Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold11
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: 5230303
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 140504 characters in sequence are not A, C, G, or T
File 25 of 29
Found at i:4147775 original size:2 final size:2
Alignment explanation
Indices: 4147768--4147797 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4147758 ATACATAGAC
4147768 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4147798 TTGTGTCTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4148287 original size:21 final size:21
Alignment explanation
Indices: 4148263--4148302 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4148253 TTAAAAATAT
*
4148263 TATTTTAT-ATTAATATTTATA
1 TATTTAATAATTAAT-TTTATA
4148284 TATTTAATAATTAATTTTA
1 TATTTAATAATTAATTTTA
4148303 AATAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTAATAATTAATTTTATA
Found at i:4149576 original size:30 final size:29
Alignment explanation
Indices: 4149536--4149613 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 29
4149526 GTTTATATTA
*
4149536 AAAAATTATTTGAATATAAATTAAAAATT
1 AAAATTTATTTGAATATAAATTAAAAATT
* * *
4149565 GAAAATTTATTTAAATACAAATTAAATATT
1 -AAAATTTATTTGAATATAAATTAAAAATT
*
4149595 AAGATCTTATTTGAATATA
1 AAAAT-TTATTTGAATATA
4149614 TATAATAAAG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.40
Consensus pattern (29 bp):
AAAATTTATTTGAATATAAATTAAAAATT
Found at i:4149687 original size:15 final size:15
Alignment explanation
Indices: 4149667--4149695 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4149657 TCAAATCCAA
4149667 TTATTTTATTTTAAT
1 TTATTTTATTTTAAT
4149682 TTATTTTATTTTAA
1 TTATTTTATTTTAA
4149696 CCATTTGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTATTTTATTTTAAT
Found at i:4151552 original size:34 final size:34
Alignment explanation
Indices: 4151506--4151723 Score: 282
Period size: 34 Copynumber: 6.5 Consensus size: 34
4151496 GTAAAAACCA
*
4151506 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
4151540 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
4151574 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
4151608 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
4151641 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
4151675 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
4151708 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
4151724 TCTCCCACTT
Statistics
Matches: 162, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
33 45 0.28
34 115 0.71
35 2 0.01
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:4151620 original size:68 final size:67
Alignment explanation
Indices: 4151504--4151723 Score: 323
Period size: 67 Copynumber: 3.3 Consensus size: 67
4151494 TGGTAAAAAC
* * *
4151504 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
4151569 AT
66 AT
* * *
4151571 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
4151636 AAT
65 AAT
* * * * * *
4151639 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
4151704 AT
66 AT
4151706 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
4151724 TCTCCCACTT
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 75 0.55
68 61 0.45
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:4155814 original size:19 final size:19
Alignment explanation
Indices: 4155787--4155849 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
4155777 TCACGTGTAC
* *
4155787 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
4155806 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
4155825 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
4155844 AGTACC
1 AGTACC
4155850 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:4156197 original size:34 final size:34
Alignment explanation
Indices: 4156151--4156367 Score: 244
Period size: 34 Copynumber: 6.4 Consensus size: 34
4156141 GTAAAAACCA
*
4156151 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
4156185 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
4156219 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
**
4156253 CCATTTAATCAACAATGGTAAGTTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
4156286 CCATTTAGTCAACAATGGACAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG--TAACCTACCAAATCTC
* * * * *
4156321 TCATTTAATCAACAATGATAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
4156354 CCATTTAATCAACA
1 CCATTTAATCAACA
4156368 GTATCCTCCT
Statistics
Matches: 155, Mismatches: 22, Indels: 13
0.82 0.12 0.07
Matches are distributed among these distances:
33 34 0.22
34 102 0.66
35 19 0.12
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:4156265 original size:68 final size:67
Alignment explanation
Indices: 4156149--4156367 Score: 285
Period size: 68 Copynumber: 3.2 Consensus size: 67
4156139 TAGTAAAAAC
* * *
4156149 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
4156214 AT
66 AT
* * * *
4156216 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGTTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
4156281 AAT
65 AAT
* * * * * * * *
4156284 CTCCATTTAGTCAACAATGGACAAACCACCAAATCACTCATTTAATCAACAATGATAAACTACTA
1 CACCATTTAATCAACAATGG-CAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
4156349 AAT
65 AAT
4156352 CACCATTTAATCAACA
1 CACCATTTAATCAACA
4156368 GTATCCTCCT
Statistics
Matches: 130, Mismatches: 20, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
67 19 0.15
68 111 0.85
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:4156327 original size:102 final size:101
Alignment explanation
Indices: 4156149--4156367 Score: 316
Period size: 102 Copynumber: 2.2 Consensus size: 101
4156139 TAGTAAAAAC
* *
4156149 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAA
* *
4156214 ATCACCCATTTAATCAACAATGGTAAGCTACCAAATTT
66 ATCACCCATTTAATCAACAATGATAAACTACCAAA--T
* **
4156252 C-CCATTTAATCAACAATGGTAAGTTACCAAATCT-CCATTTAGTCAACAATGGACAAACCACCA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGG-CAAACCACCA
* *
4156315 AATCACTCATTTAATCAACAATGATAAACTACTAAAT
65 AATCACCCATTTAATCAACAATGATAAACTACCAAAT
4156352 CACCATTTAATCAACA
1 CACCATTTAATCAACA
4156368 GTATCCTCCT
Statistics
Matches: 105, Mismatches: 9, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
100 2 0.02
101 32 0.30
102 70 0.67
103 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGATAAACTACCAAAT
Found at i:4162320 original size:3 final size:3
Alignment explanation
Indices: 4162312--4162350 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
4162302 TATCTGTCTC
4162312 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4162351 AAATTTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:4164103 original size:2 final size:2
Alignment explanation
Indices: 4164096--4164122 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4164086 TGAAAACATC
4164096 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4164123 TGAAAGGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4168523 original size:23 final size:25
Alignment explanation
Indices: 4168497--4168542 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
4168487 TGTCCTTGTT
*
4168497 TTTCCATTTC-CCTTT-TTATTTTC
1 TTTCAATTTCACCTTTGTTATTTTC
4168520 TTTCAATTTCACCTTTGTTATTT
1 TTTCAATTTCACCTTTGTTATTT
4168543 GTATTTGTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 5 0.25
25 6 0.30
ACGTcount: A:0.13, C:0.22, G:0.02, T:0.63
Consensus pattern (25 bp):
TTTCAATTTCACCTTTGTTATTTTC
Found at i:4173883 original size:26 final size:26
Alignment explanation
