Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 71 of 295
Found at i:20504594 original size:43 final size:43
Alignment explanation
Indices: 20504547--20504651 Score: 122
Period size: 43 Copynumber: 2.4 Consensus size: 43
20504537 AGTATGATTA
* * *
20504547 CTTTGATTTATCTAATGATGCAATAT-GTGTGCCACTATAATTG
1 CTTTGATTCATCCAATGATGCAAT-TCGTGTGCCAATATAATTG
* * *
20504590 CTTTGGTTCATCCAATGATGCACTTCTTGTGCCAATATAATTG
1 CTTTGATTCATCCAATGATGCAATTCGTGTGCCAATATAATTG
* *
20504633 CTTTGGTTCATCCGATGAT
1 CTTTGATTCATCCAATGAT
20504652 ACTCCTCGTG
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
42 1 0.02
43 53 0.98
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41
Consensus pattern (43 bp):
CTTTGATTCATCCAATGATGCAATTCGTGTGCCAATATAATTG
Found at i:20504669 original size:43 final size:43
Alignment explanation
Indices: 20504573--20504677 Score: 138
Period size: 43 Copynumber: 2.4 Consensus size: 43
20504563 GATGCAATAT
* * *
20504573 GTGTGCCACTATAATTGCTTTGGTTCATCCAATGATGCACTTC
1 GTGTGCCAATATAATTGCTTTGGTTCATCCAATGATACACCTC
* * *
20504616 TTGTGCCAATATAATTGCTTTGGTTCATCCGATGATACTCCTC
1 GTGTGCCAATATAATTGCTTTGGTTCATCCAATGATACACCTC
* *
20504659 GTGTGTCAATACAATTGCT
1 GTGTGCCAATATAATTGCT
20504678 CCGACTTGCT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 53 1.00
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (43 bp):
GTGTGCCAATATAATTGCTTTGGTTCATCCAATGATACACCTC
Found at i:20506594 original size:28 final size:28
Alignment explanation
Indices: 20506554--20506609 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
20506544 AAAAAAACAA
*
20506554 AAACTGTTTAAAAAAATTGATGTGACAG
1 AAACTGTTAAAAAAAATTGATGTGACAG
20506582 AAACTGTTAAAAAAAATTGATGTGACAG
1 AAACTGTTAAAAAAAATTGATGTGACAG
20506610 GGATGGAGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.48, C:0.07, G:0.18, T:0.27
Consensus pattern (28 bp):
AAACTGTTAAAAAAAATTGATGTGACAG
Found at i:20506682 original size:26 final size:27
Alignment explanation
Indices: 20506625--20506687 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
20506615 GAGGGCATGC
**
20506625 CAGAGGCGGCACTGGTGAAGCCTGTGG
1 CAGAGGCGGCACCAGTGAAGCCTGTGG
20506652 CAGAGGCGGCACCAGTGAAG-CTGTGG
1 CAGAGGCGGCACCAGTGAAGCCTGTGG
20506678 CAGAGGCGGC
1 CAGAGGCGGC
20506688 GCCCACTCCC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
26 16 0.47
27 18 0.53
ACGTcount: A:0.21, C:0.24, G:0.44, T:0.11
Consensus pattern (27 bp):
CAGAGGCGGCACCAGTGAAGCCTGTGG
Found at i:20506888 original size:16 final size:16
Alignment explanation
Indices: 20506867--20506905 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
20506857 AAATTATTAT
*
20506867 AAAAAATAAAATACTA
1 AAAAAATAAAATACCA
* *
20506883 AAAAAATAATATGCCA
1 AAAAAATAAAATACCA
20506899 AAAAAAT
1 AAAAAAT
20506906 TTCTCAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.72, C:0.08, G:0.03, T:0.18
Consensus pattern (16 bp):
AAAAAATAAAATACCA
Found at i:20507267 original size:17 final size:17
Alignment explanation
Indices: 20507245--20507280 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
20507235 TAATTTTTAA
20507245 TTGCTAAAATATAATAT
1 TTGCTAAAATATAATAT
*
20507262 TTGCTAGAATATAATAT
