Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 68 of 199
Found at i:20409371 original size:6 final size:6
Alignment explanation
Indices: 20409351--20409407 Score: 62
Period size: 6 Copynumber: 9.2 Consensus size: 6
20409341 ACCAATTTAG
* *
20409351 TTTATC TTTATTT TTTATT TTTATT TTTATT TGTAATGT TTTATT TTTA-T
1 TTTATT TTTA-TT TTTATT TTTATT TTTATT T-TTAT-T TTTATT TTTATT
20409401 TTTATT T
1 TTTATT T
20409408 GAATTCCAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
5 5 0.11
6 26 0.59
7 11 0.25
8 2 0.05
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.77
Consensus pattern (6 bp):
TTTATT
Found at i:20409438 original size:3 final size:3
Alignment explanation
Indices: 20409430--20409475 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
20409420 ATTTTAATCC
20409430 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
20409476 CCTTCTTTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:20409539 original size:18 final size:18
Alignment explanation
Indices: 20409501--20409537 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
20409491 AAATTGCGTC
20409501 TTAACTTTAACTTGATTT
1 TTAACTTTAACTTGATTT
20409519 TTAA-TTTAACTTGATTT
1 TTAACTTTAACTTGATTT
20409536 TT
1 TT
20409538 TATTAGTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.27, C:0.08, G:0.05, T:0.59
Consensus pattern (18 bp):
TTAACTTTAACTTGATTT
Found at i:20414663 original size:12 final size:12
Alignment explanation
Indices: 20414648--20414681 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
20414638 AAGAAGAAAA
20414648 AAAATCAAAATC
1 AAAATCAAAATC
20414660 AAAATCAAAATC
1 AAAATCAAAATC
*
20414672 AAAAACAAAA
1 AAAATCAAAA
20414682 AAGAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.74, C:0.15, G:0.00, T:0.12
Consensus pattern (12 bp):
AAAATCAAAATC
Found at i:20414664 original size:41 final size:41
Alignment explanation
Indices: 20414613--20414713 Score: 132
Period size: 41 Copynumber: 2.5 Consensus size: 41
20414603 CAATTCAAAA
* *
20414613 AAAAACAAAATCAAAAAGACAAAA-AAAGAAGAAAAAAAATC
1 AAAATCAAAATCAAAAAGA-AAAACAAAAAAGAAAAAAAATC
**
20414654 AAAATCAAAATCAAAATCAAAAACAAAAAAGAAAAAAAATC
1 AAAATCAAAATCAAAAAGAAAAACAAAAAAGAAAAAAAATC
* *
20414695 AAAGTCAAAAGCAAAAAGA
1 AAAATCAAAATCAAAAAGA
20414714 GAAATCAATC
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
40 4 0.08
41 47 0.92
ACGTcount: A:0.75, C:0.11, G:0.07, T:0.07
Consensus pattern (41 bp):
AAAATCAAAATCAAAAAGAAAAACAAAAAAGAAAAAAAATC
Found at i:20414676 original size:29 final size:31
Alignment explanation
Indices: 20414655--20414733 Score: 103
Period size: 29 Copynumber: 2.7 Consensus size: 31
20414645 AAAAAAATCA
*
20414655 AAATCAAAATCAAAATCAAAAACAAAAA-AG
1 AAATCAAAATCAAAGTCAAAAACAAAAAGAG
* *
20414685 AAA-AAAAATCAAAGTCAAAAGCAAAAAGAG
1 AAATCAAAATCAAAGTCAAAAACAAAAAGAG
20414715 AAATC--AATCAAAGTCAAAA
1 AAATCAAAATCAAAGTCAAAA
20414734 TAAAAATATG
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
29 35 0.81
30 8 0.19
ACGTcount: A:0.70, C:0.13, G:0.08, T:0.10
Consensus pattern (31 bp):
AAATCAAAATCAAAGTCAAAAACAAAAAGAG
Found at i:20414739 original size:29 final size:28
Alignment explanation
Indices: 20414660--20414748 Score: 90
Period size: 29 Copynumber: 3.0 Consensus size: 28
20414650 AATCAAAATC
*
20414660 AAAATCAAAATCAAAAACAAAAAAGAAAA
1 AAAATCAAAGTC-AAAACAAAAAAGAAAA
20414689 AAAATCAAAGTCAAAAGC-AAAAAGAGAAA
1 AAAATCAAAGTCAAAA-CAAAAAAGA-AAA
** *
20414718 TCAATCAAAGTCAAAATAAAAATATGAAAA
1 AAAATCAAAGTCAAAACAAAAA-A-GAAAA
20414748 A
1 A
20414749 GATAAAAAAG
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
28 11 0.22
29 33 0.66
30 4 0.08
31 2 0.04
ACGTcount: A:0.71, C:0.10, G:0.08, T:0.11
Consensus pattern (28 bp):
AAAATCAAAGTCAAAACAAAAAAGAAAA
Found at i:20415645 original size:6 final size:7
Alignment explanation
Indices: 20415632--20415665 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
20415622 AAAAAAAGGG
20415632 ATGAAAA
1 ATGAAAA
20415639 ATGAAAA
1 ATGAAAA
20415646 ATG-AAA
1 ATGAAAA
20415652 ATGAAAA
1 ATGAAAA
20415659 ATGAAAA
1 ATGAAAA
20415666 GTAAGGACGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (7 bp):
ATGAAAA
Found at i:20415652 original size:13 final size:13
Alignment explanation
Indices: 20415636--20415665 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
20415626 AAAGGGATGA
20415636 AAAATGAAAAATG
1 AAAATGAAAAATG
20415649 AAAATGAAAAATG
1 AAAATGAAAAATG
20415662 AAAA
1 AAAA
20415666 GTAAGGACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (13 bp):
AAAATGAAAAATG
Found at i:20416952 original size:21 final size:22
Alignment explanation
Indices: 20416923--20416973 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
20416913 TCTCTCTCGC
*
20416923 TTTCCTTTTCGCCTTTTTCA-T
1 TTTCATTTTCGCCTTTTTCACT
**
20416944 TTTCATTTTCTTCTTTTTCACT
1 TTTCATTTTCGCCTTTTTCACT
20416966 TTT-ATTTT
1 TTTCATTTT
20416974 TCTCTTCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.08, C:0.22, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTCATTTTCGCCTTTTTCACT
Found at i:20418842 original size:18 final size:18
Alignment explanation
Indices: 20418819--20418855 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
20418809 GCAGCAAGAA
20418819 AGAGGGAAATTATAGATT
1 AGAGGGAAATTATAGATT
20418837 AGAGGGAAATTATAGATT
1 AGAGGGAAATTATAGATT
20418855 A
1 A
20418856 AGAATGATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.27, T:0.27
Consensus pattern (18 bp):
AGAGGGAAATTATAGATT
Found at i:20427061 original size:26 final size:26
Alignment explanation
Indices: 20427028--20427077 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
20427018 TTTATGCATA
*
20427028 TTTTATAATTTAAATATATATACATT
1 TTTTATAATATAAATATATATACATT
*
20427054 TTTTATAATATATATATATATACA
1 TTTTATAATATAAATATATATACA
20427078 CATACACTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (26 bp):
TTTTATAATATAAATATATATACATT
Found at i:20430421 original size:21 final size:20
Alignment explanation
Indices: 20430383--20430425 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
20430373 TTCTGCCAAA
*
20430383 TCATTCATTCGTTCATATTAT
1 TCATACATTCGTTCATA-TAT
* *
20430404 TCATACATTCTTTTATATAT
1 TCATACATTCGTTCATATAT
20430424 TC
1 TC
20430426 TTTGGTACCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.26, C:0.19, G:0.02, T:0.53
Consensus pattern (20 bp):
TCATACATTCGTTCATATAT
Found at i:20432712 original size:50 final size:50
Alignment explanation
Indices: 20432566--20432724 Score: 156
Period size: 50 Copynumber: 3.2 Consensus size: 50
20432556 ACTTCCTTAG
*
20432566 CAGTGCAGTGGAACAGATAGAAGCTACGACGGCGGATCTGGTTTCCCTGA
1 CAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGA
* * * ** * * * * * ***
20432616 TATTGCAATTAAAAAGATTAAAGCCACAACGGTGGATCTTACTTCCCTGA
1 CAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGA
* * *
20432666 CGGTGCGGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCCGA
1 CAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGA
*
20432716 CATTGCAGT
1 CAGTGCAGT
20432725 TAAATAAATT
Statistics
Matches: 76, Mismatches: 33, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
50 76 1.00
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (50 bp):
CAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGA
Found at i:20436643 original size:12 final size:12
Alignment explanation
Indices: 20436626--20436650 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20436616 GTCTTATTCA
20436626 ACCTTTAGAGAC
1 ACCTTTAGAGAC
20436638 ACCTTTAGAGAC
1 ACCTTTAGAGAC
20436650 A
1 A
20436651 TGATTTTGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (12 bp):
ACCTTTAGAGAC
Found at i:20440860 original size:23 final size:23
Alignment explanation
Indices: 20440830--20440878 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
20440820 AACCCATATA
*
20440830 TATGCATGCTAATATACTATTAT
1 TATGCATGCCAATATACTATTAT
*
20440853 TATGCATGCCGATATACTATTAT
1 TATGCATGCCAATATACTATTAT
20440876 TAT
1 TAT
20440879 TCTTTTAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (23 bp):
TATGCATGCCAATATACTATTAT
Found at i:20441619 original size:43 final size:43
Alignment explanation
Indices: 20441385--20441858 Score: 294
Period size: 43 Copynumber: 11.0 Consensus size: 43
20441375 TCTTTTGCCG
* * * * *
20441385 CGCCACTATAGAT-GTGGCTCTTTAGCGGCGCTTACATACAAAA
1 CGCCACTATAGATAG-GGTTCTATAGCGGCGCTTATACAAAAAA
* ** * *
20441428 CGCCACTATAGATCGGCCTCTCTAGCGGCGCTTATCCAAAAAA
1 CGCCACTATAGATAGGGTTCTATAGCGGCGCTTATACAAAAAA
** * * * **
20441471 CGCCACTATAGAGGGTGGGTCTAT-TCTGGCGATTATACTCAAAA
1 CGCCACTATAGATAG-GGTTCTATAGC-GGCGCTTATACAAAAAA
* *
20441515 CGCCACTATAGAT-GTGATCTATAGCGGCGCTTATACAAAAAAA
1 CGCCACTATAGATAGGGTTCTATAGCGGCGCTTATAC-AAAAAA
* * * * *
20441558 CGCCACTATAGCTTGGGTTCTATAGCGGCGCTTGTACGACAAA
1 CGCCACTATAGATAGGGTTCTATAGCGGCGCTTATACAAAAAA
* * * ** * *
20441601 CGCCACTAGAGAGAGGGTTCTTTTCCGGTGCTTATACAAGAAA
1 CGCCACTATAGATAGGGTTCTATAGCGGCGCTTATACAAAAAA
** * * **
20441644 CGCCACTATAGATAGGGTTCT-TCTCCAGCGCTTCA-ATAGGAAA
1 CGCCACTATAGATAGGGTTCTAT-AGCGGCGCTT-ATACAAAAAA
* * * ** * *
20441687 CGCCACGATAGATAAGGTTCTTTTCCGGCGCTTATGCAAGAAA
1 CGCCACTATAGATAGGGTTCTATAGCGGCGCTTATACAAAAAA
* * * *
20441730 CGCCACGATAGATAGGGTTCTTTTGCGGCGCTTATACAAGAAA
1 CGCCACTATAGATAGGGTTCTATAGCGGCGCTTATACAAAAAA
* * * * *
20441773 CGCCACAATAGATAGGGTTCTTTTGCGACGCTTAGT-CTAAAAA
1 CGCCACTATAGATAGGGTTCTATAGCGGCGCTTA-TACAAAAAA
* * ** * * * *
20441816 CACCACTACAGACGGGGATCTTTCGCGGCGCTTATGCAAAAAA
1 CGCCACTATAGATAGGGTTCTATAGCGGCGCTTATACAAAAAA
20441859 ATGCCACAAT
Statistics
Matches: 351, Mismatches: 68, Indels: 24
0.79 0.15 0.05
Matches are distributed among these distances:
42 19 0.05
43 278 0.79
44 54 0.15
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.25
Consensus pattern (43 bp):
CGCCACTATAGATAGGGTTCTATAGCGGCGCTTATACAAAAAA
Found at i:20441706 original size:129 final size:129
Alignment explanation
Indices: 20441555--20441794 Score: 327
Period size: 129 Copynumber: 1.9 Consensus size: 129
20441545 TTATACAAAA
* * ** * * * *
20441555 AAACGCCACTATAGCTTGGGTTCTATAGCGGCGCTTGTACGACAAACGCCACTAGAGAGAGGGTT
1 AAACGCCACGATAGATAAGGTTCTATACCGGCGCTTATACAACAAACGCCACGAGAGAGAGGGTT
* *
20441620 CTTTTCCGGTGCTTATACAAGAAACGCCACTATAGATAGGGTTCTTCTCCAGCGCTTCAATAGG
66 CTTTTCCGGCGCTTATACAAGAAACGCCACAATAGATAGGGTTCTTCTCCAGCGCTTCAATAGG
* * * * * *
20441684 AAACGCCACGATAGATAAGGTTCTTTTCCGGCGCTTATGCAAGAAACGCCACGATAGATAGGGTT
1 AAACGCCACGATAGATAAGGTTCTATACCGGCGCTTATACAACAAACGCCACGAGAGAGAGGGTT
*
20441749 CTTTTGCGGCGCTTATACAAGAAACGCCACAATAGATAGGGTTCTT
66 CTTTTCCGGCGCTTATACAAGAAACGCCACAATAGATAGGGTTCTT
20441795 TTGCGACGCT
Statistics
Matches: 94, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
129 94 1.00
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (129 bp):
AAACGCCACGATAGATAAGGTTCTATACCGGCGCTTATACAACAAACGCCACGAGAGAGAGGGTT
CTTTTCCGGCGCTTATACAAGAAACGCCACAATAGATAGGGTTCTTCTCCAGCGCTTCAATAGG
Found at i:20442342 original size:21 final size:21
Alignment explanation
Indices: 20442300--20442345 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
20442290 TTGAACCTCA
* *
20442300 GCTTCTCTCACTGCTGCCTCT
1 GCTTCTCTCACTGCCGCATCT
**
20442321 GCTTCTCTCGTTGCCGCATCT
1 GCTTCTCTCACTGCCGCATCT
20442342 GCTT
1 GCTT
20442346 TAAGTTGTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.04, C:0.39, G:0.17, T:0.39
Consensus pattern (21 bp):
GCTTCTCTCACTGCCGCATCT
Found at i:20442406 original size:87 final size:87
Alignment explanation
Indices: 20442219--20442395 Score: 275
Period size: 87 Copynumber: 2.0 Consensus size: 87
20442209 CTCTAATTCC
* * * *
20442219 CTCACTGCAGCCTCTGCTTCTCTCGTTGCTGCATCTGCTTTAAGCTGCCGCTGGAGTTCTTCGTA
1 CTCACTGCTGCCTCTGCTTCTCTCGTTGCCGCATCTGCTTTAAGCTGCAGCTGGAGTTCTTCATA
20442284 CTTTCGTTGAACCTCAGCTTCT
66 CTTTCGTTGAACCTCAGCTTCT
* *
20442306 CTCACTGCTGCCTCTGCTTCTCTCGTTGCCGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATA
1 CTCACTGCTGCCTCTGCTTCTCTCGTTGCCGCATCTGCTTTAAGCTGCAGCTGGAGTTCTTCATA
*
20442371 TCTTT-TTTGAACCTCAGCTTCT
66 -CTTTCGTTGAACCTCAGCTTCT
20442393 CTC
1 CTC
20442396 GATGTTGCCT
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
87 78 0.95
88 4 0.05
ACGTcount: A:0.12, C:0.31, G:0.18, T:0.39
Consensus pattern (87 bp):
CTCACTGCTGCCTCTGCTTCTCTCGTTGCCGCATCTGCTTTAAGCTGCAGCTGGAGTTCTTCATA
CTTTCGTTGAACCTCAGCTTCT
Found at i:20447954 original size:9 final size:9
