Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D09
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: 51526817
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 216316 characters in sequence are not A, C, G, or T
File 108 of 172
Found at i:31098155 original size:38 final size:38
Alignment explanation
Indices: 31098086--31098161 Score: 91
Period size: 39 Copynumber: 1.9 Consensus size: 38
31098076 ATAAAAATTT
* *
31098086 AAAATTTTATATTTTCAAAAATTCTAAAAAATATATAAA
1 AAAATTTAAAATTTTCAAAAATTCTAAAAAATA-ATAAA
31098125 AAAATTTAAAATTTT-AAAAATTTTCTAAAATAATAAT
1 AAAATTTAAAATTTTCAAAAA--TTCTAAAA-AATAAT
31098162 TTTGGGAGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
38 5 0.16
39 13 0.41
40 10 0.31
41 4 0.12
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (38 bp):
AAAATTTAAAATTTTCAAAAATTCTAAAAAATAATAAA
Found at i:31099185 original size:16 final size:18
Alignment explanation
Indices: 31099156--31099188 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
31099146 ACTAAAAATA
31099156 TTAAAGAAATTAAATTTG
1 TTAAAGAAATTAAATTTG
31099174 TTAAA-AAA-TAAATTT
1 TTAAAGAAATTAAATTT
31099189 TATAAAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (18 bp):
TTAAAGAAATTAAATTTG
Found at i:31114343 original size:10 final size:10
Alignment explanation
Indices: 31114323--31114376 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
31114313 TTTAAGATTC
31114323 AAAAAAGTTAT
1 AAAAAA-TTAT
31114334 AAAAAATTAT
1 AAAAAATTAT
**
31114344 TTAAAATT-T
1 AAAAAATTAT
31114353 -AAAAATTAT
1 AAAAAATTAT
*
31114362 -TAAAATTAT
1 AAAAAATTAT
31114371 AAAAAA
1 AAAAAA
31114377 ATATTTTTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
8 6 0.17
9 10 0.28
10 14 0.39
11 6 0.17
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:31114359 original size:8 final size:9
Alignment explanation
Indices: 31114324--31114375 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
31114314 TTAAGATTCA
31114324 AAAAAGTTAT
1 AAAAA-TTAT
31114334 AAAAAATTATT
1 -AAAAATTA-T
*
31114345 TAAAATT-T
1 AAAAATTAT
31114353 AAAAATTAT
1 AAAAATTAT
*
31114362 TAAAATTAT
1 AAAAATTAT
31114371 AAAAA
1 AAAAA
31114376 AATATTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
8 7 0.20
9 13 0.37
10 9 0.26
11 6 0.17
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (9 bp):
AAAAATTAT
Found at i:31114364 original size:17 final size:19
Alignment explanation
Indices: 31114325--31114375 Score: 70
Period size: 18 Copynumber: 2.7 Consensus size: 19
31114315 TAAGATTCAA
31114325 AAAAGTTATAAAAAATTATTT
1 AAAA-TTAT-AAAAATTATTT
31114346 AAAATT-TAAAAATTA-TT
1 AAAATTATAAAAATTATTT
31114363 AAAATTATAAAAA
1 AAAATTATAAAAA
31114376 AATATTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 8 0.28
18 14 0.48
19 1 0.03
20 2 0.07
21 4 0.14
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
AAAATTATAAAAATTATTT
Found at i:31120918 original size:4 final size:4
Alignment explanation
Indices: 31120909--31120953 Score: 90
Period size: 4 Copynumber: 11.2 Consensus size: 4
31120899 ATTAAAACAA
31120909 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG T
31120954 CACAGAATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:31132520 original size:13 final size:13
Alignment explanation
Indices: 31132504--31132529 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31132494 TTTCATCTGT
31132504 ATTTTTAAATTTG
1 ATTTTTAAATTTG
31132517 ATTTTTAAATTTG
1 ATTTTTAAATTTG
31132530 TTGTAAAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
ATTTTTAAATTTG
Found at i:31133640 original size:22 final size:20
Alignment explanation
Indices: 31133606--31133648 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 20
31133596 TTTTGTACAA
31133606 TAATAATATTATTTTAATTT
1 TAATAATATTATTTTAATTT
31133626 TAATATATATATATTTTAATTT
1 TAATA-ATAT-TATTTTAATTT
31133648 T
1 T
31133649 TTTTAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.24
21 4 0.19
22 12 0.57
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TAATAATATTATTTTAATTT
Found at i:31145592 original size:46 final size:44
Alignment explanation
Indices: 31145490--31146081 Score: 354
Period size: 44 Copynumber: 13.7 Consensus size: 44
31145480 TTTAAGTCTA
** * *
31145490 CTCCACTGTAATATCAGGGAGATAAGACCTCTG--GCTTCAATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGA--TCTGATTCTTCGATCTG
* * *
31145534 CTCCACTGTAACCTCAGGGGGATAAGATCTGCAATTCTTCGGTCTA
1 CTCCACTGTAACCTCAGGGAGATAAGATCTG--ATTCTTCGATCTG
* * * *
31145580 CTCCACTGTAACCTCAGAGAGATAAGACCTGA---TGCGATCTA
1 CTCCACTGTAACCTCAGGGAGATAAGATCTGATTCTTCGATCTG
* * * * * * *
31145621 CTCTACTGTAACTTCAGAGAGATGAGATCCTTTATT-TT-AATCCG
1 CTCCACTGTAACCTCAGGGAGATAAGAT-C-TGATTCTTCGATCTG
* *
31145665 CTCCACTGTAACTTCAGGGAGATAGGAT-T-ATATCTTCGATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGATCTGAT-TCTTCGATCTG
* *
31145708 CTCCGCTGTAACCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTG
1 CTCCACTGTAACCTCAGGGAGATAAGATCTG--ATTCTTCGATCTG
* * * * *
31145754 TTCCACTGTAATCTCAGGGAGATAAGACCTGA---TGCGATCTA
1 CTCCACTGTAACCTCAGGGAGATAAGATCTGATTCTTCGATCTG
* * * * * *
31145795 CTCTACTGTAACTTCAGAGAGATAAGATCCTTTATT-TT-AATCCG
1 CTCCACTGTAACCTCAGGGAGATAAGAT-C-TGATTCTTCGATCTG
* *
31145839 CTCCACTGTAACTTCAGGGAGATAGGAT-T-ATATCTTCGATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGATCTGAT-TCTTCGATCTG
* * *
31145882 CTCCGCTGTAACCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTG
1 CTCCACTGTAACCTCAGGGAGATAAGATCTG--ATTCTTCGATCTG
* * * * *
31145928 TTCCACTGTAATCTCAGGGAGATAAGACCTGA-T-GT-GATCTT
1 CTCCACTGTAACCTCAGGGAGATAAGATCTGATTCTTCGATCTG
* * * ** *
31145969 CTCTACTGTAACTTCAGAGAGATAAGATC-----CTTTAATCCG
1 CTCCACTGTAACCTCAGGGAGATAAGATCTGATTCTTCGATCTG
* * * * *
31146008 CTCCATTGTAATCTCAAGGAGATAGGAT-T-ACTATCTTTGATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGATCTGA-T-TCTTCGATCTG
* *
31146052 CTCCGCTGTAATCTCAGGGAGATAAGATCT
1 CTCCACTGTAACCTCAGGGAGATAAGATCT
31146082 CTGGCTTCAA
Statistics
Matches: 424, Mismatches: 89, Indels: 69
0.73 0.15 0.12
Matches are distributed among these distances:
38 1 0.00
39 24 0.06
40 4 0.01
41 90 0.21
42 11 0.03
43 63 0.15
44 116 0.27
45 3 0.01
46 108 0.25
47 4 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (44 bp):
CTCCACTGTAACCTCAGGGAGATAAGATCTGATTCTTCGATCTG
Found at i:31145638 original size:41 final size:42
Alignment explanation
Indices: 31145486--31145995 Score: 235
Period size: 46 Copynumber: 11.7 Consensus size: 42
31145476 TAGGTTTAAG
* ** *
31145486 TCTACTCCACTGTAA-TATCAGGGAGATAAGACCTCTGGCTTCAA
1 TCTACTCCACTGTAACT-TCAGAGAGATAAGA-C-CTGATTTCGA
* * * * * *
31145530 TCTGCTCCACTGTAACCTCAGGGGGATAAGATCTGCAATTCTTCGG
1 TCTACTCCACTGTAACTTCAGAGAGATAAGACCTG--A-T-TTCGA
* *
31145576 TCTACTCCACTGTAACCTCAGAGAGATAAGACCTGA-TGCGA
1 TCTACTCCACTGTAACTTCAGAGAGATAAGACCTGATTTCGA
* * * **
31145617 TCTACTCTACTGTAACTTCAGAGAGATGAGATCCTTTATTTTAA
1 TCTACTCCACTGTAACTTCAGAGAGATAAGA-CC-TGATTTCGA
** * * * *
31145661 TCCGCTCCACTGTAACTTCAGGGAGATAGGA-TTATATCTTCGA
1 TCTACTCCACTGTAACTTCAGAGAGATAAGACCT-GAT-TTCGA
* * * * * *
31145704 TCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGCAATTCTTCGG
1 TCTACTCCACTGTAACTTCAGAGAGATAAGACCTG--A-T-TTCGA
** * *
31145750 TCTGTTCCACTGTAA-TCTCAGGGAGATAAGACCTGA-TGCGA
1 TCTACTCCACTGTAACT-TCAGAGAGATAAGACCTGATTTCGA
* * **
31145791 TCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAA
1 TCTACTCCACTGTAACTTCAGAGAGATAAGA-CC-TGATTTCGA
** * * * *
31145835 TCCGCTCCACTGTAACTTCAGGGAGATAGGA-TTATATCTTCGA
1 TCTACTCCACTGTAACTTCAGAGAGATAAGACCT-GAT-TTCGA
* * * * * * *
31145878 TCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAATTCTTTGG
1 TCTACTCCACTGTAACTTCAGAGAGATAAGACCTG--A-T-TTCGA
** * *
31145924 TCTGTTCCACTGTAA-TCTCAGGGAGATAAGACCTGATGT-GA
1 TCTACTCCACTGTAACT-TCAGAGAGATAAGACCTGATTTCGA
* *
31145965 TCTTCTCTACTGTAACTTCAGAGAGATAAGA
1 TCTACTCCACTGTAACTTCAGAGAGATAAGA
31145996 TCCTTTAATC
Statistics
Matches: 362, Mismatches: 77, Indels: 57
0.73 0.16 0.11
Matches are distributed among these distances:
41 87 0.24
42 16 0.04
43 65 0.18
44 87 0.24
45 2 0.01
46 105 0.29
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (42 bp):
TCTACTCCACTGTAACTTCAGAGAGATAAGACCTGATTTCGA
Found at i:31145705 original size:87 final size:87
Alignment explanation
Indices: 31145614--31146080 Score: 363
Period size: 87 Copynumber: 5.4 Consensus size: 87
31145604 AGACCTGATG
* *
31145614 CGATCTACTCTACTGTAACTTCAGAGAGATGAGATCCTTTATTTTAATCCGCTCCACTGTAA-CT
1 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTAATTTTAATCCGCTCCACTGTAATC-
31145678 TCAGGGAGATAGGATTATATCTT
65 TCAGGGAGATAGGATTATATCTT
* ** * * * ** * *
31145701 CGATCTGCTCCGCTGTAACCTCAGGGAGATAAGAT-CTGCAATTCTTCGGTCTGTTCCACTGTAA
1 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCT-TAATT-TT-AATCCGCTCCACTGTAA
* * * *
31145765 TCTCAGGGAGATAAGACCT-GA--TG
63 TCTCAGGGAGATAGGA-TTATATCTT
*
31145788 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAA-CT
1 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTAATTTTAATCCGCTCCACTGTAATC-
31145852 TCAGGGAGATAGGATTATATCTT
65 TCAGGGAGATAGGATTATATCTT
* ** * * * ** * *
31145875 CGATCTGCTCCGCTGTAACCTCAGGGAGATAAGAT-CTGAAATTCTTTGGTCTGTTCCACTGTAA
1 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCT-TAA-T-TTTAATCCGCTCCACTGTAA
* * * *
31145939 TCTCAGGGAGATAAGACCT-GAT-GT
63 TCTCAGGGAGATAGGA-TTATATCTT
* *
31145963 -GATCTTCTCTACTGTAACTTCAGAGAGATAAGATCC-----TTTAATCCGCTCCATTGTAATCT
1 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTAATTTTAATCCGCTCCACTGTAATCT
*
31146022 CAAGGAGATAGGATTACTATCTT
66 CAGGGAGATAGGATTA-TATCTT
* * ** *
31146045 TGATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGATC
1 CGATCTACTCTACTGTAACT-TCAGAGAGATAAGATC
31146081 TCTGGCTTCA
Statistics
Matches: 294, Mismatches: 65, Indels: 46
0.73 0.16 0.11
Matches are distributed among these distances:
79 1 0.00
80 29 0.10
81 2 0.01
82 2 0.01
83 29 0.10
84 2 0.01
85 27 0.09
86 6 0.02
87 127 0.43
88 7 0.02
89 58 0.20
90 4 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.32
Consensus pattern (87 bp):
CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTAATTTTAATCCGCTCCACTGTAATCT
CAGGGAGATAGGATTATATCTT
Found at i:31145744 original size:174 final size:174
