Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167827.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_10, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 24162007
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 47000 characters in sequence are not A, C, G, or T
File 15 of 131
Found at i:3807606 original size:2 final size:2
Alignment explanation
Indices: 3807599--3807631 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3807589 GCTTATCATG
*
3807599 TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3807632 GTATGTTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3821142 original size:20 final size:20
Alignment explanation
Indices: 3821113--3821151 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3821103 TGGTATAAAT
*
3821113 CTTTCTCATTTACCACTAGG
1 CTTTCCCATTTACCACTAGG
*
3821133 CTTTCCCATTTACCTCTAG
1 CTTTCCCATTTACCACTAG
3821152 TGAGGCTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.33, G:0.08, T:0.41
Consensus pattern (20 bp):
CTTTCCCATTTACCACTAGG
Found at i:3826645 original size:20 final size:19
Alignment explanation
Indices: 3826589--3826657 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 19
3826579 ATAAAATTTT
*
3826589 AATATATTATTTTTATATAA
1 AATATAATA-TTTTATATAA
**
3826609 AATATAATATAAATATATAA
1 AATATAATAT-TTTATATAA
*
3826629 ATTATTAATATTTTATATAA
1 AATA-TAATATTTTATATAA
*
3826649 CATA-AATAT
1 AATATAATAT
3826658 ATCAAATACT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
18 5 0.13
19 1 0.03
20 27 0.69
21 6 0.15
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (19 bp):
AATATAATATTTTATATAA
Found at i:3830962 original size:30 final size:30
Alignment explanation
Indices: 3830926--3831001 Score: 134
Period size: 30 Copynumber: 2.5 Consensus size: 30
3830916 TTCTTCGCTC
3830926 ATTTTTTTTCTTTTTAATCTTTCATCCCAT
1 ATTTTTTTTCTTTTTAATCTTTCATCCCAT
* *
3830956 ATTTTTTTCCTTTTTACTCTTTCATCCCAT
1 ATTTTTTTTCTTTTTAATCTTTCATCCCAT
3830986 ATTTTTTTTCTTTTTA
1 ATTTTTTTTCTTTTTA
3831002 TTTTTACTTG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.14, C:0.20, G:0.00, T:0.66
Consensus pattern (30 bp):
ATTTTTTTTCTTTTTAATCTTTCATCCCAT
Found at i:3834453 original size:24 final size:25
Alignment explanation
Indices: 3834408--3834469 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 25
3834398 AAAAAATATA
*
3834408 TTTTAAATTATTAATTTAATTTAAT
1 TTTTATATTATTAATTTAATTTAAT
3834433 TTTTATATT-TTATATTT-ATTTAAT
1 TTTTATATTATTA-ATTTAATTTAAT
*
3834457 TTATATA-TATTAA
1 TTTTATATTATTAA
3834470 AAATAATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 2 0.06
24 19 0.58
25 12 0.36
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
TTTTATATTATTAATTTAATTTAAT
Found at i:3834490 original size:21 final size:22
Alignment explanation
Indices: 3834455--3834505 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
3834445 TATTTATTTA
3834455 ATTTATATATATT-AAAAATAAT
1 ATTT-TATATATTAAAAAATAAT
*
3834477 ATTTTATATTTTAAAAAATAAT
1 ATTTTATATATTAAAAAATAAT
3834499 ATTTTAT
1 ATTTTAT
3834506 TAATTTCGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 7 0.26
22 20 0.74
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTTTATATATTAAAAAATAAT
Found at i:3838719 original size:39 final size:39
Alignment explanation
Indices: 3838665--3838742 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
3838655 ATGATGCTGT
*
3838665 CATGGCATGAACTGTTATAGTAAT-TGGCTTATTATTAGG
1 CATGGCATGAACTGTTATAGTAATCT-GATTATTATTAGG
3838704 CATGGCATGAACTGTTATAGTAATCTGATTATTATTAGG
1 CATGGCATGAACTGTTATAGTAATCTGATTATTATTAGG
3838743 TAATAAGACT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
39 36 0.97
40 1 0.03
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.38
Consensus pattern (39 bp):
CATGGCATGAACTGTTATAGTAATCTGATTATTATTAGG
Found at i:3841176 original size:33 final size:35
Alignment explanation
Indices: 3841138--3841223 Score: 94
Period size: 33 Copynumber: 2.6 Consensus size: 35
3841128 TAAATCAGAC
3841138 AATATTATTTCATTAATAAATTT-TTTTAAAA-TA
1 AATATTATTTCATTAATAAATTTATTTTAAAATTA
* *
3841171 AATATTAATTT--TT-ATATATTTATTTTAAAATTT
1 AATATT-ATTTCATTAATAAATTTATTTTAAAATTA
3841204 AATATT-TATTCATTAATAAA
1 AATATTAT-TTCATTAATAAA
3841224 AAAATATAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
31 8 0.19
32 12 0.28
33 13 0.30
34 6 0.14
35 4 0.09
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (35 bp):
AATATTATTTCATTAATAAATTTATTTTAAAATTA
Found at i:3844526 original size:106 final size:106
Alignment explanation
Indices: 3844333--3844532 Score: 332
Period size: 106 Copynumber: 1.9 Consensus size: 106
3844323 ACACTTCAGA
*
3844333 ACTATAAAATTTTCATTTTCTTTTCTGAAAATGAGAACATGTGCGGTGATTAATTTAATCCTGTA
1 ACTATAAAATTTTCATTTTCTTTTCTGAAAATGAGAACATGTGCAGTGATTAATTTAATCCTGTA
*
3844398 CGAACTGTCCCGAGACATTGATAGGCAAATGGCATTTTAGG
66 CCAACTGTCCCGAGACATTGATAGGCAAATGGCATTTTAGG
*
3844439 ACTA-AAAGATTTTCATTTTCTTTTCT-AGAAATGAGAATATGTGCAGTGATTAATTTAATCCTG
1 ACTATAAA-ATTTTCATTTTCTTTTCTGA-AAATGAGAACATGTGCAGTGATTAATTTAATCCTG
*
3844502 TACCAACTGTCCCGAGATATTGATAGGCAAA
64 TACCAACTGTCCCGAGACATTGATAGGCAAA
3844533 AACGGGGCAG
Statistics
Matches: 88, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
105 4 0.05
106 84 0.95
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (106 bp):
ACTATAAAATTTTCATTTTCTTTTCTGAAAATGAGAACATGTGCAGTGATTAATTTAATCCTGTA
CCAACTGTCCCGAGACATTGATAGGCAAATGGCATTTTAGG
Found at i:3849080 original size:22 final size:22
Alignment explanation
Indices: 3849055--3849097 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3849045 AAAATTTTTT
*
3849055 AAAAATT-ATATATAAATTTAA
1 AAAAATTAAAATATAAATTTAA
*
3849076 AAAAATTAAAATATATATTTAA
1 AAAAATTAAAATATAAATTTAA
3849098 TATTTAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAAATTAAAATATAAATTTAA
Found at i:3854792 original size:33 final size:33
Alignment explanation
Indices: 3854754--3854818 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
3854744 TTACCTAATC
* *
3854754 AATATCTAATATTCTTTAAATCAATATCAAATT
1 AATATCTAATATTCTCTAAATAAATATCAAATT
3854787 AATATCTAATATTCTCTAAATAAATATCAAAT
1 AATATCTAATATTCTCTAAATAAATATCAAAT
3854819 CAATTTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (33 bp):
AATATCTAATATTCTCTAAATAAATATCAAATT
Found at i:3854831 original size:33 final size:33
Alignment explanation
Indices: 3854750--3854832 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 33
3854740 ATAATTACCT
** * *
3854750 AATCAATATCTAATATTCTTTAAATCAATATCA
1 AATCAATATAAAATATTCTCTAAATAAATATCA
* **
3854783 AATTAATATCTAATATTCTCTAAATAAATATCA
1 AATCAATATAAAATATTCTCTAAATAAATATCA
*
3854816 AATCAATTTAAAATATT
1 AATCAATATAAAATATT
3854833 ATTGGTACAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (33 bp):
AATCAATATAAAATATTCTCTAAATAAATATCA
Found at i:3854884 original size:11 final size:11
Alignment explanation
Indices: 3854868--3854894 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3854858 ATCAATTTAT
3854868 AATATTACTAA
1 AATATTACTAA
3854879 AATATTACTAA
1 AATATTACTAA
3854890 AATAT
1 AATAT
3854895 CATTGACACT
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:0.07, G:0.00, T:0.37
Consensus pattern (11 bp):
AATATTACTAA
Found at i:3859345 original size:43 final size:41
Alignment explanation
Indices: 3859298--3859382 Score: 98
Period size: 41 Copynumber: 2.0 Consensus size: 41
3859288 CTAATATTCT
* *
3859298 CTAAATTAATATCAAATCAATTTAAAATATAACTAAAATATTA
1 CTAAAATAATATC--ATCAATCTAAAATATAACTAAAATATTA
* * * *
3859341 CTAAAATGATATCATCAATCTATAATATTACTATAATATTA
1 CTAAAATAATATCATCAATCTAAAATATAACTAAAATATTA
3859382 C
1 C
3859383 GAGAATATCA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
41 25 0.69
43 11 0.31
ACGTcount: A:0.51, C:0.12, G:0.01, T:0.36
Consensus pattern (41 bp):
CTAAAATAATATCATCAATCTAAAATATAACTAAAATATTA
Found at i:3860980 original size:59 final size:58
Alignment explanation
Indices: 3860880--3861243 Score: 459
Period size: 59 Copynumber: 6.1 Consensus size: 58
3860870 ATGATTTTTT
3860880 TTTTTATAGGGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTGGAAATTTCGA
1 TTTTTA-A-GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTT--A
*
3860941 TTTTTAAGGAAAATTGATACTTTCAACTTTTTCCC-AAAAATATTTTTTTTGAAATTTTGA
1 TTTTTAAGGAAAATTGATACTTTCAAC-TTTTCCCTAAAAATATTTTTTTGGAAA-TTT-A
* *
3861001 TTTTTAAGGAAAATTGATACTTTTAACTTTTCCCCAAAAATATATTTTTTTTGGAAATTTA
1 TTTTTAAGGAAAATTGATACTTTCAACTTTT-CCCTAAAA-ATA-TTTTTTTGGAAATTTA
*
3861062 TTTTTCTTTTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTCGAAATTTA
1 ----T-TTTTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTTGGAAATTTA
* *
3861126 TTTCTGAGGAAAATTGATACTTTCAACTTTTCTCC-AAAAATA-TTTTTTGGAAATTTA
1 TTTTTAAGGAAAATTGATACTTTCAACTTTTC-CCTAAAAATATTTTTTTGGAAATTTA
* * *
3861183 TTTCTAAGGAAAATTGATACTTTCAATTTTTCCCTAAAAATATTTTTTTTGAAATTT-
1 TTTTTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTTA
3861240 TTTT
1 TTTT
3861244 ATTTTTATTT
Statistics
Matches: 275, Mismatches: 13, Indels: 34
0.85 0.04 0.11
Matches are distributed among these distances:
56 2 0.01
57 54 0.20
58 13 0.05
59 67 0.24
60 52 0.19
61 14 0.05
62 6 0.02
63 11 0.04
64 19 0.07
65 8 0.03
66 29 0.11
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.48
Consensus pattern (58 bp):
TTTTTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTTA
Found at i:3861353 original size:19 final size:17
Alignment explanation
Indices: 3861319--3861367 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 17
3861309 AATAAATAAA
*
3861319 AAATAAAATAAACAAAG
1 AAATAAAAAAAACAAAG
3861336 AAATAAAAAAAATTCAAAG
1 AAATAAAAAAAA--CAAAG
*
3861355 AAAGAAAGAAAAA
1 AAATAAA-AAAAA
3861368 AAAAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 11 0.41
19 11 0.41
20 5 0.19
ACGTcount: A:0.78, C:0.04, G:0.08, T:0.10
Consensus pattern (17 bp):
AAATAAAAAAAACAAAG
Found at i:3861362 original size:27 final size:27
Alignment explanation
Indices: 3861309--3861375 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
3861299 AACCTAATCT
*
3861309 AATAAATAAAAAATAAAATAAACAAAGA
1 AATAAA-AAAAAATAAAAGAAACAAAGA
* * *
3861337 AATAAAAAAAATTCAAAGAAAGAAAGA
1 AATAAAAAAAAATAAAAGAAACAAAGA
*
3861364 AAAAAAAAAAAA
1 AATAAAAAAAAA
3861376 AACCTGGAGC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 27 0.82
28 6 0.18
ACGTcount: A:0.81, C:0.03, G:0.06, T:0.10
Consensus pattern (27 bp):
AATAAAAAAAAATAAAAGAAACAAAGA
