Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 367 of 378
Found at i:109953397 original size:84 final size:86
Alignment explanation
Indices: 109953250--109953421 Score: 249
Period size: 84 Copynumber: 2.0 Consensus size: 86
109953240 TTGAGGTATT
* * *
109953250 TTCAATTTCTGCTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACG
1 TTCAATTTATGCTTTTCAAGAAAATCAACTCATATTACGAAAGGTGAGTTGAGCCTCAAGACACG
* *
109953315 TTGAGGTATTTTCAATTCCTG
66 CTGAGGTAATTTCAATTCCTG
* * *
109953336 TTCAATTTATGTTTTTC-A-AAAATTAACTCATATTACGAAAGGTGAGTTGAGCCTCAGGACACG
1 TTCAATTTATGCTTTTCAAGAAAATCAACTCATATTACGAAAGGTGAGTTGAGCCTCAAGACACG
*
109953399 CTGAGGTAATTTCAATTTCTG
66 CTGAGGTAATTTCAATTCCTG
109953420 TT
1 TT
109953422 TCTCAAAAAT
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
84 61 0.79
85 1 0.01
86 15 0.19
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (86 bp):
TTCAATTTATGCTTTTCAAGAAAATCAACTCATATTACGAAAGGTGAGTTGAGCCTCAAGACACG
CTGAGGTAATTTCAATTCCTG
Found at i:109953428 original size:73 final size:73
Alignment explanation
Indices: 109953336--109953767 Score: 522
Period size: 73 Copynumber: 5.7 Consensus size: 73
109953326 TCAATTCCTG
* * * *
109953336 TTCAATTTATGTTTTTCAAAAATTAACTCATATTACGAAAGGTGAGTTGAGCCTCAGGACACGCT
1 TTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
*
109953401 GAGGTAAT
66 GAGGTATT
* * * *
109953409 TTCAATTTCTGTTTCTCAAAAATCAACTCATATTGCGAGAGGTTAGTTGAGCCTCAAGACACGCC
1 TTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
109953474 GAGGTATT
66 GAGGTATT
* ** * *
109953482 TTCAATTTCTATTTTTTCAAAAAGATCAACTCACGTTGCGAGAGGTAAGTTGAGCCTCGGGTCAC
1 TTCAATTTCT-GTTTTTC-AAAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--AC
**
109953547 ACGCCAAGGTATT
61 ACGCTGAGGTATT
**
109953560 TTCAATTTCTGTTTTTTCAAAAAGATCAACTCACGTTGCGAGAGGTGAGTTGAGCCTCAGGACAC
1 TTCAATTTCTG-TTTTTC-AAAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
*
109953625 GCTGAGGTAAT
63 GCTGAGGTATT
* * * *
109953636 TTCAATTTCTGTTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGGCACACT
1 TTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
109953701 GAGGTATT
66 GAGGTATT
* *
109953709 TTCAATTAATGTTTTTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 TTC----AAT-TTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
109953768 TAGCTCACGT
Statistics
Matches: 315, Mismatches: 33, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
73 122 0.39
74 9 0.03
75 10 0.03
76 55 0.17
77 3 0.01
78 116 0.37
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (73 bp):
TTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
GAGGTATT
Found at i:109953848 original size:227 final size:225
Alignment explanation
Indices: 109953181--109953848 Score: 657
Period size: 227 Copynumber: 2.9 Consensus size: 225
109953171 TGATGTTTTT
** *
109953181 ATTTCTGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGGCACATTGAGG
1 ATTTCTGTTTCTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGGCACACTGAGG
* **
109953246 TATTTTC---AATTTCTGCTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
66 TATTTTCAATAATTTTTTTTTTTCAA-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-A
* * * *
109953308 AGACACGT--TGAGGTATTTTCAATTCCTGTTCAATTTATGTTTTTCAAAAATTAACTCATATTA
129 AGTCACGTGCTGAGGTA-TTTC--TT-C--TT-AATTTCTATTTTTC-AAAA--AACTCATATTG
109953371 CGA-AAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCA
184 CGAGAA-GTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCA
* * * * *
109953413 ATTTCTGTTTCTCAAAAATCAACTCATATTGCGAGAGGTTAGTTGAGCCTCAAGACACGCCGAGG
1 ATTTCTGTTTCTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGGCACACTGAGG
* * ** * *
109953478 TATTTTCAAT--TTCTATTTTTTCAAAAAGATCAACTCACGTTGCGAGAGGTAAGTTGAGCCTCG
66 TATTTTCAATAATTTTTTTTTTTCAAAAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-A
* ** ** *
109953541 GGTCACACGCCAAGGTA-TT-TTC--AATTTCTGTTTTTTCAAAAAGA-TCAACTCACGTTGCGA
129 AGTCACGTGCTGAGGTATTTCTTCTTAATTTCT-ATTTTTCAAAAA-ACTC-A-T-A--TTGCGA
*
109953601 GAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCA
187 GAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCA
* * *
109953640 ATTTCTGTTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGGCACACTGAGG
1 ATTTCTGTTTCTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGGCACACTGAGG
*
109953705 TATTTTCAATTAATGTTTTTTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT
66 TATTTTCAA-TAAT-TTTTTTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTA
* * * *
109953769 AGCTCACGTGCTGAGCTATTTCTGTCTTAATGTCTATTTTT-AAAAAACTTCATATTGTGAGAAA
129 AG-TCACGTGCTGAGGTATTTCT-TCTTAATTTCTATTTTTCAAAAAAC-TCATATTGCGAGAAG
109953833 TGAGTTGAG-CTCAGGA
191 TGAGTTGAGCCTCAGGA
109953849 TCACAGGCCG
Statistics
Matches: 358, Mismatches: 52, Indels: 57
0.77 0.11 0.12
Matches are distributed among these distances:
222 3 0.01
223 2 0.01
224 11 0.03
225 7 0.02
227 114 0.32
228 19 0.05
229 41 0.11
230 10 0.03
231 12 0.03
232 75 0.21
233 53 0.15
234 6 0.02
235 5 0.01
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (225 bp):
ATTTCTGTTTCTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGGCACACTGAGG
TATTTTCAATAATTTTTTTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAAG
TCACGTGCTGAGGTATTTCTTCTTAATTTCTATTTTTCAAAAAACTCATATTGCGAGAAGTGAGT
TGAGCCTCAGGACACGCTGAGGTAATTTCA
Found at i:109956123 original size:38 final size:37
Alignment explanation
Indices: 109956073--109956165 Score: 100
Period size: 37 Copynumber: 2.5 Consensus size: 37
109956063 ATATATGTAA
* *
109956073 ATATTATGTATATAT-TTTTAAATACTATATT-GTAT
1 ATATTATATATATATATTTTTAATACTATATTAGTAT
* * *
109956108 ATGTATATATATATATATTCTTAGTACTATATTACGTAT
1 ATAT-TATATATATATATTTTTAATACTATATTA-GTAT
*
109956147 ATATTATGTATATATATTT
1 ATATTATATATATATATTT
109956166 ATTTTTACCC
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
35 3 0.07
36 10 0.22
37 13 0.28
38 13 0.28
39 7 0.15
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.53
Consensus pattern (37 bp):
ATATTATATATATATATTTTTAATACTATATTAGTAT
Found at i:109957070 original size:109 final size:108
Alignment explanation
Indices: 109956938--109957149 Score: 370
Period size: 109 Copynumber: 2.0 Consensus size: 108
109956928 GGATCGGTGG
*
109956938 CGACTCCCTGTTTATTTCAAAATCAAACGTCAAATTTCAAACTTTTTTCCATAAATCGCCACAAT
1 CGACTCCCTGTTTATTTCAAAATCAAACGTCAAATTTCAAACTTTTTTCCATAAATCACCACAAT
*
109957003 TAGTGACCAAGCTACGCTAAAATTTTTACGTCACTACAGCTGC
66 TAGCGACCAAGCTACGCTAAAATTTTTACGTCACTACAGCTGC
*
109957046 CGACTCCACTGTTTGTTTCAAAATCAAACGTCAAATTTCAAACTTTTTTCCATAAATCACCACAA
1 CGACTCC-CTGTTTATTTCAAAATCAAACGTCAAATTTCAAACTTTTTTCCATAAATCACCACAA
* *
109957111 TTAGCGACCAAGCTACGCTAAATTTTTTACGTCGCTACA
65 TTAGCGACCAAGCTACGCTAAAATTTTTACGTCACTACA
109957150 CAAACAATCC
Statistics
Matches: 98, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
108 7 0.07
109 91 0.93
ACGTcount: A:0.33, C:0.26, G:0.10, T:0.32
Consensus pattern (108 bp):
CGACTCCCTGTTTATTTCAAAATCAAACGTCAAATTTCAAACTTTTTTCCATAAATCACCACAAT
TAGCGACCAAGCTACGCTAAAATTTTTACGTCACTACAGCTGC
Found at i:109958134 original size:22 final size:22
Alignment explanation
Indices: 109958109--109958152 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
109958099 TCCGCCAAAG
109958109 TTAAATAAGTGTGGTCAAGCCA
1 TTAAATAAGTGTGGTCAAGCCA
109958131 TTAAATAAGTGTGGTCAAGCCA
1 TTAAATAAGTGTGGTCAAGCCA
109958153 CCAGAATTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (22 bp):
TTAAATAAGTGTGGTCAAGCCA
Found at i:109961915 original size:2 final size:2
Alignment explanation
Indices: 109961908--109961944 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
109961898 GGTTCCATTG
109961908 AT 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 AT A
109961945 ACTAGGACCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:109963386 original size:4 final size:4
Alignment explanation
Indices: 109963377--109963432 Score: 58
Period size: 4 Copynumber: 14.0 Consensus size: 4
109963367 TAGGTAGCAT
* * * * *
109963377 CATA CATA CATG CTTA CGTA CATA CATA CATA CATA CATG CATG CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
109963425 TATA CATA
1 CATA CATA
109963433 TATATATGTA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.41, C:0.23, G:0.07, T:0.29
Consensus pattern (4 bp):
CATA
Found at i:109963414 original size:16 final size:16
Alignment explanation
Indices: 109963373--109963432 Score: 68
Period size: 16 Copynumber: 3.8 Consensus size: 16
109963363 AGATTAGGTA
109963373 GCAT-CATACATACAT
1 GCATACATACATACAT
* *
109963388 GCTTACGTACATACAT
1 GCATACATACATACAT
* *
109963404 ACATACATACATGCAT
1 GCATACATACATACAT
*
109963420 GCATATATACATA
1 GCATACATACATA