1 TTGCTAAAATATAATAT
20507279 TT
1 TT
20507281 AGAAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (17 bp):
TTGCTAAAATATAATAT
Found at i:20507467 original size:17 final size:17
Alignment explanation
Indices: 20507445--20507479 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
20507435 TAGGCTTCAC
*
20507445 TGGTGCCGTCTATGGCA
1 TGGTGCCGCCTATGGCA
20507462 TGGTGCCGCCTATGGCA
1 TGGTGCCGCCTATGGCA
20507479 T
1 T
20507480 AGGCTTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.11, C:0.26, G:0.34, T:0.29
Consensus pattern (17 bp):
TGGTGCCGCCTATGGCA
Found at i:20507510 original size:27 final size:27
Alignment explanation
Indices: 20507462--20507514 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
20507452 GTCTATGGCA
* *
20507462 TGGTGCCGCCTATGGCATAGGCTTCAT
1 TGGTGCCGCCTATGCCACAGGCTTCAT
*
20507489 TGGTGCCGCCTCTGCCACAGGCTTCA
1 TGGTGCCGCCTATGCCACAGGCTTCA
20507515 CCAGTGTCGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.13, C:0.32, G:0.28, T:0.26
Consensus pattern (27 bp):
TGGTGCCGCCTATGCCACAGGCTTCAT
Found at i:20507575 original size:27 final size:27
Alignment explanation
Indices: 20507545--20507598 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
20507535 CCCTCCATCC
*
20507545 CTGTCACATCGGTTTTTTTAACAGTTT
1 CTGTCACATCAGTTTTTTTAACAGTTT
20507572 CTGTCACATCAGTTTTTTTAACAGTTT
1 CTGTCACATCAGTTTTTTTAACAGTTT
20507599 TTGTTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.20, C:0.19, G:0.13, T:0.48
Consensus pattern (27 bp):
CTGTCACATCAGTTTTTTTAACAGTTT
Found at i:20509284 original size:93 final size:92
Alignment explanation
Indices: 20509125--20509341 Score: 296
Period size: 93 Copynumber: 2.3 Consensus size: 92
20509115 TGATGCCATA
* *
20509125 GTATCTTTC-AACTATGGTCTTACTCATTTTC-TGTCATGTTGCCGTGGTATCTTTCAACCATGG
1 GTATCTTTCAAAC-ATGGTCTTACTCA-TTTCATGTCACGTTGCCATGGTATCTTTCAACCATGG
* *
20509188 TCTTATTCATA-TCCCCGTCATGTTGTCATG
64 TCTTA--CATATTCCACATCATGTTGTCATG
*
20509218 GTATCTTTCAAACATGGTCTTATTCATTTCATGTCACGTTGCCATGGTATCTTTCAACCATGGTC
1 GTATCTTTCAAACATGGTCTTACTCATTTCATGTCACGTTGCCATGGTATCTTTCAACCATGGTC
* *
20509283 TTACATATTTCATATCATGTTGTCATG
66 TTACATATTCCACATCATGTTGTCATG
* *
20509310 GTATCTTTCAACCATGGTCTTACACATTTCAT
1 GTATCTTTCAAACATGGTCTTACTCATTTCAT
20509342 TTCAGAAAGC
Statistics
Matches: 111, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
91 4 0.04
92 48 0.43
93 56 0.50
94 3 0.03
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (92 bp):
GTATCTTTCAAACATGGTCTTACTCATTTCATGTCACGTTGCCATGGTATCTTTCAACCATGGTC
TTACATATTCCACATCATGTTGTCATG
Found at i:20509339 original size:46 final size:46
Alignment explanation
Indices: 20509113--20509341 Score: 282
Period size: 46 Copynumber: 5.0 Consensus size: 46
20509103 TTATCTTCGA
* * *
20509113 CATGATGCCATAGTATCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATGT
* * * **
20509159 CATGTTGCCGTGGTATCTTTCAACCATGGTCTTATTCATATCCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCAT-TTCATGT
* * *
20509206 CATGTTGTCATGGTATCTTTCAAACATGGTCTTATTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* *
