Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 269 of 292
Found at i:77399957 original size:16 final size:16
Alignment explanation
Indices: 77399923--77399960 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
77399913 AAATTTTGAG
77399923 TTTTTGTCAAAAACGTA
1 TTTTTGTCAAAAAC-TA
77399940 TTTTATGTCAAAAA-TA
1 TTTT-TGTCAAAAACTA
77399956 TTTTT
1 TTTTT
77399961 TAGAAACATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 1 0.05
16 6 0.30
17 4 0.20
18 9 0.45
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.50
Consensus pattern (16 bp):
TTTTTGTCAAAAACTA
Found at i:77402340 original size:28 final size:27
Alignment explanation
Indices: 77402275--77402345 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 27
77402265 ATTTAATTAC
*
77402275 CGTGTTATTATTTTTTCTTTTTAACTTT
1 CGTG-TATTATTTTTTCTTATTAACTTT
* *
77402303 CTTGTCATTATTTTTTCTTATT-AGTTAT
1 CGTGT-ATTATTTTTTCTTATTAACTT-T
77402331 CGTGCTATTATTTTT
1 CGTG-TATTATTTTT
77402346 CACATTTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
27 4 0.11
28 31 0.86
29 1 0.03
ACGTcount: A:0.15, C:0.11, G:0.08, T:0.65
Consensus pattern (27 bp):
CGTGTATTATTTTTTCTTATTAACTTT
Found at i:77403624 original size:20 final size:20
Alignment explanation
Indices: 77403601--77403652 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 20
77403591 AAATCCAAAT
77403601 TAAAATACTGAAATTCAGGA
1 TAAAATACTGAAATTCAGGA
*
77403621 TAAAAT-CTTTAAATTCAGGA
1 TAAAATAC-TGAAATTCAGGA
77403641 TAAAAATACTGA
1 T-AAAATACTGA
77403653 TGTGGCATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 1 0.04
20 18 0.67
21 7 0.26
22 1 0.04
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.29
Consensus pattern (20 bp):
TAAAATACTGAAATTCAGGA
Found at i:77404473 original size:38 final size:37
Alignment explanation
Indices: 77404429--77404539 Score: 97
Period size: 38 Copynumber: 3.0 Consensus size: 37
77404419 TAATTATGTA
77404429 AATATATATAATTTAATTATTAATTACTT-TTTTATTT
1 AATATATATAATTTAATTATTAATTA-TTATTTTATTT
* * *
77404466 AAGTATATAGATATTT-ATTATTTATTATTATTCTA-TT
1 AA-TATATATA-ATTTAATTATTAATTATTATTTTATTT
*
77404503 AA-AT-TATAATTTATATTATTAAATTATGATTATTATT
1 AATATATATAATTTA-ATTATT-AATTATTATT-TTATT
77404540 ATTATTAAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
33 4 0.07
34 3 0.05
35 8 0.14
36 8 0.14
37 10 0.17
38 22 0.37
39 4 0.07
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.57
Consensus pattern (37 bp):
AATATATATAATTTAATTATTAATTATTATTTTATTT
Found at i:77404522 original size:20 final size:20
Alignment explanation
Indices: 77404489--77404543 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 20
77404479 TTTATTATTT
77404489 ATTATTATTCTATTAAATTATA
1 ATTATTA-T-TATTAAATTATA
*
77404511 ATT-TATATTATTAAATTATG
1 ATTAT-TATTATTAAATTATA
77404531 ATTATTATTATTA
1 ATTATTATTATTA
77404544 TTAAAAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
20 22 0.73
21 3 0.10
22 5 0.17
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
ATTATTATTATTAAATTATA
Found at i:77404528 original size:25 final size:26
Alignment explanation
Indices: 77404480--77404546 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
77404470 ATATAGATAT
* **
77404480 TTATTATTTATTATTATTCTATTAAA
1 TTATAATTTATTATTATTAAATTAAA
*
77404506 TTATAATTTA-TATTATTAAATTATGA
1 TTATAATTTATTATTATTAAATTA-AA
*
77404532 TTATTA-TTATTATTA
1 TTATAATTTATTATTA
77404547 AAAATAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
25 14 0.41
26 20 0.59
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (26 bp):
TTATAATTTATTATTATTAAATTAAA
Found at i:77404832 original size:13 final size:14
Alignment explanation
Indices: 77404816--77404854 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
77404806 AATTAAAGTT
77404816 AATAAAATAAAAG-
1 AATAAAATAAAAGA
* *
77404829 AATAAAAGAAATGA
1 AATAAAATAAAAGA
77404843 AATAAAATAAAA
1 AATAAAATAAAA
77404855 TAAAGAAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (14 bp):
AATAAAATAAAAGA
Found at i:77405250 original size:22 final size:22
Alignment explanation
Indices: 77405225--77405270 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
77405215 TAAGTAGTTA
77405225 GATGTGAGTTTGATAAGAAATT
1 GATGTGAGTTTGATAAGAAATT
*
77405247 GATGTGAGTTTGGTAAGAAATT
1 GATGTGAGTTTGATAAGAAATT
77405269 GA
1 GA
77405271 GTAGTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.30, T:0.35
Consensus pattern (22 bp):
GATGTGAGTTTGATAAGAAATT
Found at i:77405986 original size:45 final size:45
Alignment explanation
Indices: 77405935--77406047 Score: 174
Period size: 45 Copynumber: 2.5 Consensus size: 45
77405925 CGACTATTGT
*
77405935 TACTGTTACCGTTACTGTTACTGATTC-GACACTTTGTGTGTTGAA
1 TACTGTTACCGTTACTGTTACTGATTCAG-CACTTTGTATGTTGAA
*
77405980 TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTATGTTGAA
1 TACTGTTACCGTTACTGTTACTGATTCAGCACTTTGTATGTTGAA
* *
77406025 TACTGTTACTGTTACTGCTACTG
1 TACTGTTACCGTTACTGTTACTG
77406048 CTACCGTTAC
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
45 61 0.98
46 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.42
Consensus pattern (45 bp):
TACTGTTACCGTTACTGTTACTGATTCAGCACTTTGTATGTTGAA
Found at i:77406056 original size:18 final size:18
Alignment explanation
Indices: 77406025--77406059 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
77406015 GTATGTTGAA
* *
77406025 TACTGTTACTGTTACTGC
1 TACTGCTACCGTTACTGC
77406043 TACTGCTACCGTTACTG
1 TACTGCTACCGTTACTG
77406060 ATTACTGATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.40
Consensus pattern (18 bp):
TACTGCTACCGTTACTGC
Found at i:77406779 original size:14 final size:14
Alignment explanation
Indices: 77406760--77406789 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
77406750 TTATATCGAG
77406760 ACCAATCCAAATCA
1 ACCAATCCAAATCA
*
77406774 ACCAATCCAATTCA
1 ACCAATCCAAATCA
77406788 AC
1 AC
77406790 ATATTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.17
Consensus pattern (14 bp):
ACCAATCCAAATCA
Found at i:77411546 original size:14 final size:14
Alignment explanation
Indices: 77411529--77411572 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
77411519 TGAAGTTCAT
*
77411529 GATTTAAATTTTGA
1 GATTTAAATTTTAA
*
77411543 GATTTAAAATTTAA
1 GATTTAAATTTTAA
* *
77411557 AATTTAAATTTAAA
1 GATTTAAATTTTAA
77411571 GA
1 GA
77411573 CTCAAATCCG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (14 bp):
GATTTAAATTTTAA
Found at i:77411812 original size:17 final size:17
Alignment explanation
Indices: 77411790--77411822 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
77411780 ACTTAAATTT
*
77411790 AAAATCTCGAAATTTTA
1 AAAATCTCAAAATTTTA
77411807 AAAATCTCAAAATTTT
1 AAAATCTCAAAATTTT
77411823 TTATTGTCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.12, G:0.03, T:0.36
Consensus pattern (17 bp):
AAAATCTCAAAATTTTA
Found at i:77420097 original size:34 final size:34
Alignment explanation
Indices: 77419987--77420096 Score: 130
Period size: 34 Copynumber: 3.2 Consensus size: 34
77419977 ACACATAAAT
* * * *
77419987 AATCGGTTCAAAAGAAGCAATATTCTAACATAGC
1 AATCGATTCAAAAGAAGTAATATTCCAACATAAC
* * *
77420021 AATCGATTCAAAAGAAATAATATTTCAACATGAC
1 AATCGATTCAAAAGAAGTAATATTCCAACATAAC
* * *
77420055 AATAGATTTAAAAGAAGTAGTATTCCAACATAAC
1 AATCGATTCAAAAGAAGTAATATTCCAACATAAC
77420089 AATCGATT
1 AATCGATT
77420097 TCAATATAAA
Statistics
Matches: 62, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 62 1.00
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.26
Consensus pattern (34 bp):
AATCGATTCAAAAGAAGTAATATTCCAACATAAC
Found at i:77420123 original size:55 final size:55
Alignment explanation
Indices: 77420064--77420181 Score: 182
Period size: 55 Copynumber: 2.1 Consensus size: 55
77420054 CAATAGATTT
* *
77420064 AAAAGAAGTAGTATTCCAACATAACAATCGATTTCAATATAAAAACAATCAATTC
1 AAAAGAAGTAGTATTCCAACATAACAATCGATTTAAACATAAAAACAATCAATTC
* * **
77420119 AAAAGAAGTAGTATTCCAATATAACAATCGATTTAAACATAAAAATAATTGATTC
1 AAAAGAAGTAGTATTCCAACATAACAATCGATTTAAACATAAAAACAATCAATTC
77420174 AAAAGAAG
1 AAAAGAAG
77420182 AAGCAGTATT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.53, C:0.13, G:0.09, T:0.25
Consensus pattern (55 bp):
AAAAGAAGTAGTATTCCAACATAACAATCGATTTAAACATAAAAACAATCAATTC
Found at i:77420326 original size:55 final size:55
Alignment explanation
Indices: 77420199--77420335 Score: 148
Period size: 55 Copynumber: 2.5 Consensus size: 55
77420189 ATTCTACTAT
* * * ** *
77420199 AACAATCAATTCAAAAGAAACAATATTTCAACATTACAATCGATTTAAACATATA
1 AACAATAAATCCAAAAGAAACAATATTCCAACAGGACAATCGATTTAAACATAAA
* ** * * *
77420254 AATAATTTATTCAAAAGAACCAATATTCCAACAGGATAATCGATTTAAACATAAA
1 AACAATAAATCCAAAAGAAACAATATTCCAACAGGACAATCGATTTAAACATAAA
* *
77420309 AACAATAAATCCGAAAGAAGCAATATT
1 AACAATAAATCCAAAAGAAACAATATT