Alignment explanation
Indices: 20447915--20448200 Score: 194
Period size: 9 Copynumber: 32.8 Consensus size: 9
20447905 TATGTATTAA
*
20447915 GTAAATTAT
1 GTAAGTTAT
20447924 GTAAGTTAT
1 GTAAGTTAT
20447933 GTACGAG-TA-
1 GTA--AGTTAT
20447942 -TAAGTTAT
1 GTAAGTTAT
*
20447950 GTAAGTCAT
1 GTAAGTTAT
*
20447959 GT-A-TTAA
1 GTAAGTTAT
*
20447966 GTAAGCTAT
1 GTAAGTTAT
20447975 GTAAGTTAT
1 GTAAGTTAT
* *
20447984 CATAA-ATAT
1 -GTAAGTTAT
*
20447993 GTATGTTAT
1 GTAAGTTAT
20448002 GTAAG-T-T
1 GTAAGTTAT
20448009 GTAAGTTATT
1 GTAAGTTA-T
*
20448019 GTGTA-TTAT
1 GT-AAGTTAT
*
20448028 GTAACTTAT
1 GTAAGTTAT
20448037 GTAAGTTAT
1 GTAAGTTAT
* *
20448046 -CAAATTAAT
1 GTAAGTT-AT
*
20448055 GTATGTTAT
1 GTAAGTTAT
20448064 GTAAG-T-T
1 GTAAGTTAT
20448071 GTAAGTTATT
1 GTAAGTTA-T
*
20448081 GTGTA-TTAT
1 GT-AAGTTAT
20448090 GTAAGTTAT
1 GTAAGTTAT
20448099 GTAAGTTAT
1 GTAAGTTAT
20448108 GTAAGTTAT
1 GTAAGTTAT
*
20448117 GT-A-TTAC
1 GTAAGTTAT
*
20448124 GTAGGTTAT
1 GTAAGTTAT
20448133 GTAAGTTAT
1 GTAAGTTAT
20448142 GTAAGTTAT
1 GTAAGTTAT
20448151 GT-A-TTAT
1 GTAAGTTAT
* *
20448158 GTAGGTTTT
1 GTAAGTTAT
*
20448167 GTAAGTTGT
1 GTAAGTTAT
20448176 GTAA-TATAT
1 GTAAGT-TAT
*
20448185 TTAAGTTAT
1 GTAAGTTAT
20448194 GTAAGTT
1 GTAAGTT
20448201 TTGTTTATAT
Statistics
Matches: 215, Mismatches: 35, Indels: 54
0.71 0.12 0.18
Matches are distributed among these distances:
6 2 0.01
7 29 0.13
8 19 0.09
9 140 0.65
10 21 0.10
11 4 0.02
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.45
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:20447980 original size:34 final size:33
Alignment explanation
Indices: 20447942--20448200 Score: 180
Period size: 34 Copynumber: 8.2 Consensus size: 33
20447932 TGTACGAGTA
* *
20447942 TAAGTTATGTAAGTCATGTATTAAGTAAGCTATG
1 TAAGTTATGTAAGT-ATGTATTATGTAAGTTATG
* *
20447976 TAAGTTATCATAAATATGTATGTTATGTAAG-T-TG
1 TAAGTTAT-GTAAGTATGTA--TTATGTAAGTTATG
*
20448010 TAAGTTAT-T--G--TGTATTATGTAACTTATG
1 TAAGTTATGTAAGTATGTATTATGTAAGTTATG
** *
20448038 TAAGTTATCAAATTAATGTATGTTATGTAAG-T-TG
1 TAAGTTATGTAAGT-ATGTA--TTATGTAAGTTATG
20448072 TAAGTTAT-T--G--TGTATTATGTAAGTTATG
1 TAAGTTATGTAAGTATGTATTATGTAAGTTATG
* *
20448100 TAAGTTATGTAAGTTATGTATTACGTAGGTTATG
1 TAAGTTATGTAAG-TATGTATTATGTAAGTTATG
* *
20448134 TAAGTTATGTAAGTTATGTATTATGTAGGTTTTG
1 TAAGTTATGTAAG-TATGTATTATGTAAGTTATG
*
20448168 TAAGTTGTGTAA-TA--TA-T-T-TAAGTTATG
1 TAAGTTATGTAAGTATGTATTATGTAAGTTATG
20448195 TAAGTT
1 TAAGTT
20448201 TTGTTTATAT
Statistics
Matches: 187, Mismatches: 17, Indels: 49
0.74 0.07 0.19
Matches are distributed among these distances:
26 17 0.09
27 15 0.08
28 29 0.16
29 2 0.01
30 2 0.01
31 1 0.01
32 3 0.02
34 96 0.51
35 6 0.03
36 16 0.09
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.46
Consensus pattern (33 bp):
TAAGTTATGTAAGTATGTATTATGTAAGTTATG
Found at i:20448038 original size:62 final size:62
Alignment explanation
Indices: 20447958--20448107 Score: 241
Period size: 62 Copynumber: 2.4 Consensus size: 62
20447948 ATGTAAGTCA
*
20447958 TGTATTAAGTAAGC-TATGTAAGTTATCATAAAT-ATGTATGTTATGTAAGTTGTAAGTTATTG
1 TGTATTATGTAA-CTTATGTAAGTTATCA-AAATAATGTATGTTATGTAAGTTGTAAGTTATTG
*
20448020 TGTATTATGTAACTTATGTAAGTTATCAAATTAATGTATGTTATGTAAGTTGTAAGTTATTG
1 TGTATTATGTAACTTATGTAAGTTATCAAAATAATGTATGTTATGTAAGTTGTAAGTTATTG
*
20448082 TGTATTATGTAAGTTATGTAAGTTAT
1 TGTATTATGTAACTTATGTAAGTTAT
20448108 GTAAGTTATG
Statistics
Matches: 83, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
61 4 0.05
62 79 0.95
ACGTcount: A:0.33, C:0.03, G:0.19, T:0.46
Consensus pattern (62 bp):
TGTATTATGTAACTTATGTAAGTTATCAAAATAATGTATGTTATGTAAGTTGTAAGTTATTG
Found at i:20448039 original size:28 final size:27
Alignment explanation
Indices: 20447998--20448107 Score: 89
Period size: 28 Copynumber: 3.8 Consensus size: 27
20447988 AATATGTATG
*
20447998 TTATGTAAGT-TGTAAGTTATTGTGTA
1 TTATGTAATTATGTAAGTTATTGTGTA
*
20448024 TTATGTAACTTATGTAAGTTATCAAATTAATGTA
1 TTATGTAA-TTATGTAAG-T-T---ATT-GTGTA
*
20448058 TGTTATGTAAGT-TGTAAGTTATTGTGTA
1 --TTATGTAATTATGTAAGTTATTGTGTA
20448086 TTATGTAAGTTATGTAAGTTAT
1 TTATGTAA-TTATGTAAGTTAT
20448108 GTAAGTTATG
Statistics
Matches: 67, Mismatches: 5, Indels: 22
0.71 0.05 0.23
Matches are distributed among these distances:
26 16 0.24
27 2 0.03
28 20 0.30
29 4 0.06
30 1 0.01
32 1 0.01
33 4 0.06
34 10 0.15
35 1 0.01
36 8 0.12
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (27 bp):
TTATGTAATTATGTAAGTTATTGTGTA
Found at i:20448136 original size:62 final size:61
Alignment explanation
Indices: 20447904--20448204 Score: 216
Period size: 62 Copynumber: 5.0 Consensus size: 61
20447894 GTTACATAAT
* * ** * *
20447904 TTATGT-ATTAAGTAAATTATGTAAGTTATGTACGAGTATAAGTTATGTAAGTCA---TGTA
1 TTATGTAATTATGTAAGTTATGTAAGTTATGTATTA-TGTAAGTTATGTAAGTTATTGTGTA
* * * *
20447962 TTAAGTAAGCTATGTAAGTTATCATAA-ATATGTATGTTATGTAAG-T-TGTAAGTTATTGTGTA
1 TTATGTAA-TTATGTAAGTTAT-GTAAGTTATGTA--TTATGTAAGTTATGTAAGTTATTGTGTA
* *
20448024 TTATGTAACTTATGTAAGTTAT-CAAATTAATGTATGTTATGTAAG-T-TGTAAGTTATTGTGTA
1 TTATGTAA-TTATGTAAGTTATGTAAGTT-ATGTA--TTATGTAAGTTATGTAAGTTATTGTGTA
* * *
20448086 TTATGTAAGTTATGTAAGTTATGTAAGTTATGTATTACGTAGGTTATGTAAGTTA-TGT-AA
1 TTATGTAA-TTATGTAAGTTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTATTGTGTA
* * * *
20448146 GTTATGT-ATTATGTAGGTTTTGTAAGTTGTGTAATATATTTAAGTTATGTAAGTT-TTGT
1 -TTATGTAATTATGTAAGTTATGTAAGTTATGT-AT-TATGTAAGTTATGTAAGTTATTGT
20448205 TTATATTTGT
Statistics
Matches: 199, Mismatches: 27, Indels: 31
0.77 0.11 0.12
Matches are distributed among these distances:
58 5 0.03
59 30 0.15
60 30 0.15
61 38 0.19
62 92 0.46
63 4 0.02
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.46
Consensus pattern (61 bp):
TTATGTAATTATGTAAGTTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTATTGTGTA
Found at i:20448145 original size:43 final size:44
Alignment explanation
Indices: 20447915--20448200 Score: 143
Period size: 43 Copynumber: 6.6 Consensus size: 44
20447905 TATGTATTAA
* * * *
20447915 GTAAATTATGTAAGTTATGTACGAG-TAT-AAGTTATGTAAGTCAT
1 GTAAGTTATGTAAGTTATGTA--AGTTATGTAGTTACGTAAGTTAT
* * * ** * *
20447959 GT-A-TTAAGTAAGCTATGTAAGTTATCATAAATATGTATGTTAT
1 GTAAGTTATGTAAGTTATGTAAGTTAT-GTAGTTACGTAAGTTAT
* * *
20448002 GTAAG-T-TGTAAGTTATTGTGTA-TTATGTAACTTATGTAAGTTAT
1 GTAAGTTATGTAAGTTA-TGT-AAGTTATGT-AGTTACGTAAGTTAT
* * * * *
20448046 -CAAATTAATGTATGTTATGTAAG-T-TGTAAGTTATTGTGTA-TTAT
1 GTAAGTT-ATGTAAGTTATGTAAGTTATGT-AGTTA-CGT-AAGTTAT
*
20448090 GTAAGTTATGTAAGTTATGTAAGTTATGTA-TTACGTAGGTTAT
1 GTAAGTTATGTAAGTTATGTAAGTTATGTAGTTACGTAAGTTAT
** *
20448133 GTAAGTTATGTAAGTTATGT-A-TTATGTAGGTTTTGTAAGTTGT
1 GTAAGTTATGTAAGTTATGTAAGTTATGTA-GTTACGTAAGTTAT
*
20448176 GTAA-TATATTTAAGTTATGTAAGTT
1 GTAAGT-TATGTAAGTTATGTAAGTT
20448201 TTGTTTATAT
Statistics
Matches: 188, Mismatches: 31, Indels: 45
0.71 0.12 0.17
Matches are distributed among these distances:
40 2 0.01
41 10 0.05
42 16 0.09
43 84 0.45
44 52 0.28
45 13 0.07
46 11 0.06
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.45
Consensus pattern (44 bp):
GTAAGTTATGTAAGTTATGTAAGTTATGTAGTTACGTAAGTTAT
Found at i:20448311 original size:13 final size:15
Alignment explanation
Indices: 20448292--20448332 Score: 59
Period size: 13 Copynumber: 2.8 Consensus size: 15
20448282 CATATAAGTT
20448292 TATGTAAGTTATG-A
1 TATGTAAGTTATGTA
20448306 -ATGTAAGTTATGTA
1 TATGTAAGTTATGTA
20448320 TTATGTAAGTTAT
1 -TATGTAAGTTAT
20448333 TTAAATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.50
14 1 0.04
16 11 0.46
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (15 bp):
TATGTAAGTTATGTA
Found at i:20448327 original size:16 final size:16
Alignment explanation
Indices: 20448291--20448369 Score: 74
Period size: 16 Copynumber: 5.0 Consensus size: 16
20448281 ACATATAAGT
20448291 TTATGTAAGTTATG-A
1 TTATGTAAGTTATGTA
20448306 --ATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
*
20448320 TTATGTAAGTTATTTAAA
1 TTATGTAAGTTATGT--A
* *
20448338 TTATTTAAGTTGTGTA
1 TTATGTAAGTTATGTA
* *
20448354 TTAAGTAAGTCATGTA
1 TTATGTAAGTTATGTA
20448370 GGCTATGTGT
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
13 12 0.24
14 1 0.02
16 25 0.49
18 13 0.25
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:20448444 original size:21 final size:22
Alignment explanation
Indices: 20448420--20448470 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
20448410 ATTTTTCAAG
*
20448420 TATATATATAATTTTA-ATAAA
1 TATATATATAACTTTATATAAA
*
20448441 TATAT-TAAAACTTTATATAAA
1 TATATATATAACTTTATATAAA
20448462 TATATATAT
1 TATATATAT
20448471 CAAAGATGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 8 0.32
21 15 0.60
22 2 0.08
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TATATATATAACTTTATATAAA
Found at i:20451152 original size:11 final size:11
Alignment explanation
Indices: 20451136--20451162 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
20451126 TTACTCAACC
20451136 AGTAATATGAA
1 AGTAATATGAA
20451147 AGTAATATGAA
1 AGTAATATGAA
20451158 AGTAA
1 AGTAA
20451163 ATTAAACAAA
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:0.56, C:0.00, G:0.19, T:0.26
Consensus pattern (11 bp):
AGTAATATGAA
Found at i:20452162 original size:2 final size:2
Alignment explanation
Indices: 20452155--20452208 Score: 51
Period size: 2 Copynumber: 28.5 Consensus size: 2
20452145 AATTAATAAC
* *
20452155 TA TA TA TA TA TA TA TA TA TC CA TA TA TA TA -A T- TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
20452194 TC CA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
20452209 CAAAAATAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
1 3 0.07
2 38 0.93
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:20453506 original size:15 final size:14
Alignment explanation
Indices: 20453483--20453549 Score: 59
Period size: 14 Copynumber: 4.9 Consensus size: 14
20453473 ATGACCGTTG
20453483 AAACCCTAAATCTC
1 AAACCCTAAATCTC
*
20453497 AAACCCCTAAACCTC
1 AAA-CCCTAAATCTC
*
20453512 TAACCCTAAAT-T-
1 AAACCCTAAATCTC
* *
20453524 -AACCTTAAATCTT
1 AAACCCTAAATCTC
*
20453537 AAACCTTAAATCT
1 AAACCCTAAATCT
20453550 ATACCCCGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
11 9 0.20
12 1 0.02
13 1 0.02
14 22 0.49
15 12 0.27
ACGTcount: A:0.42, C:0.31, G:0.00, T:0.27
Consensus pattern (14 bp):
AAACCCTAAATCTC
Found at i:20454104 original size:41 final size:41
Alignment explanation
Indices: 20454043--20454241 Score: 136
Period size: 41 Copynumber: 4.8 Consensus size: 41
20454033 AAGGTAATAA
* *
20454043 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAA-AGCCGGAGG
1 ATTACCGGCGCTTAGATAAAAACGCCGCTAAAGAGCC-GAGC
* * * *
20454084 ATTACTGGCGCTTAGATAAAAACGTCACTAAAGATCCGAGC
1 ATTACCGGCGCTTAGATAAAAACGCCGCTAAAGAGCCGAGC
* * * * **
20454125 ATTACCGACGCTTATACAAAATCGCCGCTAAATGCA-AAGAGC
1 ATTACCGGCGCTTAGATAAAAACGCCGCTAAA-G-AGCCGAGC
** * * *
20454167 ATTAGTGGCGCTCAGA-ATAAAACGCCACTAAAGATG-CAAGC
1 ATTACCGGCGCTTAGATA-AAAACGCCGCTAAAGA-GCCGAGC
* * * *
20454208 ATTAGCGGCGCTGAAATAAAATCGCCGCTAAAGA
1 ATTACCGGCGCTTAGATAAAAACGCCGCTAAAGA
20454242 CCAGAGATAT
Statistics
Matches: 122, Mismatches: 29, Indels: 14
0.74 0.18 0.08
Matches are distributed among these distances:
40 1 0.01
41 88 0.72
42 32 0.26
43 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (41 bp):
ATTACCGGCGCTTAGATAAAAACGCCGCTAAAGAGCCGAGC
Found at i:20454196 original size:83 final size:83
Alignment explanation
Indices: 20454084--20454239 Score: 206
Period size: 83 Copynumber: 1.9 Consensus size: 83
20454074 AAGCCGGAGG
* * * * *
20454084 ATTACTGGCGCTTAGATAAAAACGTCACTAAAGATCCGAGCATTACCGACGCTTATACAAAATCG
1 ATTACTGGCGCTCAGATAAAAACGCCACTAAAGATCCAAGCATTACCGACGCTGAAACAAAATCG
20454149 CCGCTAAATGCAAAGAGC
66 CCGCTAAATGCAAAGAGC
* * * * *
20454167 ATTAGTGGCGCTCAGA-ATAAAACGCCACTAAAGATGCAAGCATTAGCGGCGCTGAAATAAAATC
1 ATTACTGGCGCTCAGATA-AAAACGCCACTAAAGATCCAAGCATTACCGACGCTGAAACAAAATC
20454231 GCCGCTAAA
65 GCCGCTAAA
20454240 GACCAGAGAT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
82 1 0.02
83 61 0.98
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (83 bp):
ATTACTGGCGCTCAGATAAAAACGCCACTAAAGATCCAAGCATTACCGACGCTGAAACAAAATCG
CCGCTAAATGCAAAGAGC
Found at i:20458131 original size:16 final size:17
Alignment explanation
Indices: 20458105--20458149 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
20458095 CCAATTTAAT
* *