Found at i:3861851 original size:31 final size:31
Alignment explanation
Indices: 3861793--3861853 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
3861783 GGGCAGGTAG
* ** *
3861793 CCGGAAACTTCAAGGTTGGCCGAAATTTTCA
1 CCGGAAAATTCAAACTTCGCCGAAATTTTCA
*
3861824 CCGGAAAATTCAAACTTCGCCGGAATTTTC
1 CCGGAAAATTCAAACTTCGCCGAAATTTTC
3861854 GTCGGAATCT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.26
Consensus pattern (31 bp):
CCGGAAAATTCAAACTTCGCCGAAATTTTCA
Found at i:3861908 original size:26 final size:24
Alignment explanation
Indices: 3861869--3861922 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
3861859 AATCTGGAAA
*
3861869 TTTCCCAGAAATTTCCAGAAAAAAT
1 TTTCCCAAAAATTTCCA-AAAAAAT
* *
3861894 TTTCGCCAAAAATTTCTAAAAAATT
1 TTTC-CCAAAAATTTCCAAAAAAAT
3861919 TTTC
1 TTTC
3861923 TCACTCTCAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.35
Consensus pattern (24 bp):
TTTCCCAAAAATTTCCAAAAAAAT
Found at i:3862412 original size:35 final size:35
Alignment explanation
Indices: 3862351--3862438 Score: 94
Period size: 35 Copynumber: 2.6 Consensus size: 35
3862341 ATATATATAC
*
3862351 ATAAATAATAAA-ATACACATAAATATTAACAAAAA
1 ATAAATAATAAATATATACAT-AATATTAACAAAAA
* * *
3862386 ATAAATAAATAAATATATACAT-ATATTAATACATA
1 ATAAAT-AATAAATATATACATAATATTAACAAAAA
3862421 AT-AATAATAAATA-ATACA
1 ATAAATAATAAATATATACA
3862439 ATACATAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
32 5 0.11
33 8 0.17
34 3 0.06
35 18 0.38
36 6 0.13
37 7 0.15
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (35 bp):
ATAAATAATAAATATATACATAATATTAACAAAAA
Found at i:3863337 original size:2 final size:2
Alignment explanation
Indices: 3863332--3863377 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
3863322 AAAACAAATC
* *
3863332 AT AT AT AT AT AT AT AT AT AT AT GT AT AT -T AT AT -T AT A- AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3863371 AT AT AT A
1 AT AT AT A
3863378 AACATCCGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
1 3 0.08
2 35 0.92
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3877843 original size:23 final size:23
Alignment explanation
Indices: 3877792--3877843 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
3877782 TTTAATTGTT
* * *
3877792 AAAAAATAAATAATTTTTTCTAT
1 AAAAAATAAATAATTATATCTAC
**
3877815 TTAAAATAAATAATTATATCTAC
1 AAAAAATAAATAATTATATCTAC
3877838 AAAAAA
1 AAAAAA
3877844 GATACTTATT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.37
Consensus pattern (23 bp):
AAAAAATAAATAATTATATCTAC
Found at i:3880641 original size:25 final size:23
Alignment explanation
Indices: 3880613--3880678 Score: 60
Period size: 25 Copynumber: 2.7 Consensus size: 23
3880603 AATAATATAT
* *
3880613 ATAATTTTTTAATTAAAATTAAATA
1 ATAATTTTTAAATAAAAATT-AA-A
**
3880638 ATAATAATTAAATAAAAATTAAA
1 ATAATTTTTAAATAAAAATTAAA
3880661 ATAATTTTATCAAATAAA
1 ATAATTTT-T-AAATAAA
3880679 TAACTTAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
23 7 0.21
24 3 0.09
25 23 0.70
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
ATAATTTTTAAATAAAAATTAAA
Found at i:3881277 original size:23 final size:22
Alignment explanation
Indices: 3881212--3881279 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 22
3881202 TTTAATAATT
*
3881212 ATAAT-AAAAATATAAT-TTTA
1 ATAATAAAAAATATATTATTTA
* * *
3881232 ATATTAAATAA-AT-TTAATTA
1 ATAATAAAAAATATATTATTTA
3881252 ATAATAAAAAATATATTATTTAA
1 ATAATAAAAAATATATTATTT-A
3881275 ATAAT
1 ATAAT
3881280 TTAATCAATT
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
19 1 0.03
20 18 0.50
21 6 0.17
22 5 0.14
23 6 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
ATAATAAAAAATATATTATTTA
Found at i:3883078 original size:16 final size:16
Alignment explanation
Indices: 3883057--3883090 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3883047 TCAATTGAAT
3883057 TATATTTACAAATATA
1 TATATTTACAAATATA
* *
3883073 TATATTTATATATATA
1 TATATTTACAAATATA
3883089 TA
1 TA
3883091 AGACAAACCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
TATATTTACAAATATA
Found at i:3887345 original size:12 final size:12
Alignment explanation
Indices: 3887330--3887385 Score: 60
Period size: 12 Copynumber: 4.4 Consensus size: 12
3887320 TTATTTTTTA
3887330 AATTTTATATTT
1 AATTTTATATTT
3887342 AATTTTATATATT
1 AATTTTATAT-TT
*
3887355 -TTTATATATATTT
1 AATT-T-TATATTT
3887368 AATTTTATATTT
1 AATTTTATATTT
3887380 ATATTT
1 A-ATTT
3887386 AAAATAACAT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
12 20 0.54
13 10 0.27
14 7 0.19
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
AATTTTATATTT
Found at i:3887352 original size:14 final size:14
Alignment explanation
Indices: 3887326--3887377 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
3887316 AAAATTATTT
*
3887326 TTTAAATTT-TATA
1 TTTAATTTTATATA
3887339 TTTAATTTTATATA
1 TTTAATTTTATATA
*
3887353 TTT--TTATATATA
1 TTTAATTTTATATA
3887365 TTTAATTTTATAT
1 TTTAATTTTATAT
3887378 TTATATTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
12 11 0.33
13 8 0.24
14 14 0.42
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTAATTTTATATA
Found at i:3889751 original size:3 final size:3
Alignment explanation
Indices: 3889745--3889797 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
3889735 AAAAAATTAA
3889745 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3889793 AAT AA
1 AAT AA
3889798 CAACAACAAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3893032 original size:14 final size:14
Alignment explanation
Indices: 3892998--3893024 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3892988 GCAAGCTTTC
3892998 AAAATTTAACTAAG
1 AAAATTTAACTAAG
3893012 AAAATTTAACTAA
1 AAAATTTAACTAA
3893025 AAGGATTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.07, G:0.04, T:0.30
Consensus pattern (14 bp):
AAAATTTAACTAAG
Found at i:3897136 original size:25 final size:25
Alignment explanation
Indices: 3897108--3897155 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
3897098 AGCTCGGTTG
*
3897108 TAGAGATTTTTA-TTCATTTTTATTT
1 TAGA-ATTTTTATTTCATATTTATTT
*
3897133 TAGATTTTTTATTTCATATTTAT
1 TAGAATTTTTATTTCATATTTAT
3897156 CATTTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.25, C:0.04, G:0.06, T:0.65
Consensus pattern (25 bp):
TAGAATTTTTATTTCATATTTATTT
Found at i:3899159 original size:18 final size:17
Alignment explanation
Indices: 3899131--3899169 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 17
3899121 TATTTGTTTT
3899131 TTTTACAAAAAAATAAAAA
1 TTTTAC-AAAAAA-AAAAA
3899150 TTTT-CAAAAAAAAAAA
1 TTTTACAAAAAAAAAAA
3899166 TTTT
1 TTTT
3899170 TGAGGAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 9 0.45
17 6 0.30
18 1 0.05
19 4 0.20
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (17 bp):
TTTTACAAAAAAAAAAA
Found at i:3899164 original size:16 final size:17
Alignment explanation
Indices: 3899138--3899169 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3899128 TTTTTTTACA
3899138 AAAAAATAAAAATTTTC
1 AAAAAATAAAAATTTTC
3899155 AAAAAA-AAAAATTTT
1 AAAAAATAAAAATTTT
3899170 TGAGGAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (17 bp):
AAAAAATAAAAATTTTC
Found at i:3899309 original size:58 final size:58
Alignment explanation
Indices: 3899157--3899493 Score: 396
Period size: 58 Copynumber: 5.7 Consensus size: 58
3899147 AAATTTTCAA
* * *
3899157 AAAAAAAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGATTTC
1 AAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGATTTC
* *
3899215 AGAAAAAAATATATTTTTGGAA-AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTC
1 ---AAAAAA-ATATTTTT-GAAGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGATTTC
*** * *
3899277 AAAAACGGATTTTTGAAGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAA-AGTTTC
1 AAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGA-TTTC
* *
3899335 TAAAAAATATTTTTG-AGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTC
1 AAAAAAATATTTTTGAAG-AAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGATTTC
* * * *
3899393 TAAAAAATATTTTTGAAGAAAAGTTGAAAGTATAAATTTT-CTTCGAAATTAAAATTTC
1 AAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTCCTT-GAAAATAAGATTTC
* *
3899451 TAAAAAATATTTTGGGAA-AAAAGTTGAAAGTATCAATTTTCCT
1 AAAAAAATATTTT-TGAAGAAAAGTTGAAAGTATCAATTTTCCT
3899494 GTACGAAAGC
Statistics
Matches: 241, Mismatches: 25, Indels: 22
0.84 0.09 0.08
Matches are distributed among these distances:
57 8 0.03
58 169 0.70
59 12 0.05
61 6 0.02
62 44 0.18
63 2 0.01
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.35
Consensus pattern (58 bp):
AAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGATTTC
Found at i:3899384 original size:116 final size:116
Alignment explanation
Indices: 3899158--3899493 Score: 471
Period size: 116 Copynumber: 2.9 Consensus size: 116
3899148 AATTTTCAAA
* * * * *
3899158 AAAAAAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAAT-AAGATTTCAGAAAAA
1 AAAAAAGATTTTTGAAGAAAAGTTGAAAGTATCAATTTTCTTCGAAATTAAAG-TTTC---TAAA
*
3899222 AATATATTTTTGGAAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTC-
62 AA-ATATTTTTGGAAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGCTTTCT
* *
3899277 AAAAACGGATTTTTGAAGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTCTAAAAAA
1 AAAAA-AGATTTTTGAAGAAAAGTTGAAAGTATCAATTTTCTTCGAAATTAAAGTTTCTAAAAAA
*
3899342 TATTTTT-GAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTCT
65 TATTTTTGGA-AAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGCTTTCT
* * *
3899394 AAAAAATATTTTTGAAGAAAAGTTGAAAGTATAAATTTTCTTCGAAATTAAAATTTCTAAAAAAT
1 AAAAAAGATTTTTGAAGAAAAGTTGAAAGTATCAATTTTCTTCGAAATTAAAGTTTCTAAAAAAT
*
3899459 ATTTTGGGAAAAAAGTTGAAAGTATCAATTTTCCT
66 ATTTTTGGAAAAAAGTTGAAAGTATCAATTTTCCT
3899494 GTACGAAAGC
Statistics
Matches: 197, Mismatches: 15, Indels: 13
0.88 0.07 0.06
Matches are distributed among these distances:
115 2 0.01
116 133 0.68
117 12 0.06
119 5 0.03
120 42 0.21
121 3 0.02
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.35
Consensus pattern (116 bp):
AAAAAAGATTTTTGAAGAAAAGTTGAAAGTATCAATTTTCTTCGAAATTAAAGTTTCTAAAAAAT
ATTTTTGGAAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGCTTTCT
Found at i:3899480 original size:174 final size:176
Alignment explanation
Indices: 3899158--3899493 Score: 459
Period size: 174 Copynumber: 1.9 Consensus size: 176
3899148 AATTTTCAAA
* *