Indices: 4173847--4173898 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
4173837 TGATAGGTAA
4173847 AAGCTCATTCAATGGCCATTATTGTT
1 AAGCTCATTCAATGGCCATTATTGTT
4173873 AAGCTCATTCAATGGCCATTATTGTT
1 AAGCTCATTCAATGGCCATTATTGTT
4173899 CTTTTACTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (26 bp):
AAGCTCATTCAATGGCCATTATTGTT
Found at i:4178752 original size:7 final size:7
Alignment explanation
Indices: 4178727--4178781 Score: 55
Period size: 7 Copynumber: 8.1 Consensus size: 7
4178717 TTTAAGTTTA
4178727 ATTA-TT
1 ATTATTT
4178733 ATTA-TT
1 ATTATTT
4178739 ATATATTT
1 AT-TATTT
4178747 ATTATTT
1 ATTATTT
4178754 ATTA-TT
1 ATTATTT
4178760 -TTATTT
1 ATTATTT
*
4178766 ATTTTTT
1 ATTATTT
4178773 ATTAATTT
1 ATT-ATTT
4178781 A
1 A
4178782 AATGTTAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
5 3 0.07
6 12 0.29
7 19 0.45
8 8 0.19
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
ATTATTT
Found at i:4178772 original size:11 final size:11
Alignment explanation
Indices: 4178723--4178780 Score: 53
Period size: 11 Copynumber: 5.0 Consensus size: 11
4178713 AAATTTTAAG
*
4178723 TTTAATTATTAT
1 TTTATTTATT-T
*
4178735 TATTATATATTT
1 T-TTATTTATTT
*
4178747 ATTATTTATTAT
1 TTTATTTATT-T
4178759 TTTATTTATTT
1 TTTATTTATTT
*
4178770 TTTATTAATTT
1 TTTATTTATTT
4178781 AAATGTTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
11 19 0.50
12 12 0.32
13 7 0.18
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTATTTATTT
Found at i:4179421 original size:27 final size:27
Alignment explanation
Indices: 4179386--4179446 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 27
4179376 ATTTAATTTT
4179386 ATTTAAAATTTA-A-AAATATTATTTAAAA
1 ATTT-AAATTTATATAAATATTA--TAAAA
4179414 ATTTAAATTTATATTAAATATTATAAAA
1 ATTTAAATTTATA-TAAATATTATAAAA
4179442 ATTTA
1 ATTTA
4179447 TTATTATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
27 7 0.23
28 15 0.50
30 8 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
ATTTAAATTTATATAAATATTATAAAA
Found at i:4179449 original size:20 final size:19
Alignment explanation
Indices: 4179383--4179448 Score: 73
Period size: 19 Copynumber: 3.3 Consensus size: 19
4179373 TTTATTTAAT
4179383 TTTATTTAAAATTTAAAAA
1 TTTATTTAAAATTTAAAAA
4179402 TATTATTTAAAAATTT--AAA
1 T-TTATTT-AAAATTTAAAAA
4179421 TTTATATTAAATATTATAAAAA
1 TTTAT-TTAAA-ATT-TAAAAA
4179443 TTTATT
1 TTTATT
4179449 ATTATTTAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
18 7 0.17
19 10 0.25
20 7 0.17
21 8 0.20
22 8 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTATTTAAAATTTAAAAA
Found at i:4179456 original size:38 final size:38
Alignment explanation
Indices: 4179374--4179459 Score: 97
Period size: 38 Copynumber: 2.3 Consensus size: 38
4179364 AAAATTATAT
*
4179374 TTATTTAATTTTATTTAAAATTTAAAAATATTATTTAA
1 TTATTTAAATTTATTTAAAATTTAAAAATATTATTTAA
**
4179412 AAATTTAAATTTATATTAAATATTATAAAAAT-TTA-TT-A
1 TTATTTAAATTTAT-TTAAA-ATT-TAAAAATATTATTTAA
4179450 TTATTTAAAT
1 TTATTTAAAT
4179460 AAATTTTATT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
38 20 0.50
39 7 0.17
40 6 0.15
41 7 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (38 bp):
TTATTTAAATTTATTTAAAATTTAAAAATATTATTTAA
Found at i:4179476 original size:22 final size:23
Alignment explanation
Indices: 4179417--4179476 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 23
4179407 TTTAAAAATT
*
4179417 TAAATTTATATTAAATA-TTATAA
1 TAAATTT-TATTTAATATTTATAA
*
4179440 -AAA-TTTA-TTATTATTTA-AA
1 TAAATTTTATTTAATATTTATAA
4179459 TAAATTTTATTTAATATT
1 TAAATTTTATTTAATATT
4179477 ATTTATAACT
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
19 6 0.20
20 8 0.27
21 6 0.20
22 10 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TAAATTTTATTTAATATTTATAA
Found at i:4179847 original size:45 final size:45
Alignment explanation
Indices: 4179798--4179900 Score: 106
Period size: 45 Copynumber: 2.3 Consensus size: 45
4179788 TTTATAATTT
*
4179798 TAAAAAATAAAAATATTATTAT-TC-AATTAA-TTAATAATTTTTAT-A
1 TAAAAAATAAAAA-ATT-TTATCTCGAA-TAACAT-ATAATTTTTATCA
* *
4179843 TAAAAAATTATAAAATTTTATCTCGAATAACATATAATTTTTGTCA
1 TAAAAAA-TAAAAAATTTTATCTCGAATAACATATAATTTTTATCA
4179889 TAAAAAATAAAA
1 TAAAAAATAAAA
4179901 TAATATAAGA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
44 4 0.08
45 29 0.59
46 16 0.33
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (45 bp):
TAAAAAATAAAAAATTTTATCTCGAATAACATATAATTTTTATCA
Found at i:4180751 original size:16 final size:14
Alignment explanation
Indices: 4180717--4180759 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
4180707 AACATAATTT
*
4180717 TATAAAATTTAATA
1 TATAAAATTTAAAA
4180731 TATAAAATATTAAAA
1 TATAAAAT-TTAAAA
*
4180746 -ATATAATTTAAAA
1 TATAAAATTTAAAA
4180759 T
1 T
4180760 TATGTTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 6 0.24
14 14 0.56
15 5 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TATAAAATTTAAAA
Found at i:4181391 original size:22 final size:21
Alignment explanation
Indices: 4181334--4181394 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 21
4181324 TTTATAAAAT
*
4181334 ATTAAAATATTAATTTTAATA
1 ATTAAAATATAAATTTTAATA
4181355 ATTAAAAGT-TAAAATTTTAATA
1 ATTAAAA-TAT-AAATTTTAATA
*
4181377 ATTTTAAATATAAATTTT
1 A-TTAAAATATAAATTTT
4181395 TAAAAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
21 8 0.24
22 20 0.59
23 6 0.18
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
ATTAAAATATAAATTTTAATA
Found at i:4181684 original size:22 final size:21
Alignment explanation
Indices: 4181637--4181678 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
4181627 TTGAAACATA
4181637 TATTTAAATAAAAATAAAATT
1 TATTTAAATAAAAATAAAATT
*
4181658 TATTTAAA-ATAAATAAAATT
1 TATTTAAATAAAAATAAAATT
4181678 T
1 T
4181679 TAATTTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TATTTAAATAAAAATAAAATT
Found at i:4181733 original size:18 final size:18
Alignment explanation
Indices: 4181710--4181748 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
4181700 AATTTATTTT
4181710 TTAA-TTATATAATATATA
1 TTAATTTATAT-ATATATA
*
4181728 TTAATTTATATTTATATA
1 TTAATTTATATATATATA
4181746 TTA
1 TTA
4181749 TATAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAATTTATATATATATA
Found at i:4181799 original size:14 final size:14
Alignment explanation
Indices: 4181743--4181801 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 14
4181733 TTATATTTAT
**
4181743 ATATTATATAATTT
1 ATATTATATAATAA
* *
4181757 TTATTATATAAAAA
1 ATATTATATAATAA
*
4181771 ATA-AATAT-A-AA
1 ATATTATATAATAA
4181782 ATATTATATAATAA
1 ATATTATATAATAA
4181796 ATATTA
1 ATATTA
4181802 AAAAATAGAT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
11 5 0.14
12 5 0.14
13 5 0.14
14 20 0.57
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATATTATATAATAA
Found at i:4181851 original size:21 final size:21
Alignment explanation
Indices: 4181827--4181866 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4181817 TATTTATTTT
4181827 TTAAAAT-TTAATAATAAATTA
1 TTAAAATATTAA-AATAAATTA
*
4181848 TTAAATTATTAAAATAAAT
1 TTAAAATATTAAAATAAAT
4181867 AAATTATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAAAATATTAAAATAAATTA
Found at i:4181867 original size:25 final size:24
Alignment explanation
Indices: 4181839--4181944 Score: 85
Period size: 27 Copynumber: 4.2 Consensus size: 24
4181829 AAAATTTAAT
4181839 AATAAATTATTAAATTATTAAAATA
1 AATAAATTATTAAATTA-TAAAATA
*
4181864 AATAAATTATATAATATAATATAAATA
1 AATAAATTAT-TAA-ATTATA-AAATA
* *
4181891 AATTTAAATTATTTATTTATAAATATA