77420336 TTTGAAAATT
Statistics
Matches: 67, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
55 67 1.00
ACGTcount: A:0.53, C:0.15, G:0.07, T:0.26
Consensus pattern (55 bp):
AACAATAAATCCAAAAGAAACAATATTCCAACAGGACAATCGATTTAAACATAAA
Found at i:77421035 original size:14 final size:14
Alignment explanation
Indices: 77421018--77421049 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
77421008 TGTATATTTA
77421018 AAAATAAAATAAAT
1 AAAATAAAATAAAT
*
77421032 AAAATAAAATATAT
1 AAAATAAAATAAAT
77421046 AAAA
1 AAAA
77421050 CATAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAATAAAATAAAT
Found at i:77423708 original size:15 final size:14
Alignment explanation
Indices: 77423690--77423720 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
77423680 TTAATTTATT
77423690 TAATAATAATGCTAA
1 TAATAATAAT-CTAA
77423705 TAATAATAATCTAA
1 TAATAATAATCTAA
77423719 TA
1 TA
77423721 TAAAACCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (14 bp):
TAATAATAATCTAA
Found at i:77423731 original size:21 final size:20
Alignment explanation
Indices: 77423707--77423775 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
77423697 AATGCTAATA
77423707 ATAATAATCTAATATAAAACC
1 ATAATAAT-TAATATAAAACC
* **
77423728 ATAAT-GTTAAT-TAATAATT
1 ATAATAATTAATATAA-AACC
77423747 ATAATAATTTAATATAAAACC
1 ATAATAA-TTAATATAAAACC
77423768 ATAATAAT
1 ATAATAAT
77423776 AATCATTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
18 3 0.08
19 11 0.29
20 2 0.05
21 19 0.50
22 3 0.08
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.36
Consensus pattern (20 bp):
ATAATAATTAATATAAAACC
Found at i:77423787 original size:33 final size:32
Alignment explanation
Indices: 77423739--77423816 Score: 78
Period size: 30 Copynumber: 2.6 Consensus size: 32
77423729 TAATGTTAAT
* *
77423739 TAATAATTATAATAATTTAATATAAAACC-ATAA
1 TAATAATCATTATAATTT-ATATAAAACCTA-AA
77423772 TAATAATCATTATAA--TATATAAAACCTAAA
1 TAATAATCATTATAATTTATATAAAACCTAAA
77423802 TAA-AATC-TT-TAATTT
1 TAATAATCATTATAATTT
77423817 TATTTCACCA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
27 3 0.08
28 2 0.05
29 5 0.12
30 15 0.38
31 2 0.05
33 13 0.32
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (32 bp):
TAATAATCATTATAATTTATATAAAACCTAAA
Found at i:77425164 original size:68 final size:72
Alignment explanation
Indices: 77425087--77425221 Score: 188
Period size: 72 Copynumber: 1.9 Consensus size: 72
77425077 TTTTAATAAT
* * * *
77425087 TTAATATTAAATTAAATTTAATACTTAT-TT-T-GAT-AGTATTTTATTAATTTAATATTAAAGT
1 TTAATATTAAATTAAAGTTAATACTTATCTTGTAAATAAATATTCTATTAATTTAATATTAAAGT
77425148 GACTATC
66 GACTATC
* *
77425155 TTAATATTAAATTTAAGTTAATATTTATCTTGTAAATAAATATTCTATTAATTTAATATTAAAGT
1 TTAATATTAAATTAAAGTTAATACTTATCTTGTAAATAAATATTCTATTAATTTAATATTAAAGT
77425220 GA
66 GA
77425222 TTAATTTTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
68 25 0.44
69 2 0.04
70 1 0.02
71 2 0.04
72 27 0.47
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (72 bp):
TTAATATTAAATTAAAGTTAATACTTATCTTGTAAATAAATATTCTATTAATTTAATATTAAAGT
GACTATC
Found at i:77429277 original size:14 final size:14
Alignment explanation
Indices: 77429258--77429297 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
77429248 GTGTGCTCTA
77429258 ATATTAATTTATAT
1 ATATTAATTTATAT
**
77429272 ATATTAAAATATAT
1 ATATTAATTTATAT
*
77429286 ATAATAATTTAT
1 ATATTAATTTAT
77429298 TTGATCCTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATATTAATTTATAT
Found at i:77429648 original size:16 final size:16
Alignment explanation
Indices: 77429627--77429659 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
77429617 ATGTAAATTT
77429627 AAAAATTAAAAAAATA
1 AAAAATTAAAAAAATA
*
77429643 AAAAATTAAATAAATA
1 AAAAATTAAAAAAATA
77429659 A
1 A
77429660 CTAAAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAAATTAAAAAAATA
Found at i:77439068 original size:53 final size:53
Alignment explanation
Indices: 77438988--77439098 Score: 215
Period size: 53 Copynumber: 2.1 Consensus size: 53
77438978 AAGTTATCTT
77438988 GATACTGTCCTTTTCTATTTTACTTCTCTTGGGGTAGTCCTTTCACTTTTTTA
1 GATACTGTCCTTTTCTATTTTACTTCTCTTGGGGTAGTCCTTTCACTTTTTTA
77439041 GATACTGTCCTTTTCTATTTTACTTCTCTTGGGGTAGTCCTTTCACTTTTTTA
1 GATACTGTCCTTTTCTATTTTACTTCTCTTGGGGTAGTCCTTTCACTTTTTTA
77439094 G-TACT
1 GATACT
77439099 TGATATTGCA
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 4 0.07
53 54 0.93
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.52
Consensus pattern (53 bp):
GATACTGTCCTTTTCTATTTTACTTCTCTTGGGGTAGTCCTTTCACTTTTTTA
Found at i:77456370 original size:24 final size:23
Alignment explanation
Indices: 77456318--77456371 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
77456308 ATGCTGAGGC
*
77456318 AATTTTAATATATTTATTCTTTA
1 AATTTTAATATATTTATTATTTA
77456341 AA-TTTAATTTATATTTA-TATTTA
1 AATTTTAA--TATATTTATTATTTA
77456364 AATTTTAA
1 AATTTTAA
77456372 GGAATCAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 5 0.19
23 9 0.33
24 13 0.48
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
AATTTTAATATATTTATTATTTA
Found at i:77456580 original size:75 final size:75
Alignment explanation
Indices: 77456496--77456647 Score: 304
Period size: 75 Copynumber: 2.0 Consensus size: 75
77456486 TTAATTGAAC
77456496 TAAGAATAAATTTATGTATTATTTGTAATATTTATAATACATAATATTCTAAATTAAATATTTTC
1 TAAGAATAAATTTATGTATTATTTGTAATATTTATAATACATAATATTCTAAATTAAATATTTTC
77456561 AAATTAAGGG
66 AAATTAAGGG
77456571 TAAGAATAAATTTATGTATTATTTGTAATATTTATAATACATAATATTCTAAATTAAATATTTTC
1 TAAGAATAAATTTATGTATTATTTGTAATATTTATAATACATAATATTCTAAATTAAATATTTTC
77456636 AAATTAAGGG
66 AAATTAAGGG
77456646 TA
1 TA
77456648 TGTTCGATAA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 77 1.00
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (75 bp):
TAAGAATAAATTTATGTATTATTTGTAATATTTATAATACATAATATTCTAAATTAAATATTTTC
AAATTAAGGG
Found at i:77457428 original size:10 final size:10
Alignment explanation
Indices: 77457388--77457450 Score: 63
Period size: 10 Copynumber: 6.0 Consensus size: 10
77457378 AGGAATAAAT
77457388 AAAAAGAAAA
1 AAAAAGAAAA
*
77457398 AGAAAGCCAAAA
1 AAAAAG--AAAA
*
77457410 AAATTAGAAAA
1 AAA-AAGAAAA
77457421 AAAAAGAAAA
1 AAAAAGAAAA
* *
77457431 GAAAAGAAAG
1 AAAAAGAAAA
77457441 AAAAAGAAAA
1 AAAAAGAAAA
77457451 TTCCAAATGG
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
10 27 0.64
11 7 0.17
12 6 0.14
13 2 0.05
ACGTcount: A:0.79, C:0.03, G:0.14, T:0.03
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:77462816 original size:32 final size:32
Alignment explanation
Indices: 77462779--77462844 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
77462769 TAAAAAAAAC
77462779 TTAACTCATAAATTAGTATCTAAATTATACTT
1 TTAACTCATAAATTAGTATCTAAATTATACTT
77462811 TTAACTCATAAATTAGTATCTAAATTATACTT
1 TTAACTCATAAATTAGTATCTAAATTATACTT
77462843 TT
1 TT
77462845 TTTTTCTCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.39, C:0.12, G:0.03, T:0.45
Consensus pattern (32 bp):
TTAACTCATAAATTAGTATCTAAATTATACTT
Found at i:77464467 original size:6 final size:6
Alignment explanation
Indices: 77464456--77464481 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
77464446 AATTAAACTC
77464456 AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AA
77464482 CGAAAAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:77469170 original size:6 final size:6
Alignment explanation
Indices: 77469161--77469185 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
77469151 TTTATTTTAT
77469161 TTAATA TTAATA TTAATA TTAATA T
1 TTAATA TTAATA TTAATA TTAATA T
77469186 AAAATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAATA
Found at i:77469210 original size:12 final size:11
Alignment explanation
Indices: 77469159--77469210 Score: 50
Period size: 12 Copynumber: 4.4 Consensus size: 11
77469149 TTTTTATTTT
77469159 ATTTAATATTA
1 ATTTAATATTA
77469170 ATATTAATATTA
1 AT-TTAATATTA
* *
77469182 ATATAAAATTTAA
1 ATTTAATA-TT-A
77469195 ATTTAATATTA
1 ATTTAATATTA
77469206 TATTT
1 -ATTT
77469211 TTTAAATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
11 7 0.21
12 19 0.58
13 7 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
ATTTAATATTA
Found at i:77469210 original size:18 final size:16
Alignment explanation
Indices: 77469154--77469210 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 16
77469144 GGGGATTTTT
*
77469154 ATTTTATTTAATATTA
1 ATTTAATTTAATATTA
*
77469170 ATATTAATATTAATATAAA
1 AT-TTAAT-TTAATAT-TA
77469189 ATTTAAATTTAATATTA
1 ATTT-AATTTAATATTA
77469206 TATTT
1 -ATTT
77469211 TTTAAATATT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
16 2 0.06
17 5 0.15
18 20 0.61
19 6 0.18
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTTAATTTAATATTA
Found at i:77469291 original size:21 final size:20