3899158 AAAAAAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGATTTCAGAAAAAA
1 AAAAAAAATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGATTTC--AAAAAA
* ** *
3899223 ATATATTTTTGGAAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTCAAAAACGGATT
64 ATATATTTTTGGAAAAAAGTTGAAAGTATAAATTTTCCTTAAAAATAAAATTTCAAAAACAGATT
*
3899288 TTTGAAGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTCT
129 TTGGAAGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTCT
* * *
3899336 AAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTC-TAAAAA-
1 AAAAAAAATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGATTTCAAAAAAAT
* * *
3899399 ATATTTTT-GAAGAAAAGTTGAAAGTATAAATTTT-CTTCGAAATTAAAATTTCTAAAAA-ATAT
66 ATATTTTTGGAA-AAAAGTTGAAAGTATAAATTTTCCTT-AAAAATAAAATTTC-AAAAACAGAT
3899461 TTTGGGAA-AAAAGTTGAAAGTATCAATTTTCCT
128 TTT-GGAAGAAAAGTTGAAAGTATCAATTTTCCT
3899494 GTACGAAAGC
Statistics
Matches: 141, Mismatches: 13, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
173 6 0.04
174 69 0.49
175 13 0.09
178 53 0.38
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.35
Consensus pattern (176 bp):
AAAAAAAATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGATTTCAAAAAAAT
ATATTTTTGGAAAAAAGTTGAAAGTATAAATTTTCCTTAAAAATAAAATTTCAAAAACAGATTTT
GGAAGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTCT
Found at i:3903234 original size:30 final size:27
Alignment explanation
Indices: 3903199--3903278 Score: 88
Period size: 30 Copynumber: 2.8 Consensus size: 27
3903189 TATCAACAAT
3903199 GGATGAAAAATGAGAAAAAAGAAAAGAAGA
1 GGATGAAAAATGA-AAAAAAGAAAA-AA-A
*
3903229 TGATGAAAAATGAAAAATAAAGAAAAAAA
1 GGATGAAAAATG-AAAA-AAAGAAAAAAA
**
3903258 GGAAAAAAAATGAAAAAAAGA
1 GGATGAAAAATGAAAAAAAGA
3903279 TTCAAATTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
27 5 0.11
28 4 0.09
29 10 0.23
30 16 0.36
31 9 0.20
ACGTcount: A:0.71, C:0.00, G:0.20, T:0.09
Consensus pattern (27 bp):
GGATGAAAAATGAAAAAAAGAAAAAAA
Found at i:3903253 original size:10 final size:9
Alignment explanation
Indices: 3903234--3903276 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 9
3903224 GAAGATGATG
*
3903234 AAAAATGAA
1 AAAAAAGAA
3903243 AAATAAAGAA
1 AAA-AAAGAA
*
3903253 AAAAAGGAA
1 AAAAAAGAA
3903262 AAAAAATGAA
1 AAAAAA-GAA
3903272 AAAAA
1 AAAAA
3903277 GATTCAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
9 13 0.45
10 16 0.55
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.07
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:3903256 original size:19 final size:19
Alignment explanation
Indices: 3903204--3903277 Score: 71
Period size: 19 Copynumber: 3.8 Consensus size: 19
3903194 ACAATGGATG
3903204 AAAAATGAGAAAAAA-GAAA
1 AAAAATGA-AAAAAAGGAAA
* * *
3903223 AGAAGATGATGAAAAATGAAA
1 A-AAAATGA-AAAAAAGGAAA
3903244 AATAAA-GAAAAAAAGGAAA
1 AA-AAATGAAAAAAAGGAAA
3903263 AAAAATGAAAAAAAG
1 AAAAATGAAAAAAAG
3903278 ATTCAAATTG
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
18 3 0.07
19 21 0.47
20 14 0.31
21 7 0.16
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (19 bp):
AAAAATGAAAAAAAGGAAA
Found at i:3903515 original size:11 final size:11
Alignment explanation
Indices: 3903499--3903523 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3903489 ACATACCATT
3903499 CATCCCAATGA
1 CATCCCAATGA
3903510 CATCCCAATGA
1 CATCCCAATGA
3903521 CAT
1 CAT
3903524 GTATCCAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.36, G:0.08, T:0.20
Consensus pattern (11 bp):
CATCCCAATGA
Found at i:3904043 original size:63 final size:63
Alignment explanation
Indices: 3903975--3904098 Score: 194
Period size: 63 Copynumber: 2.0 Consensus size: 63
3903965 AAACTAGTGC
*** *
3903975 TGAGAAGCTTATGAACGATGACCAAGTGACAGGTGATAAAATTTGTTTTGAAATGGCTAGTAT
1 TGAGAAGCTTATGAACGATGACCAAGTGACAGAACATAAAATTTATTTTGAAATGGCTAGTAT
* *
3904038 TGAGAAGCTTATGAACGATGACCAAGTGACAGAACATGAAATTTATTTTGAAATGGTTAGT
1 TGAGAAGCTTATGAACGATGACCAAGTGACAGAACATAAAATTTATTTTGAAATGGCTAGT
3904099 GCTGATAAGC
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (63 bp):
TGAGAAGCTTATGAACGATGACCAAGTGACAGAACATAAAATTTATTTTGAAATGGCTAGTAT
Found at i:3905410 original size:42 final size:42
Alignment explanation
Indices: 3905134--3905533 Score: 309
Period size: 42 Copynumber: 9.5 Consensus size: 42
3905124 ATGATTATTA
*
3905134 AGGAGCAATTTATTTTT-CAAAGTCGGGGTT-A-CCTCTATTTAG
1 AGGAGCAATTTATTTTTCCAAAGTC---GTTGAGCCTCTGTTTAG
* * * * * *
3905176 AGGAGCAATTTACTTTT-CAAAATTGTGGTGCCCCTGTTTAG
1 AGGAGCAATTTATTTTTCCAAAGTCGTTGAGCCTCTGTTTAG
* * * * * **
3905217 AGGAGC-ATTTATTTTT--GAAGT-ATGGTGCTTCTACTTAG
1 AGGAGCAATTTATTTTTCCAAAGTCGTTGAGCCTCTGTTTAG
* *** * *
3905255 AGAATTTATTTATTTTGT--AAAGTCGTTGAACCTCTGATTAG
1 AGGAGCAATTTATTTT-TCCAAAGTCGTTGAGCCTCTGTTTAG
* *
3905296 AGGAGCCATTTA-TTTTCCAAAGTCGTTGAGCCTCTGATTAG
1 AGGAGCAATTTATTTTTCCAAAGTCGTTGAGCCTCTGTTTAG
* * * *
3905337 ATGAGCCATTTATTTTTTCAAAAGTCATTGAGCCTCTGTTTAG
1 AGGAGCAATTTA-TTTTTCCAAAGTCGTTGAGCCTCTGTTTAG
*
3905380 AGGAGCAATTTATTTTTCCAAAGTCGTTGAGCCTTTGTTTAG
1 AGGAGCAATTTATTTTTCCAAAGTCGTTGAGCCTCTGTTTAG
* *
3905422 AGGAGCAATTTATTTTTCCAAAGTTGTTGAGCCTCTGCTTAG
1 AGGAGCAATTTATTTTTCCAAAGTCGTTGAGCCTCTGTTTAG
* * * * *
3905464 AGGAGCCTTTATTTATTTTTTCAAAGTTGTTGAGCTTCTGCTTAG
1 AGGAG-C--AATTTATTTTTCCAAAGTCGTTGAGCCTCTGTTTAG
*
3905509 AGGAGCCTTTATTTATTTTTCCAAA
1 AGGAG-C--AATTTATTTTTCCAAA
3905534 TTTGTTGAAT
Statistics
Matches: 299, Mismatches: 47, Indels: 21
0.81 0.13 0.06
Matches are distributed among these distances:
38 15 0.05
39 15 0.05
40 17 0.06
41 66 0.22
42 92 0.31
43 37 0.12
45 57 0.19
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.41
Consensus pattern (42 bp):
AGGAGCAATTTATTTTTCCAAAGTCGTTGAGCCTCTGTTTAG
Found at i:3905541 original size:45 final size:42
Alignment explanation
Indices: 3905273--3905533 Score: 317
Period size: 42 Copynumber: 6.1 Consensus size: 42
3905263 TTTATTTTGT
*
3905273 AAAGTCGTTGAACCTCTGATTAGAGGAGCCATTTA-TTTTCC
1 AAAGTCGTTGAGCCTCTGATTAGAGGAGCCATTTATTTTTCC
* *
3905314 AAAGTCGTTGAGCCTCTGATTAGATGAGCCATTTATTTTTTCA
1 AAAGTCGTTGAGCCTCTGATTAGAGGAGCCATTTA-TTTTTCC
* * *
3905357 AAAGTCATTGAGCCTCTGTTTAGAGGAGCAATTTATTTTTCC
1 AAAGTCGTTGAGCCTCTGATTAGAGGAGCCATTTATTTTTCC
* * *
3905399 AAAGTCGTTGAGCCTTTGTTTAGAGGAGCAATTTATTTTTCC
1 AAAGTCGTTGAGCCTCTGATTAGAGGAGCCATTTATTTTTCC
* * *
3905441 AAAGTTGTTGAGCCTCTGCTTAGAGGAGCCTTTATTTATTTTTTC
1 AAAGTCGTTGAGCCTCTGATTAGAGGAGCC---ATTTATTTTTCC
* * *
3905486 AAAGTTGTTGAGCTTCTGCTTAGAGGAGCCTTTATTTATTTTTCC
1 AAAGTCGTTGAGCCTCTGATTAGAGGAGCC---ATTTATTTTTCC
3905531 AAA
1 AAA
3905534 TTTGTTGAAT
Statistics
Matches: 198, Mismatches: 17, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
41 33 0.17
42 72 0.36
43 36 0.18
45 57 0.29
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.40
Consensus pattern (42 bp):
AAAGTCGTTGAGCCTCTGATTAGAGGAGCCATTTATTTTTCC
Found at i:3907860 original size:16 final size:15
Alignment explanation
Indices: 3907840--3907876 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
3907830 TTTTTTGGTA
3907840 TTTTATTCATTTGTT
1 TTTTATTCATTTGTT
*
3907855 TATTTATTTATTTGTT
1 T-TTTATTCATTTGTT
3907871 TTTTAT
1 TTTTAT
3907877 GTGTTAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.16, C:0.03, G:0.05, T:0.76
Consensus pattern (15 bp):
TTTTATTCATTTGTT
Found at i:3907990 original size:61 final size:62
Alignment explanation
Indices: 3907923--3908063 Score: 198
Period size: 62 Copynumber: 2.3 Consensus size: 62
3907913 TTTTTACAAA
* *
3907923 AAAATAAAAATTTTAAAAAAAA-ATATTTTTT-AGGAAAAGTTGAAAGTATCAATTTTCTTTG
1 AAAAT-AAAATTTCAAAAAAAATATATTTTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTTG
*
3907984 AAAATAAAATTTCAAAAAAAATATATTTTTTGAGAAAAAGTTGAAAGTATCAATTTT-TCTTA
1 AAAATAAAATTTCAAAAAAAATATATTTTTTGAGAAAAAGTTGAAAGTATCAATTTTCT-TTG
**
3908046 AAAATAAGTTTTCAAAAA
1 AAAATAAAATTTCAAAAA
3908064 TGGCTCGAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
60 15 0.21
61 15 0.21
62 42 0.58
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (62 bp):
AAAATAAAATTTCAAAAAAAATATATTTTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTTG
Found at i:3908241 original size:58 final size:58
Alignment explanation
Indices: 3908067--3908242 Score: 239
Period size: 58 Copynumber: 3.0 Consensus size: 58
3908057 TCAAAAATGG
* * * *
3908067 CTCGAAATTAAAGTTTCTAAAAAATATTTTTGAGGAAAAGTTGAAAATATCAATTTTT
1 CTCGAAATTAAAATTTCTAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTC
* * ** *
3908125 CTTGAAAATAAGCTTTCTAAAGAATATTTTTG-GAGAAAAGTTGAAAGTATCAATTTTC
1 CTCGAAATTAAAATTTCTAAAAAATATTTTTGAGA-AAAAGTTGAAAGTATCAATTTTC
3908183 CTCGAAATTAAAATTTCTAAAAAATA-TTTTGAGAAAAAGTTGAAAGTATCAAATTTTC
1 CTCGAAATTAAAATTTCTAAAAAATATTTTTGAGAAAAAGTTGAAAGTATC-AATTTTC
3908241 CT
1 CT
3908243 GTACAAAAGC
Statistics
Matches: 102, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
57 22 0.22
58 80 0.78
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (58 bp):
CTCGAAATTAAAATTTCTAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTC
Found at i:3909759 original size:39 final size:38
Alignment explanation
Indices: 3909706--3909785 Score: 124
Period size: 39 Copynumber: 2.1 Consensus size: 38
3909696 TTTTTCAATG
* * *
3909706 TAGTTTTTTTTTACATATATTTTTTAACAATAACATTT
1 TAGTTTTTTCTTACATATATTCTTCAACAATAACATTT
3909744 TAGTATTTTTCTTACATATATTCTTCAACAATAACATTT
1 TAGT-TTTTTCTTACATATATTCTTCAACAATAACATTT
3909783 TAG
1 TAG
3909786 GTGAGTGAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
38 4 0.11
39 34 0.89
ACGTcount: A:0.33, C:0.11, G:0.04, T:0.53
Consensus pattern (38 bp):
TAGTTTTTTCTTACATATATTCTTCAACAATAACATTT
Found at i:3911621 original size:3 final size:3
Alignment explanation
Indices: 3911609--3911641 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
3911599 TCCATTTTTT
*
3911609 TAA TAA -AA TAA TAA TAA CAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3911642 TTATAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:3912402 original size:58 final size:58
Alignment explanation
Indices: 3912223--3912610 Score: 357
Period size: 58 Copynumber: 6.6 Consensus size: 58
3912213 TATACAGGGG
** *
3912223 AAAATTGATACTTTCAACTTTTCCCGTAAAAT-TTTTTTGGAAACTTTAATTTTGAGA
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATACTTTTTGGAAACTTTAATTTTGAGA
* * * ** * * * *
3912280 AAAATTGATACTTCCAACTTTTCCTCAAAAAAAAACTTTTTTAAAAATTTATTTTTAAAA
1 AAAATTGATACTTTCAACTTTTCC-C-CAAAAATACTTTTTGGAAACTTTAATTTTGAGA