Alignment explanation
Indices: 31145524--31146081 Score: 912
Period size: 174 Copynumber: 3.2 Consensus size: 174
31145514 AGACCTCTGG
* * * **
31145524 CTTCAATCTGCTCCACTGTAACCTCAGGGGGATAAGATCTGCAATTCTTCGGTCTACTCCACTGT
1 CTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTGTTCCACTGT
* * *
31145589 AACCTCAGAGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATGAGATCCTTT
66 AATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTT
31145654 ATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTATAT
131 ATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTATAT
31145698 CTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTGTTCCACTGT
1 CTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTGTTCCACTGT
31145763 AATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTT
66 AATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTT
31145828 ATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTATAT
131 ATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTATAT
* *
31145872 CTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCACTGT
1 CTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTGTTCCACTGT
* *
31145937 AATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCC---
66 AATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTT
* *
31145999 --TTTAATCCGCTCCATTGTAA-TCTCAAGGAGATAGGATTACTAT
131 ATTTTAATCCGCTCCACTGTAACT-TCAGGGAGATAGGATTA-TAT
* *
31146042 CTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT
1 CTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCT
31146082 CTGGCTTCAA
Statistics
Matches: 366, Mismatches: 16, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
168 1 0.00
169 35 0.10
170 41 0.11
174 289 0.79
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (174 bp):
CTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTGTTCCACTGT
AATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTT
ATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTATAT
Found at i:31146145 original size:86 final size:87
Alignment explanation
Indices: 31146041--31146439 Score: 382
Period size: 88 Copynumber: 4.6 Consensus size: 87
31146031 AGGATTACTA
* * * ** * * * *
31146041 TCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATC-TCTGGCTTCAATCTGCTCCAAT-G
1 TCTTTGATCTGCTTCGCTGTAATGT-AGGAAGGCAAGATCTTCTGTCTTCAACCAGCT-CAATCA
**
31146104 CAACCGATGGAGGCAAGGCTT-TG
64 CAACCGAAAGAGGCAAGGCTTGTG
* * * * * *
31146127 TCTTTGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTACT-TCTTTAACTAGCTCCA-CTG
1 TCTTTGATCTGCTTCGCTG-TAATGTAGGAAGGCAAGATCTTCTGTCTTCAACCAGCTCAATC-A
* ** *
31146190 CAATCGATGGATGCAAGGCTT-TG
64 CAACCGAAAGAGGCAAGGCTTGTG
* *
31146213 T-TTTCGATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCA
1 TCTTT-GATCTGCTTCGCTG-TAATGTAGGAAGGCAAGATCTTCTGTCTTCAACCAGCTCAATCA
*
31146277 CAACCGAAAGAGGCAAGGTTTGTG
64 CAACCGAAAGAGGCAAGGCTTGTG
* * *
31146301 TCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCAC
1 TCTTTGATCTGCTTCGCTGT-AATGTAGGAAGGCAAGATCTTCTGTCTTCAACCAGCTCAATCAC
*
31146366 AACCGAAAGAGGCAAGGTTTGTG
65 AACCGAAAGAGGCAAGGCTTGTG
* * *
31146389 TCTTCGATCTGCTTCGCTGTCAATGCAGAAAGGCAAGATCCTT-TGTCTTCA
1 TCTTTGATCTGCTTCGCTGT-AATGTAGGAAGGCAAGAT-CTTCTGTCTTCA
31146440 TTGATCTGTC
Statistics
Matches: 272, Mismatches: 30, Indels: 20
0.84 0.09 0.06
Matches are distributed among these distances:
85 5 0.02
86 96 0.35
87 36 0.13
88 130 0.48
89 5 0.02
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (87 bp):
TCTTTGATCTGCTTCGCTGTAATGTAGGAAGGCAAGATCTTCTGTCTTCAACCAGCTCAATCACA
ACCGAAAGAGGCAAGGCTTGTG
Found at i:31146163 original size:43 final size:43
Alignment explanation
Indices: 31146114--31146249 Score: 104
Period size: 43 Copynumber: 3.2 Consensus size: 43
31146104 CAACCGATGG
31146114 AGGCAAGGCTTTGTCTTTGATCTGCTTCGCTGTTAATGCAGGA
1 AGGCAAGGCTTTGTCTTTGATCTGCTTCGCTGTTAATGCAGGA
* * * * * *
31146157 AGGCAAGATCTACT-TCTTT-AACTAGCTCCACTG-CAAT-CGATGG-
1 AGGCAAG-GCT-TTGTCTTTGATCT-GCTTCGCTGTTAATGC-A-GGA
* *
31146200 ATGCAAGGCTTTGT-TTTCGATCTGCTTCGCTGTTAATGTAGGA
1 AGGCAAGGCTTTGTCTTT-GATCTGCTTCGCTGTTAATGCAGGA
31146243 AGGCAAG
1 AGGCAAG
31146250 ATCTTTTGTC
Statistics
Matches: 67, Mismatches: 15, Indels: 22
0.64 0.14 0.21
Matches are distributed among these distances:
41 4 0.06
42 13 0.19
43 33 0.49
44 16 0.24
45 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (43 bp):
AGGCAAGGCTTTGTCTTTGATCTGCTTCGCTGTTAATGCAGGA
Found at i:31146291 original size:44 final size:44
Alignment explanation
Indices: 31146243--31146381 Score: 138
Period size: 44 Copynumber: 3.2 Consensus size: 44
31146233 TAATGTAGGA
31146243 AGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCGAAAG
1 AGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCGAAAG
* * * * * ** ** * * *
31146287 AGGCAAGGT-TTGTGTCTTCGATCTGCTTCGCTGTCAA-TGTAGG
1 AGGCAAGATCTTTTGTCTTCAACCAGC-TCTATCACAACCGAAAG
31146330 AAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCGAAAG
1 -AGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCGAAAG
31146375 AGGCAAG
1 AGGCAAG
31146382 GTTTGTGTCT
Statistics
Matches: 67, Mismatches: 24, Indels: 8
0.68 0.24 0.08
Matches are distributed among these distances:
43 16 0.24
44 35 0.52
45 16 0.24
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.27
Consensus pattern (44 bp):
AGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCGAAAG
Found at i:31146326 original size:88 final size:88
Alignment explanation
Indices: 31146104--31146439 Score: 439
Period size: 88 Copynumber: 3.9 Consensus size: 88
31146094 TGCTCCAATG
** * * *
31146104 CAACCGATGGAGGCAAGGCTT-TGTCTTTGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
** * * * *
31146168 ACT-TCTTTAACTAGCTCCA-CTG
66 TTTGTCTTCAACCAGCTCTATC-A
* ** * * *
31146190 CAATCGATGGATGCAAGGCTTTGT-T-TTCGATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATC
1 CAACCGAAAGAGGCAAGG-TTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATC
31146253 TTTTGTCTTCAACCAGCTCTATCA
65 TTTTGTCTTCAACCAGCTCTATCA
*
31146277 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
31146342 TTTGTCTTCAACCAGCTCTATCA
66 TTTGTCTTCAACCAGCTCTATCA
* *
31146365 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAGGCAAGATCC
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
31146430 TTTGTCTTCA
66 TTTGTCTTCA
31146440 TTGATCTGTC
Statistics
Matches: 225, Mismatches: 19, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
86 59 0.26
87 31 0.14
88 135 0.60
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (88 bp):
CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
TTTGTCTTCAACCAGCTCTATCA
Found at i:31146423 original size:44 final size:44
Alignment explanation
Indices: 31146287--31146425 Score: 124
Period size: 44 Copynumber: 3.2 Consensus size: 44
31146277 CAACCGAAAG
* *
31146287 AGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGA
1 AGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAA
* * * * * * * *
31146331 AGGCAAGATCTTTTGTCTTCAACCAGC-T--CTATCACA-ACCGAAA
1 AGGCAAGGT-TTGTGTCTTCGATCTGCTTCGCTGTCA-ATGCAG-AA
31146374 GAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAA
1 -AGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAA
31146419 AGGCAAG
1 AGGCAAG
31146426 ATCCTTTGTC
Statistics
Matches: 69, Mismatches: 18, Indels: 16
0.67 0.17 0.16
Matches are distributed among these distances:
42 6 0.09
43 15 0.22
44 25 0.36
45 16 0.23
46 7 0.10
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (44 bp):
AGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAA
Found at i:31146436 original size:176 final size:173
Alignment explanation
Indices: 31146104--31146439 Score: 433
Period size: 174 Copynumber: 1.9 Consensus size: 173
31146094 TGCTCCAATG
** * *
31146104 CAACCGATGGAGGCAAGGCTTTGTCTTTGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTA
1 CAACCGAAAGAGGCAAGGCTTTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTA
* * * * ** * *
31146169 CTTCTTTAACTAGCTCCACTGCAATCGATGGATGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTT
66 CTTCTTCAACCAGCTCCACTACAACCGAAAGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTC
* * *
31146234 AATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCA
131 AATGCAGAAAGGCAAGATCCTTTGTCTTCAACCAGCTCTATCA
* *
31146277 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGCTT-TGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
** *
31146342 TTTGTCTTCAACCAGCTCTA-TCACAACCGAAAGAGGCAAGG-TTTGTGTCTTCGATCTGCTTCG
65 ACT-TCTTCAACCAGCTCCACT-ACAACCGAAAGAGGCAAGGCTTTGT-T-TTCGATCTGCTTCG
31146405 CTGTCAATGCAGAAAGGCAAGATCCTTTGTCTTCA
126 CTGTCAATGCAGAAAGGCAAGATCCTTTGTCTTCA
31146440 TTGATCTGTC
Statistics
Matches: 138, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
173 18 0.13
174 47 0.34
175 28 0.20
176 45 0.33
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (173 bp):
CAACCGAAAGAGGCAAGGCTTTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTA
CTTCTTCAACCAGCTCCACTACAACCGAAAGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTC
AATGCAGAAAGGCAAGATCCTTTGTCTTCAACCAGCTCTATCA
Found at i:31154952 original size:25 final size:25
Alignment explanation
Indices: 31154924--31154971 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
31154914 CCTCATACAT
31154924 ATTTCAATACAAATACGATGCTGTA
1 ATTTCAATACAAATACGATGCTGTA
31154949 ATTTCAATACAAATACGATGCTG
1 ATTTCAATACAAATACGATGCTG
31154972 ACAGTTTCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (25 bp):
ATTTCAATACAAATACGATGCTGTA
Found at i:31160348 original size:15 final size:16
Alignment explanation
Indices: 31160322--31160354 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
31160312 GTTAAAAGTT
31160322 TTTTGAATTTGGGTTA
1 TTTTGAATTTGGGTTA
*
31160338 TTTTG-ATTTGGTTTA
1 TTTTGAATTTGGGTTA
31160353 TT
1 TT
31160355 ATAAGAGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.15, C:0.00, G:0.21, T:0.64
Consensus pattern (16 bp):
TTTTGAATTTGGGTTA
Found at i:31161257 original size:17 final size:17
Alignment explanation
Indices: 31161235--31161268 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
31161225 ATCCACTAAT
*
31161235 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