20509252 CACGTTGCCATGGTATCTTTCAACCATGGTCTTACAT-ATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTAC-TCATTTCATGT
* *
20509298 CATGTTGTCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCAT
20509342 TTCAGAAAGC
Statistics
Matches: 158, Mismatches: 21, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
45 1 0.01
46 118 0.75
47 39 0.25
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.41
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
Found at i:20517167 original size:93 final size:93
Alignment explanation
Indices: 20517000--20517168 Score: 232
Period size: 93 Copynumber: 1.8 Consensus size: 93
20516990 TGATGCCATA
* * * * *
20517000 GTATCTTTCAACTATAGTCTTACTCATTTTCTGTCATGTTGTCATGGTATCTTTCAAACATGGTC
1 GTATCTTTCAACCATAGTCTTACACATTTTCTATCACGTTGCCATGGTATCTTTCAAACATGGTC
**
20517065 TTATTCATTTCCCCGTCATGTTGTCATG
66 TTACACATTTCCCCGTCATGTTGTCATG
* * *
20517093 GTATCTTTCAACCATGGTCTTACACA-TTTCATATTACGTTGCCATGGTATCTTTCAACCATGGT
1 GTATCTTTCAACCATAGTCTTACACATTTTC-TATCACGTTGCCATGGTATCTTTCAAACATGGT
20517157 CTTACACATTTC
65 CTTACACATTTC
20517169 ATTTCAGAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
92 4 0.06
93 61 0.94
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.43
Consensus pattern (93 bp):
GTATCTTTCAACCATAGTCTTACACATTTTCTATCACGTTGCCATGGTATCTTTCAAACATGGTC
TTACACATTTCCCCGTCATGTTGTCATG
Found at i:20517168 original size:46 final size:46
Alignment explanation
Indices: 20516988--20517170 Score: 206
Period size: 46 Copynumber: 4.0 Consensus size: 46
20516978 TTATCTTCGA
* * * * *
20516988 CATGATGCCATAGTATCTTTCAACTATAGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATGT
* * ** **
20517034 CATGTTGTCATGGTATCTTTCAAACATGGTCTTATTCATTTCCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTT-CATGT
* *
20517081 CATGTTGTCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGT
* *
20517127 TACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
20517171 TTCAGAAAGC
Statistics
Matches: 118, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
45 3 0.03
46 75 0.64
47 40 0.34
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.42
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGT
Found at i:20519281 original size:11 final size:11
Alignment explanation
Indices: 20519265--20519312 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
20519255 CCTTTTATAC
20519265 TAATAAAATAA
1 TAATAAAATAA
*
20519276 TAATAAAATATCT
1 TAATAAAATA--A
* *
20519289 TATTAAAATAT
1 TAATAAAATAA
20519300 TAATAAAATAA
1 TAATAAAATAA
20519311 TA
1 TA
20519313 TTTATCTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 22 0.71
13 9 0.29
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:20520701 original size:20 final size:20
Alignment explanation
Indices: 20520676--20520714 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
20520666 GTCATTTTCT
*
20520676 GTTAAAAAGGAAAAAAAAGA
1 GTTAAAAACGAAAAAAAAGA
20520696 GTTAAAAACGAAAAAAAAG
1 GTTAAAAACGAAAAAAAAG
20520715 GATTGTGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.69, C:0.03, G:0.18, T:0.10
Consensus pattern (20 bp):
GTTAAAAACGAAAAAAAAGA
Found at i:20521008 original size:16 final size:16
Alignment explanation