20458105 AAATATATTTATTTTTA
1 AAATATTTTTAATTTTA
20458122 AAAT-TTTTTAATTTTA
1 AAATATTTTTAATTTTA
20458138 AAATATTTTTAA
1 AAATATTTTTAA
20458150 AATACTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
AAATATTTTTAATTTTA
Found at i:20458180 original size:21 final size:21
Alignment explanation
Indices: 20458142--20458181 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20458132 ATTTTAAAAT
**
20458142 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
20458163 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
20458182 GGTATTTATT
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:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:20458188 original size:22 final size:21
Alignment explanation
Indices: 20458141--20458199 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
20458131 AATTTTAAAA
* *
20458141 TATTTTTAAAAT-ACTTTTTT
1 TATTTTTAAAATAAATTTTTG
20458161 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAATAAATTTTT-G
20458184 TATTTATTAAAA-AAAT
1 TATTT-TTAAAATAAAT
20458200 GGGCCGACCC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 1 0.03
21 11 0.33
22 14 0.42
23 7 0.21
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (21 bp):
TATTTTTAAAATAAATTTTTG
Found at i:20459514 original size:21 final size:21
Alignment explanation
Indices: 20459466--20459518 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
20459456 AAATTGTAGG
20459466 AAAAAGA-AGAAAAAAATGAA
1 AAAAAGATAGAAAAAAATGAA
* *
20459486 AAATAGATAGATAAAAAT-AA
1 AAAAAGATAGAAAAAAATGAA
20459506 ACAAAAGAT-GAAA
1 A-AAAAGATAGAAA
20459519 TAATCAAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.74, C:0.02, G:0.13, T:0.11
Consensus pattern (21 bp):
AAAAAGATAGAAAAAAATGAA
Found at i:20465815 original size:14 final size:14
Alignment explanation
Indices: 20465796--20465828 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
20465786 GGGAAGACAA
20465796 GATCTGCTTTCTTC
1 GATCTGCTTTCTTC
20465810 GATCTGCTTTCTTC
1 GATCTGCTTTCTTC
20465824 GATCT
1 GATCT
20465829 ACTTCACGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.09, C:0.27, G:0.15, T:0.48
Consensus pattern (14 bp):
GATCTGCTTTCTTC
Found at i:20465862 original size:58 final size:59
Alignment explanation
Indices: 20465760--20465872 Score: 174
Period size: 58 Copynumber: 1.9 Consensus size: 59
20465750 AAGACTTGTA
* **
20465760 TCTTCGATCTACTTCACTACCAGTATGGGAAGACAAGATCTGCTTTCTTCGATCTGCTT
1 TCTTCGATCTACTTCACTACCAATACAGGAAGACAAGATCTGCTTTCTTCGATCTGCTT
* *
20465819 TCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGATCTGCTTTCTTCGATCT
1 TCTTCGATCTACTTCACTACCAATACAGGAAGACAAGATCTGCTTTCTTCGATCT
20465873 ATTCCACTGT
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
58 32 0.65
59 17 0.35
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.35
Consensus pattern (59 bp):
TCTTCGATCTACTTCACTACCAATACAGGAAGACAAGATCTGCTTTCTTCGATCTGCTT
Found at i:20466349 original size:133 final size:132
Alignment explanation
Indices: 20465863--20466927 Score: 1638
Period size: 132 Copynumber: 8.1 Consensus size: 132
20465853 AGATCTGCTT
* * * *
20465863 TCTTCGATCTATTCCACTG-TCGACC-GGGGAGATAGAATTACTGGCTTCAATATACTCCACTGC
1 TCTTCAATCTATTCCACTGCT-GCCCAGGGAAG-TAGAATTACTGGCTTCAATATACTCCACTGT
* * *
20465926 AACCTCAAGGAGGTAAAATTTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
64 AACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
*
20465991 GTAA
129 GAAA
* * * * *
20465995 -CTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAAAATTATTGGCTTTAATGTACTCCACTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATATACTCCACTGTAA
* * *
20466059 CCACAGGGAGGTAAAATCTGTCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGA
66 CCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGA
20466124 AA
131 AA
* * *
20466126 TCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTAGCTTCAATGTACTCCACTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATATACTCCACTGTAA
* * *
20466191 CCTCAGGGAGGTAGAATCCGCCATCTTCGATCTGCTCCCCTACTGCTTAGGGAGATAAGATCTGA
66 CCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGA
20466256 AA
131 AA
* *
20466258 TCTTCAATCTATTCCACTGTTGCCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTA
1 TCTTCAATCTATTCCACTGCTG-CCCAGGGAAGTAGAATTACTGGCTTCAATATACTCCACTGTA
***
20466323 ACCTCAGGGAGGTAAAATCCATCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG
65 ACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG
20466388 AAA
130 AAA
* *
20466391 TCTTCAATCTATTCCACTGTTGCCCCAGGGAAGTAGAATTATTGGCTTCAATATACTCCACTGTA
1 TCTTCAATCTATTCCACTGCTG-CCCAGGGAAGTAGAATTACTGGCTTCAATATACTCCACTGTA
* *
20466456 ACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCTACTACTGCTTAGGGAGATAAGATCTG
65 ACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG
20466521 AAA
130 AAA
* ** *
20466524 TCTTCAATCTATTCCACTGTTGCCCCAGGGAAGTAGAATTGTTGGCTTCAATGTACTCCACTGTA
1 TCTTCAATCTATTCCACTGCTG-CCCAGGGAAGTAGAATTACTGGCTTCAATATACTCCACTGTA
* * * *
20466589 ACCACA-GGAGGTAAAATCTGCCATCTTTGATTTGCTCCACTACTGCTTAGGGAGACAAGATCTG
65 ACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG
20466653 AAA
130 AAA
*
20466656 TCTTCAATCTATTCCACTGCTGCTCAGGG-AGATAGAATTACTGGCTTCAATATACTCCACTGTA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAAG-TAGAATTACTGGCTTCAATATACTCCACTGTA
* *
20466720 ACCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTACTTAGGGAGATAAGATCTG
65 ACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG
20466785 AAA
130 AAA
20466788 TCTTCAATCTATTCCACTGCTGCCCAGGG-AGATAGAATTACTGGCTTCAATATACTCCACTGTA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAAG-TAGAATTACTGGCTTCAATATACTCCACTGTA
20466852 ACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG
65 ACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG
*
20466917 TAA
130 AAA
20466920 TCTTCAAT
1 TCTTCAAT
20466928 TTGTTCAACT
Statistics
Matches: 870, Mismatches: 57, Indels: 12
0.93 0.06 0.01
Matches are distributed among these distances:
130 2 0.00
131 149 0.17
132 418 0.48
133 301 0.35
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (132 bp):
TCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATATACTCCACTGTAA
CCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGA
AA
Found at i:20466905 original size:44 final size:44
Alignment explanation
Indices: 20465929--20466927 Score: 249
Period size: 44 Copynumber: 22.7 Consensus size: 44
20465919 CCACTGCAAC
* * * ** *
20465929 CTCAAGGAGGTAAAATTTGCCATCTTTGATCTGCTCCACTACTG
1 CTCAGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTG
* * * * * * *
20465973 CTTAGGGAGATAAGATCTG-TAACTTCAATCTATTCCGCTGCTG
1 CTCAGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTG
* * * *
20466016 CCCAGGGA-AGTAAAATTATTGGC-T-TT-AATGTACTCCACTGTAAC--
1 CTCAGGGAGA-TAAAA-T-CTGCCATCTTCAATCTACTCCAC--T-ACTG
* * * ** *
20466060 CACAGGGAGGTAAAATCTGTCATCTTTGATCTGCTCCACTACTG
1 CTCAGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTG
* * ** * * *
20466104 CTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCGCTGCTG
1 CTCAGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTG
* * * * * *
20466148 CCCAGGGA-AGTAGAAT-TACTAGCTTCAATGTACTCCACTGTAAC--
1 CTCAGGGAGA-TAAAATCTGCCATCTTCAATCTACTCCAC--T-ACTG
* * * * * *
20466192 CTCAGGGAGGTAGAATCCGCCATCTTCGATCTGCTCCCCTACTG
1 CTCAGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTG
* * ** * **
20466236 CTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTG
1 CTCAGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTG
* * * *** *
20466280 CCCCAGGGA-AGTAGAAT-TACTGGCTTCAATGTACTCCACTGTAAC--
1 -CTCAGGGAGA-TAAAATCTGCCATCTTCAATCTACTCCAC--T-ACTG
* *** * *
20466325 CTCAGGGAGGTAAAATCCATCATCTTCGATCTGCTCCACTACTG
1 CTCAGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTG
* * ** * **
20466369 CTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTG
1 CTCAGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTG
* * ***** *
20466413 CCCCAGGGA-AGTAGAAT-TATTGGCTTCAATATACTCCACTGTAAC--
1 -CTCAGGGAGA-TAAAATCTGCCATCTTCAATCTACTCCAC--T-ACTG
* * * * *
20466458 CTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCTACTACTG
1 CTCAGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTG
* * ** * **
20466502 CTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTG
1 CTCAGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTG
* * **** *
20466546 CCCCAGGGA-AGTAGAAT-TGTTGGCTTCAATGTACTCCACTGTAAC--
1 -CTCAGGGAGA-TAAAATCTGCCATCTTCAATCTACTCCAC--T-ACTG
* * ** * *
20466591 CACA-GGAGGTAAAATCTGCCATCTTTGATTTGCTCCACTACTG
1 CTCAGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTG
* * * ** * *
20466634 CTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTG
1 CTCAGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTG
* * *** *
20466678 CTCAGGGAGATAGAAT-TACTGGCTTCAATATACTCCACTGTAAC--
1 CTCAGGGAGATAAAATCTGCCATCTTCAATCTACTCCAC--T-ACTG
* ** * *
20466722 CTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTA
1 CTCAGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTG
* * ** * *
20466766 CTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTG
1 CTCAGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTG
* * * *** *
20466810 CCCAGGGAGATAGAAT-TACTGGCTTCAATATACTCCACTGTAAC--
1 CTCAGGGAGATAAAATCTGCCATCTTCAATCTACTCCAC--T-ACTG
* * *
20466854 CTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTG
1 CTCAGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTG
* * **
20466898 CTTAGGGAGATAAGATCTGTAATCTTCAAT
1 CTCAGGGAGATAAAATCTGCCATCTTCAAT
20466928 TTGTTCAACT
Statistics
Matches: 646, Mismatches: 248, Indels: 122
0.64 0.24 0.12
Matches are distributed among these distances:
41 2 0.00
42 17 0.03
43 99 0.15
44 407 0.63
45 114 0.18
46 7 0.01
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (44 bp):
CTCAGGGAGATAAAATCTGCCATCTTCAATCTACTCCACTACTG
Found at i:20466983 original size:50 final size:50
Alignment explanation
Indices: 20466921--20467290 Score: 330
Period size: 50 Copynumber: 7.4 Consensus size: 50
20466911 GATCTGTAAT
* * *
20466921 CTTCAATTTGTTCAACTGTAATGTCAGGGAAACCAGATCCGCCGTCGTAG
1 CTTCAATCTGTTCAACTGCAATATCAGGGAAACCAGATCCGCCGTCGTAG
* ** *** * * *
20466971 CTTCAATCTGTTCTACTGCAACGTCAGGGAAGTAAGATCAGCCGTTGTGG
1 CTTCAATCTGTTCAACTGCAATATCAGGGAAACCAGATCCGCCGTCGTAG
* * * *
20467021 CTTCAATCTTTTTAATTACAATATCAGGGAAACCAGATCCGCCGTCGTAG
1 CTTCAATCTGTTCAACTGCAATATCAGGGAAACCAGATCCGCCGTCGTAG
* * * *** * * *
20467071 CTTCAATCTGTTCCACTGCACTA-CTAAGGAAGTAAGATTCGCCGTTGTGG
1 CTTCAATCTGTTCAACTGCAATATC-AGGGAAACCAGATCCGCCGTCGTAG
* * *
20467121 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAG
1 CTTCAATCTGTTCAACTGCAATATCAGGGAAACCAGATCCGCCGTCGTAG
* * * * *** * *
20467171 GTTCAATCTGTTCCACTGCACTGAT-AAGGAAGTAAGATCCGCCGTTGTGG
1 CTTCAATCTGTTCAACTGCAAT-ATCAGGGAAACCAGATCCGCCGTCGTAG
* * *
20467221 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAG
1 CTTCAATCTGTTCAACTGCAATATCAGGGAAACCAGATCCGCCGTCGTAG
* *
20467271 CTTCAATCTATTCCACTGCA
1 CTTCAATCTGTTCAACTGCA
20467291 TTGCAAGGAA
Statistics
Matches: 240, Mismatches: 76, Indels: 8
0.74 0.23 0.02
Matches are distributed among these distances:
49 3 0.01
50 234 0.98
51 3 0.01
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.29
Consensus pattern (50 bp):
CTTCAATCTGTTCAACTGCAATATCAGGGAAACCAGATCCGCCGTCGTAG
Found at i:20467069 original size:100 final size:98
Alignment explanation
Indices: 20466944--20467290 Score: 563
Period size: 100 Copynumber: 3.5 Consensus size: 98
20466934 AACTGTAATG
* *
20466944 TCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCTACTGCAACGTCAGGGAAGTAAGAT
1 TCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGC-ACGTCAAGGAAGTAAGAT
*
20467009 CAGCCGTTGTGGCTTCAATCTTTTTAATTACAATA
65 C-GCCGTTGTGGCTTCAATCTTTTTAATTGCAATA
20467044 TCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCAC-TACTAAGGAAGTAAGA
1 TCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACGT-C-AAGGAAGTAAGA
20467108 TTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATA
64 -TCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATA
*
20467144 TCAGGGAAACCAGATCCGCCGTCGTAGGTTCAATCTGTTCCACTGCACTGAT-AAGGAAGTAAGA
1 TCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCAC-G-TCAAGGAAGTAAGA
20467208 TCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATA
64 T-CGCCGTTGTGGCTTCAATCTTTTTAATTGCAATA
*
20467244 TCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCACTGCA
1 TCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCA
20467291 TTGCAAGGAA
Statistics
Matches: 234, Mismatches: 6, Indels: 14
0.92 0.02 0.06
Matches are distributed among these distances:
98 1 0.00
99 4 0.02
100 226 0.97
101 2 0.01
103 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (98 bp):
TCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACGTCAAGGAAGTAAGATC
GCCGTTGTGGCTTCAATCTTTTTAATTGCAATA
Found at i:20468663 original size:7 final size:7
Alignment explanation
Indices: 20468643--20468795 Score: 167
Period size: 7 Copynumber: 22.0 Consensus size: 7
20468633 TTAGCCTCTC
20468643 CATTTTT
1 CATTTTT
20468650 -ACTTTTT
1 CA-TTTTT
*
20468657 CCATTTTC
1 -CATTTTT
20468665 CATTTTT
1 CATTTTT
20468672 CATTTTT
1 CATTTTT
20468679 CATTTTT
1 CATTTTT
20468686 CATTTTT
1 CATTTTT
20468693 CA-TTTT
1 CATTTTT
20468699 CATTTTTT
1 CA-TTTTT
** *
20468707 CACATCT
1 CATTTTT
20468714 -ATTTTCTT
1 CA-TTT-TT
20468722 C-TCTTTT
1 CAT-TTTT
20468729 --TTTTT
1 CATTTTT
20468734 CATTTTT
1 CATTTTT
20468741 CATTTTT
1 CATTTTT
20468748 CATTTTT
1 CATTTTT
20468755 CATTTTT
1 CATTTTT
20468762 CATTTTT
1 CATTTTT
20468769 CATTTTT
1 CATTTTT
20468776 CATTTTT
1 CATTTTT
20468783 CA-TTTT
1 CATTTTT
20468789 CATTTTT
1 CATTTTT
20468796 TCACATCTCA
Statistics
Matches: 126, Mismatches: 8, Indels: 24
0.80 0.05 0.15
Matches are distributed among these distances:
5 4 0.03
6 15 0.12
7 93 0.74
8 13 0.10
9 1 0.01
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (7 bp):
CATTTTT
Found at i:20471873 original size:16 final size:16
Alignment explanation
Indices: 20471852--20471886 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
20471842 TTCTATAATG
20471852 AAATGTCATGCAGTCA
1 AAATGTCATGCAGTCA
*
20471868 AAATGTCATGCATTCA
1 AAATGTCATGCAGTCA
20471884 AAA
1 AAA
20471887 CAAAACACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (16 bp):
AAATGTCATGCAGTCA
Found at i:20476828 original size:2 final size:2
Alignment explanation
Indices: 20476821--20476855 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
20476811 NNNNNAAATA
20476821 AT AT AT AT AT 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 AT AT A
20476856 CAAATAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20479922 original size:4 final size:4
Alignment explanation
Indices: 20479915--20479957 Score: 59
Period size: 4 Copynumber: 10.8 Consensus size: 4
20479905 CACACACAAT
* * *
20479915 ATAC ATAC ATAT ATAC ATAT ATAC ATAC ATAC AAAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
20479958 TATATATATA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.53, C:0.19, G:0.00, T:0.28
Consensus pattern (4 bp):
ATAC
Found at i:20479930 original size:12 final size:12
Alignment explanation
Indices: 20479913--20479965 Score: 61
Period size: 12 Copynumber: 4.4 Consensus size: 12
20479903 AACACACACA
20479913 ATATACATACAT
1 ATATACATACAT
*
20479925 ATATACATATAT
1 ATATACATACAT
* *
20479937 ACATACATACAA
1 ATATACATACAT
* *
20479949 ACATACATATAT
1 ATATACATACAT
20479961 ATATA
1 ATATA
20479966 TATGCCTACC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (12 bp):
ATATACATACAT
Found at i:20479932 original size:8 final size:8
Alignment explanation
Indices: 20479919--20479968 Score: 64
Period size: 8 Copynumber: 6.2 Consensus size: 8
20479909 CACAATATAC
20479919 ATACATAT
1 ATACATAT
20479927 ATACATAT
1 ATACATAT
*
20479935 ATACATAC
1 ATACATAT
* *
20479943 ATACAAAC
1 ATACATAT
20479951 ATACATAT
1 ATACATAT
*
20479959 ATATATAT
1 ATACATAT
20479967 AT
1 AT
20479969 GCCTACCTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 37 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (8 bp):
ATACATAT
Found at i:20481096 original size:2 final size:2
Alignment explanation
Indices: 20481091--20481122 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
20481081 AATGAATAGT
20481091 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
20481123 ATGCACCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20481536 original size:22 final size:22
Alignment explanation
Indices: 20481509--20481570 Score: 106
Period size: 22 Copynumber: 2.8 Consensus size: 22
20481499 ATCTCATACC
20481509 CTTCAAAAATTCTCTCAATTTA
1 CTTCAAAAATTCTCTCAATTTA
*
20481531 CTTCAAAAATTCTCTCAATTTC
1 CTTCAAAAATTCTCTCAATTTA
*
20481553 CTTCCAAAATTCTCTCAA
1 CTTCAAAAATTCTCTCAA
20481571 ACTCTCAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.34, C:0.27, G:0.00, T:0.39
Consensus pattern (22 bp):
CTTCAAAAATTCTCTCAATTTA
Found at i:20481578 original size:30 final size:30
Alignment explanation
Indices: 20481542--20481600 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
20481532 TTCAAAAATT
* *
20481542 CTCTCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAAA
20481572 CTCTCAAATTCCTTCCAAAATCCTCTCAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAA
20481601 TTTCCTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.36, G:0.00, T:0.34
Consensus pattern (30 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAAA
Found at i:20481598 original size:52 final size:51
Alignment explanation
Indices: 20481520--20481622 Score: 143
Period size: 52 Copynumber: 2.0 Consensus size: 51
20481510 TTCAAAAATT
* * * *
20481520 CTCTCAATTTACTTCAAAAATTCTCTCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAAATTACTTCAAAAATCCTCTCAATTTCCTTCAAAAAATCTC-CAAA
* *
20481572 CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
1 CTCTCAAATTACTTCAAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
20481623 TCCATATCAT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
51 4 0.09
52 41 0.91
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.35
Consensus pattern (51 bp):
CTCTCAAATTACTTCAAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
Found at i:20481611 original size:21 final size:22
Alignment explanation
Indices: 20481572--20481613 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
20481562 TTCTCTCAAA
20481572 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
20481594 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
20481614 ATCTCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:20481719 original size:30 final size:30
Alignment explanation
Indices: 20481655--20481711 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
20481645 ATTCAATTTC
*
20481655 ATTTTTTTAAGAAAATTTTATATATTTTTT
1 ATTTTTTTAAGAAAATTTTATAAATTTTTT
*
20481685 ATTTTTTTAA-ATAATTTTA-AAATTTTT
1 ATTTTTTTAAGAAAATTTTATAAATTTTT
20481712 AATATTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 7 0.28
29 8 0.32
30 10 0.40
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (30 bp):
ATTTTTTTAAGAAAATTTTATAAATTTTTT
Found at i:20481839 original size:14 final size:15
Alignment explanation
Indices: 20481810--20481843 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
20481800 AAATTTTAAA
20481810 TTTTATTTAAGATAT
1 TTTTATTTAAGATAT
*
20481825 TTTTATTTATG-TAT
1 TTTTATTTAAGATAT
20481839 TTTTA
1 TTTTA
20481844 GATAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTTAAGATAT
Found at i:20483947 original size:28 final size:28
Alignment explanation
Indices: 20483922--20484598 Score: 935
Period size: 28 Copynumber: 25.8 Consensus size: 28
20483912 AACCCTAACC
20483922 TAATTTAATTAAAAACCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAACCTAATT
20483950 TAATTTAATTAAAAACCCTAACC-----
1 TAATTTAATTAAAAACCCTAACCTAATT
*
20483973 TAATTTAATTAAAAACCCTCACCTAATT
1 TAATTTAATTAAAAACCCTAACCTAATT
20484001 TAATTTAATTAAAAACCCTAACC-----
1 TAATTTAATTAAAAACCCTAACCTAATT
*
20484024 TAATTTAATTAAAAACCTTAACCTAATT
1 TAATTTAATTAAAAACCCTAACCTAATT
20484052 TAATTTAATTAAAAACCCTAACC-----
1 TAATTTAATTAAAAACCCTAACCTAATT
20484075 TAATTTAATTAAAAACCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAACCTAATT
20484103 TAATTTAATTAAAAACCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAACCTAATT
*
20484131 TAATTTAATTAAAAGCCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAACCTAATT
20484159 TAATTTAATTAAAAACCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAACCTAATT
20484187 TAATTTAATTAAAAACCCTAACC-----
1 TAATTTAATTAAAAACCCTAACCTAATT
20484210 TAATTTAATTAAAAACCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAACCTAATT
20484238 TAATTTAATTAAAAACCCTAACC-----
1 TAATTTAATTAAAAACCCTAACCTAATT
20484261 TAATTTAATTAAAAACCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAACCTAATT
20484289 TAATTTAATTAAAAACCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAACCTAATT
20484317 TAATTTAATTAAAAACCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAACCTAATT
20484345 TAATTTAATTAAAAACCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAACCTAATT
*
20484373 TAATTTAATTAAAAATCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAACCTAATT
20484401 TAATTTAATTAAAAACCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAACCTAATT
20484429 TAATTTAATTAAAAACCCTAACC-----
1 TAATTTAATTAAAAACCCTAACCTAATT
20484452 TAATTTAATTAAAAACCCTAACC-----
1 TAATTTAATTAAAAACCCTAACCTAATT
20484475 TAATTTAATTAAAAACCCTAACC-----
1 TAATTTAATTAAAAACCCTAACCTAATT
* **
20484498 TAATTTAATTAAAATCCCTAACCCTAACC
1 TAATTTAATTAAAAACCCTAA-CCTAATT
*
20484527 TAATTTAATTTAAAACCCTAACC-----
1 TAATTTAATTAAAAACCCTAACCTAATT
20484550 TAATTTAATT-AAAACCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAACCTAATT
20484577 TAA-TTAATGTAAAAACCCTAAC
1 TAATTTAAT-TAAAAACCCTAAC
20484599 ATAACTCAGC
Statistics
Matches: 600, Mismatches: 11, Indels: 76
0.87 0.02 0.11
Matches are distributed among these distances:
22 12 0.02
23 189 0.31
24 2 0.00
26 5 0.01
27 4 0.01
28 369 0.62
29 19 0.03
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.34
Consensus pattern (28 bp):
TAATTTAATTAAAAACCCTAACCTAATT
Found at i:20483971 original size:51 final size:51
Alignment explanation
Indices: 20483906--20484598 Score: 916
Period size: 51 Copynumber: 13.3 Consensus size: 51
20483896 TTTCCGAGTT
20483906 ATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTTA
1 ATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTTA
*
20483957 ATTAAAAACCCTAACCTAATTTAATTAAAAACCCTCACCTAATTTAATTTA
1 ATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTTA
*
20484008 ATTAAAAACCCTAACCTAATTTAATTAAAAACCTTAACCTAATTTAATTTA
1 ATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTTA
20484059 ATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTTA
1 ATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTTA
20484110 ATTAAAAACCCTAACCTAATTTAATTTAATTAAAAGCCCTAACCTAATTTAATTTA
1 ATTAAAAACCCTAACCTAATTTAA-TT-A--AAAA-CCCTAACCTAATTTAATTTA
20484166 ATTAAAAACCCTAACCTAATTTAATTTAATTAAAAACCCTAACC-----TAATTTA
1 ATTAAAAACCCTAACC-----TAATTTAATTAAAAACCCTAACCTAATTTAATTTA
20484217 ATTAAAAACCCTAACCTAATTTAATTTAATTAAAAACCCTAACC-----TAATTTA
1 ATTAAAAACCCTAACC-----TAATTTAATTAAAAACCCTAACCTAATTTAATTTA
20484268 ATTAAAAACCCTAACCTAATTTAATTTAATTAAAAACCCTAACCTAATTTAATTTA
1 ATTAAAAACCCTAACC-----TAATTTAATTAAAAACCCTAACCTAATTTAATTTA
20484324 ATTAAAAACCCTAACCTAATTTAATTTAATTAAAAACCCTAACCTAATTTAATTTA
1 ATTAAAAACCCTAACC-----TAATTTAATTAAAAACCCTAACCTAATTTAATTTA
*
20484380 ATTAAAAATCCTAACCTAATTTAATTTAATTAAAAACCCTAACCTAATTTAATTTA
1 ATTAAAAACCCTAACC-----TAATTTAATTAAAAACCCTAACCTAATTTAATTTA
20484436 ATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACC-----TAATTTA
1 ATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTTA
* **
20484482 ATTAAAAACCCTAACCTAATTTAATTAAAATCCCTAACCCTAACCTAATTTA
1 ATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAA-CCTAATTTAATTTA
*
20484534 ATTTAAAACCCTAACCTAATTTAATT-AAAACCCTAACCTAATTTAA-TTA
1 ATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTTA
20484583 ATGTAAAAACCCTAAC
1 AT-TAAAAACCCTAAC
20484599 ATAACTCAGC
Statistics
Matches: 608, Mismatches: 12, Indels: 45
0.91 0.02 0.07
Matches are distributed among these distances:
46 43 0.07
47 2 0.00
49 5 0.01
50 20 0.03
51 307 0.50
52 34 0.06
53 1 0.00
55 4 0.01
56 177 0.29
57 4 0.01
59 1 0.00
60 2 0.00
61 8 0.01
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (51 bp):
ATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTTA
Found at i:20484101 original size:18 final size:19
Alignment explanation
Indices: 20484056--20484102 Score: 51
Period size: 23 Copynumber: 2.3 Consensus size: 19
20484046 CTAATTTAAT
20484056 TTAATTAAAAACCCTAACC
1 TTAATTAAAAACCCTAACC
20484075 TAATTTAATTAAAAACCCTAACC