31161252 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
31161269 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:31165896 original size:17 final size:17
Alignment explanation
Indices: 31165874--31165907 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
31165864 ATCCACTAAT
*
31165874 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
31165891 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
31165908 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:31168529 original size:3 final size:3
Alignment explanation
Indices: 31168521--31168549 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
31168511 CTTAAGATAC
31168521 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
31168550 AGAGTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:31169847 original size:110 final size:106
Alignment explanation
Indices: 31169657--31169855 Score: 308
Period size: 110 Copynumber: 1.8 Consensus size: 106
31169647 ATATTTGGCT
*
31169657 ATTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGGGTACGTTCCTCAAATTTCCAAACGCAA
1 ATTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCAAATTTCCAAACGCAA
31169722 AACATTGCCTTATTTTGAAAATTTTTAAAATGATCTTAAGCC
66 AACATTGCCTTATTTTG-AAATTTTTAAAATGATCTTAAGCC
* * * * *
31169764 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACG
1 ATTTGGTTAAACGAG--AAATCGAAACCCAGCACCTTAGGGCACG-TTCCTCAAATTTCCAAACG
31169829 CAAAACATTGCCTTATTTTGAAATTTT
63 CAAAACATTGCCTTATTTTGAAATTTT
31169856 AGAAAAATTC
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
107 14 0.17
109 32 0.39
110 37 0.45
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.31
Consensus pattern (106 bp):
ATTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCAAATTTCCAAACGCAA
AACATTGCCTTATTTTGAAATTTTTAAAATGATCTTAAGCC
Found at i:31170776 original size:21 final size:21
Alignment explanation
Indices: 31170750--31170791 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
31170740 TTAAAATGTG
31170750 TATATAAATACATACATATAAAT
1 TATA-AAATACATA-ATATAAAT
*
31170773 TATAAAATAGATAATATAA
1 TATAAAATACATAATATAA
31170792 TCATGTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 8 0.44
23 4 0.22
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (21 bp):
TATAAAATACATAATATAAAT
Found at i:31176366 original size:17 final size:18
Alignment explanation
Indices: 31176339--31176598 Score: 144
Period size: 18 Copynumber: 13.9 Consensus size: 18
31176329 ACAATAATAA
31176339 TTTTTGAAAACACGAAGA-
1 TTTTTGAAAACACGAA-AT
31176357 TTTTTG-AAACACGAAAAT
1 TTTTTGAAAACACG-AAAT
31176375 TTTTTGAAAACACGGAAAT
1 TTTTTGAAAACAC-GAAAT
*
31176394 TTTTTGAAAACAAGGAAA-
1 TTTTTGAAAAC-ACGAAAT
* * *
31176412 TTTTCG-ATACATGAGAAT
1 TTTTTGAAAACACGA-AAT
*
31176430 TTTTTG---ACACGAAAA
1 TTTTTGAAAACACGAAAT
*
31176445 ATTTTGAAAACACGAAA-
1 TTTTTGAAAACACGAAAT
* * * *
31176462 ATTTCGAAAACATGAATTTT
1 TTTTTGAAAACACGAA--AT
* *
31176482 TTTTTTAAAACATGAAATT
1 TTTTTGAAAACACGAAA-T
*
31176501 TTTTTAACAAAACACGAGAAT
1 TTTTT--GAAAACACGA-AAT
31176522 TTTTTGAAAACACGAAAACAT
1 TTTTTGAAAACACG--AA-AT
* *
31176543 GAAAATTTTGAAAACACGAAAA
1 ----TTTTTGAAAACACGAAAT
31176565 TTTTTG-AAACACGAGAAT
1 TTTTTGAAAACACGA-AAT
31176583 TTTTT-AAAACACGAAA
1 TTTTTGAAAACACGAAA
31176599 ACACGAATTT
Statistics
Matches: 194, Mismatches: 22, Indels: 53
0.72 0.08 0.20
Matches are distributed among these distances:
15 7 0.04
16 8 0.04
17 37 0.19
18 52 0.27
19 39 0.20
20 16 0.08
21 17 0.09
22 3 0.02
23 2 0.01
25 13 0.07
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAT
Found at i:31176512 original size:21 final size:21
Alignment explanation
Indices: 31176468--31176526 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
31176458 GAAAATTTCG
***
31176468 AAAACATG-AATTTTTTTTTT
1 AAAACATGAAATTTTTTTAAC
31176488 AAAACATGAAATTTTTTTAAC
1 AAAACATGAAATTTTTTTAAC
*
31176509 AAAACACGAGAATTTTTT
1 AAAACATGA-AATTTTTT
31176527 GAAAACACGA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.24
21 17 0.52
22 8 0.24
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (21 bp):
AAAACATGAAATTTTTTTAAC
Found at i:31176637 original size:18 final size:18
Alignment explanation
Indices: 31176610--31176676 Score: 57
Period size: 18 Copynumber: 3.8 Consensus size: 18
31176600 CACGAATTTT
*
31176610 TTTTTAAAAACACGGGAA
1 TTTTTGAAAACACGGGAA
*
31176628 TTTTTGAAAACAC-GAAA
1 TTTTTGAAAACACGGGAA
** ** *
31176645 TTTTTTTATTCACGAGAA
1 TTTTTGAAAACACGGGAA
31176663 TTTTTG-AAACACGG
1 TTTTTGAAAACACGG
31176677 ATTTTTTTTA
Statistics
Matches: 36, Mismatches: 12, Indels: 3
0.71 0.24 0.06
Matches are distributed among these distances:
17 17 0.47
18 19 0.53
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (18 bp):
TTTTTGAAAACACGGGAA
Found at i:31176664 original size:35 final size:34
Alignment explanation
Indices: 31176620--31176686 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
31176610 TTTTTAAAAA
*
31176620 CACGGGAATTTTTGAAAACACGAAATTTTTTTATT
1 CACGAGAATTTTTG-AAACACGAAATTTTTTTATT
* *
31176655 CACGAGAATTTTTGAAACACGGATTTTTTTTA
1 CACGAGAATTTTTGAAACACGAAATTTTTTTA
31176687 AAGAAAGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (34 bp):
CACGAGAATTTTTGAAACACGAAATTTTTTTATT
Found at i:31176675 original size:17 final size:17
Alignment explanation
Indices: 31176617--31176675 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
31176607 TTTTTTTTAA
*
31176617 AAACACGGGAATTTTTG
1 AAACACGAGAATTTTTG
*
31176634 AAAACACGA-AATTTTTTT
1 -AAACACGAGAA-TTTTTG
**
31176652 ATTCACGAGAATTTTTG
1 AAACACGAGAATTTTTG
31176669 AAACACG
1 AAACACG
31176676 GATTTTTTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
17 18 0.56
18 14 0.44
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (17 bp):
AAACACGAGAATTTTTG
Found at i:31176761 original size:17 final size:18
Alignment explanation
Indices: 31176739--31176786 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 18
31176729 TATTATTATT
31176739 ATTTTGAAACACGTG-AA
1 ATTTTGAAACACGTGAAA
31176756 ATTTTGAAGACA--TGAAA
1 ATTTTGAA-ACACGTGAAA
31176773 ATTTTTGAAACACG
1 A-TTTTGAAACACG
31176787 ATTTTTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
16 2 0.08
17 14 0.54
18 10 0.38
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (18 bp):
ATTTTGAAACACGTGAAA
Found at i:31177398 original size:24 final size:24
Alignment explanation
Indices: 31177370--31177424 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
31177360 CACAAAGTGG
31177370 GCTGCTTCTTTCTTCTTCTTTTTT
1 GCTGCTTCTTTCTTCTTCTTTTTT
*
31177394 TCTGCTTCTTTCTTCTTCTTTTTT
1 GCTGCTTCTTTCTTCTTCTTTTTT
31177418 GCTGCTT
1 GCTGCTT
31177425 TTTTTTTGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.00, C:0.25, G:0.09, T:0.65
Consensus pattern (24 bp):
GCTGCTTCTTTCTTCTTCTTTTTT
Found at i:31177434 original size:11 final size:11
Alignment explanation
Indices: 31177371--31177436 Score: 60
Period size: 11 Copynumber: 5.6 Consensus size: 11
31177361 ACAAAGTGGG
31177371 CTGCTTCTTTCTT
1 CTGCTT-TTT-TT
*
31177384 CTTCTTTTTTT
1 CTGCTTTTTTT
31177395 CTGCTTCTTTCTT
1 CTGCTT-TTT-TT
* *
31177408 CTTCTTTTTTG
1 CTGCTTTTTTT
31177419 CTGCTTTTTTT
1 CTGCTTTTTTT
*
31177430 TTGCTTT
1 CTGCTTT
31177437 GGTTTTTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
11 23 0.52
12 9 0.20
13 12 0.27
ACGTcount: A:0.00, C:0.23, G:0.08, T:0.70
Consensus pattern (11 bp):
CTGCTTTTTTT
Found at i:31178027 original size:30 final size:29
Alignment explanation
Indices: 31177987--31178088 Score: 132
Period size: 30 Copynumber: 3.4 Consensus size: 29
31177977 ATTTAGGATT
31177987 AAAATGAAATTTAATAAAAGTTTAGGGGTC
1 AAAATGAAATTTAA-AAAAGTTTAGGGGTC
* * *
31178017 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAA-AAAGTTTAGGGGTC
*
31178047 AAAATGAAATTTAGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTA-AAAAAGTTTAGGGGTC
*
31178077 AAAATGCAATTT
1 AAAATGAAATTT
31178089 TTATTTTTTT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
29 1 0.02
30 60 0.97
31 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.22, T:0.29
Consensus pattern (29 bp):
AAAATGAAATTTAAAAAAGTTTAGGGGTC
Found at i:31178116 original size:8 final size:8
Alignment explanation
Indices: 31178105--31178131 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
31178095 TTTTTAAAAA
31178105 AAATTTTG
1 AAATTTTG
31178113 AAATTTTG
1 AAATTTTG
31178121 AAATTTTG
1 AAATTTTG
31178129 AAA
1 AAA
31178132 ATTAAACACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (8 bp):
AAATTTTG
Found at i:31178521 original size:196 final size:196
Alignment explanation
Indices: 31178174--31178579 Score: 627
Period size: 196 Copynumber: 2.1 Consensus size: 196
31178164 AGTGCTTACA
* * * * *
31178174 ATAGAAATTTTGGTATGGCTTTAAAAATTTTGGTTCAAGCTATTGGTGAGACCACGAGTTAGAAA
1 ATAGAAATTTTGGTATGACTTTAAAAATTTGGGTTCAAGCTATTGGTGAGACCACAAGCTACAAA
* * * *
31178239 AGAGAATTTTAATATACCAAATTATCTAATGGTTTCATTAAAAGTATTAGTATAGCGTTAGAAAT
66 AAAGAATTTTAATATACCAAAATATCTAATGGTTTCATTAAAAATATTAGTATAGCATTAGAAAT
* * * *
31178304 TTTGATCGAAGCTCTTACGGGTGAGAAAGGGAAAATTTTGATA-TTAAATTAGGAATTTTGATAT
131 TTTGATCGAAACTCGTACGGGTGAAAAAGGGAAAATTTTGATATTTAAA-TAGGAATTTTAATAT
31178368 CC
195 CC
*
31178370 ATAGAAATTTTGGTATGACTTTAAAAATTTGGGTTCAAGCTATTGGTGAGACTACAAGCTACAAA
1 ATAGAAATTTTGGTATGACTTTAAAAATTTGGGTTCAAGCTATTGGTGAGACCACAAGCTACAAA
31178435 AAAGAATTTTAATATACCAAAATATCTAATGGTTTCATTAAAAATATTAGTATAGCATTAGAAAT
66 AAAGAATTTTAATATACCAAAATATCTAATGGTTTCATTAAAAATATTAGTATAGCATTAGAAAT
*
31178500 TTTGATAC-AAACTCGTACGGGTGAAAAAGGGGAAATTTTGATATTTAAATAGGAATTTTAATAT
131 TTTGAT-CGAAACTCGTACGGGTGAAAAAGGGAAAATTTTGATATTTAAATAGGAATTTTAATAT
31178564 CC
195 CC
* *
31178566 ATAAAAAATTTGGT
1 ATAGAAATTTTGGT
31178580 TCAAGCTATA
Statistics
Matches: 191, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
196 185 0.97
197 6 0.03
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (196 bp):
ATAGAAATTTTGGTATGACTTTAAAAATTTGGGTTCAAGCTATTGGTGAGACCACAAGCTACAAA
AAAGAATTTTAATATACCAAAATATCTAATGGTTTCATTAAAAATATTAGTATAGCATTAGAAAT
TTTGATCGAAACTCGTACGGGTGAAAAAGGGAAAATTTTGATATTTAAATAGGAATTTTAATATC
C
Found at i:31180521 original size:19 final size:19
Alignment explanation
Indices: 31180497--31180550 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
31180487 ATTTATTATT