Alignment explanation
Indices: 77469249--77469302 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
77469239 TTTTTTATGT
* **
77469249 TTATTTATTTTTAAAATTTA
1 TTATTTATTTTAAAAAAATA
77469269 TTATTATATTTTAAAAAAATA
1 TTATT-TATTTTAAAAAAATA
*
77469290 TTTATGTATTTTA
1 -TTATTTATTTTA
77469303 TATTATAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 5 0.18
21 19 0.68
22 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TTATTTATTTTAAAAAAATA
Found at i:77483539 original size:3 final size:3
Alignment explanation
Indices: 77483531--77483563 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
77483521 AAAAGCAAAG
77483531 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
77483564 ACAACTAGAC
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:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:77484570 original size:15 final size:16
Alignment explanation
Indices: 77484552--77484590 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
77484542 TTTGTTTGGA
77484552 TTTTTTAAT-TTTCAG
1 TTTTTTAATATTTCAG
* *
77484567 TTTTTTCATATTTGAG
1 TTTTTTAATATTTCAG
77484583 TTTTTTAA
1 TTTTTTAA
77484591 GTTTAAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.21, C:0.05, G:0.08, T:0.67
Consensus pattern (16 bp):
TTTTTTAATATTTCAG
Found at i:77484656 original size:13 final size:13
Alignment explanation
Indices: 77484638--77484662 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
77484628 TGTAATAAGA
77484638 ATAAAAATTTTAT
1 ATAAAAATTTTAT
77484651 ATAAAAATTTTA
1 ATAAAAATTTTA
77484663 ATTTTAATAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAAAATTTTAT
Found at i:77484950 original size:14 final size:14
Alignment explanation
Indices: 77484912--77484950 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
77484902 TTGTCATTAC
*
77484912 ACTATTATATTGCT
1 ACTATTATGTTGCT
*
77484926 ACTATTGTGTTGCT
1 ACTATTATGTTGCT
77484940 ACTATTATGTT
1 ACTATTATGTT
77484951 ATTGTTGTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.51
Consensus pattern (14 bp):
ACTATTATGTTGCT
Found at i:77486464 original size:24 final size:25
Alignment explanation
Indices: 77486422--77486470 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
77486412 CCTGCGGATA
** *
77486422 GCCGCATCTATTGTTTACAT-TTAT
1 GCCGCATCTATAATCTACATGTTAT
77486446 GCCGCATCTATAATCTACATGTTAT
1 GCCGCATCTATAATCTACATGTTAT
77486471 ATCTAAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.41
Consensus pattern (25 bp):
GCCGCATCTATAATCTACATGTTAT
Found at i:77487220 original size:12 final size:12
Alignment explanation
Indices: 77487190--77487221 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
77487180 AATAATTAAA
*
77487190 TAAATTAGAAAT
1 TAAATTCGAAAT
77487202 TAAATTCGAAAT
1 TAAATTCGAAAT
77487214 TAAATTCG
1 TAAATTCG
77487222 GATTTTGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.34
Consensus pattern (12 bp):
TAAATTCGAAAT
Found at i:77488597 original size:50 final size:50
Alignment explanation
Indices: 77488554--77488652 Score: 153
Period size: 50 Copynumber: 2.0 Consensus size: 50
77488544 CTAGGAGTAG
*
77488554 GGCCTTAATTACCACCTTCCGTAAGCCTCTTCCCATGCGTCTAGAAGCAA
1 GGCCTTAATTACCACCTTCCGTAAGCCTCCTCCCATGCGTCTAGAAGCAA
* * * *
77488604 TGCCTTTATTACCACCTTCTGTAAGCCTCCTCCTATGCGTCTAGAAGCA
1 GGCCTTAATTACCACCTTCCGTAAGCCTCCTCCCATGCGTCTAGAAGCA
77488653 GAGTCATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.22, C:0.33, G:0.15, T:0.29
Consensus pattern (50 bp):
GGCCTTAATTACCACCTTCCGTAAGCCTCCTCCCATGCGTCTAGAAGCAA
Found at i:77488682 original size:49 final size:50
Alignment explanation
Indices: 77488561--77488696 Score: 143
Period size: 50 Copynumber: 2.7 Consensus size: 50
77488551 TAGGGCCTTA
* * * * *
77488561 ATTACCACCTTCCGTAAGCCTCTTCCCATGCGTCTAGAAGCAATGCCTTT
1 ATTAACACCTTTCGTAAGCCTCCTCCTATGCGTCTAGAAGCAATGCCATT
* *
77488611 ATTACCACC-TTCTGTAAGCCTCCTCCTATGCGTCTAGAAGCAGA-GTCATT
1 ATTAACACCTTTC-GTAAGCCTCCTCCTATGCGTCTAGAAGCA-ATGCCATT
* * *
77488661 -TTAATACCTTTCGTAAGCCTCCCCCTATGCATCTAG
1 ATTAACACCTTTCGTAAGCCTCCTCCTATGCGTCTAG
77488697 GAGTAGGACA
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
49 30 0.41
50 43 0.58
51 1 0.01
ACGTcount: A:0.23, C:0.32, G:0.14, T:0.31
Consensus pattern (50 bp):
ATTAACACCTTTCGTAAGCCTCCTCCTATGCGTCTAGAAGCAATGCCATT
Found at i:77491888 original size:75 final size:73
Alignment explanation
Indices: 77491800--77491971 Score: 217
Period size: 75 Copynumber: 2.4 Consensus size: 73
77491790 GGTTTTCCTC
*** * * **
77491800 ATTGAAATACCATACCTACATTTTTTAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
77491864 TCAGTATGG
65 TCAGTATGG
*
77491873 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
77491938 CTCAGTATGG
64 CTCAGTATGG
77491948 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
77491972 CTTTGCCATG
Statistics
Matches: 88, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
70 21 0.24
73 3 0.03
74 7 0.08
75 57 0.65
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:77491969 original size:35 final size:35
Alignment explanation
Indices: 77491805--77491971 Score: 192
Period size: 35 Copynumber: 4.6 Consensus size: 35
77491795 TCCTCATTGA
*** *
77491805 AATACCATACCTACATTTTTTAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
77491840 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
77491880 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
77491915 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
77491950 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
77491972 CTTTGCCATG
Statistics
Matches: 118, Mismatches: 9, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
35 88 0.75
39 3 0.03
40 27 0.23
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.32
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:77499386 original size:75 final size:73
Alignment explanation
Indices: 77499298--77499469 Score: 217
Period size: 75 Copynumber: 2.4 Consensus size: 73
77499288 GGTTTTCCTC
*** * * **
77499298 ATTGAAATACCATACCTACATTTTTTAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
77499362 TCAGTATGG
65 TCAGTATGG
*
77499371 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
77499436 CTCAGTATGG
64 CTCAGTATGG
77499446 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
77499470 CTTTGCCATG
Statistics
Matches: 88, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
70 21 0.24
73 3 0.03
74 7 0.08
75 57 0.65
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:77499467 original size:35 final size:35
Alignment explanation
Indices: 77499303--77499469 Score: 192
Period size: 35 Copynumber: 4.6 Consensus size: 35
77499293 TCCTCATTGA
*** *
77499303 AATACCATACCTACATTTTTTAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
77499338 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
77499378 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
77499413 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
77499448 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
77499470 CTTTGCCATG
Statistics
Matches: 118, Mismatches: 9, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
35 88 0.75
39 3 0.03
40 27 0.23
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.32
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:77502028 original size:51 final size:50
Alignment explanation
Indices: 77501910--77502087 Score: 250
Period size: 51 Copynumber: 3.5 Consensus size: 50
77501900 CCATGGCAAC
*
77501910 AAGTGATAAGTGATAGCTTTGGCTACACTTATCTAATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTAATCAAGGACAAATGA
* * *
77501960 AAGTGATGAGT-AGTAGCTTCGGCTACACTTATCTGATCAAAGGACAAGTGA
1 AAGTGATAAGTGA-TAGCTTCGGCTACACTTATCTAATC-AAGGACAAATGA
* *
77502011 AAGTGATAAGTGATAGCTTCGGCTACACCTATCTAATCAGGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTAATCAAGGACAAATGA
* *
77502061 CAAGTGAAAAGTGGTAGCTTCGGCTAC
1 -AAGTGATAAGTGATAGCTTCGGCTAC
77502088 CTGATCAGTG
Statistics
Matches: 113, Mismatches: 11, Indels: 7
0.86 0.08 0.05
Matches are distributed among these distances:
49 1 0.01
50 43 0.38
51 68 0.60
52 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTAATCAAGGACAAATGA
Found at i:77502101 original size:31 final size:31
Alignment explanation
Indices: 77502063--77502211 Score: 235
Period size: 31 Copynumber: 4.8 Consensus size: 31
77502053 ACAAATGACA
77502063 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
77502094 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
77502125 AGTGAAAAGTGGTAGCTCCGGCTACCTAATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
77502156 AGTGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
77502187 AGTGAATAGTGGTAGCTTCGACTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
77502212 AAGTGACAAG
