Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 133 of 335
Found at i:39425015 original size:31 final size:29
Alignment explanation
Indices: 39424952--39425015 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
39424942 TTGTGTTTAT
*
39424952 GGTTTGAAAAAAATTAGGATTGTGCTTAG
1 GGTTTGAAAAAAATTAGGATTGTACTTAG
* *
39424981 GGTTTGAAAAAAATTAAGAGATTGTATTTGG
1 GGTTTGAAAAAAATT-AG-GATTGTACTTAG
39425012 GGTT
1 GGTT
39425016 ATAAAGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 15 0.50
30 2 0.07
31 13 0.43
ACGTcount: A:0.34, C:0.02, G:0.28, T:0.36
Consensus pattern (29 bp):
GGTTTGAAAAAAATTAGGATTGTACTTAG
Found at i:39425462 original size:21 final size:21
Alignment explanation
Indices: 39425427--39425470 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
39425417 TATTTTTTGA
*
39425427 TTAACATGTTATTTTTATTATT
1 TTAACATGATATTTTT-TTATT
39425449 TTAACAT-ATATTTTTTTATT
1 TTAACATGATATTTTTTTATT
39425469 TT
1 TT
39425471 TTATGTAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.33
21 7 0.33
22 7 0.33
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (21 bp):
TTAACATGATATTTTTTTATT
Found at i:39434692 original size:2 final size:2
Alignment explanation
Indices: 39434685--39434714 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
39434675 TGTAGCTTTA
39434685 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
39434715 TAGATTTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39439320 original size:30 final size:31
Alignment explanation
Indices: 39439266--39439332 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 31
39439256 TAATTTAATC
*
39439266 AATTTTAATTTTTGTATTTTTTGAAATATTT
1 AATTTTAATTTTTGTATCTTTTGAAATATTT
*
39439297 AATTTT-ATTCTTTGTA-CTTTTGAAATTTTT
1 AATTTTAATT-TTTGTATCTTTTGAAATATTT
39439327 AATTTT
1 AATTTT
39439333 TGGTCATGAC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 21 0.64
31 12 0.36
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.64
Consensus pattern (31 bp):
AATTTTAATTTTTGTATCTTTTGAAATATTT
Found at i:39440200 original size:18 final size:17
Alignment explanation
Indices: 39440166--39440208 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
39440156 GCTTTTATAA
39440166 TTTTATAATTATT-TATT
1 TTTTATAATT-TTATATT
39440183 TTTTATAGATTTTATATT
1 TTTTATA-ATTTTATATT
*
39440201 TTTAATAA
1 TTTTATAA
39440209 ATTTCTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
TTTTATAATTTTATATT
Found at i:39440212 original size:18 final size:17
Alignment explanation
Indices: 39440158--39440217 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
39440148 TTACTGCTGC
* *
39440158 TTTTATAATTTTATAAT
1 TTTTATATTTTTATAAA
*
39440175 TATTTAT-TTTTTATAGA
1 T-TTTATATTTTTATAAA
39440192 TTTTATATTTTTAATAAA
1 TTTTATATTTTT-ATAAA
39440210 TTTCTATA
1 TTT-TATA
39440218 ATTTCTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 5 0.14
17 14 0.40
18 12 0.34
19 4 0.11
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (17 bp):
TTTTATATTTTTATAAA
Found at i:39441964 original size:23 final size:25
Alignment explanation
Indices: 39441901--39441971 Score: 76
Period size: 27 Copynumber: 2.8 Consensus size: 25
39441891 TTTTGTCCAT
*
39441901 TTATTTTATAAAATTTATTTATTTA
1 TTATTTTATAAAATTTATATATTTA
*
39441926 TTTTACTTTATCAAAATTTA-ATATTTA
1 --TTATTTTAT-AAAATTTATATATTTA
39441953 -TATTTTATAAAATTT-TATA
1 TTATTTTATAAAATTTATATA
39441972 AAAATTAATC
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
23 10 0.26
24 7 0.18
27 14 0.36
28 8 0.21
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (25 bp):
TTATTTTATAAAATTTATATATTTA
Found at i:39451471 original size:3 final size:3
Alignment explanation
Indices: 39451463--39451488 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
39451453 ATACACACAA
39451463 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
39451489 ACCATAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:39456409 original size:44 final size:43
Alignment explanation
Indices: 39456349--39456431 Score: 139
Period size: 44 Copynumber: 1.9 Consensus size: 43
39456339 ATAGAAGTTC
*
39456349 TGATAATTATACATTTAAAAATAATTATAATTTAATATTATTTG
1 TGATAATTAAACATTTAAAAATAATTATAATTTAA-ATTATTTG
*
39456393 TGATAATTAAATATTTAAAAATAATTATAATTTAAATTA
1 TGATAATTAAACATTTAAAAATAATTATAATTTAAATTA
39456432 CAATTATAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
43 4 0.11
44 33 0.89
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (43 bp):
TGATAATTAAACATTTAAAAATAATTATAATTTAAATTATTTG
Found at i:39456418 original size:18 final size:17
Alignment explanation
Indices: 39456395--39456428 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
39456385 ATTATTTGTG
39456395 ATAATTAAATATTTAAAA
1 ATAATTAAA-ATTTAAAA
*
39456413 ATAATTATAATTTAAA
1 ATAATTAAAATTTAAA
39456429 TTACAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAATTAAAATTTAAAA
Found at i:39456933 original size:2 final size:2
Alignment explanation
Indices: 39456926--39456962 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
39456916 GCTAACCTAT
39456926 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39456963 CAACAATTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39458231 original size:22 final size:22
Alignment explanation
Indices: 39458203--39458247 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
39458193 TACCAATGTG
39458203 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
39458225 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
39458247 T
1 T
39458248 TTTTTATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:39462830 original size:22 final size:22
Alignment explanation
Indices: 39462802--39462846 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
39462792 AGGGGGAGTG
39462802 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
39462824 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
39462846 T
1 T
39462847 TTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:39470472 original size:21 final size:21
Alignment explanation
Indices: 39470446--39470491 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
39470436 ATTTTAAACC
39470446 TAAATATTAAATCCTAAACAA
1 TAAATATTAAATCCTAAACAA
39470467 TAAATATTAAATCCTAAACAA
1 TAAATATTAAATCCTAAACAA
39470488 TAAA
1 TAAA
39470492 CCTTAAACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.59, C:0.13, G:0.00, T:0.28
Consensus pattern (21 bp):
TAAATATTAAATCCTAAACAA
Found at i:39470505 original size:21 final size:21
Alignment explanation
Indices: 39470446--39470498 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
39470436 ATTTTAAACC
*
39470446 TAAATATTAAATCCTAAACAA
1 TAAACATTAAATCCTAAACAA
*
39470467 TAAATATTAAATCCTAAACAA
1 TAAACATTAAATCCTAAACAA
*
39470488 TAAACCTTAAA
1 TAAACATTAAA
39470499 CCTTAAATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
TAAACATTAAATCCTAAACAA
Found at i:39471655 original size:20 final size:20
Alignment explanation
Indices: 39471630--39471669 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
39471620 TATCACTCCT
39471630 CAACCCTTCAACAAGTTTCA
1 CAACCCTTCAACAAGTTTCA
39471650 CAACCCTTCAACAAGTTTCA
1 CAACCCTTCAACAAGTTTCA
39471670 GGAGGATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.35, G:0.05, T:0.25
Consensus pattern (20 bp):
CAACCCTTCAACAAGTTTCA
Found at i:39475762 original size:6 final size:6
Alignment explanation
Indices: 39475743--39475779 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
39475733 GGACACAATA
*
39475743 AAGG-G AAGGAG AAGGGG AAGGAG AAGGAG AAGGAG AA
1 AAGGAG AAGGAG AAGGAG AAGGAG AAGGAG AAGGAG AA
39475780 AGCGTTTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 4 0.14
6 25 0.86
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (6 bp):
AAGGAG
Found at i:39478372 original size:2 final size:2
Alignment explanation
Indices: 39478365--39478391 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39478355 TTGAGAAACT
39478365 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
39478392 GTATGTATGC
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:39479888 original size:32 final size:32
Alignment explanation
Indices: 39479822--39479889 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 32
39479812 TTTTTGTTAA
* * *
39479822 TGTTGGATTCTGAAATTTTAGTTTATTATGTT
1 TGTTGGATTCTAAAATTTTAGTCTATGATGTT
39479854 TGTTGGATTCTAAAATTATTATGTCT-TGAT-TT
1 TGTTGGATTCTAAAATT-TTA-GTCTATGATGTT
39479886 TGTT
1 TGTT
39479890 AGATATTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
32 22 0.71
33 6 0.19
34 3 0.10
ACGTcount: A:0.22, C:0.04, G:0.18, T:0.56
Consensus pattern (32 bp):