1 AA--TAAATTATTAAATTATAAA-ATA
4181918 AATAAA-T-TTAAA-TA-AAATATA
1 AATAAATTATTAAATTATAAA-ATA
4181939 AATAAA
1 AATAAA
4181945 ATTTAAAACT
Statistics
Matches: 69, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
21 13 0.19
22 2 0.03
23 3 0.04
24 1 0.01
25 14 0.20
26 7 0.10
27 19 0.28
28 2 0.03
29 8 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
AATAAATTATTAAATTATAAAATA
Found at i:4181869 original size:17 final size:19
Alignment explanation
Indices: 4181849--4181889 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
4181839 AATAAATTAT
4181849 TAAATTAT-TAAAATAA-A
1 TAAATTATATAAAATAATA
*
4181866 TAAATTATATAATATAATA
1 TAAATTATATAAAATAATA
4181885 TAAAT
1 TAAAT
4181890 AAATTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.38
18 7 0.33
19 6 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TAAATTATATAAAATAATA
Found at i:4181898 original size:10 final size:10
Alignment explanation
Indices: 4181862--4181951 Score: 65
Period size: 11 Copynumber: 8.4 Consensus size: 10
4181852 ATTATTAAAA
4181862 TAAATAAATT
1 TAAATAAATT
*
4181872 ATATAATATAATA
1 -TA-AATA-AATT
4181885 TAAATAAATT
1 TAAATAAATT
*
4181895 TAAAT-TATT
1 TAAATAAATT
* *
4181904 TATTTATAAATA
1 TA--AATAAATT
4181916 TAAATAAATT
1 TAAATAAATT
*
4181926 TAAATAAAATA
1 TAAAT-AAATT
4181937 TAAATAAAATT
1 TAAAT-AAATT
4181948 TAAA
1 TAAA
4181952 ACTCATATCG
Statistics
Matches: 63, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
9 5 0.08
10 19 0.30
11 26 0.41
12 10 0.16
13 3 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
TAAATAAATT
Found at i:4181899 original size:54 final size:53
Alignment explanation
Indices: 4181841--4181951 Score: 154
Period size: 54 Copynumber: 2.1 Consensus size: 53
4181831 AATTTAATAA
*
4181841 TAAATTATTAAATTATTAAA-ATAAATAAATTATATAATATAATATAAAT-AAATT
1 TAAATTATTAAATTA-TAAATATAAATAAATT-TA-AATAAAATATAAATAAAATT
* *
4181895 TAAATTATTTATTTATAAATATAAATAAATTTAAATAAAATATAAATAAAATT
1 TAAATTATTAAATTATAAATATAAATAAATTTAAATAAAATATAAATAAAATT
4181948 TAAA
1 TAAA
4181952 ACTCATATCG
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
52 13 0.25
53 15 0.29
54 24 0.46
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (53 bp):
TAAATTATTAAATTATAAATATAAATAAATTTAAATAAAATATAAATAAAATT
Found at i:4181944 original size:31 final size:31
Alignment explanation
Indices: 4181862--4181944 Score: 103
Period size: 31 Copynumber: 2.6 Consensus size: 31
4181852 ATTATTAAAA
4181862 TAAATAAATTATATAATATAATATAAATAAATT
1 TAAATAAATTATA-AATA-AATATAAATAAATT
* * **
4181895 TAAATTATTTATTTATAAATATAAATAAATT
1 TAAATAAATTATAAATAAATATAAATAAATT
*
4181926 TAAATAAAATATAAATAAA
1 TAAATAAATTATAAATAAA
4181945 ATTTAAAACT
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
31 28 0.68
32 3 0.07
33 10 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (31 bp):
TAAATAAATTATAAATAAATATAAATAAATT
Found at i:4181959 original size:22 final size:21
Alignment explanation
Indices: 4181862--4181951 Score: 76
Period size: 21 Copynumber: 4.2 Consensus size: 21
4181852 ATTATTAAAA
* *
4181862 TAAATAAATTATATAATATAATA
1 TAAATAAAATATA-AATA-AATT
* *
4181885 TAAAT-AAATTTAAAT-TATT
1 TAAATAAAATATAAATAAATT
**
4181904 TATTTATAAATATAAATAAATT
1 TAAATA-AAATATAAATAAATT
4181926 TAAATAAAATATAAATAAAATT
1 TAAATAAAATATAAAT-AAATT
4181948 TAAA
1 TAAA
4181952 ACTCATATCG
Statistics
Matches: 53, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
19 5 0.09
21 22 0.42
22 21 0.40
23 5 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATAAAATATAAATAAATT
Found at i:4186043 original size:22 final size:19
Alignment explanation
Indices: 4186009--4186048 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 19
4185999 ATTTTTAAAA
4186009 TTTTTTAAATTATATATTAT
1 TTTTTTAAATTATA-ATTAT
4186029 TTTTATTATAATTATAATTA
1 TTTT-TTA-AATTATAATTA
4186049 AAATATTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTTTAAATTATAATTAT
Found at i:4188190 original size:18 final size:19
Alignment explanation
Indices: 4188163--4188204 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
4188153 CATTCATAAA
4188163 TTAT-TTTACTAAATT-TT
1 TTATATTTACTAAATTATT
4188180 TTATATTTACTAAATTATT
1 TTATATTTACTAAATTATT
4188199 TT-TATT
1 TTATATT
4188205 AAATTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.17
18 15 0.65
19 4 0.17
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATATTTACTAAATTATT
Found at i:4188390 original size:17 final size:19
Alignment explanation
Indices: 4188368--4188408 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
4188358 TAAAATTATT
4188368 TATTATTTATT-T-AATAA
1 TATTATTTATTATAAATAA
4188385 TATTA-TTATTATAAATAA
1 TATTATTTATTATAAATAA
4188403 T-TTATT
1 TATTATT
4188409 AATATCAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.24
17 9 0.43
18 7 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TATTATTTATTATAAATAA
Found at i:4188418 original size:17 final size:18
Alignment explanation
Indices: 4188380--4188418 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
4188370 TTATTTATTT
*
4188380 AATAATATTATTATTATA
1 AATAATATTATTAATATA
*
4188398 AATAAT-TTATTAATATC
1 AATAATATTATTAATATA
4188415 AATA
1 AATA
4188419 TTTGATGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
AATAATATTATTAATATA
Found at i:4188781 original size:74 final size:75
Alignment explanation
Indices: 4188687--4188866 Score: 310
Period size: 75 Copynumber: 2.4 Consensus size: 75
4188677 AAATGTGGGA
4188687 GGTCACTTAGAGGAACTATGAAACCAATACACAATAATTG-AAAAAAAAAATGCGAAA-TGTGGG
1 GGTCACTTAGAGGAACTATGAAACCAATACACAATAATTGAAAAAAAAAAATGCGAAATTG-GGG
4188750 ATTCGAAACCT
65 ATTCGAAACCT
*
4188761 GGTCACTTAGAGGAACTATGAAACCAATACACAATAATTGAAAAAAAAAAATGTGAAATTGGGGA
1 GGTCACTTAGAGGAACTATGAAACCAATACACAATAATTGAAAAAAAAAAATGCGAAATTGGGGA
4188826 TTCGAAACCT
66 TTCGAAACCT
* *
4188836 GGTCACTTAGAGGAACTAAGAAACCAGTACA
1 GGTCACTTAGAGGAACTATGAAACCAATACA
4188867 GCTAAAAGCT
Statistics
Matches: 101, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
74 40 0.40
75 59 0.58
76 2 0.02
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.20
Consensus pattern (75 bp):
GGTCACTTAGAGGAACTATGAAACCAATACACAATAATTGAAAAAAAAAAATGCGAAATTGGGGA
TTCGAAACCT
Found at i:4190831 original size:26 final size:22
Alignment explanation
Indices: 4190780--4190823 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
4190770 TTTTTAAGAT
4190780 TGATTCTGTAAGTTCCTTCGTC
1 TGATTCTGTAAGTTCCTTCGTC
4190802 TGATTCTGTAAGTTCCTTCGTC
1 TGATTCTGTAAGTTCCTTCGTC
4190824 CCCGTGATAA
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:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (22 bp):
TGATTCTGTAAGTTCCTTCGTC
Found at i:4192115 original size:18 final size:18
Alignment explanation
Indices: 4192055--4192121 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 18
4192045 GATCAGAATA
4192055 ATTAAATTAAATTATTTAAT
1 ATTAAA-TAAA-TATTTAAT
4192075 -TTAAA-AAAT-TTTAAGT
1 ATTAAATAAATATTTAA-T
4192091 ATTAAATAAATATTTAAT
1 ATTAAATAAATATTTAAT
*
4192109 ATGAAATATAATA
1 ATTAAATA-AATA
4192122 AAATATTTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
15 5 0.12
16 2 0.05
17 8 0.20
18 12 0.29
19 14 0.34
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (18 bp):
ATTAAATAAATATTTAAT
Found at i:4192121 original size:19 final size:19
Alignment explanation
Indices: 4192080--4192121 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
4192070 TTAATTTAAA
*
4192080 AAAT-TTTAAGTATTAAAT
1 AAATATTTAAGTATGAAAT
4192098 AAATATTTAA-TATGAAAT
1 AAATATTTAAGTATGAAAT
4192116 ATAATA
1 A-AATA