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 108 1.00
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:77503044 original size:46 final size:46
Alignment explanation
Indices: 77502863--77503044 Score: 258
Period size: 46 Copynumber: 4.0 Consensus size: 46
77502853 TTTGACATGA
* * * * * *
77502863 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
*** *
77502909 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
77502955 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
77503001 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
77503045 AGAGCACACT
Statistics
Matches: 124, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 4 0.03
46 120 0.97
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.40
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:77504386 original size:7 final size:7
Alignment explanation
Indices: 77504376--77504400 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
77504366 ATTCAGAATT
77504376 CTAAACC
1 CTAAACC
77504383 CTAAACC
1 CTAAACC
77504390 CTAAACC
1 CTAAACC
77504397 CTAA
1 CTAA
77504401 TTATTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.40, G:0.00, T:0.16
Consensus pattern (7 bp):
CTAAACC
Found at i:77505697 original size:47 final size:46
Alignment explanation
Indices: 77505644--77505746 Score: 125
Period size: 46 Copynumber: 2.2 Consensus size: 46
77505634 GGGGTATTAC
* * * * *
77505644 ATATGGCATCTGTGTGATATATGCTACTGTATAAGACCATATCTGGG
1 ATATGGCATCAGTGAGATATATGATAC-GCATAAGACCATAGCTGGG
* *
77505691 ATATGGCATCAGTGAGATATGTGATTCGCATAAGACCATAGCTGGG
1 ATATGGCATCAGTGAGATATATGATACGCATAAGACCATAGCTGGG
*
77505737 TTATGGCATC
1 ATATGGCATC
77505747 GATATATGAA
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
46 26 0.54
47 22 0.46
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (46 bp):
ATATGGCATCAGTGAGATATATGATACGCATAAGACCATAGCTGGG
Found at i:77505784 original size:42 final size:43
Alignment explanation
Indices: 77505721--77505832 Score: 147
Period size: 42 Copynumber: 2.7 Consensus size: 43
77505711 GTGATTCGCA
* * *
77505721 TAAGACCATAGCTGGGTTATGGCATCGA-TATATGAATATGTG
1 TAAGACCATAGTTGGGATATGGCATCGATTATATGAAGATGTG
* *
77505763 TAAGACCATAGTTGGGCTATGGCATC-ATTATGTGAAGATGTG
1 TAAGACCATAGTTGGGATATGGCATCGATTATATGAAGATGTG
**
77505805 TAAGACCATAGTTGAAATATGGCATCGA
1 TAAGACCATAGTTGGGATATGGCATCGA
77505833 GAAAATGAAG
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
41 1 0.02
42 59 0.97
43 1 0.02
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.29
Consensus pattern (43 bp):
TAAGACCATAGTTGGGATATGGCATCGATTATATGAAGATGTG
Found at i:77507896 original size:21 final size:21
Alignment explanation
Indices: 77507871--77507914 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
77507861 GTCGAGAGGG
77507871 AAAGAAAATGCGAGAACCGAC
1 AAAGAAAATGCGAGAACCGAC
*
77507892 AAAGAAAATGCGAGAGCCGAC
1 AAAGAAAATGCGAGAACCGAC
77507913 AA
1 AA
77507915 CGAGTAGTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.52, C:0.18, G:0.25, T:0.05
Consensus pattern (21 bp):
AAAGAAAATGCGAGAACCGAC
Found at i:77525655 original size:2 final size:2
Alignment explanation
Indices: 77525648--77525675 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
77525638 CTTGTACTTT
77525648 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
77525676 AACAACTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:77526130 original size:19 final size:18
Alignment explanation
Indices: 77526108--77526175 Score: 57
Period size: 19 Copynumber: 3.6 Consensus size: 18
77526098 CATTTAATTA
77526108 ATTTTTAATATTTTAAAAT
1 ATTTTTAATATTTT-AAAT
*
77526127 ATTTTTTATATATTTTTAAT
1 A-TTTTTA-ATATTTTAAAT
* *
77526147 AATTTTAATGATTTTTAA-
1 ATTTTTAAT-ATTTTAAAT
*
77526165 ATTTTAAATAT
1 ATTTTTAATAT
77526176 AATTTTTTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
17 2 0.05
18 9 0.21
19 14 0.33
20 10 0.24
21 7 0.17
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (18 bp):
ATTTTTAATATTTTAAAT
Found at i:77526142 original size:10 final size:9
Alignment explanation
Indices: 77526108--77526175 Score: 66
Period size: 10 Copynumber: 7.2 Consensus size: 9
77526098 CATTTAATTA
77526108 ATTTTTAAT
1 ATTTTTAAT
*
77526117 ATTTTAAAAT
1 ATTTT-TAAT
77526127 ATTTTTTATAT
1 A-TTTTTA-AT
77526138 ATTTTTAAT
1 ATTTTTAAT
*
77526147 AATTTTAAT
1 ATTTTTAAT
77526156 GATTTTTAA-
1 -ATTTTTAAT
*
77526165 ATTTTAAAT
1 ATTTTTAAT
77526174 AT
1 AT
77526176 AATTTTTTTG
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
8 7 0.14
9 17 0.35
10 18 0.37
11 7 0.14
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (9 bp):
ATTTTTAAT
Found at i:77526203 original size:49 final size:49
Alignment explanation
Indices: 77526108--77526200 Score: 131
Period size: 49 Copynumber: 1.9 Consensus size: 49
77526098 CATTTAATTA
77526108 ATTTTTAATATTTTAAAATATTTTTTATATATTTTTAATAATTTTAATG
1 ATTTTTAATATTTTAAAATATTTTTTATATATTTTTAATAATTTTAATG
77526157 ATTTTTAA-ATTTTAAATATAATTTTTT-TGA-ATTTTTAA-AATTTT
1 ATTTTTAATATTTTAAA-AT-ATTTTTTAT-ATATTTTTAATAATTTT
77526201 TAAAAAATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
48 14 0.34
49 19 0.46
50 8 0.20
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (49 bp):
ATTTTTAATATTTTAAAATATTTTTTATATATTTTTAATAATTTTAATG
Found at i:77531429 original size:25 final size:24
Alignment explanation
Indices: 77531401--77531447 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
77531391 TTACATATAT
77531401 TTTTATAATTTAAATTTTATTTACC
1 TTTTATAATTTAAATTTT-TTTACC
* * *
77531426 TTTTTTAGTTTAGATTTTTTTA
1 TTTTATAATTTAAATTTTTTTA
77531448 ATTTTTTAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 4 0.21
25 15 0.79
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.66
Consensus pattern (24 bp):
TTTTATAATTTAAATTTTTTTACC
Found at i:77533036 original size:46 final size:46
Alignment explanation
Indices: 77532971--77533132 Score: 218
Period size: 46 Copynumber: 3.5 Consensus size: 46
77532961 TTATCTTTGA
* * * * *
77532971 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATAT
**
77533017 CATGTTGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
*
77533063 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
* *
77533109 CAGGTTGTCATGGTATCTTTCAAC
1 CATGTTGCCATGGTATCTTTCAAC
77533133 ACAGGTTGCA
Statistics
Matches: 103, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
45 4 0.04
46 99 0.96
ACGTcount: A:0.21, C:0.22, G:0.15, T:0.41
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
Found at i:77533163 original size:24 final size:25
Alignment explanation
Indices: 77533109--77533156 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 25
77533099 CATTTCATAT
77533109 CAGGTTGTCATGGTATCTTTCAACA
1 CAGGTTGTCATGGTATCTTTCAACA
77533134 CAGGTTG-CATGGTATCTTTCAAC
1 CAGGTTGTCATGGTATCTTTCAAC
77533157 CATGGTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (25 bp):
CAGGTTGTCATGGTATCTTTCAACA
Found at i:77535309 original size:11 final size:11
Alignment explanation
Indices: 77535293--77535344 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
77535283 TATACTAAAT
77535293 AAATAATAATA
1 AAATAATAATA
*
77535304 AAATAAT-ATT
1 AAATAATAATA
* *
77535314 AAATATCTCATA
1 AAATA-ATAATA
*
77535326 AAATATTAATA
1 AAATAATAATA
77535337 AAATAATA
1 AAATAATA
77535345 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:77547385 original size:20 final size:20
Alignment explanation
Indices: 77547362--77547400 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
77547352 TAGAAAACCG
77547362 AAAAAAAAAGCTGAAGCAGA
1 AAAAAAAAAGCTGAAGCAGA
77547382 AAAAAAAAAGCTGAAGCAG
1 AAAAAAAAAGCTGAAGCAG
77547401 GTAGAGCGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.64, C:0.10, G:0.21, T:0.05
Consensus pattern (20 bp):
AAAAAAAAAGCTGAAGCAGA
Found at i:77547516 original size:3 final size:3
Alignment explanation
Indices: 77547496--77547553 Score: 59
Period size: 3 Copynumber: 19.3 Consensus size: 3
77547486 CTCATTTTGG
*
77547496 GAA GAAA GAA GGA GAA GAA GAA -AA GAAA GAA G-A GAA GAA GAA GAA
1 GAA G-AA GAA GAA GAA GAA GAA GAA G-AA GAA GAA GAA GAA GAA GAA
77547541 GGAA -AA GAA GAA G
1 -GAA GAA GAA GAA G
77547554 CAGGCAGCAT
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
2 6 0.13
3 32 0.68
4 9 0.19
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:77547532 original size:26 final size:26
Alignment explanation
Indices: 77547496--77547553 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
77547486 CTCATTTTGG
*
77547496 GAAGAA-AGAAGGAGAAGAA-GAAAA
1 GAAGAAGAGAAGAAGAAGAAGGAAAA
77547520 GAAAGAAGAGAAGAAGAAGAAGGAAAA
1 G-AAGAAGAGAAGAAGAAGAAGGAAAA
77547547 GAAGAAG
1 GAAGAAG
77547554 CAGGCAGCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 1 0.03
25 5 0.17
26 18 0.60
27 6 0.20