1 ----TTAATTAAAAACCCTAACC
20484098 -TAATT
1 TTAATT
20484103 TAATTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 5 0.21
23 19 0.79
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (19 bp):
TTAATTAAAAACCCTAACC
Found at i:20484236 original size:18 final size:19
Alignment explanation
Indices: 20484191--20484237 Score: 51
Period size: 23 Copynumber: 2.3 Consensus size: 19
20484181 CTAATTTAAT
20484191 TTAATTAAAAACCCTAACC
1 TTAATTAAAAACCCTAACC
20484210 TAATTTAATTAAAAACCCTAACC
1 ----TTAATTAAAAACCCTAACC
20484233 -TAATT
1 TTAATT
20484238 TAATTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 5 0.21
23 19 0.79
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (19 bp):
TTAATTAAAAACCCTAACC
Found at i:20484287 original size:18 final size:19
Alignment explanation
Indices: 20484242--20484288 Score: 51
Period size: 23 Copynumber: 2.3 Consensus size: 19
20484232 CTAATTTAAT
20484242 TTAATTAAAAACCCTAACC
1 TTAATTAAAAACCCTAACC
20484261 TAATTTAATTAAAAACCCTAACC
1 ----TTAATTAAAAACCCTAACC
20484284 -TAATT
1 TTAATT
20484289 TAATTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 5 0.21
23 19 0.79
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (19 bp):
TTAATTAAAAACCCTAACC
Found at i:20484471 original size:18 final size:20
Alignment explanation
Indices: 20484429--20484511 Score: 85
Period size: 23 Copynumber: 3.7 Consensus size: 20
20484419 TAACCTAATT
20484429 TAATTTAATTAAAAACCCTAACC
1 TAATTTAATTAAAAA-CC--ACC
20484452 TAATTTAATTAAAAACCCTAACC
1 TAATTTAATTAAAAA-CC--ACC
20484475 TAATTTAATTAAAAACCCTAACC
1 TAATTTAATTAAAAA-CC--ACC
20484498 TAATTTAATTAAAA
1 TAATTTAATTAAAA
20484512 TCCCTAACCC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 60 1.00
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (20 bp):
TAATTTAATTAAAAACCACC
Found at i:20484682 original size:56 final size:57
Alignment explanation
Indices: 20484611--20484720 Score: 161
Period size: 56 Copynumber: 1.9 Consensus size: 57
20484601 AACTCAGCAG
* ** *
20484611 ATTTGATAATCTTACTAACCATTAACACACTTTTTTGGGCT-TAATAATTTTACATA
1 ATTTGATAATCTTACTAACCATTAACAAAAGTTTTTGGGATGTAATAATTTTACATA
20484667 ATTTGATAAGT-TTACTAACCATTAACAAAAGTTTTTGGGATGTAATAATTTTAC
1 ATTTGATAA-TCTTACTAACCATTAACAAAAGTTTTTGGGATGTAATAATTTTAC
20484721 CTAGTTTTAC
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
56 35 0.73
57 13 0.27
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (57 bp):
ATTTGATAATCTTACTAACCATTAACAAAAGTTTTTGGGATGTAATAATTTTACATA
Found at i:20488849 original size:126 final size:125
Alignment explanation
Indices: 20488625--20488869 Score: 418
Period size: 126 Copynumber: 2.0 Consensus size: 125
20488615 CCATGAGGGC
*
20488625 GCGATTTGACACTATTTACTCAGAAACGTCAAAAAATAATTATTTCCTACATGACCAACTGTAGT
1 GCGATTTGACACTATTTACTCAGAAACGTCAAAAAATAATTATTTCCTACATGACCAACTGTAGC
* * *
20488690 GAAATCGTGTCCACGAGGGCGCGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCA
66 GAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTATCA
* * *
20488750 GCGATTTTATACTATTTGCTCAGAAAACGTCAAAAAATAATTATTTCCTACATGACCAACTGTAG
1 GCGATTTGACACTATTTACTCAG-AAACGTCAAAAAATAATTATTTCCTACATGACCAACTGTAG
20488815 CGAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTG
65 CGAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTG
20488870 CTGGAGGCGA
Statistics
Matches: 112, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
125 20 0.18
126 92 0.82
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.30
Consensus pattern (125 bp):
GCGATTTGACACTATTTACTCAGAAACGTCAAAAAATAATTATTTCCTACATGACCAACTGTAGC
GAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTATCA
Found at i:20488880 original size:126 final size:126
Alignment explanation
Indices: 20488625--20488907 Score: 412
Period size: 126 Copynumber: 2.3 Consensus size: 126
20488615 CCATGAGGGC
* *
20488625 GCGATTTGACACTATTTACTCAG-AAACGTCAAAAAATAATTATTTCCTACATGACCAACTGTAG
1 GCGATTTCACACTATTTGCTCAGAAAACGTCAAAAAATAATTATTTCCTACATGACCAACTGTAG
* * * * * *
20488689 TGAAATCGTGTCCACGAGGGCGCGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCA
66 CGAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGCTAGCA
* *
20488750 GCGATTTTATACTATTTGCTCAGAAAACGTCAAAAAATAATTATTTCCTACATGACCAACTGTAG
1 GCGATTTCACACTATTTGCTCAGAAAACGTCAAAAAATAATTATTTCCTACATGACCAACTGTAG
*
20488815 CGAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGCT-GGA
66 CGAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGCTAGCA
*
20488875 GGCGATTTCCCACTATTTGAC-CA-AAAACGTCAA
1 -GCGATTTCACACTATTTG-CTCAGAAAACGTCAA
20488908 CTCAAAAAAA
Statistics
Matches: 142, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
125 31 0.22
126 110 0.77
127 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (126 bp):
GCGATTTCACACTATTTGCTCAGAAAACGTCAAAAAATAATTATTTCCTACATGACCAACTGTAG
CGAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGCTAGCA
Found at i:20493249 original size:108 final size:108
Alignment explanation
Indices: 20493056--20493256 Score: 375
Period size: 108 Copynumber: 1.9 Consensus size: 108
20493046 GGAAATCGCG
* *
20493056 TCCACGTCAGCATCTCGCGTTGACGTGGACGCGATTTCGGCCCGCGCGTGAACAGTACCCAACGG
1 TCCACGTCAGCATCTCGCGCTGACGTGGACGCGATTTCGGCCCACGCGTGAACAGTACCCAACGG
20493121 TCAAAAAAATAAAATACCGGGCCCATTTCGAGCGCGATTTCCT
66 TCAAAAAAATAAAATACCGGGCCCATTTCGAGCGCGATTTCCT
20493164 TCCACGTCAGCATCTCGCGCTGACGTGGACGCGATTTCGGCCCACGCGTGAACAGTACCCAACGG
1 TCCACGTCAGCATCTCGCGCTGACGTGGACGCGATTTCGGCCCACGCGTGAACAGTACCCAACGG
*
20493229 TCAAAAAAATAAAATCCCGGGCCCATTT
66 TCAAAAAAATAAAATACCGGGCCCATTT
20493257 TGATAAATTT
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 90 1.00
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.19
Consensus pattern (108 bp):
TCCACGTCAGCATCTCGCGCTGACGTGGACGCGATTTCGGCCCACGCGTGAACAGTACCCAACGG
TCAAAAAAATAAAATACCGGGCCCATTTCGAGCGCGATTTCCT
Found at i:20497089 original size:21 final size:21
Alignment explanation
Indices: 20497056--20497117 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
20497046 AAACATATCT
20497056 AAAATAT-TTAAAATTTTATA
1 AAAATATATTAAAATTTTATA
*
20497076 AAAATATATTAAAATTCTATA
1 AAAATATATTAAAATTTTATA
*
20497097 AAAAT-CA-TAAAA-TTTATA
1 AAAATATATTAAAATTTTATA
20497115 AAA
1 AAA
20497118 TTATTATAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 8 0.21
19 5 0.13
20 8 0.21
21 17 0.45
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAATATATTAAAATTTTATA
Found at i:20497115 original size:9 final size:9
Alignment explanation
Indices: 20497055--20497151 Score: 56
Period size: 9 Copynumber: 10.3 Consensus size: 9
20497045 AAAACATATC
20497055 TAAAATATT-
1 TAAAAT-TTA
20497064 TAAAATTTTA
1 TAAAA-TTTA
*
20497074 TAAAAATATA
1 T-AAAATTTA
20497084 TTAAAATTCTA
1 -TAAAATT-TA
* *
20497095 TAAAAATCA
1 TAAAATTTA
20497104 TAAAATTTA
1 TAAAATTTA
20497113 TAAAA-TTA
1 TAAAATTTA
* *
20497121 TTATAATTGA
1 -TAAAATTTA
*
20497131 TATAAACTTA
1 TA-AAATTTA
20497141 T-AAATTTA
1 TAAAATTTA
20497149 TAA
1 TAA
20497152 TAAAAAAACC
Statistics
Matches: 67, Mismatches: 12, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
8 10 0.15
9 27 0.40
10 23 0.34
11 7 0.10
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (9 bp):
TAAAATTTA
Found at i:20497906 original size:22 final size:22
Alignment explanation
Indices: 20497876--20497918 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
20497866 ACACCAAAAC
* *
20497876 AGGCTTTTAGTGGCGCTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
20497898 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
20497919 AGCGCCGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.19, G:0.28, T:0.44
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Found at i:20498118 original size:43 final size:43
Alignment explanation
Indices: 20498046--20498232 Score: 252
Period size: 43 Copynumber: 4.4 Consensus size: 43
20498036 AGACTAAGAC
* * *
20498046 CTTTAGCGGCGCTTTAGTG-GAAGCGCCGCTAAAGATCAGGGT
1 CTTTAGCGGCGTTTTTGCGAGAAGCGCCGCTAAAGATCAGGGT
*
20498088 CTTTAGCGGCGTTTTTGCTAGAAGCGCCGCTAAAGATCAGGGT
1 CTTTAGCGGCGTTTTTGCGAGAAGCGCCGCTAAAGATCAGGGT
* * *
20498131 CTTTAGCGGCGTTTTTTCGAG-AGTAGCCGCTGAAGATCAGGGT
1 CTTTAGCGGCGTTTTTGCGAGAAG-CGCCGCTAAAGATCAGGGT
* * *
20498174 CTTTAGTGGCGTTTTTGCGACAAGCGCCGCTAAAGATTAGGGT
1 CTTTAGCGGCGTTTTTGCGAGAAGCGCCGCTAAAGATCAGGGT
*
20498217 CTTTAGCGGCGCTTTT
1 CTTTAGCGGCGTTTTT
20498233 CCCACAAACA
Statistics
Matches: 126, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
42 17 0.13
43 107 0.85
44 2 0.02
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.29
Consensus pattern (43 bp):
CTTTAGCGGCGTTTTTGCGAGAAGCGCCGCTAAAGATCAGGGT
Found at i:20498252 original size:43 final size:43
Alignment explanation
Indices: 20498071--20498405 Score: 141
Period size: 43 Copynumber: 7.8 Consensus size: 43
20498061 AGTGGAAGCG
* * * * * * *
20498071 CCGCTAAAGATCAGGGTCTTTAGCGGCGTTTTTGCTAGAAGCG
1 CCGCAAAAGATCAGGGTCTTTAGCGGCGCTTTTCCCACAAACA
* * * * * * *
20498114 CCGCTAAAGATCAGGGTCTTTAGCGGCGTTTTTTCGAGAGTA-G
1 CCGCAAAAGATCAGGGTCTTTAGCGGCGCTTTTCCCACA-AACA
** * * * * * *
20498157 CCGCTGAAGATCAGGGTCTTTAGTGGCGTTTTTGCGACAAGCG
1 CCGCAAAAGATCAGGGTCTTTAGCGGCGCTTTTCCCACAAACA
* *
20498200 CCGCTAAAGATTAGGGTCTTTAGCGGCGCTTTTCCCACAAACA
1 CCGCAAAAGATCAGGGTCTTTAGCGGCGCTTTTCCCACAAACA
* * ** * * * * *** *
20498243 CCTCAAAAGACCCTGATCTATAGCAGCGCCTCGACCACAAACG
1 CCGCAAAAGATCAGGGTCTTTAGCGGCGCTTTTCCCACAAACA
* * *** * *
20498286 CCACTAAAGATCATAATCTTTAGCGGCGCTTTCCCCACAAACG
1 CCGCAAAAGATCAGGGTCTTTAGCGGCGCTTTTCCCACAAACA
* * * * * * *
20498329 CCGCTAAAGACCATGATCTTTAGTGGCGCTTTTTTCCACAAACG
1 CCGCAAAAGATCAGGGTCTTTAGCGGCGC-TTTTCCCACAAACA
* * ****
20498373 CCGCTAAAGACCCTTATCTTTAGCGGCGCTTTT
1 CCGCAAAAGATCAGGGTCTTTAGCGGCGCTTTT
20498406 ACCAAAAAAC
Statistics
Matches: 237, Mismatches: 52, Indels: 6
0.80 0.18 0.02
Matches are distributed among these distances:
43 199 0.84
44 38 0.16
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (43 bp):
CCGCAAAAGATCAGGGTCTTTAGCGGCGCTTTTCCCACAAACA
Found at i:20498424 original size:44 final size:43
Alignment explanation
Indices: 20498216--20498425 Score: 204
Period size: 43 Copynumber: 4.8 Consensus size: 43
20498206 AAGATTAGGG
* * * * *
20498216 TCTTTAGCGGCGCTTTTCCCACAAACACCTCAAAAGACCCTGA
1 TCTTTAGCGGCGCTTTTACCACAAACGCCACTAAAGACCATGA
* * * ** * *
20498259 TCTATAGCAGCGCCTCGACCACAAACGCCACTAAAGATCATAA
1 TCTTTAGCGGCGCTTTTACCACAAACGCCACTAAAGACCATGA
** *
20498302 TCTTTAGCGGCGCTTTCCCCACAAACGCCGCTAAAGACCATGA
1 TCTTTAGCGGCGCTTTTACCACAAACGCCACTAAAGACCATGA
* * * * *
20498345 TCTTTAGTGGCGCTTTTTTCCACAAACGCCGCTAAAGACCCTTA
1 TCTTTAGCGGCGC-TTTTACCACAAACGCCACTAAAGACCATGA
* *
20498389 TCTTTAGCGGCGCTTTTACCAAAAAACTCCACTAAAG
1 TCTTTAGCGGCGCTTTTACC-ACAAACGCCACTAAAG
20498426 GCCAACACCT
Statistics
Matches: 134, Mismatches: 31, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
43 83 0.62
44 51 0.38
ACGTcount: A:0.29, C:0.32, G:0.15, T:0.24
Consensus pattern (43 bp):
TCTTTAGCGGCGCTTTTACCACAAACGCCACTAAAGACCATGA
Found at i:20498449 original size:87 final size:87
Alignment explanation
Indices: 20498277--20498468 Score: 213
Period size: 88 Copynumber: 2.2 Consensus size: 87
20498267 AGCGCCTCGA
* * * * *
20498277 CCACAAACGCCACTAAAGATCATAATCTTTAGCGGCGCTTTCCCCACAAACGCCGCTAAAGACCA
1 CCACAAACGCCACTAAAGACCATAATCTTTAGCGGCGCTTTACCAAAAAACGCCACTAAAGACCA
** * *
20498342 TGATCTTTAGTGGCGCTTTTTT
66 ACACCTTCAGTGGCGCTTTTTT
* * * * *
20498364 CCACAAACGCCGCTAAAGACCCTTATCTTTAGCGGCGCTTTTACCAAAAAACTCCACTAAAGGCC
1 CCACAAACGCCACTAAAGACCATAATCTTTAGCGGCGC-TTTACCAAAAAACGCCACTAAAGACC
*
20498429 AACACCTTCAGTGGCGTTTTTTT
65 AACACCTTCAGTGGCGCTTTTTT
** *
20498452 TGAAAAACGCCACTAAA
1 CCACAAACGCCACTAAA
20498469 TTTGGCAGAT
Statistics
Matches: 85, Mismatches: 19, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
87 34 0.40
88 51 0.60
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25
Consensus pattern (87 bp):
CCACAAACGCCACTAAAGACCATAATCTTTAGCGGCGCTTTACCAAAAAACGCCACTAAAGACCA
ACACCTTCAGTGGCGCTTTTTT
Found at i:20498802 original size:21 final size:21
Alignment explanation
Indices: 20498776--20498888 Score: 109
Period size: 21 Copynumber: 5.4 Consensus size: 21
20498766 TTTGACGCTG
*
20498776 CTCTGCTTCCCTCGCTGTAGC
1 CTCTGCTTCCCTCGCTGCAGC
* **
20498797 CTCTGCTTCCCTTGCTTTAGC
1 CTCTGCTTCCCTCGCTGCAGC
20498818 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * * * *
20498839 CTGTACTTCTCTCGTTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
* * *
20498860 CTCTGCTTCTCTTGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
*
20498881 ATCTGCTT
1 CTCTGCTT
20498889 TAAGCTNNNN
Statistics
Matches: 77, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 77 1.00
ACGTcount: A:0.04, C:0.41, G:0.18, T:0.37
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:20508248 original size:16 final size:16
Alignment explanation
Indices: 20508227--20508260 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
20508217 ATAGTTAAGC
20508227 TATGTAAGTTATGTAT
1 TATGTAAGTTATGTAT
*
20508243 TATGTAAGTTATTTAT
1 TATGTAAGTTATGTAT
20508259 TA
1 TA
20508261 CCCAAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Found at i:20508310 original size:9 final size:9
Alignment explanation
Indices: 20508298--20508381 Score: 68
Period size: 9 Copynumber: 9.8 Consensus size: 9
20508288 AAAATTATGC
20508298 TATGTAAGT
1 TATGTAAGT
20508307 TATGTAAGT
1 TATGTAAGT
* *
20508316 CATATAAGT
1 TATGTAAGT
*
20508325 TACGTAAG-
1 TATGTAAGT
20508333 T-TGTAAGT
1 TATGTAAGT
20508341 TATGTAAGT
1 TATGTAAGT
* *
20508350 TGT-TTA-T
1 TATGTAAGT
* *
20508357 TATGAAAAT
1 TATGTAAGT
*
20508366 TAAGTAAGT
1 TATGTAAGT
20508375 TATGTAA
1 TATGTAA
20508382 TTTACGAATA
Statistics
Matches: 56, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
7 8 0.14
8 5 0.09
9 43 0.77
ACGTcount: A:0.37, C:0.02, G:0.19, T:0.42
Consensus pattern (9 bp):
TATGTAAGT
Found at i:20508341 original size:16 final size:16
Alignment explanation
Indices: 20508300--20508352 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
20508290 AATTATGCTA
20508300 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
* *
20508316 CATATAAGTTACGTAAGT
1 --TGTAAGTTATGTAAGT
20508334 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
20508350 TGT
1 TGT
20508353 TTATTATGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
16 17 0.55
18 14 0.45
ACGTcount: A:0.32, C:0.04, G:0.23, T:0.42
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Found at i:20508476 original size:22 final size:22
Alignment explanation
Indices: 20508451--20508496 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
20508441 TAACTAACTT
*
20508451 ATGTAATTTAAGTATAATATTA
1 ATGTAAGTTAAGTATAATATTA
*
20508473 ATGTAAGTTATGTATAATATTA
1 ATGTAAGTTAAGTATAATATTA
20508495 AT
1 AT
20508497 TAACAAAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (22 bp):
ATGTAAGTTAAGTATAATATTA
Found at i:20508480 original size:56 final size:56
Alignment explanation
Indices: 20508418--20508607 Score: 254
Period size: 56 Copynumber: 3.2 Consensus size: 56
20508408 TTATGTAAGT
* *
20508418 TGTAAGTTATGTATAATATTAATTAACTAACTTATGTAATTTAAGTATAATATTAA
1 TGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATAATATTAA
*
20508474 TGTAAGTTATGTATAATATTAATTAACAAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATAATATTAA
* *
20508530 TGTAATTAGTTATGTAATTTATGTATATTAATTAATTAAGTTATATAATTTATGTATAATATTAA
1 TGT-A--AGTTATGT-A--TA---ATATTAATTAACTAAGTTATGTAATTTATGTATAATATTAA
20508595 TGTAAGTTATGTA
1 TGTAAGTTATGTA
20508608 ATTTATGAAT
Statistics
Matches: 119, Mismatches: 6, Indels: 13
0.86 0.04 0.09
Matches are distributed among these distances:
56 56 0.47
57 1 0.01
59 8 0.07
60 1 0.01
61 1 0.01
62 10 0.08
64 1 0.01
65 41 0.34
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.47
Consensus pattern (56 bp):
TGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATAATATTAA
Found at i:20508519 original size:9 final size:9
Alignment explanation
Indices: 20508505--20508614 Score: 50
Period size: 9 Copynumber: 11.6 Consensus size: 9
20508495 ATTAACAAAG
20508505 TTATGTAAT
1 TTATGTAAT
20508514 TTATGTATAAT
1 TTATG--TAAT
20508525 ATTAATGTAATT
1 -TT-ATGTAA-T
20508537 AGTTATGTAAT
1 --TTATGTAAT
20508548 TTATGT-A-
1 TTATGTAAT
20508555 -TAT-TAAT
1 TTATGTAAT
* *
20508562 TAAT-TAAG
1 TTATGTAAT
*
20508570 TTATATAAT
1 TTATGTAAT
20508579 TTATGTATAAT
1 TTATG--TAAT
*
20508590 ATTAATGTAAG
1 -TT-ATGTAAT
20508601 TTATGTAAT
1 TTATGTAAT
20508610 TTATG
1 TTATG
20508615 AATAATTATA
Statistics
Matches: 79, Mismatches: 8, Indels: 28
0.69 0.07 0.24
Matches are distributed among these distances:
5 1 0.01
6 4 0.05
8 9 0.11
9 29 0.37
10 2 0.03
11 15 0.19
12 11 0.14
13 8 0.10
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (9 bp):
TTATGTAAT
Found at i:20508532 original size:22 final size:22
Alignment explanation
Indices: 20508505--20508607 Score: 67
Period size: 22 Copynumber: 4.7 Consensus size: 22
20508495 ATTAACAAAG
20508505 TTATGTAATTTATGTA-TAATA
1 TTATGTAATTTATGTATTAATA
20508526 TTAATGTAA-TTA-GTTATGTAAT-
1 TT-ATGTAATTTATG-TAT-TAATA
* *
20508548 TTATGTATATTAAT-TAATTAA-G
1 TTATGTA-ATTTATGT-ATTAATA
*
20508570 TTATATAATTTATGTA-TAATA
1 TTATGTAATTTATGTATTAATA
*
20508591 TTAATGTAAGTTATGTA
1 TT-ATGTAATTTATGTA
20508608 ATTTATGAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 23
0.69 0.06 0.25
Matches are distributed among these distances:
20 4 0.06
21 20 0.31
22 32 0.50
23 8 0.12
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (22 bp):
TTATGTAATTTATGTATTAATA
Found at i:20508561 original size:31 final size:31
Alignment explanation
Indices: 20508489--20508642 Score: 159
Period size: 31 Copynumber: 4.8 Consensus size: 31
20508479 GTTATGTATA
**
20508489 ATATTAATTAACAAAGTTATGTAATTTATGTAT
1 ATATTAATTAATTAAGTTATGTAATTTATG--T
20508522 AATATTAATGTAATT-AGTTATGTAATTTATGT
1 -ATATTAAT-TAATTAAGTTATGTAATTTATGT
*
20508554 ATATTAATTAATTAAGTTATATAATTTATGT
1 ATATTAATTAATTAAGTTATGTAATTTATGT
* *
20508585 ATAAT-ATTAATGTAAGTTATGTAATTTATGA
1 ATATTAATTAAT-TAAGTTATGTAATTTATGT
**
20508616 ATAATTATAAAAATGTAAGTTATGTAA
1 AT-ATTA-ATTAAT-TAAGTTATGTAA
20508643 GTTGTAAGTT
Statistics
Matches: 105, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
30 11 0.10
31 47 0.45
32 3 0.03
34 41 0.39
35 3 0.03
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (31 bp):
ATATTAATTAATTAAGTTATGTAATTTATGT
Found at i:20508561 original size:65 final size:62
Alignment explanation
Indices: 20508489--20508614 Score: 198
Period size: 65 Copynumber: 2.0 Consensus size: 62
20508479 GTTATGTATA
*
20508489 ATATTAATTAACAAAGTTATGTAATTTATGTATAATATTAATGTAATTAGTTATGTAATTTATGT
1 ATATTAATTAACAAAGTTATATAATTTATGTATAATATTAATGT-A--AGTTATGTAATTTATGT
**
20508554 ATATTAATTAATTAAGTTATATAATTTATGTATAATATTAATGTAAGTTATGTAATTTATG
1 ATATTAATTAACAAAGTTATATAATTTATGTATAATATTAATGTAAGTTATGTAATTTATG
20508615 AATAATTATA
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
62 16 0.28
64 1 0.02
65 41 0.71
ACGTcount: A:0.40, C:0.01, G:0.10, T:0.48
Consensus pattern (62 bp):
ATATTAATTAACAAAGTTATATAATTTATGTATAATATTAATGTAAGTTATGTAATTTATGT
Found at i:20508635 original size:65 final size:64
Alignment explanation
Indices: 20508502--20508638 Score: 188
Period size: 65 Copynumber: 2.1 Consensus size: 64
20508492 TTAATTAACA
* * **
20508502 AAGTTATGTAATTTATGTATAATATTAATGTAATTAGTTATGTAATTTATGTATATTAATTAATT
1 AAGTTATATAATTTATGTATAATATTAATGTAA-TAGTTATGTAATTTATGAATATTAAAAAATT
20508567 AAGTTATATAATTTATGTATAATATTAATGT-A-AGTTATGTAATTTATGAATAATTATAAAAAT
1 AAGTTATATAATTTATGTATAATATTAATGTAATAGTTATGTAATTTATGAAT-ATTA-AAAAAT
20508630 GT
64 -T
20508632 AAGTTAT
1 AAGTTAT
20508639 GTAAGTTGTA
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
62 18 0.28
63 4 0.06
64 5 0.08
65 38 0.58
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (64 bp):
AAGTTATATAATTTATGTATAATATTAATGTAATAGTTATGTAATTTATGAATATTAAAAAATT
Found at i:20508636 original size:34 final size:31
Alignment explanation
Indices: 20508473--20508642 Score: 182
Period size: 34 Copynumber: 5.2 Consensus size: 31
20508463 TATAATATTA
*
20508473 ATGTAAGTTATGTATAATATTAAT-TAACAAAGTT
1 ATGTAATTTATGTATAATATTAATGT----AAGTT
20508507 ATGTAATTTATGTATAATATTAATGTAATTAGTT
1 ATGTAATTTATGTATAATATTAATGT-A--AGTT
*
20508541 ATGTAATTTATGTATATTAATTAAT-TAAGTT
1 ATGTAATTTATGTATAAT-ATTAATGTAAGTT
*
20508572 ATATAATTTATGTATAATATTAATGTAAGTT
1 ATGTAATTTATGTATAATATTAATGTAAGTT
* *
20508603 ATGTAATTTATGAATAATTATAAAAATGTAAGTT
1 ATGTAATTTATGTATAA-TAT--TAATGTAAGTT
20508637 ATGTAA
1 ATGTAA
20508643 GTTGTAAGTT
Statistics
Matches: 121, Mismatches: 7, Indels: 16
0.84 0.05 0.11
Matches are distributed among these distances:
30 6 0.05
31 41 0.34
32 5 0.04
33 1 0.01
34 61 0.50
35 7 0.06
ACGTcount: A:0.42, C:0.01, G:0.11, T:0.46
Consensus pattern (31 bp):
ATGTAATTTATGTATAATATTAATGTAAGTT
Found at i:20510133 original size:84 final size:83
Alignment explanation
Indices: 20509991--20510260 Score: 247
Period size: 76 Copynumber: 3.3 Consensus size: 83
20509981 CCGTAAAGGC
* * * *
20509991 AAAACGGCATCGTTTTGTTTAAAAAACCCGAAACTTTGCGGCGTTTTCACCATAGCGCCACTAAT
1 AAAACGACACCGTTTGGTTTAAAAAACCCGAAACTTTGCGGCCTTTTCACCATAGCGCCACTAAT
* *
20510056 GTCGTTAATGTGCCAGGG
66 GCCCTTAATGTGCCAGGG
20510074 AAAACGACACCGTTTGGTTTAAAAAACCCGAAAACTTTGCGGCACTTTT-ACCATAGCGCCACTA
1 AAAACGACACCGTTTGGTTTAAAAAACCCG-AAACTTTGCGGC-CTTTTCACCATAGCGCCACTA
20510138 ATGCCCTTAATGT-------
64 ATGCCCTTAATGTGCCAGGG
** * * ** * **
20510151 -AAACGACACCGTTTCATTAAAAAAACCCCGACAA-TTTGCGGCATTTTCGGCGTAATGCCACTA
1 AAAACGACACCGTTTGGTTTAAAAAA-CCCGA-AACTTTGCGGCCTTTTCACCATAGCGCCACTA
* * *
20510214 ATGCCATTAATATGCCAGGC
64 ATGCCCTTAATGTGCCAGGG
20510234 AAAACGACACCGCTTT-GTTTACAAAAA
1 AAAACGACACCG-TTTGGTTTA-AAAAA
20510261 TGATAAAATT
Statistics
Matches: 153, Mismatches: 19, Indels: 28
0.76 0.09 0.14
Matches are distributed among these distances:
75 4 0.03
76 52 0.34
77 6 0.04
83 27 0.18
84 52 0.34
85 12 0.08
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (83 bp):
AAAACGACACCGTTTGGTTTAAAAAACCCGAAACTTTGCGGCCTTTTCACCATAGCGCCACTAAT
GCCCTTAATGTGCCAGGG
Found at i:20510599 original size:20 final size:20
Alignment explanation
Indices: 20510554--20510606 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
20510544 TAAAATTAAA
*
20510554 AATTTTAGAGTTTTTATATTT
1 AATTTT-GATTTTTTATATTT
*
20510575 CATTTTGATTTTTGTAT-TTT
1 AATTTTGATTTTT-TATATTT
*
20510595 AATTTTAATTTT
1 AATTTTGATTTT
20510607 AATTTTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 19 0.70
21 8 0.30
ACGTcount: A:0.25, C:0.02, G:0.08, T:0.66
Consensus pattern (20 bp):
AATTTTGATTTTTTATATTT
Found at i:20513745 original size:114 final size:113
Alignment explanation
Indices: 20513541--20513873 Score: 551
Period size: 114 Copynumber: 2.9 Consensus size: 113
20513531 NNNNNNNNNN
* *
20513541 AGCGGCGC-ATTGAAAAAACGCCACTAAAGTCACCGAAGTGTCTCCAAACGACGTCGTCTGGGGT
1 AGCGGCGCTATTCAAAAAACGCCACTAATGTCACCGAAGTGTCTCCAAACGACGTCGTCT-GGGT
*
20513605 TTAGTTTTTGCGGCATTTTTATAGAAACGCCGCTAATACTCATATTATT
65 TTAGTTTTTGCGGCATTTTTATAGAAACGCTGCTAATACTCATATTATT
* *
20513654 AGCGGCGCTATTCAAAAAATGCCACTAATGTCACCGAAGTGTCCCCAAACGACGTCGTCTGGGTT
1 AGCGGCGCTATTCAAAAAACGCCACTAATGTCACCGAAGTGTCTCCAAACGACGTCGTCTGGG-T
* *
20513719 TTAGTTTTTGCGGCATTTTTACAGAAACGCTGCTAATTCTCATATTATT
65 TTAGTTTTTGCGGCATTTTTATAGAAACGCTGCTAATACTCATATTATT
* *
20513768 AGCGGCGCTATTCGAAAAACGCCACTAATGTCACCGAAGTTTCTCCAAACGACGTCGTCTGGGTT
1 AGCGGCGCTATTCAAAAAACGCCACTAATGTCACCGAAGTGTCTCCAAACGACGTCGTCTGGGTT
*
20513833 TAGTTTTTGCGGCGTTTTTATAGAAACGCTGCTAATACTCA
66 TAGTTTTTGCGGCATTTTTATAGAAACGCTGCTAATACTCA
20513874 ATCGGTTGCG
Statistics
Matches: 204, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
113 51 0.25
114 153 0.75
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.30
Consensus pattern (113 bp):
AGCGGCGCTATTCAAAAAACGCCACTAATGTCACCGAAGTGTCTCCAAACGACGTCGTCTGGGTT
TAGTTTTTGCGGCATTTTTATAGAAACGCTGCTAATACTCATATTATT
Found at i:20521370 original size:65 final size:65
Alignment explanation
Indices: 20521239--20521361 Score: 221
Period size: 64 Copynumber: 1.9 Consensus size: 65
20521229 NNNNNTCATA
*
20521239 TAAAATTGGATCAATTAGGTATAATCAAGTAAACAACTTGATTAAAAAACAAATATTCAATATAT
1 TAAAATTGGATCAATTAGATATAATCAAGTAAACAACTTGATTAAAAAACAAATATTCAATATAT
*
20521304 TAAAATTGGATC-ATTAGATATAATCAAGTAAACAACTTGATTAAAAAATAAATATTCA
1 TAAAATTGGATCAATTAGATATAATCAAGTAAACAACTTGATTAAAAAACAAATATTCA
20521362 TTGTTATTAT
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
64 44 0.79
65 12 0.21
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (65 bp):
TAAAATTGGATCAATTAGATATAATCAAGTAAACAACTTGATTAAAAAACAAATATTCAATATAT
Found at i:20521539 original size:145 final size:145
Alignment explanation