31180497 TGTTTTATAATATTTTAAA
1 TGTTTTATAATATTTTAAA
***
31180516 TGTTTTATAATATACCAAA
1 TGTTTTATAATATTTTAAA
31180535 TGATTTTA-AATATTTT
1 TG-TTTTATAATATTTT
31180551 TTTTAAAACG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
19 23 0.82
20 5 0.18
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.54
Consensus pattern (19 bp):
TGTTTTATAATATTTTAAA
Found at i:31180615 original size:13 final size:13
Alignment explanation
Indices: 31180597--31180621 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31180587 AATAATAATT
31180597 AATTAAAAAAACA
1 AATTAAAAAAACA
31180610 AATTAAAAAAAC
1 AATTAAAAAAAC
31180622 GTTTGAATAA
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:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (13 bp):
AATTAAAAAAACA
Found at i:31180663 original size:10 final size:10
Alignment explanation
Indices: 31180632--31180664 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
31180622 GTTTGAATAA
31180632 AAAATATTAT
1 AAAATATTAT
*
31180642 AAAACATT-T
1 AAAATATTAT
31180651 AAAATATTAT
1 AAAATATTAT
31180661 AAAA
1 AAAA
31180665 ACTAATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAATATTAT
Found at i:31180674 original size:19 final size:18
Alignment explanation
Indices: 31180631--31180691 Score: 68
Period size: 19 Copynumber: 3.3 Consensus size: 18
31180621 CGTTTGAATA
*
31180631 AAAAATATTATAAAACATT
1 AAAAATATTATAAAA-ACT
*
31180650 TAAAATATTATAAAAACT
1 AAAAATATTATAAAAACT
* *
31180668 AATAAATATTTTAAAAAAT
1 AA-AAATATTATAAAAACT
31180687 AAAAA
1 AAAAA
31180692 AATGTTTGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
18 6 0.17
19 30 0.83
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAAATATTATAAAAACT
Found at i:31180805 original size:94 final size:87
Alignment explanation
Indices: 31180646--31180815 Score: 250
Period size: 94 Copynumber: 1.9 Consensus size: 87
31180636 TATTATAAAA
* *
31180646 CATTTAAAATATTATAAAAACTAATAAATATTTTAAAAAATAAAAAAATGTTTGAATAAACAAAT
1 CATTTAAAATATTATAAAAAATAATAAATATTTTAAAAAATAAAAAAATGTTTGAATAAAAAAAT
31180711 ATTATAAAACATTTAAAATATG
66 ATTATAAAACATTTAAAATATG
*
31180733 CATTTACAATATTATAAAACAAATAATAAATAATTTTAAAAAAAATTCAAAAAAATGTTTGAATA
1 CATTTAAAATATTAT-AAA-AAATAATAAAT-ATTTT--AAAAAA-T-AAAAAAATGTTTGAATA
31180798 AAAAAATATTATAAAACA
59 AAAAAATATTATAAAACA
31180816 AATAATAAAT
Statistics
Matches: 73, Mismatches: 3, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
87 14 0.19
88 3 0.04
89 10 0.14
90 5 0.07
92 6 0.08
93 1 0.01
94 34 0.47
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.32
Consensus pattern (87 bp):
CATTTAAAATATTATAAAAAATAATAAATATTTTAAAAAATAAAAAAATGTTTGAATAAAAAAAT
ATTATAAAACATTTAAAATATG
Found at i:31190234 original size:32 final size:31
Alignment explanation
Indices: 31190188--31190247 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
31190178 CTCTCCATTG
31190188 ATTCAATAATATAAT-TAAAATATTTTAATTT
1 ATTCAATAATATAATAT-AAATATTTTAATTT
* *
31190219 ATTCAAATATTATAATATAAATTTTTTAA
1 ATTC-AATAATATAATATAAATATTTTAA
31190248 ATAATAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 4 0.16
32 20 0.80
33 1 0.04
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (31 bp):
ATTCAATAATATAATATAAATATTTTAATTT
Found at i:31191540 original size:15 final size:16
Alignment explanation
Indices: 31191507--31191540 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
31191497 AAAGCTATGT
*
31191507 TAAAAAACAAAAGTGA
1 TAAAAAACAAAAGTAA
31191523 TAAAAAACAAAA-TAA
1 TAAAAAACAAAAGTAA
31191538 TAA
1 TAA
31191541 TAATAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.74, C:0.06, G:0.06, T:0.15
Consensus pattern (16 bp):
TAAAAAACAAAAGTAA
Found at i:31191695 original size:18 final size:18
Alignment explanation
Indices: 31191681--31191714 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
31191671 TACTTTTATT
31191681 TAATTTT-T-AATTTTTA
1 TAATTTTATAAATTTTTA
31191697 TAATTTTATAAATTTTTA
1 TAATTTTATAAATTTTTA
31191715 AAAATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 1 0.06
18 8 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TAATTTTATAAATTTTTA
Found at i:31199715 original size:27 final size:28
Alignment explanation
Indices: 31199685--31199743 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
31199675 TGAACTTTTT
* *
31199685 ATAA-TTTTT-TTATTTTTTAAATATGTC
1 ATAACTTTTTATTATTTGTT-AATATGAC
31199712 ATAACTTTTTAATTATTTGTTAATATGAC
1 ATAACTTTTT-ATTATTTGTTAATATGAC
31199741 ATA
1 ATA
31199744 TAAGATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 4 0.15
28 5 0.19
29 10 0.37
30 8 0.30
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (28 bp):
ATAACTTTTTATTATTTGTTAATATGAC
Found at i:31203288 original size:26 final size:28
Alignment explanation
Indices: 31203259--31203310 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
31203249 TTATTAAAAC
*
31203259 TCTTCTAAAAG-AAACTC-AAGAGAAAT
1 TCTTCAAAAAGAAAACTCAAAGAGAAAT
*
31203285 TCTTGAAAAAGAAAACTCAAAGAGAA
1 TCTTCAAAAAGAAAACTCAAAGAGAA
31203311 TTTATTAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 9 0.41
27 6 0.27
28 7 0.32
ACGTcount: A:0.54, C:0.13, G:0.13, T:0.19
Consensus pattern (28 bp):
TCTTCAAAAAGAAAACTCAAAGAGAAAT
Found at i:31203697 original size:17 final size:19
Alignment explanation
Indices: 31203664--31203698 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
31203654 ATTGTTTGGA
31203664 TATTGTATAACTTTTGTTT
1 TATTGTATAACTTTTGTTT
31203683 TATTGT-TAA-TTTTGTT
1 TATTGTATAACTTTTGTT
31203699 ACTATTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.20, C:0.03, G:0.11, T:0.66
Consensus pattern (19 bp):
TATTGTATAACTTTTGTTT
Found at i:31203876 original size:10 final size:11
Alignment explanation
Indices: 31203844--31203876 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
31203834 TATATTTTTT
31203844 AAAATTATATA
1 AAAATTATATA
*
31203855 AAAATAATATA
1 AAAATTATATA
31203866 AAAATTA-ATA
1 AAAATTATATA
31203876 A
1 A
31203877 GGGCGGGCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 4 0.20
11 16 0.80
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AAAATTATATA
Found at i:31204169 original size:8 final size:8
Alignment explanation
Indices: 31204158--31204184 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
31204148 TAAAAATTCA
31204158 AAATAATT
1 AAATAATT
31204166 AAATAATT
1 AAATAATT
31204174 AAATAATT
1 AAATAATT
31204182 AAA
1 AAA
31204185 GCTGATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AAATAATT
Found at i:31209224 original size:57 final size:57
Alignment explanation
Indices: 31209154--31209268 Score: 185
Period size: 57 Copynumber: 2.0 Consensus size: 57
31209144 CTTAGCCTCT
* * *
31209154 CTAATTTTTCTTGCTATAGCTTATGCAACCTGAGAATGAAATTTGACTCATTTATAG
1 CTAATTTTTCTTGCCATAACTTATACAACCTGAGAATGAAATTTGACTCATTTATAG
* *
31209211 CTAATTTTTCTTGCCGTAACTTATACAACCTGATAATGAAATTTGACTCATTTATAG
1 CTAATTTTTCTTGCCATAACTTATACAACCTGAGAATGAAATTTGACTCATTTATAG
31209268 C
1 C
31209269 CTAAGGCCAA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40
Consensus pattern (57 bp):
CTAATTTTTCTTGCCATAACTTATACAACCTGAGAATGAAATTTGACTCATTTATAG
Found at i:31209628 original size:125 final size:125
Alignment explanation
Indices: 31209287--31209803 Score: 628
Period size: 125 Copynumber: 4.1 Consensus size: 125
31209277 AAACAAAAAT
* * *
31209287 TACTGTAAAAAAAGAGCGTTC-ACGTGAGAGCTTTTTTC-ATCAATTTTGCTAACAGTGCATCCT
1 TACTGTAGAAAAAGAGCG-TCAACGTGGGAGCTTTTTTCAAT-AATTTTGCTGACAGTGCATCCT
* * *
31209350 GCTTGAAGCATTTTTGACACCATTTATTCAGAACTGTCTTCTCAAAATTATTTTTTCAGGAAC
64 GCTTAAAGCATTTTTGACACCATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTT-AGGAAC
* * * * *
31209413 TACTATAGAAAAAGAGCGTCAATGTGGAAGCTTTTTTTTCAGTATTTTTGCTGACAGTGCATCCT
1 TACTGTAGAAAAAGAGCGTCAACGTGGGAGC--TTTTTTCAATAATTTTGCTGACAGTGCATCCT
* ** *
31209478 GCTTAAAGCATTTTTTACACCATTTGTTCAGAATTGCCTTCTCAAAATTATTTTTTAGGAAC
64 GCTTAAAGCATTTTTGACACCATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTAGGAAC
*
31209540 TACTGTAGAAAAAGAGCGTTC-ACGTGGGAGCTTTTTTCAATATTTTTGCTGACAGTGCATCCTG
1 TACTGTAGAAAAAGAGCG-TCAACGTGGGAGCTTTTTTCAATAATTTTGCTGACAGTGCATCCTG
* * * * * *
31209604 CTTGAAGCGTTTTTAACACTATTTGTTCAGAATCGTCTTCTCAAAATTATTTTTCAGGAAC
65 CTTAAAGCATTTTTGACACCATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTAGGAAC
* * * * *
31209665 TACTGTAGAAAAAGAGCGTCTACGTTGGAGCTTTTTTCAGTAATTTTGATGACAGTGCATTCTGC
1 TACTGTAGAAAAAGAGCGTCAACGTGGGAGCTTTTTTCAATAATTTTGCTGACAGTGCATCCTGC
* ** * * *
31209730 TTAAAGCGTTTTTGACATTATCTT-TTCAGAACCGTATTCTCAAAATTAATTTTTTTGAAAC
66 TTAAAGCATTTTTGACACCAT-TTGTTCAGAACCGTCTTCTCAAAATT-ATTTTTTAGGAAC
*
31209791 TATTGTAGAAAAA
1 TACTGTAGAAAAA
31209804 AACTAAAATC
Statistics
Matches: 345, Mismatches: 38, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
124 2 0.01
125 184 0.53
126 47 0.14
127 31 0.09
128 80 0.23
129 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (125 bp):
TACTGTAGAAAAAGAGCGTCAACGTGGGAGCTTTTTTCAATAATTTTGCTGACAGTGCATCCTGC
TTAAAGCATTTTTGACACCATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTAGGAAC
Found at i:31209953 original size:32 final size:32
Alignment explanation
Indices: 31209857--31209963 Score: 105
Period size: 33 Copynumber: 3.4 Consensus size: 32
31209847 ACCTACACAA
31209857 AATTATTTTTAAAAAAA-T-TAAACCCTAATTT
1 AATTA-TTTTAAAAAAACTCTAAACCCTAATTT
* *** *
31209888 AATTAATTTATTTTAAACCCTAAACCCTAATTT
1 AATTATTTTA-AAAAAACTCTAAACCCTAATTT
* *
31209921 AATTATTTTAAAAAAACTCTAAACCTTGATTT
1 AATTATTTTAAAAAAACTCTAAACCCTAATTT
31209953 -ATT-TTTTAAAA
1 AATTATTTTAAAA
31209964 CTCTTAAACC
Statistics
Matches: 61, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
30 12 0.20
31 11 0.18
32 16 0.26
33 22 0.36
ACGTcount: A:0.44, C:0.12, G:0.01, T:0.43
Consensus pattern (32 bp):
AATTATTTTAAAAAAACTCTAAACCCTAATTT
Found at i:31210031 original size:34 final size:34
Alignment explanation
Indices: 31209988--31210093 Score: 142
Period size: 33 Copynumber: 3.1 Consensus size: 34
31209978 ACCTTAACCC
**
31209988 TAAATTATTTTAACAAAACTTTAAACCCTAAACT
1 TAAATTATTTTAACAAAACCCTAAACCCTAAACT
* * *
31210022 TAAATTATTTTAACAAAACCCT-AATCCTAACCC
1 TAAATTATTTTAACAAAACCCTAAACCCTAAACT
*
31210055 TAAATTATTTTAATAAAACCCTAAACCCTAAACT
1 TAAATTATTTTAACAAAACCCTAAACCCTAAACT