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (26 bp):
GAAGAAGAGAAGAAGAAGAAGGAAAA
Found at i:77547591 original size:13 final size:13
Alignment explanation
Indices: 77547573--77547603 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
77547563 TTGGTGAGGG
77547573 AAGAAAAAAGAAA
1 AAGAAAAAAGAAA
*
77547586 AAGAAAAAAGAAG
1 AAGAAAAAAGAAA
77547599 AAGAA
1 AAGAA
77547604 GAGGAGGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
AAGAAAAAAGAAA
Found at i:77548079 original size:17 final size:16
Alignment explanation
Indices: 77548056--77548098 Score: 68
Period size: 17 Copynumber: 2.6 Consensus size: 16
77548046 TATCCTAATG
77548056 AAAAAATAAAATACGA
1 AAAAAATAAAATACGA
*
77548072 AAAGAAATAAAATATGA
1 AAA-AAATAAAATACGA
77548089 AAAAAATAAA
1 AAAAAATAAA
77548099 TTTTCTGGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 10 0.40
17 15 0.60
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (16 bp):
AAAAAATAAAATACGA
Found at i:77548509 original size:139 final size:136
Alignment explanation
Indices: 77548134--77548744 Score: 643
Period size: 139 Copynumber: 4.5 Consensus size: 136
77548124 GGTTTTTTAT
* * **
77548134 TAAAATAATATAAAAATAAAATACGGAAATAGTATATTTTAAAAAATAATATCCGAAAATTTAAA
1 TAAAATAATA-AAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCTAAAAATTTAAA
* * * * *
77548199 AAATACAAATAAAGTGACAAAATTA-AGGTTATTT-------ACTAAAATTATACATTTGAAACA
65 AAATACAAACAAAGGGCCAAAATCAGA-GTTATTTAAAAAACACTAAAATAATACATTTGAAACA
77548256 TTATGTAC
129 TTATGTAC
* * * * *
77548264 TAAAATAATATAAAAATAAAATAGGAAAATAATATATTTT-AAAAA-AAAGTTTAAAAATTTTAA
1 TAAAATAATA-AAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCTAAAAATTTAAA
* *
77548327 AAATACAAACAAAGGGCCAAAATCAGGGTTATTTAAAAAACACTAAAATAACACATTTGAAACAT
65 AAATACAAACAAAGGGCCAAAATCAGAGTTATTTAAAAAACACTAAAATAATACATTTGAAACAT
77548392 TATGTAC
130 TATGTAC
77548399 TAAAATAAGATAAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCTAAAAAGTTT
1 TAAAAT-A-AT-AAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCTAAAAA-TTT
*
77548464 -AAAAATACAAACAAAGGGCCAAAATCAGAGTTATTTAAAAAACACTAAAATAATATATTTGAAA
62 AAAAAATACAAACAAAGGGCCAAAATCAGAGTTATTTAAAAAACACTAAAATAATACATTTGAAA
77548528 CATTATGTAC
127 CATTATGTAC
* * *
77548538 --------T--AAAATAAAATACGAAAATAATATATTTTAAAAAATAAAGTCTGAAAATTTAAAA
1 TAAAATAATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCTAAAAATTTAAAA
** * *
77548593 AATACAAACAAATAGCCAAAATCAGAGTTATTTACTAAATTAATATAAAAAATTAAAATAATACA
66 AATACAAACAAAGGGCCAAAATCAGAG----TTA-T---TT-A-A-AAAACACTAAAATAATACA
77548658 TTTGAAACATTATGTAC
120 TTTGAAACATTATGTAC
** * *
77548675 TAAAATAATATAAAAAATAAAATATAAAAATAGTATATTTTAAAAAATAAAATCCAAAAATTTCA
1 TAAAAT-A-ATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCTAAAAATTTAA
77548740 AAAAT
64 AAAAT
77548745 TTTAAAAATA
Statistics
Matches: 405, Mismatches: 38, Indels: 57
0.81 0.08 0.11
Matches are distributed among these distances:
125 3 0.01
126 72 0.18
128 40 0.10
129 6 0.01
130 40 0.10
131 1 0.00
134 2 0.00
135 36 0.09
136 2 0.00
137 62 0.15
138 6 0.01
139 81 0.20
140 3 0.01
147 1 0.00
149 50 0.12
ACGTcount: A:0.58, C:0.07, G:0.07, T:0.28
Consensus pattern (136 bp):
TAAAATAATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCTAAAAATTTAAAA
AATACAAACAAAGGGCCAAAATCAGAGTTATTTAAAAAACACTAAAATAATACATTTGAAACATT
ATGTAC
Found at i:77548963 original size:15 final size:16
Alignment explanation
Indices: 77548932--77548989 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
77548922 ACCGAGTGTA
**
77548932 TTAAATATATTATATT
1 TTAAATATAAAATATT
77548948 TTAAATA-AAAATATT
1 TTAAATATAAAATATT
** *
77548963 TTACTTATTAAATATT
1 TTAAATATAAAATATT
77548979 TTAAATTATAA
1 TTAAA-TATAA
77548990 TAAAAATATT
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
15 11 0.34
16 17 0.53
17 4 0.12
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAATATAAAATATT
Found at i:77548974 original size:38 final size:38
Alignment explanation
Indices: 77548930--77549026 Score: 108
Period size: 38 Copynumber: 2.5 Consensus size: 38
77548920 ATACCGAGTG
77548930 TATTAAATATATTATATTTTAAATAAAAATATTT-TACT
1 TATTAAATATATTATATTTT-AATAAAAATATTTGTACT
* * * *
77548968 TATTAAATATTTTAAATTATAATAAAAATATTTGTATT
1 TATTAAATATATTATATTTTAATAAAAATATTTGTACT
*
77549006 TGAGTTGAATATATT-TATTTT
1 T-A-TTAAATATATTATATTTT
77549027 TTTAATGTAG
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
37 13 0.27
38 21 0.44
39 5 0.10
40 9 0.19
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (38 bp):
TATTAAATATATTATATTTTAATAAAAATATTTGTACT
Found at i:77552721 original size:17 final size:18
Alignment explanation
Indices: 77552699--77552732 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
77552689 AAAATTATTT
77552699 TTTTCATATTTT-TTTTC
1 TTTTCATATTTTATTTTC
77552716 TTTTCATATTTTATTTT
1 TTTTCATATTTTATTTT
77552733 TTCGTTAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTCATATTTTATTTTC
Found at i:77552734 original size:15 final size:15
Alignment explanation
Indices: 77552697--77552765 Score: 57
Period size: 16 Copynumber: 4.4 Consensus size: 15
77552687 AAAAAATTAT
*
77552697 TTTTTTCATATTTTTT
1 TTTTTTCATA-TTTTA
77552713 TTCTTTTCATATTTTA
1 TT-TTTTCATATTTTA
* ***
77552729 TTTTTTCGTTAAGATA
1 TTTTTTC-ATATTTTA
*
77552745 TTTTTTAATATTTTA
1 TTTTTTCATATTTTA
77552760 TTTTTT
1 TTTTTT
77552766 TATACTATTT
Statistics
Matches: 41, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
15 15 0.37
16 18 0.44
17 8 0.20
ACGTcount: A:0.19, C:0.06, G:0.03, T:0.72
Consensus pattern (15 bp):
TTTTTTCATATTTTA
Found at i:77553257 original size:38 final size:36
Alignment explanation
Indices: 77553175--77553258 Score: 87
Period size: 38 Copynumber: 2.2 Consensus size: 36
77553165 TCCTTTTTTT
** * *
77553175 TCTTTCTTTTTCCTTCCCTCCCTCTTCTTCTGCTTC
1 TCTTTCTTTTTCCTTCCCTCCCAATGCTGCTGCTTC
*
77553211 TCTTTTTCTTTTTTCTTCCCTCACCAATGCTGCGTGCTTC
1 TC--TTTCTTTTTCCTTCCCTC-CCAATGCTGC-TGCTTC
77553251 TCTTTCTT
1 TCTTTCTT
77553259 CTCCTTCTCC
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
36 2 0.05
38 23 0.59
39 6 0.15
40 8 0.21
ACGTcount: A:0.04, C:0.36, G:0.06, T:0.55
Consensus pattern (36 bp):
TCTTTCTTTTTCCTTCCCTCCCAATGCTGCTGCTTC
Found at i:77553261 original size:9 final size:9
Alignment explanation
Indices: 77553247--77553314 Score: 54
Period size: 9 Copynumber: 7.6 Consensus size: 9
77553237 ATGCTGCGTG
77553247 CTTCTCTTT
1 CTTCTCTTT
*
77553256 CTTCTCCTT
1 CTTCTCTTT
*
77553265 CTCCTTCTTCT
1 CTTC-TCTT-T
77553276 CTTC-CTTT
1 CTTCTCTTT
77553284 CTTCTC-TT
1 CTTCTCTTT
77553292 CTT-TCTTTT
1 CTTCTC-TTT
77553301 CTTCT-TCTT
1 CTTCTCT-TT
77553310 CTTCT
1 CTTCT
77553315 TTCTTCCCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
7 2 0.04
8 11 0.23
9 27 0.56
10 4 0.08
11 4 0.08
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (9 bp):
CTTCTCTTT
Found at i:77553274 original size:3 final size:3
Alignment explanation
Indices: 77553254--77553320 Score: 61
Period size: 3 Copynumber: 23.0 Consensus size: 3
77553244 GTGCTTCTCT
* * *
77553254 TTC TTC TCC TTC TCC TTC TTC -TC TTC CT- TTC TTC -TC TTC TTTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC
77553297 TT- TTC TTC TTC TTC TTC TTTC TTC
1 TTC TTC TTC TTC TTC TTC -TTC TTC
77553321 CCAAAATGAG
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
2 7 0.13
3 39 0.75
4 6 0.12
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:77553281 original size:12 final size:12
Alignment explanation
Indices: 77553247--77553311 Score: 62
Period size: 12 Copynumber: 5.4 Consensus size: 12
77553237 ATGCTGCGTG
*
77553247 CTTCTCTTTCTT
1 CTTCTCTTCCTT
*
77553259 CTCCT-TCTCCTT
1 CTTCTCT-TCCTT
77553271 CTTCTCTTCCTTT
1 CTTCTCTTCC-TT
*
77553284 CTTCTCTTCTTT
1 CTTCTCTTCCTT
*
77553296 CTTTTCTT-CTT
1 CTTCTCTTCCTT
77553307 CTTCT
1 CTTCT
77553312 TCTTTCTTCC
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
11 7 0.16
12 24 0.56
13 12 0.28
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (12 bp):
CTTCTCTTCCTT
Found at i:77553440 original size:27 final size:27
Alignment explanation
Indices: 77553402--77553472 Score: 124
Period size: 27 Copynumber: 2.6 Consensus size: 27
77553392 GTCTTCTCCA
*
77553402 CGGTGCTGCCTCTGGCACTGGCACCAT
1 CGGTGCCGCCTCTGGCACTGGCACCAT
77553429 CGGTGCCGCCTCTGGCACTGGCACCAT
1 CGGTGCCGCCTCTGGCACTGGCACCAT
*
77553456 CGGTGCCGCCTGTGGCA
1 CGGTGCCGCCTCTGGCA
77553473 GGCCCACCAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.10, C:0.38, G:0.32, T:0.20
Consensus pattern (27 bp):
CGGTGCCGCCTCTGGCACTGGCACCAT
Found at i:77553480 original size:27 final size:28
Alignment explanation
Indices: 77553402--77553504 Score: 99
Period size: 27 Copynumber: 3.8 Consensus size: 28
77553392 GTCTTCTCCA
* *
77553402 CGGTGCTGCCTCTGGCACTGG--CACCAT
