Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr6
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: 26303135
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 1968672 characters in sequence are not A, C, G, or T
File 53 of 66
Found at i:19246883 original size:4 final size:4
Alignment explanation
Indices: 19246804--19247130 Score: 196
Period size: 4 Copynumber: 81.8 Consensus size: 4
19246794 AAAGCCAATG
* * * * * *
19246804 ATAT ATAC ATAT ACAT ATAT ACAT ACAT ATAC ATAT ATAC ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * * * * *
19246852 ACAT ATAC ATAT ACAT ATAC ATAC ATAT ATAT ATAT ACAT ATAC ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * *
19246900 ACAT ATAT ATAC ATAT ACAT ACAT ATAT ATAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * * ** * * * * *
19246948 ATAT ATAT AGTGGT -TCAT AAAG ATACG GGAT GTA- AAAT GTNAG ATAC
1 ATAT ATAT A-T-AT AT-AT ATAT ATA-T ATAT ATAT ATAT AT-AT ATAT
* * * * *
19246995 ATAT ATAC ATAC ATAT A-AT ATAT ACAT ATAT ATA- ACAT ATAC ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * * * * *
19247041 ACAT ATAC ATAC ATAT AT-T ATGT ATAT GTAT ATGT ATAT ATAT ACAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* *
19247088 ATAC ATAC ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATA
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATA
19247131 GTGGTTCATA
Statistics
Matches: 247, Mismatches: 67, Indels: 18
0.74 0.20 0.05
Matches are distributed among these distances:
3 9 0.04
4 232 0.94
5 5 0.02
6 1 0.00
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.38
Consensus pattern (4 bp):
ATAT
Found at i:19247038 original size:6 final size:6
Alignment explanation
Indices: 19246995--19247130 Score: 125
Period size: 6 Copynumber: 23.2 Consensus size: 6
19246985 TGTNAGATAC
* * * * *
19246995 ATATAT ACATAC ATATA- ATATAT ACATAT ATATA- ACATAT ACATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* * * * * * *
19247041 ACATAT ACATAC ATATAT -TATGT ATATGT ATATGT ATATAT ATACAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* *
19247088 ATACAT ACATAT ATATAT ATATAT ATATAT ATATAT ATATAT A
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT A
19247131 GTGGTTCATA
Statistics
Matches: 112, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
5 13 0.12
6 99 0.88
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (6 bp):
ATATAT
Found at i:19248054 original size:23 final size:25
Alignment explanation
Indices: 19248021--19248072 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
19248011 TAAGCCTAAA
19248021 TTTTAGAAATT-TTTCTT-TCACTTT
1 TTTTAGAAATTATTTCTTATC-CTTT
*
19248045 TTTTAG-AATTATTTTTTATCCTTT
1 TTTTAGAAATTATTTCTTATCCTTT
19248069 TTTT
1 TTTT
19248073 CTTTTTTCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 4 0.16
24 19 0.76
25 2 0.08
ACGTcount: A:0.19, C:0.10, G:0.04, T:0.67
Consensus pattern (25 bp):
TTTTAGAAATTATTTCTTATCCTTT
Found at i:19248093 original size:16 final size:15
Alignment explanation
Indices: 19248056--19248095 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
19248046 TTTAGAATTA
*
19248056 TTTTTTATCCTTTTT
1 TTTTTTTTCCTTTTT
*
19248071 TTCTTTTTTCCTTTTC
1 TT-TTTTTTCCTTTTT
19248087 TTTTTTTTC
1 TTTTTTTTC
19248096 TTGGGTTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTTTTCCTTTTT
Found at i:19252055 original size:2 final size:2
Alignment explanation
Indices: 19252050--19252080 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
19252040 GAGGCGGGAG
19252050 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
19252081 TGTGAGTGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:19255365 original size:2 final size:2
Alignment explanation
Indices: 19255308--19255350 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
19255298 TTCAATGAGT
19255308 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19255350 T
1 T
19255351 TTTGTGATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19259725 original size:24 final size:24
Alignment explanation
Indices: 19259683--19259732 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
19259673 CAGTGATGAC
* * * *
19259683 GAAGATGGTGACGATGAAGAGGAT
1 GAAGATGGCGACAAGGAAGAAGAT
19259707 GAAGATGGCGACAAGGAAGAAGAT
1 GAAGATGGCGACAAGGAAGAAGAT
19259731 GA
1 GA
19259733 GGAAGATGAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.42, C:0.06, G:0.40, T:0.12
Consensus pattern (24 bp):
GAAGATGGCGACAAGGAAGAAGAT
Found at i:19270553 original size:14 final size:14
Alignment explanation
Indices: 19270510--19270553 Score: 72
Period size: 14 Copynumber: 3.1 Consensus size: 14
19270500 AAAATATCTA
19270510 TTGAAAAATTATA-
1 TTGAAAAATTATAT
19270523 TTGAAAAAATTATAT
1 TTG-AAAAATTATAT
19270538 TTGAAAAATTATAT
1 TTGAAAAATTATAT
19270552 TT
1 TT
19270554 ATTGAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
13 3 0.10
14 23 0.79
15 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (14 bp):
TTGAAAAATTATAT
Found at i:19272543 original size:151 final size:150
Alignment explanation
Indices: 19272340--19272638 Score: 526
Period size: 151 Copynumber: 2.0 Consensus size: 150
19272330 CCGAGACCGC
* * *
19272340 CAAGGCTGTTTATTGTCACACACACAAACACATTTCACCTCTGACAACACAGCCGTTCCTTGGCG
1 CAAGGCTGTTTATTGTCACACACACAAACACATTTCACCTCTGACAACACAGCCATTCCTCGACG
* *
19272405 TTGGCTGAGTCCCACTTTCACGTGGTGGCCAGCGTGAAGTGTACTCAAATCCTACCTCGGGAGTT
66 TTAGCTGAGTCCCACTTTCACGTGGTGGCCAGCGTGAAGTGTACTCAAATCCTACCTCGAGAGTT
*
19272470 ATCCTACGTGCCTCTCCANGT
131 ATCCTACGCGCCTCTCCA-GT
19272491 CAAGGCTGTTTATTGTCACACACACAAACACATTTCACCTCTGACAACACAGCCATTCCTCGACG
1 CAAGGCTGTTTATTGTCACACACACAAACACATTTCACCTCTGACAACACAGCCATTCCTCGACG
*
19272556 TTAGCTGAGTCCCAGTTTCACGTGGTGGCCAGCGTGAAGTGTACTCAAATCCTACCTCGAGAGTT
66 TTAGCTGAGTCCCACTTTCACGTGGTGGCCAGCGTGAAGTGTACTCAAATCCTACCTCGAGAGTT
19272621 ATCCTACGCGCCTCTCCA
131 ATCCTACGCGCCTCTCCA
19272639 ATTGAGGTAA
Statistics
Matches: 141, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
151 141 1.00
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.26
Consensus pattern (150 bp):
CAAGGCTGTTTATTGTCACACACACAAACACATTTCACCTCTGACAACACAGCCATTCCTCGACG
TTAGCTGAGTCCCACTTTCACGTGGTGGCCAGCGTGAAGTGTACTCAAATCCTACCTCGAGAGTT
ATCCTACGCGCCTCTCCAGT
Found at i:19276947 original size:19 final size:18
Alignment explanation
Indices: 19276912--19276967 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
19276902 NNNNNNNNNN
*
19276912 TTCCTTTTTTTTCCTTTCT
1 TTCCTTTTTTCT-CTTTCT
19276931 TTCCTTTCTTTCTCTTT-T
1 TTCCTTT-TTTCTCTTTCT
*
19276949 TTTC-TTTTTCTCTTTCT
1 TTCCTTTTTTCTCTTTCT
19276966 TT
1 TT
19276968 TCTTCTCCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 9 0.27
17 5 0.15
18 4 0.12
19 11 0.33
20 4 0.12
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (18 bp):
TTCCTTTTTTCTCTTTCT
Found at i:19276960 original size:16 final size:17
Alignment explanation
Indices: 19276919--19276971 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
19276909 NNNTTCCTTT
*
19276919 TTTTTC-CTTTCTTTCC
1 TTTTTCTCTTTCTTTTC
19276935 TTTCTTTCTCTTT-TTTTC
1 -TT-TTTCTCTTTCTTTTC
19276953 TTTTTCTCTTTCTTTTC
1 TTTTTCTCTTTCTTTTC
19276970 TT
1 TT
19276972 CTCCCTCCCC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
16 9 0.28
17 11 0.34
18 8 0.25
19 4 0.12
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTCTCTTTCTTTTC
Found at i:19276974 original size:14 final size:13
Alignment explanation
Indices: 19276921--19276971 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
19276911 NTTCCTTTTT
*
19276921 TTTCCTTTCTTTCC
1 TTTCTTTTCTTT-C
*
19276935 TTTCTTTCTCTTTT
1 TTTCTTT-TCTTTC
*
19276949 TTTCTTTT-TCTC
1 TTTCTTTTCTTTC
19276961 TTTCTTTTCTT
1 TTTCTTTTCTT
19276972 CTCCCTCCCC
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
12 10 0.33
13 2 0.07
14 13 0.43
15 5 0.17
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTCTTTTCTTTC
Found at i:19277126 original size:116 final size:120
Alignment explanation
Indices: 19276976--19277196 Score: 360
Period size: 123 Copynumber: 1.9 Consensus size: 120
19276966 TTTCTTCTCC
* *
19276976 CTCCCCGCGGTTCCCCCTTCTC-TTTTTTTTT-TTCTTCTTC-CTTCCTTTCTTTCTCTTTCTCA
1 CTCCCCGCGGGTCCCCCTTCTCTTTTTTTTTTCTTCTTCTTCTCTTCCTTTCTTTCTCATTCTCA
19277038 TTCTTCT-CCCGTTGGCTTCTTCTTTCTTTCTTTCTCATTCTCTTTCTCTCCTTT
66 TTCTTCTCCCCGTTGGCTTCTTCTTTCTTTCTTTCTCATTCTCTTTCTCTCCTTT
19277092 CTCCCCGCGGGTCCCCCTTCTCTTTTTTTTTTTCTTCTTCTTCTTTCTTCCTTTCTTTCTCATTC
1 CTCCCCGCGGGTCCCCCTTCTC-TTTTTTTTTTCTTCTTCTTC--TCTTCCTTTCTTTCTCATTC
*
19277157 TCCTTCTTCTCCCCGTTGGCTTCTTCTTTCTTTCTTTCTC
63 TCATTCTTCTCCCCGTTGGCTTCTTCTTTCTTTCTTTCTC
19277197 TTTTGCCGAC
Statistics
Matches: 95, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