109963433 TATATATGTA
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
15 3 0.09
16 32 0.91
ACGTcount: A:0.40, C:0.23, G:0.08, T:0.28
Consensus pattern (16 bp):
GCATACATACATACAT
Found at i:109967108 original size:19 final size:17
Alignment explanation
Indices: 109967076--109967119 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
109967066 ATAAATATTT
109967076 TTAAAATAAAATAATAA
1 TTAAAATAAAATAATAA
109967093 TTAATAATAAATATAATAA
1 TTAA-AATAAA-ATAATAA
*
109967112 TTTAAATA
1 TTAAAATA
109967120 TGTTTTAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 10 0.42
19 10 0.42
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAAAATAAAATAATAA
Found at i:109969497 original size:53 final size:53
Alignment explanation
Indices: 109969437--109969545 Score: 218
Period size: 53 Copynumber: 2.1 Consensus size: 53
109969427 TTACGTCTTA
109969437 TTGCTCTTTGCAATGTTCTCTATAAAATTGTAGCCAAAGTTCTTGCCAATAGG
1 TTGCTCTTTGCAATGTTCTCTATAAAATTGTAGCCAAAGTTCTTGCCAATAGG
109969490 TTGCTCTTTGCAATGTTCTCTATAAAATTGTAGCCAAAGTTCTTGCCAATAGG
1 TTGCTCTTTGCAATGTTCTCTATAAAATTGTAGCCAAAGTTCTTGCCAATAGG
109969543 TTG
1 TTG
109969546 AAAGCTATTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (53 bp):
TTGCTCTTTGCAATGTTCTCTATAAAATTGTAGCCAAAGTTCTTGCCAATAGG
Found at i:109974952 original size:17 final size:17
Alignment explanation
Indices: 109974930--109974965 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
109974920 CTAATTTATT
*
109974930 TGAGCCTTAATTACTTA
1 TGAGCCCTAATTACTTA
109974947 TGAGCCCTAATTACTTA
1 TGAGCCCTAATTACTTA
109974964 TG
1 TG
109974966 TTCAATCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (17 bp):
TGAGCCCTAATTACTTA
Found at i:109975797 original size:29 final size:29
Alignment explanation
Indices: 109975758--109975849 Score: 141
Period size: 29 Copynumber: 3.1 Consensus size: 29
109975748 AGCCCCCTCC
109975758 AAAAAAAACCTAACCCAAAAAAAAAAAAA
1 AAAAAAAACCTAACCCAAAAAAAAAAAAA
109975787 AAAAAAAACCTAACCCAAAAAAAAAGAAGAA
1 AAAAAAAACCTAACCCAAAAAAAAA-AA-AA
*
109975818 AAAGAAAAACCTAA-CCAAAAAAAATAAAA
1 AAA-AAAAACCTAACCCAAAAAAAAAAAAA
109975847 AAA
1 AAA
109975850 CCTAGCCACC
Statistics
Matches: 59, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
29 30 0.51
30 4 0.07
31 15 0.25
32 10 0.17
ACGTcount: A:0.77, C:0.15, G:0.03, T:0.04
Consensus pattern (29 bp):
AAAAAAAACCTAACCCAAAAAAAAAAAAA
Found at i:109976082 original size:18 final size:17
Alignment explanation
Indices: 109976042--109976080 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
109976032 CCTAAAGGTG
*
109976042 ATTTTATCTTCTTTATT
1 ATTTTATCTTATTTATT
109976059 ATTTTACTCTTATTT-TT
1 ATTTTA-TCTTATTTATT
109976076 ATTTT
1 ATTTT
109976081 TATTTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTTATCTTATTTATT
Found at i:109976152 original size:13 final size:13
Alignment explanation
Indices: 109976134--109976183 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
109976124 TATATACATC
109976134 ATAATAAAAAAAT
1 ATAATAAAAAAAT
*
109976147 ATAATAAAAATAT
1 ATAATAAAAAAAT
*
109976160 ATATACAAAACAAAT
1 ATA-ATAAAA-AAAT
109976175 ATAA-AAAAA
1 ATAATAAAAA
109976184 TTACATTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
12 1 0.03
13 19 0.59
14 6 0.19
15 6 0.19
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (13 bp):
ATAATAAAAAAAT
Found at i:109976367 original size:29 final size:29
Alignment explanation
Indices: 109976311--109976367 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
109976301 TCTCTTCTTT
* *
109976311 TTTCATTTATTTTTCGTATTTACCTTAGA
1 TTTCATTTATTTTGCGTATTTAACTTAGA
*
109976340 TTTCATATTATTTTGC-TATTTAATTTAG
1 TTTCAT-TTATTTTGCGTATTTAACTTAG
109976368 CTTTAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.23, C:0.11, G:0.07, T:0.60
Consensus pattern (29 bp):
TTTCATTTATTTTGCGTATTTAACTTAGA
Found at i:109976628 original size:11 final size:11
Alignment explanation
Indices: 109976610--109976639 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
109976600 GTGTATATTG
109976610 TATATATTATA
1 TATATATTATA
*
109976621 TTTATATTATA
1 TATATATTATA
109976632 TATATATT
1 TATATATT
109976640 CTTAATGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATATATTATA
Found at i:109978212 original size:26 final size:26
Alignment explanation
Indices: 109978183--109978404 Score: 213
Period size: 26 Copynumber: 8.6 Consensus size: 26
109978173 AAACGAAACA
* *
109978183 AAATAATATATAAAACAATTTGAAGT
1 AAATAATATATAAAACAATTTAAAAT
* *
109978209 AAAT-A-GTACAAAACAATTTAAAAT
1 AAATAATATATAAAACAATTTAAAAT
* *
109978233 AAATAATATGTAAAACAAATTAAAAT
1 AAATAATATATAAAACAATTTAAAAT
* *
109978259 AAATAATATACAAAGCAATTTAAAAT
1 AAATAATATATAAAACAATTTAAAAT
* *
109978285 AAATAATATATAAGACACTTT---AT
1 AAATAATATATAAAACAATTTAAAAT
* * *
109978308 -AATAACATATAAAAGAATTTAAGAT
1 AAATAATATATAAAACAATTTAAAAT
*
109978333 AAATAATATATAAAAGAAATTTAAAAAT
1 AAATAATATATAAAA-CAATTT-AAAAT
* *
109978361 AAATAATATACAAAACAGTTTAAAAAT
1 AAATAATATATAAAACAATTT-AAAAT
109978388 AAATGATATATATAAAA
1 AAAT-A-ATATATAAAA
109978405 AAACCAATTC
Statistics
Matches: 159, Mismatches: 27, Indels: 17
0.78 0.13 0.08
Matches are distributed among these distances:
22 16 0.10
23 2 0.01
24 19 0.12
25 4 0.03
26 71 0.45
27 19 0.12
28 19 0.12
29 9 0.06
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (26 bp):
AAATAATATATAAAACAATTTAAAAT
Found at i:109978327 original size:48 final size:50
Alignment explanation
Indices: 109978183--109978495 Score: 230
Period size: 50 Copynumber: 6.2 Consensus size: 50
109978173 AAACGAAACA
* * * * * *
109978183 AAATAATATATAAAACAATTTGAAGTAAATAGTACAAAACAATTTAAAAT
1 AAATAATATATAAAACAAATTAAAATAAATAATATAAAAGAATTTAAAAT
*
109978233 AAATAATATGTAAAACAAATTAAAATAAATAATATACAAAGCAATTTAAAAT
1 AAATAATATATAAAACAAATTAAAATAAATAATATA-AAAG-AATTTAAAAT
* ** * * *
109978285 AAATAATATATAAGACACTTTATAAT-AA-CATATAAAAGAATTTAAGAT
1 AAATAATATATAAAACAAATTAAAATAAATAATATAAAAGAATTTAAAAT
*
109978333 AAATAATATATAAAAGAAATTTAAAAATAAATAATATACAAA-ACAGTTTAAAAAT
1 AAATAATATATAAAACAAA-TT-AAAATAAATAATATA-AAAGA-A-TTT-AAAAT
** * * *
109978388 AAATGATATATATAAAA-AAA-CCAATTCAA-AATGAATAATAG--TTTAAAAT
1 AAAT-A-ATATATAAAACAAATTAAAATAAATAAT--ATAAAAGAATTTAAAAT
* * * * *
109978437 ACATAATATGTGAAA-AACTTAAAATAAATAATAATAAAATAATTTAAAAT
1 AAATAATATATAAAACAAATTAAAATAAATAAT-ATAAAAGAATTTAAAAT
109978487 AAATAATAT
1 AAATAATAT
109978496 GTGAAAAACT
Statistics
Matches: 207, Mismatches: 37, Indels: 38
0.73 0.13 0.13
Matches are distributed among these distances:
47 10 0.05
48 36 0.17
49 17 0.08
50 58 0.28
51 7 0.03
52 40 0.19
53 11 0.05
54 6 0.03
55 8 0.04
56 4 0.02
57 10 0.05
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (50 bp):
AAATAATATATAAAACAAATTAAAATAAATAATATAAAAGAATTTAAAAT
Found at i:109978462 original size:25 final size:25
Alignment explanation
Indices: 109978430--109978506 Score: 102
Period size: 25 Copynumber: 3.1 Consensus size: 25
109978420 GAATAATAGT
*
109978430 TTAAAATACATAATATGTGAAAAAC
1 TTAAAATAAATAATATGTGAAAAAC
* * *
109978455 TTAAAATAAATAATA-ATAAAATAAT
1 TTAAAATAAATAATATGTGAAA-AAC
109978480 TTAAAATAAATAATATGTGAAAAAC
1 TTAAAATAAATAATATGTGAAAAAC
109978505 TT
1 TT
109978507 CTGCTATAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
24 4 0.09
25 35 0.81
26 4 0.09
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.31
Consensus pattern (25 bp):
TTAAAATAAATAATATGTGAAAAAC
Found at i:109978487 original size:15 final size:16
Alignment explanation
Indices: 109978456--109978495 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
109978446 GTGAAAAACT
109978456 TAAAATAA-ATAATAA
1 TAAAATAATATAATAA
*
109978471 TAAAATAATTTAA-AA
1 TAAAATAATATAATAA
109978486 T-AAATAATAT
1 TAAAATAATAT
109978496 GTGAAAAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 8 0.36
15 11 0.50
16 3 0.14
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAAATAATATAATAA
Found at i:109988879 original size:17 final size:17
Alignment explanation
Indices: 109988857--109988899 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
109988847 TATTTTATAA
109988857 TATAATTGTATTGTACT
1 TATAATTGTATTGTACT
* *
109988874 TATAATTATATTGTATT
1 TATAATTGTATTGTACT
*
109988891 TATACTTGT
1 TATAATTGT
109988900 TAATTTGTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.56
Consensus pattern (17 bp):
TATAATTGTATTGTACT
Found at i:109990209 original size:2 final size:2
Alignment explanation
Indices: 109990204--109990229 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
109990194 TCATTTGCAT
109990204 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
109990230 CTTTATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:109997224 original size:2 final size:2