TGTTGGATTCTAAAATTTTAGTCTATGATGTT
Found at i:39479915 original size:27 final size:27
Alignment explanation
Indices: 39479885--39479957 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 27
39479875 TGTCTTGATT
39479885 TTGTTAGATATTGATTATGTTTCAAGC
1 TTGTTAGATATTGATTATGTTTCAAGC
*
39479912 TTGTTAGATATTGAATTTATTATGTTTTAAGC
1 TTGTTAGATATTG-----ATTATGTTTCAAGC
*
39479944 TTGTTGGATATTGA
1 TTGTTAGATATTGA
39479958 AATGATTGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
27 14 0.36
32 25 0.64
ACGTcount: A:0.26, C:0.04, G:0.19, T:0.51
Consensus pattern (27 bp):
TTGTTAGATATTGATTATGTTTCAAGC
Found at i:39479937 original size:32 final size:32
Alignment explanation
Indices: 39479898--39479958 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
39479888 TTAGATATTG
39479898 ATTATGTTTCAAGCTTGTTAGATATTGAATTT
1 ATTATGTTTCAAGCTTGTTAGATATTGAATTT
* *
39479930 ATTATGTTTTAAGCTTGTTGGATATTGAA
1 ATTATGTTTCAAGCTTGTTAGATATTGAA
39479959 ATGATTGACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.28, C:0.05, G:0.18, T:0.49
Consensus pattern (32 bp):
ATTATGTTTCAAGCTTGTTAGATATTGAATTT
Found at i:39480971 original size:22 final size:22
Alignment explanation
Indices: 39480940--39480988 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
39480930 GGACAATGTT
39480940 GTTATAATGTGCTGTAATATTA
1 GTTATAATGTGCTGTAATATTA
* *
39480962 GTTATCATGTGGTGTAATATTA
1 GTTATAATGTGCTGTAATATTA
39480984 GTTAT
1 GTTAT
39480989 GCACTTGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.04, G:0.20, T:0.47
Consensus pattern (22 bp):
GTTATAATGTGCTGTAATATTA
Found at i:39481001 original size:22 final size:22
Alignment explanation
Indices: 39480911--39481001 Score: 59
Period size: 22 Copynumber: 4.2 Consensus size: 22
39480901 TAATGTGGTG
39480911 TAATATTAGTTATGCACT-TGGA
1 TAATATTAGTTAT-CACTGTGGA
* * *
39480933 CAATGTT-GTTAT-AATGTGCTG-
1 TAATATTAGTTATCACTGTG--GA
*
39480954 TAATATTAGTTATCA-TGTGGTG
1 TAATATTAGTTATCACTGTGG-A
39480976 TAATATTAGTTATGCACT-TGGA
1 TAATATTAGTTAT-CACTGTGGA
39480998 TAAT
1 TAAT
39481002 GTTGTTGTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 18
0.69 0.08 0.23
Matches are distributed among these distances:
19 2 0.04
20 3 0.06
21 10 0.19
22 32 0.59
23 6 0.11
24 1 0.02
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.43
Consensus pattern (22 bp):
TAATATTAGTTATCACTGTGGA
Found at i:39481363 original size:16 final size:16
Alignment explanation
Indices: 39481331--39481363 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
39481321 AACAAAGAAA
39481331 AAATAATAAATTCTTT
1 AAATAATAAATTCTTT
39481347 AAATATATAAATT-TTT
1 AAATA-ATAAATTCTTT
39481363 A
1 A
39481364 TTATAAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATAATAAATTCTTT
Found at i:39481487 original size:15 final size:14
Alignment explanation
Indices: 39481466--39481520 Score: 83
Period size: 14 Copynumber: 3.9 Consensus size: 14
39481456 ATAATTTTTT
39481466 AGAAATTATTTTCC
1 AGAAATTATTTTCC
39481480 AGGAAATTATTTTCC
1 A-GAAATTATTTTCC
*
39481495 AGAAATTATTTTTC
1 AGAAATTATTTTCC
*
39481509 AGAAAATATTTT
1 AGAAATTATTTT
39481521 ACCTGCAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
14 24 0.63
15 14 0.37
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (14 bp):
AGAAATTATTTTCC
Found at i:39481498 original size:29 final size:28
Alignment explanation
Indices: 39481466--39481520 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
39481456 ATAATTTTTT
*
39481466 AGAAATTATTTTCCAGGAAATTATTTTCC
1 AGAAATTATTTTCCA-GAAAATATTTTCC
*
39481495 AGAAATTATTTTTCAGAAAATATTTT
1 AGAAATTATTTTCCAGAAAATATTTT
39481521 ACCTGCAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (28 bp):
AGAAATTATTTTCCAGAAAATATTTTCC
Found at i:39482381 original size:16 final size:16
Alignment explanation
Indices: 39482342--39482372 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39482332 GACTCGTCTC
39482342 AAATATATTATATTAT
1 AAATATATTATATTAT
*
39482358 AAAAATATTATATTA
1 AAATATATTATATTA
39482373 ATTATATATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATATATTATATTAT
Found at i:39483381 original size:17 final size:19
Alignment explanation
Indices: 39483359--39483395 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
39483349 ATTATTATCC
39483359 TAACTTT-TTTAAA-ATTT
1 TAACTTTCTTTAAATATTT
39483376 TAACTTTCTTTAAATATTT
1 TAACTTTCTTTAAATATTT
39483395 T
1 T
39483396 TTGAAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 6 0.33
19 5 0.28
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.59
Consensus pattern (19 bp):
TAACTTTCTTTAAATATTT
Found at i:39483410 original size:13 final size:13
Alignment explanation
Indices: 39483392--39483419 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
39483382 TCTTTAAATA
39483392 TTTTTTGAAATTT
1 TTTTTTGAAATTT
39483405 TTTTTTGAAATTT
1 TTTTTTGAAATTT
39483418 TT
1 TT
39483420 ATAAATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.71
Consensus pattern (13 bp):
TTTTTTGAAATTT
Found at i:39483437 original size:19 final size:19
Alignment explanation
Indices: 39483407--39483468 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
39483397 TGAAATTTTT
39483407 TTTTGAAATTTTTATAAATA
1 TTTTG-AATTTTTATAAATA
39483427 TTTTGAA-TTTTA-AAATTTA
1 TTTTGAATTTTTATAAA--TA
* *
39483446 TTTTGATTTTTTTTAAAT-
1 TTTTGAATTTTTATAAATA
39483464 TTTTG
1 TTTTG
39483469 TTGAGAAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 11 0.31
20 9 0.25
21 3 0.08
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (19 bp):
TTTTGAATTTTTATAAATA
Found at i:39483619 original size:23 final size:22
Alignment explanation
Indices: 39483581--39483623 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
39483571 ATTCAACTCG
39483581 ACTCGAATTCGAAACTCAAATA
1 ACTCGAATTCGAAACTCAAATA
39483603 ACTC-AATTCGATTAACTCAAA
1 ACTCGAATTCGA--AACTCAAA
39483624 ATTCGAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 4 0.21
23 8 0.42
ACGTcount: A:0.44, C:0.23, G:0.07, T:0.26
Consensus pattern (22 bp):
ACTCGAATTCGAAACTCAAATA
Found at i:39491587 original size:21 final size:21
Alignment explanation
Indices: 39491548--39491588 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
39491538 CTTATTTATA
* *
39491548 TTTTAATTAATCATGATTTAG
1 TTTTAATCAATCATAATTTAG
*
39491569 TTTTAATCAATCTTAATTTA
1 TTTTAATCAATCATAATTTA
39491589 CTTAATTAAG
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:0.34, C:0.07, G:0.05, T:0.54
Consensus pattern (21 bp):
TTTTAATCAATCATAATTTAG
Found at i:39492395 original size:46 final size:46
Alignment explanation
Indices: 39492327--39492521 Score: 318
Period size: 46 Copynumber: 4.2 Consensus size: 46
39492317 AGCCCCAAAC
* *
39492327 ACACATTTTATATCTTGTTGCCATGGTATCTTTCAACCATGGTCTT
1 ACACATTTCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTT
* *
39492373 GCACATTTCATGTCATGTTGCCATGGTATCTTTCAACCATGGTCTT
1 ACACATTTCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTT
* *
39492419 GCACATTTCATATCATGTTGCCATGGCATCTTTCAACCATGGTCTT
1 ACACATTTCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTT
* *
39492465 ACACATTTCATATCATGTTGCCATTGTGTCTTTCAACCATGGTCTT
1 ACACATTTCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTT
39492511 ACACATTTCAT
1 ACACATTTCAT
39492522 TTCAAAAAGC
Statistics
Matches: 139, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 139 1.00
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.40
Consensus pattern (46 bp):
ACACATTTCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTT
Found at i:39492427 original size:21 final size:21
Alignment explanation
Indices: 39492403--39492474 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 21
39492393 CCATGGTATC
39492403 TTTCAACCATGGTCTTGCACA
1 TTTCAACCATGGTCTTGCACA
* * *
39492424 TTTCATATCATGTTGCCATGGCATC-
1 TTTCA-ACCATG--GTC-TTGCA-CA
*
39492449 TTTCAACCATGGTCTTACACA
1 TTTCAACCATGGTCTTGCACA
39492470 TTTCA
1 TTTCA
39492475 TATCATGTTG
Statistics
Matches: 38, Mismatches: 7, Indels: 12
0.67 0.12 0.21
Matches are distributed among these distances:
20 1 0.03
21 13 0.34
22 7 0.18
24 7 0.18
25 9 0.24
26 1 0.03
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.38
Consensus pattern (21 bp):
TTTCAACCATGGTCTTGCACA
Found at i:39492452 original size:25 final size:25
Alignment explanation
Indices: 39492378--39492453 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
39492368 GTCTTGCACA
* *
39492378 TTTCATGTCATGTTGCCATGGTATC
1 TTTCATATCATGTTGCCATGGCATC
* * *
39492403 TTTCA-ACCATG--GTC-TTGCA-C
1 TTTCATATCATGTTGCCATGGCATC
39492423 ATTTCATATCATGTTGCCATGGCATC