116 21 0.22
118 9 0.09
119 9 0.09
122 27 0.28
123 29 0.31
ACGTcount: A:0.01, C:0.37, G:0.06, T:0.56
Consensus pattern (120 bp):
CTCCCCGCGGGTCCCCCTTCTCTTTTTTTTTTCTTCTTCTTCTCTTCCTTTCTTTCTCATTCTCA
TTCTTCTCCCCGTTGGCTTCTTCTTTCTTTCTTTCTCATTCTCTTTCTCTCCTTT
Found at i:19277788 original size:47 final size:47
Alignment explanation
Indices: 19277719--19277812 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
19277709 ATATAATAAA
19277719 AAGTATGTCCACTTTTACCAATCAATTTTTTTTTTGTAATCCATACT
1 AAGTATGTCCACTTTTACCAATCAATTTTTTTTTTGTAATCCATACT
19277766 AAGTATGTCCACTTTTACCAATCAATTTTTTTTTTGTAATCCATACT
1 AAGTATGTCCACTTTTACCAATCAATTTTTTTTTTGTAATCCATACT
19277813 TTTATATATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (47 bp):
AAGTATGTCCACTTTTACCAATCAATTTTTTTTTTGTAATCCATACT
Found at i:19283796 original size:60 final size:60
Alignment explanation
Indices: 19283719--19283834 Score: 148
Period size: 60 Copynumber: 1.9 Consensus size: 60
19283709 AAAATTTTTT
19283719 ATATATTACATATA-TTTTAAATGAG-CCC-AAAATAAATTTTTTTATTAAATTATTAATACA
1 ATATATTACATATATTTTTAAATGAGCCCCTAAAAT-AA--TTTTTATTAAATTATTAATACA
** * *
19283779 ATATATTTTATATATTTTTTAATGGGCCCCTAAAATAATTTTTATTAAATTATTAA
1 ATATATTACATATATTTTTAAATGAGCCCCTAAAATAATTTTTATTAAATTATTAA
19283835 GATAAATAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
60 30 0.61
61 9 0.18
62 5 0.10
63 5 0.10
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.47
Consensus pattern (60 bp):
ATATATTACATATATTTTTAAATGAGCCCCTAAAATAATTTTTATTAAATTATTAATACA
Found at i:19287968 original size:18 final size:18
Alignment explanation
Indices: 19287945--19287980 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
19287935 TTTTTTCTTC
19287945 TTTTTTATTTAAGGTTAT
1 TTTTTTATTTAAGGTTAT
*
19287963 TTTTTTATTTAATGTTAT
1 TTTTTTATTTAAGGTTAT
19287981 CCAAATATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.69
Consensus pattern (18 bp):
TTTTTTATTTAAGGTTAT
Found at i:19289204 original size:21 final size:21
Alignment explanation
Indices: 19289180--19289245 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
19289170 GGTAAAGTTT
19289180 TTATTTAATT-TTT-TATTTAT
1 TTATTT-ATTATTTATATTTAT
19289200 ATTA-TTATTATTTATATTTAT
1 -TTATTTATTATTTATATTTAT
* *
19289221 TTATTTTTTCAATTATATTCTAT
1 TTATTTATT-ATTTATATT-TAT
19289244 TT
1 TT
19289246 GCTCATATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
19 3 0.08
20 8 0.21
21 14 0.37
22 8 0.21
23 5 0.13
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (21 bp):
TTATTTATTATTTATATTTAT
Found at i:19289212 original size:15 final size:13
Alignment explanation
Indices: 19289177--19289226 Score: 66
Period size: 15 Copynumber: 3.7 Consensus size: 13
19289167 AAAGGTAAAG
19289177 TTTTTATTTA-AT
1 TTTTTATTTATAT
19289189 TTTTTATTTATAT
1 TTTTTATTTATAT
19289202 TATTATTATTTATAT
1 T-TT-TTATTTATAT
19289217 TTATTTATTT
1 TT-TTTATTT
19289227 TTTCAATTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
12 10 0.29
13 3 0.09
14 9 0.26
15 12 0.35
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTTATTTATAT
Found at i:19299465 original size:21 final size:21
Alignment explanation
Indices: 19299441--19299481 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
19299431 TTATGTATTA
*
19299441 ATTCCTTTGATGAATCTGAAT
1 ATTCCTTTAATGAATCTGAAT
* *
19299462 ATTCTTTTAATGAATTTGAA
1 ATTCCTTTAATGAATCTGAA
19299482 AAGATACTTA
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:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (21 bp):
ATTCCTTTAATGAATCTGAAT
Found at i:19302706 original size:2 final size:2
Alignment explanation
Indices: 19302699--19302723 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19302689 ACTTCATTTA
19302699 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
19302724 GTGCCGACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19303284 original size:2 final size:2
Alignment explanation
Indices: 19303279--19303306 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19303269 TTTAAAATGC
19303279 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19303307 TATTTTTAAA
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):
AT
Found at i:19303611 original size:2 final size:2
Alignment explanation
Indices: 19303604--19303630 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19303594 AAATCGCCTT
19303604 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
19303631 TTCATTACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19304313 original size:34 final size:35
Alignment explanation
Indices: 19304243--19304316 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 35
19304233 AAATTAAAAT
*
19304243 TTAAATAATCAAAAATAAATATCTCAAATATCAAC
1 TTAAATAATCAAAAACAAATATCTCAAATATCAAC
* *
19304278 TTAAATATTTAAAAACAAATATC-CAAATAAT-AAC
1 TTAAATAATCAAAAACAAATATCTCAAAT-ATCAAC
19304312 TTAAA
1 TTAAA
19304317 CAACATTACA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
34 13 0.37
35 22 0.63
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (35 bp):
TTAAATAATCAAAAACAAATATCTCAAATATCAAC
Found at i:19304481 original size:15 final size:15
Alignment explanation
Indices: 19304461--19304498 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
19304451 AGTATATATA
19304461 TTATAATTAATAA-TT
1 TTATAATT-ATAACTT
19304476 TTATAAATTATAACTT
1 TTAT-AATTATAACTT
19304492 TTATAAT
1 TTATAAT
19304499 GTTAATACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (15 bp):
TTATAATTATAACTT
Found at i:19304493 original size:16 final size:16
Alignment explanation
Indices: 19304461--19304497 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
19304451 AGTATATATA
19304461 TTAT-AATTAATAATT
1 TTATAAATTAATAATT
19304476 TTATAAATT-ATAACTT
1 TTATAAATTAATAA-TT
19304492 TTATAA
1 TTATAA
19304498 TGTTAATACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (16 bp):
TTATAAATTAATAATT
Found at i:19309551 original size:25 final size:22
Alignment explanation
Indices: 19309523--19309576 Score: 54
Period size: 25 Copynumber: 2.3 Consensus size: 22
19309513 AATGACAATC
*
19309523 TTAATTAATTNTTAAAAATCCTAAA
1 TTAATTAAAT-TTAAAAAT-CT-AA
*
19309548 TTAATCTAAATTTAATAATCTAA
1 TTAAT-TAAATTTAAAAATCTAA
19309571 TTAATT
1 TTAATT
19309577 GCTTAATTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 1 0.04
23 7 0.27
24 2 0.08
25 12 0.46
26 4 0.15
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.44
Consensus pattern (22 bp):
TTAATTAAATTTAAAAATCTAA
Found at i:19309742 original size:123 final size:124
Alignment explanation
Indices: 19309502--19309743 Score: 301
Period size: 122 Copynumber: 2.0 Consensus size: 124
19309492 GTTAAATTCC
* * * *
19309502 TTAATTACCCCAATGACAATCTTAATTAATTNTTAAAAATCCTAAATTAATCTAAATTTAATAAT
1 TTAATTAACCCAATAACAATCTTAATTAATTATTAAAAATCCTAAATTAATCTAAATTCAATAAT
* * *
19309567 CTAATTAATTGCTTAATTACTTATTACAACACACAACATTACTTACTTAACTATATTAT
66 CTAATTAATTGCTTAATTAATTATTACAACACACAACATTACTTAATGAACTATATTAT
* ** ** *
19309626 TTAATTAACCCATTAAC-ATCTTAATTAA-T-TTAAATAATTTTAAATTAATCTAAATTCGTTAC
1 TTAATTAACCCAATAACAATCTTAATTAATTATTAAA-AATCCTAAATTAATCTAAATTCAATAA
* **
19309688 TTTAATTAATTGCTTAATTAATTACTTACAACACATTACATTACTTAATGAACTAT
65 TCTAATTAATTGCTTAATTAATTA-TTACAACACACAACATTACTTAATGAACTAT
19309744 GTACATTATT
Statistics
Matches: 101, Mismatches: 15, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
121 5 0.05
122 44 0.44
123 38 0.38
124 14 0.14
ACGTcount: A:0.41, C:0.15, G:0.02, T:0.41
Consensus pattern (124 bp):
TTAATTAACCCAATAACAATCTTAATTAATTATTAAAAATCCTAAATTAATCTAAATTCAATAAT
CTAATTAATTGCTTAATTAATTATTACAACACACAACATTACTTAATGAACTATATTAT
Found at i:19309786 original size:123 final size:121
Alignment explanation
Indices: 19309544--19309776 Score: 286
Period size: 122 Copynumber: 1.9 Consensus size: 121
19309534 TTAAAAATCC
* *
19309544 TAAATTAATCTAAATTTAATAATCTAATTAATTGCTTAATTACTTATTACAACACACAACATTAC
1 TAAATTAATCTAAATTCAATAATCTAATTAATTGCTTAATTAATTATTACAACACACAACATTAC
* * *
19309609 TTACTTAACTATATTATTTAATTAACCCATTAACATCTTAATTAATTTAAATAATTT
66 TTAATGAACTATATTATTTAATTAACCCATTAACACCTTAA-TAATTTAAATAATTT
** * * **
19309666 TAAATTAATCTAAATTCGTTACTTTAATTAATTGCTTAATTAATTACTTACAACACATTACATTA
1 TAAATTAATCTAAATTCAATAATCTAATTAATTGCTTAATTAATTA-TTACAACACACAACATTA
* **
19309731 CTTAATGAACTATGTACATTATTTATTTAAGTCATTAACACCTTAA
65 CTTAATGAACTA--T--ATTATTTAATTAACCCATTAACACCTTAA
19309777 ATTAAATAAT
Statistics
Matches: 92, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
122 40 0.43
123 26 0.28
125 1 0.01
127 25 0.27
ACGTcount: A:0.41, C:0.14, G:0.03, T:0.42
Consensus pattern (121 bp):
TAAATTAATCTAAATTCAATAATCTAATTAATTGCTTAATTAATTATTACAACACACAACATTAC
