment explanation
Indices: 19786832--19786957 Score: 180
Period size: 42 Copynumber: 3.0 Consensus size: 42
19786822 CAGCTCATAT
* *
19786832 GCAACAGCTTATGCGCACTCCTACTCGCCCATAGCCGGGTCA
1 GCAACGGCTTATGCGCACTCCTACTCGCACATAGCCGGGTCA
* * *
19786874 GCAACGGCTTATGCGCACTCCCACTCGTACATAGCCTGGTCA
1 GCAACGGCTTATGCGCACTCCTACTCGCACATAGCCGGGTCA
* * *
19786916 GCAACGGCTTATGCACACTCCTACTAGCACATAGCTGGGTCA
1 GCAACGGCTTATGCGCACTCCTACTCGCACATAGCCGGGTCA
19786958 ATATCATTAC
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 73 1.00
ACGTcount: A:0.23, C:0.35, G:0.21, T:0.21
Consensus pattern (42 bp):
GCAACGGCTTATGCGCACTCCTACTCGCACATAGCCGGGTCA
Found at i:19787801 original size:19 final size:19
Alignment explanation
Indices: 19787760--19787801 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
19787750 GAAGAAGGAG
*
19787760 AAGAAGCTGTTGGAGAATG
1 AAGAAGCTGTTGGAGAATA
19787779 AAGAAGCTGTTGGAAGAA-A
1 AAGAAGCTGTTGG-AGAATA
19787798 AAGA
1 AAGA
19787802 TATTTATAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.45, C:0.05, G:0.33, T:0.17
Consensus pattern (19 bp):
AAGAAGCTGTTGGAGAATA
Found at i:19788414 original size:2 final size:2
Alignment explanation
Indices: 19788407--19788462 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
19788397 ACTTGTCCAT
19788407 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
19788449 TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA
19788463 CACCACCGTC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:19788551 original size:35 final size:35
Alignment explanation
Indices: 19788485--19788557 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
19788475 CTTACTTGGC
*
19788485 TCATGTGCACTCCCTACACGCGCAAGGCAATATCA
1 TCATGTGCACTCCCTACACGCACAAGGCAATATCA
***
19788520 TCATGTGCACTCCCTACACGCACATTTCAATATCA
1 TCATGTGCACTCCCTACACGCACAAGGCAATATCA
19788555 TCA
1 TCA
19788558 CACGCACTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.29, C:0.34, G:0.12, T:0.25
Consensus pattern (35 bp):
TCATGTGCACTCCCTACACGCACAAGGCAATATCA
Found at i:19788565 original size:35 final size:35
Alignment explanation
Indices: 19788491--19788568 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
19788481 TGGCTCATGT
* ***
19788491 GCACTCCCTACACGCGCAAGGCAATATCATCATGT
1 GCACTCCCTACACGCACAAGGCAATATCATCACAC
***
19788526 GCACTCCCTACACGCACATTTCAATATCATCACAC
1 GCACTCCCTACACGCACAAGGCAATATCATCACAC
19788561 GCACTCCC
1 GCACTCCC
19788569 GCCCACATCA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.28, C:0.40, G:0.12, T:0.21
Consensus pattern (35 bp):
GCACTCCCTACACGCACAAGGCAATATCATCACAC
Found at i:19789831 original size:19 final size:19
Alignment explanation
Indices: 19789807--19789848 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
19789797 CGTGGTAAGG
19789807 TGAAAATAGCATGGGAGCA
1 TGAAAATAGCATGGGAGCA
* *
19789826 TGAAAATGGCGTGGGAGCA
1 TGAAAATAGCATGGGAGCA
19789845 TGAA
1 TGAA
19789849 GGAGAAGAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.36, T:0.17
Consensus pattern (19 bp):
TGAAAATAGCATGGGAGCA
Found at i:19794686 original size:35 final size:35
Alignment explanation
Indices: 19794647--19794719 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
19794637 CTTACTTAGC
19794647 TCATGTGCACTCCCTACACGCACAAGGCAATATCA
1 TCATGTGCACTCCCTACACGCACAAGGCAATATCA
***
19794682 TCATGTGCACTCCCTACACGCACATTTCAATATCA
1 TCATGTGCACTCCCTACACGCACAAGGCAATATCA
19794717 TCA
1 TCA
19794720 CACGCACTCC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.30, C:0.34, G:0.11, T:0.25
Consensus pattern (35 bp):
TCATGTGCACTCCCTACACGCACAAGGCAATATCA
Found at i:19794727 original size:35 final size:35
Alignment explanation
Indices: 19794653--19794730 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 35
19794643 TAGCTCATGT
***
19794653 GCACTCCCTACACGCACAAGGCAATATCATCATGT
1 GCACTCCCTACACGCACAAGGCAATATCATCACAC
***
19794688 GCACTCCCTACACGCACATTTCAATATCATCACAC
1 GCACTCCCTACACGCACAAGGCAATATCATCACAC
19794723 GCACTCCC
1 GCACTCCC
19794731 GCCCACATCA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.29, C:0.40, G:0.10, T:0.21
Consensus pattern (35 bp):
GCACTCCCTACACGCACAAGGCAATATCATCACAC
Found at i:19795567 original size:10 final size:10
Alignment explanation
Indices: 19795552--19795580 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
19795542 GCCTTTCCTA
19795552 ACATATCCAC
1 ACATATCCAC
19795562 ACATATCCAC
1 ACATATCCAC
19795572 ACATATCCA
1 ACATATCCA
19795581 AACTTCCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.21
Consensus pattern (10 bp):
ACATATCCAC
Found at i:19800732 original size:12 final size:12
Alignment explanation
Indices: 19800715--19800744 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
19800705 CCATCCTTTC
19800715 TCTCTTTTTCTT
1 TCTCTTTTTCTT
19800727 TCTCTTTTTCTT
1 TCTCTTTTTCTT
*
19800739 CCTCTT
1 TCTCTT
19800745 GGGTGGAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (12 bp):
TCTCTTTTTCTT
Found at i:19801208 original size:17 final size:17
Alignment explanation
Indices: 19801186--19801221 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
19801176 CACCAATCTC
19801186 TTTACATGCAAATAGAT
1 TTTACATGCAAATAGAT
19801203 TTTACATGCAAATAGAT
1 TTTACATGCAAATAGAT
19801220 TT
1 TT
19801222 AGGCTTATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (17 bp):
TTTACATGCAAATAGAT
Found at i:19806198 original size:2 final size:2
Alignment explanation
Indices: 19806155--19806190 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
19806145 AAACAAAATC
*
19806155 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AC AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19806191 AAATATATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:19809376 original size:46 final size:46
Alignment explanation
Indices: 19809284--19809380 Score: 110
Period size: 46 Copynumber: 2.1 Consensus size: 46
19809274 AATTATAATT
**
19809284 ATTTTTGTATTTAGGATAAATATGTGATAAAATATAATTATGGATA
1 ATTTTTGTATTTAGGATAAATATGTGATAAAATATAATTAACGATA
* *
19809330 ATTTTTGCT-TTTGGGATAAATATGT-ATTTAAATTATAA-TAACGATA
1 ATTTTTG-TATTTAGGATAAATATGTGA--TAAAATATAATTAACGATA
19809376 ATTTT
1 ATTTT
19809381 GTTCTTTATG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
45 1 0.02
46 33 0.75
47 10 0.23
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.46
Consensus pattern (46 bp):
ATTTTTGTATTTAGGATAAATATGTGATAAAATATAATTAACGATA
Found at i:19810806 original size:2 final size:2
Alignment explanation
Indices: 19810794--19810823 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
19810784 ACCATATACC
*
19810794 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19810824 CAATCATCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19810911 original size:42 final size:40
Alignment explanation
Indices: 19810864--19810960 Score: 131
Period size: 42 Copynumber: 2.3 Consensus size: 40