31210089 CTAAA
1 -TAAA
31210094 CAAAAAACTC
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
33 29 0.48
34 28 0.46
35 4 0.07
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (34 bp):
TAAATTATTTTAACAAAACCCTAAACCCTAAACT
Found at i:31210059 original size:33 final size:33
Alignment explanation
Indices: 31209982--31210085 Score: 136
Period size: 34 Copynumber: 3.1 Consensus size: 33
31209972 CCATACACCT
**
31209982 TAACCCTAAATTATTTTAACAAAACTTTAAACCC
1 TAACCCTAAATTATTTTAACAAAACCCT-AACCC
* * *
31210016 TAAACTTAAATTATTTTAACAAAACCCTAATCC
1 TAACCCTAAATTATTTTAACAAAACCCTAACCC
*
31210049 TAACCCTAAATTATTTTAATAAAACCCTAAACCC
1 TAACCCTAAATTATTTTAACAAAACCCT-AACCC
31210083 TAA
1 TAA
31210086 ACTCTAAACA
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
33 29 0.48
34 31 0.52
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.32
Consensus pattern (33 bp):
TAACCCTAAATTATTTTAACAAAACCCTAACCC
Found at i:31216525 original size:33 final size:33
Alignment explanation
Indices: 31216475--31216549 Score: 98
Period size: 34 Copynumber: 2.2 Consensus size: 33
31216465 AAACTAATCA
* *
31216475 TCTCTCAAATTTCCTCTC-AATTTCTTCTAAATT
1 TCTCTC-AATTTCCTCTCAAATTCCTTCAAAATT
*
31216508 TCCTCTCAATTTGCTCTCAAATTCCTTCAAAATT
1 T-CTCTCAATTTCCTCTCAAATTCCTTCAAAATT
31216542 TCTCTCAA
1 TCTCTCAA
31216550 ATCCATATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 18 0.49
34 19 0.51
ACGTcount: A:0.25, C:0.29, G:0.01, T:0.44
Consensus pattern (33 bp):
TCTCTCAATTTCCTCTCAAATTCCTTCAAAATT
Found at i:31216532 original size:22 final size:22
Alignment explanation
Indices: 31216475--31216551 Score: 97
Period size: 22 Copynumber: 3.5 Consensus size: 22
31216465 AAACTAATCA
31216475 TCTCTCAAATTTCCTCTCAATT
1 TCTCTCAAATTTCCTCTCAATT
31216497 TCT-TCTAAATTTCCTCTCAATT
1 TCTCTC-AAATTTCCTCTCAATT
31216519 TGCTCTCAAA-TTCCT-TCAAAATT
1 T-CTCTCAAATTTCCTCTC--AATT
31216542 TCTCTCAAAT
1 TCTCTCAAAT
31216552 CCATATTTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 11
0.82 0.00 0.18
Matches are distributed among these distances:
21 4 0.08
22 33 0.67
23 10 0.20
24 2 0.04
ACGTcount: A:0.26, C:0.29, G:0.01, T:0.44
Consensus pattern (22 bp):
TCTCTCAAATTTCCTCTCAATT
Found at i:31216551 original size:11 final size:11
Alignment explanation
Indices: 31216475--31216551 Score: 72
Period size: 11 Copynumber: 6.9 Consensus size: 11
31216465 AAACTAATCA
31216475 TCTCTCAAATT
1 TCTCTCAAATT
31216486 TCCTCTC-AATT
1 T-CTCTCAAATT
31216497 TCT-TCTAAATT
1 TCTCTC-AAATT
31216508 TCCTCTC-AATT
1 T-CTCTCAAATT
31216519 TGCTCTCAAATT
1 T-CTCTCAAATT
*
31216531 CCT-TCAAAATT
1 TCTCTC-AAATT
31216542 TCTCTCAAAT
1 TCTCTCAAAT
31216552 CCATATTTAT
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
9 2 0.04
10 4 0.07
11 34 0.62
12 13 0.24
13 2 0.04
ACGTcount: A:0.26, C:0.29, G:0.01, T:0.44
Consensus pattern (11 bp):
TCTCTCAAATT
Found at i:31216575 original size:51 final size:51
Alignment explanation
Indices: 31216513--31216610 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 51
31216503 AAATTTCCTC
31216513 TCAATTTGCTCTCAAATTCCT-TCAAAATTTCTCTCAAATCCATATTTATTT
1 TCAATTTGCTCTCAAATTCCTCT-AAAATTTCTCTCAAATCCATATTTATTT
* * * *
31216564 TCAATTTGCTCTCAAGTTCCTCTTAAATTTCTCTTAAATCCCTATTT
1 TCAATTTGCTCTCAAATTCCTCTAAAATTTCTCTCAAATCCATATTT
31216611 TTAAATAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 41 0.98
52 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.03, T:0.46
Consensus pattern (51 bp):
TCAATTTGCTCTCAAATTCCTCTAAAATTTCTCTCAAATCCATATTTATTT
Found at i:31223138 original size:33 final size:33
Alignment explanation
Indices: 31223096--31223161 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
31223086 TTCTTGACTG
*
31223096 GTCAGCCGTGAGTTTGGACAAAGAGACAAAACC
1 GTCAGCCGTGAGTTTGGACAAAGAGAAAAAACC
31223129 GTCAGCCGTGAGTTTGGACAAAGAGAAAAAACC
1 GTCAGCCGTGAGTTTGGACAAAGAGAAAAAACC
31223162 TCTTGGCGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.38, C:0.20, G:0.27, T:0.15
Consensus pattern (33 bp):
GTCAGCCGTGAGTTTGGACAAAGAGAAAAAACC
Found at i:31227097 original size:9 final size:10
Alignment explanation
Indices: 31227055--31227140 Score: 70
Period size: 10 Copynumber: 8.8 Consensus size: 10
31227045 CATGTGGCAA
31227055 AAAAATT-TT
1 AAAAATTATT
*
31227064 AAAAACTATT
1 AAAAATTATT
*
31227074 AAAAATCA-T
1 AAAAATTATT
31227083 AAAAATTATT
1 AAAAATTATT
* *
31227093 AAAATTTAGT
1 AAAAATTATT
*
31227103 AAAAAAT-TT
1 AAAAATTATT
**
31227112 AAAAAAAATTT
1 AAAAATTA-TT
*
31227123 AAAATTTATT
1 AAAAATTATT
31227133 AAAAATTA
1 AAAAATTA
31227141 GAAAAAAAAA
Statistics
Matches: 59, Mismatches: 14, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
9 21 0.36
10 31 0.53
11 7 0.12
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (10 bp):
AAAAATTATT
Found at i:31227105 original size:29 final size:28
Alignment explanation
Indices: 31227055--31227138 Score: 80
Period size: 29 Copynumber: 2.9 Consensus size: 28
31227045 CATGTGGCAA
**
31227055 AAAAATT-TTAAAAACTATTAAAAATCAT
1 AAAAATTATTAAAATTTATTAAAAAT-AT
* *
31227083 AAAAATTATTAAAATTTAGTAAAAAATTT
1 AAAAATTATTAAAATTTA-TTAAAAATAT
**
31227112 AAAAAAAATTTAAAATTTATTAAAAAT
1 AAAAATTA-TTAAAATTTATTAAAAAT
31227139 TAGAAAAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
28 7 0.15
29 22 0.48
30 17 0.37
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (28 bp):
AAAAATTATTAAAATTTATTAAAAATAT
Found at i:31227117 original size:11 final size:11
Alignment explanation
Indices: 31227093--31227126 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
31227083 AAAAATTATT
*
31227093 AAAATTTAGTAA
1 AAAATTTA-AAA
31227105 AAAATTTAAAA
1 AAAATTTAAAA
31227116 AAAATTTAAAA
1 AAAATTTAAAA
31227127 TTTATTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 13 0.62
12 8 0.38
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (11 bp):
AAAATTTAAAA
Found at i:31227139 original size:29 final size:29
Alignment explanation
Indices: 31227052--31227149 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 29
31227042 TGACATGTGG
* **
31227052 CAAAAAAATTTTAAAAACTATTAAAAA-T
1 CAAAAAAAATTTAAAATTTATTAAAAATT
* * *
31227080 CATAAAAATTATTAAAATTTAGTAAAAAATT
1 CAAAAAAAAT-TTAAAATTTA-TTAAAAATT
*
31227111 TAAAAAAAATTTAAAATTTATTAAAAATT
1 CAAAAAAAATTTAAAATTTATTAAAAATT
*
31227140 AGAAAAAAAA
1 -CAAAAAAAA
31227150 ATGTAAAAAC
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
28 9 0.16
29 16 0.28
30 24 0.42
31 8 0.14
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (29 bp):
CAAAAAAAATTTAAAATTTATTAAAAATT
Found at i:31238352 original size:21 final size:22
Alignment explanation
Indices: 31238315--31238357 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
31238305 ATTGGTTTAT
*
31238315 AATTTATAATTATTTTTTGTTAA
1 AATTTATAA-TATTTTTAGTTAA
31238338 AATTTATAA-ATTTTTAGTTA
1 AATTTATAATATTTTTAGTTA
31238358 TTTATTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
23 9 0.47
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (22 bp):
AATTTATAATATTTTTAGTTAA
Found at i:31243491 original size:15 final size:16
Alignment explanation
Indices: 31243461--31243491 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
31243451 GGCATTATCA
31243461 TATTTGCCTGCAGCTT
1 TATTTGCCTGCAGCTT
31243477 TATTTGCCT-CAGCTT
1 TATTTGCCTGCAGCTT
31243492 CAACAAACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.13, C:0.26, G:0.16, T:0.45
Consensus pattern (16 bp):
TATTTGCCTGCAGCTT
Found at i:31245557 original size:2 final size:2
Alignment explanation
Indices: 31245552--31245584 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
31245542 ATATAATATA
31245552 TG TG TG 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 TG TG TG T
31245585 TGAATCACTA
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:31253119 original size:24 final size:23
Alignment explanation
Indices: 31253084--31253131 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
31253074 GTTACTTATA
31253084 AATATGTAAAAATTCAAAAAAATT
1 AATATGTAAAAA-TCAAAAAAATT
*
31253108 AATATTGT-AAAATGAAAAAAATT
1 AATA-TGTAAAAATCAAAAAAATT
31253131 A
1 A
31253132 TTTGGAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 11 0.50
24 8 0.36
25 3 0.14
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.29
Consensus pattern (23 bp):
AATATGTAAAAATCAAAAAAATT
Found at i:31253249 original size:20 final size:20
Alignment explanation
Indices: 31253226--31253271 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
31253216 CAAGTTTCTT
*
31253226 TAAAA-ATACAAAACAATCCC
1 TAAAATATA-AAAAAAATCCC
*
31253246 TAAAATTTAAAAAAAATCCC
1 TAAAATATAAAAAAAATCCC
31253266 TAAAAT
1 TAAAAT
31253272 TTGCCCAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.61, C:0.17, G:0.00, T:0.22
Consensus pattern (20 bp):
TAAAATATAAAAAAAATCCC
Found at i:31253272 original size:20 final size:20
Alignment explanation
Indices: 31253235--31253273 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
31253225 TTAAAAATAC
*
31253235 AAAACAATCCCTAAAATTTA
1 AAAAAAATCCCTAAAATTTA
31253255 AAAAAAATCCCTAAAATTT
1 AAAAAAATCCCTAAAATTT
31253274 GCCCAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.18, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAAAAATCCCTAAAATTTA
Found at i:31255985 original size:28 final size:30
Alignment explanation
Indices: 31255928--31255996 Score: 88
Period size: 28 Copynumber: 2.3 Consensus size: 30
31255918 TTTAAAAAAT
31255928 ATATAAAAACTATTTTTTAAAAATATTTAAA
1 ATATAAAAA-TATTTTTTAAAAATATTTAAA
* *
31255959 ATATAAAAATA-TTTTT-AATATTTTTAAA
1 ATATAAAAATATTTTTTAAAAATATTTAAA
*
31255987 ATTTAAAAAT
1 ATATAAAAAT
31255997 TAATTAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
28 19 0.54
29 5 0.14
30 2 0.06
31 9 0.26
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (30 bp):
ATATAAAAATATTTTTTAAAAATATTTAAA
Found at i:31256006 original size:28 final size:28
Alignment explanation
Indices: 31255944--31256008 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
31255934 AAACTATTTT
* * *
31255944 TTAAAAATATTTAAAATATAAAAATATT
1 TTAAATATTTTTAAAATATAAAAATATA
* *
31255972 TTTAATATTTTTAAAATTTAAAAAT-TAA
1 TTAAATATTTTTAAAATATAAAAATAT-A
31256000 TTAAATATT
1 TTAAATATT
31256009 GATGTGTTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