TTAATGAACTATATTATTTAATTAACCCATTAACACCTTAATAATTTAAATAATTT
Found at i:19315343 original size:85 final size:85
Alignment explanation
Indices: 19315103--19315357 Score: 338
Period size: 84 Copynumber: 3.0 Consensus size: 85
19315093 CCTAGATTCG
* * *
19315103 TTTTTCTCATAAAAAGAGATTTTTTA-AATTATTTTACTCAATTTTCACTCTCCTATTA-TTGAT
1 TTTTTTTCATAAAAAGAG-TTTTTTATAATTATTTTACTCAATTTTCAATCTCCTACTACTTGAT
19315166 TACCTAAGTTAAGGTGACACC
65 TACCTAAGTTAAGGTGACACC
* * * * * *
19315187 ATTTTTTCTTAAAAAGAGTTTTTTATAATTGTTTTATTCAATTTTCAATCTCCTACTTC-TAATT
1 TTTTTTTCATAAAAAGAGTTTTTTATAATTATTTTACTCAATTTTCAATCTCCTACTACTTGATT
*
19315251 TCCTAAGTTAAGGTGACACC
66 ACCTAAGTTAAGGTGACACC
* * *
19315271 TTTTTTTCATAAAAGGAGTTGTTTTATAACTATTTTACTCAATTTTGAATCTCCTA-TACTTGAT
1 TTTTTTTCATAAAAAGAGTT-TTTTATAATTATTTTACTCAATTTTCAATCTCCTACTACTTGAT
*
19315335 TACTTAAGTTAAGGTGACACC
65 TACCTAAGTTAAGGTGACACC
19315356 TT
1 TT
19315358 AATGCAAAAT
Statistics
Matches: 146, Mismatches: 21, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
83 7 0.05
84 84 0.58
85 55 0.38
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.46
Consensus pattern (85 bp):
TTTTTTTCATAAAAAGAGTTTTTTATAATTATTTTACTCAATTTTCAATCTCCTACTACTTGATT
ACCTAAGTTAAGGTGACACC
Found at i:19330884 original size:2 final size:2
Alignment explanation
Indices: 19330877--19330931 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
19330867 AAAATACTGG
19330877 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19330919 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
19330932 CAGTTCCTTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19331020 original size:2 final size:2
Alignment explanation
Indices: 19331009--19331050 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
19330999 TTCAATCTTC
19331009 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19331050 A
1 A
19331051 AAACTTAACC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19370692 original size:16 final size:16
Alignment explanation
Indices: 19370671--19370707 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
19370661 CCAAGACAGC
**
19370671 AGCAACAAAGCCAAGA
1 AGCAACAAAAACAAGA
19370687 AGCAACAAAAACAAGA
1 AGCAACAAAAACAAGA
19370703 AGCAA
1 AGCAA
19370708 AACAACCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.62, C:0.22, G:0.16, T:0.00
Consensus pattern (16 bp):
AGCAACAAAAACAAGA
Found at i:19371634 original size:9 final size:9
Alignment explanation
Indices: 19371610--19371671 Score: 55
Period size: 9 Copynumber: 7.3 Consensus size: 9
19371600 AAATAGAATA
19371610 AAATTAAA-
1 AAATTAAAT
*
19371618 AAAATAAAT
1 AAATTAAAT
19371627 AAATTAAAT
1 AAATTAAAT
19371636 ATAATT-AAT
1 A-AATTAAAT
19371645 -AA-TAATAT
1 AAATTAA-AT
19371653 AAA-TAAA-
1 AAATTAAAT
19371660 AAATTAAAT
1 AAATTAAAT
19371669 AAA
1 AAA
19371672 AATTTTACTT
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
6 1 0.02
7 6 0.13
8 14 0.31
9 20 0.44
10 4 0.09
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
AAATTAAAT
Found at i:19371669 original size:21 final size:24
Alignment explanation
Indices: 19371618--19371671 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
19371608 TAAAATTAAA
19371618 AAAATAAATAAATTAAATATAATT
1 AAAATAAATAAATTAAATATAATT
19371642 AATAATAATATAAA-TAAA-A-AATT
1 AA-AATAA-ATAAATTAAATATAATT
19371665 -AAATAAA
1 AAAATAAA
19371672 AATTTTACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
20 1 0.04
21 5 0.18
22 1 0.04
23 4 0.14
24 3 0.11
25 9 0.32
26 5 0.18
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (24 bp):
AAAATAAATAAATTAAATATAATT
Found at i:19371908 original size:33 final size:32
Alignment explanation
Indices: 19371853--19371939 Score: 122
Period size: 33 Copynumber: 2.7 Consensus size: 32
19371843 TTGAAAAAAT
*
19371853 TATTAAAAAA-AAATATATAATATATAAAATTA
1 TATTAAAAAATAAA-ATAAAATATATAAAATTA
*
19371885 TATTAAAAAATAAAACTAAAATATATAAGATTA
1 TATTAAAAAATAAAA-TAAAATATATAAAATTA
*
19371918 TAATAAAAAATAAAATAAAATA
1 TATTAAAAAATAAAATAAAATA
19371940 AAATATATGA
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
32 18 0.36
33 32 0.64
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (32 bp):
TATTAAAAAATAAAATAAAATATATAAAATTA
Found at i:19372179 original size:15 final size:15
Alignment explanation
Indices: 19372159--19372221 Score: 54
Period size: 15 Copynumber: 4.2 Consensus size: 15
19372149 CAATATTATC
*
19372159 TTATTTATAATCACA
1 TTATTTACAATCACA
* *
19372174 TTATTTGCAATTACA
1 TTATTTACAATCACA
* *
19372189 TTACTTACAATCATA
1 TTATTTACAATCACA
* * *
19372204 TTGTATATAATCACA
1 TTATTTACAATCACA
19372219 TTA
1 TTA
19372222 CATTATAAAG
Statistics
Matches: 35, Mismatches: 13, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.38, C:0.14, G:0.03, T:0.44
Consensus pattern (15 bp):
TTATTTACAATCACA
Found at i:19372838 original size:122 final size:121
Alignment explanation
Indices: 19372619--19372845 Score: 321
Period size: 122 Copynumber: 1.9 Consensus size: 121
19372609 AATCAAGTCA
* *
19372619 ATCAAACTTAAATTAATTTAAACTCGAATTTAATCAAAAATCCATTTGTCAAAAAATTATAATGA
1 ATCAAACTTAAATTAATTTAAACTCGAACTTAATCAAAAATCCATCTGTCAAAAAATTATAATGA
* * *
19372684 AGTGGGCTTTTCTTGATAAAAACTATTTGAGATCCAATTCGCTTTTCGAAAATATAT
66 AGTGGGCTTCTATTGATAAAAACTATTCGAGATCC-ATTCGCTTTTCGAAAATATAT
* * * * *
19372741 ATCAAATTTATATTAATTTAAACTCGAACTTAATCAAAAATTCATCTGTTAAAAAATTCTAAT-A
1 ATCAAACTTAAATTAATTTAAACTCGAACTTAATCAAAAATCCATCTGTCAAAAAATTATAATGA
**
19372805 AGATGGGCTTCTATTGATAGGAACTATTCGAGATCCATTCG
66 AG-TGGGCTTCTATTGATAAAAACTATTCGAGATCCATTCG
19372846 AGATCCAGTT
Statistics
Matches: 92, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
121 8 0.09
122 84 0.91
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.36
Consensus pattern (121 bp):
ATCAAACTTAAATTAATTTAAACTCGAACTTAATCAAAAATCCATCTGTCAAAAAATTATAATGA
AGTGGGCTTCTATTGATAAAAACTATTCGAGATCCATTCGCTTTTCGAAAATATAT
Found at i:19384909 original size:24 final size:24
Alignment explanation
Indices: 19384882--19384931 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
19384872 ACTTTCCTTA
*
19384882 CAAAACAATCTCTTGAAAATCCTG
1 CAAAACAATCTCTTGAAAACCCTG
19384906 CAAAACAATCTCTTGAAAACCCTG
1 CAAAACAATCTCTTGAAAACCCTG
19384930 CA
1 CA
19384932 CGTCTAAGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.42, C:0.28, G:0.08, T:0.22
Consensus pattern (24 bp):
CAAAACAATCTCTTGAAAACCCTG
Found at i:19385040 original size:3 final size:3
Alignment explanation
Indices: 19385032--19385065 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
19385022 TCGTCTAAAC
19385032 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
19385066 TGAAAAAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:19385971 original size:29 final size:29
Alignment explanation
Indices: 19385917--19385972 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
19385907 ATCATCACTC
**
19385917 AAGAAAAAAAATAGAATAACGCAAAATTT
1 AAGAAAAAAAATAGAATAACAAAAAATTT
*
19385946 AAGAAAAAAAATACGAA-GACAAAAAAT
1 AAGAAAAAAAATA-GAATAACAAAAAAT
19385973 AAAATAAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 20 0.87
30 3 0.13
ACGTcount: A:0.70, C:0.07, G:0.11, T:0.12
Consensus pattern (29 bp):
AAGAAAAAAAATAGAATAACAAAAAATTT
Found at i:19389412 original size:18 final size:19
Alignment explanation
Indices: 19389391--19389432 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
19389381 TGACATAATA
19389391 TTTTAAATA-ATTTAAATT
1 TTTTAAATATATTTAAATT
**
19389409 TTTTAAATATATTTTTATT
1 TTTTAAATATATTTAAATT
19389428 TTTTA
1 TTTTA
19389433 TTGTATTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTAAATATATTTAAATT
Found at i:19389444 original size:27 final size:27
Alignment explanation
Indices: 19389414--19389490 Score: 70
Period size: 26 Copynumber: 2.9 Consensus size: 27
19389404 AAATTTTTTA
*
19389414 AATATA-TTTTTATTTTTTATTGTATTC
1 AATATAGTTTTTATTTTTTATT-TAATC
* * *
19389441 AATAAATTTTTTATATTTT-TTTAATC
1 AATATAGTTTTTATTTTTTATTTAATC
19389467 AA-ATAAGTTTTTATATTTTTATTT
1 AATAT-AGTTTTTAT-TTTTTATTT
19389491 TAAATCAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
25 1 0.03
26 14 0.35
27 11 0.28
28 14 0.35
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (27 bp):
AATATAGTTTTTATTTTTTATTTAATC
Found at i:19389468 original size:26 final size:27
Alignment explanation
Indices: 19389420--19389486 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 27
19389410 TTTAAATATA
* * *
19389420 TTTTTATTTTTTATTGTATTC-AATAAAT
1 TTTTTATATTTT-TTGTAATCAAAT-AAG
19389448 TTTTTATATTTTTT-TAATCAAATAAG
1 TTTTTATATTTTTTGTAATCAAATAAG
19389474 TTTTTATATTTTT
1 TTTTTATATTTTT
19389487 ATTTTAAATC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 19 0.54
27 5 0.14
28 11 0.31