19810854 CATCTCATAT
19810864 GCAACGGCTTATGCACACTCCCACTCACACATAGTCGGGTCA
1 GCAACGGCTTATG--CACTCCCACTCACACATAGTCGGGTCA
**
19810906 GCAACGGCTTTTATGCACTCCCACTTGCACATAGTCGGGTCA
1 GCAACGGC--TTATGCACTCCCACTCACACATAGTCGGGTCA
*
19810948 GCAACGACTTATG
1 GCAACGGCTTATG
19810961 TGCATTCCTA
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
40 5 0.10
42 40 0.80
44 5 0.10
ACGTcount: A:0.25, C:0.32, G:0.21, T:0.23
Consensus pattern (40 bp):
GCAACGGCTTATGCACTCCCACTCACACATAGTCGGGTCA
Found at i:19810974 original size:42 final size:42
Alignment explanation
Indices: 19810879--19810989 Score: 143
Period size: 42 Copynumber: 2.6 Consensus size: 42
19810869 GGCTTATGCA
** * *
19810879 CACTCCCACTCACACATAGTCGGGTCAGCAACGGCTTTTATG
1 CACTCCCACTTGCACATAGTCGGGTCAGCAACGACTTATATG
*
19810921 CACTCCCACTTGCACATAGTCGGGTCAGCAACGACTTATGTG
1 CACTCCCACTTGCACATAGTCGGGTCAGCAACGACTTATATG
* *
19810963 CATTCCTACTTGCACATAG-CTGGGTCA
1 CACTCCCACTTGCACATAGTC-GGGTCA
19810990 ATATCATTAC
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
41 1 0.02
42 60 0.98
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.25
Consensus pattern (42 bp):
CACTCCCACTTGCACATAGTCGGGTCAGCAACGACTTATATG
Found at i:19821278 original size:42 final size:42
Alignment explanation
Indices: 19821231--19821349 Score: 148
Period size: 42 Copynumber: 2.8 Consensus size: 42
19821221 TATGCAACGG
* *
19821231 CTTATGCGCACTCCCACACGCACATAGCCAGGTCAGCAATAA
1 CTTATGCGCACTCCCACTCGCACATAGCCAGGTCAGCAACAA
* * * **
19821273 CTTATGTGCACTCCCACTCACACAAAGCCAGGTCAGCAACGG
1 CTTATGCGCACTCCCACTCGCACATAGCCAGGTCAGCAACAA
* * *
19821315 CTTATGCGCCCTCCTACTCGCACATAGCCGGGTCA
1 CTTATGCGCACTCCCACTCGCACATAGCCAGGTCA
19821350 ATATCATTAC
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.26, C:0.37, G:0.18, T:0.18
Consensus pattern (42 bp):
CTTATGCGCACTCCCACTCGCACATAGCCAGGTCAGCAACAA
Found at i:19822499 original size:35 final size:35
Alignment explanation
Indices: 19822403--19822574 Score: 122
Period size: 35 Copynumber: 5.0 Consensus size: 35
19822393 GCCACTAAGC
* *
19822403 TATTGCCAATGAGTGAGGCAGAAATACCA-ACATCA
1 TATTGCCAATGAGTGGGGTAGAAATACCACA-ATCA
* * ** **
19822438 TATAGTCAA--AGTGGGCG-A-ATGTACCACAATGT
1 TATTGCCAATGAGTGGG-GTAGAAATACCACAATCA
* * *
19822470 TATTGTCAATGAGTGGGGTAGAACTACCACCATCA
1 TATTGCCAATGAGTGGGGTAGAAATACCACAATCA
*
19822505 TATTGCCAATGAGTGGGGTGGAAATACCATC-ATCA
1 TATTGCCAATGAGTGGGGTAGAAATACCA-CAATCA
* * * * *
19822540 TATTGCTAAAGAGTAGGGTGGAAATACCACCATCA
1 TATTGCCAATGAGTGGGGTAGAAATACCACAATCA
19822575 AATACTCTAA
Statistics
Matches: 110, Mismatches: 19, Indels: 16
0.76 0.13 0.11
Matches are distributed among these distances:
32 16 0.15
33 8 0.07
34 9 0.08
35 76 0.69
36 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (35 bp):
TATTGCCAATGAGTGGGGTAGAAATACCACAATCA
Found at i:19824126 original size:22 final size:22
Alignment explanation
Indices: 19824101--19824143 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
19824091 GGATGGTTGA
19824101 GGTGCCAAGGAGTCATGGCTGT
1 GGTGCCAAGGAGTCATGGCTGT
19824123 GGTGCCAAGGAGTCATGGCTG
1 GGTGCCAAGGAGTCATGGCTG
19824144 CGGCACCACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.42, T:0.21
Consensus pattern (22 bp):
GGTGCCAAGGAGTCATGGCTGT
Found at i:19831462 original size:16 final size:16
Alignment explanation
Indices: 19831438--19831468 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19831428 GCCACTTAAA
19831438 TAGCCTCCAAAATCCT
1 TAGCCTCCAAAATCCT
*
19831454 TAGCTTCCAAAATCC
1 TAGCCTCCAAAATCC
19831469 CATAAGCTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.35, G:0.06, T:0.26
Consensus pattern (16 bp):
TAGCCTCCAAAATCCT
Found at i:19834278 original size:42 final size:42
Alignment explanation
Indices: 19834231--19834356 Score: 180
Period size: 42 Copynumber: 3.0 Consensus size: 42
19834221 CAGCTCATAT
*
19834231 GCATCGGCTTATGCGCACTCCCACTCGCACTTAGCTGGGTCA
1 GCATCGGCTTATGCGCACTCCCACTCGCACATAGCTGGGTCA
* * *
19834273 GCATCGGCTTATGTGCACTCCCACTCGCACATAACCGGGTCA
1 GCATCGGCTTATGCGCACTCCCACTCGCACATAGCTGGGTCA
* ***
19834315 GCATCGGCTTATGCACACTGTTACTCGCACATAGCTGGGTCA
1 GCATCGGCTTATGCGCACTCCCACTCGCACATAGCTGGGTCA
19834357 ATATCATTAC
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 73 1.00
ACGTcount: A:0.20, C:0.33, G:0.23, T:0.24
Consensus pattern (42 bp):
GCATCGGCTTATGCGCACTCCCACTCGCACATAGCTGGGTCA
Found at i:19836564 original size:80 final size:80
Alignment explanation
Indices: 19836425--19836588 Score: 197
Period size: 80 Copynumber: 2.0 Consensus size: 80
19836415 TATGAGTTCC
* * * * * ** *
19836425 ATTTATGAGATTATGACATGTATGCCCTCAGATATATGTGTTGAGAATATCATGTACACTATGGG
1 ATTTATGAGATTATAAAATGCATGCCATCAGATATATGTGTTGAGAATATAATACACACTATGAG
19836490 CGAAGCATG-TGAGTG
66 CGAAGCATGATGA-TG
* *
19836505 ATTTATGAGATTATAAAATGCATGCCATGAGATGTATGTGTTGAG-ATAGTAATACACACTATGA
1 ATTTATGAGATTATAAAATGCATGCCATCAGATATATGTGTTGAGAATA-TAATACACACTATGA
*
19836569 GCTAAGCATGATGATG
65 GCGAAGCATGATGATG
19836585 ATTT
1 ATTT
19836589 GTGAAAGTGT
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
79 3 0.04
80 65 0.92
81 3 0.04
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (80 bp):
ATTTATGAGATTATAAAATGCATGCCATCAGATATATGTGTTGAGAATATAATACACACTATGAG
CGAAGCATGATGATG
Found at i:19838326 original size:79 final size:80
Alignment explanation
Indices: 19838127--19838344 Score: 303
Period size: 80 Copynumber: 2.7 Consensus size: 80
19838117 GGATGTGACA
* * * * * *
19838127 TTAGCCCATTGTGTATATGAAATTCTCAACACATACATCTAATGGCATACATTTCATTATCTCAT
1 TTAGACCATAGTGTACATGAAATTCTCAACACATACATCTCATGGCATACATGTCATAATCTCAT
*
19838192 AATTCATTCCCATTC
66 AATTCATTCCCATGC
* * *
19838207 TTAGTCCATAGTGTACATGACATTCTCATCACATACATCTCATGGCATACATGTCATAATCTCAT
1 TTAGACCATAGTGTACATGAAATTCTCAACACATACATCTCATGGCATACATGTCATAATCTCAT
*
19838272 AATTCATT-TCATGC
66 AATTCATTCCCATGC
* * *
19838286 TTAGACCTTAGTGTACATGATATTCTCAACACATACATCTCATGGCATACATGTTATAA
1 TTAGACCATAGTGTACATGAAATTCTCAACACATACATCTCATGGCATACATGTCATAA
19838345 CCTTATAGAT
Statistics
Matches: 123, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
79 58 0.47
80 65 0.53
ACGTcount: A:0.32, C:0.23, G:0.10, T:0.36
Consensus pattern (80 bp):
TTAGACCATAGTGTACATGAAATTCTCAACACATACATCTCATGGCATACATGTCATAATCTCAT
AATTCATTCCCATGC
Found at i:19847922 original size:68 final size:68
Alignment explanation
Indices: 19847659--19847969 Score: 312
Period size: 68 Copynumber: 4.6 Consensus size: 68
19847649 CACCTACATG
* * * * *
19847659 CTTACTCATCTCATAAGGTATATGGGATTTACATCATATACATAATCTCATGGC---AATTATGC
1 CTTAATCATCTCATATGGTATATGGAATTTACATCATATACATATTCTCATGGCATTAATCATGC
19847721 -TA
66 ATA
* * * * * **
19847723 GCTGAATTATCTCATGTAGTATATGGAATATACATCATATACATATTCTCATGGCATTAATCACA
1 -CTTAATCATCTCATATGGTATATGGAATTTACATCATATACATATTCTCATGGCATTAATCATG
19847788 CATA
65 CATA
* * * * *
19847792 GTTAATCATCTCATGTAGTATATGGAATATACATCATGTACATATTCTCATGGCATTAATCATGC