1 -TTTCATATCATGTTGCCATGGCATC
39492449 TTTCA
1 TTTCA
39492454 ACCATGGTCT
Statistics
Matches: 37, Mismatches: 8, Indels: 12
0.65 0.14 0.21
Matches are distributed among these distances:
20 1 0.03
21 8 0.22
22 7 0.19
24 6 0.16
25 14 0.38
26 1 0.03
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.41
Consensus pattern (25 bp):
TTTCATATCATGTTGCCATGGCATC
Found at i:39496396 original size:40 final size:40
Alignment explanation
Indices: 39496288--39496497 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
39496278 CGGGATTTAA
* * * * *
39496288 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
39496328 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
39496368 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
39496408 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
39496448 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
39496488 CCGGATATAT
1 CCGGATATAT
39496498 TTCAATGTTC
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 152 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:39498949 original size:101 final size:101
Alignment explanation
Indices: 39498814--39499016 Score: 318
Period size: 101 Copynumber: 2.0 Consensus size: 101
39498804 CACAGCTCTG
* *
39498814 CCATGGTCTTACGTTCATAGTGCCATAACTCAGTTATGGTCTTATCATCAGAATG-TCATAGCCC
1 CCATGGTCATACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCT-ATAGCCC
39498878 AGCTATAGTCTTACATATAAACACTATCATGGACCAA
65 AGCTATAGTCTTACATATAAACACTATCATGGACCAA
*
39498915 CCATGGTCATACGTTCATAGTGCCATAACCCAGTTATGGTTTTATCATCAGAATGCTATAGCCCA
1 CCATGGTCATACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCTATAGCCCA
* * * * *
39498980 GCTATGGTCTTACATATATACATTGTCATGGTCCAA
66 GCTATAGTCTTACATATAAACACTATCATGGACCAA
39499016 C
1 C
39499017 TGTGGTTTTA
Statistics
Matches: 93, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 92 0.99
102 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.32
Consensus pattern (101 bp):
CCATGGTCATACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCTATAGCCCA
GCTATAGTCTTACATATAAACACTATCATGGACCAA
Found at i:39502089 original size:50 final size:49
Alignment explanation
Indices: 39502014--39502176 Score: 236
Period size: 50 Copynumber: 3.2 Consensus size: 49
39502004 CCATGGCAAC
* *
39502014 AAGTGATAAGTGATAGTTTCGGCTACATTTATCTAATCAAGAACAAGTGA
1 AAGTGATAAGTGATAGTTTCGGCTACACTTATCTGATCAAG-ACAAGTGA
39502064 AAGTGATAAGTGATAGTTTCGGCTACACTTATCTGATCAAGGACAAGTGA
1 AAGTGATAAGTGATAGTTTCGGCTACACTTATCTGATCAA-GACAAGTGA
* * *
39502114 AAGTGATAAGTGATAGCTTCGGTTACACTTATCTGATCAATGACAAATGA
1 AAGTGATAAGTGATAGTTTCGGCTACACTTATCTGATCAA-GACAAGTGA
*
39502164 CAAGTGAAAAGTG
1 -AAGTGATAAGTG
39502177 GTAACTTCAG
Statistics
Matches: 104, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
50 92 0.88
51 12 0.12
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (49 bp):
AAGTGATAAGTGATAGTTTCGGCTACACTTATCTGATCAAGACAAGTGA
Found at i:39502279 original size:31 final size:31
Alignment explanation
Indices: 39502166--39502277 Score: 118
Period size: 31 Copynumber: 3.6 Consensus size: 31
39502156 ACAAATGACA
* *
39502166 AGTGAAAAGTGGTAACTTCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCAGCTGCCTGATC
* *
39502197 -GATGAAAAGTGGTAGCTTCAGCAGCCTAATC
1 AG-TGAAAAGTGGTAGCTTCAGCTGCCTGATC
* ** * *
39502228 AGTGAAAAATGACAGCTTCGGTTGCCTGATC
1 AGTGAAAAGTGGTAGCTTCAGCTGCCTGATC
*
39502259 AGTGAATAGTGGTAGCTTC
1 AGTGAAAAGTGGTAGCTTC
39502278 GGCTACAAGT
Statistics
Matches: 64, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
30 1 0.02
31 62 0.97
32 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCAGCTGCCTGATC
Found at i:39505209 original size:16 final size:15
Alignment explanation
Indices: 39505184--39505214 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
39505174 ACCCAAATTT
39505184 AAAAAAAAAAAAAGA
1 AAAAAAAAAAAAAGA
39505199 AAAAGAAAAAAAAAGA
1 AAAA-AAAAAAAAAGA
39505215 TGGATTCACC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAGA
Found at i:39509737 original size:23 final size:23
Alignment explanation
Indices: 39509706--39509750 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
39509696 AGTTGTCCAA
* *
39509706 TTTTTCTTTTCTATTCTTCTTTC
1 TTTTCCTTTTCTAATCTTCTTTC
39509729 TTTTCCTTTTCTAATCTTCTTT
1 TTTTCCTTTTCTAATCTTCTTT
39509751 TTTCTTCTTC
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:0.07, C:0.22, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTTCCTTTTCTAATCTTCTTTC
Found at i:39515181 original size:5 final size:5
Alignment explanation
Indices: 39515171--39515198 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
39515161 AATAATTAAG
39515171 TATAT TATAT TATAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TAT
39515199 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:39537122 original size:2 final size:2
Alignment explanation
Indices: 39537115--39537153 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
39537105 TAAAAATTTA
*
39537115 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39537154 AATTCTAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39537493 original size:2 final size:2
Alignment explanation
Indices: 39537486--39537521 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
39537476 GATTTTGTAA
39537486 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
39537522 TGTTTATTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39545535 original size:13 final size:13
Alignment explanation
Indices: 39545517--39545545 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
39545507 GGGTATGGTG
39545517 GAATGATGTTTTA
1 GAATGATGTTTTA
39545530 GAATGATGTTTTA
1 GAATGATGTTTTA
39545543 GAA
1 GAA
39545546 AATGGCTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.24, T:0.41
Consensus pattern (13 bp):
GAATGATGTTTTA
Found at i:39547925 original size:31 final size:31
Alignment explanation
Indices: 39547890--39547948 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
39547880 ATGGTAGTTT
39547890 TCACCAGCAAAAACGGTGGTGGTGAAAACTC
1 TCACCAGCAAAAACGGTGGTGGTGAAAACTC
39547921 TCACCAGCAAAAACGGTGGTGGTGAAAA
1 TCACCAGCAAAAACGGTGGTGGTGAAAA
39547949 ACTCATGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.37, C:0.20, G:0.27, T:0.15
Consensus pattern (31 bp):
TCACCAGCAAAAACGGTGGTGGTGAAAACTC
Found at i:39549372 original size:49 final size:48
Alignment explanation
Indices: 39549276--39549614 Score: 214
Period size: 49 Copynumber: 7.0 Consensus size: 48
39549266 ATCTTTCATG
* * * * ** *
39549276 AAAATAATAACCTTGCTCCCAAATGCATAGGGGAAGAATTACAGAAGGT
1 AAAATAATAACCCTGCTCCCAGACGCAT-GGGGGAGGCTTACGGAAGGT
** * * *
39549325 AAAATAATAACATTGCTCTCAGATGCATGTGGGGAGGCTTATGGAAGGT
1 AAAATAATAACCCTGCTCCCAGACGCATG-GGGGAGGCTTACGGAAGGT
* * * * * * * * *
39549374 AGAATGATAACCCTACTCTCAGATGTATGGGGGAAGCTTGCGAAAGGT
1 AAAATAATAACCCTGCTCCCAGACGCATGGGGGAGGCTTACGGAAGGT
* * * * * * *
39549422 AAAATAATAACCTTGTTCCCAAACGTATGAGAGGAGACTTACGAAAGGT
1 AAAATAATAACCCTGCTCCCAGACGCATG-GGGGAGGCTTACGGAAGGT
*** *
39549471 AGTAAATAATAACCCTGCTTTTAGACGCATGGGGGAGGCTTATGGAAGGT
1 A--AAATAATAACCCTGCTCCCAGACGCATGGGGGAGGCTTACGGAAGGT
* * * * * * * *
39549521 AGAGTAATAACCTTGCTCCCATACACATGAAGGGAGACTTATGGAAGGT
1 AAAATAATAACCCTGCTCCCAGACGCATG-GGGGAGGCTTACGGAAGGT
* * * *
39549570 ATAA-AATAACCCTACTCCCAAATGCAT-GGGGAGGCTTACGGAAGG
1 AAAATAATAACCCTGCTCCCAGACGCATGGGGGAGGCTTACGGAAGG
39549615 CTCAATGTCT
Statistics
Matches: 224, Mismatches: 61, Indels: 13
0.75 0.20 0.04
Matches are distributed among these distances:
46 15 0.07
48 75 0.33
49 97 0.43
50 16 0.07
51 21 0.09
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (48 bp):
AAAATAATAACCCTGCTCCCAGACGCATGGGGGAGGCTTACGGAAGGT
Found at i:39549945 original size:36 final size:36
Alignment explanation
Indices: 39549905--39549978 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
39549895 GCAATTGATT
*
39549905 TGAGATAGTTTGCGTTGCTTTAGTAATGTAATGTGA
1 TGAGATAGTTTGCATTGCTTTAGTAATGTAATGTGA
39549941 TGAGATAGTTTGCATTGCTTTAGTAATGTAATGTGA
1 TGAGATAGTTTGCATTGCTTTAGTAATGTAATGTGA
39549977 TG
1 TG
39549979 TCATGCATGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.26, C:0.05, G:0.27, T:0.42
Consensus pattern (36 bp):
TGAGATAGTTTGCATTGCTTTAGTAATGTAATGTGA
Found at i:39550624 original size:30 final size:29
Alignment explanation
Indices: 39550572--39550629 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
39550562 TTTTTTTTAT
39550572 TTTCTCCTAAATTTTCACTCCC-TCCCAC
1 TTTCTCCTAAATTTTCACTCCCTTCCCAC
39550600 TTTCTCCCTAAAACTTTT-ACTCCCTTCCCA
1 TTTCT-CCT-AAA-TTTTCACTCCCTTCCCA