Indices: 20520964--20521010 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
20520954 TGTTTTTGCG
20520964 GTTATTATTATTGTT-
1 GTTATTATTATTGTTA
20520979 GATT-TT-TT-TTGTTA
1 G-TTATTATTATTGTTA
20520993 GTTATTATTATTGTTA
1 GTTATTATTATTGTTA
20521009 GT
1 GT
20521011 AAAAAATCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
13 7 0.26
14 5 0.19
15 5 0.19
16 10 0.37
ACGTcount: A:0.19, C:0.00, G:0.15, T:0.66
Consensus pattern (16 bp):
GTTATTATTATTGTTA
Found at i:20521042 original size:38 final size:38
Alignment explanation
Indices: 20520993--20521118 Score: 152
Period size: 38 Copynumber: 3.3 Consensus size: 38
20520983 TTTTTTGTTA
20520993 GTTA-TTATTATTGTTAGTAAAAAATCCTTATTATTATT
1 GTTAGTTATTATTGTTAGTAAAAAA-CCTTATTATTATT
* **
20521031 GTT-GTTATTATTGTTAGTAAAAAACTATTATTAGGATT
1 GTTAGTTATTATTGTTAGTAAAAAAC-CTTATTATTATT
* *
20521069 GTTGGTTATTATTGTTAGTAAAAAAACCCTA--ATTATT
1 GTTAGTTATTATTGTTAGT-AAAAAACCTTATTATTATT
20521106 GTTAGTTATTATT
1 GTTAGTTATTATT
20521119 ATTGTTGATT
Statistics
Matches: 76, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
37 17 0.22
38 35 0.46
39 17 0.22
40 7 0.09
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.49
Consensus pattern (38 bp):
GTTAGTTATTATTGTTAGTAAAAAACCTTATTATTATT
Found at i:20521121 original size:16 final size:17
Alignment explanation
Indices: 20521100--20521134 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
20521090 AAAAACCCTA
20521100 ATTATTGTT-AGTTATT
1 ATTATTGTTGAGTTATT
*
20521116 ATTATTGTTGATTTATT
1 ATTATTGTTGAGTTATT
20521133 AT
1 AT
20521135 AATTTTGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (17 bp):
ATTATTGTTGAGTTATT
Found at i:20521227 original size:18 final size:18
Alignment explanation
Indices: 20521185--20521227 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
20521175 ATGCAAAGAA
* *
20521185 TGTTTTATTTTTTTTATG
1 TGTTTTATTTGTTATATG
**
20521203 TAATTTATTTGTTATATG
1 TGTTTTATTTGTTATATG
20521221 TGTTTTA
1 TGTTTTA
20521228 GGTGGGTTTT
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.19, C:0.00, G:0.12, T:0.70
Consensus pattern (18 bp):
TGTTTTATTTGTTATATG
Found at i:20526640 original size:35 final size:33
Alignment explanation
Indices: 20526601--20526677 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 33
20526591 ATAATTTTAA
*
20526601 TAATAATAAACATCTAATAAATATCTTTT-ACTAAT
1 TAATAATAAA-ATAT-A-AAATATCTTTTCACTAAT
20526636 TAATAAT-AAATATAAAATATCTTTTCACTAAT
1 TAATAATAAAATATAAAATATCTTTTCACTAAT
20526668 T-ATACATAAA
1 TAATA-ATAAA
20526678 TAATACAAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
31 14 0.37
32 10 0.26
33 5 0.13
34 2 0.05
35 7 0.18
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (33 bp):
TAATAATAAAATATAAAATATCTTTTCACTAAT
Found at i:20526654 original size:31 final size:32
Alignment explanation
Indices: 20526619--20526679 Score: 99
Period size: 31 Copynumber: 1.9 Consensus size: 32
20526609 AACATCTAAT
20526619 AAATATCTTTT-ACTAATTAATA-ATAAATATA
1 AAATATCTTTTCACTAATT-ATACATAAATATA
20526650 AAATATCTTTTCACTAATTATACATAAATA
1 AAATATCTTTTCACTAATTATACATAAATA
20526680 ATACAAACGT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
31 14 0.50