Indices: 20521276--20521587 Score: 572
Period size: 145 Copynumber: 2.2 Consensus size: 145
20521266 AGTAAACAAC
*
20521276 TTGATTAAAAAACAAATATTCAATATATTAAAATTGGATCATTAGATATAATCAAGTAAACAACT
1 TTGATTAGAAAACAAATATTCAATATATTAAAATTGGATCATTAGATATAATCAAGTAAACAACT
*
20521341 TGATTAAAAAATAAATATTCATTGTTATTATGATTGATTAAAAAACAACTTGATTA-AAAAGCAA
66 TGATTAAAAAACAAATATTCATTGTTATTATGATTGATTAAAAAACAACTTGATTACAAAA-CAA
20521405 GTATTTGGTAACATTG
130 GTATTTGGTAACATTG
*
20521421 TTGATTAGAAAACAAATATTCAATATATTAAAATTGGATCATTAGATATAATCAATTAAACAACT
1 TTGATTAGAAAACAAATATTCAATATATTAAAATTGGATCATTAGATATAATCAAGTAAACAACT
*
20521486 TGATTAAAAAACAAATATTCATTGTTATTATGATTGATTAAAAAATAACTTGATTACAAAACAAG
66 TGATTAAAAAACAAATATTCATTGTTATTATGATTGATTAAAAAACAACTTGATTACAAAACAAG
20521551 TATTTGGTAACATTG
131 TATTTGGTAACATTG
20521566 TTGATTAGAAAACAAATATTCA
1 TTGATTAGAAAACAAATATTCA
20521588 TTGTTAATGT
Statistics
Matches: 162, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
145 158 0.98
146 4 0.02
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.35
Consensus pattern (145 bp):
TTGATTAGAAAACAAATATTCAATATATTAAAATTGGATCATTAGATATAATCAAGTAAACAACT
TGATTAAAAAACAAATATTCATTGTTATTATGATTGATTAAAAAACAACTTGATTACAAAACAAG
TATTTGGTAACATTG
Found at i:20525135 original size:44 final size:45
Alignment explanation
Indices: 20525070--20525160 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
20525060 ACCTCTATTC
* * *
20525070 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
20525114 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
20525159 CA
1 CA
20525161 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:20525162 original size:16 final size:16
Alignment explanation
Indices: 20525141--20525209 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
20525131 GATTAGCTAT
20525141 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
20525157 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
20525174 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
20525190 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
20525206 TACA
1 TACA
20525210 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:20525183 original size:33 final size:32
Alignment explanation
Indices: 20525141--20525209 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
20525131 GATTAGCTAT
20525141 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
20525174 TACACCTCTAATCCAATACACCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
20525206 TACA
1 TACA
20525210 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 8 0.22
33 28 0.78
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:20526746 original size:14 final size:13
Alignment explanation
Indices: 20526718--20526751 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
20526708 TATTCTAATA
20526718 TTTAATTTATTAT
1 TTTAATTTATTAT
*
20526731 TTTATTTTAGTTAT
1 TTTAATTTA-TTAT
20526745 TTTAATT
1 TTTAATT
20526752 ATTTTATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (13 bp):
TTTAATTTATTAT
Found at i:20527400 original size:42 final size:42
Alignment explanation
Indices: 20527260--20527413 Score: 191
Period size: 42 Copynumber: 3.6 Consensus size: 42
20527250 ACGGCCTAGA
* * * * * *
20527260 CACATGCCCATGTCCTTGTCCATGTGGCTCACACGGCATGGG
1 CACACGCCCATGTCCTTGCCCGTGTGGCTCACACAGCCTGAG
* *
20527302 CACACGCCCATGTCCTTGCTCGCGTGGCTCACACAGCCTGAG
1 CACACGCCCATGTCCTTGCCCGTGTGGCTCACACAGCCTGAG
20527344 CACACGCCCATGTCCTTGCCCGTGTGGCTCACACAGCCTGAG
1 CACACGCCCATGTCCTTGCCCGTGTGGCTCACACAGCCTGAG
* * * *
20527386 CACACACTCTTGTCCTCTACCCGTGTGG
1 CACACGCCCATGTCCT-TGCCCGTGTGG
20527414 TTCTAAAACA
Statistics
Matches: 97, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
42 87 0.90
43 10 0.10
ACGTcount: A:0.16, C:0.38, G:0.23, T:0.22
Consensus pattern (42 bp):
CACACGCCCATGTCCTTGCCCGTGTGGCTCACACAGCCTGAG
Found at i:20530491 original size:30 final size:30
Alignment explanation
Indices: 20530457--20530517 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
20530447 GAGAAAGTGA
20530457 ACACCTAACCAGCAGACAACAGACCACGAC
1 ACACCTAACCAGCAGACAACAGACCACGAC
20530487 ACACCTAACCAGCAGACAACAGACCACGAC
1 ACACCTAACCAGCAGACAACAGACCACGAC
20530517 A
1 A
20530518 TGAAATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.44, C:0.39, G:0.13, T:0.03
Consensus pattern (30 bp):
ACACCTAACCAGCAGACAACAGACCACGAC
Found at i:20530512 original size:15 final size:15
Alignment explanation
Indices: 20530464--20530512 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
20530454 TGAACACCTA
20530464 ACCAGCAGACAACAG
1 ACCAGCAGACAACAG
20530479 ACCA-C-GACACACCTA-
1 ACCAGCAGACA-A-C-AG
20530494 ACCAGCAGACAACAG
1 ACCAGCAGACAACAG
20530509 ACCA
1 ACCA
20530513 CGACATGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
13 4 0.14
14 3 0.11
15 14 0.50
16 3 0.11
17 4 0.14
ACGTcount: A:0.45, C:0.39, G:0.14, T:0.02
Consensus pattern (15 bp):
ACCAGCAGACAACAG
Found at i:20538960 original size:17 final size:17
Alignment explanation
Indices: 20538923--20538960 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
20538913 AAAGTGATCG
20538923 AAAAAGTACAAAAAAAT
1 AAAAAGTACAAAAAAAT
20538940 -AAAA-TACGAAAAAAAT
1 AAAAAGTAC-AAAAAAAT
20538956 AAAAA
1 AAAAA
20538961 AAATTATGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 3 0.16
16 12 0.63
17 4 0.21
ACGTcount: A:0.79, C:0.05, G:0.05, T:0.11
Consensus pattern (17 bp):
AAAAAGTACAAAAAAAT
Found at i:20539469 original size:237 final size:237
Alignment explanation
Indices: 20539054--20539518 Score: 894
Period size: 237 Copynumber: 2.0 Consensus size: 237
20539044 TTTGGAAATC
*
20539054 AGGAACACCATCAAGTTTCTTCACAATTTTTCGAGTTTTTGGGTGTTAGCAATTTTCATTTGACT
1 AGGAACACCATCAAGTTTCTTCACAATTTTTCAAGTTTTTGGGTGTTAGCAATTTTCATTTGACT
*
20539119 CTTAGCTTTAAGTTTTCATTTGTTTTTACTTTTTATTTGTTCCTTTACACATTCTAACACTTTCT
66 CTTAACTTTAAGTTTTCATTTGTTTTTACTTTTTATTTGTTCCTTTACACATTCTAACACTTTCT
20539184 TGTTTCTTGTGTTAGTAGGTTAAAGCACATTGCATATTCTTTCCTCCGTGCAATAGAATTCTTTG
131 TGTTTCTTGTGTTAGTAGGTTAAAGCACATTGCATATTCTTTCCTCCGTGCAATAGAATTCTTTG
*
20539249 ATGTCTAAGCCAATTTTAGACTCATTGTGTTATAGTGTTATT
196 ATGTCTAAGCCAATTTTAGACTCATAGTGTTATAGTGTTATT
*
20539291 AGGAACACCATCAAGTTTCTTCACAATTTTTCAAGTTTTTGGGTTTTAGCAATTTTCATTTGACT
1 AGGAACACCATCAAGTTTCTTCACAATTTTTCAAGTTTTTGGGTGTTAGCAATTTTCATTTGACT
20539356 CTTAACTTTAAGTTTTCATTTGTTTTTACTTTTTATTTGTTCCTTTACACATTCTAACACTTTCT
66 CTTAACTTTAAGTTTTCATTTGTTTTTACTTTTTATTTGTTCCTTTACACATTCTAACACTTTCT
20539421 TGTTTCTTGTGTTAGTAGGTTAAAGCACATTGCATATTCTTTCCTCCGTGCAATAGAATTCTTTG
131 TGTTTCTTGTGTTAGTAGGTTAAAGCACATTGCATATTCTTTCCTCCGTGCAATAGAATTCTTTG
20539486 ATGTCTAAGCCAATTTTAGACTCATAGTGTTAT
196 ATGTCTAAGCCAATTTTAGACTCATAGTGTTAT
20539519 TAGGTTTTCT
Statistics
Matches: 224, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
237 224 1.00
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.47
Consensus pattern (237 bp):
AGGAACACCATCAAGTTTCTTCACAATTTTTCAAGTTTTTGGGTGTTAGCAATTTTCATTTGACT
CTTAACTTTAAGTTTTCATTTGTTTTTACTTTTTATTTGTTCCTTTACACATTCTAACACTTTCT
TGTTTCTTGTGTTAGTAGGTTAAAGCACATTGCATATTCTTTCCTCCGTGCAATAGAATTCTTTG
ATGTCTAAGCCAATTTTAGACTCATAGTGTTATAGTGTTATT
Found at i:20551934 original size:31 final size:26
Alignment explanation
Indices: 20551869--20551926 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
20551859 TGAATTTTTC
20551869 TCGAATCGAGTCGAGTGAGATGGAAT
1 TCGAATCGAGTCGAGTGAGATGGAAT
20551895 TCGAATCGAGTCGAGTGAGATGGAAT
1 TCGAATCGAGTCGAGTGAGATGGAAT
20551921 TCGAAT
1 TCGAAT
20551927 GGAATCGAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.31, C:0.12, G:0.33, T:0.24
Consensus pattern (26 bp):
TCGAATCGAGTCGAGTGAGATGGAAT
Found at i:20552232 original size:20 final size:20
Alignment explanation
Indices: 20552207--20552246 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
20552197 CGTAAAATGA
*
20552207 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
20552227 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
20552247 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:20552236 original size:34 final size:35
Alignment explanation
Indices: 20552192--20552258 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
20552182 CAGTAAAATA
*
20552192 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
20552226 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
20552259 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:20552262 original size:14 final size:15
Alignment explanation
Indices: 20552186--20552262 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
20552176 GATTGCCAGT
* *
20552186 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
20552200 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
20552214 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
20552234 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
20552249 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
20552263 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:20553041 original size:17 final size:17
Alignment explanation
Indices: 20553021--20553473 Score: 190
Period size: 18 Copynumber: 25.7 Consensus size: 17
20553011 AAAAAAAACG
20553021 AAATTTTTGAAACACGA
1 AAATTTTTGAAACACGA
*
20553038 AAATTTTAGAAACACGAAAA
1 AAATTTTTGAAACACG---A
*
20553058 AAAATTTT--AACACGA
1 AAATTTTTGAAACACGA
*
20553073 CAATTTTTGAAACACGA
1 AAATTTTTGAAACACGA
* *
20553090 GAATTTTTTGAAATAC--
1 -AAATTTTTGAAACACGA
*** *
20553106 AAATTTAAAAAAAAAACATGA
1 AAATTT----TTGAAACACGA
* * *
20553127 CAATTTGTGAAACACTA
1 AAATTTTTGAAACACGA
* * ** *
20553144 GAGTCGTTGAAAACACGG
1 AAATTTTTG-AAACACGA
* *
20553162 AAATTTGTGAAAAAACGA
1 AAATTTTTG-AAACACGA
*
20553180 AAATTTTTGAAACACGG
1 AAATTTTTGAAACACGA
20553197 AAATTTTTAGAAAACACGA
1 AAATTTTT-G-AAACACGA
* * *
20553216 AAA-TTTTGGATCTCCG-
1 AAATTTTTGAAAC-ACGA
* *
20553232 GAATTTTTGAAAACACAA
1 AAATTTTTG-AAACACGA
20553250 AAATTTTTGAAACACCG-
1 AAATTTTTGAAACA-CGA
*
20553267 GAATTTTTGAAAACACGA
1 AAATTTTTG-AAACACGA
**
20553285 GGATTTTT-ACAACACGA
1 AAATTTTTGA-AACACGA
** * *
20553302 ATTTTTTTTAAATACGA
1 AAATTTTTGAAACACGA
20553319 AAATTTTTGAAAACAC-A
1 AAATTTTTG-AAACACGA
* * *
20553336 GAAATTTTTAAAACATGG
1 -AAATTTTTGAAACACGA
20553354 AAATTTTTGAAACATC-A
1 AAATTTTTGAAACA-CGA
20553371 AAATTTTTGAAAACACGA
1 AAATTTTTG-AAACACGA
** **
20553389 GGATTTTTGAAAACAAAAA
1 AAATTTTTG-AAAC-ACGA
20553408 AAATTTTTGAAA-ACGCA
1 AAATTTTTGAAACACG-A
* *
20553425 GAAATTTTTAAAACACGGG
1 -AAATTTTTGAAACAC-GA
* *
20553444 AATTTTTTGAAAACATGA
1 AAATTTTTG-AAACACGA
*
20553462 AAACTTTTGAAA
1 AAATTTTTGAAA
20553474 AATAGATTTT
Statistics
Matches: 320, Mismatches: 80, Indels: 72
0.68 0.17 0.15
Matches are distributed among these distances:
15 12 0.04
16 6 0.02
17 127 0.40
18 132 0.41
19 30 0.09
20 8 0.03
21 5 0.02
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (17 bp):
AAATTTTTGAAACACGA
Found at i:20553099 original size:18 final size:17
Alignment explanation
Indices: 20553018--20553400 Score: 94
Period size: 17 Copynumber: 21.9 Consensus size: 17
20553008 TTTAAAAAAA
20553018 ACGA-AATTTTTGAAAC
1 ACGACAATTTTTGAAAC
* *
20553034 ACGAAAATTTTAGAAAC
1 ACGACAATTTTTGAAAC
* *
20553051 ACGAAAAAAAATTTT--AAC
1 ACG---ACAATTTTTGAAAC
20553069 ACGACAATTTTTGAAAC
1 ACGACAATTTTTGAAAC
* *
20553086 ACGAGAATTTTTTGAAAT
1 ACGACAA-TTTTTGAAAC
***
20553104 AC-A-AATTTAAAAAAAAAAC
1 ACGACAATTT----TTGAAAC
* *
20553123 ATGACAATTTGTGAAAC
1 ACGACAATTTTTGAAAC
* * * **
20553140 ACTAGAGTCGTTGAAAAC
1 ACGACAATTTTTG-AAAC
* *
20553158 ACGGA-AATTTGTGAAAAA
1 AC-GACAATTTTTG-AAAC
*
20553176 ACGAAAATTTTTGAAAC
1 ACGACAATTTTTGAAAC
20553193 ACGGA-AATTTTTAGAAAAC
1 AC-GACAATTTTT-G-AAAC
* * *
20553212 ACGA-AAATTTTGGATC
1 ACGACAATTTTTGAAAC
* *
20553228 TCCG-GAATTTTTGAAAAC
1 -ACGACAATTTTTG-AAAC
* *
20553246 ACAAAAATTTTTGAAAC
1 ACGACAATTTTTGAAAC
*
20553263 ACCG-GAATTTTTGAAAAC
1 A-CGACAATTTTTG-AAAC
**
20553281 ACGAGGATTTTT-ACAAC
1 ACGACAATTTTTGA-AAC
* * *
20553298 ACGA-ATTTTTTTTAAAT
1 ACGACA-ATTTTTGAAAC
*
20553315 ACGAAAATTTTTGAAAAC
1 ACGACAATTTTTG-AAAC
*
20553333 ACAGA-AATTTTTAAAAC
1 AC-GACAATTTTTGAAAC
*
20553350 ATGGA-AATTTTTGAAAC
1 A-CGACAATTTTTGAAAC
*
20553367 ATC-AAAATTTTTGAAAAC
1 A-CGACAATTTTTG-AAAC
**
20553385 ACGAGGATTTTTGAAA
1 ACGACAATTTTTGAAA
20553401 ACAAAAAAAA
Statistics
Matches: 276, Mismatches: 55, Indels: 71
0.69 0.14 0.18
Matches are distributed among these distances:
15 10 0.04