1 CTTAATCATCTCATATGGTATATGGAATTTACATCATATACATATTCTCATGGCATTAATCATGC
19847857 ATA
66 ATA
* * * *
19847860 CTTAATCATCTCATATGGTATATGGAATTTACATCATATACACCATCCT-ATAGTA-TACATCAT
1 CTTAATCATCTCATATGGTATATGGAATTTACATCATATACA-TATTCTCATGGCATTA-ATCAT
19847923 GCATA
64 GCATA
* ** *
19847928 CTTGATCATC-CTATATGGTATACAGAATTCACATCATATACA
1 CTTAATCATCTC-ATATGGTATATGGAATTTACATCATATACA
19847970 GAATCTTATA
Statistics
Matches: 208, Mismatches: 31, Indels: 11
0.83 0.12 0.04
Matches are distributed among these distances:
65 45 0.22
67 3 0.01
68 154 0.74
69 6 0.03
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (68 bp):
CTTAATCATCTCATATGGTATATGGAATTTACATCATATACATATTCTCATGGCATTAATCATGC
ATA
Found at i:19847989 original size:68 final size:68
Alignment explanation
Indices: 19847845--19847990 Score: 177
Period size: 68 Copynumber: 2.1 Consensus size: 68
19847835 ATTCTCATGG
* ** * *
19847845 CATTAATCATGCATACTTAATCATCTCATATGGTATATGGAATTTACATCATATACACCATCCTA
1 CATTCATCATGCATACTTAATCATCTCATATGGTATACAGAATTCACATCATATACACAATCCTA
*
19847910 TAG
66 TAA
* * * * *
19847913 TATACATCATGCATACTTGATCATC-CTATATGGTATACAGAATTCACATCATATACAGAATCTT
1 CATTCATCATGCATACTTAATCATCTC-ATATGGTATACAGAATTCACATCATATACACAATCCT
19847977 ATAA
65 ATAA
19847981 CATTCATCAT
1 CATTCATCAT
19847991 AACAACATGC
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
67 1 0.02
68 63 0.98
ACGTcount: A:0.36, C:0.21, G:0.08, T:0.35
Consensus pattern (68 bp):
CATTCATCATGCATACTTAATCATCTCATATGGTATACAGAATTCACATCATATACACAATCCTA
TAA
Found at i:19849446 original size:35 final size:35
Alignment explanation
Indices: 19849407--19849655 Score: 261
Period size: 35 Copynumber: 7.1 Consensus size: 35
19849397 TTAACTGTTT
* *
19849407 AATTTAGTCAATTAGGCCCAATAACTTAATTAAAC
1 AATTTAATTAATTAGGCCCAATAACTTAATTAAAC
* * * * *
19849442 AATTTAATTAATTAAGACCAACAATTTAATTAAAT
1 AATTTAATTAATTAGGCCCAATAACTTAATTAAAC
* * *
19849477 AATTTTAATCAATTAGGCCCAATGACTCAATTAAAC
1 AA-TTTAATTAATTAGGCCCAATAACTTAATTAAAC
* * ****
19849513 AAATTTAATCAATTAGTCCCAATAACTTAATTGTTT
1 -AATTTAATTAATTAGGCCCAATAACTTAATTAAAC
* * *
19849549 AATTTAATTAATTAGGTCGAATGACTTAATTAAAC
1 AATTTAATTAATTAGGCCCAATAACTTAATTAAAC
* *
19849584 AATTTAATTAATTAGGCCCAATGATTTAATTAAAC
1 AATTTAATTAATTAGGCCCAATAACTTAATTAAAC
*
19849619 AATTTAATTAATTAGG--C-ACAACTTAATTAAAC
1 AATTTAATTAATTAGGCCCAATAACTTAATTAAAC
19849651 AATTT
1 AATTT
19849656 TAATCAAGTG
Statistics
Matches: 175, Mismatches: 37, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
32 17 0.10
33 1 0.01
35 104 0.59
36 51 0.29
37 2 0.01
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (35 bp):
AATTTAATTAATTAGGCCCAATAACTTAATTAAAC
Found at i:19849495 original size:71 final size:70
Alignment explanation
Indices: 19849406--19849655 Score: 274
Period size: 71 Copynumber: 3.6 Consensus size: 70
19849396 CTTAACTGTT
* * *
19849406 TAATTTAGTCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAGACCAACAATTTAA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCCCAATAATTTAA
19849471 TTAAA
66 TTAAA
* * * *
19849476 TAATTTTAATCAATTAGGCCCAATGACTCAATTAAACAAATTTAATCAATT-AGTCCCAATAACT
1 TAA-TTTAATCAATTAGGCCCAATAACTTAATTAAAC-AATTTAATTAATTAAG-CCCAATAATT
***
19849540 TAATTGTT
63 TAATTAAA
* * * * * *
19849548 TAATTTAATTAATTAGGTCGAATGACTTAATTAAACAATTTAATTAATTAGGCCCAATGATTTAA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCCCAATAATTTAA
19849613 TTAAA
66 TTAAA
* * *
19849618 CAATTTAATTAATTAGG--C-ACAACTTAATTAAACAATTT
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTT
19849656 TAATCAAGTG
Statistics
Matches: 151, Mismatches: 25, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
67 18 0.12
70 44 0.29
71 62 0.41
72 27 0.18
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (70 bp):
TAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCCCAATAATTTAA
TTAAA
Found at i:19849541 original size:142 final size:139
Alignment explanation
Indices: 19849387--19849662 Score: 374
Period size: 142 Copynumber: 2.0 Consensus size: 139
19849377 CCTTAAGAAG
*
19849387 CCCAATTAACTTAACTGTTTAATTTAGTCAATTAGGCCCAATAACTTAATTAAACAATTTAATTA
1 CCCAATTAACTTAACTGTTTAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTA
* *
19849452 ATTAAGACCAACAATTTAATTAAATAATTTTAATCAATTAGGCCCAATGACTCAATTAAACAAAT
66 ATTAAGACCAACAATTTAATTAAACAA-TTTAATCAATTAGGCAC-A--ACTCAATTAAACAAAT
19849517 TTAATCAATTAGT
127 TTAATCAATTAGT
* * * * *
19849530 CCCAA-TAACTTAATTGTTTAATTTAATTAATTAGGTCGAATGACTTAATTAAACAATTTAATTA
1 CCCAATTAACTTAACTGTTTAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTA
* * ** * * *
19849594 ATTAGGCCCAATGATTTAATTAAACAATTTAATTAATTAGGCACAACTTAATTAAACAATTTTAA
66 ATTAAGACCAACAATTTAATTAAACAATTTAATCAATTAGGCACAACTCAATTAAACAAATTTAA
19849659 TCAA
131 TCAA
19849663 GTGCTTGAGA
Statistics
Matches: 118, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
138 22 0.19
140 1 0.01
141 15 0.13
142 75 0.64
143 5 0.04
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (139 bp):
CCCAATTAACTTAACTGTTTAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTA
ATTAAGACCAACAATTTAATTAAACAATTTAATCAATTAGGCACAACTCAATTAAACAAATTTAA
TCAATTAGT
Found at i:19868098 original size:43 final size:43
Alignment explanation
Indices: 19868018--19868143 Score: 159
Period size: 43 Copynumber: 3.0 Consensus size: 43
19868008 TTATGTGATA
* * *
19868018 ATGATGGCCCAGCTATGTGCG-TGTGGGAGTGCACATGAGCTT
1 ATGATGACCAAGCTATGTGCGATGTGGGAGTGCACATGAGCTG
19868060 ATGATGACCAAGCTATGTGCGATGTGGGAGTGCACATGAGCTG
1 ATGATGACCAAGCTATGTGCGATGTGGGAGTGCACATGAGCTG
* * *
19868103 ATGATAACCCAA-CTATGTGC-AAGTAGAGAGTGCACATGAGC
1 ATGATGA-CCAAGCTATGTGCGATGT-GGGAGTGCACATGAGC
19868144 AGAGTATGGC
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
42 22 0.29
43 49 0.65
44 4 0.05
ACGTcount: A:0.27, C:0.18, G:0.32, T:0.23
Consensus pattern (43 bp):
ATGATGACCAAGCTATGTGCGATGTGGGAGTGCACATGAGCTG
Found at i:19870963 original size:35 final size:35
Alignment explanation
Indices: 19870938--19871193 Score: 259
Period size: 35 Copynumber: 7.3 Consensus size: 35
19870928 TTAATTGTTT
*
19870938 AATTTAATCGATTAGGCCCAATAACTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* * * *
19870973 AATTTAATTAATTA-ACCCTAACAATTTAATTAAAC
1 AATTTAATCAATTAGGCCC-AATAACTTAATTAAAC
* *
19871008 AATTTTAATCAATTAGGCCCAATGACTCAATTAAAC
1 AA-TTTAATCAATTAGGCCCAATAACTTAATTAAAC
* ****
19871044 AAATTTAATCAATGAGGCCCAATAACTTAATTGTTT
1 -AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* *
19871080 AATTTAATTAATTAGGCCCAATAACTTATTTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* ** *
19871115 AATTTAATTAATTAGGCCCAACGATTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* * *
19871150 AATTTAATTAATTAGG--C-ACAACTTAATTAAAA
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
19871182 AATTTTAATCAA
1 AA-TTTAATCAA
19871194 GTACTTGAGA
Statistics