39550630 TCCCACCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
28 5 0.19
29 3 0.12
30 9 0.35
31 9 0.35
ACGTcount: A:0.19, C:0.41, G:0.00, T:0.40
Consensus pattern (29 bp):
TTTCTCCTAAATTTTCACTCCCTTCCCAC
Found at i:39551034 original size:86 final size:86
Alignment explanation
Indices: 39550944--39551117 Score: 321
Period size: 86 Copynumber: 2.0 Consensus size: 86
39550934 ATTAAAATTG
* *
39550944 AATTATTAATTATGCCATAAAATATTCGTGTTAAAATTTTATATTGGTATCAATTTCACATTTTA
1 AATTATCAATTATGCCATAAAATATTCGTGTTAAAATTTTATATTGGTATAAATTTCACATTTTA
39551009 TCTTTAAAATAACTTTTATTA
66 TCTTTAAAATAACTTTTATTA
*
39551030 AATTATCAATTATGTCATAAAATATTCGTGTTAAAATTTTATATTGGTATAAATTTCACATTTTA
1 AATTATCAATTATGCCATAAAATATTCGTGTTAAAATTTTATATTGGTATAAATTTCACATTTTA
39551095 TCTTTAAAATAACTTTTATTA
66 TCTTTAAAATAACTTTTATTA
39551116 AA
1 AA
39551118 AAATCACATT
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
86 85 1.00
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.47
Consensus pattern (86 bp):
AATTATCAATTATGCCATAAAATATTCGTGTTAAAATTTTATATTGGTATAAATTTCACATTTTA
TCTTTAAAATAACTTTTATTA
Found at i:39551380 original size:10 final size:10
Alignment explanation
Indices: 39551361--39551391 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
39551351 GAACAAATAT
39551361 ATTCGTTTCG
1 ATTCGTTTCG
*
39551371 ATTCGATTCG
1 ATTCGTTTCG
39551381 ATTCGTTTCG
1 ATTCGTTTCG
39551391 A
1 A
39551392 ATTCCATCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.16, C:0.19, G:0.19, T:0.45
Consensus pattern (10 bp):
ATTCGTTTCG
Found at i:39553753 original size:17 final size:17
Alignment explanation
Indices: 39553721--39553774 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
39553711 TATGTGTTAT
39553721 AAATTATATAAATATAAA
1 AAATTATAT-AATATAAA
*
39553739 AAATAATATAATATAAA
1 AAATTATATAATATAAA
* *
39553756 ATATTATA-AATTTAAA
1 AAATTATATAATATAAA
39553772 AAA
1 AAA
39553775 AAATCTAGAC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 9 0.29
17 14 0.45
18 8 0.26
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATTATATAATATAAA
Found at i:39554306 original size:3 final size:3
Alignment explanation
Indices: 39554298--39554324 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
39554288 ACTAGTTAAA
39554298 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
39554325 TTAAGAGAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:39556308 original size:70 final size:69
Alignment explanation
Indices: 39556195--39556334 Score: 253
Period size: 70 Copynumber: 2.0 Consensus size: 69
39556185 TTTTTAAATA
*
39556195 TATAATTACTGTTTAATAGCTAGTTTTTATTTAAATTTAATTTAAAATATATAAACATAATAATA
1 TATAATTACTGTTTAATAGCTAGTTTTTATTTAAAATTAATTT-AAATATATAAACATAATAATA
39556260 ATTAT
65 ATTAT
*
39556265 TATAATTACTGTTTAATAGTTAGTTTTTATTTAAAATTAATTTAAATATATAAACATAATAATAA
1 TATAATTACTGTTTAATAGCTAGTTTTTATTTAAAATTAATTTAAATATATAAACATAATAATAA
39556330 TTAT
66 TTAT
39556334 T
1 T
39556335 TTTTATTAGG
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
69 27 0.40
70 41 0.60
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (69 bp):
TATAATTACTGTTTAATAGCTAGTTTTTATTTAAAATTAATTTAAATATATAAACATAATAATAA
TTAT
Found at i:39557580 original size:31 final size:31
Alignment explanation
Indices: 39557533--39557593 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
39557523 AAAAATCAAC
* *
39557533 TCTTTTTGAAAGGTTGATG-GTCAAATTTAAT
1 TCTTTTTAAAAGGTTGA-GCGCCAAATTTAAT
*
39557564 TCTTTTTAAAATGTTGAGCGCCAAATTTAA
1 TCTTTTTAAAAGGTTGAGCGCCAAATTTAA
39557594 CTCAAAAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 1 0.04
31 25 0.96
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (31 bp):
TCTTTTTAAAAGGTTGAGCGCCAAATTTAAT
Found at i:39559003 original size:14 final size:16
Alignment explanation
Indices: 39558969--39559005 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
39558959 TTTGTAATAT
*
39558969 AAATTTAGCACTTATA
1 AAATTTAGCACGTATA
39558985 AAATTTAGCA-GTA-A
1 AAATTTAGCACGTATA
39558999 AAATTTA
1 AAATTTA
39559006 TTATTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 8 0.40
15 2 0.10
16 10 0.50
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (16 bp):
AAATTTAGCACGTATA
Found at i:39560029 original size:2 final size:2
Alignment explanation
Indices: 39560022--39560054 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
39560012 TAAATATCAC
39560022 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39560055 CCACTTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39561685 original size:29 final size:30
Alignment explanation
Indices: 39561653--39561711 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
39561643 TTTAGTCTAA
*
39561653 TGTGTAATTTTATACATG-AACTTTGATTT
1 TGTGCAATTTTATACATGAAACTTTGATTT
* *
39561682 TGTGCAATTTTATATATGAAATTTTGATTT
1 TGTGCAATTTTATACATGAAACTTTGATTT
39561712 GATCTAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.53
Consensus pattern (30 bp):
TGTGCAATTTTATACATGAAACTTTGATTT
Found at i:39563989 original size:36 final size:36
Alignment explanation
Indices: 39563853--39564017 Score: 110
Period size: 36 Copynumber: 4.8 Consensus size: 36
39563843 AATGAGAGTT
* * * * * *
39563853 CTCTAATTCCCTATTAGGTCGAGAACACATTATTAT
1 CTCTAATTCCCTATTGGGTCAAGAATACAATGTTAC
* *
39563889 CTCTAATTCCCTATTAGGTTAAGAAT---A-GTT--
1 CTCTAATTCCCTATTGGGTCAAGAATACAATGTTAC
*** * * *
39563919 CTCTAACAACCTACTGGGTCGAGAA-AAAAGTGTTAC
1 CTCTAATTCCCTATTGGGTCAAGAATACAA-TGTTAC
* * *
39563955 CTTTAATTCCCTATTGGGTCAATAATACAATGTTAT
1 CTCTAATTCCCTATTGGGTCAAGAATACAATGTTAC
*
39563991 CTCTAATTCCCTTTTGGGTCAAGAATA
1 CTCTAATTCCCTATTGGGTCAAGAATA
39564018 TATCATTAGC
Statistics
Matches: 97, Mismatches: 24, Indels: 16
0.71 0.18 0.12
Matches are distributed among these distances:
30 18 0.19
32 3 0.03
34 3 0.03
36 70 0.72
37 3 0.03
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (36 bp):
CTCTAATTCCCTATTGGGTCAAGAATACAATGTTAC
Found at i:39566719 original size:41 final size:41
Alignment explanation
Indices: 39566626--39566742 Score: 155
Period size: 41 Copynumber: 2.9 Consensus size: 41
39566616 TGAGTTACCA
* * * *
39566626 TAGTGAATCAGGAACAAGTCCTATCCACTTT-ATATATTTC
1 TAGTGAATCAGGAATAAATCCTATTCACTTTAATTTATTTC
* * *
39566666 TAGTGAATCAGGAATAAATCCTATTCGCTTTAATTTCTTTT
1 TAGTGAATCAGGAATAAATCCTATTCACTTTAATTTATTTC
39566707 TAGTGAATCAGGAATAAATCCTATTCACTTTTAATT
1 TAGTGAATCAGGAATAAATCCTATTCAC-TTTAATT
39566743 CTCGAGAATG
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
40 27 0.40
41 33 0.49
42 7 0.10
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.39
Consensus pattern (41 bp):
TAGTGAATCAGGAATAAATCCTATTCACTTTAATTTATTTC
Found at i:39567622 original size:16 final size:18
Alignment explanation
Indices: 39567596--39567634 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
39567586 TAAACCCCAA
39567596 TTTCTCCTTTTT-CTTTC
1 TTTCTCCTTTTTCCTTTC
39567613 TTTC-CCTTTTTCCTTTC
1 TTTCTCCTTTTTCCTTTC
39567630 TTTCT
1 TTTCT
39567635 TTCTCCCCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTCTCCTTTTTCCTTTC
Found at i:39567868 original size:8 final size:8
Alignment explanation
Indices: 39567855--39567885 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
39567845 TTTAATTAAT
39567855 ATAATATA
1 ATAATATA
39567863 ATAATATA
1 ATAATATA
39567871 ATAATATA
1 ATAATATA
39567879 ATAATAT
1 ATAATAT
39567886 TTACTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
ATAATATA
Found at i:39570220 original size:26 final size:26
Alignment explanation
Indices: 39570191--39570299 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
39570181 TGATACAAAT
39570191 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
39570217 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
39570243 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
39570269 TGATAATGGTTTAGGTAAATGTT-CA
1 TGATAATGGGTTAGGTAAATGTTCCA
39570294 TGATAA
1 TGATAA
39570300 GAAATTCATG
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
25 8 0.10
26 69 0.90
ACGTcount: A:0.34, C:0.06, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:39572333 original size:134 final size:135
Alignment explanation
Indices: 39572072--39572339 Score: 504
Period size: 134 Copynumber: 2.0 Consensus size: 135
39572062 AGTCTCCCCA
39572072 AATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACTGTT
1 AATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACTGTT
39572137 ATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCCTGGCCCAGTACCACTGT
66 ATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCCTGGCCCAGTACCACTGT
39572202 TACCC
131 TACCC
*