Alignment explanation
Indices: 109997211--109997244 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
109997201 TAGAGTGCAA
*
109997211 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
109997245 GTAAATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:110005861 original size:16 final size:16
Alignment explanation
Indices: 110005840--110005873 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
110005830 CCTTTACAAG
110005840 AAAGAACTAGTTGGTT
1 AAAGAACTAGTTGGTT
110005856 AAAGAACTAGTTGGTT
1 AAAGAACTAGTTGGTT
110005872 AA
1 AA
110005874 GTAATTAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.06, G:0.24, T:0.29
Consensus pattern (16 bp):
AAAGAACTAGTTGGTT
Found at i:110007518 original size:25 final size:25
Alignment explanation
Indices: 110007488--110007539 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
110007478 GCTAAAAACC
110007488 CAACTTCCCTAACATTAAAAATCAG
1 CAACTTCCCTAACATTAAAAATCAG
110007513 CAACTTCCCTAACATTAAAAATCAG
1 CAACTTCCCTAACATTAAAAATCAG
110007538 CA
1 CA
110007540 GATTAAGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.44, C:0.29, G:0.04, T:0.23
Consensus pattern (25 bp):
CAACTTCCCTAACATTAAAAATCAG
Found at i:110008286 original size:35 final size:30
Alignment explanation
Indices: 110008240--110008315 Score: 91
Period size: 29 Copynumber: 2.4 Consensus size: 30
110008230 TTTTCAAATA
110008240 AATAGTTTTTTTTATTTTGTAAAAAAAATAAGGCT
1 AATAGTTTTTTTT-TTTTG---AAAAAA-AAGGCT
110008275 AATAG-TTTTTTTTTTTGAAAAAAAAGGCT
1 AATAGTTTTTTTTTTTTGAAAAAAAAGGCT
*
110008304 AATAGTTATTTT
1 AATAGTTTTTTT
110008316 AGTAGAGAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
29 11 0.28
30 11 0.28
33 5 0.13
34 7 0.18
35 5 0.13
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (30 bp):
AATAGTTTTTTTTTTTTGAAAAAAAAGGCT
Found at i:110009301 original size:2 final size:2
Alignment explanation
Indices: 110009296--110009332 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
110009286 CCAAATCCCC
110009296 AT 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 AT A
110009333 AGTCATAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:110009861 original size:2 final size:2
Alignment explanation
Indices: 110009854--110009879 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
110009844 AGACATTAAG
110009854 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
110009880 ATAAAGTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:110010124 original size:21 final size:22
Alignment explanation
Indices: 110010098--110010142 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
110010088 TGATATTACA
110010098 TTATTATTATTTT-CTTTCTAT
1 TTATTATTATTTTCCTTTCTAT
* *
110010119 TTATTATTTTTTTCCTTTTTAT
1 TTATTATTATTTTCCTTTCTAT
110010141 TT
1 TT
110010143 TATTTTCGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.76
Consensus pattern (22 bp):
TTATTATTATTTTCCTTTCTAT
Found at i:110010868 original size:15 final size:14
Alignment explanation
Indices: 110010842--110010877 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 14
110010832 TATATTTTTG
110010842 TTATACTTATATATA
1 TTATA-TTATATATA
110010857 TGTATATTATATATA
1 T-TATATTATATATA
110010872 TTATAT
1 TTATAT
110010878 AGTATTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 5 0.25
15 11 0.55
16 4 0.20
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (14 bp):
TTATATTATATATA
Found at i:110011591 original size:3 final size:3
Alignment explanation
Indices: 110011583--110011633 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
110011573 AATTTTACTT
* * * *
110011583 TTA TTA TTA CTA CTA -TA TTA TTA TTA TTA TCA TTA TCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
110011630 TTA T
1 TTA T
110011634 CATATTTATA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:110011854 original size:3 final size:3
Alignment explanation
Indices: 110011846--110011899 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
110011836 TATCTCTAAC
110011846 TAT TAT TAT TAT T-T TA- TAT ATAT TAT TAT CTA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT -TAT TAT TAT TAT TAT
*
110011890 TAC TAT TAT T
1 TAT TAT TAT T
110011900 CTTTATTGTC
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
2 6 0.14
3 33 0.75
4 5 0.11
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:110016446 original size:52 final size:52
Alignment explanation
Indices: 110016368--110016471 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 52
110016358 TATTCAAAAG
* * *
110016368 TTAGTTTATTCCAAGTCTTGATCAAGATGACAGACCCATTTTCTGTCCTATC
1 TTAGTTTATTCCAAGTCTCGATCAAGATGACAGACCCATTTTATGTACTATC
110016420 TTAGTTTATTCCAAGTCTCGATCAAGATGACAGACCCATTTTATGTACTATC
1 TTAGTTTATTCCAAGTCTCGATCAAGATGACAGACCCATTTTATGTACTATC
110016472 AATAGGATTA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (52 bp):
TTAGTTTATTCCAAGTCTCGATCAAGATGACAGACCCATTTTATGTACTATC
Found at i:110025627 original size:25 final size:25
Alignment explanation
Indices: 110025593--110025643 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
110025583 GAGTAGGAGT
110025593 TCACCTACGTGGTGAAGCGAACCCA
1 TCACCTACGTGGTGAAGCGAACCCA
110025618 TCACCTACGTGGTGAAGCGAACCCA
1 TCACCTACGTGGTGAAGCGAACCCA
110025643 T
1 T
110025644 GTAGGCGAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.31, G:0.24, T:0.18
Consensus pattern (25 bp):
TCACCTACGTGGTGAAGCGAACCCA
Found at i:110028204 original size:16 final size:17
Alignment explanation
Indices: 110028178--110028209 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
110028168 CCTTAAAAAA
110028178 TTAACATATATTTTTTT
1 TTAACATATATTTTTTT
110028195 TTAA-ATATATTTTTT
1 TTAACATATATTTTTT
110028210 AATATTTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (17 bp):
TTAACATATATTTTTTT
Found at i:110030881 original size:23 final size:22
Alignment explanation
Indices: 110030847--110030893 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
110030837 AGAGTTAAAA
*
110030847 TTTAGGGTTTTAAAATTTGTAGT
1 TTTAGGGTTTT-AAATTTGAAGT
110030870 TTTA-GGTATTTAAATTTGAAGT
1 TTTAGGGT-TTTAAATTTGAAGT
110030892 TT
1 TT
110030894 AGTGTTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.28, C:0.00, G:0.19, T:0.53
Consensus pattern (22 bp):
TTTAGGGTTTTAAATTTGAAGT
Found at i:110036794 original size:61 final size:62
Alignment explanation
Indices: 110036697--110036856 Score: 182
Period size: 62 Copynumber: 2.6 Consensus size: 62
110036687 TTAATATAGT
* * *
110036697 AACAAAATTAGCCCTCTAATGTATAC-ACATTCTATCA-TTTTGATCCTAAATAT-AAAAAATTC
1 AACAAATTTAGCCCTC-AATGTTTACAAAATT-TATCATTTTTG-TCCTAAATATAAAAAAATTC
** * *
110036759 AACAAATTTAGCCCTCAATGTTTACAAAATTTATCATTTTTGTTGTAATTCTAAAAAAATTC
1 AACAAATTTAGCCCTCAATGTTTACAAAATTTATCATTTTTGTCCTAAATATAAAAAAATTC
* * *
110036821 AATAAATTTAGCCCTCAATATTTATAAAATTTATCA
1 AACAAATTTAGCCCTCAATGTTTACAAAATTTATCA
110036857 CTTTAGTCAT
Statistics
Matches: 85, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
61 19 0.22
62 66 0.78
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (62 bp):
AACAAATTTAGCCCTCAATGTTTACAAAATTTATCATTTTTGTCCTAAATATAAAAAAATTC
Found at i:110036874 original size:62 final size:62
Alignment explanation
Indices: 110036750--110036877 Score: 184
Period size: 62 Copynumber: 2.1 Consensus size: 62
110036740 TCCTAAATAT
* * * ** *
110036750 AAAAAATTCAACAAATTTAGCCCTCAATGTTTACAAAATTTATCATTTTTGTTGTAATTCTA
1 AAAAAATTCAACAAATTTAGCCCTCAATATTTACAAAATTTATCACTTTAGTCATAACTCTA
* *
110036812 AAAAAATTCAATAAATTTAGCCCTCAATATTTATAAAATTTATCACTTTAGTCATAACTCTA
1 AAAAAATTCAACAAATTTAGCCCTCAATATTTACAAAATTTATCACTTTAGTCATAACTCTA
110036874 AAAA
1 AAAA
110036878 TAAAAAAATA
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.43, C:0.15, G:0.05, T:0.38
Consensus pattern (62 bp):
AAAAAATTCAACAAATTTAGCCCTCAATATTTACAAAATTTATCACTTTAGTCATAACTCTA
Found at i:110038201 original size:2 final size:2
Alignment explanation
Indices: 110038194--110038225 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
110038184 AGAATTTCAG
*
110038194 CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
110038226 ATGTGTGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:110039310 original size:103 final size:103
Alignment explanation
Indices: 110039131--110039338 Score: 398
Period size: 103 Copynumber: 2.0 Consensus size: 103
110039121 TACCACATTC
110039131 AACCTCAATTTATCTAAACCCCTTATCTTAGCCCATAATTAGATATATATTGTAATTAATAATAA
1 AACCTCAATTTATCTAAACCCCTTATCTTAGCCCATAATTAGATATATATTGTAATTAATAATAA
110039196 GTGTTGGTTGCAGTAATTAAACAAATTGCATTTTTAAA
66 GTGTTGGTTGCAGTAATTAAACAAATTGCATTTTTAAA
*
110039234 AACCTCAATTTATCTAAACCCCTTATCTTAGCCCATAATTAGATATATATTGTAATTAATAATAG