27 1 0.03
28 29 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
TTAAATATTTTTAAAATATAAAAATATA
Found at i:31258148 original size:16 final size:17
Alignment explanation
Indices: 31258127--31258161 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
31258117 TGATATAACA
31258127 AATAAAA-GTATTTTTG
1 AATAAAATGTATTTTTG
*
31258143 AATAAAATTTATTTTTG
1 AATAAAATGTATTTTTG
31258160 AA
1 AA
31258162 CAAAGAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (17 bp):
AATAAAATGTATTTTTG
Found at i:31259327 original size:16 final size:17
Alignment explanation
Indices: 31259304--31259344 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
31259294 GTTGCCTCAA
* *
31259304 GTGTTGGGCCGCTGTTG
1 GTGTTGGGCAGCTGCTG
31259321 G-GTTGGGCAGCTGCTG
1 GTGTTGGGCAGCTGCTG
31259337 GTGTTGGG
1 GTGTTGGG
31259345 TTGTTGCTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.02, C:0.15, G:0.51, T:0.32
Consensus pattern (17 bp):
GTGTTGGGCAGCTGCTG
Found at i:31259438 original size:23 final size:23
Alignment explanation
Indices: 31259387--31259465 Score: 106
Period size: 23 Copynumber: 3.3 Consensus size: 23
31259377 CGCTGCTGGA
*
31259387 GTCTGCTGGATTGGGCCTCTACTAG
1 GTCTGCTGGATTGGG--TCTGCTAG
*
31259412 GTCTGCTGGATTGGGTTTGCTAG
1 GTCTGCTGGATTGGGTCTGCTAG
31259435 GTCTGCTGGATTGGGTCTGCT-G
1 GTCTGCTGGATTGGGTCTGCTAG
31259457 AGTCTGCTG
1 -GTCTGCTG
31259466 TATTTGGTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
22 1 0.02
23 34 0.68
25 15 0.30
ACGTcount: A:0.09, C:0.19, G:0.37, T:0.35
Consensus pattern (23 bp):
GTCTGCTGGATTGGGTCTGCTAG
Found at i:31259477 original size:46 final size:47
Alignment explanation
Indices: 31259387--31259478 Score: 125
Period size: 46 Copynumber: 2.0 Consensus size: 47
31259377 CGCTGCTGGA
31259387 GTCTGCTGGATTGGGCCTCTACTAGGTCTGCTGGATTGGGTTTGCTAG
1 GTCTGCTGGATTGGG-CTCTACTAGGTCTGCTGGATTGGGTTTGCTAG
* * *
31259435 GTCTGCTGGATTGGG-TCTGCT-GAGTCTGCTGTATTTGGTTTGCT
1 GTCTGCTGGATTGGGCTCTACTAG-GTCTGCTGGATTGGGTTTGCT
31259479 GGATTGGGCC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
45 1 0.03
46 24 0.60
48 15 0.38
ACGTcount: A:0.09, C:0.17, G:0.35, T:0.39
Consensus pattern (47 bp):
GTCTGCTGGATTGGGCTCTACTAGGTCTGCTGGATTGGGTTTGCTAG
Found at i:31259478 original size:23 final size:24
Alignment explanation
Indices: 31259387--31259479 Score: 102
Period size: 23 Copynumber: 3.9 Consensus size: 24
31259377 CGCTGCTGGA
* *
31259387 GTCTGCTGGATTGGGCCTCTACT-AG
1 GTCTGCTGGATTGGG--TTTGCTGAG
31259412 GTCTGCTGGATTGGGTTTGCT-AG
1 GTCTGCTGGATTGGGTTTGCTGAG
*
31259435 GTCTGCTGGATTGGGTCTGCTGA-
1 GTCTGCTGGATTGGGTTTGCTGAG
* *
31259458 GTCTGCTGTATTTGGTTTGCTG
1 GTCTGCTGGATTGGGTTTGCTG
31259480 GATTGGGCCT
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
23 45 0.74
24 1 0.02
25 15 0.25
ACGTcount: A:0.09, C:0.17, G:0.35, T:0.39
Consensus pattern (24 bp):
GTCTGCTGGATTGGGTTTGCTGAG
Found at i:31259612 original size:14 final size:16
Alignment explanation
Indices: 31259582--31259617 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
31259572 GATCCGACTG
31259582 TTTTT-TTCTTTCTTC
1 TTTTTCTTCTTTCTTC
31259597 TTTTTCTTC-TTC-TC
1 TTTTTCTTCTTTCTTC
31259611 TTTTTCT
1 TTTTTCT
31259618 CTCTAACCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 9 0.45
15 8 0.40
16 3 0.15
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTCTTCTTTCTTC
Found at i:31260361 original size:31 final size:30
Alignment explanation
Indices: 31260326--31260415 Score: 110
Period size: 31 Copynumber: 3.0 Consensus size: 30
31260316 AGGATACAAC
31260326 ATAATTTTAGAAAAAGTGGGGGGCTAAAAAT
1 ATAATTTTAGAAAAAGTGGGGGGC-AAAAAT
* * * *
31260357 ATAATTTTAGAAAAAATAGGAGGCCAAAAT
1 ATAATTTTAGAAAAAGTGGGGGGCAAAAAT
* *
31260387 GTAATTTTA-AAAAAGTGGGGGGCCAAAAT
1 ATAATTTTAGAAAAAGTGGGGGGCAAAAAT
31260416 GTAAATAGTA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
29 17 0.33
30 13 0.25
31 21 0.41
ACGTcount: A:0.47, C:0.06, G:0.23, T:0.24
Consensus pattern (30 bp):
ATAATTTTAGAAAAAGTGGGGGGCAAAAAT
Found at i:31260410 original size:29 final size:30
Alignment explanation
Indices: 31260327--31260419 Score: 125
Period size: 29 Copynumber: 3.1 Consensus size: 30
31260317 GGATACAACA
* *
31260327 TAATTTTAGAAAAAGTGGGGGGCTAAAAATA
1 TAATTTTAGAAAAAGTGGGGGGC-CAAAATG
* * *
31260358 TAATTTTAGAAAAAATAGGAGGCCAAAATG
1 TAATTTTAGAAAAAGTGGGGGGCCAAAATG
31260388 TAATTTTA-AAAAAGTGGGGGGCCAAAATG
1 TAATTTTAGAAAAAGTGGGGGGCCAAAATG
31260417 TAA
1 TAA
31260420 ATAGTATTCT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
29 21 0.39
30 13 0.24
31 20 0.37
ACGTcount: A:0.46, C:0.05, G:0.24, T:0.25
Consensus pattern (30 bp):
TAATTTTAGAAAAAGTGGGGGGCCAAAATG
Found at i:31261133 original size:76 final size:76
Alignment explanation
Indices: 31261005--31261457 Score: 577
Period size: 76 Copynumber: 6.0 Consensus size: 76
31260995 TAAAAGACTA
* * * * * *
31261005 AAATTTAAAATACCTTGACGTGCGATCCGAAGCTCAACTCACCTATCGGATTATGAGTTGA-TCT
1 AAATTGAAAATACCTCGACGTGCAACCCGAGGCTCAACTCACCTATCGGATTATGAGTTGATTTT
31261069 TTGAAAAAATAG
66 TTG-AAAAATAG
* * * *
31261081 AAATTAAAAATACCTCGATGTGCGACCCGAGGCTCAACTCACCTATCAGATTATGAGTTGATTTT
1 AAATTGAAAATACCTCGACGTGCAACCCGAGGCTCAACTCACCTATCGGATTATGAGTTGATTTT
*
31261146 TTGAAAAACAG
66 TTGAAAAATAG
* * * *
31261157 AAATTGAAAATAGCTCGGCGTGCAACCCGAGGCTCAACTCACCTATCGGATTATGGGTTTATTTT
1 AAATTGAAAATACCTCGACGTGCAACCCGAGGCTCAACTCACCTATCGGATTATGAGTTGATTTT
31261222 TTGAAAAATAG
66 TTGAAAAATAG
* * * * * * *
31261233 AAGTTGAAAATATCTCGGCGTGCAACCTGAGGCTCAACTCACCTCTTGAATTATGAGTTGATTTT
1 AAATTGAAAATACCTCGACGTGCAACCCGAGGCTCAACTCACCTATCGGATTATGAGTTGA-TTT
31261298 TTTGAAAAATAG
65 TTTGAAAAATAG
* * * * *
31261310 AAGTTGAAAATACCTCGGCGTGCAACCCGAAGCTCAACTCACCTATTGGATTATGAGTTGA-TAT
1 AAATTGAAAATACCTCGACGTGCAACCCGAGGCTCAACTCACCTATCGGATTATGAGTTGATTTT
31261374 TTGAAAAATAG
66 TTGAAAAATAG
* * * * * *
31261385 AAATTGAAAATACCTCGATGTGCAACCCAAGGCTCAACTTATCTCTCAGATTATGAGTTGATTTT
1 AAATTGAAAATACCTCGACGTGCAACCCGAGGCTCAACTCACCTATCGGATTATGAGTTGATTTT
31261450 TTGAAAAA
66 TTGAAAAA
31261458 CGAAAAAAGA
Statistics
Matches: 332, Mismatches: 42, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
75 64 0.19
76 192 0.58
77 76 0.23
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (76 bp):
AAATTGAAAATACCTCGACGTGCAACCCGAGGCTCAACTCACCTATCGGATTATGAGTTGATTTT
TTGAAAAATAG
Found at i:31272947 original size:17 final size:16
Alignment explanation
Indices: 31272897--31272948 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 16
31272887 GGATGAGAAG
31272897 TAAAAGTTTAAAGGGAAAA
1 TAAAAGTTT--AGGG-AAA
*
31272916 TAAAAAGTTTTGGGAAA
1 T-AAAAGTTTAGGGAAA
31272933 TAAAAGTTTGAGGGAA
1 TAAAAGTTT-AGGGAA
31272949 TGTAAATAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 8 0.28
17 9 0.31
18 3 0.10
19 1 0.03
20 8 0.28
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (16 bp):
TAAAAGTTTAGGGAAA
Found at i:31273061 original size:16 final size:16
Alignment explanation
Indices: 31273040--31273070 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
31273030 GATGAGAAGG
31273040 GAATAAAAGTTTTAGA
1 GAATAAAAGTTTTAGA
31273056 GAATAAAAGTTTTAG
1 GAATAAAAGTTTTAG
31273071 GGGAAAAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.32
Consensus pattern (16 bp):
GAATAAAAGTTTTAGA
Found at i:31273335 original size:9 final size:9
Alignment explanation
Indices: 31273321--31273357 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
31273311 TATAGTTTGA
31273321 TATTCGAAT
1 TATTCGAAT
31273330 TATTCGAAT
1 TATTCGAAT
*
31273339 TATTCGAGT
1 TATTCGAAT
31273348 TATTCGAAT
1 TATTCGAAT
31273357 T
1 T
31273358 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:31274927 original size:17 final size:16
Alignment explanation
Indices: 31274880--31274927 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
31274870 GCCTCAAGTT
*
31274880 TTGGGCCGTTGCTGGG
1 TTGGGCAGTTGCTGGG
* *
31274896 TTGGGCAGCTACTGGTG
1 TTGGGCAGTTGCTGG-G
*
31274913 TTGGGCTGTTGCTGG
1 TTGGGCAGTTGCTGG
31274928 ACGGGCTTCC
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.04, C:0.17, G:0.46, T:0.33
Consensus pattern (16 bp):
TTGGGCAGTTGCTGGG
Found at i:31275031 original size:23 final size:23
Alignment explanation
Indices: 31275011--31275055 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
31275001 AGTTTGCTGG
*
31275011 GTCTACTGGATTGGGTCTGCTAA
1 GTCTACTAGATTGGGTCTGCTAA
*
31275034 GTCTGCTAGATTGGGTCTGCTA
1 GTCTACTAGATTGGGTCTGCTA
31275056 GATTGGGTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.16, C:0.18, G:0.31, T:0.36
Consensus pattern (23 bp):
GTCTACTAGATTGGGTCTGCTAA
Found at i:31275086 original size:17 final size:14
Alignment explanation
Indices: 31275034--31275082 Score: 89
Period size: 14 Copynumber: 3.5 Consensus size: 14
31275024 GGTCTGCTAA
31275034 GTCTGCTAGATTGG
1 GTCTGCTAGATTGG
31275048 GTCTGCTAGATTGG
1 GTCTGCTAGATTGG
31275062 GTCTGCTAGATTGG
1 GTCTGCTAGATTGG
*
31275076 GCCTGCT
1 GTCTGCT
31275083 GCTACTGGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.12, C:0.18, G:0.35, T:0.35
Consensus pattern (14 bp):
GTCTGCTAGATTGG
Found at i:31275864 original size:30 final size:30
Alignment explanation
Indices: 31275778--31275874 Score: 128
Period size: 29 Copynumber: 3.3 Consensus size: 30
31275768 TCCCAAGGCT
*
31275778 AAAATGTAATTTTTGAAAAAGTAGG-GGG-C
1 AAAATGTAATTTTAGAAAAAGT-GGAGGGCC
*
31275807 AAAATGTAATTTTAGAAAAAGT-AAGGGCC
1 AAAATGTAATTTTAGAAAAAGTGGAGGGCC
* *
31275836 AAAATATAATTTTAGAAAAAATGGAGGGCC
1 AAAATGTAATTTTAGAAAAAGTGGAGGGCC
31275866 AAAATGTAA
1 AAAATGTAA
31275875 ATAGTATTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
28 3 0.05
29 42 0.71
30 14 0.24
ACGTcount: A:0.48, C:0.05, G:0.22, T:0.25
Consensus pattern (30 bp):
AAAATGTAATTTTAGAAAAAGTGGAGGGCC
Found at i:31278106 original size:13 final size:14
Alignment explanation
Indices: 31278085--31278111 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31278075 TTACTTTTCC
31278085 TTGCTTTTTTTTTT
1 TTGCTTTTTTTTTT
31278099 TTGCTTTTTTTTT
1 TTGCTTTTTTTTT
31278112 CTATTTTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.85
Consensus pattern (14 bp):
TTGCTTTTTTTTTT
Found at i:31281298 original size:13 final size:13
Alignment explanation