32 14 0.50
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (32 bp):
AAATATCTTTTCACTAATTATACATAAATATA
Found at i:20528185 original size:33 final size:32
Alignment explanation
Indices: 20528115--20528196 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
20528105 GGGGAGTGGA
* **
20528115 GTACTGCGGTGGTTACGGGCCGGGGGTGTGCT
1 GTACTGCGGTGGATACGGGCCGGGGAAGTGCT
* * *
20528147 ATACTGCGGTGGATATGGGCTGGGAGAAGTGCT
1 GTACTGCGGTGGATACGGGCCGGG-GAAGTGCT
*
20528180 GTACTGCAGTGGATACG
1 GTACTGCGGTGGATACG
20528197 ACCCAAAGAT
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
32 20 0.50
33 20 0.50
ACGTcount: A:0.16, C:0.16, G:0.44, T:0.24
Consensus pattern (32 bp):
GTACTGCGGTGGATACGGGCCGGGGAAGTGCT
Found at i:20530361 original size:18 final size:18
Alignment explanation
Indices: 20530340--20530394 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
20530330 CATTGGGAAA
* *
20530340 TAAAAATTTTCATATTTT
1 TAAAAATTTTAAAATTTT
*
20530358 TAAAATTTTTAAAATTTT
1 TAAAAATTTTAAAATTTT
*
20530376 TAAAATTTTTAAAATTTT
1 TAAAAATTTTAAAATTTT
20530394 T
1 T
20530395 GGATCTTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
TAAAAATTTTAAAATTTT
Found at i:20530365 original size:9 final size:9
Alignment explanation
Indices: 20530353--20530394 Score: 84
Period size: 9 Copynumber: 4.7 Consensus size: 9
20530343 AAATTTTCAT
20530353 ATTTTTAAA
1 ATTTTTAAA
20530362 ATTTTTAAA
1 ATTTTTAAA
20530371 ATTTTTAAA
1 ATTTTTAAA
20530380 ATTTTTAAA
1 ATTTTTAAA
20530389 ATTTTT
1 ATTTTT
20530395 GGATCTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:20530370 original size:27 final size:27
Alignment explanation
Indices: 20530340--20530394 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
20530330 CATTGGGAAA
* *
20530340 TAAAAATTTTCATATTTTTAAAATTTT
1 TAAAAATTTTAAAATTTTTAAAATTTT
*
20530367 TAAAATTTTTAAAATTTTTAAAATTTT
1 TAAAAATTTTAAAATTTTTAAAATTTT
20530394 T
1 T
20530395 GGATCTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (27 bp):
TAAAAATTTTAAAATTTTTAAAATTTT
Found at i:20530454 original size:13 final size:12
Alignment explanation
Indices: 20530412--20530455 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
20530402 ATTTTTTAAA
20530412 ATATATTATTTT
1 ATATATTATTTT
*
20530424 CATATTTTATTTT
1 -ATATATTATTTT
*
20530437 TTATATTATTTT
1 ATATATTATTTT
20530449 AGTATAT
1 A-TATAT
20530456 AATGTTTCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (12 bp):
ATATATTATTTT
Found at i:20530543 original size:129 final size:128
Alignment explanation
Indices: 20530401--20530668 Score: 419
Period size: 129 Copynumber: 2.1 Consensus size: 128
20530391 TTTTGGATCT
* * *
20530401 TATTTTTTAAAATATATTATTTTCATATTTTATTTTTTATATTATTTTAGTATATAATGTTTCAA
1 TATTTTTAAAAATATACTATTTTCATATTTTATTTTTTATATTATTTTAGTACATAATGTTTCAA
* * *
20530466 ATGTATTATTTTAGTGTTTTTTATATTAATTTAGTAAATAACCCTAATTTTATCCTTTTGTTTG
66 ATGTATTATTTTAGTG-TTTTTATATTAATCTAGTAAATAACCCTAATTTTAGCCATTTGTTTG
* *
20530530 TATTTTTAAAAATATACTATTTTCGTATTTTATTTTTTATATTATTTTAGTACATAATGTTTTAA
1 TATTTTTAAAAATATACTATTTTCATATTTTATTTTTTATATTATTTTAGTACATAATGTTTCAA
* * * *
20530595 ATGTATTATTTTAGTGTTTTTATATTAATCTAGTAAATCATCCTGATTTTGGCCATTTGTTTG