39572207 AATGGGCTTGCATATG-TTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACTGTT
1 AATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACTGTT
39572271 ATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCT-GCCCAGTACCACTG
66 ATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGC-CTGGCCCAGTACCACTG
39572335 TTACC
130 TTACC
39572340 TGAATGTGCT
Statistics
Matches: 131, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
134 113 0.86
135 18 0.14
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (135 bp):
AATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACTGTT
ATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCCTGGCCCAGTACCACTGT
TACCC
Found at i:39576303 original size:13 final size:14
Alignment explanation
Indices: 39576287--39576316 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
39576277 AATTATTTAA
39576287 AATAATAATA-TAT
1 AATAATAATATTAT
39576300 AATAATAATATTAT
1 AATAATAATATTAT
39576314 AAT
1 AAT
39576317 TACTGTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATAATAATATTAT
Found at i:39577601 original size:31 final size:31
Alignment explanation
Indices: 39577554--39577614 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
39577544 AAAAATCAAC
* *
39577554 TCTTTTTGAAAGGTTGATG-GTCAAATTTAAT
1 TCTTTTTAAAAGGTTGA-GCGCCAAATTTAAT
*
39577585 TCTTTTTAAAATGTTGAGCGCCAAATTTAA
1 TCTTTTTAAAAGGTTGAGCGCCAAATTTAA
39577615 CTCAAAAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 1 0.04
31 25 0.96
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (31 bp):
TCTTTTTAAAAGGTTGAGCGCCAAATTTAAT
Found at i:39579020 original size:14 final size:16
Alignment explanation
Indices: 39578986--39579022 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
39578976 TTTGTAATAT
*
39578986 AAATTTAGCACTTATA
1 AAATTTAGCACGTATA
39579002 AAATTTAGCA-GTA-A
1 AAATTTAGCACGTATA
39579016 AAATTTA
1 AAATTTA
39579023 TTATTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 8 0.40
15 2 0.10
16 10 0.50
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (16 bp):
AAATTTAGCACGTATA
Found at i:39580043 original size:2 final size:2
Alignment explanation
Indices: 39580031--39580070 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
39580021 TTGTGAGTAA
39580031 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39580071 CCACTTTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:39581701 original size:29 final size:30
Alignment explanation
Indices: 39581669--39581727 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
39581659 TTTAGTCTAA
*
39581669 TGTGTAATTTTATACATG-AACTTTGATTT
1 TGTGCAATTTTATACATGAAACTTTGATTT
* *
39581698 TGTGCAATTTTATATATGAAATTTTGATTT
1 TGTGCAATTTTATACATGAAACTTTGATTT
39581728 GATCTAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.53
Consensus pattern (30 bp):
TGTGCAATTTTATACATGAAACTTTGATTT
Found at i:39584005 original size:36 final size:36
Alignment explanation
Indices: 39583869--39584033 Score: 110
Period size: 36 Copynumber: 4.8 Consensus size: 36
39583859 AATGAGAGTT
* * * * * *
39583869 CTCTAATTCCCTATTAGGTCGAGAACACATTATTAT
1 CTCTAATTCCCTATTGGGTCAAGAATACAATGTTAC
* *
39583905 CTCTAATTCCCTATTAGGTTAAGAAT---A-GTT--
1 CTCTAATTCCCTATTGGGTCAAGAATACAATGTTAC
*** * * *
39583935 CTCTAACAACCTACTGGGTCGAGAA-AAAAGTGTTAC
1 CTCTAATTCCCTATTGGGTCAAGAATACAA-TGTTAC
* * *
39583971 CTTTAATTCCCTATTGGGTCAATAATACAATGTTAT
1 CTCTAATTCCCTATTGGGTCAAGAATACAATGTTAC
*
39584007 CTCTAATTCCCTTTTGGGTCAAGAATA
1 CTCTAATTCCCTATTGGGTCAAGAATA
39584034 TATCATTAGC
Statistics
Matches: 97, Mismatches: 24, Indels: 16
0.71 0.18 0.12
Matches are distributed among these distances:
30 18 0.19
32 3 0.03
34 3 0.03
36 70 0.72
37 3 0.03
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (36 bp):
CTCTAATTCCCTATTGGGTCAAGAATACAATGTTAC
Found at i:39586686 original size:40 final size:40
Alignment explanation
Indices: 39586642--39586752 Score: 152
Period size: 40 Copynumber: 2.8 Consensus size: 40
39586632 TGAGTTACCA
* * *
39586642 TAGTGAATCAGGAACAAGTCCTATCCACTTTATATAT-TTC
1 TAGTGAATCAGGAATAAATCCTATTCACTTTA-ATATCTTC
* * *
39586682 TAGTGAATCAGGAATAAATCCTATTCGCTTTAATTTCTTT
1 TAGTGAATCAGGAATAAATCCTATTCACTTTAATATCTTC
39586722 TAGTGAATCAGGAATAAATCCTATTCACTTT
1 TAGTGAATCAGGAATAAATCCTATTCACTTT
39586753 TAATTCTCGA
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
39 3 0.05
40 60 0.95
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (40 bp):
TAGTGAATCAGGAATAAATCCTATTCACTTTAATATCTTC
Found at i:39587639 original size:16 final size:18
Alignment explanation
Indices: 39587613--39587651 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
39587603 TAAACCCCAA
39587613 TTTCTCCTTTTT-CTTTC
1 TTTCTCCTTTTTCCTTTC
39587630 TTTC-CCTTTTTCCTTTC
1 TTTCTCCTTTTTCCTTTC
39587647 TTTCT
1 TTTCT
39587652 TTCTCCCCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTCTCCTTTTTCCTTTC
Found at i:39587885 original size:8 final size:8
Alignment explanation
Indices: 39587872--39587902 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
39587862 TTTAATTAAT
39587872 ATAATATA
1 ATAATATA
39587880 ATAATATA
1 ATAATATA
39587888 ATAATATA
1 ATAATATA
39587896 ATAATAT
1 ATAATAT
39587903 TTACTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
ATAATATA
Found at i:39590238 original size:26 final size:26
Alignment explanation
Indices: 39590209--39590318 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
39590199 TGATACAAAT
39590209 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
39590235 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
39590261 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
39590287 TGATAATGGTTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
39590313 TGATAA
1 TGATAA
39590319 GAAATTCATG
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:39592345 original size:136 final size:137
Alignment explanation
Indices: 39592100--39592374 Score: 525
Period size: 136 Copynumber: 2.0 Consensus size: 137
39592090 GAGTAGTCTC
39592100 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
*
39592165 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTAGCCCAGTACC
39592230 ACTGTTA
131 ACTGTTA
*
39592237 CCCAAATGGGCTTGCATATG-TTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
39592301 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTAGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTAGCCCAGTACC
39592366 ACTGTTA
131 ACTGTTA
39592373 CC
1 CC
39592375 TGAATGTGCT
Statistics
Matches: 136, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
136 116 0.85
137 20 0.15
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.31
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTAGCCCAGTACC
ACTGTTA
Found at i:39595617 original size:13 final size:13
Alignment explanation
Indices: 39595599--39595623 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39595589 ATCTCACTAT
39595599 ATATATATATATA
1 ATATATATATATA
39595612 ATATATATATAT
1 ATATATATATAT
39595624 TAGTTTTATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATATATATATA
Found at i:39595927 original size:9 final size:9
Alignment explanation
Indices: 39595913--39595943 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
39595903 ATAATTTTAT
39595913 AATTTGAAC
1 AATTTGAAC
39595922 AATTTGAAC
1 AATTTGAAC
*
39595931 AATTTGAAT
1 AATTTGAAC
39595940 AATT
1 AATT
39595944 GATTGGTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (9 bp):
AATTTGAAC
Found at i:39601138 original size:16 final size:16
Alignment explanation
Indices: 39601117--39601148 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39601107 TAAAAATAAA
39601117 AATAAAATTTATTATC
1 AATAAAATTTATTATC
*
39601133 AATAAATTTTATTATC
1 AATAAAATTTATTATC
39601149 TATAGATGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (16 bp):
AATAAAATTTATTATC
Found at i:39605098 original size:46 final size:46
Alignment explanation
Indices: 39605031--39605205 Score: 185
Period size: 46 Copynumber: 3.8 Consensus size: 46
39605021 TGTAACCCGC
* *
39605031 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
* * **
39605077 CCATAAGTAAACTCGGACTCAACTCAACGAGCTTGGATGCCTATTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C-ATTCGCAT
* * * * *
39605127 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
*
39605170 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
39605206 ATGCCCAAAT
Statistics
Matches: 104, Mismatches: 18, Indels: 14
0.76 0.13 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 60 0.58
47 24 0.23
48 3 0.03
49 2 0.02
50 5 0.05
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