Matches: 183, Mismatches: 33, Indels: 12
0.80 0.14 0.05
Matches are distributed among these distances:
32 14 0.08
33 9 0.05
34 3 0.02
35 103 0.56
36 49 0.27
37 5 0.03
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (35 bp):
AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
Found at i:19871029 original size:107 final size:106
Alignment explanation
Indices: 19870938--19871186 Score: 265
Period size: 107 Copynumber: 2.4 Consensus size: 106
19870928 TTAATTGTTT
* * *
19870938 AATTTAATCGATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTA-ACCCTAACAATTTAA
1 AATTTAATCAATGAGGCCCAATAACTTAATTAAACAATTTAATTAATTAGACCC-AACAACTTAA
*
19871002 TTAAACAATTTTAATCAATTAGGCCCAATGACTCAATTAAACA
65 TTAAACAA-TTTAATCAATTAGGCCCAATAACTCAATTAAACA
**** * * *
19871045 AATTTAATCAATGAGGCCCAATAACTTAATTGTTTAATTTAATTAATTAGGCCCAATAACTTATT
1 AATTTAATCAATGAGGCCCAATAACTTAATTAAACAATTTAATTAATTAGACCCAACAACTTAAT
* ** * *
19871110 TAAACAATTTAATTAATTAGGCCCAACGATTTAATTAAAC-
66 TAAACAATTTAATCAATTAGGCCCAATAACTCAATTAAACA
* * * *
19871150 AATTTAATTAATTAGG--C-ACAACTTAATTAAAAAATTT
1 AATTTAATCAATGAGGCCCAATAACTTAATTAAACAATTT
19871187 TAATCAAGTA
Statistics
Matches: 120, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
102 15 0.12
103 1 0.01
105 14 0.12
106 29 0.24
107 58 0.48
108 3 0.03
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (106 bp):
AATTTAATCAATGAGGCCCAATAACTTAATTAAACAATTTAATTAATTAGACCCAACAACTTAAT
TAAACAATTTAATCAATTAGGCCCAATAACTCAATTAAACA
Found at i:19872787 original size:15 final size:15
Alignment explanation
Indices: 19872746--19872792 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
19872736 TTTTGGATTC
*
19872746 AATAA-AAATATCAA
1 AATAATAAAAATCAA
19872760 AATAATAAAAATCCAA
1 AATAATAAAAAT-CAA
*
19872776 AA-AATCAAAATCAA
1 AATAATAAAAATCAA
19872790 AAT
1 AAT
19872793 CTTGCTTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 10 0.36
15 13 0.46
16 5 0.18
ACGTcount: A:0.70, C:0.11, G:0.00, T:0.19
Consensus pattern (15 bp):
AATAATAAAAATCAA
Found at i:19874565 original size:30 final size:28
Alignment explanation
Indices: 19874530--19874609 Score: 90
Period size: 31 Copynumber: 2.7 Consensus size: 28
19874520 GCTCCAAACA
19874530 AAAGGTAGTGTAAAGGTTATACCTCTTTGG
1 AAAGGTAGTGT-AAGGTTATACCTCTTT-G
*
19874560 AAAGGTAATGTTGAAGGTTATACCTCTTTG
1 AAAGGTAGTG-T-AAGGTTATACCTCTTTG
*
19874590 AAAGATTAGTG-AAGGTTATA
1 AAAG-GTAGTGTAAGGTTATA
19874610 ACTCCTCTAG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
28 9 0.20
30 14 0.32
31 21 0.48
ACGTcount: A:0.34, C:0.07, G:0.25, T:0.34
Consensus pattern (28 bp):
AAAGGTAGTGTAAGGTTATACCTCTTTG
Found at i:19874577 original size:31 final size:28
Alignment explanation
Indices: 19874542--19874609 Score: 91
Period size: 31 Copynumber: 2.3 Consensus size: 28
19874532 AGGTAGTGTA
*
19874542 AAGGTTATACCTCTTTGGAAAGGTAATGTTG
1 AAGGTTATACCTCTTT-GAAAGATAA-G-TG
*
19874573 AAGGTTATACCTCTTTGAAAGATTAGTG
1 AAGGTTATACCTCTTTGAAAGATAAGTG
19874601 AAGGTTATA
1 AAGGTTATA
19874610 ACTCCTCTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
28 11 0.31
29 1 0.03
30 7 0.20
31 16 0.46
ACGTcount: A:0.32, C:0.09, G:0.24, T:0.35
Consensus pattern (28 bp):
AAGGTTATACCTCTTTGAAAGATAAGTG
Found at i:19881536 original size:22 final size:22
Alignment explanation
Indices: 19881510--19881556 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
19881500 TGAAGGAAAG
19881510 TCATTCACATTGAAGAGTAGAT
1 TCATTCACATTGAAGAGTAGAT
19881532 TCATTCACATTGAAGAGTAGAT
1 TCATTCACATTGAAGAGTAGAT
19881554 TCA
1 TCA
19881557 CTACATCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (22 bp):
TCATTCACATTGAAGAGTAGAT
Found at i:19883051 original size:14 final size:14
Alignment explanation
Indices: 19883034--19883108 Score: 91
Period size: 14 Copynumber: 5.5 Consensus size: 14
19883024 TGGAATAAAA
19883034 TAATATTAAAATAT
1 TAATATTAAAATAT
* *
19883048 TAAT-TTAAAAAAA
1 TAATATTAAAATAT
19883061 TAATATTAAAATAT
1 TAATATTAAAATAT
* * *
19883075 TAGT-TTAAAAAAA
1 TAATATTAAAATAT
19883088 TAATATTAAAATAT
1 TAATATTAAAATAT
19883102 TAATATT
1 TAATATT
19883109 TTATTTAGTG
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
13 21 0.43
14 28 0.57
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (14 bp):
TAATATTAAAATAT
Found at i:19883065 original size:27 final size:27
Alignment explanation
Indices: 19883030--19883105 Score: 143
Period size: 27 Copynumber: 2.8 Consensus size: 27
19883020 TTTTTGGAAT
19883030 AAAATAATATTAAAATATTAATTTAAA
1 AAAATAATATTAAAATATTAATTTAAA
*
19883057 AAAATAATATTAAAATATTAGTTTAAA
1 AAAATAATATTAAAATATTAATTTAAA
19883084 AAAATAATATTAAAATATTAAT
1 AAAATAATATTAAAATATTAAT
19883106 ATTTTATTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (27 bp):
AAAATAATATTAAAATATTAATTTAAA
Found at i:19884710 original size:35 final size:35
Alignment explanation
Indices: 19884662--19884769 Score: 162
Period size: 35 Copynumber: 3.1 Consensus size: 35
19884652 GGAGTGTGTG
* *
19884662 TGATGATAGTGAAATGTGCGTGTAGGGAATGCACA
1 TGATGATATTGAAATGTGCGTGTAGGGAGTGCACA
*
19884697 TGATGATATTGAAATGTGTGTGTAGGGAGTGCACA
1 TGATGATATTGAAATGTGCGTGTAGGGAGTGCACA
***
19884732 TGATGATATTGCCTTGTGCGTGTAGGGAGTGCACA
1 TGATGATATTGAAATGTGCGTGTAGGGAGTGCACA
19884767 TGA
1 TGA
19884770 GCTTAGTAAG
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 66 1.00
ACGTcount: A:0.27, C:0.09, G:0.34, T:0.30
Consensus pattern (35 bp):
TGATGATATTGAAATGTGCGTGTAGGGAGTGCACA
Found at i:19885391 original size:2 final size:2
Alignment explanation
Indices: 19885384--19885413 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
19885374 TTGGGGATGT
19885384 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19885414 CTTGGTTCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19886183 original size:28 final size:28
Alignment explanation
Indices: 19886152--19886455 Score: 334
Period size: 29 Copynumber: 10.8 Consensus size: 28
19886142 TGTTATGTTC
* * * *
19886152 TCTAAATTGAGGCAAATATGCTTTCTTG
1 TCTAAATTAAGACAAACATGTTTTCTTG
* * * *
19886180 TCTAGATTAAGGCAAAACATATTTTTTTG
1 TCTAAATTAAGAC-AAACATGTTTTCTTG
*
19886209 TCTTAAATTAAGACAAACATATTTTCTTG
1 TC-TAAATTAAGACAAACATGTTTTCTTG
*
19886238 TCTAAATTAAGACAATACATGTTTACTTG
1 TCTAAATTAAGACAA-ACATGTTTTCTTG
*
19886267 TTTAAATTAAGAC-AACTATGTTTCTCTTG
1 TCTAAATTAAGACAAAC-ATGTTT-TCTTG
*
19886296 TCTAAATTAAGATAAAACATGTTTTCTT-
1 TCTAAATTAAGA-CAAACATGTTTTCTTG
19886324 TC-----TAAGACATAACATGTTTTCTTG
1 TCTAAATTAAGACA-AACATGTTTTCTTG
*
19886348 TCTAAATTAAGACAAACATATTTTCTTG
1 TCTAAATTAAGACAAACATGTTTTCTTG
19886376 TCTAAATTAAGACCAAACATGTTTTCTTG
1 TCTAAATTAAGA-CAAACATGTTTTCTTG
*
19886405 TCTAAATTAAGACAAAACATGTTTTCTTT
1 TCTAAATTAAGAC-AAACATGTTTTCTTG
* *
19886434 TGTAAATTAAGACATACATGTT
1 TCTAAATTAAGACAAACATGTT
19886456 AATGCTGTCA
Statistics
Matches: 239, Mismatches: 21, Indels: 32
0.82 0.07 0.11