66 ATGTATTATTTTAGTGTTTTTATATTAATCTAGTAAATAACCCTAATTTTAGCCATTTGTTTG
20530658 TATTTTTAAAA
1 TATTTTTAAAA
20530669 TTTTCGGATT
Statistics
Matches: 127, Mismatches: 12, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
128 51 0.40
129 76 0.60
ACGTcount: A:0.29, C:0.06, G:0.07, T:0.57
Consensus pattern (128 bp):
TATTTTTAAAAATATACTATTTTCATATTTTATTTTTTATATTATTTTAGTACATAATGTTTCAA
ATGTATTATTTTAGTGTTTTTATATTAATCTAGTAAATAACCCTAATTTTAGCCATTTGTTTG
Found at i:20530701 original size:150 final size:150
Alignment explanation
Indices: 20530530--20531783 Score: 1872
Period size: 150 Copynumber: 8.3 Consensus size: 150
20530520 CTTTTGTTTG
*
20530530 TATTTTTAAAAATATACTATTTTCGTATTTTATTTTTTATATTATTTTAGTACATAATGTTTTAA
1 TATTTTTAAAAATATACTATTTTCGTATTTTATTTTTTATATTATTTTAGTACATAATGTTTCAA
* * *
20530595 ATGTATTATTTTAGTGTTTTTATATTAATCTAGTAAATCATCCTGATTTTGGCCATTTGTTTGTA
66 ATGTATTATTTTAGTGTTTTTATATTAATTTAGTAAATAACCCTGATTTTGGCCATTTGTTTGTA
20530660 TTTTTAAAATTTTCGGATTT
131 TTTTTAAAATTTTCGGATTT
* * *
20530680 TATTTTTAAAAATATACTATTTTCTTATTTTATTTTTTTTACATTATTTTAGTACATAATGTTTT
1 TATTTTTAAAAATATACTATTTTCGTATTTTA--TTTTTTATATTATTTTAGTACATAATGTTTC
* * * **
20530745 AAATATATTATTTTAGTGTTTTTTATATTAATTTAGTAAATAACCCTAAATTTT-TCTTTTTGTT
64 AAATGTATTATTTTAGTG-TTTTTATATTAATTTAGTAAATAACCCT-GATTTTGGCCATTTGTT
** *
20530809 TGTATTTTTAAAATTCCCAGATTT
127 TGTATTTTTAAAATTTTCGGATTT
* * *
20530833 TATTTTTAAAAATATATTATTTTCGTATATTATTTTTTTATATTATTTTAGTACATAATGTTTTA
1 TATTTTTAAAAATATACTATTTTCGTATTTTA-TTTTTTATATTATTTTAGTACATAATGTTTCA
* ** * * * *
20530898 AATGTATTATTTTAGTATTTTTTTATATTAATTTAGTAAATAACTTTAAATTTGTCCTTTTGTTT
65 AATGTATTATTTTAG--TGTTTTTATATTAATTTAGTAAATAACCCTGATTTTGGCCATTTGTTT
* **
20530963 GTATTTTTAAAATTCTCAAATTT
128 GTATTTTTAAAATTTTCGGATTT
* * *
20530986 TATTTTTAAAAATATATTATTTTTGTATTTTATTTTTTGTATTATTTTAGTACATAATGTTTCAA
1 TATTTTTAAAAATATACTATTTTCGTATTTTATTTTTTATATTATTTTAGTACATAATGTTTCAA
* *
20531051 ATGTATTATTTTAGTGTTTTTATATTAATTTAGAAAATAACCCTGATTTTGGCCCTTTGTTTGTA
66 ATGTATTATTTTAGTGTTTTTATATTAATTTAGTAAATAACCCTGATTTTGGCCATTTGTTTGTA
20531116 TTTTTAAAATTTTCGGATTT
131 TTTTTAAAATTTTCGGATTT
*
20531136 TATTTTTAAAAATATACTATTTTCGTATTTTATTTTTTATATTATTTTAGTACATAATATTTCAA
1 TATTTTTAAAAATATACTATTTTCGTATTTTATTTTTTATATTATTTTAGTACATAATGTTTCAA
*
20531201 ATGTATTATTTTAGTGTTTTTATATTAATTTAGTAAATACCCCTGATTTTGGCCATTTGTTTGTA
66 ATGTATTATTTTAGTGTTTTTATATTAATTTAGTAAATAACCCTGATTTTGGCCATTTGTTTGTA
*
20531266 TTTTTAAAATTTTTGGATTT
131 TTTTTAAAATTTTCGGATTT
* *
20531286 TATTTTTAAAAATATACTATTTTCGTATTTTATTTTTTATATTATTTTAGTACATAATATTTTAA
1 TATTTTTAAAAATATACTATTTTCGTATTTTATTTTTTATATTATTTTAGTACATAATGTTTCAA
*
20531351 AT-TATTATTTTAGTGTTTTTATATTAATTTAGTAAATAACCCTGATTTTGGCCCTTTGTTTGTA
66 ATGTATTATTTTAGTGTTTTTATATTAATTTAGTAAATAACCCTGATTTTGGCCATTTGTTTGTA
* *
20531415 TTTTTAATATTTTCAGATTT
131 TTTTTAAAATTTTCGGATTT
* * *
20531435 TATTTTTTAAAATATATTATTTTCGTATTTTATTTTTTATATT-TTTTCGTACATAATGTTTCAA
1 TATTTTTAAAAATATACTATTTTCGTATTTTATTTTTTATATTATTTTAGTACATAATGTTTCAA
* *
20531499 ATGTATTATTTTAGTGTTTTTTATATTAATTTAATAAATAATCCTGATTTTGGCCATTTGTTTGT
66 ATGTATTATTTTAGTG-TTTTTATATTAATTTAGTAAATAACCCTGATTTTGGCCATTTGTTTGT