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (27 bp):
TTTTTATATTTTTTGTAATCAAATAAG
Found at i:19389499 original size:30 final size:29
Alignment explanation
Indices: 19389413--19389500 Score: 94
Period size: 27 Copynumber: 3.1 Consensus size: 29
19389403 TAAATTTTTT
* * *
19389413 AAATATATTTTTAT-TTTTTATTGTATTC
1 AAATAAATTTTTATATTTTTATTTTAATC
*
19389441 -AATAAATTTTT-TATATTT-TTTTAATC
1 AAATAAATTTTTATATTTTTATTTTAATC
*
19389467 AAATAAGTTTTTATATTTTTATTTTAAATC
1 AAATAAATTTTTATATTTTTATTTT-AATC
19389497 AAAT
1 AAAT
19389501 TAACTCTTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
26 7 0.14
27 24 0.49
28 6 0.12
29 4 0.08
30 8 0.16
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.59
Consensus pattern (29 bp):
AAATAAATTTTTATATTTTTATTTTAATC
Found at i:19390307 original size:16 final size:17
Alignment explanation
Indices: 19390280--19390312 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
19390270 ACTTTTCAGA
*
19390280 TTATTAAGTATCTTTTC
1 TTATTAAGTATCATTTC
19390297 TTATT-AGTATCATTTC
1 TTATTAAGTATCATTTC
19390313 AATAATACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.24, C:0.12, G:0.06, T:0.58
Consensus pattern (17 bp):
TTATTAAGTATCATTTC
Found at i:19398993 original size:30 final size:30
Alignment explanation
Indices: 19398957--19399016 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
19398947 ACTTACTCAA
19398957 CTTTTGGTATGAAATCAGGCTTTTTTTTCT
1 CTTTTGGTATGAAATCAGGCTTTTTTTTCT
19398987 CTTTTGGTATGAAATCAGGCTTTTTTTTCT
1 CTTTTGGTATGAAATCAGGCTTTTTTTTCT
19399017 TACTTATTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.17, C:0.13, G:0.17, T:0.53
Consensus pattern (30 bp):
CTTTTGGTATGAAATCAGGCTTTTTTTTCT
Found at i:19412981 original size:28 final size:28
Alignment explanation
Indices: 19412923--19412983 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
19412913 GGTAAATACA
* * *
19412923 TGTAATCACTTTTTTTTTCAACATAGTG
1 TGTAATAACTTTTTTTTTCAACAGAGCG
* *
19412951 TGTAATAATTTTTTTTTTCAACAGGGCG
1 TGTAATAACTTTTTTTTTCAACAGAGCG
19412979 TGTAA
1 TGTAA
19412984 GTTAGTCTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.48
Consensus pattern (28 bp):
TGTAATAACTTTTTTTTTCAACAGAGCG
Found at i:19419615 original size:125 final size:126
Alignment explanation
Indices: 19419393--19419642 Score: 423
Period size: 125 Copynumber: 2.0 Consensus size: 126
19419383 ACCAGAGTTG
19419393 TGTCCAATCACTTTGATAAAATGAATCAAACCTATATTCTTTAATGCTCAAATGGTCATTACTTA
1 TGTCCAATCACTTTGATAAAATGAATCAAACCTATATTCTTTAATGCTCAAATGGTCATTACTTA
* **
19419458 TATAAGATACTAGCCATAAACAAGTCATATTTGTAA-TTTTGACACTGAAACAATTATCTC
66 TACAAGATACTAGCCATAAACAAGTCATATTTGTAACTTAAGACACTGAAACAATTATCTC
* *
19419518 TGTCCAGTCACTTTGATAAAATGAATCAAATCC-ATATTCTTTAATGCTCAAATGGTCATTGCTT
1 TGTCCAATCACTTTGATAAAATGAATCAAA-CCTATATTCTTTAATGCTCAAATGGTCATTACTT
*
19419582 ATACAAGATACTAGCCATAAACAAGTCATATTTGTAACTTAAGACACTGAAACGATTATCT
65 ATACAAGATACTAGCCATAAACAAGTCATATTTGTAACTTAAGACACTGAAACAATTATCT
19419643 GAAACAATTA
Statistics
Matches: 117, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
125 95 0.81
126 22 0.19
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (126 bp):
TGTCCAATCACTTTGATAAAATGAATCAAACCTATATTCTTTAATGCTCAAATGGTCATTACTTA
TACAAGATACTAGCCATAAACAAGTCATATTTGTAACTTAAGACACTGAAACAATTATCTC
Found at i:19423930 original size:2 final size:2
Alignment explanation
Indices: 19423923--19423953 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
19423913 AGACAGAAAA
*
19423923 AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
19423954 TTTGATCGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19425096 original size:12 final size:12
Alignment explanation
Indices: 19425079--19425106 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
19425069 ATAAAAATAT
19425079 TAAAAATGATAA
1 TAAAAATGATAA
19425091 TAAAAATGATAA
1 TAAAAATGATAA
19425103 TAAA
1 TAAA
19425107 TAAAATTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (12 bp):
TAAAAATGATAA
Found at i:19427293 original size:7 final size:7
Alignment explanation
Indices: 19427268--19427312 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
19427258 AGCAACAAAT
*
19427268 AAGAATA
1 AAGAAAA
*
19427275 AATAAAA
1 AAGAAAA
19427282 AAGAAAA
1 AAGAAAA
*
19427289 GAGAAAA
1 AAGAAAA
*
19427296 GAGAAAA
1 AAGAAAA
19427303 AAGAAAA
1 AAGAAAA
19427310 AAG
1 AAG
19427313 TACAATGGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (7 bp):
AAGAAAA
Found at i:19428623 original size:144 final size:144
Alignment explanation
Indices: 19428363--19428641 Score: 344
Period size: 144 Copynumber: 1.9 Consensus size: 144
19428353 AAATAAAGAG
* * * * *
19428363 GATTTCATGCATGTTGATAATCTCATACAGTCTTTGAACAAAATTAAGATTAGTATCTGTTAATA
1 GATTTCATACATGTTGATAATCCCATACAGTCCTTGAACAAAATTAAGATTACTATCTGCTAATA
* * * * *
19428428 TGCATTTGCATATATCTGTGATGGTAAAGGTAATTGTCCTATATAAAAGTTAACATCAAATAGTT
66 TGCATTTACAGATATCTGTGATAGTAAAGGCAATTGTCCTATACAAAAGTTAACATCAAATAGTT
19428493 GAAATCATCAAGCT
131 GAAATCATCAAGCT
* ** *
19428507 GATTTCATACATGTTGATAATCCCCTGTAGTCCTTGAACAAAATTAAGATTACTATCTGCTACTA
1 GATTTCATACATGTTGATAATCCCATACAGTCCTTGAACAAAATTAAGATTACTATCTGCTAATA
* * * * * * * *
19428572 TGCATTTATAGATATTTGTGTTAGTAGAGGCAGTTGTTGC-ATACAAAAGTTAACATTAGATAGT
66 TGCATTTACAGATATCTGTGATAGTAAAGGCAATTG-TCCTATACAAAAGTTAACATCAAATAGT
19428636 TGAAAT
130 TGAAAT
19428642 TGTCAAATTG
Statistics
Matches: 112, Mismatches: 22, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
144 110 0.98
145 2 0.02
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (144 bp):
GATTTCATACATGTTGATAATCCCATACAGTCCTTGAACAAAATTAAGATTACTATCTGCTAATA
TGCATTTACAGATATCTGTGATAGTAAAGGCAATTGTCCTATACAAAAGTTAACATCAAATAGTT
GAAATCATCAAGCT
Found at i:19431805 original size:15 final size:15
Alignment explanation
Indices: 19431785--19431816 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
19431775 TAACATTATA
19431785 ATTAAAATAAAAAAT
1 ATTAAAATAAAAAAT
*
19431800 ATTAAAATAAAATAT
1 ATTAAAATAAAAAAT
19431815 AT
1 AT
19431817 AATATAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATTAAAATAAAAAAT
Found at i:19431820 original size:20 final size:21
Alignment explanation
Indices: 19431773--19431821 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
19431763 AAAAATATGT
* *
19431773 TATAACATTATAATTAAAATA
1 TATAATATTATAAATAAAATA
* *
19431794 AAAAATATTA-AAATAAAATA
1 TATAATATTATAAATAAAATA
19431814 TATAATAT
1 TATAATAT
19431822 AAGAATTAGA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
TATAATATTATAAATAAAATA
Found at i:19431855 original size:31 final size:33
Alignment explanation
Indices: 19431800--19431866 Score: 95
Period size: 31 Copynumber: 2.1 Consensus size: 33
19431790 AATAAAAAAT
*
19431800 ATTAAAATAAAATATATAATATAAG-AATTAGAA
1 ATTAAAATAAAAGATATAATATAAGAAATTA-AA
19431833 ATTAAAATAAAAGA-A-AATATAAGAAATTAAA
1 ATTAAAATAAAAGATATAATATAAGAAATTAAA
19431864 ATT
1 ATT
19431867 CATATAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 13 0.41
32 6 0.19
33 13 0.41
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (33 bp):
ATTAAAATAAAAGATATAATATAAGAAATTAAA
Found at i:19432209 original size:15 final size:15
Alignment explanation
Indices: 19432189--19432228 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
19432179 ATTCTCTTTA
19432189 CAATCACATTACTTG
1 CAATCACATTACTTG
19432204 CAATCACATTACTTG
1 CAATCACATTACTTG
*
19432219 TAATCACATT
1 CAATCACATT
19432229 GCATTGTAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (15 bp):
CAATCACATTACTTG
Found at i:19434800 original size:17 final size:17
Alignment explanation
Indices: 19434769--19434801 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
19434759 TTCTTGATAA
19434769 AATAAAACTCATTATTG
1 AATAAAACTCATTATTG
19434786 AATAATAACTC-TTATT
1 AATAA-AACTCATTATT
19434802 TTATTGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.39
Consensus pattern (17 bp):
AATAAAACTCATTATTG
Found at i:19435021 original size:57 final size:57
Alignment explanation
Indices: 19434953--19435083 Score: 167
Period size: 57 Copynumber: 2.3 Consensus size: 57
19434943 TCTTGTTTTT
* * * *
19434953 AATTAAGACAAAATATGTTATCTTGTCTAAATTTAGATAAA-ACATGTTTTTTGTCTA
1 AATTAAGACAAAACATGTTATCTTGTCTAAATTAAGACAAATACAT-TTTCTTGTCTA
* * * *
19435010 AATTAAAACAAAACATGTTTTCTTGTCTAAATTAAGGCAAATATATTTTCTTGTCTA
1 AATTAAGACAAAACATGTTATCTTGTCTAAATTAAGACAAATACATTTTCTTGTCTA
19435067 AATTAAGAC-AAACATGT
1 AATTAAGACAAAACATGT
19435084 AAAAACTATC
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
56 8 0.12
57 53 0.83
58 3 0.05
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.39
Consensus pattern (57 bp):
AATTAAGACAAAACATGTTATCTTGTCTAAATTAAGACAAATACATTTTCTTGTCTA