Matches are distributed among these distances:
22 1 0.00
23 18 0.08
24 2 0.01
27 2 0.01
28 67 0.28
29 131 0.55
30 15 0.06
31 3 0.01
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (28 bp):
TCTAAATTAAGACAAACATGTTTTCTTG
Found at i:19886355 original size:138 final size:138
Alignment explanation
Indices: 19886195--19886445 Score: 391
Period size: 138 Copynumber: 1.8 Consensus size: 138
19886185 ATTAAGGCAA
*
19886195 AACATATTTTTTTGTCTTAAATTAAGACAAACATATTTTCTTGTCTAAATTAAGA-CAATACATG
1 AACATATTTTCTTGTCTTAAATTAAGACAAACATATTTTCTTGTCTAAATTAAGACCAA-ACATG
*
19886259 TTTACTTGTTTAAATTAAGAC-AACTATGTTTCTCTTGTCTAAATTAAGATAAAACATGTTTTCT
65 TTTACTTGTCTAAATTAAGACAAAC-ATGTTT-TCTTGTCTAAATTAAGATAAAACATGTTTTCT
19886323 TTCTAAGACAT
128 TTCTAAGACAT
*
19886334 AACATGTTTTCTTGTC-TAAATTAAGACAAACATATTTTCTTGTCTAAATTAAGACCAAACATGT
1 AACATATTTTCTTGTCTTAAATTAAGACAAACATATTTTCTTGTCTAAATTAAGACCAAACATGT
* * *
19886398 TTTCTTGTCTAAATTAAGACAAAACATGTTTTCTTTTGTAAATTAAGA
66 TTACTTGTCTAAATTAAGAC-AAACATGTTTTCTTGTCTAAATTAAGA
19886446 CATACATGTT
Statistics
Matches: 103, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
138 77 0.75
139 23 0.22
140 3 0.03
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.41
Consensus pattern (138 bp):
AACATATTTTCTTGTCTTAAATTAAGACAAACATATTTTCTTGTCTAAATTAAGACCAAACATGT
TTACTTGTCTAAATTAAGACAAACATGTTTTCTTGTCTAAATTAAGATAAAACATGTTTTCTTTC
TAAGACAT
Found at i:19886410 original size:109 final size:109
Alignment explanation
Indices: 19886217--19886433 Score: 341
Period size: 109 Copynumber: 2.0 Consensus size: 109
19886207 TGTCTTAAAT
* *
19886217 TAAGACAAACATATTTTCTTGTCTAAATTAAGACAATACATGTTTACTTGTTTAAATTAAGACAA
1 TAAGACAAACATATTTTCTTGTCTAAATTAAGACAATACATATTTACTTGTCTAAATTAAGACAA
*
19886282 CTATGTTTCTCTTGTCTAAATTAAGATAAAACATGTTTTCTTTC
66 CTATGTTTCTCTTGTCTAAATTAAGACAAAACATGTTTTCTTTC
* *
19886326 TAAGACATAACATGTTTTCTTGTCTAAATTAAGACAA-ACATATTTTCTTGTCTAAATTAAGACC
1 TAAGACA-AACATATTTTCTTGTCTAAATTAAGACAATACATATTTACTTGTCTAAATTAAGA-C
19886390 AAAC-ATGTTT-TCTTGTCTAAATTAAGACAAAACATGTTTTCTTT
64 -AACTATGTTTCTCTTGTCTAAATTAAGACAAAACATGTTTTCTTT
19886434 TGTAAATTAA
Statistics
Matches: 100, Mismatches: 5, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
109 62 0.62
110 35 0.35
111 3 0.03
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (109 bp):
TAAGACAAACATATTTTCTTGTCTAAATTAAGACAATACATATTTACTTGTCTAAATTAAGACAA
CTATGTTTCTCTTGTCTAAATTAAGACAAAACATGTTTTCTTTC
Found at i:19888340 original size:43 final size:42
Alignment explanation
Indices: 19888277--19888412 Score: 157
Period size: 43 Copynumber: 3.2 Consensus size: 42
19888267 AGCCAGCTTA
* *
19888277 TCATCATCGACTTATACGCACTCCCTACTCGCACATAGCCAGG
1 TCATCATCGGCTTATGCGCACTCCCTACTCGCACATAGCC-GG
*
19888320 TCATCATCGGCTTATGCGCACTCCCTACTTGCACATAGCCGG
1 TCATCATCGGCTTATGCGCACTCCCTACTCGCACATAGCCGG
* * * * *
19888362 CTCATCATCAGCTCATGTGCACTCTC-ACATCGCACATAGCTGGG
1 -TCATCATCGGCTTATGCGCACTCCCTAC-TCGCACATAGC-CGG
19888406 TCATCAT
1 TCATCAT
19888413 TATCACACAA
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
42 4 0.05
43 75 0.93
44 2 0.02
ACGTcount: A:0.23, C:0.35, G:0.16, T:0.26
Consensus pattern (42 bp):
TCATCATCGGCTTATGCGCACTCCCTACTCGCACATAGCCGG
Found at i:19889253 original size:11 final size:11
Alignment explanation
Indices: 19889223--19889255 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
19889213 AGGAAGAAGA
19889223 AAAGTTGCTGG
1 AAAGTTGCTGG
19889234 -AAGTTGCTGG
1 AAAGTTGCTGG
*
19889244 AAATTTGCTGG
1 AAAGTTGCTGG
19889255 A
1 A
19889256 GCTTTAGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.27, C:0.09, G:0.33, T:0.30
Consensus pattern (11 bp):
AAAGTTGCTGG
Found at i:19895571 original size:43 final size:43
Alignment explanation
Indices: 19895521--19895611 Score: 137
Period size: 43 Copynumber: 2.1 Consensus size: 43
19895511 CTGACTTATG
* *
19895521 ATCATCGACTTATGCACACTCCCTACTCGCATATAGCCGGCTC
1 ATCATCGACTTATGCACACTCCCTACTCGCACATAGCCAGCTC
* **
19895564 ATCATCGACTTATGCGCACTCTTTACTCGCACATAGCCAGCTC
1 ATCATCGACTTATGCACACTCCCTACTCGCACATAGCCAGCTC
19895607 ATCAT
1 ATCAT
19895612 TATCTCATGT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.24, C:0.35, G:0.13, T:0.27
Consensus pattern (43 bp):
ATCATCGACTTATGCACACTCCCTACTCGCACATAGCCAGCTC
Found at i:19898249 original size:40 final size:39
Alignment explanation
Indices: 19898151--19898255 Score: 131
Period size: 38 Copynumber: 2.7 Consensus size: 39
19898141 TGATAGTGTT
* * * *
19898151 CATGTGCATGATGTGGGGGGATGTACACGATGGCACTGA
1 CATGTGCACGATGTGGGGGGATGCACACGATGACACCGA
* * *
19898190 C-TGTGCACGATGTGAGGGGATGCACACGATGACTCCGG
1 CATGTGCACGATGTGGGGGGATGCACACGATGACACCGA
19898228 CTATGTGCACGATGTGGGGGGATGCACA
1 C-ATGTGCACGATGTGGGGGGATGCACA
19898256 TGAGCTGGGT
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
38 31 0.55
39 1 0.02
40 24 0.43
ACGTcount: A:0.22, C:0.19, G:0.38, T:0.21
Consensus pattern (39 bp):
CATGTGCACGATGTGGGGGGATGCACACGATGACACCGA
Found at i:19909207 original size:54 final size:54
Alignment explanation
Indices: 19909145--19909294 Score: 237
Period size: 54 Copynumber: 2.8 Consensus size: 54
19909135 CACCACCATT
* * *
19909145 TCACCCAACTCATGTGCATCCCCCCAGATTGTGCACATAGCCTGACACCCAGTC
1 TCACCCAACTCATGTGCATCCCCCCACATTGTGCACATAGCCGGACACCCAATC
**
19909199 TCACCCAACTCATGTGCATCCCCCCACATCATGCACATAGCCGGACACCCAATC
1 TCACCCAACTCATGTGCATCCCCCCACATTGTGCACATAGCCGGACACCCAATC
* *
19909253 TCACCCAGCTCATGTGCATCCCCCAACATTGTGCACATAGCC
1 TCACCCAACTCATGTGCATCCCCCCACATTGTGCACATAGCC
19909295 AAAGTCATCG
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 87 1.00
ACGTcount: A:0.25, C:0.42, G:0.13, T:0.19
Consensus pattern (54 bp):
TCACCCAACTCATGTGCATCCCCCCACATTGTGCACATAGCCGGACACCCAATC
Found at i:19909567 original size:2 final size:2
Alignment explanation
Indices: 19909560--19909587 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19909550 TTATGACATA
19909560 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19909588 CAATATTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19920056 original size:2 final size:2
Alignment explanation
Indices: 19920043--19920091 Score: 89
Period size: 2 Copynumber: 24.0 Consensus size: 2
19920033 TTAGCCAAGC
19920043 AT AT ACT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19920086 AT AT AT
1 AT AT AT
19920092 CAATCATCAT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 44 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19920194 original size:42 final size:42
Alignment explanation
Indices: 19920132--19920417 Score: 319
Period size: 42 Copynumber: 6.8 Consensus size: 42
19920122 CATCTCATAT
* * *
19920132 GCAACGGCTTATGCGTACTCCCACTCGCATATAGCTAGGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCTAGGTCA
** **
19920174 GCAACGGCTTATGTGCACTCCCACTCATACATAGCCGGGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCTAGGTCA
* ** *