Found at i:39605151 original size:93 final size:93
Alignment explanation
Indices: 39605038--39605210 Score: 285
Period size: 93 Copynumber: 1.9 Consensus size: 93
39605028 CGCCCATAAG
* * *
39605038 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTAAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTAAACTCGGACTCAACTCA
39605103 ACGAGCTT-GGATGCCTATTTACATCTCA
66 ACGAG-TTCGGATGCCTATTTACATCTCA
* *
39605131 CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTAAACTCGGACTCAACTCA
39605196 ACGAGTTCGGATGCC
66 ACGAGTTCGGATGCC
39605211 CAAATATCCT
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
92 2 0.03
93 72 0.97
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTAAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTATTTACATCTCA
Found at i:39609377 original size:2 final size:2
Alignment explanation
Indices: 39609372--39609397 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39609362 ATATTGTGTG
39609372 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
39609398 AATGTGTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39610851 original size:21 final size:21
Alignment explanation
Indices: 39610800--39610856 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
39610790 TTTTTTGTTA
*
39610800 ACTTAAAACTCATTTTAAAATG
1 ACTTAAAAAT-ATTTTAAAATG
**
39610822 -CTTCTAAATGATTTT-AAATG
1 ACTTAAAAAT-ATTTTAAAATG
39610842 ACTTAAAAATATTTT
1 ACTTAAAAATATTTT
39610857 TAATCAAGAC
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (21 bp):
ACTTAAAAATATTTTAAAATG
Found at i:39614402 original size:19 final size:20
Alignment explanation
Indices: 39614366--39614403 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
39614356 TGGGACACAG
39614366 TCTGGGCTATGTTCACACGA
1 TCTGGGCTATGTTCACACGA
39614386 TCTGGGCTATG-TCACACG
1 TCTGGGCTATGTTCACACG
39614404 GCCTGCCCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.29
Consensus pattern (20 bp):
TCTGGGCTATGTTCACACGA
Found at i:39615036 original size:51 final size:52
Alignment explanation
Indices: 39614961--39615083 Score: 162
Period size: 51 Copynumber: 2.4 Consensus size: 52
39614951 TCCCAAACTT
* * *
39614961 ACTTCATACTTT-ATCCGG-TATTATTACTTTGTTGTTCTGGCCTCAACAAGA
1 ACTTCATA-TTTCATCCGGATATTATTACTTTATTGCTCTAGCCTCAACAAGA
**
39615012 ACTTCATATTTCATCCGGAT-TTATTACTTTATTGCTCTAGTTTCAACAAGA
1 ACTTCATATTTCATCCGGATATTATTACTTTATTGCTCTAGCCTCAACAAGA
*
39615063 GCTTCATATTTCATCCGGATA
1 ACTTCATATTTCATCCGGATA
39615084 ACTTAGTTCT
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
50 3 0.05
51 59 0.94
52 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.41
Consensus pattern (52 bp):
ACTTCATATTTCATCCGGATATTATTACTTTATTGCTCTAGCCTCAACAAGA
Found at i:39617706 original size:22 final size:22
Alignment explanation
Indices: 39617680--39617722 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
39617670 TATATCTTTA
39617680 AATAAAAATAAAAAAATTAAAG
1 AATAAAAATAAAAAAATTAAAG
**
39617702 AATAAAAATAAATCAATTAAA
1 AATAAAAATAAAAAAATTAAA
39617723 TAATTTTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (22 bp):
AATAAAAATAAAAAAATTAAAG
Found at i:39618472 original size:30 final size:30
Alignment explanation
Indices: 39618436--39618504 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
39618426 AAAACAGAAT
* *
39618436 AGAGCAGAACAAAACCAAATGGTA-TAGAGC
1 AGAGCAGAACAAAACAAAATGG-AGCAGAGC
*
39618466 AGAGCAGAACAGAACAAAATGGAGCAGAGC
1 AGAGCAGAACAAAACAAAATGGAGCAGAGC
*
39618496 AGAACAGAA
1 AGAGCAGAA
39618505 AGAGTAGAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 1 0.03
30 33 0.97
ACGTcount: A:0.52, C:0.16, G:0.26, T:0.06
Consensus pattern (30 bp):
AGAGCAGAACAAAACAAAATGGAGCAGAGC
Found at i:39618492 original size:20 final size:19
Alignment explanation
Indices: 39618466--39618518 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
39618456 GGTATAGAGC
39618466 AGAGCAGAACAGAACA-AA
1 AGAGCAGAACAGAACAGAA
*
39618484 ATGGAGCAGAGCAGAACAGAA
1 A--GAGCAGAACAGAACAGAA
*
39618505 AGAGTAGAACAGAA
1 AGAGCAGAACAGAA
39618519 TAGAGCTTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 1 0.03
19 11 0.38
20 14 0.48
21 3 0.10
ACGTcount: A:0.55, C:0.13, G:0.28, T:0.04
Consensus pattern (19 bp):
AGAGCAGAACAGAACAGAA
Found at i:39618513 original size:14 final size:15
Alignment explanation
Indices: 39618491--39618524 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
39618481 AAAATGGAGC
39618491 AGAGCAGAACAGAA-
1 AGAGCAGAACAGAAT
*
39618505 AGAGTAGAACAGAAT
1 AGAGCAGAACAGAAT
39618520 AGAGC
1 AGAGC
39618525 TTGTATGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.53, C:0.12, G:0.29, T:0.06
Consensus pattern (15 bp):
AGAGCAGAACAGAAT
Found at i:39625305 original size:29 final size:29
Alignment explanation
Indices: 39625263--39625323 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
39625253 CTAACACTTT
*
39625263 TCCTTTTCGAATACGCGGTCCCATGTCTC
1 TCCTTTTCGAATACACGGTCCCATGTCTC
* **
39625292 TCCTTTTCGAATACATGGTCTTATGTCTC
1 TCCTTTTCGAATACACGGTCCCATGTCTC
39625321 TCC
1 TCC
39625324 AAATAACTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.15, C:0.31, G:0.15, T:0.39
Consensus pattern (29 bp):
TCCTTTTCGAATACACGGTCCCATGTCTC
Found at i:39627289 original size:37 final size:37
Alignment explanation
Indices: 39627239--39627311 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
39627229 AGAGGTGCAC
39627239 GAACAAGAGCAGCACTAATAGTCAAGAAATACATCAG
1 GAACAAGAGCAGCACTAATAGTCAAGAAATACATCAG
39627276 GAACAAGAGCAGCACTAATAGTCAAGAAATACATCA
1 GAACAAGAGCAGCACTAATAGTCAAGAAATACATCA
39627312 ATGCCTAGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.49, C:0.19, G:0.18, T:0.14
Consensus pattern (37 bp):
GAACAAGAGCAGCACTAATAGTCAAGAAATACATCAG
Found at i:39627491 original size:14 final size:15
Alignment explanation
Indices: 39627467--39627495 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
39627457 GGTTCACTCA
39627467 TATTAATTTTTATAT
1 TATTAATTTTTATAT
39627482 TATT-ATTTTTATAT
1 TATTAATTTTTATAT
39627496 AAAAATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TATTAATTTTTATAT
Found at i:39627696 original size:14 final size:14
Alignment explanation
Indices: 39627673--39627713 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
39627663 TACAATATCC
*
39627673 AAATAATAACAATA
1 AAATAGTAACAATA
39627687 AAATAGTAACAATA
1 AAATAGTAACAATA
*
39627701 TAATAGTAA-AATA
1 AAATAGTAACAATA
39627714 GCAGCAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 4 0.16
14 21 0.84
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (14 bp):
AAATAGTAACAATA
Found at i:39628360 original size:21 final size:22
Alignment explanation
Indices: 39628336--39628379 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
39628326 TTTATTTTTC
*
39628336 TGTTTTATTGCTATTTT-TTAT
1 TGTTTTATTACTATTTTATTAT
*
39628357 TGTTTTGTTACTATTTTATTAT
1 TGTTTTATTACTATTTTATTAT
39628379 T
1 T
39628380 ATTATTCACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.16, C:0.05, G:0.09, T:0.70
Consensus pattern (22 bp):
TGTTTTATTACTATTTTATTAT
Found at i:39629038 original size:27 final size:27
Alignment explanation
Indices: 39628984--39629042 Score: 66
Period size: 30 Copynumber: 2.1 Consensus size: 27
39628974 TAAAATTTAA
39628984 AAAAATAATTTATTCTTTAATCTAAAATAT
1 AAAAATAATTTA-T-TTTAATCTAAAAT-T
* *
39629014 AAAAATAATTTA-TTTAATTTTAAATT
1 AAAAATAATTTATTTTAATCTAAAATT
39629040 AAA
1 AAA
39629043 TGAAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 4 0.15
27 11 0.41
30 12 0.44
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (27 bp):
AAAAATAATTTATTTTAATCTAAAATT
Found at i:39632027 original size:23 final size:21
Alignment explanation
Indices: 39631997--39632038 Score: 66
Period size: 23 Copynumber: 1.9 Consensus size: 21
39631987 AGCCACCCTC
39631997 TTACTTTTTTGACTTTGTTTTTT
1 TTACTTTTTT-ACTTT-TTTTTT
39632020 TTACTTTTTTACTTTTTTT
1 TTACTTTTTTACTTTTTTT
39632039 ACTTTTGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
22 5 0.26
23 10 0.53
ACGTcount: A:0.10, C:0.10, G:0.05, T:0.76
Consensus pattern (21 bp):
TTACTTTTTTACTTTTTTTTT
Found at i:39632035 original size:7 final size:8
Alignment explanation
Indices: 39631997--39632044 Score: 55
Period size: 9 Copynumber: 6.0 Consensus size: 8
39631987 AGCCACCCTC
39631997 TTACTTTT
1 TTACTTTT
*
39632005 TTGACTTTG
1 TT-ACTTTT
39632014 TT--TTTT
1 TTACTTTT
39632020 TTACTTTT
1 TTACTTTT
39632028 TTACTTTTT
1 TTAC-TTTT
39632037 TTACTTTT
1 TTACTTTT
39632045 GTCATATTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
6 5 0.15
8 14 0.41
9 15 0.44