* *
3912340 AAAATTGATACTTTTAACTTTTCCCCAAAAATACTTTTTGGAAACTTTAATTTCGAGA
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATACTTTTTGGAAACTTTAATTTTGAGA
* * * * * *
3912398 AAAATTGGTACTTTCAACTTTTCCTCAAAAATAAACTTTTTTTGAAAATTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCCCAAAAAT--AC-TTTTTGGAAACTTTAATTTTGAGA
* * *
3912459 AAAATTGATACTTTCAACTTTTCTCCAAAAATA-TTTCTTGAAAACTTTAATTTCGAGA
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATACTTT-TTGGAAACTTTAATTTTGAGA
* *** * ** * * * * *
3912517 AAAATTGATACTTTTAACTTTTGTTCAAAATCTTTTTTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCCCAAAA---ATACTTTTTGGAAACTTTAATTTTGAGA
*
3912578 AAAATTGATACTTTCAACTTTTTCCCAAAAATA
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATA
3912611 TATATTTTTT
Statistics
Matches: 263, Mismatches: 57, Indels: 21
0.77 0.17 0.06
Matches are distributed among these distances:
57 26 0.10
58 97 0.37
59 6 0.02
60 42 0.16
61 89 0.34
62 3 0.01
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCCCCAAAAATACTTTTTGGAAACTTTAATTTTGAGA
Found at i:3912480 original size:119 final size:118
Alignment explanation
Indices: 3912223--3912611 Score: 548
Period size: 119 Copynumber: 3.3 Consensus size: 118
3912213 TATACAGGGG
** * *
3912223 AAAATTGATACTTTCAACTTTTCCCGTAAAATTTTTTTGGAAACTTTAATTTTGAGAAAAATTGA
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTGGAAACTTTAATTTCGAGAAAAATTGA
* * * *
3912288 TACTTCCAACTTTTCCTCAAAAAAAAAC-TTTTTTAAAAATTTATTTTTAAAA
66 TACTTTCAACTTTTCCTCAAAAATAAACTTTTTTTGAAAATTTATTTTTAAGA
*
3912340 AAAATTGATACTTTTAACTTTTCCCCAAAAATACTTTTTGGAAACTTTAATTTCGAGAAAAATTG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTGGAAACTTTAATTTCGAGAAAAATTG
*
3912405 GTACTTTCAACTTTTCCTCAAAAATAAACTTTTTTTGAAAATTTATTTTTAAGA
65 ATACTTTCAACTTTTCCTCAAAAATAAACTTTTTTTGAAAATTTATTTTTAAGA
* *
3912459 AAAATTGATACTTTCAACTTTTCTCCAAAAATATTTCTTGAAAACTTTAATTTCGAGAAAAATTG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTT-TTGGAAACTTTAATTTCGAGAAAAATTG
* ** **** *
3912524 ATACTTTTAACTTTTGTTC-AAAATCTTTTTTTTTTTGAAAATTTATTTTTAAGG
65 ATACTTTCAACTTTTCCTCAAAAAT-AAACTTTTTTTGAAAATTTATTTTTAAGA
*
3912578 AAAATTGATACTTTCAACTTTTTCCCAAAAATAT
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATAT
3912612 ATATTTTTTT
Statistics
Matches: 244, Mismatches: 24, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
117 29 0.12
118 64 0.26
119 151 0.62
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (118 bp):
AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTGGAAACTTTAATTTCGAGAAAAATTGA
TACTTTCAACTTTTCCTCAAAAATAAACTTTTTTTGAAAATTTATTTTTAAGA
Found at i:3912675 original size:6 final size:6
Alignment explanation
Indices: 3912636--3912713 Score: 67
Period size: 6 Copynumber: 13.5 Consensus size: 6
3912626 TTGTTTAAAG
* * * *
3912636 AAAAT- AAAATA ATAAA-A CAAAATG AAAGTG AAAATA AAAAT- -AAAGA
1 AAAATA AAAATA A-AAATA -AAAATA AAAATA AAAATA AAAATA AAAATA
3912682 AAAAT- AAAATA AAAATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAA
3912714 GAATGTTAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
4 3 0.05
5 10 0.17
6 43 0.72
7 4 0.07
ACGTcount: A:0.78, C:0.01, G:0.05, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:3912702 original size:12 final size:11
Alignment explanation
Indices: 3912636--3912713 Score: 77
Period size: 12 Copynumber: 6.8 Consensus size: 11
3912626 TTGTTTAAAG
3912636 AAAATAAAATAA
1 AAAATAAAAT-A
* *
3912648 TAAAACAAAATG
1 -AAAATAAAATA
*
3912660 AAAGTGAAAATA
1 AAAAT-AAAATA
*
3912672 AAAAT-AAAGA
1 AAAATAAAATA
3912682 AAAATAAAATA
1 AAAATAAAATA
3912693 AAAATAAAAATA
1 AAAAT-AAAATA
3912705 AAAATAAAA
1 AAAATAAAA
3912714 GAATGTTAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
10 9 0.17
11 16 0.30
12 20 0.37
13 9 0.17
ACGTcount: A:0.78, C:0.01, G:0.05, T:0.15
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:3912737 original size:3 final size:3
Alignment explanation
Indices: 3912729--3912760 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
3912719 TTAAACAAAT
3912729 ATA ATA ATA ATA ATA ATA ATA ATA ATA TATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA A
3912761 ATATATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3913279 original size:32 final size:31
Alignment explanation
Indices: 3913216--3913281 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
3913206 CAGCTGGCCA
* *
3913216 AAAAATTCAAACTTGGCGAGAATAGTCATCG
1 AAAAATTCAAACTTCGCGAGAAAAGTCATCG
* * *
3913247 AAAAATTCAACCTTCGCTAGAAAATTCAATCG
1 AAAAATTCAAACTTCGCGAGAAAAGTC-ATCG
3913279 AAA
1 AAA
3913282 TTTGGAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 22 0.76
32 7 0.24
ACGTcount: A:0.45, C:0.18, G:0.14, T:0.23
Consensus pattern (31 bp):
AAAAATTCAAACTTCGCGAGAAAAGTCATCG
Found at i:3913813 original size:11 final size:11
Alignment explanation
Indices: 3913792--3913880 Score: 51
Period size: 11 Copynumber: 7.8 Consensus size: 11
3913782 TATATAATAG
3913792 TAATAAATAAA
1 TAATAAATAAA
3913803 TAA-ATAATAAA
1 TAATA-AATAAA
3913814 TACATAAGATAAA
1 TA-ATAA-ATAAA
*
3913827 -AATAAAAGAAA
1 TAAT-AAATAAA
* *
3913838 AAATATATAAAA
1 TAATAAAT-AAA
*
3913850 TAATAATAAAAA
1 TAATAA-ATAAA
3913862 TAA-AAATAAAA
1 TAATAAAT-AAA
3913873 TAA-AAATA
1 TAATAAATA
3913881 CAAAATACAA
Statistics
Matches: 62, Mismatches: 7, Indels: 19
0.70 0.08 0.22
Matches are distributed among these distances:
10 3 0.05
11 31 0.50
12 21 0.34
13 7 0.11
ACGTcount: A:0.74, C:0.01, G:0.02, T:0.22
Consensus pattern (11 bp):
TAATAAATAAA
Found at i:3913847 original size:27 final size:25
Alignment explanation
Indices: 3913800--3913894 Score: 77
Period size: 27 Copynumber: 3.6 Consensus size: 25
3913790 AGTAATAAAT
* * *
3913800 AAATAAATAATAAATACATAAGATAA
1 AAATAAAAAAAAAATATATAA-ATAA
3913826 AAATAAAAGAAAAAATATATAAAATAA
1 AAATAAAA-AAAAAATATAT-AAATAA
* *
3913853 TAATAAAAATAAAA-ATA-AAATAA
1 AAATAAAAAAAAAATATATAAATAA
3913876 AAATACAAAATACAAAATA
1 AAATA-AAAA-A-AAAATA
3913895 AAAAAAGAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
23 10 0.18
24 4 0.07
25 3 0.05
26 16 0.29
27 21 0.38
28 2 0.04
ACGTcount: A:0.75, C:0.03, G:0.02, T:0.20
Consensus pattern (25 bp):
AAATAAAAAAAAAATATATAAATAA
Found at i:3913870 original size:39 final size:42
Alignment explanation
Indices: 3913796--3913878 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 42
3913786 TAATAGTAAT
3913796 AAATAAATAAATAATAAATACATAAGATAAAAATAAAAGAAA
1 AAATAAATAAATAATAAATACATAAGATAAAAATAAAAGAAA
* *
3913838 AAATATATAAAATAAT-AATA-A-AA-ATAAAAATAAAATAAA
1 AAATAAAT-AAATAATAAATACATAAGATAAAAATAAAAGAAA
3913877 AA
1 AA
3913879 TACAAAATAC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
39 17 0.45
40 2 0.05
41 1 0.03
42 11 0.29
43 7 0.18
ACGTcount: A:0.76, C:0.01, G:0.02, T:0.20
Consensus pattern (42 bp):
AAATAAATAAATAATAAATACATAAGATAAAAATAAAAGAAA
Found at i:3913885 original size:7 final size:6
Alignment explanation
Indices: 3913800--3913898 Score: 85
Period size: 6 Copynumber: 15.5 Consensus size: 6
3913790 AGTAATAAAT
* *
3913800 AAATAA ATAATAA ATACAT-A AGATAA AAATAA AAGAAAA AATATATA
1 AAATAA A-AATAA A-A-ATAA AAATAA AAATAA AA-ATAA AA-ATA-A
*
3913847 AAATAA TAATAA AAATAA AAAT-A AAATAA AAATACA AAATACA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATA-A AAATA-A AAATAA
3913896 AAA
1 AAA
3913899 AAGAAAATGG
Statistics
Matches: 79, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
5 7 0.09
6 34 0.43
7 33 0.42
8 5 0.06
ACGTcount: A:0.76, C:0.03, G:0.02, T:0.19
Consensus pattern (6 bp):
AAATAA
Found at i:3913899 original size:7 final size:7
Alignment explanation
Indices: 3913796--3913899 Score: 53
Period size: 7 Copynumber: 15.4 Consensus size: 7
3913786 TAATAGTAAT
3913796 AAATAAA
1 AAATAAA
*
3913803 TAAATAAT
1 -AAATAAA
3913811 AAATACATA
1 AAATA-A-A
*
3913820 AGAT-AA
1 AAATAAA
3913826 AAATAAA
1 AAATAAA
3913833 AGAA-AAA
1 A-AATAAA
* *
3913840 ATATATA
1 AAATAAA
3913847 AAAT-AA
1 AAATAAA
*
3913853 TAAT-AA
1 AAATAAA
3913859 AAAT-AA
1 AAATAAA
3913865 AAAT--A
1 AAATAAA
3913870 AAAT-AA
1 AAATAAA
*
3913876 AAATACA
1 AAATAAA
*
3913883 AAATACA
1 AAATAAA
3913890 AAATAAA
1 AAATAAA
3913897 AAA
1 AAA
3913900 AGAAAATGGG
Statistics
Matches: 77, Mismatches: 12, Indels: 15
0.74 0.12 0.14
Matches are distributed among these distances:
5 5 0.06
6 25 0.32
7 35 0.45
8 9 0.12
9 3 0.04
ACGTcount: A:0.76, C:0.03, G:0.02, T:0.19
Consensus pattern (7 bp):
AAATAAA
Found at i:3913906 original size:20 final size:20
Alignment explanation
Indices: 3913851--3913906 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
3913841 TATATAAAAT
* *
3913851 AATAATAAAAATAAAA-ATAA
1 AATAA-AAAAACAAAATACAA
*
3913871 AATAAAAATACAAAATACAA
1 AATAAAAAAACAAAATACAA
*
3913891 AATAAAAAAAGAAAAT
1 AATAAAAAAACAAAAT
3913907 GGGCCTACCC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 8 0.27
20 22 0.73
ACGTcount: A:0.79, C:0.04, G:0.02, T:0.16
Consensus pattern (20 bp):
AATAAAAAAACAAAATACAA
Found at i:3914135 original size:43 final size:42
Alignment explanation
Indices: 3914078--3914456 Score: 256
Period size: 43 Copynumber: 9.0 Consensus size: 42
3914068 TTAAAACTCT
* * *
3914078 TCTAAGCAGAGGCTCAACGACTTTGAAAAACATAAATGGCTCT
1 TCTAAACAGAGGCTCAACAACTTTGAAAAA-ATAAATGGCTCC
** * * *
3914121 TCTAATTAGAGGCTCAACGACTTTGAAAAAGTAAAATAAAGCTCC
1 TCTAAACAGAGGCTCAACAACTTTGAAAAAAT-AAAT--GGCTCC
* * **** * *
3914166 TCTTAATAGAGG-T-AATTTTTTTTAAAATTTGATTAAA--GCTCC
1 TCTAAACAGAGGCTCAACAACTTTGAAAA----AATAAATGGCTCC
* * * *
3914208 TCTAAGCAGAGGCTCAACGACTTTGAGAAACATAAATGGCTCT
1 TCTAAACAGAGGCTCAACAACTTTGA-AAAAATAAATGGCTCC
* * * *
3914251 TCTAATCAGAGGCTCAACAACTTTGGAAAAGTAAAATTGCTCC
1 TCTAAACAGAGGCTCAACAACTTTGAAAAAAT-AAATGGCTCC
* * *
3914294 TCTAAATAGAGGCTCAACAACTTT-AGAAGAGTAAATGGCTCC
1 TCTAAACAGAGGCTCAACAACTTTGA-AAAAATAAATGGCTCC
* *
3914336 TCTAAACAGAAGCTCAACAACTTTG--AAAATAAATAGCTCC
1 TCTAAACAGAGGCTCAACAACTTTGAAAAAATAAATGGCTCC
*
3914376 TCTAAACAGAGGCATC-ACAACTTTG-GAAAATAAATGGCTCC
1 TCTAAACAGAGGC-TCAACAACTTTGAAAAAATAAATGGCTCC
* ** * * *
3914417 TCTAAACAAAGGCTTGACGATTTTG-AAAAATAAATTGCTC
1 TCTAAACAGAGGCTCAACAACTTTGAAAAAATAAATGGCTC
3914457 TTTGACAATC
Statistics
Matches: 269, Mismatches: 49, Indels: 38
0.76 0.14 0.11
Matches are distributed among these distances:
40 34 0.13
41 52 0.19
42 50 0.19
43 104 0.39
44 7 0.03
45 17 0.06
46 3 0.01
47 2 0.01
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.27