1 AACCTCAATTTATCTAAACCCCTTATCTTAGCCCATAATTAGATATATATTGTAATTAATAATAA
*
110039299 GTGTTGGTTGCAGTAATTAAATAAATTGCATTTTTAAA
66 GTGTTGGTTGCAGTAATTAAACAAATTGCATTTTTAAA
110039337 AA
1 AA
110039339 AGAATGCAGG
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 103 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (103 bp):
AACCTCAATTTATCTAAACCCCTTATCTTAGCCCATAATTAGATATATATTGTAATTAATAATAA
GTGTTGGTTGCAGTAATTAAACAAATTGCATTTTTAAA
Found at i:110047788 original size:20 final size:22
Alignment explanation
Indices: 110047744--110047789 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
110047734 TTTTAGTATC
* *
110047744 ATTTTTATTTGTTTTAATATTT
1 ATTTTTATGTGTTTTAATATAT
110047766 ATTTTTATGT-TTTTAA-ATAT
1 ATTTTTATGTGTTTTAATATAT
110047786 ATTT
1 ATTT
110047790 GATTTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.32
21 6 0.27
22 9 0.41
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (22 bp):
ATTTTTATGTGTTTTAATATAT
Found at i:110047806 original size:26 final size:24
Alignment explanation
Indices: 110047760--110047819 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
110047750 ATTTGTTTTA
*
110047760 ATATTTATTTTTATGTTTTTAAAT
1 ATATTTATTTTTATATTTTTAAAT
110047784 ATATTTGATTTATTATATTTTTAAAT
1 ATATTT-ATTT-TTATATTTTTAAAT
* *
110047810 TTTTTTATTT
1 ATATTTATTT
110047820 AATGAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 8 0.26
26 17 0.55
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.68
Consensus pattern (24 bp):
ATATTTATTTTTATATTTTTAAAT
Found at i:110053316 original size:20 final size:20
Alignment explanation
Indices: 110053288--110053326 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
110053278 AAATTTTAAA
110053288 ATTT-AAAAATTATAAAAACT
1 ATTTAAAAAATTA-AAAAACT
*
110053308 ATTTTAAAAATTAAAAAAC
1 ATTTAAAAAATTAAAAAAC
110053327 ATTAATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
ATTTAAAAAATTAAAAAACT
Found at i:110053506 original size:12 final size:12
Alignment explanation
Indices: 110053491--110053530 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
110053481 AAAAGAAGTA
110053491 AAAAAATTAAAT
1 AAAAAATTAAAT
*
110053503 AAAAAATAAAAAT
1 AAAAAAT-TAAAT
*
110053516 AAAAAATTTAAT
1 AAAAAATTAAAT
110053528 AAA
1 AAA
110053531 GTTGAATGGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAAAATTAAAT
Found at i:110058808 original size:16 final size:16
Alignment explanation
Indices: 110058787--110058822 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
110058777 AAAAAAGAGC
*
110058787 AAAAAATTCCAGCAAA
1 AAAAAATTCAAGCAAA
110058803 AAAAAATTCAAGCAAA
1 AAAAAATTCAAGCAAA
110058819 AAAA
1 AAAA
110058823 TCCAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.69, C:0.14, G:0.06, T:0.11
Consensus pattern (16 bp):
AAAAAATTCAAGCAAA
Found at i:110059081 original size:19 final size:19
Alignment explanation
Indices: 110059044--110059084 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
110059034 TGTTTTCATA
* *
110059044 TTTTCTTTCCTTGGTTTTT
1 TTTTCTTTCCTTAGATTTT
*
110059063 TTTTCTTTCTTTAGATTTT
1 TTTTCTTTCCTTAGATTTT
110059082 TTT
1 TTT
110059085 ATTTTATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.05, C:0.12, G:0.07, T:0.76
Consensus pattern (19 bp):
TTTTCTTTCCTTAGATTTT
Found at i:110064757 original size:21 final size:18
Alignment explanation
Indices: 110064720--110064754 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
110064710 GAAGAAAGAT
110064720 GGTGGGAAGAAAGATGAA
1 GGTGGGAAGAAAGATGAA
*
110064738 GGTGGGAAGAAGGATGA
1 GGTGGGAAGAAAGATGA
110064755 TGATAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.49, T:0.11
Consensus pattern (18 bp):
GGTGGGAAGAAAGATGAA
Found at i:110066138 original size:20 final size:21
Alignment explanation
Indices: 110066103--110066149 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
110066093 AAGCTAATTT
* *
110066103 AAAATT-TAAAAGTTATTAA-
1 AAAATTATAAAAATTATAAAC
110066122 AAAATTATAAAAATTATAAAC
1 AAAATTATAAAAATTATAAAC
110066143 AAAATTA
1 AAAATTA
110066150 CTAATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 6 0.25
20 11 0.46
21 7 0.29
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (21 bp):
AAAATTATAAAAATTATAAAC
Found at i:110068666 original size:28 final size:28
Alignment explanation
Indices: 110068626--110068704 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
110068616 GCAATCAAAT
* * *
110068626 ATGGTACTCAGTGTACGAAATATTGAGA
1 ATGGAACTTAGTGTGCGAAATATTGAGA
* *
110068654 ATGGCACTTAGTGTGCGAGATATTGAGA
1 ATGGAACTTAGTGTGCGAAATATTGAGA
* *
110068682 ATGAAACTTAGTGTGCAAAATAT
1 ATGGAACTTAGTGTGCGAAATAT
110068705 CGAATGATTC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.29
Consensus pattern (28 bp):
ATGGAACTTAGTGTGCGAAATATTGAGA
Found at i:110071765 original size:5 final size:5
Alignment explanation
Indices: 110071755--110071836 Score: 60
Period size: 5 Copynumber: 16.2 Consensus size: 5
110071745 GTGAGAGGTA
* * * *
110071755 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTA ATATT AATTT A-ATT ATTTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT A-TTTT
* * *
110071805 ATTTAT ATAATT -TTTT ATTTA ATTAT ATTTT A
1 ATTT-T AT-TTT ATTTT ATTTT ATTTT ATTTT A
110071837 ATGAGATAAT
Statistics
Matches: 59, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
4 5 0.08
5 46 0.78
6 7 0.12
7 1 0.02
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (5 bp):
ATTTT
Found at i:110071807 original size:30 final size:31
Alignment explanation
Indices: 110071753--110071836 Score: 86
Period size: 30 Copynumber: 2.8 Consensus size: 31
110071743 AGGTGAGAGG
* * *
110071753 TAATT-TT-ATTTTATTTTATTTTATTTTATT
1 TAATTATTAATTTAATTATATTTTA-TTTATA
110071783 TAA-TATTAATTTAATTAT-TTTTATTTATA
1 TAATTATTAATTTAATTATATTTTATTTATA
* *
110071812 TAATTTTTTATTTAATTATATTTTA
1 TAATTATTAATTTAATTATATTTTA
110071837 ATGAGATAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
29 9 0.20
30 23 0.51
31 13 0.29
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (31 bp):
TAATTATTAATTTAATTATATTTTATTTATA
Found at i:110073725 original size:4 final size:4
Alignment explanation
Indices: 110073716--110073754 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
110073706 AAGTTTTTAT
110073716 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
110073755 AATGGTGGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:110073976 original size:24 final size:25
Alignment explanation
Indices: 110073929--110073976 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
110073919 CATGGATAAA
* *
110073929 TTTGGTTAATTAATCATTTTGGTCT
1 TTTGGATAATTAATCATTTAGGTCT
*
110073954 TTTGGATAATT-ATTATTTAGGTC
1 TTTGGATAATTAATCATTTAGGTC
110073977 CCTAAGTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.23, C:0.06, G:0.17, T:0.54
Consensus pattern (25 bp):
TTTGGATAATTAATCATTTAGGTCT
Found at i:110076588 original size:19 final size:20
Alignment explanation
Indices: 110076555--110076594 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
110076545 ATATATGTAT
110076555 ATAAAATAAAGAAAAT-AAA
1 ATAAAATAAAGAAAATGAAA
110076574 ATAAAATAACA-AAAATGAAA
1 ATAAAATAA-AGAAAATGAAA
110076594 A
1 A
110076595 ATGAACAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.15
Consensus pattern (20 bp):
ATAAAATAAAGAAAATGAAA
Found at i:110076888 original size:9 final size:9
Alignment explanation
Indices: 110076842--110076883 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
110076832 AAATGTTAGG
*
110076842 TTTTTTTTC
1 TTTTTTTTA
*
110076851 TTTTTCTTCA
1 TTTTT-TTTA
110076861 TTTTTTTTA
1 TTTTTTTTA
110076870 TTTTTTTT-
1 TTTTTTTTA
110076878 TTTTTT
1 TTTTTT
110076884 ATTTTGGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
8 6 0.21
9 16 0.55
10 7 0.24
ACGTcount: A:0.05, C:0.07, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:110077608 original size:22 final size:23
Alignment explanation
Indices: 110077583--110077629 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
110077573 TCCCTTAACA
*
110077583 CTCACTCTCTCTTTC-ACTTCAC
1 CTCACTCTCTCATTCTACTTCAC
* *
110077605 CTCATTCTCTCATTCTTCTTCAC
1 CTCACTCTCTCATTCTACTTCAC
110077628 CT
1 CT
110077630 AATATTCTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.13, C:0.43, G:0.00, T:0.45
Consensus pattern (23 bp):
CTCACTCTCTCATTCTACTTCAC
Found at i:110083195 original size:30 final size:30
Alignment explanation
Indices: 110083161--110083222 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
110083151 GAAGAATTAG
110083161 AAGATAAATTTTAATTTCCATTAGTAACGA
1 AAGATAAATTTTAATTTCCATTAGTAACGA
110083191 AAGATAAATTTTAATTTCCATTAGTAACGA
1 AAGATAAATTTTAATTTCCATTAGTAACGA
110083221 AA
1 AA