Found at i:19435022 original size:28 final size:28
Alignment explanation
Indices: 19434953--19435083 Score: 158
Period size: 28 Copynumber: 4.6 Consensus size: 28
19434943 TCTTGTTTTT
*
19434953 AATTAAGACAAAATATGTTATCTTGTCTA
1 AATTAAGACAAAACATGTT-TCTTGTCTA
* * *
19434982 AATTTAGATAAAACATGTTTTTTGTCTA
1 AATTAAGACAAAACATGTTTCTTGTCTA
*
19435010 AATTAAAACAAAACATGTTTTCTTGTCTA
1 AATTAAGACAAAACATG-TTTCTTGTCTA
* *
19435039 AATTAAGGCAAATATAT-TTTCTTGTCTA
1 AATTAAGACAAA-ACATGTTTCTTGTCTA
19435067 AATTAAGAC-AAACATGT
1 AATTAAGACAAAACATGT
19435084 AAAAACTATC
Statistics
Matches: 86, Mismatches: 13, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
26 3 0.03
27 3 0.03
28 41 0.48
29 36 0.42
30 3 0.03
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.39
Consensus pattern (28 bp):
AATTAAGACAAAACATGTTTCTTGTCTA
Found at i:19435701 original size:19 final size:19
Alignment explanation
Indices: 19435677--19435714 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
19435667 CCATTTAACT
*
19435677 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATTTGAG
19435696 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
19435715 GGTTTGACAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:19439486 original size:19 final size:20
Alignment explanation
Indices: 19439454--19439493 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
19439444 TCACTTCTAA
19439454 ACTTCAAATAATACTCCAAT
1 ACTTCAAATAATACTCCAAT
* *
19439474 ACTT-AAATCATACTCGAAT
1 ACTTCAAATAATACTCCAAT
19439493 A
1 A
19439494 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.45, C:0.23, G:0.03, T:0.30
Consensus pattern (20 bp):
ACTTCAAATAATACTCCAAT
Found at i:19439918 original size:13 final size:13
Alignment explanation
Indices: 19439900--19439924 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19439890 AGAGAAATTG
19439900 TGATTTTATAAAA
1 TGATTTTATAAAA
19439913 TGATTTTATAAA
1 TGATTTTATAAA
19439925 TTTTCTAGAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:19446197 original size:13 final size:13
Alignment explanation
Indices: 19446179--19446203 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19446169 CAATTTGATT
19446179 ATTATCATTAAAC
1 ATTATCATTAAAC
19446192 ATTATCATTAAA
1 ATTATCATTAAA
19446204 GCTTCGACAA
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:0.12, G:0.00, T:0.40
Consensus pattern (13 bp):
ATTATCATTAAAC
Found at i:19447565 original size:14 final size:15
Alignment explanation
Indices: 19447529--19447565 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
19447519 TAATGATTTG
19447529 ATACATTAAATTTTT
1 ATACATTAAATTTTT
*
19447544 ATAGATTAAATTTTT
1 ATACATTAAATTTTT
19447559 -TACATTA
1 ATACATTA
19447566 TTTAACTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (15 bp):
ATACATTAAATTTTT
Found at i:19451403 original size:17 final size:18
Alignment explanation
Indices: 19451367--19451404 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
19451357 ATTTGACCAT
*
19451367 TTTAATATAATTAAAATA
1 TTTAATATAAATAAAATA
*
19451385 TTTAATA-AAATAAATTA
1 TTTAATATAAATAAAATA
19451402 TTT
1 TTT
19451405 TCTTGTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTAATATAAATAAAATA
Found at i:19456231 original size:67 final size:67
Alignment explanation
Indices: 19456123--19456255 Score: 214
Period size: 67 Copynumber: 2.0 Consensus size: 67
19456113 AAATTGGATT
* *
19456123 ATTGAAAATTATTAATAAGAGTTTGAAGTTTGTACAAACACAGAACACCAAAAGGATAATAATCA
1 ATTGAAAATTATTAATAAAAGTTTGAAGTTTGTACAAACACAAAACACCAAAAGGATAATAATCA
19456188 AA
66 AA
* *
19456190 ATTGAAAATTATCT-ATAAAATTTTGAAGTTTGTACAAACACAAAACATCAAAAGGATAATAATC
1 ATTGAAAATTAT-TAATAAAAGTTTGAAGTTTGTACAAACACAAAACACCAAAAGGATAATAATC
19456254 AA
65 AA
19456256 TTATAAAACA
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
67 60 0.98
68 1 0.02
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.27
Consensus pattern (67 bp):
ATTGAAAATTATTAATAAAAGTTTGAAGTTTGTACAAACACAAAACACCAAAAGGATAATAATCA
AA
Found at i:19461724 original size:132 final size:136
Alignment explanation
Indices: 19461578--19461846 Score: 406
Period size: 132 Copynumber: 2.0 Consensus size: 136
19461568 TTATAAAACG
*
19461578 TAATCATATAAATAAAGTTTATTATAAGCTATAGTAATGCTTATGTATAAATTAAATATATGTAT
1 TAATCATATAAATAAAGTCTATTATAAGCTATAGTAATGCTTATGTATAAATTAAATATATGTAT
* *
19461643 ATAGATAATATATTACATTATTATATATATA-AT-TAA-TGAT-ACA-AATTT-TATGTTAAAAT
66 AT--ATAATATATGACATTATTATATATATATATATAATTAATAACATAATTTATATGTTAAAAT
19461702 GTTTTATA
129 GTTTTATA
* * *
19461710 TAATTATATAAATAAAGTCTATTATAAGTTATAGTAATGCTTATGTATAAATTAAATATGTGTAT
1 TAATCATATAAATAAAGTCTATTATAAGCTATAGTAATGCTTATGTATAAATTAAATATATGTAT
* *
19461775 ATATAATATATGACTTTATTATATATATATATATAATTAATAACATAATTTATATGTTATAATGT
66 ATATAATATATGACATTATTATATATATATATATAATTAATAACATAATTTATATGTTAAAATGT
19461840 TTTATA
131 TTTATA
19461846 T
1 T
19461847 CAAAGTTTGT
Statistics
Matches: 123, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
130 25 0.20
131 2 0.02
132 66 0.54
133 3 0.02
134 3 0.02
135 5 0.04
136 19 0.15
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.45
Consensus pattern (136 bp):
TAATCATATAAATAAAGTCTATTATAAGCTATAGTAATGCTTATGTATAAATTAAATATATGTAT
ATATAATATATGACATTATTATATATATATATATAATTAATAACATAATTTATATGTTAAAATGT
TTTATA
Found at i:19461776 original size:66 final size:65
Alignment explanation
Indices: 19461578--19461784 Score: 167
Period size: 66 Copynumber: 3.2 Consensus size: 65
19461568 TTATAAAACG
* * *
19461578 TAATCATATAAATAAAGTTTATTATAAGCTATAGTAATGCTTATGTATAAATTAAATATATGTAT
1 TAATAATATAAATAAAG-TTATTATAAGTTATAGTAATGCTTATGTATAAATTAAATATGTGTAT
19461643 A
65 A
* * * ** * **
19461644 TAGATAATAT-ATTACA-TTATTAT-A-TATATAATTAATGATACAAAT-TTTATGTTAAA-ATG
1 TA-ATAATATAAATAAAGTTATTATAAGT-TAT-AGTAATG---CTTATGTATAAATTAAATATG
*
19461703 TTTTATA
60 -TGTATA
*
19461710 TAATTATATAAATAAAGTCTATTATAAGTTATAGTAATGCTTATGTATAAATTAAATATGTGTAT
1 TAATAATATAAATAAAGT-TATTATAAGTTATAGTAATGCTTATGTATAAATTAAATATGTGTAT
19461775 A
65 A
19461776 T-ATAATATA
1 TAATAATATA
19461785 TGACTTTATT
Statistics
Matches: 104, Mismatches: 23, Indels: 29
0.67 0.15 0.19
Matches are distributed among these distances:
63 4 0.04
64 13 0.12
65 18 0.17
66 39 0.38
67 13 0.12
68 12 0.12
69 4 0.04
70 1 0.01
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.43
Consensus pattern (65 bp):
TAATAATATAAATAAAGTTATTATAAGTTATAGTAATGCTTATGTATAAATTAAATATGTGTATA
Found at i:19465024 original size:43 final size:43
Alignment explanation
Indices: 19464976--19465059 Score: 132
Period size: 43 Copynumber: 2.0 Consensus size: 43
19464966 ATCAAGAATC
** *
19464976 GTCTTTTGATGAAGAAGTATTTATACGTCGCCTAAGAACTGTT
1 GTCTTTTGATGAAGAAGTACCTATAAGTCGCCTAAGAACTGTT
*
19465019 GTCTTTTGATGAAGAAGTACCTATAAGTTGCCTAAGAACTG
1 GTCTTTTGATGAAGAAGTACCTATAAGTCGCCTAAGAACTG
19465060 CTGCTAATAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (43 bp):
GTCTTTTGATGAAGAAGTACCTATAAGTCGCCTAAGAACTGTT
Found at i:19474883 original size:15 final size:15
Alignment explanation
Indices: 19474863--19474910 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
19474853 ATTTTGTTAG
19474863 AAATGTGATTATTGA
1 AAATGTGATTATTGA
* *
19474878 AAATGTGATTACTGG
1 AAATGTGATTATTGA
* *
19474893 ATATGTGATTGTTGA
1 AAATGTGATTATTGA
19474908 AAA
1 AAA
19474911 AATAATTTTG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.38
Consensus pattern (15 bp):
AAATGTGATTATTGA
Found at i:19480161 original size:2 final size:2
Alignment explanation
Indices: 19480156--19480187 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
19480146 TGGTATACAA
19480156 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19480188 TTTCGACGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19482759 original size:17 final size:19
Alignment explanation
Indices: 19482724--19482760 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
19482714 ATGGAGTATC
19482724 ATCATCATATTCTTGTTATT
1 ATCATCATA-TCTTGTTATT
19482744 ATCATCATA-CTT-TTATT
1 ATCATCATATCTTGTTATT
19482761 TGTTCTAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.29
18 3 0.18
20 9 0.53
ACGTcount: A:0.27, C:0.16, G:0.03, T:0.54
Consensus pattern (19 bp):
ATCATCATATCTTGTTATT
Found at i:19499282 original size:3 final size:3
Alignment explanation
Indices: 19499274--19499309 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
19499264 CCTTCCACCT
*
19499274 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA TAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
19499310 TTATGACCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:19503380 original size:43 final size:43
Alignment explanation
Indices: 19503330--19503411 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 43