Consensus pattern (42 bp):
TCTAAACAGAGGCTCAACAACTTTGAAAAAATAAATGGCTCC
Found at i:3914196 original size:130 final size:128
Alignment explanation
Indices: 3914053--3914305 Score: 407
Period size: 130 Copynumber: 2.0 Consensus size: 128
3914043 ACATTTTTTA
* *
3914053 TTTTTTAAGATTTGATTAAAACTCTTCTAAGCAGAGGCTCAACGACTTTGAAAAACATAAATGGC
1 TTTTTTAAAATTTGATTAAAACTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAACATAAATGGC
* * *
3914118 TCTTCTAATTAGAGGCTCAACGACTTTGAAAAAGTAAAATAAAGCTCCTCTTAATAGAGGTAATT
66 TCTTCTAATCAGAGGCTCAACAACTTTGAAAAAGTAAAAT--AGCTCCTCTAAATAGAGGTAATT
* *
3914183 TTTTTTAAAATTTGATTAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGAGAAACATAAATGGC
1 TTTTTTAAAATTTGATTAAAACTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAACATAAATGGC
* *
3914248 TCTTCTAATCAGAGGCTCAACAACTTTGGAAAAGTAAAATTGCTCCTCTAAATAGAGG
66 TCTTCTAATCAGAGGCTCAACAACTTTGAAAAAGTAAAATAGCTCCTCTAAATAGAGG
3914306 CTCAACAACT
Statistics
Matches: 114, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
128 16 0.14
130 98 0.86
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (128 bp):
TTTTTTAAAATTTGATTAAAACTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAACATAAATGGC
TCTTCTAATCAGAGGCTCAACAACTTTGAAAAAGTAAAATAGCTCCTCTAAATAGAGGTAATT
Found at i:3914417 original size:41 final size:41
Alignment explanation
Indices: 3914203--3914430 Score: 289
Period size: 43 Copynumber: 5.5 Consensus size: 41
3914193 TTTGATTAAA
* *
3914203 GCTCCTCTAAGCAGAGGCTCAACGACTTTGAGAAACATAAATG
1 GCTCCTCTAAACAGAGGCTCAACAACTTTG-GAAA-ATAAATG
* * *
3914246 GCTCTTCTAATCAGAGGCTCAACAACTTTGGAAAAGTAAAATT
1 GCTCCTCTAAACAGAGGCTCAACAACTTTGGAAAA-T-AAATG
* * *
3914289 GCTCCTCTAAATAGAGGCTCAACAACTTTAGAAGAGTAAATG
1 GCTCCTCTAAACAGAGGCTCAACAACTTTGGAA-AATAAATG
* *
3914331 GCTCCTCTAAACAGAAGCTCAACAACTTT-GAAAATAAATA
1 GCTCCTCTAAACAGAGGCTCAACAACTTTGGAAAATAAATG
3914371 GCTCCTCTAAACAGAGGCATC-ACAACTTTGGAAAATAAATG
1 GCTCCTCTAAACAGAGGC-TCAACAACTTTGGAAAATAAATG
*
3914412 GCTCCTCTAAACAAAGGCT
1 GCTCCTCTAAACAGAGGCT
3914431 TGACGATTTT
Statistics
Matches: 163, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
40 32 0.20
41 33 0.20
42 36 0.22
43 61 0.37
44 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCTCAACAACTTTGGAAAATAAATG
Found at i:3914447 original size:41 final size:41
Alignment explanation
Indices: 3914203--3914456 Score: 278
Period size: 43 Copynumber: 6.1 Consensus size: 41
3914193 TTTGATTAAA
* *
3914203 GCTCCTCTAAGCAGAGGCTCAACGACTTTGAGAAACATAAATG
1 GCTCCTCTAAACAGAGGCTCAACAACTTTGA-AAA-ATAAATG
* * * *
3914246 GCTCTTCTAATCAGAGGCTCAACAACTTTGGAAAAGTAAAATT
1 GCTCCTCTAAACAGAGGCTCAACAACTTT-GAAAAAT-AAATG
* * *
3914289 GCTCCTCTAAATAGAGGCTCAACAACTTTAGAAGAGTAAATG
1 GCTCCTCTAAACAGAGGCTCAACAACTTT-GAAAAATAAATG
* *
3914331 GCTCCTCTAAACAGAAGCTCAACAACTTTG-AAAATAAATA
1 GCTCCTCTAAACAGAGGCTCAACAACTTTGAAAAATAAATG
*
3914371 GCTCCTCTAAACAGAGGCATC-ACAACTTTGGAAAATAAATG
1 GCTCCTCTAAACAGAGGC-TCAACAACTTTGAAAAATAAATG
* ** * * *
3914412 GCTCCTCTAAACAAAGGCTTGACGATTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCTCAACAACTTTGAAAAATAAATG
3914453 GCTC
1 GCTC
3914457 TTTGACAATC
Statistics
Matches: 182, Mismatches: 24, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
40 34 0.19
41 49 0.27
42 32 0.18
43 65 0.36
44 2 0.01
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCTCAACAACTTTGAAAAATAAATG
Found at i:3914447 original size:82 final size:82
Alignment explanation
Indices: 3914202--3914456 Score: 282
Period size: 82 Copynumber: 3.1 Consensus size: 82
3914192 ATTTGATTAA
* * * * *
3914202 AGCTCCTCTAAGCAGAGGCTCAACGACTTTGAGAAACATAAATGGCTCTTCTAATCAGAGGCTCA
1 AGCTCCTCTAAACAGAGGCTCAACAACTTTG-GAAA-ATAAATGGCTCCTCTAAACAAAGGCTCA
* *
3914267 ACAACTTTGGAAAAGTAAAAT
64 ACAA-TTTTGAAAAAT-AAAT
* * * *
3914288 TGCTCCTCTAAATAGAGGCTCAACAACTTTAGAAGAGTAAATGGCTCCTCTAAACAGAA-GCTCA
1 AGCTCCTCTAAACAGAGGCTCAACAACTTTGGAA-AATAAATGGCTCCTCTAAACA-AAGGCTCA
*
3914352 ACAACTTTG-AAAATAAAT
64 ACAATTTTGAAAAATAAAT
**
3914370 AGCTCCTCTAAACAGAGGCATC-ACAACTTTGGAAAATAAATGGCTCCTCTAAACAAAGGCTTGA
1 AGCTCCTCTAAACAGAGGC-TCAACAACTTTGGAAAATAAATGGCTCCTCTAAACAAAGGCTCAA
*
3914434 CGATTTTGAAAAATAAAT
65 CAATTTTGAAAAATAAAT
*
3914452 TGCTC
1 AGCTC
3914457 TTTGACAATC
Statistics
Matches: 143, Mismatches: 21, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
80 2 0.01
81 30 0.21
82 45 0.31
83 6 0.04
84 3 0.02
85 29 0.20
86 28 0.20
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.24
Consensus pattern (82 bp):
AGCTCCTCTAAACAGAGGCTCAACAACTTTGGAAAATAAATGGCTCCTCTAAACAAAGGCTCAAC
AATTTTGAAAAATAAAT
Found at i:3915476 original size:18 final size:16
Alignment explanation
Indices: 3915453--3915511 Score: 64
Period size: 18 Copynumber: 3.4 Consensus size: 16
3915443 TTGAGTCCTC
3915453 ATTTTTCATTCATTTTTT
1 ATTTTTCATT--TTTTTT
3915471 ATTTTTCATTTTTTTT
1 ATTTTTCATTTTTTTT
*
3915487 ATTTTTTTATATTATTTTT
1 A-TTTTTCAT-TT-TTTTT
3915506 ATTTTT
1 ATTTTT
3915512 TTTCAAGCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
16 7 0.19
17 7 0.19
18 17 0.46
19 6 0.16
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (16 bp):
ATTTTTCATTTTTTTT
Found at i:3915476 original size:19 final size:18
Alignment explanation
Indices: 3915454--3915512 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 18
3915444 TGAGTCCTCA
3915454 TTTTTCATTCATTTTTTA-
1 TTTTTCATT-ATTTTTTAT
3915472 TTTTTCATT-TTTTTTAT
1 TTTTTCATTATTTTTTAT
*
3915489 TTTTTTA-TATTATTTTTAT
1 TTTTTCATTA-T-TTTTTAT
3915508 TTTTT
1 TTTTT
3915513 TTCAAGCATA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
16 8 0.22
17 6 0.17
18 10 0.28
19 12 0.33
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTTCATTATTTTTTAT
Found at i:3915490 original size:9 final size:9
Alignment explanation
Indices: 3915472--3915514 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
3915462 TCATTTTTTA
*
3915472 TTTTTCATT
1 TTTTTTATT
3915481 TTTTTTATT
1 TTTTTTATT
3915490 TTTTTATATT
1 TTTTT-TATT
*
3915500 ATTTTTATT
1 TTTTTTATT
3915509 TTTTTT
1 TTTTTT
3915515 CAAGCATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
9 22 0.73
10 8 0.27
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTATT
Found at i:3915513 original size:19 final size:17
Alignment explanation
Indices: 3915465--3915513 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 17
3915455 TTTTCATTCA
*
3915465 TTTTTTA-TTTTTCATT
1 TTTTTTATTTTTTTATT
3915481 TTTTTTATTTTTTTATAT
1 TTTTTTATTTTTTTAT-T
3915499 TATTTTTATTTTTTT
1 T-TTTTTATTTTTTT
3915514 TCAAGCATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 7 0.24
17 7 0.24
18 2 0.07
19 13 0.45
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTTTATTTTTTTATT
Found at i:3925997 original size:58 final size:58
Alignment explanation
Indices: 3925872--3926323 Score: 443
Period size: 58 Copynumber: 7.7 Consensus size: 58
3925862 TTTATACAGG
* * *
3925872 GAAAAATTGATACTTTCAACTTTTTCC-C--CAAAATTTTTTTGAAAACTTTAATTTCGA
1 GAAAAATTGATACTTTCAAC-TTTTCCTCAAAAAAATTTTTTTG-AAACTTTATTTTCAA
* * * *
3925929 GAAAAATTGATACTTCCAACTTTTCCTCAAAAAAATTTTTTTAAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTTGAAACTTTATTTTCAA
* * * *
3925987 GAAAAATTGATACTTTCAACTTTTCC-CCAAAATATCTTTTTGAAACTTTAATTTCGAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTTGAAACTTTATTTTC-AA
* * * * *
3926045 G-AAAATTAATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAACTTTAATTTCGA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTTGAAACTTTATTTTCAA
* ** * * *
3926102 GGAAAATTGGCACTTTCAACTTTTCCTAAAAAATAAACTTTTTTTGAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCT-CAAAA-AAA-TTTTTTTGAAACTTTATTTTCAA
* * *
3926163 GAAAAATTGATACTTTCAACTTTTTCCT--AAAAAATATTTCTTGAAAACTTTAATTTCGA
1 GAAAAATTGATACTTTCAAC-TTTTCCTCAAAAAAAT-TTTTTTG-AAACTTTATTTTCAA
* *** * *
3926222 GGAAAATTGATACTTTCAACTTTTCCTCAAAATCTTTTTTTTTTGAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAA--AAATTTTTTTGAAACTTTATTTTCAA
* *
3926282 GAAAAATTGGTACTTTCAACTTTT-CTCCAAAAATATTTTTTT
1 GAAAAATTGATACTTTCAACTTTTCCT-CAAAAAAATTTTTTT
3926324 TTATTTTGTT
Statistics
Matches: 327, Mismatches: 51, Indels: 33
0.80 0.12 0.08
Matches are distributed among these distances:
56 6 0.02
57 68 0.21
58 111 0.34
59 50 0.15
60 43 0.13
61 41 0.13
62 8 0.02
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.43
Consensus pattern (58 bp):
GAAAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTTGAAACTTTATTTTCAA
Found at i:3926195 original size:119 final size:115
Alignment explanation
Indices: 3925874--3926322 Score: 528
Period size: 115 Copynumber: 3.8 Consensus size: 115
3925864 TATACAGGGA
* * **
3925874 AAAATTGATACTTTCAACTTTTTCC-CCAAA-ATTTTTTTGAAAACTTTAATTTCGAGAAAAATT
1 AAAATTGATACTTTCAAC-TTTTCCTCAAAATATTTTTTTGAAAA-TTTATTTTTAAGAAAAATT
* * * * * ** *
3925937 GATACTTCCAACTTTTCCTCAAAAAAATTTTTTTAAAAATTTATTTTTAAGA
64 GATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAACTTTAATTTCGAGG
* * * ** *
3925989 AAAATTGATACTTTCAACTTTTCCCCAAAATATCTTTTTGAAACTTTAATTTCGAAG-AAAATTA
1 AAAATTGATACTTTCAACTTTTCCTCAAAATATTTTTTTGAAAATTT-ATTTTTAAGAAAAATTG
*
3926053 ATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAACTTTAATTTCGAGG
65 ATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAACTTTAATTTCGAGG
** *
3926104 AAAATTGGCACTTTCAACTTTTCCTAAAAAATAAACTTTTTTTGAAAATTTATTTTTAAGAAAAA
1 AAAATTGATACTTTCAACTTTTCCT-CAAAAT--A-TTTTTTTGAAAATTTATTTTTAAGAAAAA
* *
3926169 TTGATACTTTCAACTTTTTCCTAAAAAATATTTCTTGAAAACTTTAATTTCGAGG
62 TTGATACTTTCAAC-TTTTCCTCAAAAATATTTTTTGAAAACTTTAATTTCGAGG
*
3926224 AAAATTGATACTTTCAACTTTTCCTCAAAATCTTTTTTTTTTGAAAATTTATTTTTAAGAAAAAT
1 AAAATTGATACTTTCAACTTTTCCTCAAAA---TATTTTTTTGAAAATTTATTTTTAAGAAAAAT
*
3926289 TGGTACTTTCAACTTTT-CTCCAAAAATATTTTTT
63 TGATACTTTCAACTTTTCCT-CAAAAATATTTTTT
3926323 TTTATTTTGT
Statistics
Matches: 285, Mismatches: 36, Indels: 23
0.83 0.10 0.07
Matches are distributed among these distances:
114 6 0.02
115 95 0.33
116 21 0.07
117 2 0.01
118 24 0.08
119 76 0.27
120 60 0.21
122 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (115 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAATATTTTTTTGAAAATTTATTTTTAAGAAAAATTGA
TACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAACTTTAATTTCGAGG
Found at i:3926347 original size:5 final size:5
Alignment explanation
Indices: 3926339--3926436 Score: 60
Period size: 5 Copynumber: 18.8 Consensus size: 5