19920216 GCAACTG-TTATGTGCACTCTTACTCGCACATAG-TCGAGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCTAG-GTCA
* * * *
19920257 GCAACGGCTTATGTGCACTCCCACTCACAGATGGCCAGGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCTAGGTCA
* *
19920299 GCAACGGCTTATGTGCACTCCTACTCGCACATAGC-CGAGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCTAG-GTCA
* *
19920341 GCAACGGCTTATGTGCACTCCCACTCACACATAGCTTA-GTTA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGC-TAGGTCA
* * *
19920383 GCAATGGCTTATGTGCACTTCTACTCGCACATAGC
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGC
19920418 CGAGTCCATA
Statistics
Matches: 203, Mismatches: 35, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
40 1 0.00
41 33 0.16
42 168 0.83
43 1 0.00
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.24
Consensus pattern (42 bp):
GCAACGGCTTATGTGCACTCCCACTCGCACATAGCTAGGTCA
Found at i:19920349 original size:84 final size:84
Alignment explanation
Indices: 19920132--19920423 Score: 401
Period size: 84 Copynumber: 3.5 Consensus size: 84
19920122 CATCTCATAT
* * * * *
19920132 GCAACGGCTTATGCGTACTCCCACTCGCATATAG-CTAGGTCAGCAACGGCTTATGTGCACTCCC
1 GCAACGGCTTATGTGCACTCCTACTCGCACATAGCCGA-GTCAGCAACGGCTTATGTGCACTCCC
* *
19920196 ACTCATACATAGCCGGGTCA
65 ACTCACACATAGCCAGGTCA
* * *
19920216 GCAACTG-TTATGTGCACTCTTACTCGCACATAGTCGAGTCAGCAACGGCTTATGTGCACTCCCA
1 GCAACGGCTTATGTGCACTCCTACTCGCACATAGCCGAGTCAGCAACGGCTTATGTGCACTCCCA
* *
19920280 CTCACAGATGGCCAGGTCA
66 CTCACACATAGCCAGGTCA
19920299 GCAACGGCTTATGTGCACTCCTACTCGCACATAGCCGAGTCAGCAACGGCTTATGTGCACTCCCA
1 GCAACGGCTTATGTGCACTCCTACTCGCACATAGCCGAGTCAGCAACGGCTTATGTGCACTCCCA
* *
19920364 CTCACACATAGCTTA-GTTA
66 CTCACACATAGC-CAGGTCA
* *
19920383 GCAATGGCTTATGTGCACTTCTACTCGCACATAGCCGAGTC
1 GCAACGGCTTATGTGCACTCCTACTCGCACATAGCCGAGTC
19920424 CATATCAACA
Statistics
Matches: 185, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
83 69 0.37
84 115 0.62
85 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.24
Consensus pattern (84 bp):
GCAACGGCTTATGTGCACTCCTACTCGCACATAGCCGAGTCAGCAACGGCTTATGTGCACTCCCA
CTCACACATAGCCAGGTCA
Found at i:19924437 original size:54 final size:54
Alignment explanation
Indices: 19924222--19924437 Score: 315
Period size: 54 Copynumber: 4.0 Consensus size: 54
19924212 ATAAGCACAT
* * *
19924222 ACACCACCATTTCACCCAGCTCATGTGCATCCCCCCAGATCGTGCACATAGCTAG
1 ACACC-CCATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCTGG
* * *
19924277 ACACCCCGTCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCCGA
1 ACACCCCATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCTGG
* * * * *
19924331 ACATCCTATCTCACCCAACTCATGTGCATCCCCCCACACCCTGCACATAGCTGG
1 ACACCCCATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCTGG
*
19924385 ACACCCCATCTCACCCAGCTCATGTGCATCCCCTCACATCGTGCACATAGCTG
1 ACACCCCATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCTG
19924438 AAGTCATCGT
Statistics
Matches: 141, Mismatches: 20, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
54 136 0.96
55 5 0.04
ACGTcount: A:0.24, C:0.44, G:0.13, T:0.19
Consensus pattern (54 bp):
ACACCCCATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCTGG
Found at i:19924535 original size:41 final size:41
Alignment explanation
Indices: 19924407--19924590 Score: 165
Period size: 41 Copynumber: 4.6 Consensus size: 41
19924397 ACCCAGCTCA
* *
19924407 TGTGCATCCCCTCACATCGTGCACATAGCTGAA--GTCATCG
1 TGTGCATCCCCTCACATCGTGCACA-AGCAGAATCATCATCG
* *
19924447 TGTGCATCCCCTCACATTGTGTACAAGC--AAT-ATCATCG
1 TGTGCATCCCCTCACATCGTGCACAAGCAGAATCATCATCG
* *
19924485 CTTTATGCATCCCCCCACATCGTGCACAAG-AGATATCATCATCG
1 ---TGTGCATCCCCTCACATCGTGCACAAGCAGA-ATCATCATCG
**
19924529 TGTGCATCCCCTCACATCGTGCAC-AG-TTAATGC--CATCG
1 TGTGCATCCCCTCACATCGTGCACAAGCAGAAT-CATCATCG
19924567 TGTGCATCCCC-CACATCGTGCACA
1 TGTGCATCCCCTCACATCGTGCACA
19924591 CGAGCAATAT
Statistics
Matches: 123, Mismatches: 11, Indels: 22
0.79 0.07 0.14
Matches are distributed among these distances:
37 14 0.11
38 22 0.18
39 5 0.04
40 27 0.22
41 45 0.37
42 1 0.01
43 2 0.02
44 7 0.06
ACGTcount: A:0.24, C:0.34, G:0.17, T:0.26
Consensus pattern (41 bp):
TGTGCATCCCCTCACATCGTGCACAAGCAGAATCATCATCG
Found at i:19924566 original size:82 final size:78
Alignment explanation
Indices: 19924441--19924590 Score: 194
Period size: 82 Copynumber: 1.9 Consensus size: 78
19924431 ATAGCTGAAG
* * *
19924441 TCATCGTGTGCATCCCCTCACATTGTGTACAAGCAATATCATCGCTTTATGCATCCCCCCACATC
1 TCATCGTGTGCATCCCCTCACATCGTGCACAAGCAATACCATCG---TATGCAT-CCCCCACATC
19924506 GTGCACAAGAGATATCA
62 GTGCACAAGAGATATCA
* * *
19924523 TCATCGTGTGCATCCCCTCACATCGTGCAC-AGTTAATGCCATCGTGTGCATCCCCCACATCGTG
1 TCATCGTGTGCATCCCCTCACATCGTGCACAAG-CAATACCATCGTATGCATCCCCCACATCGTG
19924587 CACA
65 CACA
19924591 CGAGCAATAT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
78 17 0.28
79 6 0.10
81 2 0.03
82 36 0.59
ACGTcount: A:0.24, C:0.34, G:0.16, T:0.26
Consensus pattern (78 bp):
TCATCGTGTGCATCCCCTCACATCGTGCACAAGCAATACCATCGTATGCATCCCCCACATCGTGC
ACAAGAGATATCA
Found at i:19929594 original size:27 final size:27
Alignment explanation
Indices: 19929543--19929605 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
19929533 AACAGCCCAA
* *
19929543 ATGTGGGCTGCACACCCGTAGAAGCCC
1 ATGTGGGCTGCACACCCATAAAAGCCC
*
19929570 ATGTGGGCTGCACACTCATAAAAGCCC
1 ATGTGGGCTGCACACCCATAAAAGCCC
*
19929597 ATATGGGCT
1 ATGTGGGCT
19929606 ACTGCATGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.25, C:0.29, G:0.27, T:0.19
Consensus pattern (27 bp):
ATGTGGGCTGCACACCCATAAAAGCCC
Found at i:19931148 original size:28 final size:27
Alignment explanation
Indices: 19931104--19931462 Score: 380
Period size: 28 Copynumber: 12.5 Consensus size: 27
19931094 CTTATCTTTG
* *
19931104 ATTAAGACAAAAATATGTTATCTTGTCAAA
1 ATTAAGAC--AAACATGTT-TCTTGTCTAA
* * *
19931134 ATTAAGGCAAATATGTTTTCTTGTCCAA
1 ATTAAGACAAACATG-TTTCTTGTCTAA
*
19931162 ATTAAGACAAAAACATATTTTTCTTGTCCTAA
1 ATTAAGAC--AAAC--ATGTTTCTTGT-CTAA
* * *
19931194 ATTAAAACAAAAATATTTGCTTGTCTAA
1 ATTAAGACAAACATGTTT-CTTGTCTAA
19931222 ATTAAGACAAAACATGTTTGCTTGTCTAA
1 ATTAAGAC-AAACATGTTT-CTTGTCTAA
*
19931251 ATTAAGATAAACATGTTTCCTTGTCTAA
1 ATTAAGACAAACATGTTT-CTTGTCTAA
19931279 ATTAAGACATAACATGCTTTCTTGTCTAA
1 ATTAAGACA-AACATG-TTTCTTGTCTAA
*
19931308 ATTAAGACAAACAAGTTTTCTTGTCTAA
1 ATTAAGACAAACATG-TTTCTTGTCTAA
*
19931336 ATTAAGACAAACAAT-TTCCTTGTCTAA
1 ATTAAGACAAAC-ATGTTTCTTGTCTAA
19931363 ATTAAGACATAACATGCTTTCTTGTCTAA
1 ATTAAGACA-AACATG-TTTCTTGTCTAA
*
19931392 ATTAAGACAAACAAGTTTTCTTGTCTAA
1 ATTAAGACAAACATG-TTTCTTGTCTAA
19931420 ATTAAGACAAAACATGCTTTCTTGT-TCAA
1 ATTAAGAC-AAACATG-TTTCTTGTCT-AA
19931449 ATTAAGACAAACAT
1 ATTAAGACAAACAT
19931463 TTCAAAACTT
Statistics
Matches: 289, Mismatches: 24, Indels: 34
0.83 0.07 0.10
Matches are distributed among these distances:
27 22 0.08
28 130 0.45