*
20531564 ATTTTTAATATTTTCGGATTT
130 ATTTTTAAAATTTTCGGATTT
*
20531585 TATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTTATATTATTTTAGTACATAATGTTTCA
1 TATTTTTAAAAATATACTATTTTCGTATTTTA-TTTTTTATATTATTTTAGTACATAATGTTTCA
* * *
20531650 AATGTATTATTTTAGTGTTTTTTATATTAATTTAGTAAATAACCCT-AATTTGTCCCTTTGTTTG
65 AATGTATTATTTTAGTG-TTTTTATATTAATTTAGTAAATAACCCTGATTTTGGCCATTTGTTTG
*
20531714 TATTATTT-AAATTTTTGGATTT
129 TATT-TTTAAAATTTTCGGATTT
* **
20531736 TATTTTT-AAAATAAACTATTTTTATATTTTATTTTTTATATTATTTTA
1 TATTTTTAAAAATATACTATTTTCGTATTTTATTTTTTATATTATTTTA
20531784 AAAAAACCCG
Statistics
Matches: 1017, Mismatches: 75, Indels: 25
0.91 0.07 0.02
Matches are distributed among these distances:
148 20 0.02
149 148 0.15
150 416 0.41
151 49 0.05
152 209 0.21
153 169 0.17
154 6 0.01
ACGTcount: A:0.29, C:0.06, G:0.08, T:0.57
Consensus pattern (150 bp):
TATTTTTAAAAATATACTATTTTCGTATTTTATTTTTTATATTATTTTAGTACATAATGTTTCAA
ATGTATTATTTTAGTGTTTTTATATTAATTTAGTAAATAACCCTGATTTTGGCCATTTGTTTGTA
TTTTTAAAATTTTCGGATTT
Found at i:20530866 original size:16 final size:13
Alignment explanation
Indices: 20530845--20530881 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
20530835 TTTTTAAAAA
**
20530845 TATATTATTTTCG
1 TATATTATTTTTT
20530858 TATATTATTTTTT
1 TATATTATTTTTT
20530871 TATATTATTTT
1 TATATTATTTT
20530882 AGTACATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.70
Consensus pattern (13 bp):
TATATTATTTTTT
Found at i:20530896 original size:26 final size:27
Alignment explanation
Indices: 20530844--20530914 Score: 72
Period size: 26 Copynumber: 2.6 Consensus size: 27
20530834 ATTTTTAAAA
* * *
20530844 ATATATTATTTTCGTATATTAT-TTTT
1 ATATATTATTTTAGTACATAATGTTTT
*
20530870 TTATATTATTTTAGTACATAATGTTTT
1 ATATATTATTTTAGTACATAATGTTTT
*
20530897 AAATGTATTATTTTAGTA
1 --ATATATTATTTTAGTA
20530915 TTTTTTTATA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
26 18 0.50
27 4 0.11
29 14 0.39
ACGTcount: A:0.31, C:0.03, G:0.07, T:0.59
Consensus pattern (27 bp):
ATATATTATTTTAGTACATAATGTTTT
Found at i:20531469 original size:299 final size:302
Alignment explanation
Indices: 20530530--20531783 Score: 1907
Period size: 299 Copynumber: 4.2 Consensus size: 302
20530520 CTTTTGTTTG
*
20530530 TATTTTTAAAAATATACTATTTTCGTATTTTATTTTTTATATTATTTTAGTACATAATGTTTTAA
1 TATTTTTAAAAATATACTATTTTCGTATTTTATTTTTTATATTATTTTAGTACATAATGTTTCAA
* * *
20530595 ATGTATTATTTTAGTGTTTTTATATTAATCTAGTAAATCATCCTGATTTTGGCCATTTGTTTGTA
66 ATGTATTATTTTAGTGTTTTTATATTAATTTAGTAAATAACCCTGATTTTGGCCATTTGTTTGTA
* *
20530660 TTTTTAAAATTTTCGGATTTTATTTTTAAAAATATACTATTTTCTTATTTTATTTTTTTTACATT
131 TTTTTAAAATTTTCGGATTTTATTTTTAAAAATATACTATTTTCGTATTTTA-TTTTTTTATATT
* *
20530725 ATTTTAGTACATAATGTTTTAAATATATTATTTTAGTGTTTTTTATATTAATTTAGTAAATAACC
195 ATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTATATTAATTTAGTAAATAACC
* * ** **
20530790 CTAAATTTT-TCTTTTTGTTTGTATTTTTAAAATTCCCAGATTT
260 CT-GATTTTGGCCCTTTGTTTGTATTTTTAAAATTTTCAGATTT
* * *
20530833 TATTTTTAAAAATATATTATTTTCGTATATTATTTTTTTATATTATTTTAGTACATAATGTTTTA
1 TATTTTTAAAAATATACTATTTTCGTATTTTA-TTTTTTATATTATTTTAGTACATAATGTTTCA