4192122 AAATATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (19 bp):
AAATATTTAAGTATGAAAT
Found at i:4192144 original size:24 final size:25
Alignment explanation
Indices: 4192090--4192149 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 25
4192080 AAATTTTAAG
*
4192090 TATTAA-ATAAATATTTAATATGAAA
1 TATTAATA-AAATATTTAATATAAAA
4192115 TA-TAATAAAATATTTAATA-AAAA
1 TATTAATAAAATATTTAATATAAAA
*
4192138 TATTAATTAAAT
1 TATTAATAAAAT
4192150 GATATAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 5 0.16
24 23 0.74
25 3 0.10
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
TATTAATAAAATATTTAATATAAAA
Found at i:4195563 original size:2 final size:2
Alignment explanation
Indices: 4195556--4195596 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
4195546 CCTCCTGGGC
4195556 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4195596 T
1 T
4195597 GGTAAAAACT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4196110 original size:21 final size:21
Alignment explanation
Indices: 4196086--4196148 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 21
4196076 TAATAAAATA
*
4196086 TATATTTTAT-TAAATAGTTAT
1 TATATTTTATATAAA-AATTAT
4196107 TATATTTTATATAAAAATTAT
1 TATATTTTATATAAAAATTAT
* **
4196128 T-TATTTAATATTTAAATTAT
1 TATATTTTATATAAAAATTAT
4196148 T
1 T
4196149 TTTAATTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 17 0.46
21 16 0.43
22 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
TATATTTTATATAAAAATTAT
Found at i:4197527 original size:24 final size:24
Alignment explanation
Indices: 4197499--4197547 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
4197489 TTTTTTTTTT
* *
4197499 AATAA-AAAAATATTATAATTTAAA
1 AATAAGAAAAAAATTA-AAATTAAA
4197523 AATAAGAAAAAAATTAAAATTAAA
1 AATAAGAAAAAAATTAAAATTAAA
4197547 A
1 A
4197548 TTTATTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (24 bp):
AATAAGAAAAAAATTAAAATTAAA
Found at i:4197809 original size:21 final size:21
Alignment explanation
Indices: 4197783--4197825 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
4197773 TCCATTTATG
4197783 TCTAGTG-CCCGCATTTACAAA
1 TCTAGTGTCCC-CATTTACAAA
4197804 TCTAGTGTCCCCATTTACAAA
1 TCTAGTGTCCCCATTTACAAA
4197825 T
1 T
4197826 TACGGATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.33
Consensus pattern (21 bp):
TCTAGTGTCCCCATTTACAAA
Found at i:4198131 original size:18 final size:18
Alignment explanation
Indices: 4198088--4198160 Score: 66
Period size: 22 Copynumber: 4.1 Consensus size: 18
4198078 TTTTATTATG
4198088 TTATATTTATATTTAAAATATT
1 TTATATTTATA--T-AAAT-TT
4198110 TTATATTTATATAAATTT
1 TTATATTTATATAAATTT
4198128 TTATATGTTA-AT-AA--T
1 TTATAT-TTATATAAATTT
4198143 TTAT-TTTATATAAATTT
1 TTATATTTATATAAATTT
4198160 T
1 T
4198161 AAAATTTTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
13 3 0.07
14 3 0.07
15 7 0.15
17 4 0.09
18 10 0.22
19 7 0.15
20 1 0.02
22 11 0.24
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (18 bp):
TTATATTTATATAAATTT
Found at i:4198151 original size:20 final size:19
Alignment explanation
Indices: 4198088--4198153 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 19
4198078 TTTTATTATG
4198088 TTATATTTATATTTAAAATATT
1 TTATATTTATA--T-AAATATT
4198110 TTATATTTATATAAAT-TT
1 TTATATTTATATAAATATT
*
4198128 TTATATGTTA-ATAATTTATT
1 TTATAT-TTATATAA-ATATT
4198148 TTATAT
1 TTATAT
4198154 AAATTTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
18 12 0.30
19 8 0.20
20 9 0.22
22 11 0.28
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
TTATATTTATATAAATATT
Found at i:4198769 original size:19 final size:20
Alignment explanation
Indices: 4198747--4198785 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
4198737 TTTATTAGGG
*
4198747 ATTTGAATT-TTTTAAAATA
1 ATTTGAATTATATTAAAATA
*
4198766 ATTTTAATTATATTAAAATA
1 ATTTGAATTATATTAAAATA
4198786 GTAATTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (20 bp):
ATTTGAATTATATTAAAATA
Found at i:4199265 original size:10 final size:10
Alignment explanation
Indices: 4199250--4199286 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
4199240 TTAATTAGCC
4199250 TATATAAATA
1 TATATAAATA
*
4199260 TATATATATA
1 TATATAAATA
4199270 TATATAAATA
1 TATATAAATA
*
4199280 TTTATAA
1 TATATAA
4199287 GTAGTAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
TATATAAATA
Found at i:4199610 original size:12 final size:12
Alignment explanation
Indices: 4199574--4199617 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 12
4199564 TAATAATATT
4199574 TTTTATTTAAAAAA
1 TTTTATTT--AAAA
*
4199588 TTTAAATTTAAAA
1 TTT-TATTTAAAA
4199601 TTTTATTTAAAA
1 TTTTATTTAAAA
4199613 TTTTA
1 TTTTA
4199618 AATATTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 13 0.48
13 7 0.26
14 3 0.11
15 4 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TTTTATTTAAAA
Found at i:4199619 original size:26 final size:28
Alignment explanation
Indices: 4199574--4199626 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
4199564 TAATAATATT
4199574 TTTTATTTAAAAAATTTAAAT-TTAAAA
1 TTTTATTTAAAAAATTTAAATATTAAAA
*
4199601 TTTTATTT-AAAATTTTAAATATTAAA
1 TTTTATTTAAAAAATTTAAATATTAAA
4199627 TCATTTAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 11 0.46
27 13 0.54
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
TTTTATTTAAAAAATTTAAATATTAAAA
Found at i:4202293 original size:35 final size:35
Alignment explanation
Indices: 4202232--4202302 Score: 83
Period size: 35 Copynumber: 2.0 Consensus size: 35
4202222 GTCCGGTCCA
* * *
4202232 ATTTAAAATATATATTATTAAAAAAAATATATGTTT
1 ATTTAAAATATATATAATAAAAAAAAAAATAT-TTT
4202268 ATTT-AAATATA-ATAATAAAATAAAAAAATATTTT
1 ATTTAAAATATATATAATAAAA-AAAAAAATATTTT
4202302 A
1 A
4202303 ATATATTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
34 11 0.35
35 16 0.52
36 4 0.13
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (35 bp):
ATTTAAAATATATATAATAAAAAAAAAAATATTTT
Found at i:4203879 original size:3 final size:3
Alignment explanation
Indices: 4203871--4203906 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
4203861 AGTTTAGACA
4203871 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
4203907 GATACATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4204984 original size:22 final size:23
Alignment explanation
Indices: 4204959--4205004 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
4204949 ATTATTAAAA
*
4204959 TAAATAATTAT-TAATAAAA-ATT
1 TAAAAAATTATATAA-AAAAGATT
4204981 TAAAAAATTATATAAAAAAGATT
1 TAAAAAATTATATAAAAAAGATT
4205004 T
1 T
4205005 TGCACTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (23 bp):
TAAAAAATTATATAAAAAAGATT
Found at i:4205756 original size:3 final size:3
Alignment explanation
Indices: 4205748--4205806 Score: 91
Period size: 3 Copynumber: 19.7 Consensus size: 3
4205738 TCTGAAAATT
*
4205748 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
4205796 GAA TAA AAA TA
1 TAA TAA TAA TA
4205807 TCTATATGTC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:4208468 original size:3 final size:3
Alignment explanation
Indices: 4208460--4208494 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
4208450 TTAATCCTGG
4208460 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
4208495 TAAACCCAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:4208991 original size:16 final size:14
Alignment explanation
Indices: 4208952--4208980 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4208942 AAACAAACAT
4208952 ATATATATATGTTA
1 ATATATATATGTTA
4208966 ATATATATATGTTA
1 ATATATATATGTTA
4208980 A