29 101 0.35
30 16 0.06
31 8 0.03
32 12 0.04
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.36
Consensus pattern (27 bp):
ATTAAGACAAACATGTTTCTTGTCTAA
Found at i:19931375 original size:84 final size:85
Alignment explanation
Indices: 19931124--19931462 Score: 429
Period size: 84 Copynumber: 4.0 Consensus size: 85
19931114 AAATATGTTA
* * * * * *
19931124 TCTTGTCAAAATTAAGGCAAATATGTTTTCTTGTCCAAATTAAGACAAAAACATATTTTTCTTGT
1 TCTTGTCTAAATTAAGACAAACAAGTTTTCTTGTCTAAATTAAGAC--AAACATA-TTTCCTTGT
* * *
19931189 CCTAAATTAAAACA-AAAAT-ATT
63 -CTAAATTAAGACATAACATGCTT
* * * *
19931211 TGCTTGTCTAAATTAAGACAAAACATGTTTGCTTGTCTAAATTAAGATAAACATGTTTCCTTGTC
1 T-CTTGTCTAAATTAAGAC-AAACAAGTTTTCTTGTCTAAATTAAGACAAACATATTTCCTTGTC
19931276 TAAATTAAGACATAACATGCTT
64 TAAATTAAGACATAACATGCTT
19931298 TCTTGTCTAAATTAAGACAAACAAGTTTTCTTGTCTAAATTAAGACAAACA-ATTTCCTTGTCTA
1 TCTTGTCTAAATTAAGACAAACAAGTTTTCTTGTCTAAATTAAGACAAACATATTTCCTTGTCTA
19931362 AATTAAGACATAACATGCTT
66 AATTAAGACATAACATGCTT
*
19931382 TCTTGTCTAAATTAAGACAAACAAGTTTTCTTGTCTAAATTAAGACAAAACATGCTTT-CTTGT-
1 TCTTGTCTAAATTAAGACAAACAAGTTTTCTTGTCTAAATTAAGAC-AAACAT-ATTTCCTTGTC
19931445 TCAAATTAAGACA-AACAT
64 T-AAATTAAGACATAACAT
19931463 TTCAAAACTT
Statistics
Matches: 228, Mismatches: 16, Indels: 18
0.87 0.06 0.07
Matches are distributed among these distances:
84 78 0.34
85 53 0.23
86 45 0.20
87 13 0.06
88 15 0.07
89 24 0.11
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (85 bp):
TCTTGTCTAAATTAAGACAAACAAGTTTTCTTGTCTAAATTAAGACAAACATATTTCCTTGTCTA
AATTAAGACATAACATGCTT
Found at i:19931387 original size:141 final size:143
Alignment explanation
Indices: 19931125--19931462 Score: 470
Period size: 141 Copynumber: 2.4 Consensus size: 143
19931115 AATATGTTAT
* * * * * *
19931125 CTTGTCAAAATTAAGGCAAATATGTTTTCTTGTCCAAATTAAGACAAAAACATATTTTTCTTGTC
1 CTTGTCTAAATTAAGACAAACATGCTTTCTTGTCTAAATTAAGAC--AAACATAGTTTTCTTGTC
*
19931190 CTAAATTAAAACAAAAATATTTGCTTGTCTAAATTAAGACAAAACATGTTTGCTTGTCTAAATTA
64 CTAAATTAAAACAAAAATATTTCCTTGTCTAAATTAAGACAAAACATGTTTGCTTGTCTAAATTA
* *
19931255 AGATAAACATGTTTC
129 AGACAAACAAGTTTC
19931270 CTTGTCTAAATTAAGACATAACATGCTTTCTTGTCTAAATTAAGACAAACA-AGTTTTCTTGT-C
1 CTTGTCTAAATTAAGACA-AACATGCTTTCTTGTCTAAATTAAGACAAACATAGTTTTCTTGTCC
* * *
19931333 TAAATTAAGACAAACA-ATTTCCTTGTCTAAATTAAGACATAACATGCTTT-CTTGTCTAAATTA
65 TAAATTAAAACAAAAATATTTCCTTGTCTAAATTAAGACAAAACATG-TTTGCTTGTCTAAATTA
*
19931396 AGACAAACAAGTTTT
129 AGACAAACAAGTTTC
19931411 CTTGTCTAAATTAAGACAAAACATGCTTTCTTGT-TCAAATTAAGACAAACAT
1 CTTGTCTAAATTAAGAC-AAACATGCTTTCTTGTCT-AAATTAAGACAAACAT
19931463 TTCAAAACTT
Statistics
Matches: 175, Mismatches: 13, Indels: 13
0.87 0.06 0.06
Matches are distributed among these distances:
140 1 0.01
141 100 0.57
142 19 0.11
143 10 0.06
144 5 0.03
145 16 0.09
146 24 0.14
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (143 bp):
CTTGTCTAAATTAAGACAAACATGCTTTCTTGTCTAAATTAAGACAAACATAGTTTTCTTGTCCT
AAATTAAAACAAAAATATTTCCTTGTCTAAATTAAGACAAAACATGTTTGCTTGTCTAAATTAAG
ACAAACAAGTTTC
Found at i:19931460 original size:57 final size:57
Alignment explanation
Indices: 19931104--19931461 Score: 390
Period size: 57 Copynumber: 6.2 Consensus size: 57
19931094 CTTATCTTTG
* * * * * * *
19931104 ATTAAGACAAAAATATGTTATCTTGTCAAAATTAAGGC-AAATATGTTTTCTTGTCCAA
1 ATTAAGACAAACA-A-GTTTTCTTGTCTAAATTAAGACAAAACATGCTTTCTTGTCTAA
* * *
19931162 ATTAAGACAAAAACATATTTTTCTTGTCCTAAATTAAAACAAAA-AT-ATTTGCTTGTCTAA
1 ATTAAGAC--AAACA-AGTTTTCTTGT-CTAAATTAAGACAAAACATGCTTT-CTTGTCTAA
* * *
19931222 ATTAAGACAAAACATGTTTGCTTGTCTAAATTAAGA-TAAACATG-TTTCCTTGTCTAA
1 ATTAAGAC-AAACAAGTTTTCTTGTCTAAATTAAGACAAAACATGCTTT-CTTGTCTAA
* * * *
19931279 ATTAAGACATAACATGCTTTCTTGTCTAAATTAAGAC-AAACAAGTTTTCTTGTCTAA
1 ATTAAGACA-AACAAGTTTTCTTGTCTAAATTAAGACAAAACATGCTTTCTTGTCTAA
* *
19931336 ATTAAGACAAACAA-TTTCCTTGTCTAAATTAAGACATAACATGCTTTCTTGTCTAA
1 ATTAAGACAAACAAGTTTTCTTGTCTAAATTAAGACAAAACATGCTTTCTTGTCTAA
19931392 ATTAAGACAAACAAGTTTTCTTGTCTAAATTAAGACAAAACATGCTTTCTTGT-TCAA
1 ATTAAGACAAACAAGTTTTCTTGTCTAAATTAAGACAAAACATGCTTTCTTGTCT-AA
19931449 ATTAAGACAAACA
1 ATTAAGACAAACA
19931462 TTTCAAAACT
Statistics
Matches: 262, Mismatches: 25, Indels: 27
0.83 0.08 0.09
Matches are distributed among these distances:
55 19 0.07
56 40 0.15
57 131 0.50
58 19 0.07
59 17 0.06
60 33 0.13
61 3 0.01
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (57 bp):
ATTAAGACAAACAAGTTTTCTTGTCTAAATTAAGACAAAACATGCTTTCTTGTCTAA
Found at i:19931530 original size:81 final size:80
Alignment explanation
Indices: 19931436--19931597 Score: 306
Period size: 81 Copynumber: 2.0 Consensus size: 80
19931426 ACAAAACATG
19931436 CTTTCTTGTTCAAATTAAGACAAACATTTCAAAACTTCCATTTTTGTATACAATTTAATTAATCA
1 CTTTCTTGTTCAAATTAAGACAAACATTTCAAAACTTCCATTTTTGTATACAATTTAATTAATCA
19931501 AATAAAAAATGCATT
66 AATAAAAAATGCATT
19931516 CNTTTCTTGTTCAAATTAAGACAAACATTTCAAAACTTCCATTTTTGTATACAATTTAATTAATC
1 C-TTTCTTGTTCAAATTAAGACAAACATTTCAAAACTTCCATTTTTGTATACAATTTAATTAATC
*
19931581 AAATAAAACATGCATT
65 AAATAAAAAATGCATT
19931597 C
1 C
19931598 CAACTTAAAC
Statistics
Matches: 80, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
80 1 0.01
81 79 0.99
ACGTcount: A:0.40, C:0.16, G:0.05, T:0.38
Consensus pattern (80 bp):
CTTTCTTGTTCAAATTAAGACAAACATTTCAAAACTTCCATTTTTGTATACAATTTAATTAATCA
AATAAAAAATGCATT
Found at i:19933589 original size:31 final size:28
Alignment explanation
Indices: 19933551--19933671 Score: 95
Period size: 30 Copynumber: 4.1 Consensus size: 28
19933541 ATTGTTTCTA
19933551 GTTATACCTCCAAGCAAAAGGTAGTGTAAAG
1 GTTATACCTCCAAG-AAAAGGTAGTG--AAG
**
19933582 GTTATACCTCCTTGAAAAGGTAGTGAAG
1 GTTATACCTCCAAGAAAAGGTAGTGAAG
* *
19933610 GTTATACGTCCTCTAA-AAAAGGTGGT-AATG
1 GTTATA---CCTCCAAGAAAAGGTAGTGAA-G
* *
19933640 GTTATACCTTCGAGTAAAAGGTAGTG-AG
1 GTTATACCTCCAAG-AAAAGGTAGTGAAG
19933668 GTTA
1 GTTA
19933672 AGCTTGCTCC
Statistics
Matches: 73, Mismatches: 10, Indels: 17
0.73 0.10 0.17
Matches are distributed among these distances:
27 4 0.05
28 14 0.19
29 12 0.16
30 27 0.37
31 16 0.22
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (28 bp):
GTTATACCTCCAAGAAAAGGTAGTGAAG
Found at i:19933602 original size:30 final size:30
Alignment explanation
Indices: 19933551--19933648 Score: 96
Period size: 30 Copynumber: 3.3 Consensus size: 30
19933541 ATTGTTTCTA
**
19933551 GTTATACCTCCAAGCAAAAGGTAGTGTAAAG
1 GTTATACCTCCTTG-AAAAGGTAGTGTAAAG
19933582 GTTATACCTCCTTGAAAAGGTAGTG--AAG
1 GTTATACCTCCTTGAAAAGGTAGTGTAAAG
* * *
19933610 GTTATACGTCCTCTAAAAAAGGT-G-GTAATG
1 GTTATACCTCCT-T-GAAAAGGTAGTGTAAAG
19933640 GTTATACCT
1 GTTATACCT
19933649 TCGAGTAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
28 15 0.26
29 2 0.04
30 28 0.49
31 12 0.21
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (30 bp):
GTTATACCTCCTTGAAAAGGTAGTGTAAAG
Found at i:19939403 original size:25 final size:24