Indices: 31281280--31281305 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31281270 AAAAATACTA
31281280 TTTTTTATGTGAT
1 TTTTTTATGTGAT
31281293 TTTTTTATGTGAT
1 TTTTTTATGTGAT
31281306 GACCTATCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.69
Consensus pattern (13 bp):
TTTTTTATGTGAT
Found at i:31290434 original size:14 final size:15
Alignment explanation
Indices: 31290401--31290439 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
31290391 GTTCTAATTA
31290401 TTAAAAATTATATTT
1 TTAAAAATTATATTT
* *
31290416 ATAAAATTTAT-TTT
1 TTAAAAATTATATTT
31290430 TTAAAAATTA
1 TTAAAAATTA
31290440 CTTATTTTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTAAAAATTATATTT
Found at i:31296239 original size:6 final size:6
Alignment explanation
Indices: 31296230--31296254 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
31296220 GCAATAACGG
31296230 ATTAGA ATTAGA ATTAGA ATTAGA A
1 ATTAGA ATTAGA ATTAGA ATTAGA A
31296255 CTAAATCATG
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:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (6 bp):
ATTAGA
Found at i:31297034 original size:6 final size:6
Alignment explanation
Indices: 31297019--31297057 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
31297009 GCGACAATCA
*
31297019 TATATG TATATA TATATG TATATG TATATG TATATG TAT
1 TATATG TATATG TATATG TATATG TATATG TATATG TAT
31297058 TTATGTATTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:31299961 original size:6 final size:6
Alignment explanation
Indices: 31299952--31299976 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
31299942 GCAATAACGG
31299952 ATTAGA ATTAGA ATTAGA ATTAGA A
1 ATTAGA ATTAGA ATTAGA ATTAGA A
31299977 CTAAATCATG
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:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (6 bp):
ATTAGA
Found at i:31304336 original size:21 final size:20
Alignment explanation
Indices: 31304312--31304379 Score: 50
Period size: 21 Copynumber: 3.4 Consensus size: 20
31304302 AATAAATACC
*
31304312 AAAAATTTATTTTAAAAATT
1 AAAAAATTATTTTAAAAATT
** *
31304332 AAAAAAAAAATTTAAAAATATTT
1 -AAAAAATTATTTTAAAA-A-TT
*
31304355 TAAAAA-TATTTT-AAAATT
1 AAAAAATTATTTTAAAAATT
31304373 AAAAAAT
1 AAAAAAT
31304380 AAAAAAAGTA
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
18 7 0.19
19 1 0.03
20 3 0.08
21 17 0.47
22 6 0.17
23 2 0.06
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAAAATTATTTTAAAAATT
Found at i:31304376 original size:17 final size:17
Alignment explanation
Indices: 31304354--31304437 Score: 62
Period size: 17 Copynumber: 4.7 Consensus size: 17
31304344 TAAAAATATT
31304354 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
***
31304371 TTAAAAA-ATAAAAAAAGTA
1 TTAAAAATAT-TTTAAA--A
31304390 TTTTAAAAATATTTTAAAA
1 -TT-AAAAATATTTTAAAA
*
31304409 TTAAAAAAATTTTAAAA
1 TTAAAAATATTTTAAAA
* *
31304426 ATAAATATATTT
1 TTAAAAATATTT
31304438 ATTATATCGG
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
16 2 0.04
17 33 0.65
18 2 0.04
19 2 0.04
20 2 0.04
21 8 0.16
22 2 0.04
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:31304392 original size:38 final size:39
Alignment explanation
Indices: 31304319--31304417 Score: 146
Period size: 38 Copynumber: 2.5 Consensus size: 39
31304309 ACCAAAAATT
31304319 TATTTTAAAAATTAAAAAAAAAATTTAAAAATATTTTAAAAA
1 TATTTT-AAAATTAAAAAAAAAA--TAAAAATATTTTAAAAA
* *
31304361 TATTTTAAAATTAAAAAATAAA-AAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAAAAATAAAAATATTTTAAAAA
31304399 TATTTTAAAATTAAAAAAA
1 TATTTTAAAATTAAAAAAA
31304418 TTTTAAAAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
38 33 0.61
41 15 0.28
42 6 0.11
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (39 bp):
TATTTTAAAATTAAAAAAAAAATAAAAATATTTTAAAAA
Found at i:31304424 original size:49 final size:50
Alignment explanation
Indices: 31304320--31304430 Score: 124
Period size: 48 Copynumber: 2.3 Consensus size: 50
31304310 CCAAAAATTT
* ***
31304320 ATTTTAAAAATTAAAAAAAAAATTTAAAAATATTTTAAAAATATTTTAAA
1 ATTTTAAAAAATAAAAAAAAAATTTAAAAATATTTTAAAAATATAAAAAA
* *
31304370 A--TTAAAAAATAAAAAAAGTATTTTAAAAATATTTT-AAAAT-TAAAAAA
1 ATTTTAAAAAATAAAAAAA-AAATTTAAAAATATTTTAAAAATATAAAAAA
31304417 ATTTT-AAAAATAAA
1 ATTTTAAAAAATAAA
31304431 TATATTTATT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
47 5 0.10
48 29 0.56
49 17 0.33
50 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (50 bp):
ATTTTAAAAAATAAAAAAAAAATTTAAAAATATTTTAAAAATATAAAAAA
Found at i:31304426 original size:11 final size:11
Alignment explanation
Indices: 31304342--31304370 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
31304332 AAAAAAAAAA
31304342 TTTAAAAATAT
1 TTTAAAAATAT
31304353 TTTAAAAATAT
1 TTTAAAAATAT
31304364 TTTAAAA
1 TTTAAAA
31304371 TTAAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
TTTAAAAATAT
Found at i:31315083 original size:6 final size:6
Alignment explanation
Indices: 31315074--31315100 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
31315064 TAAGTCTAAG
31315074 AAAATA AAAATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAA
31315101 CAAATGGACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:31319570 original size:136 final size:136
Alignment explanation
Indices: 31319397--31319673 Score: 502
Period size: 136 Copynumber: 2.0 Consensus size: 136
31319387 TCTGTGCTAG
*
31319397 GACCATAGGGTAAACATTCTGGATTGTTCATCCATCCTTCATTCGTATCGCACTGCATCA-TCAG
1 GACCATAGGGTAAACATTATGGATTGTTCATCCATCCTTCATTCGTATCGCACTGCATCACT-AG
* *
31319461 ATGTACCTGCATATAACCATATAAACTATCAATTTTCTTATTTAAAAGCTCTACCTGATTCGATA
65 ATGTACCTGCATAGAACCATATAAACTATCAATTTTCTTATTTAAAAGCTATACCTGATTCGATA
31319526 ACATGGT
130 ACATGGT
*
31319533 GACCATAGGGTAAACATTATGGATTGTTCATCCATCCTTCATTCGTATCGCACTGCATCACTGGA
1 GACCATAGGGTAAACATTATGGATTGTTCATCCATCCTTCATTCGTATCGCACTGCATCACTAGA
31319598 TGTACCTGCATAGAACCATATAAACTATCAATTTTCTTATTTAAAAGCTATACCTGATTCGATAA
66 TGTACCTGCATAGAACCATATAAACTATCAATTTTCTTATTTAAAAGCTATACCTGATTCGATAA
31319663 CATGGT
131 CATGGT
31319669 GACCA
1 GACCA
31319674 CATCTAAGTT
Statistics
Matches: 136, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
136 135 0.99
137 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (136 bp):
GACCATAGGGTAAACATTATGGATTGTTCATCCATCCTTCATTCGTATCGCACTGCATCACTAGA
TGTACCTGCATAGAACCATATAAACTATCAATTTTCTTATTTAAAAGCTATACCTGATTCGATAA
CATGGT
Found at i:31324328 original size:15 final size:15
Alignment explanation
Indices: 31324308--31324336 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
31324298 CGGTGGTTAT
31324308 GTGCAAGTGTACATG
1 GTGCAAGTGTACATG
31324323 GTGCAAGTGTACAT
1 GTGCAAGTGTACAT
31324337 AGTACAAGTA
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:0.14, G:0.31, T:0.28
Consensus pattern (15 bp):
GTGCAAGTGTACATG
Found at i:31324344 original size:15 final size:15
Alignment explanation
Indices: 31324311--31324345 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
31324301 TGGTTATGTG
* *
31324311 CAAGTGTACATGGTG
1 CAAGTGTACATAGTA
31324326 CAAGTGTACATAGTA
1 CAAGTGTACATAGTA
31324341 CAAGT
1 CAAGT
31324346 AATAAGTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26
Consensus pattern (15 bp):
CAAGTGTACATAGTA
Found at i:31330688 original size:42 final size:42
Alignment explanation
Indices: 31330624--31330953 Score: 335
Period size: 42 Copynumber: 7.5 Consensus size: 42
31330614 TAATAGTTAC
* * *
31330624 ACGGTGGAATCAGCACTTAGCAACCACC-TTTATATTCAAGGAT
1 ACGG-GGAATCAGCACATAGCAACC-CCTTTTATAATCAAAGAT
*
31330667 ACAGGGAATCAGCACATAGCAACCCCTTTTATAATCAAAGAT
1 ACGGGGAATCAGCACATAGCAACCCCTTTTATAATCAAAGAT
* * *
31330709 ACGGGGAATCAGCACATAACAACCCCTTTTTTTATAACCAAATAT
1 ACGGGGAATCAGCACATAGCAACCCC---TTTTATAATCAAAGAT
* *
31330754 ACGGGGAATCAGCACTTAGCACTTAGCAACCCCTTTGATAATCAGA-AT
1 ACGGGGAATCAG--C--A-CA--TAGCAACCCCTTTTATAATCAAAGAT
* *
31330802 ACGGGGAATCAGCACTTAGCAACCCCTTTGATAATC-AAGAAT
1 ACGGGGAATCAGCACATAGCAACCCCTTTTATAATCAAAG-AT
*
31330844 ACGAGGAATCAGCACATAGCAACCCCTTTTATAATCAAAGAT
1 ACGGGGAATCAGCACATAGCAACCCCTTTTATAATCAAAGAT
* * *
31330886 ACGGGGAATCAGCACTTAGCAACCCCTTTTACATTCAATA-AT
1 ACGGGGAATCAGCACATAGCAACCCCTTTTATAATCAA-AGAT
*
31330928 ATTCGGTGGAATCAGCACACAGCAAC
1 A--CGG-GGAATCAGCACATAGCAAC
31330954 TACCGTTATA
Statistics
Matches: 246, Mismatches: 23, Indels: 34
0.81 0.08 0.11
Matches are distributed among these distances:
40 1 0.00
41 22 0.09
42 130 0.53
43 8 0.03
44 4 0.02
45 43 0.17
46 1 0.00
47 1 0.00
48 14 0.06
49 11 0.04
50 2 0.01
52 9 0.04
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (42 bp):
ACGGGGAATCAGCACATAGCAACCCCTTTTATAATCAAAGAT
Found at i:31330941 original size:177 final size:178
Alignment explanation
Indices: 31330624--31330945 Score: 492
Period size: 177 Copynumber: 1.8 Consensus size: 178
31330614 TAATAGTTAC
* *
31330624 ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAAGGATACAGGGAATCAGCACATAGCAA
1 ACGGTGGAATCAGCACTTAGCAACCACCTTTATAATCAAGAATACAGGGAATCAGCACATAGCAA
** *
31330689 CCCCTTTTATAATCAAAGATACGGGGAATCAGCACATAACAACCCCTTTTTTTATAACCAAATAT
66 CCCCTTTTATAATCAAAGATACGGGGAATCAGCACATAACAACCCCTTTTTACATAACAAAATAT
31330754 ACGGGGAATCAGCACTTAGCACTTAGCAACCCCTTTGATAATCAGAAT
131 ACGGGGAATCAGCACTTAGCACTTAGCAACCCCTTTGATAATCAGAAT
31330802 ACGG-GGAATCAGCACTTAGCAACC-CCTTTGATAATCAAGAATAC-GAGGAATCAGCACATAGC
1 ACGGTGGAATCAGCACTTAGCAACCACCTTT-ATAATCAAGAATACAG-GGAATCAGCACATAGC
* * *
31330864 AACCCCTTTTATAATCAAAGATACGGGGAATCAGCACTTAGCAACCCC-TTTTACAT-TCAATAA
64 AACCCCTTTTATAATCAAAGATACGGGGAATCAGCACATAACAACCCCTTTTTACATAACAA-AA
*
31330927 TATTCGGTGGAATCAGCAC
128 TATACGG-GGAATCAGCAC
31330946 ACAGCAACTA
Statistics
Matches: 131, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
175 2 0.02
176 20 0.15
177 105 0.80
178 4 0.03
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (178 bp):
ACGGTGGAATCAGCACTTAGCAACCACCTTTATAATCAAGAATACAGGGAATCAGCACATAGCAA
CCCCTTTTATAATCAAAGATACGGGGAATCAGCACATAACAACCCCTTTTTACATAACAAAATAT
ACGGGGAATCAGCACTTAGCACTTAGCAACCCCTTTGATAATCAGAAT
Found at i:31330973 original size:87 final size:84
Alignment explanation
Indices: 31330778--31330974 Score: 229
Period size: 84 Copynumber: 2.3 Consensus size: 84
31330768 CTTAGCACTT
* * *