19503320 TACTCCCTGC
* *
19503330 TGGGAGTTGCTCTTTAATGTGAGACTTTGTTCCTTTACCCTTT
1 TGGGAGTTGCTCTTCAATGTGAGACTTTGTGCCTTTACCCTTT
* *
19503373 TGGGAGTTTCTCTTCAATGTGAGACTTTGTGGCTTTACC
1 TGGGAGTTGCTCTTCAATGTGAGACTTTGTGCCTTTACC
19503412 TGCGGGGAGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.15, C:0.18, G:0.23, T:0.44
Consensus pattern (43 bp):
TGGGAGTTGCTCTTCAATGTGAGACTTTGTGCCTTTACCCTTT
Found at i:19506744 original size:15 final size:15
Alignment explanation
Indices: 19506726--19506767 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
19506716 AATATTAATA
*
19506726 ATTAATAGTTTAAAT
1 ATTAATATTTTAAAT
**
19506741 ATTAACCTTTTAAAT
1 ATTAATATTTTAAAT
19506756 ATTAATATTTTA
1 ATTAATATTTTA
19506768 TTTATAATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (15 bp):
ATTAATATTTTAAAT
Found at i:19510907 original size:71 final size:71
Alignment explanation
Indices: 19510783--19510917 Score: 164
Period size: 71 Copynumber: 1.9 Consensus size: 71
19510773 TATAGAAAAT
* * * * * **
19510783 AAAATAGTTGTTGGAAATTATTAAATACATCTTATCGTTAGTAGATTGGAAATA-AATGAAATAG
1 AAAATAGTTGTTGGAAATCATGAAATACATATTACCCTTAGTAGATTACAAATAGAA-GAAATAG
19510847 GTGAGAA
65 GTGAGAA
* * *
19510854 AAAATTGTTGTTGGAGATCATGAAATACATATTACCCTTAGTTGATTACAAATAGAAGAAATAG
1 AAAATAGTTGTTGGAAATCATGAAATACATATTACCCTTAGTAGATTACAAATAGAAGAAATAG
19510918 TTGGGAATTA
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
71 51 0.96
72 2 0.04
ACGTcount: A:0.43, C:0.07, G:0.19, T:0.32
Consensus pattern (71 bp):
AAAATAGTTGTTGGAAATCATGAAATACATATTACCCTTAGTAGATTACAAATAGAAGAAATAGG
TGAGAA
Found at i:19511202 original size:24 final size:21
Alignment explanation
Indices: 19511162--19511210 Score: 53
Period size: 24 Copynumber: 2.2 Consensus size: 21
19511152 TCTTAAGTTT
*
19511162 TATATATTTTTAATATAATTAAA
1 TATATATTATTAATATAA--AAA
*
19511185 TATATTATTATTATTATAAAAA
1 TATA-TATTATTAATATAAAAA
19511207 TATA
1 TATA
19511211 AAATCTCTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 7 0.30
23 4 0.17
24 12 0.52
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TATATATTATTAATATAAAAA
Found at i:19512494 original size:22 final size:22
Alignment explanation
Indices: 19512459--19512533 Score: 89
Period size: 22 Copynumber: 3.4 Consensus size: 22
19512449 CTGCATAATC
* * *
19512459 AATTTTTGGGCATTAGAATACT
1 AATTTTTAGACATTAGATTACT
* *
19512481 AGTTTTTAGACATTACATTACT
1 AATTTTTAGACATTAGATTACT
19512503 AATTTTTAGACATT-GTATTACT
1 AATTTTTAGACATTAG-ATTACT
19512525 AATTTTTAG
1 AATTTTTAG
19512534 GTATTGTGTG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.47
Consensus pattern (22 bp):
AATTTTTAGACATTAGATTACT
Found at i:19512606 original size:23 final size:23
Alignment explanation
Indices: 19512558--19512636 Score: 115
Period size: 23 Copynumber: 3.5 Consensus size: 23
19512548 ATTTTTAGAT
* *
19512558 ATTGTGTGACTGGTTGAT-AGGC
1 ATTGCGTGACTGGTTAATAAGGC
19512580 ATTGCGTGACTGGTTAATAAGGC
1 ATTGCGTGACTGGTTAATAAGGC
*
19512603 ATTGCGTGACTGGTTAGTAAGGC
1 ATTGCGTGACTGGTTAATAAGGC
*
19512626 ATTACGTGACT
1 ATTGCGTGACT
19512637 TAGACATTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 16 0.31
23 36 0.69
ACGTcount: A:0.23, C:0.13, G:0.32, T:0.33
Consensus pattern (23 bp):
ATTGCGTGACTGGTTAATAAGGC
Found at i:19512675 original size:22 final size:22
Alignment explanation
Indices: 19512647--19512700 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
19512637 TAGACATTAT
*
19512647 CTAAAAATCAGTCACGCAATGC
1 CTAAAAATCAGTCACGCAATAC
* *
19512669 CTAAAAA-CTAATCACGTAATAC
1 CTAAAAATC-AGTCACGCAATAC
19512691 CT-AAAATCAG
1 CTAAAAATCAG
19512701 CGAAGCAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.46, C:0.24, G:0.09, T:0.20
Consensus pattern (22 bp):
CTAAAAATCAGTCACGCAATAC
Found at i:19513057 original size:21 final size:20
Alignment explanation
Indices: 19513017--19513057 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
19513007 AGTTATGTAA
* *
19513017 AAAATTAATTAAAAATTATT
1 AAAATTAAATAAAAAATATT
19513037 AAAATTATAATAAAAAATATT
1 AAAATTA-AATAAAAAATATT
19513058 TTTGAATTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAATTAAATAAAAAATATT
Found at i:19527813 original size:45 final size:45
Alignment explanation
Indices: 19527764--19527866 Score: 116
Period size: 45 Copynumber: 2.3 Consensus size: 45
19527754 ATTAAATTTA
* * * * *
19527764 AATAATACTATATAATAATCTTTATTACATTTATTATATTCAAAT
1 AATAATAATATATAATAATCCTTATAACATTTACTATAATCAAAT
* * * *
19527809 AATAATATTAAATAATATTCCTTATAATATTTACTATAATCAAAT
1 AATAATAATATATAATAATCCTTATAACATTTACTATAATCAAAT
*
19527854 AATATTAATATAT
1 AATAATAATATAT
19527867 TAAATAATAT
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.45
Consensus pattern (45 bp):
AATAATAATATATAATAATCCTTATAACATTTACTATAATCAAAT
Found at i:19527880 original size:19 final size:19
Alignment explanation
Indices: 19527832--19527886 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
19527822 AATATTCCTT
* *
19527832 ATAATATTTACTATAATCAA
1 ATAATATTTAATAT-ATTAA
19527852 ATAATA-TTAATATATTAA
1 ATAATATTTAATATATTAA
*
19527870 ATAATATTTAAAATATT
1 ATAATATTTAATATATT
19527887 TTTATTTCCT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 10 0.32
19 15 0.48
20 6 0.19
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAATATTTAATATATTAA
Found at i:19528270 original size:15 final size:16
Alignment explanation
Indices: 19528243--19528272 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19528233 CTTAAAAATA
19528243 TTTATAAAGATTTTAT
1 TTTATAAAGATTTTAT
19528259 TTTATAAA-ATTTTA
1 TTTATAAAGATTTTA
19528273 AATATTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (16 bp):
TTTATAAAGATTTTAT
Found at i:19544815 original size:18 final size:18
Alignment explanation
Indices: 19544792--19544828 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
19544782 TCTCACCCTG
19544792 TCCCTCACTTTTCTAGAA
1 TCCCTCACTTTTCTAGAA
19544810 TCCCTCACTTTTCTAGAA
1 TCCCTCACTTTTCTAGAA
19544828 T
1 T
19544829 AACCTCATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.32, G:0.05, T:0.41
Consensus pattern (18 bp):
TCCCTCACTTTTCTAGAA
Found at i:19550737 original size:28 final size:26
Alignment explanation
Indices: 19550697--19550752 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
19550687 TAAAAATATA
19550697 AAAATTTGATTAAATGAATATAAAAAT
1 AAAATTTGATTAAAT-AATATAAAAAT
* * *
19550724 AAAATTTTATTTAAATATTTTAAAAAT
1 AAAATTTGA-TTAAATAATATAAAAAT
19550751 AA
1 AA
19550753 TTCAAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (26 bp):
AAAATTTGATTAAATAATATAAAAAT
Found at i:19552321 original size:23 final size:23
Alignment explanation
Indices: 19552291--19552344 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 23
19552281 ATTAAACATC
19552291 AATAATTTATTATTAAATTA-TTA
1 AATAATTTA-TATTAAATTAGTTA
19552314 AATAATTTATATTAAATTAGTTA
1 AATAATTTATATTAAATTAGTTA
*
19552337 TATAATTT
1 AATAATTT
19552345 TTACTTTCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 10 0.34
23 19 0.66
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
AATAATTTATATTAAATTAGTTA
Found at i:19552366 original size:20 final size:20
Alignment explanation
Indices: 19552343--19552386 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
19552333 GTTATATAAT
* *
19552343 TTTTACTTTCATTATTTNTA
1 TTTTACTTTAATTATTTATA
* *
19552363 TTTTATTTTAATTTTTTATA
1 TTTTACTTTAATTATTTATA
19552383 TTTT
1 TTTT
19552387 TATTATATTC
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:0.20, C:0.05, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTTACTTTAATTATTTATA
Found at i:19552774 original size:33 final size:33
Alignment explanation
Indices: 19552695--19552783 Score: 101
Period size: 33 Copynumber: 2.7 Consensus size: 33
19552685 GAGAGAGGAA
** *
19552695 GAAGATCGATTGAGAGAGGACGA--AAGATAGGG
1 GAAGATCGGCTGAGAGAGGA-GATGAAGACAGGG
* *
19552727 GAAGATCGGTTGAGAGAGTAGATGAAGACAGGG
1 GAAGATCGGCTGAGAGAGGAGATGAAGACAGGG
*
19552760 GAAGGTCGGCTGAGAGAGGAGATG
1 GAAGATCGGCTGAGAGAGGAGATG
19552784 CTTTTCGGGG
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
31 2 0.04
32 18 0.37
33 29 0.59
ACGTcount: A:0.36, C:0.07, G:0.44, T:0.13
Consensus pattern (33 bp):
GAAGATCGGCTGAGAGAGGAGATGAAGACAGGG
Found at i:19553024 original size:17 final size:17
Alignment explanation
Indices: 19553002--19553034 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
19552992 GACAAATATG
*
19553002 AGGAATTTCTATTCCTT
1 AGGAATTCCTATTCCTT
19553019 AGGAATTCCTATTCCT
1 AGGAATTCCTATTCCT
19553035 CACCTTGTTT
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:0.24, C:0.21, G:0.12, T:0.42
Consensus pattern (17 bp):
AGGAATTCCTATTCCTT
Found at i:19558645 original size:33 final size:33