1 A
4208981 GTTATTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (14 bp):
ATATATATATGTTA
Found at i:4210037 original size:26 final size:26
Alignment explanation
Indices: 4209993--4210046 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
4209983 TTTACACATC
4209993 AATTATTAAAAAAATTATATT-AATT
1 AATTATTAAAAAAATTATATTAAATT
**
4210018 AATTATTTTAAAAATATATATTAAATT
1 AATTATTAAAAAAAT-TATATTAAATT
4210045 AA
1 AA
4210047 ATTAATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 13 0.52
26 6 0.24
27 6 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
AATTATTAAAAAAATTATATTAAATT
Found at i:4210242 original size:144 final size:147
Alignment explanation
Indices: 4210070--4210362 Score: 484
Period size: 147 Copynumber: 2.0 Consensus size: 147
4210060 ATCAAATAAA
* *
4210070 ATTAATAAAAATATCTAATTATATAATAATAAAAAAAT-T-ATTAACAGTATCGTAATCTTTTT-
1 ATTAATAAAAACATCTAATTATACAATAATAAAAAAATATGATTAACAGTATCGTAATCTTTTTC
*
4210132 TTCTTGAAAAATATGATTTAAAATAATTATTTTATTTATCTTAAAAAAACTGACGTTAATTTTTT
66 TTCTTGAAAAATATGATTTAAAATAATTATTTTATTTATCTTAAAAAAACTGACGTTAATTTTGT
*
4210197 TTCCTTTTTCATCTTTT
131 TTACTTTTTCATCTTTT
* * * *
4210214 ATTAATAAAAGCATTTAATTATGCAATAATAAAAAAATATGATTAATAGTATCGTAATCTTTTTC
1 ATTAATAAAAACATCTAATTATACAATAATAAAAAAATATGATTAACAGTATCGTAATCTTTTTC
*
4210279 TTCTTGAAAAATATGATTTAAAATAATTATTTTATTTATCTTAAAAAAACTGATGTTAATTTTGT
66 TTCTTGAAAAATATGATTTAAAATAATTATTTTATTTATCTTAAAAAAACTGACGTTAATTTTGT
4210344 TTACTTTTTCATCTTTT
131 TTACTTTTTCATCTTTT
4210361 AT
1 AT
4210363 ATTTTATGTG
Statistics
Matches: 137, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
144 33 0.24
145 1 0.01
146 22 0.16
147 81 0.59
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.47
Consensus pattern (147 bp):
ATTAATAAAAACATCTAATTATACAATAATAAAAAAATATGATTAACAGTATCGTAATCTTTTTC
TTCTTGAAAAATATGATTTAAAATAATTATTTTATTTATCTTAAAAAAACTGACGTTAATTTTGT
TTACTTTTTCATCTTTT
Found at i:4211332 original size:22 final size:22
Alignment explanation
Indices: 4211307--4211368 Score: 56
Period size: 22 Copynumber: 2.8 Consensus size: 22
4211297 ATATTTAATT
4211307 TTTATATTTAAAATATAATTAA
1 TTTATATTTAAAATATAATTAA
* *
4211329 TTTA-ATATAAAAATATATTTTAA
1 TTTATAT-TTAAAATATA-ATTAA
* *
4211352 ATTAT-TTTAAAAAATAA
1 TTTATATTTAAAATATAA
4211369 GGACTATTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
21 2 0.06
22 21 0.68
23 8 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TTTATATTTAAAATATAATTAA
Found at i:4211819 original size:3 final size:3
Alignment explanation
Indices: 4211811--4211869 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
4211801 TATGAAGCTT
4211811 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4211859 TAA TAA TAA TA
1 TAA TAA TAA TA
4211870 TCTATACGTC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:4212990 original size:22 final size:22
Alignment explanation
Indices: 4212965--4213006 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
4212955 TATGTAAATT
* *
4212965 AATTGAATTAAATTTATATTTA
1 AATTAAATTAAATTAATATTTA
4212987 AATTAAATTAAATTAATATT
1 AATTAAATTAAATTAATATT
4213007 AGAGTACGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
AATTAAATTAAATTAATATTTA
Found at i:4215397 original size:2 final size:2
Alignment explanation
Indices: 4215392--4215426 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4215382 TCTATATAAG
4215392 TA TA TA TA TA TA TA TA TA TA 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 TA T
4215427 CTCAAATCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4216072 original size:2 final size:2
Alignment explanation
Indices: 4216065--4216108 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
4216055 GAATAAAGAC
4216065 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4216106 AT A
1 AT A
4216109 AGTCCCTTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4217324 original size:32 final size:32
Alignment explanation
Indices: 4217285--4217377 Score: 109
Period size: 32 Copynumber: 2.8 Consensus size: 32
4217275 CGAAAATTTT
4217285 AAAATTTATATAATATAAATTATTAACAT-ATA
1 AAAATTTATATAATATAAATTA-TAACATGATA
4217317 AAAATTTATATAAATATAAA-TATAACATGATA
1 AAAATTTATAT-AATATAAATTATAACATGATA
*
4217349 AAATATATAAATATAATATAAATATATAA
1 AAA-AT-T-TATATAATATAAAT-TATAA
4217378 ATTTTTGGAT
Statistics
Matches: 53, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
31 6 0.11
32 19 0.36
33 10 0.19
34 9 0.17
35 4 0.08
36 5 0.09
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (32 bp):
AAAATTTATATAATATAAATTATAACATGATA
Found at i:4217333 original size:18 final size:18
Alignment explanation
Indices: 4217285--4217336 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
4217275 CGAAAATTTT
4217285 AAAATTTATAT-AATAT-
1 AAAATTTATATAAATATA
4217301 -AAA-TTAT-TAACATATA
1 AAAATTTATATAA-ATATA
4217317 AAAATTTATATAAATATA
1 AAAATTTATATAAATATA
4217335 AA
1 AA
4217337 TATAACATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
13 1 0.03
14 5 0.17
15 7 0.23
17 3 0.10
18 11 0.37
19 3 0.10
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATTTATATAAATATA
Found at i:4217335 original size:6 final size:6
Alignment explanation
Indices: 4217291--4217374 Score: 59
Period size: 6 Copynumber: 13.7 Consensus size: 6
4217281 TTTTAAAATT
* **
4217291 TATATAA TATAAA TTATTAACA TATAAA AATTTA TATAAA TATAAA TATAACA
1 TATA-AA TATAAA -TA-TAA-A TATAAA TATAAA TATAAA TATAAA TATAA-A
4217344 TGATAAA -AT--A TATAAA TAT-AA TATAAA TATA
1 T-ATAAA TATAAA TATAAA TATAAA TATAAA TATA
4217375 TAAATTTTTG
Statistics
Matches: 62, Mismatches: 6, Indels: 19
0.71 0.07 0.22
Matches are distributed among these distances:
3 1 0.02
4 2 0.03
5 7 0.11
6 30 0.48
7 12 0.19
8 9 0.15
9 1 0.02
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (6 bp):
TATAAA
Found at i:4217373 original size:19 final size:23
Alignment explanation
Indices: 4217330--4217379 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 23
4217320 ATTTATATAA
4217330 ATATAAATATAACATGATAAAAT
1 ATATAAATATAACATGATAAAAT
4217353 ATATAAATAT-A-AT-AT-AAAT
1 ATATAAATATAACATGATAAAAT
4217372 ATATAAAT
1 ATATAAAT
4217380 TTTTGGATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 12 0.44
20 2 0.07
21 2 0.07
22 1 0.04
23 10 0.37
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (23 bp):
ATATAAATATAACATGATAAAAT
Found at i:4219516 original size:20 final size:20
Alignment explanation
Indices: 4219473--4219516 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
4219463 ATAGAGGCTC
*
4219473 CCTCCTCCCTCTCAAGTATC
1 CCTCCTCCCTCTCAAGTATA
**
4219493 CCTCCTCCCTCTCTTGTATA
1 CCTCCTCCCTCTCAAGTATA
4219513 CCTC
1 CCTC
4219517 TTCAATTCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.50, G:0.05, T:0.34
Consensus pattern (20 bp):
CCTCCTCCCTCTCAAGTATA
Found at i:4219917 original size:220 final size:220
Alignment explanation
Indices: 4219535--4219966 Score: 819
Period size: 220 Copynumber: 2.0 Consensus size: 220
4219525 ATTCTTATAA
*
4219535 TAGAATTGGTGGTGTCCGAGGACGTAAGCATAAGTTGGCCGAACCTCGTTAAATCTTTGGTGTTG
1 TAGAATTGATGGTGTCCGAGGACGTAAGCATAAGTTGGCCGAACCTCGTTAAATCTTTGGTGTTG
4219600 TGTTTCTTCTTTTATTGTCTTTATTTTTTCAATAACTTGTAGGTGGAATATCCGCTGATTCCACC
66 TGTTTCTTCTTTTATTGTCTTTATTTTTTCAATAACTTGTAGGTGGAATATCCGCTGATTCCACC
4219665 ACAATTGGTATCAGAGCCAAGTTACTCTGAGTATGCTCTGTGGTTGCAGCTTAGGCTGATCTTCC
131 ACAATTGGTATCAGAGCCAAGTTACTCTGAGTATGCTCTGTGGTTGCAGCTTAGGCTGATCTTCC
*
4219730 ACAATAGAAAAGGTATCCGATGACG
196 ACAACAGAAAAGGTATCCGATGACG
*
4219755 TAGAATTGATGGTGTCCGAGGACGTAGGCATAAGTTGGCCGAACCTCGTTAAATCTTTGGTGTTG