1 CGGTGCCGCCTGTGGCA-TGGCCCACCAT
*
77553429 CGGTGCCGCCTCTGGCACTGG--CACCAT
1 CGGTGCCGCCTGTGGCA-TGGCCCACCAT
*
77553456 CGGTGCCGCCTGTGGCA-GGCCCACCAC
1 CGGTGCCGCCTGTGGCATGGCCCACCAT
* *
77553483 CAGTGCCGCCTGTAGCATGGCC
1 CGGTGCCGCCTGTGGCATGGCC
77553505 TCCACCTGTG
Statistics
Matches: 68, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
25 2 0.03
27 62 0.91
28 4 0.06
ACGTcount: A:0.12, C:0.40, G:0.31, T:0.17
Consensus pattern (28 bp):
CGGTGCCGCCTGTGGCATGGCCCACCAT
Found at i:77553550 original size:20 final size:21
Alignment explanation
Indices: 77553525--77553563 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
77553515 TCGCTCTGTC
77553525 TGCTTCAG-TTTTTTTTTTTT
1 TGCTTCAGCTTTTTTTTTTTT
77553545 TGCTTCAGCTTTTTTTTTT
1 TGCTTCAGCTTTTTTTTTT
77553564 CAATTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.05, C:0.13, G:0.10, T:0.72
Consensus pattern (21 bp):
TGCTTCAGCTTTTTTTTTTTT
Found at i:77554100 original size:238 final size:237
Alignment explanation
Indices: 77553690--77554262 Score: 729
Period size: 238 Copynumber: 2.4 Consensus size: 237
77553680 TATTATTCAA
* *
77553690 ATTCTTCATCTAGGAGAAGAAAGAGTCTCGATAGGTCCAGTTCTA-TAGTAA-ACACTGCTGCAG
1 ATTCTTCTTCTAGGAGAAG-AA-AGTCTTGATAGGTCCAGTTCTATTAGTAAGA-A-TGCTGCAG
**
77553753 CTGTAGTGGTTGAGATGGATGAAATGAAATCAGTTTCTAATGCAAAGGTCTCTCCCGCAACTGTT
62 CTGTAGTGGTTGAGATGGATGAAATGAAATTGGTTTCTAATGCAAAGGTCTCTCCCGCAACTGTT
* ** * * *
77553818 TATTATGTCAAAGGACCTAAGCTTGATGTACTAGATATTGATTCTAACTCCAATTCTTTGAGGGG
127 GATTACATCAAAGGACCTAAGCTCGATGTACTAGATAGTGATTCTAACTCCAATTCTTTGAGGGA
* *
77553883 TGAATCACTTCCCGGAGATCAAACTCAAACAAGGGATTATTATTTTG
192 TGAATCACTGCCCGGAGAGCAAACTCAAACAA-GGATTATTATTTTG
* * ** * *
77553930 ATTCTTCTTCTAGGATAAGAAAGTCTTGATAGGTCCAGTTCTATTGGTAAGTTTACTGCAGCTAT
1 ATTCTTCTTCTAGGAGAAGAAAGTCTTGATAGGTCCAGTTCTATTAGTAAGAATGCTGCAGCTGT
* * * * * *
77553995 AGTAGG-TCAGCTGGATGAAAGGAAATTGGTTTCTAATGCAAAGGTCTTTCCTGCGACTGTTGAT
66 AGT-GGTTGAGATGGATGAAATGAAATTGGTTTCTAATGCAAAGGTCTCTCCCGCAACTGTTGAT
* * * * *
77554059 TACATCAATGGATCTAAGCTCGGTGTTCTAGATGGTGATTCTAACTCCAATTCTTTGAGGGATGA
130 TACATCAAAGGACCTAAGCTCGATGTACTAGATAGTGATTCTAACTCCAATTCTTTGAGGGATGA
* * * * *
77554124 ATCACTGCCTGGAGGGCTAACTCAGATAAGGATTATTATTTTG
195 ATCACTGCCCGGAGAGCAAACTCAAACAAGGATTATTATTTTG
* * * *
77554167 AATCTTCTTCTCGGAGAAGAAAGTCTTGATATGTCCAGTTCTATTAGTAAGAATGTTGCAGCTGT
1 ATTCTTCTTCTAGGAGAAGAAAGTCTTGATAGGTCCAGTTCTATTAGTAAGAATGCTGCAGCTGT
77554232 AGTGGTTGAGATGGATGAAATGAAATTGGTT
66 AGTGGTTGAGATGGATGAAATGAAATTGGTT
77554263 AAAGTTGATT
Statistics
Matches: 282, Mismatches: 47, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
236 2 0.01
237 94 0.33
238 160 0.57
239 9 0.03
240 17 0.06
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.33
Consensus pattern (237 bp):
ATTCTTCTTCTAGGAGAAGAAAGTCTTGATAGGTCCAGTTCTATTAGTAAGAATGCTGCAGCTGT
AGTGGTTGAGATGGATGAAATGAAATTGGTTTCTAATGCAAAGGTCTCTCCCGCAACTGTTGATT
ACATCAAAGGACCTAAGCTCGATGTACTAGATAGTGATTCTAACTCCAATTCTTTGAGGGATGAA
TCACTGCCCGGAGAGCAAACTCAAACAAGGATTATTATTTTG
Found at i:77554465 original size:209 final size:208
Alignment explanation
Indices: 77554095--77554471 Score: 519
Period size: 209 Copynumber: 1.8 Consensus size: 208
77554085 TCTAGATGGT
* *
77554095 GATTCTAACTCCAATTCTTTGAGGGATGAATCACTGCCTGGAGGGCTAACTCAGATAAGGATTAT
1 GATTCTAACTCCAATTCTTTGAGGGATGAATCACTGCCTGAAGGGCTAACTCAGACAAGGATTAT
* * * * **
77554160 TATTTTGAATCTTCTTCTCGGAGAAGAAAGTCTTGATATGTCCAGTTCTATTAGTAAGAATGTTG
66 TATTCTGAATCTTCTTCTAGGAGAAGAAAGTCTTGATAGGTCCAGTTCTATTAGGAAGAATGCGG
* **
77554225 CAGCTGTAGTGGTTGAGATGGATGAAATGAAATTGGTTAAAGTTGATTACATTCATGGACCTTGG
131 CAGCTATAGTGGTTGAGACCGATGAAATGAAATTGGTTAAAGTTGATTACATTCATGGACCTTGG
77554290 TGTGCCGGATCGG
196 TGTGCCGGATCGG
* * * *
77554303 GATTCTAACTCCCATTCTTTGAGGGATGAATCACTTCCTGAAGGGTCTGA-TCAGACGA-GATTA
1 GATTCTAACTCCAATTCTTTGAGGGATGAATCACTGCCTGAAGGG-CTAACTCAGACAAGGATTA
* *
77554366 TTATTCT-AATTCTTCTTCTAGGAGAAGAAAGAGTCTCT-ATAGGTCCGGTTCTATTAGGAAGAC
65 TTATTCTGAA-TCTTCTTCTAGGAGAAG-AA-AGTCT-TGATAGGTCCAGTTCTATTAGGAAGAA
*
77554429 TGCGGCATCTATAGTGGTTGAGACCGATGAAATGAAATTGGTT
126 TGCGGCAGCTATAGTGGTTGAGACCGATGAAATGAAATTGGTT
77554472 TCTAGTGTTT
Statistics
Matches: 146, Mismatches: 18, Indels: 9
0.84 0.10 0.05
Matches are distributed among these distances:
206 2 0.01
207 27 0.18
208 50 0.34
209 66 0.45
210 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.33
Consensus pattern (208 bp):
GATTCTAACTCCAATTCTTTGAGGGATGAATCACTGCCTGAAGGGCTAACTCAGACAAGGATTAT
TATTCTGAATCTTCTTCTAGGAGAAGAAAGTCTTGATAGGTCCAGTTCTATTAGGAAGAATGCGG
CAGCTATAGTGGTTGAGACCGATGAAATGAAATTGGTTAAAGTTGATTACATTCATGGACCTTGG
TGTGCCGGATCGG
Found at i:77563175 original size:23 final size:23
Alignment explanation
Indices: 77563130--77563185 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
77563120 AATGCAACAA
* * * *
77563130 GAGACCAGAAGCAGTTCAGCATG
1 GAGACCAGCACCAGCTCAACATG
77563153 GAGACCAGCACCAGCTCAACATG
1 GAGACCAGCACCAGCTCAACATG
* *
77563176 AAGATCAGCA
1 GAGACCAGCA
77563186 TTGGAGTTGA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.38, C:0.27, G:0.25, T:0.11
Consensus pattern (23 bp):
GAGACCAGCACCAGCTCAACATG
Found at i:77565699 original size:17 final size:17
Alignment explanation
Indices: 77565677--77565724 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
77565667 CCCGGCCCGA
77565677 TTTTAATATTAAATTAT
1 TTTTAATATTAAATTAT
* ***
77565694 TTTTAAAATTTTTTTAT
1 TTTTAATATTAAATTAT
*
77565711 TTTTAATTTTAAAT
1 TTTTAATATTAAAT
77565725 AACTTTAGTA
Statistics
Matches: 22, Mismatches: 9, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTAATATTAAATTAT
Found at i:77565935 original size:20 final size:20
Alignment explanation
Indices: 77565912--77565951 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
77565902 TTAGTCCCAT
*
77565912 TATTTATTTTTTTGTTTTAA
1 TATTTATTTTTATGTTTTAA
*
77565932 TATTTGTTTTTATGTTTTAA
1 TATTTATTTTTATGTTTTAA
77565952 ATGTATTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.72
Consensus pattern (20 bp):
TATTTATTTTTATGTTTTAA
Found at i:77565969 original size:25 final size:23
Alignment explanation
Indices: 77565932--77565977 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
77565922 TTTGTTTTAA
*
77565932 TATTTGTTTTTATGTTTTAAATG
1 TATTTGTTTTTATATTTTAAATG
77565955 TATTTGATTTATTATATTTTAAA
1 TATTTG-TTT-TTATATTTTAAA
77565978 GTTTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 3 0.15
25 11 0.55
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (23 bp):
TATTTGTTTTTATATTTTAAATG
Found at i:77567507 original size:26 final size:28
Alignment explanation
Indices: 77567448--77567507 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 28
77567438 ACATATATGA
77567448 TATAAAAAACTAGTAATATTTCAACAAC
1 TATAAAAAACTAGTAATATTTCAACAAC
*
77567476 -A-AAAAAAATAGTAATATTT-AA-AAGC
1 TATAAAAAACTAGTAATATTTCAACAA-C
77567501 TATAAAA
1 TATAAAA
77567508 TAAGATTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
24 2 0.07
25 3 0.11
26 18 0.64
27 5 0.18
ACGTcount: A:0.60, C:0.08, G:0.05, T:0.27
Consensus pattern (28 bp):
TATAAAAAACTAGTAATATTTCAACAAC
Found at i:77569260 original size:3 final size:3
Alignment explanation
Indices: 77569252--77569310 Score: 50
Period size: 3 Copynumber: 20.3 Consensus size: 3
77569242 TTAATTTTAA
* * * *
77569252 TAT TAT TAT TGT TAT TAT TAG TAT TAT TGT TAA TAT TAT T-T TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
77569298 CAT TAT TAC TAT T
1 TAT TAT TAT TAT T
77569311 TTTCATTTTT
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
2 3 0.07
3 39 0.93
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:77569278 original size:18 final size:17
Alignment explanation
Indices: 77569255--77569310 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
77569245 ATTTTAATAT
77569255 TATTATTGTTATTATTA
1 TATTATTGTTATTATTA
*
77569272 GTATTATTGTTAATATTA
1 -TATTATTGTTATTATTA
* *
77569290 TTTTATT-TCATTATTA
1 TATTATTGTTATTATTA
77569306 CTATT
1 -TATT
77569311 TTTCATTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
16 7 0.22
17 9 0.28
18 16 0.50
ACGTcount: A:0.29, C:0.04, G:0.05, T:0.62
Consensus pattern (17 bp):
TATTATTGTTATTATTA
Found at i:77569431 original size:26 final size:26
Alignment explanation
Indices: 77569372--77569431 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
77569362 ATTTTCTTTT
*
77569372 TTATTATTATTGTTGTTAACTTATCA
1 TTATTATTATTGTTATTAACTTATCA
* * *
77569398 TCATTATTATTGTTATTTATTTATC-
1 TTATTATTATTGTTATTAACTTATCA
77569423 TTATATATT
1 TTAT-TATT
77569432 TCTATTATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
25 3 0.11
26 25 0.89
ACGTcount: A:0.27, C:0.07, G:0.05, T:0.62
Consensus pattern (26 bp):
TTATTATTATTGTTATTAACTTATCA