ACGTcount: A:0.10, C:0.10, G:0.04, T:0.75
Consensus pattern (8 bp):
TTACTTTT
Found at i:39632107 original size:18 final size:18
Alignment explanation
Indices: 39632086--39632123 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
39632076 AGTTTTATGT
*
39632086 TTTTCCTTATTTATTTTA
1 TTTTACTTATTTATTTTA
*
39632104 TTTTATTTATTTATTTTA
1 TTTTACTTATTTATTTTA
39632122 TT
1 TT
39632124 ATTAATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTACTTATTTATTTTA
Found at i:39632199 original size:22 final size:22
Alignment explanation
Indices: 39632140--39632205 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
39632130 TTTAAAAAAT
*
39632140 TAAAATGTATATTTGAAATGTTTTA
1 TAAAATATAT-TTTGAAA--TTTTA
* *
39632165 TAATATATATTTTTAAATTTTA
1 TAAAATATATTTTGAAATTTTA
39632187 -AAAATATACTTTTGAAATT
1 TAAAATATA-TTTTGAAATT
39632206 ATTTTTTGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
21 7 0.20
22 14 0.40
24 6 0.17
25 8 0.23
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (22 bp):
TAAAATATATTTTGAAATTTTA
Found at i:39632231 original size:13 final size:13
Alignment explanation
Indices: 39632215--39632273 Score: 55
Period size: 13 Copynumber: 4.2 Consensus size: 13
39632205 TATTTTTTGA
39632215 AATTTTAAATATT
1 AATTTTAAATATT
*
39632228 AATTTTAAATTTTTTTT
1 AATTTTAAA----TATT
39632245 AAATTTTAAATATT
1 -AATTTTAAATATT
*
39632259 ATTTTTAAATATT
1 AATTTTAAATATT
39632272 AA
1 AA
39632274 ATATATTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
13 22 0.59
14 3 0.08
17 3 0.08
18 9 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
AATTTTAAATATT
Found at i:39632237 original size:20 final size:19
Alignment explanation
Indices: 39632228--39632286 Score: 84
Period size: 20 Copynumber: 3.1 Consensus size: 19
39632218 TTTAAATATT
39632228 AATTTTAAAT-TTTTTTTA
1 AATTTTAAATATTTTTTTA
39632246 AATTTTAAATATTATTTTTA
1 AATTTTAAATATT-TTTTTA
*
39632266 AATATTAAATATATTTTTTA
1 AATTTTAAATAT-TTTTTTA
39632286 A
1 A
39632287 TAATATAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
18 10 0.27
19 2 0.05
20 24 0.65
21 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
AATTTTAAATATTTTTTTA
Found at i:39632238 original size:7 final size:7
Alignment explanation
Indices: 39632209--39632275 Score: 54
Period size: 7 Copynumber: 10.1 Consensus size: 7
39632199 TGAAATTATT
39632209 TTTTGAAA
1 TTTT-AAA
39632217 TTTTAAA
1 TTTTAAA
*
39632224 TATT-AA
1 TTTTAAA
39632230 TTTTAAA
1 TTTTAAA
39632237 TTTT---
1 TTTTAAA
39632241 TTTTAAA
1 TTTTAAA
39632248 TTTTAAA
1 TTTTAAA
* *
39632255 TATT-AT
1 TTTTAAA
39632261 TTTTAAA
1 TTTTAAA
*
39632268 TATTAAA
1 TTTTAAA
39632275 T
1 T
39632276 ATATTTTTTA
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
4 4 0.09
6 9 0.19
7 30 0.64
8 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (7 bp):
TTTTAAA
Found at i:39632249 original size:31 final size:32
Alignment explanation
Indices: 39632160--39632268 Score: 130
Period size: 31 Copynumber: 3.2 Consensus size: 32
39632150 ATTTGAAATG
* *
39632160 TTTTATAATATATATTTTTAAATTTTAAAAATATAC
1 TTTTA-AAT-TAT-TTTTTAAATTTTAAATAT-TAA
39632196 TTTTGAAATTATTTTTTGAAATTTTAAATATTAA
1 TTTT-AAATTATTTTTT-AAATTTTAAATATTAA
*
39632230 TTTTAAATT-TTTTTTAAATTTTAAATATTAT
1 TTTTAAATTATTTTTTAAATTTTAAATATTAA
39632261 TTTTAAAT
1 TTTTAAAT
39632269 ATTAAATATA
Statistics
Matches: 68, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
31 23 0.34
32 6 0.09
33 5 0.07
34 11 0.16
35 15 0.22
36 7 0.10
37 1 0.01
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (32 bp):
TTTTAAATTATTTTTTAAATTTTAAATATTAA
Found at i:39632282 original size:31 final size:31
Alignment explanation
Indices: 39632214--39632282 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
39632204 TTATTTTTTG
* ***
39632214 AAATTTTAAATATTAATTTTAAATTTTTTTT
1 AAATTTTAAATATTAATTTTAAATATTAAAT
*
39632245 AAATTTTAAATATTATTTTTAAATATTAAAT
1 AAATTTTAAATATTAATTTTAAATATTAAAT
*
39632276 ATATTTT
1 AAATTTT
39632283 TTAATAATAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (31 bp):
AAATTTTAAATATTAATTTTAAATATTAAAT
Found at i:39632360 original size:24 final size:24
Alignment explanation
Indices: 39632333--39632378 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
39632323 TTTCAAAGTT
*
39632333 ATTATTAGTTTTATAA-TATTTTAA
1 ATTATGAGTTTTA-AATTATTTTAA
*
39632357 ATTATGATTTTTAAATTATTTT
1 ATTATGAGTTTTAAATTATTTT
39632379 TAAAGATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.11
24 17 0.89
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (24 bp):
ATTATGAGTTTTAAATTATTTTAA
Found at i:39632984 original size:84 final size:86
Alignment explanation
Indices: 39632883--39633067 Score: 257
Period size: 84 Copynumber: 2.2 Consensus size: 86
39632873 TTTATTGGAA
* * * *
39632883 AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCATTTGTGGGAAAAACGCCGCTAAAGGT-AAG
1 AAAAACGCCGCTAAAGGTCAAAGCTTTTAGCAGCATTTGTGGGAAAAACACCGCTAAACGTCAAG
39632947 GCTTTTAGCGGCG-TTTTGGG
66 GCTTTTAGCGGCGCTTTTGGG
* * *
39632967 AAAAGCGCCGCTAAAGGTCAAAGCTTTTAGCAGCGTTTGTGGGAAAAGCACCGCTAAACGTCAAG
1 AAAAACGCCGCTAAAGGTCAAAGCTTTTAGCAGCATTTGTGGGAAAAACACCGCTAAACGTCAAG
***
39633032 GCTTTTAGCGGCGCTTTTTTT
66 GCTTTTAGCGGCGCTTTTGGG
*
39633053 ACAAACGCCGCTAAA
1 AAAAACGCCGCTAAA
39633068 TTTGGCAGAT
Statistics
Matches: 87, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
84 54 0.62
85 16 0.18
86 17 0.20
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.24
Consensus pattern (86 bp):
AAAAACGCCGCTAAAGGTCAAAGCTTTTAGCAGCATTTGTGGGAAAAACACCGCTAAACGTCAAG
GCTTTTAGCGGCGCTTTTGGG
Found at i:39632993 original size:42 final size:43
Alignment explanation
Indices: 39632883--39633044 Score: 247
Period size: 43 Copynumber: 3.8 Consensus size: 43
39632873 TTTATTGGAA
*
39632883 AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCATTTGTGGG
1 AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
39632926 AAAAACGCCGCTAAAGGT-AAGGCTTTTAGCGGCGTTT-TGGG
1 AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
* * *
39632967 AAAAGCGCCGCTAAAGGTCAAAGCTTTTAGCAGCGTTTGTGGG
1 AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
* * *
39633010 AAAAGCACCGCTAAACGTCAAGGCTTTTAGCGGCG
1 AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCG
39633045 CTTTTTTTAC
Statistics
Matches: 109, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
41 21 0.19
42 35 0.32
43 53 0.49
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
Found at i:39633467 original size:21 final size:21
Alignment explanation
Indices: 39633443--39633488 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
39633433 GCTCGTGCCT
*
39633443 CTGCCTCTCTCGCTGCAGCCG
1 CTGCCTCCCTCGCTGCAGCCG
* * *
39633464 CTGCCTCCCTCTCTGCTGCCT
1 CTGCCTCCCTCGCTGCAGCCG
39633485 CTGC
1 CTGC
39633489 TCTAAGTTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.02, C:0.50, G:0.20, T:0.28
Consensus pattern (21 bp):
CTGCCTCCCTCGCTGCAGCCG
Found at i:39639137 original size:9 final size:9
Alignment explanation
Indices: 39639123--39639348 Score: 143
Period size: 9 Copynumber: 24.6 Consensus size: 9
39639113 TATTTAAGTA
39639123 TTATGTAAG
1 TTATGTAAG
*
39639132 TTATGTAAT
1 TTATGTAAG
*
39639141 TTATGATATG
1 TTATG-TAAG
* * *
39639151 ATATAT-AT
1 TTATGTAAG
*
39639159 TTATGTAAA
1 TTATGTAAG
* *
39639168 TTATAT-AT
1 TTATGTAAG
*
39639176 TTATCTAAG
1 TTATGTAAG
*
39639185 TTATATAAG
1 TTATGTAAG
39639194 TTATGTAAG
1 TTATGTAAG
*
39639203 TTATGTAAA
1 TTATGTAAG
*
39639212 TTATGATATAAAA
1 TTATG---T-AAG
*
39639225 TATATTTAAG
1 T-TATGTAAG
39639235 TATTATGTAAG
1 --TTATGTAAG
39639246 TTATGTAAG
1 TTATGTAAG
* *
39639255 TTATAT-AT
1 TTATGTAAG
*
39639263 TTATCTAAG
1 TTATGTAAG
*
39639272 TTATATAAG
1 TTATGTAAG
*
39639281 TTATATAAG
1 TTATGTAAG
*
39639290 TTATGTATG
1 TTATGTAAG
*
39639299 TTATATAAG
1 TTATGTAAG
39639308 TTATGTAAG
1 TTATGTAAG
* *
39639317 TTATATATG
1 TTATGTAAG
*
39639326 TTATATAAG
1 TTATGTAAG
*
39639335 TTATGTAAA
1 TTATGTAAG
39639344 TTATG
1 TTATG
39639349 ATATCAAATA
Statistics
Matches: 171, Mismatches: 35, Indels: 22
0.75 0.15 0.10
Matches are distributed among these distances:
8 16 0.09
9 131 0.77
10 7 0.04
11 8 0.05
12 2 0.01
13 4 0.02
14 3 0.02
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:39639202 original size:18 final size:18
Alignment explanation
Indices: 39639123--39639348 Score: 161
Period size: 18 Copynumber: 12.3 Consensus size: 18
39639113 TATTTAAGTA
* *
39639123 TTATGTAAGTTATGTAAT
1 TTATGTAAGTTATATAAG
* * *
39639141 TTATGATATGATATAT-AT
1 TTATG-TAAGTTATATAAG
* *
39639159 TTATGTAAATTATAT-AT
1 TTATGTAAGTTATATAAG
*
39639176 TTATCTAAGTTATATAAG