1 TAGAATTGATGGTGTCCGAGGACGTAAGCATAAGTTGGCCGAACCTCGTTAAATCTTTGGTGTTG
*
4219820 TGTTTCTTCTTTTATTGTCTTTATTTTTTCAATAGCTTGTAGGTGGAATATCCGCTGATTCCACC
66 TGTTTCTTCTTTTATTGTCTTTATTTTTTCAATAACTTGTAGGTGGAATATCCGCTGATTCCACC
*
4219885 ACAATTGGTATCAGAGCCAAGTTACTCTGAGTATGCTCTGTGGTTGCAGCTTAGGTTGATCTTCC
131 ACAATTGGTATCAGAGCCAAGTTACTCTGAGTATGCTCTGTGGTTGCAGCTTAGGCTGATCTTCC
4219950 ACAACAGAAAAGGTATC
196 ACAACAGAAAAGGTATC
4219967 ATTCGACTAT
Statistics
Matches: 207, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
220 207 1.00
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (220 bp):
TAGAATTGATGGTGTCCGAGGACGTAAGCATAAGTTGGCCGAACCTCGTTAAATCTTTGGTGTTG
TGTTTCTTCTTTTATTGTCTTTATTTTTTCAATAACTTGTAGGTGGAATATCCGCTGATTCCACC
ACAATTGGTATCAGAGCCAAGTTACTCTGAGTATGCTCTGTGGTTGCAGCTTAGGCTGATCTTCC
ACAACAGAAAAGGTATCCGATGACG
Found at i:4222219 original size:21 final size:22
Alignment explanation
Indices: 4222190--4222235 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
4222180 TGTTCAGACA
** *
4222190 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
4222212 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
4222233 AGT
1 AGT
4222236 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:4223600 original size:2 final size:2
Alignment explanation
Indices: 4223593--4223623 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4223583 CGCTCTATAT
4223593 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
4223624 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4227082 original size:4 final size:4
Alignment explanation
Indices: 4227073--4227102 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
4227063 CTCCTACTCT
4227073 CATA CATA CATA CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CATA CA
4227103 AAGTACCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (4 bp):
CATA
Found at i:4238165 original size:29 final size:27
Alignment explanation
Indices: 4238133--4238206 Score: 82
Period size: 29 Copynumber: 2.7 Consensus size: 27
4238123 TATAAACATT
4238133 TTAAATTTATATAATAATTTATTAATATA
1 TTAAATTTATATAATAATTT-TTAA-ATA
4238162 TTAAATTTATATAA-ATATTTTTAAATA
1 TTAAATTTATATAATA-ATTTTTAAATA
4238189 -T-AATTATAATATAATAAT
1 TTAAATT-T-ATATAATAAT
4238207 ACAAATATGA
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
25 4 0.10
26 2 0.05
27 11 0.27
28 6 0.15
29 18 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
TTAAATTTATATAATAATTTTTAAATA
Found at i:4238170 original size:17 final size:17
Alignment explanation
Indices: 4238148--4238180 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4238138 TTTATATAAT
4238148 AATTTAT-TAATATATTA
1 AATTTATATAA-ATATTA
4238165 AATTTATATAAATATT
1 AATTTATATAAATATT
4238181 TTTAAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AATTTATATAAATATTA
Found at i:4239861 original size:76 final size:77
Alignment explanation
Indices: 4239758--4239913 Score: 233
Period size: 76 Copynumber: 2.0 Consensus size: 77
4239748 TGGGAAACCT
* * *
4239758 AATTCGGATTATTGCTTTTACTTATTTGCCTATCTGCTTTCTGCATATTTGCAAATCCGTACATT
1 AATTCGGATTATTGCATTTACTTATTTGCCTATCCGCTTTCTGCATATTTGCAAATCCATACATT
4239823 ATTTATGCGG-A
66 ATTTATGCGGTA
* * * * *
4239834 AATTTGGATTCTTGCATTTACTTATTTGCCTGTCCGCTTTCTGCATTTTTGCAAGTCCATACATT
1 AATTCGGATTATTGCATTTACTTATTTGCCTATCCGCTTTCTGCATATTTGCAAATCCATACATT
4239899 ATTTATGCGGTA
66 ATTTATGCGGTA
4239911 AAT
1 AAT
4239914 GTTGACCACA
Statistics
Matches: 71, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
76 67 0.94
77 4 0.06
ACGTcount: A:0.22, C:0.19, G:0.15, T:0.45
Consensus pattern (77 bp):
AATTCGGATTATTGCATTTACTTATTTGCCTATCCGCTTTCTGCATATTTGCAAATCCATACATT
ATTTATGCGGTA
Found at i:4253934 original size:4 final size:4
Alignment explanation
Indices: 4253925--4254014 Score: 83
Period size: 4 Copynumber: 25.0 Consensus size: 4
4253915 TACTTCCTAG
* * *
4253925 CATA CATA CAT- -ATA TATA TATA CATA CATA CAT- -ATA TATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
4253969 C--A CATA CATA CAT- -ATA CATA CATA CATA C--A CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
4254011 CATA
1 CATA
4254015 TATATATATA
Statistics
Matches: 74, Mismatches: 2, Indels: 20
0.77 0.02 0.21
Matches are distributed among these distances:
2 10 0.14
4 64 0.86
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (4 bp):
CATA
Found at i:4253949 original size:18 final size:18
Alignment explanation
Indices: 4253926--4254038 Score: 145
Period size: 18 Copynumber: 6.2 Consensus size: 18
4253916 ACTTCCTAGC
*
4253926 ATACATACATATATATAT
1 ATACATACATACATATAT
4253944 ATACATACATACATATAT
1 ATACATACATACATATAT
*
4253962 ATACATACACATACATACAT
1 ATACAT--ACATACATATAT
* *
4253982 ATACATACATACATACAC
1 ATACATACATACATATAT
4254000 ATACATACATACATATAT
1 ATACATACATACATATAT
* * *
4254018 ATATATATATATATATAT
1 ATACATACATACATATAT
4254036 ATA
1 ATA
4254039 GAGAGGCTTC
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
18 68 0.80
20 17 0.20
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (18 bp):
ATACATACATACATATAT
Found at i:4253967 original size:10 final size:10
Alignment explanation
Indices: 4253930--4254036 Score: 79
Period size: 10 Copynumber: 10.3 Consensus size: 10
4253920 CCTAGCATAC
4253930 ATACATATAT
1 ATACATATAT
* *
4253940 ATATATACATAC
1 ATACAT--ATAT
4253952 ATACATATAT
1 ATACATATAT
* *
4253962 ATACATACAC
1 ATACATATAT
*
4253972 ATACATACAT
1 ATACATATAT
*
4253982 ATACATACATAC
1 ATACAT--ATAT
* *
4253994 ATACACATAC
1 ATACATATAT
*
4254004 ATACATACAT
1 ATACATATAT
*
4254014 ATATATATAT
1 ATACATATAT
*
4254024 ATATATATAT
1 ATACATATAT
4254034 ATA
1 ATA
4254037 TAGAGAGGCT
Statistics
Matches: 78, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
10 63 0.81
12 15 0.19
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (10 bp):
ATACATATAT
Found at i:4254019 original size:4 final size:4
Alignment explanation
Indices: 4254012--4254038 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
4254002 ACATACATAC
4254012 ATAT ATAT ATAT ATAT ATAT ATAT ATA
1 ATAT ATAT ATAT ATAT ATAT ATAT ATA
4254039 GAGAGGCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
ATAT
Found at i:4254038 original size:14 final size:14
Alignment explanation
Indices: 4253930--4254030 Score: 112
Period size: 14 Copynumber: 7.2 Consensus size: 14
4253920 CCTAGCATAC
* *
4253930 ATACATATATATAT
1 ATACATACATACAT
4253944 ATACATACATACAT
1 ATACATACATACAT
* *
4253958 ATATATACATACAC
1 ATACATACATACAT
* *
4253972 ATACATACATATAC
1 ATACATACATACAT
*
4253986 ATACATACATACAC
1 ATACATACATACAT
4254000 ATACATACATACAT
1 ATACATACATACAT
* * *
4254014 ATATATATATATAT
1 ATACATACATACAT
4254028 ATA
1 ATA
4254031 TATATATAGA
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 76 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (14 bp):
ATACATACATACAT
Found at i:4254694 original size:22 final size:21
Alignment explanation
Indices: 4254657--4254706 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
4254647 TTTGTCTTGG
4254657 ATTTATTATGTTAATT-TAAA
1 ATTTATTATGTTAATTATAAA
*
4254677 ATATTATTAATTTTAATTATAAA
1 AT-TTATT-ATGTTAATTATAAA
4254700 ATTTATT
1 ATTTATT
4254707 TTAAAATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 2 0.08
21 5 0.19
22 13 0.50
23 6 0.23
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTTATTATGTTAATTATAAA
Found at i:4254733 original size:19 final size:18
Alignment explanation
Indices: 4254682--4254734 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
4254672 TTAAAATATT
4254682 ATTAA-TTTTAATTATAAA
1 ATTAATTTTTAA-TATAAA