Found at i:77569491 original size:3 final size:3
Alignment explanation
Indices: 77569483--77569650 Score: 111
Period size: 3 Copynumber: 56.3 Consensus size: 3
77569473 CACATTCATT
* * *
77569483 TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTC TTT TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
77569529 TTA TTTA CTA TTA TTA TGT- TTA CTT- TTA -TA CTA -TA GTTA -TA CTT-
1 TTA -TTA TTA TTA TTA T-TA TTA -TTA TTA TTA TTA TTA -TTA TTA -TTA
* * * * *
77569573 TCTC TTA TGA TCA TCA TTA TTC TTA TTA TT- TCT- TTA -TA TTA TTA
1 T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
77569617 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
77569651 ACTTTCTTTT
Statistics
Matches: 136, Mismatches: 13, Indels: 32
0.75 0.07 0.18
Matches are distributed among these distances:
2 14 0.10
3 109 0.80
4 13 0.10
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:77569519 original size:34 final size:34
Alignment explanation
Indices: 77569476--77569545 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
77569466 TTACTGTCAC
* *
77569476 ATTCATTTTATTATTATTATTATTTATTATTATT
1 ATTCATTTTATTAATATTATTATTTACTATTATT
*
77569510 ATTCTTTTTATTAATATTATTATTTACTATTATT
1 ATTCATTTTATTAATATTATTATTTACTATTATT
77569544 AT
1 AT
77569546 GTTTACTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (34 bp):
ATTCATTTTATTAATATTATTATTTACTATTATT
Found at i:77572320 original size:20 final size:21
Alignment explanation
Indices: 77572284--77572322 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
77572274 CACTCAACTT
77572284 TTAAAACTTATGTAATAGTCA
1 TTAAAACTTATGTAATAGTCA
77572305 TTAAAA-TTATCG-AATAGT
1 TTAAAACTTAT-GTAATAGT
77572323 TACATTTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (21 bp):
TTAAAACTTATGTAATAGTCA
Found at i:77584680 original size:6 final size:6
Alignment explanation
Indices: 77584669--77584693 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
77584659 AAACCCAGCC
77584669 GTCGAG GTCGAG GTCGAG GTCGAG G
1 GTCGAG GTCGAG GTCGAG GTCGAG G
77584694 GTTTTACAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.52, T:0.16
Consensus pattern (6 bp):
GTCGAG
Found at i:77588389 original size:6 final size:6
Alignment explanation
Indices: 77588378--77588406 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
77588368 TTTCAGCAAA
77588378 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
77588407 GCTAGAGGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:77590813 original size:15 final size:15
Alignment explanation
Indices: 77590793--77590822 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
77590783 TTACTGCCAA
77590793 TCATTTATCAACTTC
1 TCATTTATCAACTTC
77590808 TCATTTATCAACTTC
1 TCATTTATCAACTTC
77590823 GAGTTTTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.47
Consensus pattern (15 bp):
TCATTTATCAACTTC
Found at i:77592563 original size:43 final size:44
Alignment explanation
Indices: 77592474--77592563 Score: 164
Period size: 44 Copynumber: 2.1 Consensus size: 44
77592464 AATGTGAAGA
*
77592474 GTTAAATTTATTAAATTATTTAGAATTTAAGATTTGGCTATTTG
1 GTTAAATTTATTAAATTATTTAGAATTCAAGATTTGGCTATTTG
77592518 GTTAAATTTATTAAATTATTTAGAA-TCAAGATTTGGCTATTTG
1 GTTAAATTTATTAAATTATTTAGAATTCAAGATTTGGCTATTTG
77592561 GTT
1 GTT
77592564 TCTAAGCAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
43 20 0.44
44 25 0.56
ACGTcount: A:0.33, C:0.03, G:0.14, T:0.49
Consensus pattern (44 bp):
GTTAAATTTATTAAATTATTTAGAATTCAAGATTTGGCTATTTG
Found at i:77593842 original size:22 final size:22
Alignment explanation
Indices: 77593814--77593857 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
77593804 TAATACATTA
77593814 AAAATAAAAATTAATTAATAAG
1 AAAATAAAAATTAATTAATAAG
* *
77593836 AAAATAATAATTTATTAATAAG
1 AAAATAAAAATTAATTAATAAG
77593858 GTAAATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (22 bp):
AAAATAAAAATTAATTAATAAG
Found at i:77593935 original size:29 final size:31
Alignment explanation
Indices: 77593903--77593967 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
77593893 TTTTCTTCAA
*
77593903 CCAACCATGAA-A-AGTCCTTTTTTGATCAC
1 CCAACCATGAATACACTCCTTTTTTGATCAC
* *
77593932 CCAACCATTAATACACTCCTTTTTTTATCAC
1 CCAACCATGAATACACTCCTTTTTTGATCAC
*
77593963 TCAAC
1 CCAAC
77593968 TATTCAATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 10 0.33
30 1 0.03
31 19 0.63
ACGTcount: A:0.31, C:0.31, G:0.05, T:0.34
Consensus pattern (31 bp):
CCAACCATGAATACACTCCTTTTTTGATCAC
Found at i:77604731 original size:16 final size:13
Alignment explanation
Indices: 77604697--77604721 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
77604687 TCTAATCATA
77604697 TAATAATTTATAT
1 TAATAATTTATAT
77604710 TAATAATTTATA
1 TAATAATTTATA
77604722 ATTTTAATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TAATAATTTATAT
Found at i:77604745 original size:20 final size:21
Alignment explanation
Indices: 77604690--77604745 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 21
77604680 ATCTATGTCT
* * *
77604690 AATCATATAATAATTTATATT
1 AATCATTTAATATTTTATATA
*
77604711 AATAATTT-ATAATTTTA-ATA
1 AATCATTTAAT-ATTTTATATA
77604731 AATCATTTAATATTT
1 AATCATTTAATATTT
77604746 CAATTTTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (21 bp):
AATCATTTAATATTTTATATA
Found at i:77604769 original size:13 final size:14
Alignment explanation
Indices: 77604753--77604794 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
77604743 TTTCAATTTT
77604753 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
77604766 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
77604781 ATTTTAAATAATAT
1 ATTTT-AATAATAT
77604795 TCTTCATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:77604779 original size:16 final size:16
Alignment explanation
Indices: 77604757--77604793 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
77604747 AATTTTATTT
77604757 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
77604774 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
77604789 TAATA
1 TAATA
77604794 TTCTTCATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:77604847 original size:15 final size:15
Alignment explanation
Indices: 77604827--77604883 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
77604817 CTTCAATATT
77604827 AATATTTTAATAATA
1 AATATTTTAATAATA
*
77604842 AATATTTATTAAAATTATA
1 AATA-TT-TT--AATAATA
*
77604861 AATATATTAATAATA
1 AATATTTTAATAATA
*
77604876 AATGTTTT
1 AATATTTT
77604884 GTAGTGTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:77605668 original size:32 final size:32
Alignment explanation
Indices: 77605619--77605690 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 32
77605609 AACTTTTACG
* * *
77605619 AAATATTTTCAAGAAATTTA-TTAAATAATAGA
1 AAATA-TTTCAACAAATTCATTTAAATAACAGA
*
77605651 AAATATTTCACACAAATTCATTTAAATACCAGA
1 AAATATTTCA-ACAAATTCATTTAAATAACAGA
77605684 AAATATT
1 AAATATT
77605691 AATTTTTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 5 0.15
32 12 0.35
33 17 0.50
ACGTcount: A:0.51, C:0.10, G:0.04, T:0.35
Consensus pattern (32 bp):
AAATATTTCAACAAATTCATTTAAATAACAGA
Found at i:77608293 original size:19 final size:20
Alignment explanation
Indices: 77608262--77608315 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
77608252 AAAAATATAA
77608262 ATTTTGAAATTTTT-ATAAA-T
1 ATTTTG-AATTTTTGA-AAATT
77608282 ATTTTGAATTTTTGAAAATT
1 ATTTTGAATTTTTGAAAATT
77608302 ATTTTG-ATTTTTGA
1 ATTTTGAATTTTTGA
77608316 TTTTGTAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.57
Consensus pattern (20 bp):
ATTTTGAATTTTTGAAAATT
Found at i:77611298 original size:20 final size:20
Alignment explanation
Indices: 77611273--77611312 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
77611263 ACCCAGTAAG
77611273 TTAGGGCACAATCCTCCCGT
1 TTAGGGCACAATCCTCCCGT
77611293 TTAGGGCACAATCCTCCCGT
1 TTAGGGCACAATCCTCCCGT
77611313 GGATCCTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.35, G:0.20, T:0.25
Consensus pattern (20 bp):
TTAGGGCACAATCCTCCCGT
Found at i:77611568 original size:3 final size:3
Alignment explanation
Indices: 77611560--77611729 Score: 154
Period size: 3 Copynumber: 57.0 Consensus size: 3
77611550 TAGTGCCATT
* * * * * * *
77611560 ATA ATA ATA AAA ATA AAA ATA ATA AAA ATA ACA AT- ATG TTA CTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
77611607 ATA ATAA ATAA ATA TTG GTA ATA A-A TATA TATA A-A ATA ATA GTA A-A
1 ATA AT-A AT-A ATA ATA ATA ATA ATA -ATA -ATA ATA ATA ATA ATA ATA
77611653 AGTA ATA A-A ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
77611697 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
77611730 CTCTCCCCCT
Statistics
Matches: 139, Mismatches: 19, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
2 11 0.08
3 114 0.82
4 14 0.10