Alignment explanation
Indices: 19939375--19939443 Score: 66
Period size: 28 Copynumber: 2.7 Consensus size: 24
19939365 TTAATTAGGT
19939375 CATGCCCATTCTTCCTTTATTGGAC
1 CATGCCCATT-TTCCTTTATTGGAC
* * *
19939400 CATGTCCAATTTTCCTTGCTTGTTGGGC
1 CATG-CCCATTTTCC-T--TTATTGGAC
19939428 CATGCCCATTTTCCTT
1 CATGCCCATTTTCCTT
19939444 GTTATTTTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
24 1 0.03
25 8 0.22
26 7 0.19
27 9 0.25
28 11 0.31
ACGTcount: A:0.13, C:0.30, G:0.14, T:0.42
Consensus pattern (24 bp):
CATGCCCATTTTCCTTTATTGGAC
Found at i:19939462 original size:5 final size:5
Alignment explanation
Indices: 19939448--19939503 Score: 89
Period size: 5 Copynumber: 11.6 Consensus size: 5
19939438 TTCCTTGTTA
*
19939448 TTTTC TTTTC CTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC -TTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
19939497 -TTTC TTT
1 TTTTC TTT
19939504 CTCTCCCACT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
4 8 0.17
5 40 0.83
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:19939914 original size:34 final size:34
Alignment explanation
Indices: 19939818--19939900 Score: 130
Period size: 34 Copynumber: 2.4 Consensus size: 34
19939808 GCACTTTTTG
*
19939818 GCCTCCAAAATCAGCAGAAAAATGGCACTTTCCA
1 GCCTCCAAAATCAGCAGAAAAATGGCTCTTTCCA
* * *
19939852 ACCTCCAAAACCAGCAGAAAAATAGCTCTTTCCA
1 GCCTCCAAAATCAGCAGAAAAATGGCTCTTTCCA
19939886 GCCTCCAAAATCAGC
1 GCCTCCAAAATCAGC
19939901 CCTTAAATGG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.39, C:0.33, G:0.12, T:0.17
Consensus pattern (34 bp):
GCCTCCAAAATCAGCAGAAAAATGGCTCTTTCCA
Found at i:19949910 original size:28 final size:29
Alignment explanation
Indices: 19949869--19949928 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
19949859 GTCTATGGGC
*
19949869 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
19949897 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
19949927 AA
1 AA
19949929 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:19956765 original size:84 final size:83
Alignment explanation
Indices: 19956624--19956790 Score: 316
Period size: 84 Copynumber: 2.0 Consensus size: 83
19956614 TTAACCTATT
19956624 TCGGTCTTTTACCCAATAAATTGAAATACGCATCCAATTTAGCTCCAATTGATCCCATTTCTTTT
1 TCGGTCTTTTACCCAATAAATTGAAATACGCATCCAATTTAGCTCCAATTGATCCCATTTCTTTT
19956689 TCTAATGCTTCAAATCAC
66 TCTAATGCTTCAAATCAC
*
19956707 NTCGGTCTTTTACCCGATAAATTGAAATACGCATCCAATTTAGCTCCAATTGATCCCATTTCTTT
1 -TCGGTCTTTTACCCAATAAATTGAAATACGCATCCAATTTAGCTCCAATTGATCCCATTTCTTT
19956772 TTCTAATGCTTCAAATCAC
65 TTCTAATGCTTCAAATCAC
19956791 CAATGTCCAG
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 82 1.00
ACGTcount: A:0.28, C:0.25, G:0.09, T:0.37
Consensus pattern (83 bp):
TCGGTCTTTTACCCAATAAATTGAAATACGCATCCAATTTAGCTCCAATTGATCCCATTTCTTTT
TCTAATGCTTCAAATCAC
Found at i:19958031 original size:18 final size:18
Alignment explanation
Indices: 19958008--19958051 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
19957998 ACAAGTATAC
* *
19958008 ATCCACTTTTGGTGGGTG
1 ATCCACTTATGATGGGTG
* *
19958026 ATCCACCTATGATGGGTT
1 ATCCACTTATGATGGGTG
19958044 ATCCACTT
1 ATCCACTT
19958052 CTAGTGAATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (18 bp):
ATCCACTTATGATGGGTG
Found at i:19958380 original size:58 final size:57
Alignment explanation
Indices: 19958251--19958445 Score: 281
Period size: 58 Copynumber: 3.5 Consensus size: 57
19958241 TATTAAATGA
19958251 TGTCGCATTCACTTCAGGGAATGGACAGATTTATAATTTTTTTATTAGTAACTAGTT
1 TGTCGCATTCACTTCAGGGAATGGACAGATTTATAATTTTTTTATTAGTAACTAGTT
*
19958308 TGTTGCATTCACTTCAGGGAATGGACAGATTTATAATTTTTTTTATTAGTAACTAGTT
1 TGTCGCATTCACTTCAGGGAATGGACAGATTTATAA-TTTTTTTATTAGTAACTAGTT
* * * * *
19958366 TGTCGCATTTACTTCAGGGAAT-GA-ACATTCATAA--TTTTTATTAGTAGCTCGTT
1 TGTCGCATTCACTTCAGGGAATGGACAGATTTATAATTTTTTTATTAGTAACTAGTT
* *
19958419 TGTCACATTCACTTCAGAGAATGGACA
1 TGTCGCATTCACTTCAGGGAATGGACA
19958446 TTCATGGTTT
Statistics
Matches: 125, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
53 36 0.29
54 2 0.02
55 1 0.01
56 8 0.06
57 37 0.30
58 41 0.33
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (57 bp):
TGTCGCATTCACTTCAGGGAATGGACAGATTTATAATTTTTTTATTAGTAACTAGTT
Found at i:19958447 original size:53 final size:55
Alignment explanation
Indices: 19958251--19958450 Score: 253
Period size: 53 Copynumber: 3.6 Consensus size: 55
19958241 TATTAAATGA
*
19958251 TGTCGCATTCACTTCAGGGAATGGACAGATTTATAATTTTTTTATTAGTAACTAGTT
1 TGTCGCATTCACTTCAGGGAATGGACA-ATTCATAA-TTTTTTATTAGTAACTAGTT
* *
19958308 TGTTGCATTCACTTCAGGGAATGGACAGATTTATAATTTTTTTTATTAGTAACTAGTT
1 TGTCGCATTCACTTCAGGGAATGGACA-ATTCATAA--TTTTTTATTAGTAACTAGTT
* * * *
19958366 TGTCGCATTTACTTCAGGGAATGAAC-ATTCATAA-TTTTTATTAGTAGCTCGTT
1 TGTCGCATTCACTTCAGGGAATGGACAATTCATAATTTTTTATTAGTAACTAGTT
* *
19958419 TGTCACATTCACTTCAGAGAATGGAC-ATTCAT
1 TGTCGCATTCACTTCAGGGAATGGACAATTCAT
19958451 GGTTTTACAT
Statistics
Matches: 131, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
53 45 0.34
56 7 0.05
57 35 0.27
58 44 0.34
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (55 bp):
TGTCGCATTCACTTCAGGGAATGGACAATTCATAATTTTTTATTAGTAACTAGTT
Found at i:19958779 original size:19 final size:19
Alignment explanation
Indices: 19958755--19958793 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
19958745 GAGAAATATA
**
19958755 AAAGAAAGTATTTAGAGGG
1 AAAGAAAGTAAGTAGAGGG
19958774 AAAGAAAGTAAGTAGAGGG
1 AAAGAAAGTAAGTAGAGGG
19958793 A
1 A
19958794 GTAAAAAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.33, T:0.15
Consensus pattern (19 bp):
AAAGAAAGTAAGTAGAGGG
Found at i:19961298 original size:18 final size:19
Alignment explanation
Indices: 19961249--19961305 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
19961239 AGAAAATAAA
19961249 TAATTTTAT-TAATTATTTTT
1 TAATTTTATAT-A-TATTTTT
*
19961269 TACTTTTATATATATTTTT
1 TAATTTTATATATATTTTT
19961288 TAATTTT-TATATATTTTT
1 TAATTTTATATATATTTTT
19961306 AATATAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 11 0.32
19 13 0.38
20 9 0.26
21 1 0.03
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (19 bp):
TAATTTTATATATATTTTT
Found at i:19962596 original size:30 final size:28
Alignment explanation
Indices: 19962496--19962597 Score: 105
Period size: 28 Copynumber: 3.5 Consensus size: 28
19962486 ACTTTTTTAT
*
19962496 AATTTTAATTAATACTCATAATTTTTTAAAA
1 AATTTTAATTAATGCTC---ATTTTTTAAAA
**
19962527 AATTTTAGCTAATGCTCATTTTTTAAAA
1 AATTTTAATTAATGCTCATTTTTTAAAA
* *
19962555 AATTTTAATTAATGCTCATGTTCTTTGAAT
1 AATTTTAATTAATGCTCAT-TT-TTTAAAA
*
19962585 AATTTTGATTAAT
1 AATTTTAATTAAT
19962598 ACGTATAATT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
28 28 0.46
29 2 0.03
30 17 0.28
31 14 0.23
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (28 bp):
AATTTTAATTAATGCTCATTTTTTAAAA
Done.