110083223 AACATGATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (30 bp):
AAGATAAATTTTAATTTCCATTAGTAACGA
Found at i:110083341 original size:50 final size:50
Alignment explanation
Indices: 110083266--110083367 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 50
110083256 TTAAATTGGG
*
110083266 GTTTCATTTAGAACTCTACTCATTATGAGTAAATATATTCTTCTCTTTTA
1 GTTTCATCTAGAACTCTACTCATTATGAGTAAATATATTCTTCTCTTTTA
110083316 GTTTCATCTAGAACTCTACTCATTATGAGTAAATATATTCTTCTCTTTTA
1 GTTTCATCTAGAACTCTACTCATTATGAGTAAATATATTCTTCTCTTTTA
110083366 GT
1 GT
110083368 ATTATTTTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.27, C:0.17, G:0.09, T:0.47
Consensus pattern (50 bp):
GTTTCATCTAGAACTCTACTCATTATGAGTAAATATATTCTTCTCTTTTA
Found at i:110090765 original size:21 final size:21
Alignment explanation
Indices: 110090739--110090794 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
110090729 AACAGCGGTG
* *
110090739 GCGGTGAGATTAGTTATTGTA
1 GCGGTGAGATTAGATACTGTA
*
110090760 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
110090781 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
110090795 AACAGCGGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.07, G:0.38, T:0.30
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:110091034 original size:18 final size:18
Alignment explanation
Indices: 110091011--110091093 Score: 70
Period size: 18 Copynumber: 4.8 Consensus size: 18
110091001 TATTTTAATG
110091011 AATTATATAATCAATTTA
1 AATTATATAATCAATTTA
* *
110091029 AATTAT-TTATTAGA--TA
1 AATTATATAATCA-ATTTA
*
110091045 AA--ATGATAAT-AATTTTT
1 AATTAT-ATAATCAA-TTTA
110091062 AATTATATAATCAATTTA
1 AATTATATAATCAATTTA
110091080 AATTATATAATCAA
1 AATTATATAATCAA
110091094 CAGGCCAGGG
Statistics
Matches: 51, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
14 3 0.06
15 1 0.02
16 7 0.14
17 7 0.14
18 29 0.57
19 4 0.08
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (18 bp):
AATTATATAATCAATTTA
Found at i:110092499 original size:2 final size:2
Alignment explanation
Indices: 110092492--110092524 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
110092482 TGTATTTATC
110092492 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
110092525 TTTACGATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:110095582 original size:23 final size:22
Alignment explanation
Indices: 110095543--110095587 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
110095533 CATGCTTTTC
*
110095543 TTTCTTTCTTTTTTTTTTCATT
1 TTTCTTTCTTTTTTTTTCCATT
*
110095565 TTTCTTTGTTTTTATTTTCCATT
1 TTTCTTTCTTTTT-TTTTCCATT
110095588 AAATCTGGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.07, C:0.13, G:0.02, T:0.78
Consensus pattern (22 bp):
TTTCTTTCTTTTTTTTTCCATT
Found at i:110096264 original size:9 final size:9
Alignment explanation
Indices: 110096250--110096274 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
110096240 AAATCCAGCT
110096250 TTTTTTTTA
1 TTTTTTTTA
110096259 TTTTTTTTA
1 TTTTTTTTA
110096268 TTTTTTT
1 TTTTTTT
110096275 GGCTTTGCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:110098977 original size:17 final size:19
Alignment explanation
Indices: 110098944--110098982 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
110098934 TTCTTACTGT
*
110098944 TTTAAATAATCATTATATA
1 TTTAAATAATCATTATAAA
110098963 TTTAAA-AAT-ATTATAAA
1 TTTAAATAATCATTATAAA
110098980 TTT
1 TTT
110098983 GATATAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 3 0.16
19 6 0.32
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTAAATAATCATTATAAA
Found at i:110099258 original size:16 final size:17
Alignment explanation
Indices: 110099226--110099276 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 17
110099216 ATATTAAAAT
*
110099226 TTATTATGTT-AATTAA
1 TTATTATTTTGAATTAA
110099242 TTATTATTTTGAA-TAA
1 TTATTATTTTGAATTAA
**
110099258 -TGGTATTTTGAATTAA
1 TTATTATTTTGAATTAA
110099274 TTA
1 TTA
110099277 GATAAAGTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
15 10 0.36
16 15 0.54
17 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (17 bp):
TTATTATTTTGAATTAA
Found at i:110104591 original size:2 final size:2
Alignment explanation
Indices: 110104584--110104620 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
110104574 AAAATATGTG
*
110104584 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
110104621 CAATGCATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 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):
TA
Found at i:110107063 original size:2 final size:2
Alignment explanation
Indices: 110107052--110107084 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
110107042 ATTAAGTTAT
110107052 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
110107085 AAGTAAAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:110107118 original size:11 final size:10
Alignment explanation
Indices: 110107100--110107175 Score: 53
Period size: 11 Copynumber: 6.6 Consensus size: 10
110107090 AAAGGAATAA
110107100 AAAGAAAAAG
1 AAAGAAAAAG
110107110 AATAGAAAAAG
1 AA-AGAAAAAG
*
110107121 AAAGAAAGGATG
1 AAAGAAA--AAG
110107133 AAACGAAACAGAG
1 AAA-GAAA-A-AG
110107146 AAAAGAAAGAAG
1 -AAAGAAA-AAG
110107158 AAAGGAAAAAGG
1 AAA-GAAAAA-G
110107170 AAAGAA
1 AAAGAA
110107176 GAAAAAAAGT
Statistics
Matches: 54, Mismatches: 4, Indels: 15
0.74 0.05 0.21
Matches are distributed among these distances:
10 7 0.13
11 18 0.33
12 16 0.30
13 10 0.19
14 3 0.06
ACGTcount: A:0.70, C:0.03, G:0.25, T:0.03
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:110107147 original size:25 final size:24
Alignment explanation
Indices: 110107100--110107175 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 24
110107090 AAAGGAATAA
110107100 AAAGAAA-AAGAATA-G-AAAA-AG
1 AAAGAAAGAAGAA-ACGAAAAAGAG
* *
110107121 AAAGAAAGGATGAAACGAAACAGAG
1 AAAGAAA-GAAGAAACGAAAAAGAG
*
110107146 AAAAGAAAGAAGAAAGGAAAAAG-G
1 -AAAGAAAGAAGAAACGAAAAAGAG
110107170 AAAGAA
1 AAAGAA
110107176 GAAAAAAAGT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
21 7 0.16
22 1 0.02
23 11 0.25
24 4 0.09
25 14 0.32
26 7 0.16
ACGTcount: A:0.70, C:0.03, G:0.25, T:0.03
Consensus pattern (24 bp):
AAAGAAAGAAGAAACGAAAAAGAG
Found at i:110108519 original size:18 final size:19
Alignment explanation
Indices: 110108496--110108544 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
110108486 ATAACCGATC
110108496 AACTGATTGA-TACTGAAT
1 AACTGATTGATTACTGAAT
*
110108514 AACTGATT-ATTATTGAAT
1 AACTGATTGATTACTGAAT
*
110108532 AATTGATTG-TTAC
1 AACTGATTGATTAC
110108545 CGACTGTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 1 0.04
18 25 0.96
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (19 bp):
AACTGATTGATTACTGAAT
Found at i:110111002 original size:53 final size:53
Alignment explanation
Indices: 110110921--110111071 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
110110911 CTTACACGGT
* *
110110921 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
110110976 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
110111029 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
110111072 GCACACTTGT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:110119555 original size:75 final size:75
Alignment explanation
Indices: 110119437--110119607 Score: 203
Period size: 75 Copynumber: 2.4 Consensus size: 75
110119427 CATGGCAAAG
* ** *
110119437 TGTGAAACGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
110119496 CCATACTGAGC
65 CCATACCGAGC
110119507 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
110119572 CATACCGAGT
66 CATACCGAGC
***
110119582 TAAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
110119608 TGAGGAAAAC
Statistics
Matches: 86, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
70 17 0.20
73 4 0.05
74 5 0.06
75 60 0.70
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:110119575 original size:35 final size:36
Alignment explanation
Indices: 110119440--110119603 Score: 181
Period size: 35 Copynumber: 4.5 Consensus size: 36
110119430 GGCAAAGTGT
* * **
110119440 GAAACGTAGGTATGGTATCAT-CCATACTGAGTTGT
1 GAAATGTAGGTATGGTATTATCCCATACTGAGTTAA
* **
110119475 GAAATGTAGGTATGGTATTAT-CCATACTGAGCTGT
1 GAAATGTAGGTATGGTATTATCCCATACTGAGTTAA
110119510 GAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAA
1 GAAATGTAGGTATGGTATTATC----CCATACTGAGTTAA
* *
110119550 GAAATGTAGGTATGGCATT-TCCCATACCGAGTTAA
1 GAAATGTAGGTATGGTATTATCCCATACTGAGTTAA
*
110119585 AAAATGTAGGTATGGTATT
1 GAAATGTAGGTATGGTATT
110119604 TCAATGAGGA
Statistics
Matches: 114, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
35 83 0.73
39 2 0.02
40 29 0.25
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (36 bp):