16 10 0.04
17 129 0.47
18 101 0.37
19 13 0.05
20 8 0.03
21 5 0.02
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (17 bp):
ACGACAATTTTTGAAAC
Found at i:20553193 original size:35 final size:35
Alignment explanation
Indices: 20553154--20553473 Score: 260
Period size: 35 Copynumber: 9.1 Consensus size: 35
20553144 GAGTCGTTGA
* *
20553154 AAACACGGAAATTTGTGAAAAAACGAAAATTTTTG
1 AAACACGGAAATTTTTGAAAACACGAAAATTTTTG
20553189 AAACACGGAAATTTTTAGAAAACACGAAAA-TTTTG
1 AAACACGGAAATTTTT-GAAAACACGAAAATTTTTG
* * * *
20553224 GATCTCCGG-AATTTTTGAAAACACAAAAATTTTTG
1 AAAC-ACGGAAATTTTTGAAAACACGAAAATTTTTG
**
20553259 AAACACCGG-AATTTTTGAAAACACGAGGATTTTT-
1 AAACA-CGGAAATTTTTGAAAACACGAAAATTTTTG
* ** *
20553293 ACAACAC-GAATTTTTTTTAAATACGAAAATTTTTG
1 A-AACACGGAAATTTTTGAAAACACGAAAATTTTTG
* * *
20553328 AAAACACAGAAATTTTT-AAAACATGGAAATTTTTG
1 -AAACACGGAAATTTTTGAAAACACGAAAATTTTTG
* **
20553363 AAACATC-AAAATTTTTGAAAACACGAGGATTTTTG
1 AAACA-CGGAAATTTTTGAAAACACGAAAATTTTTG
*** * *
20553398 AAAACAAAAAAAATTTTTGAAAACGC-AGAAATTTTTA
1 -AAAC-ACGGAAATTTTTGAAAACACGA-AAATTTTTG
* * *
20553435 AAACACGGGAATTTTTTGAAAACATGAAAACTTTTG
1 AAACAC-GGAAATTTTTGAAAACACGAAAATTTTTG
20553471 AAA
1 AAA
20553474 AATAGATTTT
Statistics
Matches: 227, Mismatches: 41, Indels: 33
0.75 0.14 0.11
Matches are distributed among these distances:
33 1 0.00
34 46 0.20
35 100 0.44
36 56 0.25
37 24 0.11
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.30
Consensus pattern (35 bp):
AAACACGGAAATTTTTGAAAACACGAAAATTTTTG
Found at i:20553324 original size:52 final size:52
Alignment explanation
Indices: 20553250--20553473 Score: 174
Period size: 52 Copynumber: 4.2 Consensus size: 52
20553240 GAAAACACAA
* ** *
20553250 AAATTTTTGAAACACCGGAATTTTTGAAAACACGAGGATTTTTACAACA-CG
1 AAATTTTTGAAACATCAAAATTTTTGAAAACACGAGGATTTTTAAAACATCG
* ** * *
20553301 AATTTTTTTTAA-ATACGAAAATTTTTGAAAACAC-AGAAATTTTTAAAACATGG
1 AAATTTTTGAAACAT-C-AAAATTTTTGAAAACACGAG-GATTTTTAAAACATCG
***
20553354 AAATTTTTGAAACATCAAAATTTTTGAAAACACGAGGATTTTTGAAAACAAAAA
1 AAATTTTTGAAACATCAAAATTTTTGAAAACACGAGGATTTTT-AAAAC-ATCG
*
20553408 AAATTTTTGAAA-ACGCAGAAATTTTT-AAAACACG-GGAATTTTTTGAAAACAT-G
1 AAATTTTTGAAACA-TCA-AAATTTTTGAAAACACGAGG-A-TTTTT-AAAACATCG
*
20553461 AAAACTTTTGAAA
1 -AAATTTTTGAAA
20553474 AATAGATTTT
Statistics
Matches: 140, Mismatches: 20, Indels: 23
0.77 0.11 0.13
Matches are distributed among these distances:
50 1 0.01
51 12 0.09
52 49 0.35
53 21 0.15
54 38 0.27
55 19 0.14
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.32
Consensus pattern (52 bp):
AAATTTTTGAAACATCAAAATTTTTGAAAACACGAGGATTTTTAAAACATCG
Found at i:20553401 original size:18 final size:18
Alignment explanation
Indices: 20553150--20553474 Score: 196
Period size: 18 Copynumber: 18.4 Consensus size: 18
20553140 ACTAGAGTCG
20553150 TTGAAAACACG-GAAATTT
1 TTGAAAACACGAG-AATTT
* * *
20553168 GTGAAAAAACGAAAATTT
1 TTGAAAACACGAGAATTT
20553186 TTG-AAACACG-GAAATTT
1 TTGAAAACACGAG-AATTT
*
20553203 TTAGAAAACACGAAAATTT
1 TT-GAAAACACGAGAATTT
* ***
20553222 TGGATCTC-CG-GAATTT
1 TTGAAAACACGAGAATTT
* *
20553238 TTGAAAACACAAAAATTT
1 TTGAAAACACGAGAATTT
20553256 TTG-AAACACCG-GAATTT
1 TTGAAAACA-CGAGAATTT
*
20553273 TTGAAAACACGAGGATTT
1 TTGAAAACACGAGAATTT
* *
20553291 TT-ACAACACGA-ATTTT
1 TTGAAAACACGAGAATTT
** * *
20553307 TTTTAAATACGAAAATTT
1 TTGAAAACACGAGAATTT
20553325 TTGAAAACAC-AGAAATTT
1 TTGAAAACACGAG-AATTT
*
20553343 TT-AAAACATG-GAAATTT
1 TTGAAAACACGAG-AATTT
*
20553360 TTG-AAACATC-AAAATTT
1 TTGAAAACA-CGAGAATTT
*
20553377 TTGAAAACACGAGGATTT
1 TTGAAAACACGAGAATTT
** *
20553395 TTGAAAACAAAAAAAATTT
1 TTGAAAAC-ACGAGAATTT
*
20553414 TTGAAAACGC-AGAAATTT
1 TTGAAAACACGAG-AATTT
*
20553432 TT-AAAACACGGGAATTTT
1 TTGAAAACACGAGAA-TTT
* * *
20553450 TTGAAAACATGAAAACTT
1 TTGAAAACACGAGAATTT
20553468 TTGAAAA
1 TTGAAAA
20553475 ATAGATTTTT
Statistics
Matches: 233, Mismatches: 50, Indels: 48
0.70 0.15 0.15
Matches are distributed among these distances:
16 14 0.06
17 84 0.36
18 99 0.42
19 36 0.15
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (18 bp):
TTGAAAACACGAGAATTT
Found at i:20553745 original size:19 final size:20
Alignment explanation
Indices: 20553722--20553768 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
20553712 ACGCGAATAT
* *
20553722 TTTTTGAAATAGAAGAAAAA
1 TTTTTGAAAGACAAGAAAAA
*
20553742 TTTTTG-AAGACACGAAAAA
1 TTTTTGAAAGACAAGAAAAA
20553761 -TTTTGAAA
1 TTTTTGAAA
20553769 AATATAATTG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 5 0.22
19 12 0.52
20 6 0.26
ACGTcount: A:0.49, C:0.04, G:0.15, T:0.32
Consensus pattern (20 bp):
TTTTTGAAAGACAAGAAAAA
Found at i:20555847 original size:44 final size:45
Alignment explanation
Indices: 20555710--20555870 Score: 200
Period size: 45 Copynumber: 3.6 Consensus size: 45
20555700 AGCAGCGTGA
**
20555710 AGTAGATCAAAGTCAACAGATCTTGTCTCCCCATACTGGTGGTGG
1 AGTAGATCAAAGAAAACAGATCTTGTCTCCCCATACTGGTGGTGG
* * *** * *
20555755 AGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTGG-CGTGA
1 AGTAGATCAAAGAAAACAGATCTTGTCTCCCCATACTGGTGGTGG
20555799 AGTAGATCAAAG-AAACAGATCTTGTCTCCCCATACTGGTGGTGG
1 AGTAGATCAAAGAAAACAGATCTTGTCTCCCCATACTGGTGGTGG
* * *
20555843 AGTAGGTCGAAGAAAACAGATCGTGTCT
1 AGTAGATCAAAGAAAACAGATCTTGTCT
20555871 TCATGTACTG
Statistics
Matches: 95, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
43 21 0.22
44 28 0.29
45 46 0.48
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.25
Consensus pattern (45 bp):
AGTAGATCAAAGAAAACAGATCTTGTCTCCCCATACTGGTGGTGG
Found at i:20555856 original size:88 final size:88
Alignment explanation
Indices: 20555704--20555899 Score: 338
Period size: 88 Copynumber: 2.2 Consensus size: 88
20555694 GAAGAAAGCA
*
20555704 GCGTGAAGTAGATCAAAGTCAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCAAAGAA
1 GCGTGAAGTAGATCAAAG-AAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCAAAGAA
* *
20555769 AGCAGATCTTGTCTTCATGTACTG
65 AACAGATCGTGTCTTCATGTACTG
* *
20555793 GCGTGAAGTAGATCAAAGAAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGGTCGAAGAAA
1 GCGTGAAGTAGATCAAAGAAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCAAAGAAA
20555858 ACAGATCGTGTCTTCATGTACTG
66 ACAGATCGTGTCTTCATGTACTG
20555881 GCGTGAAGTAGATCAAAGA
1 GCGTGAAGTAGATCAAAGA
20555900 TAGTAGGTCC
Statistics
Matches: 102, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
88 84 0.82
89 18 0.18
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.25
Consensus pattern (88 bp):
GCGTGAAGTAGATCAAAGAAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCAAAGAAA
ACAGATCGTGTCTTCATGTACTG
Found at i:20555880 original size:45 final size:45
Alignment explanation
Indices: 20555710--20555899 Score: 197
Period size: 45 Copynumber: 4.3 Consensus size: 45
20555700 AGCAGCGTGA
** * ***
20555710 AGTAGATCAAAGTCAACAGATCTTGTCTCCCCATACTGGTGGTGG
1 AGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGTGGTGG
* * *
20555755 AGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTGG-CGTGA
1 AGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGTGGTGG
* ***
20555799 AGTAGATCAAAG-AAACAGATCTTGTCTCCCCATACTGGTGGTGG
1 AGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGTGGTGG
* * * * *
20555843 AGTAGGTCGAAGAAAACAGATCGTGTCTTCATGTACTGG-CGTGA
1 AGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGTGGTGG
20555887 AGTAGATCAAAGA
1 AGTAGATCAAAGA
20555900 TAGTAGGTCC
Statistics
Matches: 116, Mismatches: 27, Indels: 5
0.78 0.18 0.03
Matches are distributed among these distances:
43 21 0.18
44 42 0.36
45 53 0.46
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (45 bp):
AGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGTGGTGG
Found at i:20556168 original size:44 final size:45
Alignment explanation
Indices: 20556112--20556201 Score: 128
Period size: 44 Copynumber: 2.0 Consensus size: 45
20556102 ATCGATTGAA
* * *
20556112 AAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAG
1 AAAGCAGATCTTGTCTTCATATACTGGTCGAGAAGTAGATCGAAG
* *
20556156 AAAGCAGATCTTGTCTTCCTATACTGGTGGAGAAGTAGATCGAAG
1 AAAGCAGATCTTGTCTTCATATACTGGTCGAGAAGTAGATCGAAG
20556201 A
1 A
20556202 TACAAGTCTT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 24 0.60
45 16 0.40
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (45 bp):
AAAGCAGATCTTGTCTTCATATACTGGTCGAGAAGTAGATCGAAG
Found at i:20560730 original size:88 final size:89
Alignment explanation
Indices: 20560632--20560827 Score: 322
Period size: 88 Copynumber: 2.2 Consensus size: 89
20560622 GGACCTACTA
* *
20560632 TCTTTGATCTACTTCACGCCAGTACATGAAGACACGATCTGTTTTCTTCGACCTACTCCACCACC
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGACCTACTCCACCACC
20560697 AGTATAGGGAGACAAGATCTGTT-
66 AGTATAGGGAGACAAGATCTGTTG
* *
20560720 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTGATCTACTCCACCACC
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGACCTACTCCACCACC
*
20560785 AGTATGGGGAGACAAGATCTGTTG
66 AGTATAGGGAGACAAGATCTGTTG
* *
20560809 ACTTTAATCTACTTCACGC
1 TCTTTGATCTACTTCACGC
20560828 TGCTTTCTTC
Statistics
Matches: 100, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
88 83 0.83
89 17 0.17
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.31
Consensus pattern (89 bp):
TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGACCTACTCCACCACC
AGTATAGGGAGACAAGATCTGTTG
Found at i:20560766 original size:44 final size:43
Alignment explanation
Indices: 20560632--20560827 Score: 203
Period size: 45 Copynumber: 4.4 Consensus size: 43
20560622 GGACCTACTA
* *
20560632 TCTTTGATCTACTTCACGCCAGTACATGAAGACACGATCTGTTT
1 TCTTTGATCTACTTCACGCCAGTACAGGAAGACAAGATCTG-TT
* * * * * *
20560676 TCTTCGACCTACTCCACCACCAGTATAGGGAGACAAGATCTGTT
1 TCTTTGATCTACTTCA-CGCCAGTACAGGAAGACAAGATCTGTT
*
20560720 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT
1 TCTTTGATCTACTTCACGCCAGTACAGGAAGACAAGATCTG-TT
* * ** *
20560764 TCTTTGATCTACTCCACCACCAGTATGGGGAGACAAGATCTGTT
1 TCTTTGATCTACTTCA-CGCCAGTACAGGAAGACAAGATCTGTT
* *
20560808 GACTTTAATCTACTTCACGC
1 -TCTTTGATCTACTTCACGC
20560828 TGCTTTCTTC
Statistics
Matches: 123, Mismatches: 25, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
43 21 0.17
44 49 0.40
45 53 0.43
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.31
Consensus pattern (43 bp):
TCTTTGATCTACTTCACGCCAGTACAGGAAGACAAGATCTGTT
Found at i:20562389 original size:50 final size:49
Alignment explanation
Indices: 20562314--20562409 Score: 147
Period size: 50 Copynumber: 1.9 Consensus size: 49
20562304 TTTTTTTTTC
* * *
20562314 TTTTTTTTTTTACTCAAGGCTCCCTTTGTAGGGTTTCACCCTGGTCTCT
1 TTTTTTTTTTTACTCAAAGCGCCCTTTGTAGGCTTTCACCCTGGTCTCT
*
20562363 TTTTTTTTTTTGACTCAAAGCGCCCTTTGTAGGCTTTCACCTTGGTC
1 TTTTTTTTTTT-ACTCAAAGCGCCCTTTGTAGGCTTTCACCCTGGTC
20562410 CCACCTTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
49 11 0.26
50 31 0.74
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (49 bp):
TTTTTTTTTTTACTCAAAGCGCCCTTTGTAGGCTTTCACCCTGGTCTCT
Found at i:20562419 original size:50 final size:50
Alignment explanation
Indices: 20562315--20562420 Score: 131
Period size: 50 Copynumber: 2.1 Consensus size: 50
20562305 TTTTTTTTCT
* * * * * ***
20562315 TTTTTTTTTTACTCAAGGCTCCCTTTGTAGGGTTTCACCCTGGTCTCTTT
1 TTTTTTTTTGACTCAAAGCGCCCTTTGTAGGCTTTCACCCTGGTCCCACC
*
20562365 TTTTTTTTTGACTCAAAGCGCCCTTTGTAGGCTTTCACCTTGGTCCCACC
1 TTTTTTTTTGACTCAAAGCGCCCTTTGTAGGCTTTCACCCTGGTCCCACC
20562415 TTTTTT
1 TTTTTT
20562421 AAGCAGAGTA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.11, C:0.25, G:0.15, T:0.48
Consensus pattern (50 bp):
TTTTTTTTTGACTCAAAGCGCCCTTTGTAGGCTTTCACCCTGGTCCCACC
Found at i:20568604 original size:11 final size:11
Alignment explanation
Indices: 20568584--20568618 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
20568574 TTAAAAGTAT
*
20568584 TTAAAATAAAA
1 TTAAATTAAAA
20568595 TTAAATTAAAA
1 TTAAATTAAAA
20568606 TTAAATTAAAA
1 TTAAATTAAAA
20568617 TT
1 TT
20568619 TAAAAAACGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
TTAAATTAAAA
Found at i:20568605 original size:16 final size:16
Alignment explanation
Indices: 20568584--20568615 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
20568574 TTAAAAGTAT
20568584 TTAAAATAAAATTAAA
1 TTAAAATAAAATTAAA
*
20568600 TTAAAATTAAATTAAA
1 TTAAAATAAAATTAAA
20568616 ATTTAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TTAAAATAAAATTAAA
Done.