1 TTATGTAAGTTATATAAG
* *
39639194 TTATGTAAGTTATGTAAA
1 TTATGTAAGTTATATAAG
* *
39639212 TTATGATATAAAATATATTTAAG
1 TTATG---T-AAGT-TATATAAG
*
39639235 TATTATGTAAGTTATGTAAG
1 --TTATGTAAGTTATATAAG
* * *
39639255 TTATAT-ATTTATCTAAG
1 TTATGTAAGTTATATAAG
*
39639272 TTATATAAGTTATATAAG
1 TTATGTAAGTTATATAAG
*
39639290 TTATGTATGTTATATAAG
1 TTATGTAAGTTATATAAG
*
39639308 TTATGTAAGTTATATATG
1 TTATGTAAGTTATATAAG
* * *
39639326 TTATATAAGTTATGTAAA
1 TTATGTAAGTTATATAAG
39639344 TTATG
1 TTATG
39639349 ATATCAAATA
Statistics
Matches: 167, Mismatches: 31, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
17 37 0.22
18 97 0.58
19 7 0.04
20 7 0.04
21 4 0.02
22 4 0.02
23 6 0.04
25 5 0.03
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.48
Consensus pattern (18 bp):
TTATGTAAGTTATATAAG
Found at i:39639215 original size:27 final size:27
Alignment explanation
Indices: 39639176--39639348 Score: 159
Period size: 27 Copynumber: 6.2 Consensus size: 27
39639166 AATTATATAT
*
39639176 TTATCTAAGTTATATAAGTTATGTAAG
1 TTATGTAAGTTATATAAGTTATGTAAG
* * *
39639203 TTATGTAAATTATGATATAAAATATATTTAAG
1 TTATGT-AAGT-T-ATAT-AAGT-TATGTAAG
* * *
39639235 TATTATGTAAGTTATGTAAGTTATAT-AT
1 --TTATGTAAGTTATATAAGTTATGTAAG
* *
39639263 TTATCTAAGTTATATAAGTTATATAAG
1 TTATGTAAGTTATATAAGTTATGTAAG
*
39639290 TTATGTATGTTATATAAGTTATGTAAG
1 TTATGTAAGTTATATAAGTTATGTAAG
* * *
39639317 TTATATATGTTATATAAGTTATGTAAA
1 TTATGTAAGTTATATAAGTTATGTAAG
39639344 TTATG
1 TTATG
39639349 ATATCAAATA
Statistics
Matches: 120, Mismatches: 18, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
26 22 0.18
27 59 0.49
28 4 0.03
29 5 0.04
30 7 0.06
31 6 0.05
32 8 0.07
33 3 0.03
34 6 0.05
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.47
Consensus pattern (27 bp):
TTATGTAAGTTATATAAGTTATGTAAG
Found at i:39639233 original size:114 final size:114
Alignment explanation
Indices: 39639099--39639320 Score: 313
Period size: 114 Copynumber: 1.9 Consensus size: 114
39639089 ACTAGTTATG
* * * *
39639099 TATGATATGATATATATTTAAGTATTATGTAAGTTATGTAATTTATGATATGATATAT-ATTTAT
1 TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTAT-ATAT-ATATATAAGTTAT
* *
39639163 GTAAATTATAT-ATTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAAT
64 ATAAATTATATAAGTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAAT
* *
39639213 TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATATATTTATCTAAGTTATAT
1 TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATATATATATATAAGTTATAT
* * *
39639278 AAGTTATATAAGTTATGTATGTTATATAAGTTATGTAAGTTAT
66 AAATTATATAAGTTATCTAAGTTATATAAGTTATGTAAGTTAT
39639321 ATATGTTATA
Statistics
Matches: 95, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
112 4 0.04
113 18 0.19
114 73 0.77
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.48
Consensus pattern (114 bp):
TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATATATATATATAAGTTATAT
AAATTATATAAGTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAAT
Found at i:39639709 original size:24 final size:24
Alignment explanation
Indices: 39639681--39639748 Score: 102
Period size: 24 Copynumber: 2.8 Consensus size: 24
39639671 ACTTAAATGG
39639681 TAAAACGGACGATAATATTTGTAA
1 TAAAACGGACGATAATATTTGTAA
*
39639705 TAAAACGGA-GAATAATATTTGTGA
1 TAAAACGGACG-ATAATATTTGTAA
*
39639729 TAAAACGGACGAGAATATTT
1 TAAAACGGACGATAATATTT
39639749 CAATAATAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.03
24 38 0.95
25 1 0.03
ACGTcount: A:0.46, C:0.07, G:0.19, T:0.28
Consensus pattern (24 bp):
TAAAACGGACGATAATATTTGTAA
Found at i:39644297 original size:3 final size:3
Alignment explanation
Indices: 39644289--39644377 Score: 178
Period size: 3 Copynumber: 29.7 Consensus size: 3
39644279 TTTTTCTCTT
39644289 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39644337 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
39644378 TCCTATTAAT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 86 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:39644470 original size:28 final size:27
Alignment explanation
Indices: 39644418--39644471 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
39644408 GGTCTCTCTA
*
39644418 ATATATTTAAATTTTAGATTTATTTAC
1 ATATATTTAAATTTTAGATTCATTTAC
*
39644445 ATATACTTTAATTTTTA-ATATCATTTA
1 ATATA-TTTAAATTTTAGAT-TCATTTA
39644472 GTCTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.56
Consensus pattern (27 bp):
ATATATTTAAATTTTAGATTCATTTAC
Found at i:39644653 original size:12 final size:11
Alignment explanation
Indices: 39644631--39644676 Score: 60
Period size: 12 Copynumber: 4.2 Consensus size: 11
39644621 TTTTTCATTA
39644631 ATATC-TATAT
1 ATATCATATAT
39644641 ATATCAATATAT
1 ATATC-ATATAT
39644653 ATATCCATATAT
1 ATAT-CATATAT
39644665 ATAT-ATATAT
1 ATATCATATAT
39644675 AT
1 AT
39644677 TATTTATTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
10 13 0.39
12 19 0.58
13 1 0.03
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (11 bp):
ATATCATATAT
Found at i:39645435 original size:153 final size:152
Alignment explanation
Indices: 39645180--39645562 Score: 599
Period size: 153 Copynumber: 2.5 Consensus size: 152
39645170 GGCGCTTACG
* * * ** *
39645180 TAAAAACGCCGCTATAGGTCGG-TCTATAGTGGCGCTTCTCTAAAAACGCTACTAATGCTTGATC
1 TAAAAACGCCGCTATAGGT-GGATCTATAGCGGCGCTT-ACTGAAAACGCCGCTAATGCTCGATC
39645244 TTTAGCGGCGTTTTTTGAGAAGCGTCGCTAATGAACTGAAGCTTACATAATACGACATCATTCAC
64 TTTAGCGGCGTTTTTTGAGAAGCGTCGCTAATGAACTGAAGCTTACATAATACGACATCATTCAC
* *
39645309 ATTAATCTTTTGTGGCGTTTTTAA
129 ATTAATCTTTTGCGGCATTTTTAA
* *
39645333 TAAAAAAGCCGCTATAGGTGGATCTATAGCCGCGTCTTACTGAAAACGCCGCTAATGCTCGATCT
1 TAAAAACGCCGCTATAGGTGGATCTATAGCGGCG-CTTACTGAAAACGCCGCTAATGCTCGATCT
*
39645398 TTAGCGGCGTTTTTTGAGAAGCG-CTGCTAATGAACTGAAGCTTACATAATACGACGTCATTCAC
65 TTAGCGGCGTTTTTTGAGAAGCGTC-GCTAATGAACTGAAGCTTACATAATACGACATCATTCAC
39645462 ATTAATCTTTTGCGGCATTTTTAA
129 ATTAATCTTTTGCGGCATTTTTAA
*
39645486 TAAAAACGCCGCTATAGGTGGATCTATAGCGGCGCCTTACTGAAAACGCCGCTAATGCTCGATTT
1 TAAAAACGCCGCTATAGGTGGATCTATAGCGGCG-CTTACTGAAAACGCCGCTAATGCTCGATCT
39645551 TTAGCGGCGTTT
65 TTAGCGGCGTTT
39645563 CGCTAATACT
Statistics
Matches: 212, Mismatches: 15, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
152 3 0.01
153 206 0.97
154 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (152 bp):
TAAAAACGCCGCTATAGGTGGATCTATAGCGGCGCTTACTGAAAACGCCGCTAATGCTCGATCTT
TAGCGGCGTTTTTTGAGAAGCGTCGCTAATGAACTGAAGCTTACATAATACGACATCATTCACAT
TAATCTTTTGCGGCATTTTTAA
Found at i:39650273 original size:34 final size:35
Alignment explanation
Indices: 39650228--39650306 Score: 97
Period size: 35 Copynumber: 2.3 Consensus size: 35
39650218 AAGAGGTCAT
* * * *
39650228 TAAATTGTTGTACCATA-TTGATGTGATGTGTCTC
1 TAAATTATTGTACCATATTTGATGTCATATCTCTC
* *
39650262 TTAATTATTGTACTATATTTGATGTCATATCTCTC
1 TAAATTATTGTACCATATTTGATGTCATATCTCTC
39650297 TAAATTATTG
1 TAAATTATTG
39650307 CTAAAGCATC
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
34 14 0.38
35 23 0.62
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.48
Consensus pattern (35 bp):
TAAATTATTGTACCATATTTGATGTCATATCTCTC
Found at i:39652217 original size:15 final size:15
Alignment explanation
Indices: 39652180--39652213 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
39652170 AAAAACCAAA
*
39652180 AAAACAAAATAAACC
1 AAAATAAAATAAACC
39652195 AAAATAAAA-AAACC
1 AAAATAAAATAAACC
39652209 AAAAT
1 AAAAT
39652214 TAAAGTCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.76, C:0.15, G:0.00, T:0.09
Consensus pattern (15 bp):
AAAATAAAATAAACC
Found at i:39653698 original size:20 final size:21
Alignment explanation
Indices: 39653675--39653713 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
39653665 TATATATATA
39653675 TATAT-ATTTATATTGTTTTG
1 TATATCATTTATATTGTTTTG
39653695 TATATCATTTATATTGTTT
1 TATATCATTTATATTGTTT
39653714 CGTTACAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.64
Consensus pattern (21 bp):
TATATCATTTATATTGTTTTG
Found at i:39655247 original size:26 final size:26
Alignment explanation
Indices: 39655188--39655251 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 26
39655178 TACAAATAAA
39655188 TAAAATTAAAAAAATTTATTCTTTAATC
1 TAAAATTAAAAAAATTTA-T-TTTAATC
*
39655216 TAAAATATAAAAAAATTTA-TTTAATT
1 TAAAAT-TAAAAAAATTTATTTTAATC
*
39655242 TTAAATTAAA
1 TAAAATTAAA
39655252 TGAAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
25 4 0.12
26 11 0.33
28 6 0.18
29 12 0.36
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (26 bp):
TAAAATTAAAAAAATTTATTTTAATC
Done.