3926329 TTGTTTAAAG
* *
3926339 AAAAT AAAAT --AAT AAAAC AAAAT GAAAGT GAAAAT AAAAAT AAAGA-
1 AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT -AAAAT -AAAAT AAA-AT
* *
3926385 AAAGT AAAAT AAAATT AAAA- AAATAA AAAAT AAAAT AAAGAT AAAAAT
1 AAAAT AAAAT AAAA-T AAAAT AAA-AT AAAAT AAAAT AAA-AT -AAAAT
3926433 AAAA
1 AAAA
3926437 AAATGTTAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
3 3 0.04
4 3 0.04
5 39 0.52
6 27 0.36
7 3 0.04
ACGTcount: A:0.77, C:0.01, G:0.06, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:3926378 original size:6 final size:6
Alignment explanation
Indices: 3926339--3926437 Score: 51
Period size: 6 Copynumber: 15.7 Consensus size: 6
3926329 TTGTTTAAAG
* * * *
3926339 AAAAT- AAAATA ATAAA-A CAAAATG AAAGTG AAAATA AAAATA AAGAAAA
1 AAAATA AAAATA A-AAATA -AAAATA AAAATA AAAATA AAAATA AA-AATA
* *
3926388 GTAAAATA AAATTAAA AAAATA AAAA-A TAAAATA AAGATA AAAATA AAAA
1 --AAAATA AAA--ATA AAAATA AAAATA -AAAATA AAAATA AAAATA AAAA
3926438 AATGTTAAAC
Statistics
Matches: 73, Mismatches: 10, Indels: 21
0.70 0.10 0.20
Matches are distributed among these distances:
5 6 0.08
6 49 0.67
7 8 0.11
8 8 0.11
9 2 0.03
ACGTcount: A:0.77, C:0.01, G:0.06, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:3926393 original size:21 final size:21
Alignment explanation
Indices: 3926363--3926425 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
3926353 AAACAAAATG
3926363 AAAGTGAAAATAAAAATAAAGA
1 AAAGT-AAAATAAAAATAAAGA
*
3926385 AAAGTAAAATAAAATTAAA-A
1 AAAGTAAAATAAAAATAAAGA
*
3926405 AAA-TAAAAAATAAAATAAAGA
1 AAAGTAAAATA-AAAATAAAGA
3926426 TAAAAATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 6 0.17
20 11 0.31
21 14 0.39
22 5 0.14
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (21 bp):
AAAGTAAAATAAAAATAAAGA
Found at i:3926404 original size:26 final size:25
Alignment explanation
Indices: 3926339--3926439 Score: 96
Period size: 26 Copynumber: 3.7 Consensus size: 25
3926329 TTGTTTAAAG
*
3926339 AAAATAAAATAATAAAACAAAATGAAAGT
1 AAAAT-AAA-AATAAAA-AAAAT-AAAAT
*
3926368 GAAAATAAAAATAAAGAAAAGTAAAAT
1 -AAAATAAAAATAAA-AAAAATAAAAT
3926395 AAAATTAAAAA-AATAAAAAATAAAAT
1 AAAA-TAAAAATAA-AAAAAATAAAAT
3926421 AAAGATAAAAATAAAAAAA
1 AAA-ATAAAAATAAAAAAA
3926440 TGTTAAACAA
Statistics
Matches: 63, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
26 30 0.48
27 14 0.22
28 10 0.16
29 4 0.06
30 5 0.08
ACGTcount: A:0.77, C:0.01, G:0.06, T:0.16
Consensus pattern (25 bp):
AAAATAAAAATAAAAAAAATAAAAT
Found at i:3926436 original size:32 final size:31
Alignment explanation
Indices: 3926334--3926440 Score: 99
Period size: 32 Copynumber: 3.3 Consensus size: 31
3926324 TTATTTTGTT
* * *
3926334 TAAAGAAAATAAAATAATAAAACAAAATGAAAG
1 TAAA-AAAATAAAA-AATAAAATAAAATAAAAA
* * *
3926367 TGAAAATAAA-AATAAAGAAAAGTAAAATAAAAT
1 T-AAAA-AAATAAAAAATAAAA-TAAAATAAAAA
3926400 TAAAAAAATAAAAAATAAAATAAAGATAAAAA
1 TAAAAAAATAAAAAATAAAATAAA-ATAAAAA
3926432 TAAAAAAAT
1 TAAAAAAAT
3926441 GTTAAACAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
31 7 0.11
32 34 0.56
33 14 0.23
34 6 0.10
ACGTcount: A:0.76, C:0.01, G:0.07, T:0.17
Consensus pattern (31 bp):
TAAAAAAATAAAAAATAAAATAAAATAAAAA
Found at i:3927410 original size:21 final size:23
Alignment explanation
Indices: 3927347--3927430 Score: 63
Period size: 21 Copynumber: 3.9 Consensus size: 23
3927337 TTTAAAAAGA
*
3927347 AAATGATCAGATAAATA-ATAAT
1 AAATAATCAGATAAATATATAAT
* * * *
3927369 -ATTAA-CATATAACTA-AAAAT
1 AAATAATCAGATAAATATATAAT
*
3927389 AAATACT-AGATAAAT-TATAAT
1 AAATAATCAGATAAATATATAAT
*
3927410 ATATAATCAGATAAATATATA
1 AAATAATCAGATAAATATATA
3927431 TATATAAATA
Statistics
Matches: 45, Mismatches: 12, Indels: 9
0.68 0.18 0.14
Matches are distributed among these distances:
20 12 0.27
21 21 0.47
22 8 0.18
23 4 0.09
ACGTcount: A:0.58, C:0.06, G:0.05, T:0.31
Consensus pattern (23 bp):
AAATAATCAGATAAATATATAAT
Found at i:3927534 original size:15 final size:15
Alignment explanation
Indices: 3927514--3927556 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
3927504 ATTAAATAGT
3927514 AATAATAAATAAATA
1 AATAATAAATAAATA
*
3927529 AATAATAAATACATA
1 AATAATAAATAAATA
3927544 AGATAA-AAATAAA
1 A-ATAATAAATAAA
3927557 AGAAAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 21 0.84
16 4 0.16
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (15 bp):
AATAATAAATAAATA
Found at i:3927553 original size:26 final size:25
Alignment explanation
Indices: 3927524--3927628 Score: 74
Period size: 26 Copynumber: 4.1 Consensus size: 25
3927514 AATAATAAAT
3927524 AAATAAATA-ATAAATACATAAGATAA
1 AAATAAATAGATAAATACA-AA-ATAA
* * *
3927550 AAATAAA-AGAAAAATATATATATAA
1 AAATAAATAGATAAATACA-AAATAA
*
3927575 AAAAATAATA-ATAATATACAAAAT-A
1 AAATA-AATAGATAA-ATACAAAATAA
* *
3927600 AAATAAAAATATAAAATACAAAATAA
1 AAATAAATAGAT-AAATACAAAATAA
3927626 AAA
1 AAA
3927629 AAAAATGGGC
Statistics
Matches: 63, Mismatches: 9, Indels: 14
0.73 0.10 0.16
Matches are distributed among these distances:
24 3 0.05
25 25 0.40
26 30 0.48
27 5 0.08
ACGTcount: A:0.73, C:0.03, G:0.02, T:0.22
Consensus pattern (25 bp):
AAATAAATAGATAAATACAAAATAA
Found at i:3927574 original size:19 final size:17
Alignment explanation
Indices: 3927552--3927625 Score: 58
Period size: 19 Copynumber: 3.8 Consensus size: 17
3927542 TAAGATAAAA
3927552 ATAAAAGAAAAATATATAT
1 ATAAAA-AAAAATA-ATAT
3927571 ATAAAAAAATAATAATAAT
1 ATAAAAAAA-AATAAT-AT
*
3927590 ATACAAAATAAAATAAAAAT
1 ATA-AAAA-AAAAT-AATAT
3927610 ATAAAATACAAAATAA
1 ATAAAA-A-AAAATAA
3927626 AAAAAAAATG
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
18 5 0.11
19 20 0.43
20 18 0.38
21 4 0.09
ACGTcount: A:0.73, C:0.03, G:0.01, T:0.23
Consensus pattern (17 bp):
ATAAAAAAAAATAATAT
Found at i:3927626 original size:20 final size:18
Alignment explanation
Indices: 3927546--3927628 Score: 78
Period size: 20 Copynumber: 4.4 Consensus size: 18
3927536 AATACATAAG
*
3927546 ATAAAAATA-AAAGAAAA
1 ATAAAAATATAAAAAAAA
* *
3927563 ATATATATATAAAAAAATA
1 ATAAAAATATAAAAAAA-A
*
3927582 ATAATAATATACAAAATAAA
1 ATAAAAATATA-AAAA-AAA
3927602 ATAAAAATATAAAATACAAA
1 ATAAAAATATAAAA-A-AAA
3927622 ATAAAAA
1 ATAAAAA
3927629 AAAAATGGGC
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
17 7 0.13
18 6 0.11
19 12 0.23
20 26 0.49
21 2 0.04
ACGTcount: A:0.75, C:0.02, G:0.01, T:0.22
Consensus pattern (18 bp):
ATAAAAATATAAAAAAAA
Found at i:3927627 original size:12 final size:12
Alignment explanation
Indices: 3927584--3927627 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
3927574 AAAAAATAAT
*
3927584 AATAATATACAA
1 AATAAAATACAA
*
3927596 AATAAAATAAAA
1 AATAAAATACAA
3927608 ATATAAAATACAA
1 A-ATAAAATACAA
3927621 AATAAAA
1 AATAAAA
3927628 AAAAAATGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 17 0.61
13 11 0.39
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (12 bp):
AATAAAATACAA
Found at i:3927633 original size:25 final size:25
Alignment explanation
Indices: 3927517--3927634 Score: 105
Period size: 25 Copynumber: 4.6 Consensus size: 25
3927507 AAATAGTAAT
*
3927517 AATAAATAAATAAATAATAAATACATA
1 AATAAA-AAAAAAATAA-AAATACATA
* * *
3927544 AGATAAAAATAAAAGAAAAATATATA
1 A-ATAAAAAAAAAATAAAAATACATA
* *
3927570 TATAAAAAAATAATAATAATATACA-A
1 AATAAAAAAAAAATAA-AA-ATACATA
*
3927596 AATAAAATAAAAATATAAAATACA-A
1 AATAAAAAAAAAATA-AAAATACATA
3927621 AATAAAAAAAAAAT
1 AATAAAAAAAAAAT
3927635 GGGCTTACCC
Statistics
Matches: 74, Mismatches: 13, Indels: 10
0.76 0.13 0.10
Matches are distributed among these distances:
25 31 0.42
26 25 0.34
27 13 0.18
28 5 0.07
ACGTcount: A:0.74, C:0.03, G:0.02, T:0.22
Consensus pattern (25 bp):
AATAAAAAAAAAATAAAAATACATA
Found at i:3932193 original size:2 final size:2
Alignment explanation
Indices: 3932186--3932230 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
3932176 TCATGTGTTT
* * * *
3932186 TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TG TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3932228 TA T
1 TA T
3932231 TTATGTTATG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3933958 original size:15 final size:15
Alignment explanation
Indices: 3933938--3933971 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3933928 AAGAATTCCT
3933938 AATTTAAAAATAAAA
1 AATTTAAAAATAAAA
**
3933953 AATTTAAATTTAAAA
1 AATTTAAAAATAAAA
3933968 AATT
1 AATT
3933972 ACTGCATAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AATTTAAAAATAAAA
Found at i:3944172 original size:19 final size:18
Alignment explanation
Indices: 3944125--3944172 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
3944115 TATTGTTTTT
3944125 TATAATATATAATAATACA
1 TATAAT-TATAATAATACA
* *
3944144 TGATATTTATAATACTAACA
1 T-ATAATTATAATAAT-ACA
3944164 TATAATTAT
1 TATAATTAT
3944173 TTAATAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (18 bp):
TATAATTATAATAATACA
Found at i:3944516 original size:37 final size:37
Alignment explanation
Indices: 3944461--3944534 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
3944451 TGCATCTAGA
* *
3944461 ATAAATTTTATGTGTAATAATATTAAATAAATATATT
1 ATAAATTTTATATCTAATAATATTAAATAAATATATT
3944498 ATAAATTTTATATCTAATAATATTAAATAAATATATT
1 ATAAATTTTATATCTAATAATATTAAATAAATATATT
3944535 TTATGTTTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (37 bp):
ATAAATTTTATATCTAATAATATTAAATAAATATATT
Found at i:3944860 original size:40 final size:38
Alignment explanation
Indices: 3944777--3944860 Score: 89
Period size: 40 Copynumber: 2.2 Consensus size: 38
3944767 AAATTTTTAT
* * *
3944777 GTTTTTAACAAAAATTACATTTTTATCTTAAAAGTGTT
1 GTTTTTAACAAAAATCACATTTTTATATTAAAAGTGTC
* *
3944815 TTTTTTAACAAAAAATCACGTATTTTATATTAGAAA-TGTC
1 GTTTTTAAC-AAAAATCACAT-TTTTATATTA-AAAGTGTC
3944855 GTTTTT
1 GTTTTT
3944861 GTTTAATTCT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
38 8 0.22
39 9 0.24
40 17 0.46
41 3 0.08
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (38 bp):
GTTTTTAACAAAAATCACATTTTTATATTAAAAGTGTC
Found at i:3944922 original size:26 final size:25
Alignment explanation
Indices: 3944871--3944922 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
3944861 GTTTAATTCT
*
3944871 AAAAAATATTTTTTATGTTTTCAAC
1 AAAAAATATTTTTTATGTTTTAAAC
*
3944896 AAAAATTATTTTTTTAT-TTTATAAAC
1 AAAAAATA-TTTTTTATGTTT-TAAAC
3944922 A
1 A
3944923 TTATCTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (25 bp):