GAAATGTAGGTATGGTATTATCCCATACTGAGTTAA
Found at i:110121194 original size:53 final size:54
Alignment explanation
Indices: 110121113--110121263 Score: 209
Period size: 53 Copynumber: 2.8 Consensus size: 54
110121103 CTTACACGGT
* *
110121113 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAGACTATGGTCTTATACGGAATCACATTA
*
110121168 TCACATTATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGACTATGGTCTTATACGGAATCACATTA
** *
110121221 TCACATTGCACCGATGCCATAGCCCA-ACTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGACTATGGTCTTATACGG
110121264 GCACACTTGT
Statistics
Matches: 88, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
52 1 0.01
53 80 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (54 bp):
TCACATTATACCGATGCCATAGCCCAGACTATGGTCTTATACGGAATCACATTA
Found at i:110124159 original size:29 final size:28
Alignment explanation
Indices: 110124094--110124159 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
110124084 CTATATTTTT
* * *
110124094 ATAATATTATTAATTAGTTCAATATTTG
1 ATAATGTTATTAATTAGTTCAATAGTTA
110124122 ATAATGTTATTAATTAGTTCAAATAGTTA
1 ATAATGTTATTAATTAGTTC-AATAGTTA
*
110124151 ATATTGTTA
1 ATAATGTTA
110124160 GCCTTTCAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
28 19 0.58
29 14 0.42
ACGTcount: A:0.39, C:0.03, G:0.09, T:0.48
Consensus pattern (28 bp):
ATAATGTTATTAATTAGTTCAATAGTTA
Found at i:110126774 original size:2 final size:2
Alignment explanation
Indices: 110126767--110126812 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
110126757 ATTGCTACAA
*
110126767 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
110126809 AT AT
1 AT AT
110126813 TTACTGATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:110131731 original size:22 final size:22
Alignment explanation
Indices: 110131688--110131731 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
110131678 TTTTAATATA
*
110131688 AAATTATAAAAATATCTTTTAT
1 AAATTATAAAAATATCTATTAT
*
110131710 AAATTATAATTAATAT-TATTAT
1 AAATTATAA-AAATATCTATTAT
110131732 GTCACTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATTATAAAAATATCTATTAT
Found at i:110137851 original size:101 final size:102
Alignment explanation
Indices: 110137689--110137893 Score: 385
Period size: 101 Copynumber: 2.0 Consensus size: 102
110137679 TGGGACACAC
*
110137689 AGCATTTTTAGGTTGTGACATGTGGCACTGAGATGCCATAATCTATTCTTCCTATAAAAATATTT
1 AGCACTTTTAGGTTGTGACA-GTGGCACTGAGATGCCATAATCTATTCTTCCTATAAAAATATTT
110137754 AAAAATTTAAAAGAAATATATAAAAATACTTAAAATTT
65 AAAAATTTAAAAGAAATATATAAAAATACTTAAAATTT
110137792 AGCACTTTTAGGTTGTGAC-GTGGCACTGAGATGCCATAATCTATTCTTCCTATAAAAATATTTA
1 AGCACTTTTAGGTTGTGACAGTGGCACTGAGATGCCATAATCTATTCTTCCTATAAAAATATTTA
110137856 AAAATTTAAAAGAAATATATAAAAATACTTAAAATTT
66 AAAATTTAAAAGAAATATATAAAAATACTTAAAATTT
110137893 A
1 A
110137894 AGTTAGAAAA
Statistics
Matches: 101, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
101 83 0.82
103 18 0.18
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (102 bp):
AGCACTTTTAGGTTGTGACAGTGGCACTGAGATGCCATAATCTATTCTTCCTATAAAAATATTTA
AAAATTTAAAAGAAATATATAAAAATACTTAAAATTT
Found at i:110138302 original size:10 final size:10
Alignment explanation
Indices: 110138262--110138305 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
110138252 GTTTATCAAC
*
110138262 ATTTAATTGT
1 ATTTAATTAT
*
110138272 GTTTAATTAT
1 ATTTAATTAT
110138282 AATTATAATTAT
1 -ATT-TAATTAT
110138294 ATTTAATTAT
1 ATTTAATTAT
110138304 AT
1 AT
110138306 GTGTTTGAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 17 0.59
11 5 0.17
12 7 0.24
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (10 bp):
ATTTAATTAT
Found at i:110140302 original size:31 final size:31
Alignment explanation
Indices: 110140264--110140325 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
110140254 GATATTATAC
110140264 ATACAAAGGTATTTTAATAATTATTCTAGGA
1 ATACAAAGGTATTTTAATAATTATTCTAGGA
110140295 ATACAAAGGTATTTTAATAATTATTCTAGGA
1 ATACAAAGGTATTTTAATAATTATTCTAGGA
110140326 CTAAGTGGGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (31 bp):
ATACAAAGGTATTTTAATAATTATTCTAGGA
Found at i:110140908 original size:48 final size:48
Alignment explanation
Indices: 110140837--110140936 Score: 200
Period size: 48 Copynumber: 2.1 Consensus size: 48
110140827 ACATTTTCAT
110140837 CTAATTTCTCTCATTTATTTTGTGAACTCCATCTTCAAAGATAAGGGA
1 CTAATTTCTCTCATTTATTTTGTGAACTCCATCTTCAAAGATAAGGGA
110140885 CTAATTTCTCTCATTTATTTTGTGAACTCCATCTTCAAAGATAAGGGA
1 CTAATTTCTCTCATTTATTTTGTGAACTCCATCTTCAAAGATAAGGGA
110140933 CTAA
1 CTAA
110140937 AGAGAAAATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (48 bp):
CTAATTTCTCTCATTTATTTTGTGAACTCCATCTTCAAAGATAAGGGA
Found at i:110148546 original size:21 final size:21
Alignment explanation
Indices: 110148504--110148547 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
110148494 CACATCGTTT
* *
110148504 CCTCCTCTTTCTCCGCCACCG
1 CCTCCTCTGTCTACGCCACCG
* *
110148525 CCTCCTCTGTCTACTCCGCCG
1 CCTCCTCTGTCTACGCCACCG
110148546 CC
1 CC
110148548 ACCGCCAGAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.05, C:0.57, G:0.11, T:0.27
Consensus pattern (21 bp):
CCTCCTCTGTCTACGCCACCG
Found at i:110149130 original size:18 final size:20
Alignment explanation
Indices: 110149109--110149149 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
110149099 TTACTATTGA
110149109 ATAAAATTT-TATTTTAA-T
1 ATAAAATTTATATTTTAACT
*
110149127 ATAATATTTATATTTTAACT
1 ATAAAATTTATATTTTAACT
110149147 ATA
1 ATA
110149150 TTTTATTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 8 0.40
20 4 0.20
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
ATAAAATTTATATTTTAACT
Found at i:110149374 original size:15 final size:15
Alignment explanation
Indices: 110149351--110149439 Score: 57
Period size: 15 Copynumber: 6.1 Consensus size: 15
110149341 ATATTATACA
* *
110149351 TATTTATTATGTTAT
1 TATTAATTATATTAT
*
110149366 TATTAATTA-GTT-T
1 TATTAATTATATTAT
110149379 TA--AATTATA-TATT
1 TATTAATTATATTA-T
110149392 TCATTAATTATTATTAT
1 T-ATTAATTA-TATTAT
110149409 TATT-ATTATTATTAT
1 TATTAATTA-TATTAT
110149424 TATT-ATTATTATTAT
1 TATTAATTA-TATTAT
110149439 T
1 T
110149440 GAAAACACAA
Statistics
Matches: 64, Mismatches: 2, Indels: 16
0.78 0.02 0.20
Matches are distributed among these distances:
11 6 0.09
13 5 0.08
14 4 0.06
15 35 0.55
16 8 0.12
17 4 0.06
18 2 0.03
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (15 bp):
TATTAATTATATTAT
Found at i:110149406 original size:3 final size:3
Alignment explanation
Indices: 110149398--110149439 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
110149388 TATTTCATTA
110149398 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
110149440 GAAAACACAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:110149680 original size:14 final size:15
Alignment explanation
Indices: 110149661--110149689 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
110149651 TTATTAAATG
110149661 AATGAATTA-AATAT
1 AATGAATTATAATAT
110149675 AATGAATTATAATAT
1 AATGAATTATAATAT
110149690 TTTTTTTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (15 bp):
AATGAATTATAATAT
Found at i:110150020 original size:17 final size:17
Alignment explanation
Indices: 110149998--110150032 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
110149988 ATTTTTTTGT
*
110149998 AAAGTTATAATGCTAAA
1 AAAGTTATAATGCCAAA
*
110150015 AAAGTTATTATGCCAAA
1 AAAGTTATAATGCCAAA
110150032 A
1 A
110150033 TAATATCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.29
Consensus pattern (17 bp):
AAAGTTATAATGCCAAA
Found at i:110152679 original size:22 final size:22
Alignment explanation
Indices: 110152635--110152689 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
110152625 TTGAGTTTTC
* *
110152635 TTTGAAGAGAAAAATATTGGGT
1 TTTGAAGAGAAAAATAATAGGT
* *
110152657 TTTGATGAGAAAATTAATAGG-
1 TTTGAAGAGAAAAATAATAGGT
*
110152678 TTTGAAGGGAAA
1 TTTGAAGAGAAA
110152690 TTTGGGATCT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.31
Consensus pattern (22 bp):
TTTGAAGAGAAAAATAATAGGT
Found at i:110154312 original size:18 final size:18
Alignment explanation
Indices: 110154289--110154340 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
110154279 AAAATGCGAG
*
110154289 AAATGATGTTTACATTTC
1 AAATGATGTTCACATTTC
*
110154307 AAATGATATTCACATTTC
1 AAATGATGTTCACATTTC
110154325 AAATGATGTTCACATT
1 AAATGATGTTCACATT
110154341 GATGAAAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (18 bp):
AAATGATGTTCACATTTC
Found at i:110159142 original size:22 final size:23
Alignment explanation
Indices: 110159117--110159170 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