* *
4254700 ATTTATTTTAAAATATAAA
1 ATTAATTTT-TAATATAAA
4254719 ATTAATTCTTTAATAT
1 ATTAATT-TTTAATAT
4254735 GGAAGAATAG
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
18 4 0.14
19 20 0.71
20 4 0.14
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTAATTTTTAATATAAA
Found at i:4254798 original size:22 final size:22
Alignment explanation
Indices: 4254773--4254814 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
4254763 AATTTCGGGT
*
4254773 TATATTTTTAATTATAAAAAAA
1 TATATTTTTAAATATAAAAAAA
4254795 TATATTTTTAAATATAAAAA
1 TATATTTTTAAATATAAAAA
4254815 TAAATAGCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TATATTTTTAAATATAAAAAAA
Found at i:4264715 original size:12 final size:12
Alignment explanation
Indices: 4264687--4264767 Score: 75
Period size: 12 Copynumber: 7.2 Consensus size: 12
4264677 CTACAATATA
4264687 ATAAAA-ATAAT
1 ATAAAATATAAT
4264698 -TAAAATATAAT
1 ATAAAATATAAT
4264709 ATAAAAT-TAA-
1 ATAAAATATAAT
4264719 ATTAAAATATAAT
1 A-TAAAATATAAT
* *
4264732 -T-TAATATAAA
1 ATAAAATATAAT
*
4264742 ATAAAATGTAAT
1 ATAAAATATAAT
*
4264754 ATAAAAAATAAT
1 ATAAAATATAAT
4264766 AT
1 AT
4264768 TAATACTTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
10 13 0.23
11 16 0.29
12 27 0.48
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (12 bp):
ATAAAATATAAT
Found at i:4264720 original size:17 final size:17
Alignment explanation
Indices: 4264681--4264770 Score: 74
Period size: 19 Copynumber: 5.1 Consensus size: 17
4264671 TAGATACTAC
*
4264681 AATATAATAAAAATAATTAA
1 AATATAA-AATAA-AATT-A
*
4264701 AATATAATATAAAATTA
1 AATATAAAATAAAATTA
* *
4264718 AAT-TAAAATATAATTT
1 AATATAAAATAAAATTA
4264734 AATATAAAATAAAATGTA
1 AATATAAAATAAAAT-TA
* *
4264752 ATATAAAAAATAATATTA
1 A-ATATAAAATAAAATTA
4264770 A
1 A
4264771 TACTTTAAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
16 13 0.22
17 14 0.24
18 9 0.16
19 15 0.26
20 7 0.12
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (17 bp):
AATATAAAATAAAATTA
Found at i:4265650 original size:19 final size:19
Alignment explanation
Indices: 4265626--4265665 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
4265616 AGTAATTCCA
*
4265626 TTACTCATCAATTA-ATATT
1 TTACTCAT-AATAACATATT
4265645 TTACTCATAATAACATATT
1 TTACTCATAATAACATATT
4265664 TT
1 TT
4265666 TTAATAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.47
Consensus pattern (19 bp):
TTACTCATAATAACATATT
Found at i:4267129 original size:15 final size:16
Alignment explanation
Indices: 4267102--4267131 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4267092 TTGTATATTT
4267102 AATAAAGTATATATAA
1 AATAAAGTATATATAA
4267118 AATAAA-TATATATA
1 AATAAAGTATATATA
4267132 TATATGTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (16 bp):
AATAAAGTATATATAA
Found at i:4267349 original size:24 final size:25
Alignment explanation
Indices: 4267322--4267373 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
4267312 ATATGATGTG
* *
4267322 AATAAATATTAAAAATATAAT-TAA
1 AATAAATATGAAAAAAATAATATAA
*
4267346 AATATATATGAAAAAAATAATATAA
1 AATAAATATGAAAAAAATAATATAA
4267371 AAT
1 AAT
4267374 GATATCAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (25 bp):
AATAAATATGAAAAAAATAATATAA
Found at i:4267628 original size:21 final size:22
Alignment explanation
Indices: 4267596--4267636 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
4267586 AATATGAGAA
4267596 ATATAAATAAAATAT-GATATT
1 ATATAAATAAAATATAGATATT
4267617 ATATGAAA-AAAATATAGATA
1 ATAT-AAATAAAATATAGATA
4267637 CACATAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (22 bp):
ATATAAATAAAATATAGATATT
Found at i:4267705 original size:26 final size:26
Alignment explanation
Indices: 4267676--4267725 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
4267666 TCATAAAAAG
*
4267676 AATTATTAT-CATATTAAAATTTAATA
1 AATTATAATACAT-TTAAAATTTAATA
*
4267702 AATTATAATACATTTAAGATTTAA
1 AATTATAATACATTTAAAATTTAA
4267726 CACAATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 18 0.86
27 3 0.14
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (26 bp):
AATTATAATACATTTAAAATTTAATA
Found at i:4282124 original size:3 final size:3
Alignment explanation
Indices: 4282091--4282115 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4282081 AACATAGAAC
4282091 TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA T
4282116 AAATGATGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:4284706 original size:2 final size:2
Alignment explanation
Indices: 4284662--4284693 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4284652 GGTTAAAGAC
4284662 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4284694 AACGTATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4298271 original size:2 final size:2
Alignment explanation
Indices: 4298264--4298288 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4298254 AGCCATGGTG
4298264 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
4298289 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:4298293 original size:2 final size:2
Alignment explanation
Indices: 4298288--4298312 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4298278 ACACACACAC
4298288 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 A
4298313 AAATAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4298396 original size:19 final size:19
Alignment explanation
Indices: 4298372--4298409 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
4298362 ATTGAAATAT
4298372 AAATATTTTTAAGTAAAAA
1 AAATATTTTTAAGTAAAAA
*
4298391 AAATATTTTTAATTAAAAA
1 AAATATTTTTAAGTAAAAA
4298410 TGGATAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (19 bp):
AAATATTTTTAAGTAAAAA
Found at i:4298449 original size:12 final size:12
Alignment explanation
Indices: 4298423--4298464 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
4298413 ATAAAATATA
4298423 TATTATAATAATTT
1 TATT-TAAT-ATTT
*
4298437 TATTTAATTTTT
1 TATTTAATATTT
4298449 TATTTAATATTT
1 TATTTAATATTT
4298461 TATT
1 TATT
4298465 AAATCAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 18 0.69
13 4 0.15
14 4 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TATTTAATATTT
Found at i:4311108 original size:3 final size:3
Alignment explanation
Indices: 4311100--4311130 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
4311090 GTCTCAACGA
4311100 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
4311131 TATATTTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:4311508 original size:12 final size:12
Alignment explanation
Indices: 4311473--4311508 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
4311463 AACCACTTGC
*
4311473 ATATAAATATAC
1 ATATAAATATAT
4311485 ATATAAATATAT
1 ATATAAATATAT
*
4311497 ATATATATATAT
1 ATATAAATATAT
4311509 TTTTTCAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (12 bp):
ATATAAATATAT
Found at i:4315765 original size:14 final size:16
Alignment explanation
Indices: 4315746--4315803 Score: 56
Period size: 14 Copynumber: 4.0 Consensus size: 16
4315736 ATATTATTTT
4315746 TATTTTTAAATTT-AA
1 TATTTTTAAATTTAAA
4315761 T-TTTTT--ATTTAAA
1 TATTTTTAAATTTAAA
*
4315774 TATTTTTAAATATAAA
1 TATTTTTAAATTTAAA
*
4315790 TA--ATTAAATTTAAA
1 TATTTTTAAATTTAAA
4315804 CAAATAATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
12 4 0.11
13 3 0.08
14 20 0.56
15 1 0.03
16 8 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTTTTAAATTTAAA
Found at i:4316180 original size:24 final size:24
Alignment explanation
Indices: 4316152--4316198 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