AAAAAATATTTTTTATGTTTTAAAC
Found at i:3944994 original size:110 final size:110
Alignment explanation
Indices: 3944733--3944994 Score: 293
Period size: 110 Copynumber: 2.4 Consensus size: 110
3944723 ATTTTCTACT
* * * * *
3944733 TTAGAAATGTCGTTTTT-ATGAATTTTGAAAAAAAAAATTTTTATGTTTTTAACAAAAATTACAT
1 TTAGAAATGTCGTTTTTGTTGAATTCTG-AAAAATAATTTTTTATGTTTTCAACAAAAATTACAT
* *
3944797 TTTTATCTTAAAAGTGTTTTTTTTAACAAAAAATCACGTATTTTATA
65 TTTTATCTTAAAAATGTTCTTTTTAACAAAAAAT-ACGTATTTTATA
* * **
3944844 TTAGAAATGTCGTTTTTGTTTAATTCTAAAAAAT-ATTTTTTATGTTTTCAACAAAAATTATTTT
1 TTAGAAATGTCGTTTTTGTTGAATTCTGAAAAATAATTTTTTATGTTTTCAACAAAAATTACATT
* * *
3944908 TTTATTTTATAAACAT-TATCTTTTTAAC-AAAGAT-TGTATTTTTATA
66 TTTATCTTA-AAA-ATGT-TCTTTTTAACAAAAAATACGTA-TTTTATA
*
3944954 TTA-AAATGTCATTTTTGTTGAATTCTGAAAAATAATTTTTT
1 TTAGAAATGTCGTTTTTGTTGAATTCTGAAAAATAATTTTTT
3944995 TTCATGTTTT
Statistics
Matches: 128, Mismatches: 17, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
109 30 0.23
110 51 0.40
111 31 0.24
112 16 0.12
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.50
Consensus pattern (110 bp):
TTAGAAATGTCGTTTTTGTTGAATTCTGAAAAATAATTTTTTATGTTTTCAACAAAAATTACATT
TTTATCTTAAAAATGTTCTTTTTAACAAAAAATACGTATTTTATA
Found at i:3945163 original size:24 final size:25
Alignment explanation
Indices: 3945130--3945179 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
3945120 ACATAATATT
3945130 TTTTAAAATATATTA-AAAAAATTA
1 TTTTAAAATATATTATAAAAAATTA
* *
3945154 TTTTATAATATTTTATTAAAAAATTA
1 TTTTAAAATATATTA-TAAAAAATTA
3945180 CTACATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 13 0.59
26 9 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
TTTTAAAATATATTATAAAAAATTA
Found at i:3947336 original size:7 final size:7
Alignment explanation
Indices: 3947321--3947369 Score: 53
Period size: 7 Copynumber: 6.4 Consensus size: 7
3947311 AAGGTACGGT
3947321 TTTTTTA
1 TTTTTTA
*
3947328 TTTTCTA
1 TTTTTTA
3947335 TTTTTTA
1 TTTTTTA
3947342 TTTTTATA
1 TTTTT-TA
3947350 TTATATTTA
1 TT-T-TTTA
3947359 TTTTTATA
1 TTTTT-TA
3947367 TTT
1 TTT
3947370 ATATTTAACT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
7 19 0.53
8 10 0.28
9 5 0.14
10 2 0.06
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTTTA
Found at i:3947358 original size:17 final size:18
Alignment explanation
Indices: 3947338--3947376 Score: 71
Period size: 17 Copynumber: 2.2 Consensus size: 18
3947328 TTTTCTATTT
3947338 TTTATTTTTATA-TTATA
1 TTTATTTTTATATTTATA
3947355 TTTATTTTTATATTTATA
1 TTTATTTTTATATTTATA
3947373 TTTA
1 TTTA
3947377 ACTGATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTTTATATTTATA
Found at i:3947367 original size:12 final size:12
Alignment explanation
Indices: 3947322--3947399 Score: 54
Period size: 12 Copynumber: 6.4 Consensus size: 12
3947312 AGGTACGGTT
*
3947322 TTTTTATTTTCTA
1 TTTTTATATT-TA
3947335 TTTTT-TATTT-
1 TTTTTATATTTA
3947345 TTATATTATATTTA
1 TT-T-TTATATTTA
3947359 TTTTTATATTTA
1 TTTTTATATTTA
* * *
3947371 TATTTA-ACTGA
1 TTTTTATATTTA
*
3947382 TATTTTAAATTTA
1 T-TTTTATATTTA
3947395 TTTTT
1 TTTTT
3947400 GTTTTCATCG
Statistics
Matches: 52, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
10 2 0.04
11 6 0.12
12 27 0.52
13 15 0.29
14 2 0.04
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.71
Consensus pattern (12 bp):
TTTTTATATTTA
Found at i:3948842 original size:25 final size:25
Alignment explanation
Indices: 3948808--3948857 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
3948798 ATCATGCCCT
3948808 TCCCTTCATTAATATTTGGAACTAC
1 TCCCTTCATTAATATTTGGAACTAC
*
3948833 TCCCTTCATTAATTTTTGGAACTAC
1 TCCCTTCATTAATATTTGGAACTAC
3948858 ATAGGAGTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.24, G:0.08, T:0.42
Consensus pattern (25 bp):
TCCCTTCATTAATATTTGGAACTAC
Found at i:3956252 original size:12 final size:12
Alignment explanation
Indices: 3956235--3956270 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
3956225 ACAGGGGAAA
3956235 GTAGTATCAGAG
1 GTAGTATCAGAG
3956247 GTAGTATCAGAG
1 GTAGTATCAGAG
*
3956259 GTAGCATCAGAG
1 GTAGTATCAGAG
3956271 TGATTGGCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.33, C:0.11, G:0.33, T:0.22
Consensus pattern (12 bp):
GTAGTATCAGAG
Found at i:3956357 original size:3 final size:3
Alignment explanation
Indices: 3956349--3956375 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3956339 GAAAGAACAT
3956349 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
3956376 ACAAGTACAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:3957672 original size:18 final size:18
Alignment explanation
Indices: 3957649--3957685 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3957639 ACAATCAAAT
**
3957649 TAATTAATTCCTTAAAAA
1 TAATTAATTAATTAAAAA
3957667 TAATTAATTAATTAAAAA
1 TAATTAATTAATTAAAAA
3957685 T
1 T
3957686 TTTATTAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (18 bp):
TAATTAATTAATTAAAAA
Found at i:3957828 original size:25 final size:25
Alignment explanation
Indices: 3957777--3957822 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
3957767 TAACATGATT
*
3957777 ATTATTATTATTAATTTAATATAAA
1 ATTATTATTATTAATATAATATAAA
3957802 ATTATTATTA-TAA-ATAATATA
1 ATTATTATTATTAATATAATATA
3957823 TTAAATAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 3 0.15
25 10 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
ATTATTATTATTAATATAATATAAA
Found at i:3959801 original size:12 final size:12
Alignment explanation
Indices: 3959784--3959821 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3959774 ATTATAAAAT
3959784 TTTAAATTTTAA
1 TTTAAATTTTAA
3959796 TTTAAA-TTTAA
1 TTTAAATTTTAA
* *
3959807 ATTAAATTTTTA
1 TTTAAATTTTAA
3959819 TTT
1 TTT
3959822 CATTTGAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TTTAAATTTTAA
Found at i:3959925 original size:31 final size:32
Alignment explanation
Indices: 3959888--3959962 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 32
3959878 ATTTTAAATG
* *
3959888 TTTTAATTTTTTATAT-TATTTTAATATAAAA
1 TTTTAATTTTTTAAATAAATTTTAATATAAAA
* *
3959919 TTTTAATATATTTAAATAAATTTTGATATAAAA
1 TTTTAAT-TTTTTAAATAAATTTTAATATAAAA
3959952 TTATT-ATTTTT
1 TT-TTAATTTTT
3959963 ATTTTATAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
31 7 0.19
32 10 0.28
33 17 0.47
34 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (32 bp):
TTTTAATTTTTTAAATAAATTTTAATATAAAA
Found at i:3959997 original size:18 final size:19
Alignment explanation
Indices: 3959967--3960008 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
3959957 ATTTTTATTT
3959967 TATAAAAATTTAAAATATA
1 TATAAAAATTTAAAATATA
*
3959986 TATAAAAA-TTAAAGTATA
1 TATAAAAATTTAAAATATA
3960004 TATAA
1 TATAA
3960009 TTAAATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
TATAAAAATTTAAAATATA
Found at i:3960497 original size:13 final size:13
Alignment explanation
Indices: 3960460--3960489 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
3960450 TAGAATCTCT
3960460 TTTATCAAAATAA
1 TTTATCAAAATAA
3960473 TTTATCAAAATAA
1 TTTATCAAAATAA
3960486 TTTA
1 TTTA
3960490 ATAAAATAGG
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:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTATCAAAATAA
Found at i:3969963 original size:16 final size:17
Alignment explanation
Indices: 3969927--3969968 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
3969917 AATTAATTTG
*
3969927 TTATTTCTATCAATCAAA
1 TTATTT-TATCAATAAAA
3969945 TTATTTTAT-AATAAAA
1 TTATTTTATCAATAAAA
*
3969961 TTAATTTA
1 TTATTTTA
3969969 ATTAAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 13 0.59
17 3 0.14
18 6 0.27
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (17 bp):
TTATTTTATCAATAAAA
Found at i:3970517 original size:15 final size:15
Alignment explanation
Indices: 3970497--3970542 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
3970487 CCAAATTGAG
3970497 TTTAAAATAATAATT
1 TTTAAAATAATAATT
**
3970512 TTTAAAAT-ATAAAA
1 TTTAAAATAATAATT
3970526 TTTAAAATAATAATT
1 TTTAAAATAATAATT
3970541 TT
1 TT
3970543 ATTAATATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TTTAAAATAATAATT
Found at i:3970529 original size:14 final size:14
Alignment explanation
Indices: 3970497--3970568 Score: 56
Period size: 15 Copynumber: 4.9 Consensus size: 14
3970487 CCAAATTGAG
**
3970497 TTTAAAATAATAATT
1 TTTAAAAT-ATAAAA
3970512 TTTAAAATATAAAA
1 TTTAAAATATAAAA
*
3970526 TTTAAAATA-ATAAT
1 TTTAAAATATA-AAA
* *
3970540 TTTATTAATATAATA
1 TTTA-AAATATAAAA
3970555 TTTATAAATATAAA
1 TTTA-AAATATAAA
3970569 TTAAATTAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
13 1 0.02
14 19 0.41
15 25 0.54
16 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTTAAAATATAAAA
Found at i:3970530 original size:29 final size:29
Alignment explanation
Indices: 3970497--3970564 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
3970487 CCAAATTGAG
3970497 TTTAAAATAATAATTTT-TAAAATATAAAA
1 TTTAAAATAATAATTTTAT-AAATATAAAA
* *
3970526 TTTAAAATAATAATTTTATTAATATAATA
1 TTTAAAATAATAATTTTATAAATATAAAA
3970555 TTTATAAATA
1 TTTA-AAATA
3970565 TAAATTAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
29 29 0.83
30 6 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
TTTAAAATAATAATTTTATAAATATAAAA
Found at i:3972542 original size:6 final size:6
Alignment explanation
Indices: 3972533--3972557 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3972523 CTAATCCTGA
3972533 TTCCAG TTCCAG TTCCAG TTCCAG T
1 TTCCAG TTCCAG TTCCAG TTCCAG T
3972558 CAGTTTCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (6 bp):
TTCCAG
Found at i:3979855 original size:59 final size:58
Alignment explanation
Indices: 3979784--3979897 Score: 183
Period size: 59 Copynumber: 1.9 Consensus size: 58
3979774 TTCTTATTTG
*
3979784 CAAAATGTTATTAGTGGCTAACAAATTCCGAATAGGTATTGTGTCAAAACAAAGAGATA
1 CAAAATGTTATTAGTGGCTAACAAATTCCGAAAAGGTA-TGTGTCAAAACAAAGAGATA
* **
3979843 CAAAATGTTATTAGTGGCTAACAAATTCCGAAAAGTTATGTGTCGGAACAAAGAG
1 CAAAATGTTATTAGTGGCTAACAAATTCCGAAAAGGTATGTGTCAAAACAAAGAG
3979898 TGGCTTTGTT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
58 15 0.29
59 36 0.71
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.26
Consensus pattern (58 bp):
CAAAATGTTATTAGTGGCTAACAAATTCCGAAAAGGTATGTGTCAAAACAAAGAGATA
Found at i:3987747 original size:166 final size:165
Alignment explanation
Indices: 3987555--3987878 Score: 481