110159107 TTTAATTGAA
*
110159117 GAAATATATTA-TTTTAG-ATAT
1 GAAATATATAATTTTTAGAATAT
*
110159138 CGAAATAAATAATTTTTAGAATAT
1 -GAAATATATAATTTTTAGAATAT
110159162 -AAATATATA
1 GAAATATATA
110159171 GATGTGACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 17 0.63
23 6 0.22
24 4 0.15
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (23 bp):
GAAATATATAATTTTTAGAATAT
Found at i:110160320 original size:6 final size:6
Alignment explanation
Indices: 110160311--110160341 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
110160301 AGAAACAGAA
110160311 GAGTTG GAGTTG GAGTTG GAGTTG GAGTTG G
1 GAGTTG GAGTTG GAGTTG GAGTTG GAGTTG G
110160342 TTATGATTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.52, T:0.32
Consensus pattern (6 bp):
GAGTTG
Found at i:110161669 original size:42 final size:42
Alignment explanation
Indices: 110161610--110161694 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
110161600 TCCTTCTGCA
110161610 TAGATTCATACACTCTTACAGATAGCTCAAATTAGAAATAAT
1 TAGATTCATACACTCTTACAGATAGCTCAAATTAGAAATAAT
110161652 TAGATTCATACACTCTTACAGATAGCTCAAATTAGAAATAAT
1 TAGATTCATACACTCTTACAGATAGCTCAAATTAGAAATAAT
110161694 T
1 T
110161695 CTGTCTCTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.32
Consensus pattern (42 bp):
TAGATTCATACACTCTTACAGATAGCTCAAATTAGAAATAAT
Found at i:110166714 original size:16 final size:16
Alignment explanation
Indices: 110166693--110166725 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
110166683 TTATATGATC
110166693 TTGTGTGAACTATTTA
1 TTGTGTGAACTATTTA
110166709 TTGTGTGAACTATTTA
1 TTGTGTGAACTATTTA
110166725 T
1 T
110166726 CAAATGCTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.06, G:0.18, T:0.52
Consensus pattern (16 bp):
TTGTGTGAACTATTTA
Found at i:110168144 original size:2 final size:2
Alignment explanation
Indices: 110168137--110168169 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
110168127 GGTAGCAAAT
*
110168137 TA TA TA TA TA TA TA TA TC TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
110168170 TCAACACACT
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:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:110170168 original size:6 final size:6
Alignment explanation
Indices: 110170136--110170167 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
110170126 TTCTGAGAAT
*
110170136 GATAGG GATAGG GATAGG GATAGG GACAGG GA
1 GATAGG GATAGG GATAGG GATAGG GATAGG GA
110170168 CGGAGTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.34, C:0.03, G:0.50, T:0.12
Consensus pattern (6 bp):
GATAGG
Found at i:110172469 original size:18 final size:19
Alignment explanation
Indices: 110172441--110172476 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
110172431 TGGACATATT
110172441 TAAATATTTTTAAATTTTC
1 TAAATATTTTTAAATTTTC
*
110172460 TAAA-ATTTTTAAGTTTT
1 TAAATATTTTTAAATTTT
110172477 AAATAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (19 bp):
TAAATATTTTTAAATTTTC
Found at i:110172484 original size:18 final size:18
Alignment explanation
Indices: 110172439--110172486 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
110172429 AGTGGACATA
110172439 TTTAAAT-ATTTTTAAAT
1 TTTAAATAATTTTTAAAT
* *
110172456 TTTCTAA-AATTTTTAAGT
1 TTT-AAATAATTTTTAAAT
110172474 TTTAAATAATTTT
1 TTTAAATAATTTT
110172487 GAATTCAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (18 bp):
TTTAAATAATTTTTAAAT
Found at i:110178423 original size:29 final size:30
Alignment explanation
Indices: 110178363--110178424 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
110178353 AAAAAAAATA
* *
110178363 AATAAGCATGTTATTTTCATGTTTTTAATT
1 AATAAACATGTTATTTTCAAGTTTTTAATT
*
110178393 AATAAACATGTT-TTTT-AAGTTATTTATTT
1 AATAAACATGTTATTTTCAAGTT-TTTAATT
110178422 AAT
1 AAT
110178425 TTTATTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 4 0.14
29 13 0.46
30 11 0.39
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.53
Consensus pattern (30 bp):
AATAAACATGTTATTTTCAAGTTTTTAATT
Found at i:110178547 original size:16 final size:18
Alignment explanation
Indices: 110178513--110178553 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
110178503 TGTTTTTTTT
110178513 ATATATATTATTATGTTAA
1 ATATATATTA-TATGTTAA
110178532 ATATATATTA-AT-TTAA
1 ATATATATTATATGTTAA
*
110178548 AAATAT
1 ATATAT
110178554 CAACTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 9 0.43
17 2 0.10
19 10 0.48
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
ATATATATTATATGTTAA
Found at i:110178767 original size:29 final size:31
Alignment explanation
Indices: 110178734--110178797 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
110178724 ATTATATTTG
110178734 AAATAA-T-TATTTGAAATATTTCACATATA
1 AAATAATTATATTTGAAATATTTCACATATA
* * *
110178763 AAATAATTATATTTGAGATATTTTATATATA
1 AAATAATTATATTTGAAATATTTCACATATA
110178794 AAAT
1 AAAT
110178798 TAAAATAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 6 0.20
30 1 0.03
31 23 0.77
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (31 bp):
AAATAATTATATTTGAAATATTTCACATATA
Found at i:110178822 original size:19 final size:18
Alignment explanation
Indices: 110178787--110178828 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
110178777 GAGATATTTT
*
110178787 ATATATAAAATTAAAATA
1 ATATTTAAAATTAAAATA
110178805 GATATTTAAAA-TATAAATA
1 -ATATTTAAAATTA-AAATA
110178824 ATATT
1 ATATT
110178829 ACAATAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
ATATTTAAAATTAAAATA
Found at i:110191367 original size:16 final size:17
Alignment explanation
Indices: 110191339--110191371 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
110191329 AAATAGATTT
110191339 TTAATTAAAAATTTTAA
1 TTAATTAAAAATTTTAA
110191356 TTAATT-AAAATTTTAA
1 TTAATTAAAAATTTTAA
110191372 ACCTAAATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTAATTAAAAATTTTAA
Found at i:110193061 original size:47 final size:47
Alignment explanation
Indices: 110193006--110193107 Score: 161
Period size: 47 Copynumber: 2.2 Consensus size: 47
110192996 TCGATGAGAC
*
110193006 ACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTGTTCCGATGAAGT
1 ACTATGTGTACGA-TAATGTTAAAGTTCCGGATTTGTTCCGATGAAGT
* *
110193053 ACTTTGTGTACTATAATGTTAAAGTTCCGGATTTGTTCCGATGAAGT
1 ACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTCCGATGAAGT
110193100 ACTATGTG
1 ACTATGTG
110193108 CTTATCCCGG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
47 48 0.96
48 2 0.04
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (47 bp):
ACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTCCGATGAAGT
Found at i:110195650 original size:2 final size:2
Alignment explanation
Indices: 110195638--110195683 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
110195628 TCAAGTCTCA
*
110195638 AT AT A- AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
110195679 AT AT A
1 AT AT A
110195684 AAAGCTCAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:110196733 original size:30 final size:30
Alignment explanation
Indices: 110196667--110196733 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
110196657 AACTTAAATG
* **
110196667 AAAACTTTTTTGTAGTTCAGTAACCAAATT
1 AAAACTTTTTTGTAGTTAAGTAACCAAACA
**
110196697 GTAACTTTTTT-TAGTTAAGTAACCAAAACA
1 AAAACTTTTTTGTAGTTAAGTAACC-AAACA
110196727 AAAACTT
1 AAAACTT
110196734 ATCAATAATT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
29 12 0.41
30 17 0.59
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.37
Consensus pattern (30 bp):
AAAACTTTTTTGTAGTTAAGTAACCAAACA
Found at i:110197799 original size:48 final size:48
Alignment explanation
Indices: 110197744--110197841 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
110197734 AGGTTGGTAG
110197744 AATCCTAGTTGAAGTGGTAGAATACAAATAATATTATTTTAATAGAAA
1 AATCCTAGTTGAAGTGGTAGAATACAAATAATATTATTTTAATAGAAA
110197792 AATCCTAGTTGAAGTGGTAGAATACAAATAATATTATTTTAATAGAAA
1 AATCCTAGTTGAAGTGGTAGAATACAAATAATATTATTTTAATAGAAA
110197840 AA
1 AA
110197842 ATCTCTAACT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.33
Consensus pattern (48 bp):
AATCCTAGTTGAAGTGGTAGAATACAAATAATATTATTTTAATAGAAA
Found at i:110199841 original size:23 final size:23
Alignment explanation
Indices: 110199815--110199935 Score: 79
Period size: 23 Copynumber: 5.2 Consensus size: 23
110199805 ATTTTAGGTG
110199815 TTTGTCTTCCACAATTTTAAGGA
1 TTTGTCTTCCACAATTTTAAGGA
* * *
110199838 TTTGT-TTAGCTAAAATTTTAGGTGA
1 TTTGTCTT--CCACAATTTTAAG-GA
*
110199863 -TTGCCTTCCACAATTTTAAGGA
1 TTTGTCTTCCACAATTTTAAGGA
** *
110199885 TTTGTTCGGCTA-AATTTT-AGGCA
1 TTTG-TCTTCCACAATTTTAAGG-A
* * *
110199908 TTTTTCTTCCATAATTTTAAGGG