4316142 AGAAAGTATG
* *
4316152 ATTTTTAATAAATTAAAAATTTTA
1 ATTTTAAAAAAATTAAAAATTTTA
*
4316176 ATTTTAAAAAAATTTAAAATTTT
1 ATTTTAAAAAAATTAAAAATTTT
4316199 TAAACAATAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
ATTTTAAAAAAATTAAAAATTTTA
Found at i:4316429 original size:3 final size:3
Alignment explanation
Indices: 4316421--4316453 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
4316411 AAATTAAATT
4316421 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4316454 ATCTAAAGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:4316619 original size:3 final size:3
Alignment explanation
Indices: 4316611--4316655 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
4316601 AAATTAAATT
4316611 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4316656 ATCTAGAGCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:4316859 original size:18 final size:20
Alignment explanation
Indices: 4316836--4316880 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 20
4316826 TCAAAGTGAG
*
4316836 TTAATTTTGTCTA-TT-TTT
1 TTAATTTTGTCGAGTTATTT
*
4316854 TTAATTTTTTCGAGTTATTT
1 TTAATTTTGTCGAGTTATTT
4316874 TTAATTT
1 TTAATTT
4316881 ATTCAATTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 11 0.48
19 2 0.09
20 10 0.43
ACGTcount: A:0.20, C:0.04, G:0.07, T:0.69
Consensus pattern (20 bp):
TTAATTTTGTCGAGTTATTT
Found at i:4316990 original size:23 final size:22
Alignment explanation
Indices: 4316932--4317003 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 22
4316922 TTTTTTTTGT
* *
4316932 TTTAATTAGACTTTTAATTTATG
1 TTTAAATAGA-TTTTAATTTATA
* *
4316955 TTTAGAT-GAATTTTTAATTTAAA
1 TTTAAATAG-A-TTTTAATTTATA
*
4316978 TTTAAATAGATTTAAATTTATA
1 TTTAAATAGATTTTAATTTATA
4317000 TTTA
1 TTTA
4317004 TATTTTATTA
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
22 15 0.38
23 23 0.59
24 1 0.03
ACGTcount: A:0.38, C:0.01, G:0.07, T:0.54
Consensus pattern (22 bp):
TTTAAATAGATTTTAATTTATA
Found at i:4317162 original size:19 final size:18
Alignment explanation
Indices: 4317125--4317171 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
4317115 ATCGATCAAA
*
4317125 AAATAAATTAAATATATT
1 AAATAAATTTAATATATT
*
4317143 AAATAAATTTAATTTAATT
1 AAATAAATTTAATAT-ATT
*
4317162 AAATTAATTT
1 AAATAAATTT
4317172 TAACTGATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 13 0.52
19 12 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AAATAAATTTAATATATT
Found at i:4319531 original size:3 final size:3
Alignment explanation
Indices: 4319523--4319553 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
4319513 AAAAGAATCA
4319523 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
4319554 TCGAGTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:4328363 original size:2 final size:2
Alignment explanation
Indices: 4328356--4328380 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4328346 TTCTATACAC
4328356 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 A
4328381 CTTTTGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4328577 original size:2 final size:2
Alignment explanation
Indices: 4328572--4328605 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
4328562 AATATATGTG
*
4328572 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4328606 AAAGATGATT
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:4328776 original size:2 final size:2
Alignment explanation
Indices: 4328769--4328795 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4328759 CCACTAAATA
4328769 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
4328796 ACTTGTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:4329041 original size:4 final size:4
Alignment explanation
Indices: 4329032--4329059 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
4329022 ATTTACATTG
4329032 TTAA TTAA TTAA TTAA TTAA TTAA TTAA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA
4329060 GAATTATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TTAA
Found at i:4329508 original size:2 final size:2
Alignment explanation
Indices: 4329501--4329527 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4329491 TTGATTTGAT
4329501 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4329528 TTAATTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4344958 original size:24 final size:23
Alignment explanation
Indices: 4344913--4344958 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
4344903 AAATTATGTT
**
4344913 ATTTTTTATTTAATTTTTAATAA
1 ATTTTTTATTTAATTTAAAATAA
4344936 ATTTTTTATTTAGATTTAAAATA
1 ATTTTTTATTTA-ATTTAAAATA
4344959 TGATTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (23 bp):
ATTTTTTATTTAATTTAAAATAA
Found at i:4346962 original size:19 final size:19
Alignment explanation
Indices: 4346938--4346984 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
4346928 TAAAAATTTT
4346938 AAATATTATTAATAATA-AA
1 AAATATTATT-ATAATATAA
* *
4346957 AAATATAAATATAATATAA
1 AAATATTATTATAATATAA
4346976 AAATATTAT
1 AAATATTAT
4346985 CGCATAAGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATATTATTATAATATAA
Found at i:4349955 original size:3 final size:3
Alignment explanation
Indices: 4349947--4349982 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
4349937 ATCGTTTTTC
4349947 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
4349983 TTGCTGTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:4351046 original size:18 final size:18
Alignment explanation
Indices: 4351023--4351058 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
4351013 AGAAGAAGAC
4351023 CCCGATTGACAACCATCT
1 CCCGATTGACAACCATCT
4351041 CCCGATTGACAACCATCT
1 CCCGATTGACAACCATCT
4351059 GAAAGGATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.39, G:0.11, T:0.22
Consensus pattern (18 bp):
CCCGATTGACAACCATCT
Found at i:4353283 original size:2 final size:2
Alignment explanation
Indices: 4353276--4353308 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4353266 TATCGTTTAA
4353276 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 A
4353309 ATGAACAAAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4359893 original size:33 final size:33
Alignment explanation
Indices: 4359830--4359896 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 33
4359820 GTTTTAATTT
*
4359830 TATTTAAATTATTATATATTTATATTTTTTAAA
1 TATTTAAATAATTATATATTTATATTTTTTAAA
* *
4359863 TATTTTAATAATT-TATA-TTATATTTATTTTAA
1 TATTTAAATAATTATATATTTATATTT-TTTAAA
4359895 TA
1 TA
4359897 ATATGATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
31 8 0.27
32 11 0.37
33 11 0.37
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (33 bp):
TATTTAAATAATTATATATTTATATTTTTTAAA
Found at i:4365162 original size:76 final size:75
Alignment explanation
Indices: 4365056--4365207 Score: 268
Period size: 76 Copynumber: 2.0 Consensus size: 75
4365046 TGGAATGATT
4365056 ATAATCAAGCTGTAATGTCGTAATCAATCACACTTGGTCCTATAGTTGAGATTTTGTTTGCCCTT
1 ATAATCAAGCTGTAATGTCGTAATCAATCACACTTGGTCCTATAGTTGAGATTTTGTTTGCCCTT
4365121 CGCCCCCCTGC
66 C-CCCCCCTGC
* * *
4365132 ATAATCAAGCTGTAATGTCGTAGTCTATCACACTTTGTCCTATAGTTGAGATTTTGTTTGCCCTT
1 ATAATCAAGCTGTAATGTCGTAATCAATCACACTTGGTCCTATAGTTGAGATTTTGTTTGCCCTT
4365197 CCCCCCCTGC
66 CCCCCCCTGC
4365207 A
1 A
4365208 GCTAGTACAT
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
75 10 0.14
76 63 0.86
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.36
Consensus pattern (75 bp):
ATAATCAAGCTGTAATGTCGTAATCAATCACACTTGGTCCTATAGTTGAGATTTTGTTTGCCCTT
CCCCCCCTGC
Done.