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:77612120 original size:30 final size:30
Alignment explanation
Indices: 77612084--77612165 Score: 130
Period size: 30 Copynumber: 2.7 Consensus size: 30
77612074 CATAGTGGCA
*
77612084 AGTAGGGTAATGGAGTTAGTGGGGT-AGCTT
1 AGTAGGGTGATGGAGTTAGTGGGGTGA-CTT
77612114 AGTAGGGTGATGGAGTTAGTGGGGTGACTT
1 AGTAGGGTGATGGAGTTAGTGGGGTGACTT
*
77612144 AGTGGGGTGATGGAGTTAGTGG
1 AGTAGGGTGATGGAGTTAGTGG
77612166 TCAGTTTAGT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
30 48 0.98
31 1 0.02
ACGTcount: A:0.21, C:0.02, G:0.48, T:0.29
Consensus pattern (30 bp):
AGTAGGGTGATGGAGTTAGTGGGGTGACTT
Found at i:77612138 original size:17 final size:17
Alignment explanation
Indices: 77612088--77612165 Score: 64
Period size: 17 Copynumber: 5.1 Consensus size: 17
77612078 GTGGCAAGTA
*
77612088 GGGTAATGGAGTTAGTG
1 GGGTGATGGAGTTAGTG
* *
77612105 GGGT-A--G-CTTAGTA
1 GGGTGATGGAGTTAGTG
77612118 GGGTGATGGAGTTAGT-
1 GGGTGATGGAGTTAGTG
*
77612134 GGG-G-T-GACTTAGTG
1 GGGTGATGGAGTTAGTG
77612148 GGGTGATGGAGTTAGTG
1 GGGTGATGGAGTTAGTG
77612165 G
1 G
77612166 TCAGTTTAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
13 16 0.33
14 6 0.12
15 2 0.04
16 6 0.12
17 18 0.38
ACGTcount: A:0.19, C:0.03, G:0.49, T:0.29
Consensus pattern (17 bp):
GGGTGATGGAGTTAGTG
Found at i:77612147 original size:13 final size:13
Alignment explanation
Indices: 77612129--77612153 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
77612119 GGTGATGGAG
77612129 TTAGTGGGGTGAC
1 TTAGTGGGGTGAC
77612142 TTAGTGGGGTGA
1 TTAGTGGGGTGA
77612154 TGGAGTTAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.04, G:0.48, T:0.32
Consensus pattern (13 bp):
TTAGTGGGGTGAC
Found at i:77614687 original size:34 final size:35
Alignment explanation
Indices: 77614642--77614711 Score: 106
Period size: 34 Copynumber: 2.0 Consensus size: 35
77614632 TATGTTTGAA
* *
77614642 TTTTATCATTAAAATTTATCA-TCAATTTTAATTT
1 TTTTATCATTAAAATTTACCATTCAATTTCAATTT
*
77614676 TTTTATTATTAAAATTTACCATTCAATTTCAATTT
1 TTTTATCATTAAAATTTACCATTCAATTTCAATTT
77614711 T
1 T
77614712 GATAATTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 19 0.59
35 13 0.41
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.56
Consensus pattern (35 bp):
TTTTATCATTAAAATTTACCATTCAATTTCAATTT
Found at i:77614722 original size:34 final size:34
Alignment explanation
Indices: 77614649--77614723 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
77614639 GAATTTTATC
* * ** *
77614649 ATTAAAATTTATCATCAATTTTAATTTTTTTATT
1 ATTAAAATTTACCATCAATTTCAATTTTGATAAT
77614683 ATTAAAATTTACCATTCAATTTCAATTTTGATAAT
1 ATTAAAATTTACCA-TCAATTTCAATTTTGATAAT
77614718 -TTAAAA
1 ATTAAAA
77614724 ACATAATTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 19 0.54
35 16 0.46
ACGTcount: A:0.40, C:0.08, G:0.01, T:0.51
Consensus pattern (34 bp):
ATTAAAATTTACCATCAATTTCAATTTTGATAAT
Found at i:77621351 original size:19 final size:19
Alignment explanation
Indices: 77621327--77621366 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
77621317 TTAGCACCCA
77621327 CTAAACTGA-CCACTAACTC
1 CTAAACT-ACCCACTAACTC
77621346 CTAAACTATCCCACTAACTC
1 CTAAACTA-CCCACTAACTC
77621366 C
1 C
77621367 ATCACCCCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 1 0.05
19 7 0.37
20 11 0.58
ACGTcount: A:0.35, C:0.40, G:0.03, T:0.23
Consensus pattern (19 bp):
CTAAACTACCCACTAACTC
Found at i:77621769 original size:3 final size:3
Alignment explanation
Indices: 77621761--77621935 Score: 157
Period size: 3 Copynumber: 59.0 Consensus size: 3
77621751 AGGGAGAGAG
77621761 TAT TAT TAT 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 TAT TAT TAT
* *
77621809 TAT TAT TAT TAT TAT T-T TAT T-T TAT T-T TAT TACT T-T TAC TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
* * * *
77621851 TAT T-T TA- TAT ATATT TAT TAC CAT TATT TATT TAT TAT TAT TAG TAA
1 TAT TAT TAT TAT -TA-T TAT TAT TAT TA-T TA-T TAT TAT TAT TAT TAT
* * * * *
77621898 CA- TAT TGT TAT TTT TAT TAT TTT TAT TTT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
77621936 AATGACACTA
Statistics
Matches: 143, Mismatches: 18, Indels: 22
0.78 0.10 0.12
Matches are distributed among these distances:
2 13 0.09
3 116 0.81
4 13 0.09
5 1 0.01
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:77622091 original size:15 final size:16
Alignment explanation
Indices: 77622053--77622092 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
77622043 TGTTATTAGG
*
77622053 GTTATTATATTGCTAT
1 GTTATCATATTGCTAT
77622069 -TT-TCATATTGC-AT
1 GTTATCATATTGCTAT
77622082 GTTATCATATT
1 GTTATCATATT
77622093 TTTTTTAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
13 2 0.10
14 10 0.48
15 9 0.43
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.55
Consensus pattern (16 bp):
GTTATCATATTGCTAT
Found at i:77622210 original size:20 final size:20
Alignment explanation
Indices: 77622185--77622224 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
77622175 TTTAAGATCC
77622185 ACGGGAGGATTGTGCCCTAA
1 ACGGGAGGATTGTGCCCTAA
*
77622205 ACGGGATGATTGTGCCCTAA
1 ACGGGAGGATTGTGCCCTAA
77622225 CTTACTGGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.25, C:0.20, G:0.33, T:0.23
Consensus pattern (20 bp):
ACGGGAGGATTGTGCCCTAA
Found at i:77624203 original size:79 final size:79
Alignment explanation
Indices: 77624072--77624290 Score: 314
Period size: 79 Copynumber: 2.8 Consensus size: 79
77624062 TACTCTCTCG
* * * * *
77624072 ATGTAACTGTAGTGAATCAGGATTA-GCTGTTCAGGTCAAATCCTATCCACCTTAAGTTATCATA
1 ATGTAACCGTAGCGAATCAGGATTACCCTCTTCAGGTCAAATCCTATCCACCTTAAGTTACCATA
77624136 AGGAATCATATATC
66 AGGAATCATATATC
* * *
77624150 GTGTAACCGTAGCGAATCAGGATTACCCTCTTCAGATCAAATCCTATCCACCTTAGGTTACCATA
1 ATGTAACCGTAGCGAATCAGGATTACCCTCTTCAGGTCAAATCCTATCCACCTTAAGTTACCATA
*
77624215 ATGAATCATATATC
66 AGGAATCATATATC
* * * *
77624229 ATGTAACCGTAACGAATCAGGATTACCCTTTTCAGGTCAAATTCTATCCGCCTTAAGTTACC
1 ATGTAACCGTAGCGAATCAGGATTACCCTCTTCAGGTCAAATCCTATCCACCTTAAGTTACC
77624291 GTAGTGAATA
Statistics
Matches: 124, Mismatches: 16, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
78 22 0.18
79 102 0.82
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.31
Consensus pattern (79 bp):
ATGTAACCGTAGCGAATCAGGATTACCCTCTTCAGGTCAAATCCTATCCACCTTAAGTTACCATA
AGGAATCATATATC
Found at i:77624345 original size:40 final size:40
Alignment explanation
Indices: 77624266--77624403 Score: 132
Period size: 40 Copynumber: 3.5 Consensus size: 40
77624256 CTTTTCAGGT
* * * * *
77624266 CAAATTCTATCCGCCTTAAGTTACCGTAGTGAATAAGGAA
1 CAAATCCTATCCACTTTAAATTACCATAGTGAATAAGGAA
* * *
77624306 TAAATCCTATTCACTTTAAATTACCATAGTGAATCAGGAA
1 CAAATCCTATCCACTTTAAATTACCATAGTGAATAAGGAA
* ** ** *
77624346 CAAATCCTATCCACTTTGAGGTATTATAGTGAATTAGGAA
1 CAAATCCTATCCACTTTAAATTACCATAGTGAATAAGGAA
* *
77624386 CGAATCCTATCCATTTTA
1 CAAATCCTATCCACTTTA
77624404 TATTCTCGAG
Statistics
Matches: 79, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 79 1.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.32
Consensus pattern (40 bp):
CAAATCCTATCCACTTTAAATTACCATAGTGAATAAGGAA
Found at i:77627111 original size:10 final size:10
Alignment explanation
Indices: 77627096--77627120 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
77627086 AAATTCTAAT
77627096 TTTTTATATA
1 TTTTTATATA
77627106 TTTTTATATA
1 TTTTTATATA
77627116 TTTTT
1 TTTTT
77627121 GGAATTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTATATA
Found at i:77637918 original size:21 final size:20
Alignment explanation
Indices: 77637892--77637931 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
77637882 TAATAGGCAC
77637892 AATTAATCTCTATAT-TTTTAG
1 AATTAAT-T-TATATGTTTTAG
77637913 AATTAATTTATATGTTTTA
1 AATTAATTTATATGTTTTA
77637932 ATTTAGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
20 6 0.33
21 7 0.39
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (20 bp):
AATTAATTTATATGTTTTAG
Found at i:77646158 original size:20 final size:20
Alignment explanation
Indices: 77646113--77646149 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
77646103 GAGAATTGAT
*
77646113 TTAATTTATAATTAAATTAA
1 TTAATTTATAAATAAATTAA
77646133 TTAATTT-TAAATAAATT
1 TTAATTTATAAATAAATT
77646150 TATGTAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTAATTTATAAATAAATTAA
Found at i:77646183 original size:10 final size:10
Alignment explanation
Indices: 77646168--77646196 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
77646158 TAACGTAAAT
77646168 AAAATTATTA
1 AAAATTATTA
77646178 AAAATTATTA
1 AAAATTATTA
77646188 AAAA-TATTA
1 AAAATTATTA
77646197 TTTACACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.26
10 14 0.74
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
AAAATTATTA
Done.