Alignment explanation
Indices: 19558601--19558694 Score: 109
Period size: 33 Copynumber: 2.8 Consensus size: 33
19558591 AAAATATTTT
* **
19558601 TAATGTCATATATTTTATTTTTATTTCTTATTA
1 TAATTTCATATATTTTATTTTTATTTCTTAAAA
*
19558634 TAATCTT-ATATATTTTATTTTCATTTCTTAAAA
1 TAAT-TTCATATATTTTATTTTTATTTCTTAAAA
* *
19558667 TAATTTCCTATATTATATATTTTATTTC
1 TAATTTCATATATTTTAT-TTTTATTTC
19558695 AATTTCTTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
32 2 0.04
33 40 0.78
34 9 0.18
ACGTcount: A:0.30, C:0.09, G:0.01, T:0.61
Consensus pattern (33 bp):
TAATTTCATATATTTTATTTTTATTTCTTAAAA
Found at i:19562358 original size:30 final size:27
Alignment explanation
Indices: 19562292--19562361 Score: 70
Period size: 30 Copynumber: 2.5 Consensus size: 27
19562282 AAAAATAATA
*
19562292 AAAAAT-AAAAATATTTTTTATTTTTT
1 AAAAATAAAAAAAATTTTTTATTTTTT
* *
19562318 ATTAATTAAAAAAAATTATTATTATATTTTT
1 A-AAAATAAAAAAAATT-TT-TTAT-TTTTT
19562349 AAAAATAAAAAAA
1 AAAAATAAAAAAA
19562362 TAAATAGCAT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
26 1 0.03
27 3 0.09
28 8 0.24
29 2 0.06
30 14 0.41
31 6 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
AAAAATAAAAAAAATTTTTTATTTTTT
Found at i:19567823 original size:2 final size:2
Alignment explanation
Indices: 19567811--19567863 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
19567801 TGTTATAATC
*
19567811 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19567853 TA TA TA TA TA T
1 TA TA TA TA TA T
19567864 GTAAAGTGTA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:19570214 original size:35 final size:35
Alignment explanation
Indices: 19570168--19570239 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
19570158 TTCCATTTTA
19570168 ACTCCCATGGTGGCCAATACTCATTCAACACTACC
1 ACTCCCATGGTGGCCAATACTCATTCAACACTACC
*
19570203 ACTCCCATGGTGGCTAATACTCATTCAACACTACC
1 ACTCCCATGGTGGCCAATACTCATTCAACACTACC
19570238 AC
1 AC
19570240 AAGAATTGCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.29, C:0.36, G:0.11, T:0.24
Consensus pattern (35 bp):
ACTCCCATGGTGGCCAATACTCATTCAACACTACC
Found at i:19572092 original size:165 final size:167
Alignment explanation
Indices: 19571819--19572135 Score: 485
Period size: 165 Copynumber: 1.9 Consensus size: 167
19571809 TCTTGCCACT
* **
19571819 TGAACTCACTAATGCTTATTCAACACTACCACAAGAATTGTAAGAAAAAAATATTACTATGAATG
1 TGAACTCACCAACACTTATTCAACACTACCACAAGAATTGTAAGAAAAAAATATTACTATGAATG
* *
19571884 TTGGGTTCTTGCAAGTAGATGAATGTGTTGTTTTCACGCAATTTGGAAACAAAAGAACT-AAAGT
66 TTGGGTTCTTGCAAATAGATGAATATGTTGTTTTCACGCAATTTGGAAACAAAAGAACTAAAAGT
*
19571948 TGAGGATGCAATCGATAAACTTGGTCATCTTTTCACC
131 TGAGGATACAATCGATAAACTTGGTCATCTTTTCACC
* * *
19571985 TGAACTCACCAACACTTATTCAACACTACCACAAGAATTGTACG-AAAAAATATTATTATGGATG
1 TGAACTCACCAACACTTATTCAACACTACCACAAGAATTGTAAGAAAAAAATATTACTATGAATG
* *** *
19572049 TTGTGTTCTTGCAAATAGATGAATATGTTGTTTTTGTGCAATTTGGAAACAAGAGAACTAAAAGT
66 TTGGGTTCTTGCAAATAGATGAATATGTTGTTTTCACGCAATTTGGAAACAAAAGAACTAAAAGT
*
19572114 TGAGGATACAATTGATAAACTT
131 TGAGGATACAATCGATAAACTT
19572136 CCATAGATAT
Statistics
Matches: 135, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
165 70 0.52
166 65 0.48
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (167 bp):
TGAACTCACCAACACTTATTCAACACTACCACAAGAATTGTAAGAAAAAAATATTACTATGAATG
TTGGGTTCTTGCAAATAGATGAATATGTTGTTTTCACGCAATTTGGAAACAAAAGAACTAAAAGT
TGAGGATACAATCGATAAACTTGGTCATCTTTTCACC
Found at i:19572923 original size:31 final size:31
Alignment explanation
Indices: 19572879--19572940 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
19572869 TGGTCCTCGT
* *
19572879 CATTTTGTATACAAGGTTCAATGTTTTTCAG
1 CATTTTGTATACAAGATTCAATGCTTTTCAG
19572910 CATTTTGCT-TACAAGATTCAATGCTTTTCAG
1 CATTTTG-TATACAAGATTCAATGCTTTTCAG
19572941 AATTGTAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.44
Consensus pattern (31 bp):
CATTTTGTATACAAGATTCAATGCTTTTCAG
Found at i:19574900 original size:7 final size:8
Alignment explanation
Indices: 19574872--19574898 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
19574862 TTGATTTGTC
19574872 TTTTCCTT
1 TTTTCCTT
19574880 TTTTCCTT
1 TTTTCCTT
19574888 TTTTCCTT
1 TTTTCCTT
19574896 TTT
1 TTT
19574899 CCACAGTCCT
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:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTCCTT
Found at i:19575272 original size:36 final size:36
Alignment explanation
Indices: 19575232--19575308 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
19575222 GGCAGAAAAA
*
19575232 GAGGAAAATAAGAAAGAAGAAGATGAAGAGGAGGAG
1 GAGGAAAATAAGAAAGAAGAAGATGAAGAGGAAGAG
** * *
19575268 GAGGAAGTTGAGGAAGAAGAAGATGAAGAGGAAGAG
1 GAGGAAAATAAGAAAGAAGAAGATGAAGAGGAAGAG
19575304 GAGGA
1 GAGGA
19575309 GGAGGAAGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.51, C:0.00, G:0.43, T:0.06
Consensus pattern (36 bp):
GAGGAAAATAAGAAAGAAGAAGATGAAGAGGAAGAG
Found at i:19575280 original size:15 final size:15
Alignment explanation
Indices: 19575256--19575362 Score: 76
Period size: 15 Copynumber: 7.3 Consensus size: 15
19575246 AGAAGAAGAT
*
19575256 GAAGAGGAGGAGGAG
1 GAAGATGAGGAGGAG
* * *
19575271 GAAGTTGAGGAAGAA
1 GAAGATGAGGAGGAG
19575286 GAAGATGA--A-GAG
1 GAAGATGAGGAGGAG
*
19575298 GAAGAGGAGGAGGAG
1 GAAGATGAGGAGGAG
* * *
19575313 GAAGTTGAGGAAGAA
1 GAAGATGAGGAGGAG
* * * *
19575328 GAAGAAGAAGAAGAA
1 GAAGATGAGGAGGAG
*
19575343 GAAGAGGAGGAGGAG
1 GAAGATGAGGAGGAG
19575358 GAAGA
1 GAAGA
19575363 AGGAGAAGAA
Statistics
Matches: 71, Mismatches: 18, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
12 9 0.13
13 1 0.01
14 1 0.01
15 60 0.85
ACGTcount: A:0.48, C:0.00, G:0.48, T:0.05
Consensus pattern (15 bp):
GAAGATGAGGAGGAG
Found at i:19575305 original size:42 final size:42
Alignment explanation
Indices: 19575245--19575387 Score: 195
Period size: 42 Copynumber: 3.4 Consensus size: 42
19575235 GAAAATAAGA
*
19575245 AAGAAGAAGATGAAGAGGAGGAGGAGGAAGTTGAGGAAGAAG
1 AAGAAGAAGAGGAAGAGGAGGAGGAGGAAGTTGAGGAAGAAG
*
19575287 AAGATGAAGAGGAAGAGGAGGAGGAGGAAGTTGAGGAAGAAG
1 AAGAAGAAGAGGAAGAGGAGGAGGAGGAAGTTGAGGAAGAAG
*
19575329 AAGAAGAAGAAGAAGAAGAGGAGGAGGAGGAAG--AAGG-AGAAG
1 AAGAAGAAG-AG--GAAGAGGAGGAGGAGGAAGTTGAGGAAGAAG
19575371 AA-AGAGAAGAGGAAGAG
1 AAGA-AGAAGAGGAAGAG
19575388 CATGGAGAAG
Statistics
Matches: 93, Mismatches: 4, Indels: 11
0.86 0.04 0.10
Matches are distributed among these distances:
39 6 0.06
41 3 0.03
42 60 0.65
43 5 0.05
45 19 0.20
ACGTcount: A:0.50, C:0.00, G:0.45, T:0.04
Consensus pattern (42 bp):
AAGAAGAAGAGGAAGAGGAGGAGGAGGAAGTTGAGGAAGAAG
Found at i:19575387 original size:6 final size:6
Alignment explanation
Indices: 19575245--19575387 Score: 65
Period size: 6 Copynumber: 23.8 Consensus size: 6
19575235 GAAAATAAGA
* * * * * ** * *
19575245 AAGAAG AAGATG AAGAGG AGGAGG AGGAAG TTGAGG AAGAAG AAGATG
1 AAGAGG AAGAGG AAGAGG AAGAGG AAGAGG AAGAGG AAGAGG AAGAGG
* * * ** * * *
19575293 AAGAGG AAGAGG AGGAGG AGGAAG TTGAGG AAGAAG AAGAAG AAGAAG
1 AAGAGG AAGAGG AAGAGG AAGAGG AAGAGG AAGAGG AAGAGG AAGAGG
* * * *
19575341 AAGAAG AGGAGG AGGAGG AAGAAGG -AGAAG AA-AGAG AAGAGG AAGAG
1 AAGAGG AAGAGG AAGAGG AAG-AGG AAGAGG AAGAG-G AAGAGG AAGAG
19575388 CATGGAGAAG
Statistics
Matches: 108, Mismatches: 25, Indels: 8
0.77 0.18 0.06
Matches are distributed among these distances:
5 3 0.03
6 100 0.93
7 5 0.05
ACGTcount: A:0.50, C:0.00, G:0.45, T:0.04
Consensus pattern (6 bp):
AAGAGG
Found at i:19575402 original size:3 final size:3
Alignment explanation
Indices: 19575280--19575386 Score: 63
Period size: 3 Copynumber: 35.7 Consensus size: 3
19575270 GGAAGTTGAG
* * * * * * ** *
19575280 GAA GAA GAA GAT GAA GAG GAA GAG GAG GAG GAG GAA GTT GAG GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* * * * *
19575328 GAA GAA GAA GAA GAA GAA GAG GAG GAG GAG GAA GAA GGA GAA GAA -AGA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA-A
*
19575376 GAA GAG GAA GA
1 GAA GAA GAA GA
19575387 GCATGGAGAA
Statistics
Matches: 85, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
2 1 0.01
3 83 0.98
4 1 0.01
ACGTcount: A:0.52, C:0.00, G:0.45, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:19586337 original size:2 final size:2
Alignment explanation
Indices: 19586330--19586365 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
19586320 CAAAAGAAAG
19586330 TA TA TA TA TA TA TA TA TA GTA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA T
19586366 GTCTATCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19586352 original size:19 final size:19
Alignment explanation
Indices: 19586328--19586365 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
19586318 CTCAAAAGAA