1 TTTGTCTTCCACAATTTTAAGGA
110199931 TTTGT
1 TTTGT
110199936 TTCTCTTTTA
Statistics
Matches: 72, Mismatches: 17, Indels: 18
0.67 0.16 0.17
Matches are distributed among these distances:
22 11 0.15
23 38 0.53
24 19 0.26
25 4 0.06
ACGTcount: A:0.24, C:0.13, G:0.17, T:0.46
Consensus pattern (23 bp):
TTTGTCTTCCACAATTTTAAGGA
Found at i:110199871 original size:47 final size:46
Alignment explanation
Indices: 110199800--110199937 Score: 179
Period size: 47 Copynumber: 3.0 Consensus size: 46
110199790 TGCAGGTTAG
*
110199800 GCTAAATTTTAGGTGTTTGTCTTCCACAATTTTAAGGATTTGTTTA
1 GCTAAATTTTAGGTGATTGTCTTCCACAATTTTAAGGATTTGTTTA
* **
110199846 GCTAAAATTTTAGGTGATTGCCTTCCACAATTTTAAGGATTTGTTCG
1 GCT-AAATTTTAGGTGATTGTCTTCCACAATTTTAAGGATTTGTTTA
* * * *
110199893 GCTAAATTTTAGG-CATTTTTCTTCCATAATTTTAAGGGTTTGTTT
1 GCTAAATTTTAGGTGA-TTGTCTTCCACAATTTTAAGGATTTGTTT
110199938 CTCTTTTATC
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
45 1 0.01
46 37 0.46
47 42 0.52
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.46
Consensus pattern (46 bp):
GCTAAATTTTAGGTGATTGTCTTCCACAATTTTAAGGATTTGTTTA
Found at i:110201315 original size:9 final size:9
Alignment explanation
Indices: 110201301--110201335 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
110201291 TTATTTATCC
110201301 AATTAATTA
1 AATTAATTA
*
110201310 AATTAATTG
1 AATTAATTA
*
110201319 AATTAACTA
1 AATTAATTA
110201328 AATTAATT
1 AATTAATT
110201336 TCTTAATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (9 bp):
AATTAATTA
Found at i:110201322 original size:18 final size:18
Alignment explanation
Indices: 110201301--110201335 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
110201291 TTATTTATCC
*
110201301 AATTAATTAAATTAATTG
1 AATTAACTAAATTAATTG
110201319 AATTAACTAAATTAATT
1 AATTAACTAAATTAATT
110201336 TCTTAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (18 bp):
AATTAACTAAATTAATTG
Found at i:110202312 original size:16 final size:16
Alignment explanation
Indices: 110202291--110202323 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
110202281 GACTTAAAAG
110202291 TAACAATGTTAACTTT
1 TAACAATGTTAACTTT
110202307 TAACAATGTTAACTTT
1 TAACAATGTTAACTTT
110202323 T
1 T
110202324 TAGTGTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (16 bp):
TAACAATGTTAACTTT
Found at i:110213591 original size:13 final size:13
Alignment explanation
Indices: 110213573--110213599 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
110213563 ATGAGAGTAC
110213573 TTTTAGGAAACCT
1 TTTTAGGAAACCT
110213586 TTTTAGGAAACCT
1 TTTTAGGAAACCT
110213599 T
1 T
110213600 ATCAAGAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTTTAGGAAACCT
Found at i:110217002 original size:39 final size:39
Alignment explanation
Indices: 110216958--110217085 Score: 202
Period size: 39 Copynumber: 3.3 Consensus size: 39
110216948 TATGAGATTG
110216958 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGA
1 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGA
* *
110216997 AAAATATCCGGACATGAGATCCGCAGGCTATATGCTAGA
1 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGA
* * **
110217036 AATATATCCGGACTTGAGGTCCGCAGGCTACGTGCTGGA
1 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGA
110217075 AAAATATCCGG
1 AAAATATCCGG
110217086 GTTAAAGACC
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 80 1.00
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (39 bp):
AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGA
Found at i:110217099 original size:78 final size:76
Alignment explanation
Indices: 110216957--110217111 Score: 204
Period size: 78 Copynumber: 2.0 Consensus size: 76
110216947 GTATGAGATT
* * *
110216957 GAAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGAAAAATATCCGGACATGAGATCCGCA
1 GAAAATATCCGGACATGAGGTCCGCAGGCTACATGCTGGAAAAATATCCGGACATAAGACCCGCA
*
110217022 GGCTATATGCTA
66 GGCT-TACGCTA
* * **
110217034 GAAATATATCCGGACTTGAGGTCCGCAGGCTACGTGCTGGAAAAATATCCGG-GTTAAAGACCCG
1 GAAA-ATATCCGGACATGAGGTCCGCAGGCTACATGCTGGAAAAATATCCGGACAT-AAGACCCG
110217098 CAGGCTTACGCTA
64 CAGGCTTACGCTA
110217111 G
1 G
110217112 TAATGTATTC
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
77 12 0.18
78 56 0.82
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (76 bp):
GAAAATATCCGGACATGAGGTCCGCAGGCTACATGCTGGAAAAATATCCGGACATAAGACCCGCA
GGCTTACGCTA
Found at i:110224975 original size:38 final size:39
Alignment explanation
Indices: 110224927--110225053 Score: 193
Period size: 39 Copynumber: 3.3 Consensus size: 39
110224917 TATGAGATTG
110224927 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCT-GA
1 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTAGA
*
110224965 AAAATATCCGGACATGAGATCCGCAGGCTATATGCTAGA
1 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTAGA
* * ** *
110225004 AATATATCCGGACTTGAGGTCCGCAGGCTACGTGCTGGA
1 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTAGA
110225043 AAAATATCCGG
1 AAAATATCCGG
110225054 GTTAAAGACC
Statistics
Matches: 80, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
38 35 0.44
39 45 0.56
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.21
Consensus pattern (39 bp):
AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTAGA
Found at i:110225079 original size:77 final size:76
Alignment explanation
Indices: 110224926--110225079 Score: 195
Period size: 77 Copynumber: 2.0 Consensus size: 76
110224916 GTATGAGATT
* * *
110224926 GAAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGAAAAATATCCGGACATGAGATCCGCAG
1 GAAAATATCCGGACATGAGGTCCGCAGGCTACATGCTGAAAAATATCCGGACATAAGACCCGCAG
*
110224991 GCTATATGCTA
66 GCTATACGCTA
* * **
110225002 GAAATATATCCGGACTTGAGGTCCGCAGGCTACGTGCTGGAAAAATATCCGG-GTTAAAGACCCG
1 GAAA-ATATCCGGACATGAGGTCCGCAGGCTACATGCT-GAAAAATATCCGGACAT-AAGACCCG
110225066 CAGGCT-TACGCTA
63 CAGGCTATACGCTA
110225079 G
1 G
110225080 TAATGTATTC
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
76 4 0.06
77 38 0.57
78 25 0.37
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.21
Consensus pattern (76 bp):
GAAAATATCCGGACATGAGGTCCGCAGGCTACATGCTGAAAAATATCCGGACATAAGACCCGCAG
GCTATACGCTA
Found at i:110226906 original size:2 final size:2
Alignment explanation
Indices: 110226899--110227298 Score: 285
Period size: 2 Copynumber: 208.0 Consensus size: 2
110226889 GAATTATTCT
* * * * * *
110226899 TC TC TC TC TC TC TC TC TC TC CC TC CC TC CC TC CC TC CC TC CC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* *
110226941 TC CC TC TC TC TC TC TC TC TC TC TC TC TC -C CC TC TC -C T- TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * *
110226980 CC TC CC TC -C TC -C CC TC TC TC TC TC CC TC TC CC TC TC CC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* *
110227020 TC -C T- TC -C T- TC TC -C T- TC -C TC CC TC CC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * *
110227055 CC CC TC -C TC TC TC TC TC TC TC TC GC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * *
110227096 TC TC CC TC -C TC CC TC TC TC TC TC TC TC CC TC CC TC CC TC -C
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * *
110227136 CC TC TC TC TC TC TC TC TC TC TC TC CC TC TC TC CC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * *
110227178 CC TC CC TC TC TC TC TC TC TC TC AGC TC TC TC TC TC -C TC CC TC
1 TC TC TC TC TC TC TC TC TC TC TC -TC TC TC TC TC TC TC TC TC TC
* * * * * * *
110227220 TC CC TC TC TC TC TC TC TC TT TT TC TC CC TC CC TC CC TC CC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * *
110227262 TC TT TC CC CC TC TC TC TC CC TC TC TC -C CC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
110227299 CTCACACACA
Statistics
Matches: 304, Mismatches: 76, Indels: 36
0.73 0.18 0.09
Matches are distributed among these distances:
1 17 0.06
2 286 0.94
3 1 0.00
ACGTcount: A:0.00, C:0.60, G:0.01, T:0.40
Consensus pattern (2 bp):
TC
Found at i:110227306 original size:2 final size:2
Alignment explanation
Indices: 110227301--110227333 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
110227291 TCTCTCTCCT
110227301 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
110227334 GGAAAATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:110229290 original size:17 final size:17
Alignment explanation
Indices: 110229264--110229297 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
110229254 ATTTATTTAC
110229264 TATGTTCTATT-TTATT
1 TATGTTCTATTATTATT
110229280 TATGCTTCTATTATTATT
1 TATG-TTCTATTATTATT
110229298 ATTGCCTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 7 0.44
18 5 0.31
ACGTcount: A:0.21, C:0.09, G:0.06, T:0.65
Consensus pattern (17 bp):
TATGTTCTATTATTATT
Done.