Period size: 166 Copynumber: 2.0 Consensus size: 165
3987545 AACAATTATG
** *
3987555 TTATTTTTAAATTTGATTTGAATAAAAAATTATAAAATAGTCATTACTATTTTGAAAAGTATA-T
1 TTATTTTTAAATTTGACCTAAATAAAAAATTATAAAATAGTCATTACTATTTTGAAAA-TATAGT
* *
3987619 TTAAAAATGATTACAAATCAGTTATAGATTTTTACTACATAAAAAAATTAAACA-GAATTATTTA
65 TTAAAAATAACTACAAATCAGTTATAGATTTTTACTACAT-AAAAAATTAAACATG-ATTATTTA
* *
3987683 AGGCATTTTTAGTCAAAAAATGCTTTAAATTATATACA
128 AGGCATTTTTAGTCAAAAAATACCTTAAATTATATACA
*
3987721 TTATTTTTAAATTTGACCTAAATAAAAAATTATGAAATAGTCATTACTATTTTGAAAATATATGT
1 TTATTTTTAAATTTGACCTAAATAAAAAATTATAAAATAGTCATTACTATTTTGAAAATATA-GT
* * * *
3987786 TTAGAAATAACTACAAATCAGTTATAGATTTTTGCTACCTAAAAAATTGAACATGATTATTTAAG
65 TTAAAAATAACTACAAATCAGTTATAGATTTTTACTACATAAAAAATTAAACATGATTATTTAAG
*
3987851 GCATTTTTAGTCAGAAAATACCTTAAAT
130 GCATTTTTAGTCAAAAAATACCTTAAAT
3987879 AATCTCCTAA
Statistics
Matches: 142, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
165 4 0.03
166 101 0.71
167 37 0.26
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.39
Consensus pattern (165 bp):
TTATTTTTAAATTTGACCTAAATAAAAAATTATAAAATAGTCATTACTATTTTGAAAATATAGTT
TAAAAATAACTACAAATCAGTTATAGATTTTTACTACATAAAAAATTAAACATGATTATTTAAGG
CATTTTTAGTCAAAAAATACCTTAAATTATATACA
Found at i:3987953 original size:61 final size:61
Alignment explanation
Indices: 3987823--3987952 Score: 156
Period size: 61 Copynumber: 2.1 Consensus size: 61
3987813 ATTTTTGCTA
** * * * *
3987823 CCTAAAAAATTGAACATGATTATTTAAGGCATTTTTAGTCAGAAAATACCTTAAATAATCT
1 CCTAAAAAATTGAACAACATCATTTAAAGCATTTTTAATCAGAAAACACCTTAAATAATCT
* *
3987884 CCTAAAAAATTGATCAACATCATTTAAAGCATTTTCTAATTAG-AAACACCTTAAATAATCT
1 CCTAAAAAATTGAACAACATCATTTAAAGCATTTT-TAATCAGAAAACACCTTAAATAATCT
*
3987945 -TTAAAAAA
1 CCTAAAAAA
3987953 AAGTAAATAA
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
60 7 0.12
61 47 0.80
62 5 0.08
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (61 bp):
CCTAAAAAATTGAACAACATCATTTAAAGCATTTTTAATCAGAAAACACCTTAAATAATCT
Found at i:3988747 original size:161 final size:161
Alignment explanation
Indices: 3988436--3988728 Score: 376
Period size: 161 Copynumber: 1.8 Consensus size: 161
3988426 TTTTAGATAC
** * *
3988436 TATTTAAGGTATTTTTAACCAAAAACATTTTAAATAATCTCTTTTTAAAAAATATTAAAGATTAT
1 TATTTAAGGTATTTTTAACCAAAAACAACTTAAATAATCTCATTTAAAAAAATATTAAAGATTAT
** * ** *
3988501 TTAAGGCGTTTTTTACAAAAAAAACATCTTAAATAATCTTTTTTATTTTTTTAAAAGGAATTATT
66 TTAAAACGTATTGGAC-AAAAAAACATCTTAAATAATCTTTTATATTTTTTTAAAAGGAATTATT
3988566 TAAATAATATGCTTTAAAAAATTAAAGAGTAT
130 TAAATAATATGCTTTAAAAAATTAAAGAGTAT
* * * *
3988598 TATTTAAGGTATTTTTTA-TAAAAATAACTTAAATAATCTCATTTAAAAAAATATTAGAGATTAT
1 TATTTAAGGTATTTTTAACCAAAAACAACTTAAATAATCTCATTTAAAAAAATATTAAAGATTAT
* * * *
3988662 TTAAAATGTATTGGAC-AAAAAACGTCTTAAATAATCATTTTATA-TTTTTTAAATGGCATTTAT
66 TTAAAACGTATTGGACAAAAAAACATCTTAAATAATC-TTTTATATTTTTTTAAAAGG-AATTAT
3988725 TTAA
129 TTAA
3988729 GAAATTTTTA
Statistics
Matches: 111, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
159 30 0.27
160 15 0.14
161 49 0.44
162 17 0.15
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.43
Consensus pattern (161 bp):
TATTTAAGGTATTTTTAACCAAAAACAACTTAAATAATCTCATTTAAAAAAATATTAAAGATTAT
TTAAAACGTATTGGACAAAAAAACATCTTAAATAATCTTTTATATTTTTTTAAAAGGAATTATTT
AAATAATATGCTTTAAAAAATTAAAGAGTAT
Found at i:3990205 original size:27 final size:27
Alignment explanation
Indices: 3990174--3990265 Score: 67
Period size: 27 Copynumber: 3.2 Consensus size: 27
3990164 AATTTCGAGG
3990174 AAAATTGATACTTTCAACTTTTTCTCA
1 AAAATTGATACTTTCAACTTTTTCTCA
* ** * * *
3990201 AAAATTTATTTTTTTAAACATTTATTTTTAA
1 AAAATTGA-TACTTTCAAC--TT-TTTCTCA
*
3990232 GGAAAATTGATACTTTCAACTTTTTCCCA
1 --AAAATTGATACTTTCAACTTTTTCTCA
3990261 AAAAT
1 AAAAT
3990266 ATTTTTTGGA
Statistics
Matches: 46, Mismatches: 13, Indels: 12
0.65 0.18 0.17
Matches are distributed among these distances:
27 12 0.26
28 7 0.15
29 4 0.09
30 4 0.09
31 5 0.11
32 7 0.15
33 7 0.15
ACGTcount: A:0.37, C:0.13, G:0.04, T:0.46
Consensus pattern (27 bp):
AAAATTGATACTTTCAACTTTTTCTCA
Found at i:3990250 original size:118 final size:118
Alignment explanation
Indices: 3990114--3990391 Score: 427
Period size: 118 Copynumber: 2.3 Consensus size: 118
3990104 TTTTGTGCAG
*
3990114 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTCTTTT-GAAACTTT-AATTTCGAGGAAA
1 GAAAAATTGATACTTTCAACTTTTTCCCAAAAATATT-TTTTGGAAACTTTGAATTTCGAGGAAA
** * *
3990177 ATTGATACTTTCAACTTTTT-CTCAAAAATTTATTTTTTTAAACATTTATTTTTAA
65 ATTGATACTTTCAA-TTTTTCCTCAAAAA-GAACTTTTTTAAAAATTTATTTTTAA
* *
3990232 GGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGGAAACTTTGATTTTCGAGGAAAA
1 GAAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGGAAACTTTGAATTTCGAGGAAAA
3990297 TTGATACTTTCAATTTTTCCTCAAAAAGAACTTTTTTAAAAATTTATTTTTAA
66 TTGATACTTTCAATTTTTCCTCAAAAAGAACTTTTTTAAAAATTTATTTTTAA
*
3990350 GAAAAATTGATACTTTCAACTTTTTCTCAAAAATATATTTTT
1 GAAAAATTGATACTTTCAACTTTTTCCCAAAAATAT-TTTTT
3990392 TTAGGTTTTA
Statistics
Matches: 147, Mismatches: 9, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
117 4 0.03
118 104 0.71
119 39 0.27
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (118 bp):
GAAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGGAAACTTTGAATTTCGAGGAAAA
TTGATACTTTCAATTTTTCCTCAAAAAGAACTTTTTTAAAAATTTATTTTTAA
Found at i:3990301 original size:59 final size:57
Alignment explanation
Indices: 3990116--3990391 Score: 338
Period size: 59 Copynumber: 4.7 Consensus size: 57
3990106 TTGTGCAGGA
* * *
3990116 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTCTTTTGAAACTTTAATTTCGAGG
1 AAAATTGATACTTTCAACTTTTTCCCAAAAATATT-TTTTGAAACTTTATTTTCAAGG
* * *
3990174 AAAATTGATACTTTCAACTTTTTCTCAAAAATTTATTTTTTTAAACATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTTCCCAAAAA--TATTTTTTGAAAC-TTTATTTTCAAGG
*
3990234 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGGAAACTTTGATTTTCGAGG
1 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTT-GAAACTTT-ATTTTCAAGG
* * * * *
3990293 AAAATTGATACTTTCAA-TTTTTCCTCAAAAAGAACTTTTTTAAAAATTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTTCC-CAAAAA-TA-TTTTTTGAAACTTTATTTTCAAGG
*
3990352 AAAATTGATACTTTCAACTTTTTCTCAAAAATATATTTTT
1 AAAATTGATACTTTCAACTTTTTCCCAAAAATAT-TTTTT
3990392 TTAGGTTTTA
Statistics
Matches: 190, Mismatches: 18, Indels: 20
0.83 0.08 0.09
Matches are distributed among these distances:
57 1 0.01
58 53 0.28
59 73 0.38
60 57 0.30
61 6 0.03
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.45
Consensus pattern (57 bp):
AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGAAACTTTATTTTCAAGG
Found at i:3990442 original size:17 final size:16
Alignment explanation
Indices: 3990421--3990485 Score: 62
Period size: 17 Copynumber: 4.0 Consensus size: 16
3990411 AATAAAATAA
3990421 TAAAACAAAATAAAAG
1 TAAAACAAAATAAAAG
*
3990437 TGAAAA-TAAA-AAAAG
1 T-AAAACAAAATAAAAG
*
3990452 TAAAACAAAAATAAAAA
1 TAAAAC-AAAATAAAAG
*
3990469 TAAAATAAAGATAAAAG
1 TAAAACAAA-ATAAAAG
3990486 AACATTAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
14 4 0.10
15 6 0.15
16 10 0.26
17 19 0.49
ACGTcount: A:0.75, C:0.03, G:0.08, T:0.14
Consensus pattern (16 bp):
TAAAACAAAATAAAAG
Found at i:3990456 original size:6 final size:5
Alignment explanation
Indices: 3990409--3990484 Score: 59
Period size: 5 Copynumber: 14.8 Consensus size: 5
3990399 TTATTTAAAG
* * *
3990409 AAAAT AAAAT --AAT AAAAC AAAAT AAAAGT GAAAAT AAAA- AAAGT AAAACA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T -AAAAT AAAAT AAAAT AAAA-T
3990459 AAAAT AAAAAT AAAAT AAAGAT AAAA
1 AAAAT -AAAAT AAAAT AAA-AT AAAA
3990485 GAACATTAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 16
0.72 0.08 0.20
Matches are distributed among these distances:
3 3 0.05
4 3 0.05
5 31 0.54
6 16 0.28
7 4 0.07
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.14
Consensus pattern (5 bp):
AAAAT
Found at i:3990459 original size:31 final size:31
Alignment explanation
Indices: 3990408--3990477 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
3990398 TTTATTTAAA
* *
3990408 GAAAATAAAATAATAAAAC-AAAATAAAAGT
1 GAAAATAAAAAAATAAAACAAAAATAAAAAT
3990438 GAAAATAAAAAAAGTAAAACAAAAATAAAAAT
1 GAAAATAAAAAAA-TAAAACAAAAATAAAAAT
3990470 -AAAATAAA
1 GAAAATAAA
3990478 GATAAAAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
30 12 0.33
31 14 0.39
32 10 0.28
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.14
Consensus pattern (31 bp):
GAAAATAAAAAAATAAAACAAAAATAAAAAT
Found at i:3990482 original size:11 final size:11
Alignment explanation
Indices: 3990409--3990484 Score: 59
Period size: 11 Copynumber: 6.8 Consensus size: 11
3990399 TTATTTAAAG
3990409 AAAATAAAATAA
1 AAAATAAAAT-A
*
3990421 TAAAACAAAATA
1 -AAAATAAAATA
*
3990433 AAAGTGAAAAT-
1 AAAAT-AAAATA
*
3990444 AAAA-AAAGTA
1 AAAATAAAATA
3990454 AAACA-AAAATA
1 AAA-ATAAAATA
3990465 AAAATAAAATA
1 AAAATAAAATA
*
3990476 AAGATAAAA
1 AAAATAAAA
3990485 GAACATTAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
9 4 0.08
10 4 0.08
11 29 0.56
12 6 0.12
13 9 0.17
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.14
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:3990516 original size:4 final size:4
Alignment explanation
Indices: 3990507--3990546 Score: 55
Period size: 4 Copynumber: 10.0 Consensus size: 4
3990497 ATCCTAATTT
*
3990507 AATA AATAA AATA AA-A AACA AATA AATA AATA AATA AATA
1 AATA AAT-A AATA AATA AATA AATA AATA AATA AATA AATA
3990547 TAAAAAGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
3 3 0.09
4 26 0.79
5 4 0.12
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.20
Consensus pattern (4 bp):
AATA
Found at i:3991431 original size:20 final size:21
Alignment explanation
Indices: 3991375--3991459 Score: 63
Period size: 20 Copynumber: 4.0 Consensus size: 21
3991365 AATTTCCAGC
3991375 CAGATAAATCAAAAAAATAAA-
1 CAGATAAAT-AAAAAAATAAAT
3991396 -A-A-AAATTAAACGAAAATAAAT
1 CAGATAAA-TAAA--AAAATAAAT
*
3991417 CAGATAAATAAAAAAATTAA-
1 CAGATAAATAAAAAAATAAAT
3991437 CAGATAAATTAAAATTAAATAAA
1 CAGATAAA-TAAAA--AAATAAA
3991460 AGATAATACA
Statistics
Matches: 52, Mismatches: 2, Indels: 18
0.72 0.03 0.25
Matches are distributed among these distances:
18 6 0.12
19 2 0.04
20 17 0.33
21 12 0.23
22 1 0.02
23 11 0.21
24 3 0.06
ACGTcount: A:0.69, C:0.06, G:0.05, T:0.20
Consensus pattern (21 bp):
CAGATAAATAAAAAAATAAAT
Done.