19586328 AGTATATATATATATATAT
1 AGTATATATATATATATAT
19586347 AGTATATATATATATATAT
1 AGTATATATATATATATAT
19586366 GTCTATCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (19 bp):
AGTATATATATATATATAT
Found at i:19586354 original size:17 final size:17
Alignment explanation
Indices: 19586332--19586364 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
19586322 AAAGAAAGTA
19586332 TATATATATATATATAG
1 TATATATATATATATAG
19586349 TATATATATATATATA
1 TATATATATATATATA
19586365 TGTCTATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TATATATATATATATAG
Found at i:19587679 original size:13 final size:13
Alignment explanation
Indices: 19587649--19587679 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
19587639 AAAATTAGGT
19587649 TAAAATTATTTAA
1 TAAAATTATTTAA
19587662 T-AAATTATTTAA
1 TAAAATTATTTAA
19587674 TAAAAT
1 TAAAAT
19587680 AAATTATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TAAAATTATTTAA
Found at i:19591503 original size:54 final size:54
Alignment explanation
Indices: 19591421--19591575 Score: 229
Period size: 54 Copynumber: 2.9 Consensus size: 54
19591411 TGATACTATC
* * *
19591421 CAGCTATATGCACAATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGATGTA
1 CAGCTATGTACACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGATGTA
* *
19591475 CAGCTATGTACACGATGTGGTGGGATGCACATGAGCTAGGTGAGATGGGATGTC
1 CAGCTATGTACACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGATGTA
* * * *
19591529 CAGTTATGTACACGATGTGGTGGGATGCACATAAGTTGTGTGAGATG
1 CAGCTATGTACACGATGTGGTGGGATGCACATGAGCTGGGTGAGATG
19591576 CACATGATGA
Statistics
Matches: 91, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 91 1.00
ACGTcount: A:0.25, C:0.13, G:0.36, T:0.26
Consensus pattern (54 bp):
CAGCTATGTACACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGATGTA
Found at i:19592370 original size:12 final size:12
Alignment explanation
Indices: 19592355--19592379 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19592345 AAAGAATCTA
19592355 ATAAAATAAAAT
1 ATAAAATAAAAT
19592367 ATAAAATAAAAT
1 ATAAAATAAAAT
19592379 A
1 A
19592380 ATATATATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAAAATAAAAT
Found at i:19592374 original size:17 final size:17
Alignment explanation
Indices: 19592354--19592400 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
19592344 TAAAGAATCT
19592354 AATAAAATAAAATATAA
1 AATAAAATAAAATATAA
* *
19592371 AATAAAATAATATATAT
1 AATAAAATAAAATATAA
19592388 AATAATAATAAAA
1 AATAA-AATAAAA
19592401 AAGAAGAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 20 0.77
18 6 0.23
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
AATAAAATAAAATATAA
Found at i:19595711 original size:41 final size:41
Alignment explanation
Indices: 19595654--19595743 Score: 162
Period size: 41 Copynumber: 2.2 Consensus size: 41
19595644 CCTTAACGTG
*
19595654 TTTCGTGTCTAATCGTGTTTGACACGTTAAGACACGAAAAT
1 TTTCGTGTCTAATCGTGTCTGACACGTTAAGACACGAAAAT
*
19595695 TTTCGTGTCTAATCGTGTCTGACACGTTAAGACATGAAAAT
1 TTTCGTGTCTAATCGTGTCTGACACGTTAAGACACGAAAAT
19595736 TTTCGTGT
1 TTTCGTGT
19595744 TTTAACATGT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.37
Consensus pattern (41 bp):
TTTCGTGTCTAATCGTGTCTGACACGTTAAGACACGAAAAT
Found at i:19595761 original size:41 final size:41
Alignment explanation
Indices: 19595654--19595761 Score: 119
Period size: 41 Copynumber: 2.6 Consensus size: 41
19595644 CCTTAACGTG
* ***
19595654 TTTCGTGTCTAATCGTGTTTGACACGTTAAGACACGAAAAT
1 TTTCGTGTCTAATCATGTCAAACACGTTAAGACACGAAAAT
* ** *
19595695 TTTCGTGTCTAATCGTGTCTGACACGTTAAGACATGAAAAT
1 TTTCGTGTCTAATCATGTCAAACACGTTAAGACACGAAAAT
*
19595736 TTTCGTGTTTTAA-CATGTCAAACACG
1 TTTCGTG-TCTAATCATGTCAAACACG
19595762 ACAAACACGT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 56 0.93
42 4 0.07
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (41 bp):
TTTCGTGTCTAATCATGTCAAACACGTTAAGACACGAAAAT
Found at i:19595790 original size:10 final size:11
Alignment explanation
Indices: 19595764--19595793 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
19595754 CAAACACGAC
19595764 AAACACGTTTA
1 AAACACGTTTA
19595775 AAACACGTTT-
1 AAACACGTTTA
19595785 AAACACGTT
1 AAACACGTT
19595794 CATTTAATCG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27
Consensus pattern (11 bp):
AAACACGTTTA
Found at i:19596006 original size:29 final size:29
Alignment explanation
Indices: 19595957--19596012 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
19595947 TTATATTAAA
* *
19595957 TTTTATTATATTTGATGTTATTATTATTT
1 TTTTATTATAATTGATGTTATAATTATTT
*
19595986 TTTTATTATAATT-ATTTTTATAATTAT
1 TTTTATTATAATTGA-TGTTATAATTAT
19596013 AGATTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 1 0.04
29 22 0.96
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.68
Consensus pattern (29 bp):
TTTTATTATAATTGATGTTATAATTATTT
Found at i:19601800 original size:16 final size:17
Alignment explanation
Indices: 19601779--19601812 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
19601769 TGAAAAATAT
*
19601779 AATGAAA-AATGAAAAA
1 AATGAAAGAAGGAAAAA
19601795 AATGAAAGAAGGAAAAA
1 AATGAAAGAAGGAAAAA
19601812 A
1 A
19601813 GGAGAGAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.09
Consensus pattern (17 bp):
AATGAAAGAAGGAAAAA
Found at i:19614535 original size:19 final size:17
Alignment explanation
Indices: 19614482--19614545 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 17
19614472 TGTAGACACC
19614482 TAAATAAAAAAAATTAAA
1 TAAATAAAAAAAA-TAAA
*
19614500 TTAAATTAAATAAAATAAA
1 -TAAA-TAAAAAAAATAAA
*
19614519 TAAAT-AAAACAAT-AA
1 TAAATAAAAAAAATAAA
*
19614534 TAATTAAAAAAA
1 TAAATAAAAAAA
19614546 TATATGGGGA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
15 6 0.16
16 11 0.29
17 1 0.03
18 4 0.11
19 8 0.21
20 8 0.21
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (17 bp):
TAAATAAAAAAAATAAA
Found at i:19618888 original size:17 final size:17
Alignment explanation
Indices: 19618866--19618914 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
19618856 GACACCTCAA
19618866 AAAATAAAAAATATAAT
1 AAAATAAAAAATATAAT
19618883 AAAATAAAATAATAT-AT
1 AAAATAAAA-AATATAAT
*
19618900 ATAATAAAAAA-ATAA
1 AAAATAAAAAATATAA
19618915 AATACGCCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
15 2 0.07
16 3 0.10
17 19 0.66
18 5 0.17
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAATAAAAAATATAAT
Found at i:19618891 original size:22 final size:20
Alignment explanation
Indices: 19618864--19618916 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 20
19618854 TAGACACCTC
19618864 AAAAAATAAAAAATATAATAA
1 AAAAAATAAAAAATATAAT-A
* *
19618885 AATAAAATAATATATATAATA
1 AA-AAAATAAAAAATATAATA
19618906 AAAAAATAAAA
1 AAAAAATAAAA
19618917 TACGCCCAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 8 0.29
21 5 0.18
22 15 0.54
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (20 bp):
AAAAAATAAAAAATATAATA
Found at i:19620833 original size:11 final size:10
Alignment explanation
Indices: 19620798--19620835 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
19620788 AGGAAAGAAT
19620798 AAAAATAAAA
1 AAAAATAAAA
*
19620808 AAACA-AAAA
1 AAAAATAAAA
19620817 AAAAATAAAA
1 AAAAATAAAA
19620827 AATAAATAA
1 AA-AAATAA
19620836 TCCATGAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 8 0.33
10 10 0.42
11 6 0.25
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.11
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:19621569 original size:2 final size:2
Alignment explanation
Indices: 19621562--19621592 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
19621552 GCACGTTACG
19621562 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
19621593 TATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:19622913 original size:27 final size:27
Alignment explanation
Indices: 19622883--19623047 Score: 159
Period size: 27 Copynumber: 6.0 Consensus size: 27
19622873 TAACATGGTA
* * *
19622883 TGTAACAGCTAAATTTTCAACGTAATG
1 TGTAACAACTAAATTTTCAACATAACG
* ** * *
19622910 TGTAACAACTATATTTTTTTATATAGCG
1 TGTAACAACTA-AATTTTCAACATAACG
* *
19622938 TGTAATAACTAAATTTTCAACATAACA
1 TGTAACAACTAAATTTTCAACATAACG
* * * *
19622965 TATAATAACTACAATTTTTAACATAATG
1 TGTAACAACTA-AATTTTCAACATAACG
19622993 TGTAACAACTAAATTTTCAACATAACG
1 TGTAACAACTAAATTTTCAACATAACG
* * *
19623020 TATAATAACTACATTTTCAACATAACG
1 TGTAACAACTAAATTTTCAACATAACG
19623047 T
1 T
19623048 ATAATAATTA
Statistics
Matches: 110, Mismatches: 26, Indels: 4
0.79 0.19 0.03
Matches are distributed among these distances:
27 69 0.63
28 41 0.37
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.36
Consensus pattern (27 bp):
TGTAACAACTAAATTTTCAACATAACG
Done.