31330778 AGCAACCCCT-TTGATAATCAGA-ATACGGGGAATCAGCACTTAGCAACCCCTTTGATAATCAAG
1 AGCAACACCTGTT-ATAATCAAAGATACGGGGAATCAGCACTTAGCAACCCCTTTGACAATCAAG
*
31330841 AATACGAGGAATCAGCACAT
65 AATACGAGGAATCAGCACAC
* * * * *
31330861 AGCAACCCCTTTTATAATCAAAGATACGGGGAATCAGCACTTAGCAACCCCTTTTACATTCAATA
1 AGCAACACCTGTTATAATCAAAGATACGGGGAATCAGCACTTAGCAACCCCTTTGACAATCAAGA
*
31330926 ATATTCGGTGGAATCAGCACAC
66 ATA--C-GAGGAATCAGCACAC
*
31330948 AGCAACTACC-GTTATAATCATAGATAC
1 AGCAAC-ACCTGTTATAATCAAAGATAC
31330975 CCGTTTTATT
Statistics
Matches: 98, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
83 18 0.18
84 43 0.44
86 1 0.01
87 34 0.35
88 2 0.02
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.23
Consensus pattern (84 bp):
AGCAACACCTGTTATAATCAAAGATACGGGGAATCAGCACTTAGCAACCCCTTTGACAATCAAGA
ATACGAGGAATCAGCACAC
Found at i:31342032 original size:37 final size:37
Alignment explanation
Indices: 31341982--31342057 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
31341972 AGCTACGGTA
31341982 AATCGATGTATTTTCATTTATCTAAGCATAAAAAATT
1 AATCGATGTATTTTCATTTATCTAAGCATAAAAAATT
31342019 AATCGATGTATTTTCATTTATCTAAGCATAAAAAATT
1 AATCGATGTATTTTCATTTATCTAAGCATAAAAAATT
31342056 AA
1 AA
31342058 AACTTCACGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (37 bp):
AATCGATGTATTTTCATTTATCTAAGCATAAAAAATT
Found at i:31343919 original size:21 final size:22
Alignment explanation
Indices: 31343895--31343941 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
31343885 AAAGTTAAAA
31343895 TTTATTATTAACAAAT-TTTAG
1 TTTATTATTAACAAATATTTAG
**
31343916 TTTATTATTAATTAATATTTAG
1 TTTATTATTAACAAATATTTAG
31343938 TTTA
1 TTTA
31343942 AGTTAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.57
Consensus pattern (22 bp):
TTTATTATTAACAAATATTTAG
Found at i:31347133 original size:3 final size:3
Alignment explanation
Indices: 31347127--31347177 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
31347117 TAAAAAAAAC
**
31347127 TAA TAA TAA TAA TAA TGG 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
31347175 TAA
1 TAA
31347178 ACTAATTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:31347736 original size:12 final size:12
Alignment explanation
Indices: 31347721--31347753 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
31347711 AGAGCCAAGA
31347721 AAAAGAAAAAAG
1 AAAAGAAAAAAG
*
31347733 AAAAGCAAAAAG
1 AAAAGAAAAAAG
31347745 AAAA-AAAAA
1 AAAAGAAAAA
31347754 TAATGAAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 4 0.21
12 15 0.79
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAAG
Found at i:31348872 original size:20 final size:20
Alignment explanation
Indices: 31348829--31348872 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
31348819 TCCTGATTTT
* *
31348829 ATTTGATTCCAATCAATTTG
1 ATTTGATTCCAATCAAATTA
**
31348849 ATTTGATTTTAATCAAATTA
1 ATTTGATTCCAATCAAATTA
31348869 ATTT
1 ATTT
31348873 AATTACTCAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.09, G:0.07, T:0.50
Consensus pattern (20 bp):
ATTTGATTCCAATCAAATTA
Found at i:31349351 original size:20 final size:22
Alignment explanation
Indices: 31349309--31349354 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
31349299 TGCATTTTAA
*
31349309 ATATAAATATTTATTTTATTTT
1 ATATAAATATTTAGTTTATTTT
31349331 ATATAAATATTT-GTTTA-TTT
1 ATATAAATATTTAGTTTATTTT
31349351 ATAT
1 ATAT
31349355 TCTTATTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.30
21 4 0.17
22 12 0.52
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
ATATAAATATTTAGTTTATTTT
Found at i:31349758 original size:87 final size:87
Alignment explanation
Indices: 31349479--31349908 Score: 533
Period size: 87 Copynumber: 4.9 Consensus size: 87
31349469 TGAAATAAAA
* * * * *
31349479 ATTAAAATTGAATAAAATCTATTTCGGGATTTATTCCCGCCGTTCAACAGATTTTATTCCTTTTA
1 ATTAAAATTAAATAAAATTTGTTTCGGGATTTATTCCCGCCGTTCAACGGATTTTATTCC---AA
*
31349544 TTTT-ATTTTATTTCC-AAACGAGA
63 TTTTGATTTTATTTCCAAAACGAGT
* * * **
31349567 ATTAAAGTTAAATAAAATTTATTTCAGGATTTATTCCTACCGTTCAACGGATTTTATTCC-ATTT
1 ATTAAAATTAAATAAAATTTGTTTCGGGATTTATTCCCGCCGTTCAACGGATTTTATTCCAATTT
* *
31349631 TTATTTTATTTCCAAAACAAGT
66 TGATTTTATTTCCAAAACGAGT
* * * * *
31349653 ATTAAAATTAAATAAAATTTGTTCCGGGATTTATTCTCGTCGTTCAACAGAGTTTATTCCAATTT
1 ATTAAAATTAAATAAAATTTGTTTCGGGATTTATTCCCGCCGTTCAACGGATTTTATTCCAATTT
* *
31349718 TGATTTTGTTCCCAAAACGAGT
66 TGATTTTATTTCCAAAACGAGT
* * *
31349740 ATTAGAATTAAATAAAATTTGTTTCGGGATTTATTCCCGCTGTTTAACGGATTTTATTCCAATTT
1 ATTAAAATTAAATAAAATTTGTTTCGGGATTTATTCCCGCCGTTCAACGGATTTTATTCCAATTT
* *
31349805 TGACTTTGTTTCCAAAACGAGT
66 TGATTTTATTTCCAAAACGAGT
* * * *
31349827 ATTAGAATTAAATAAAATCTGTTTCGAGATTTATTCCCGCCGTTTAACGGATTTTATTCCAATTT
1 ATTAAAATTAAATAAAATTTGTTTCGGGATTTATTCCCGCCGTTCAACGGATTTTATTCCAATTT
* *
31349892 TAATTTTTTTTCCAAAA
66 TGATTTTATTTCCAAAA
31349909 TGAGAAATGG
Statistics
Matches: 300, Mismatches: 39, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
84 5 0.02
85 11 0.04
86 56 0.19
87 175 0.58
88 53 0.18
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (87 bp):
ATTAAAATTAAATAAAATTTGTTTCGGGATTTATTCCCGCCGTTCAACGGATTTTATTCCAATTT
TGATTTTATTTCCAAAACGAGT
Found at i:31350101 original size:88 final size:88
Alignment explanation
Indices: 31349935--31350154 Score: 257
Period size: 88 Copynumber: 2.5 Consensus size: 88
31349925 ATGAGAAAGG
* * * * ***
31349935 AGATTTAATTCAA-TTTAATACTCATTTTGGAAACAAAATAAAA-AATGCAATAAAATTTGTTGA
1 AGATTTTATTTAACTTTAATACTCGTTTTGGAAATAAAATAAAATAATGCAATAAAATCCATTGA
* **
31349998 ACGGTGGGAATAAATCTTAAAAC
66 ACGGCGGGAATAAATCCCAAAAC
* * * *
31350021 ATATTTTATTTAATTTTAATACTCGTTTTGAAAATAAAATAAAATAATGGAATAAAATCCATTGA
1 AGATTTTATTTAACTTTAATACTCGTTTTGGAAATAAAATAAAATAATGCAATAAAATCCATTGA
* * *
31350086 ATGGCGGGAATAAATCCCGAAAT
66 ACGGCGGGAATAAATCCCAAAAC
*
31350109 AGATTTTATTTAACTTTAATTCTCG-TTTGGAAATAAAATAAAATAA
1 AGATTTTATTTAACTTTAATACTCGTTTTGGAAATAAAATAAAATAA
31350155 AATAAAATGA
Statistics
Matches: 112, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
86 10 0.09
87 47 0.42
88 55 0.49
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.35
Consensus pattern (88 bp):
AGATTTTATTTAACTTTAATACTCGTTTTGGAAATAAAATAAAATAATGCAATAAAATCCATTGA
ACGGCGGGAATAAATCCCAAAAC
Found at i:31350208 original size:93 final size:88
Alignment explanation
Indices: 31349935--31350196 Score: 228
Period size: 88 Copynumber: 2.9 Consensus size: 88
31349925 ATGAGAAAGG
* * * * * ****
31349935 AGATTTAATTCAA-TTTAATACTCATTTTGG-AAACAAAATAAAA-AATGCAATAAAATTTGTTG
1 AGATTTTATTTAACTTTAATACTC-GTTTGGAAAATAAAATAAAATAATGGAATAAAACCCATTG
* * *** *
31349997 AACGGTGGGAATAAATCTTAAAAC
65 AATGGCGGGAATAAATCCCGAAAT
* * * *
31350021 ATATTTTATTTAATTTTAATACTCGTTTTGAAAATAAAATAAAATAATGGAATAAAATCCATTGA
1 AGATTTTATTTAACTTTAATACTCGTTTGGAAAATAAAATAAAATAATGGAATAAAACCCATTGA
31350086 ATGGCGGGAATAAATCCCGAAAT
66 ATGGCGGGAATAAATCCCGAAAT
*
31350109 AGATTTTATTTAACTTTAATTCTCGTTTGGAAATAAAATAAAATAAAATAAAAT-GAATAAAACC
1 AGATTTTATTTAACTTTAATACTCGTTTGG----AAAATAAAATAAAAT--AATGGAATAAAACC
*
31350173 CGTTGAACT-GCGGGAATAAATCCC
60 CATTGAA-TGGCGGGAATAAATCCC
31350197 ATTTTTAATT
Statistics
Matches: 144, Mismatches: 22, Indels: 13
0.80 0.12 0.07
Matches are distributed among these distances:
86 14 0.10
87 22 0.15
88 59 0.41
92 15 0.10
93 30 0.21
94 4 0.03
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (88 bp):
AGATTTTATTTAACTTTAATACTCGTTTGGAAAATAAAATAAAATAATGGAATAAAACCCATTGA
ATGGCGGGAATAAATCCCGAAAT
Found at i:31350346 original size:20 final size:21
Alignment explanation
Indices: 31350321--31350363 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
31350311 CATGTTAGCT
31350321 AACAAATATGAATAT-AAATA
1 AACAAATATGAATATAAAATA
**
31350341 AACAAATATTTATATAAAATA
1 AACAAATATGAATATAAAATA
31350362 AA
1 AA
31350364 ATAAATACTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (21 bp):
AACAAATATGAATATAAAATA
Found at i:31358680 original size:14 final size:15
Alignment explanation
Indices: 31358654--31358685 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
31358644 AATTAATTTA
31358654 AAATTTCATTTAATT
1 AAATTTCATTTAATT
31358669 AAATTT-ATTTAATT
1 AAATTTCATTTAATT
31358683 AAA
1 AAA
31358686 AACCTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
AAATTTCATTTAATT
Found at i:31359965 original size:34 final size:32
Alignment explanation
Indices: 31359927--31359989 Score: 83
Period size: 34 Copynumber: 1.9 Consensus size: 32
31359917 ATACTTAACA
31359927 TTTTTAA-TATATTTAAAAGTTTAATATATTTAAT
1 TTTTTAAGT-TATTTAAAA-TTTAA-ATATTTAAT
*
31359961 TTTTTAAGTTTTTTAAAATTTAAATATTT
1 TTTTTAAGTTATTTAAAATTTAAATATTT
31359990 TAAGAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 6 0.22
33 5 0.19
34 15 0.56
35 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (32 bp):
TTTTTAAGTTATTTAAAATTTAAATATTTAAT
Found at i:31359966 original size:17 final size:17
Alignment explanation
Indices: 31359916--31359967 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
31359906 TAAAATTGGT
*
31359916 TATACTTAACATTTTTAA
1 TATATTTAA-ATTTTTAA
**
31359934 TATATTTAAAAGTTTAA
1 TATATTTAAATTTTTAA
*
31359951 TATATTTAATTTTTTAA
1 TATATTTAAATTTTTAA
31359968 GTTTTTTAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
17 20 0.71
18 8 0.29
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (17 bp):
TATATTTAAATTTTTAA
Found at i:31361418 original size:18 final size:18
Alignment explanation
Indices: 31361389--31361429 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
31361379 TCTTTTCATA
31361389 ATTTTTTATGAACTTTTAT
1 ATTTTTTATGAA-TTTTAT
*
31361408 ATTTTTT-TGAATTTTTT
1 ATTTTTTATGAATTTTAT
31361425 ATTTT
1 ATTTT
31361430 GAACATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.48
18 4 0.19
19 7 0.33
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (18 bp):
ATTTTTTATGAATTTTAT
Found at i:31370388 original size:21 final size:21
Alignment explanation
Indices: 31370363--31370403 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
31370353 TTATGTCATT
31370363 ATTTTTATTTATAAATTTTAA
1 ATTTTTATTTATAAATTTTAA
* * *
31370384 ATTTTTTTTTCTAATTTTTA
1 ATTTTTATTTATAAATTTTA
31370404 CTTATTTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (21 bp):
ATTTTTATTTATAAATTTTAA
Done.