* ** * * * *
20530898 AATGTATTATTTTAGTATTTTTTTATATTAATTTAGTAAATAACTTTAAATTTGTCCTTTTGTTT
65 AATGTATTATTTTAG--TGTTTTTATATTAATTTAGTAAATAACCCTGATTTTGGCCATTTGTTT
* ** * * *
20530963 GTATTTTTAAAATTCTCAAATTTTATTTTTAAAAATATATTATTTTTGTATTTTA-TTTTTTGTA
128 GTATTTTTAAAATTTTCGGATTTTATTTTTAAAAATATACTATTTTCGTATTTTATTTTTTTATA
*
20531027 TTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTG-TTTTTATATTAATTTAGAAAATAA
193 TTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTATATTAATTTAGTAAATAA
*
20531091 CCCTGATTTTGGCCCTTTGTTTGTATTTTTAAAATTTTCGGATTT
258 CCCTGATTTTGGCCCTTTGTTTGTATTTTTAAAATTTTCAGATTT
*
20531136 TATTTTTAAAAATATACTATTTTCGTATTTTATTTTTTATATTATTTTAGTACATAATATTTCAA
1 TATTTTTAAAAATATACTATTTTCGTATTTTATTTTTTATATTATTTTAGTACATAATGTTTCAA
*
20531201 ATGTATTATTTTAGTGTTTTTATATTAATTTAGTAAATACCCCTGATTTTGGCCATTTGTTTGTA
66 ATGTATTATTTTAGTGTTTTTATATTAATTTAGTAAATAACCCTGATTTTGGCCATTTGTTTGTA
*
20531266 TTTTTAAAATTTTTGGATTTTATTTTTAAAAATATACTATTTTCGTATTTTA-TTTTTTATATTA
131 TTTTTAAAATTTTCGGATTTTATTTTTAAAAATATACTATTTTCGTATTTTATTTTTTTATATTA
* *
20531330 TTTTAGTACATAATATTTTAAAT-TATTATTTTAGTG-TTTTTATATTAATTTAGTAAATAACCC
196 TTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTATATTAATTTAGTAAATAACCC
*
20531393 TGATTTTGGCCCTTTGTTTGTATTTTTAATATTTTCAGATTT
261 TGATTTTGGCCCTTTGTTTGTATTTTTAAAATTTTCAGATTT
* * *
20531435 TATTTTTTAAAATATATTATTTTCGTATTTTATTTTTTATATT-TTTTCGTACATAATGTTTCAA
1 TATTTTTAAAAATATACTATTTTCGTATTTTATTTTTTATATTATTTTAGTACATAATGTTTCAA
* *
20531499 ATGTATTATTTTAGTGTTTTTTATATTAATTTAATAAATAATCCTGATTTTGGCCATTTGTTTGT
66 ATGTATTATTTTAGTG-TTTTTATATTAATTTAGTAAATAACCCTGATTTTGGCCATTTGTTTGT
* *
20531564 ATTTTTAATATTTTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTTATATT
130 ATTTTTAAAATTTTCGGATTTTATTTTTAAAAATATACTATTTTCGTATTTTATTTTTTTATATT
20531629 ATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTATATTAATTTAGTAAATAACC
195 ATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTATATTAATTTAGTAAATAACC
* * **
20531694 CT-AATTTGTCCCTTTGTTTGTATTATTT-AAATTTTTGGATTT
260 CTGATTTTGGCCCTTTGTTTGTATT-TTTAAAATTTTCAGATTT
* **
20531736 TATTTTT-AAAATAAACTATTTTTATATTTTATTTTTTATATTATTTTA
1 TATTTTTAAAAATATACTATTTTCGTATTTTATTTTTTATATTATTTTA
20531784 AAAAAACCCG
Statistics
Matches: 865, Mismatches: 76, Indels: 22
0.90 0.08 0.02
Matches are distributed among these distances:
298 35 0.04
299 215 0.25
300 185 0.21
301 55 0.06
302 81 0.09
303 115 0.13
304 92 0.11
306 87 0.10
ACGTcount: A:0.29, C:0.06, G:0.08, T:0.57
Consensus pattern (302 bp):
TATTTTTAAAAATATACTATTTTCGTATTTTATTTTTTATATTATTTTAGTACATAATGTTTCAA
ATGTATTATTTTAGTGTTTTTATATTAATTTAGTAAATAACCCTGATTTTGGCCATTTGTTTGTA
TTTTTAAAATTTTCGGATTTTATTTTTAAAAATATACTATTTTCGTATTTTATTTTTTTATATTA
TTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTATATTAATTTAGTAAATAACCC
TGATTTTGGCCCTTTGTTTGTATTTTTAAAATTTTCAGATTT
Found at i:20531891 original size:17 final size:17
Alignment explanation
Indices: 20531821--20531901 Score: 58
Period size: 17 Copynumber: 4.9 Consensus size: 17
20531811 AAAAAAATTA
20531821 TTTTTTT-ATATTTTAT
1 TTTTTTTAATATTTTAT
* **
20531837 TTCTTTTCGTATTTTA-
1 TTTTTTTAATATTTTAT
* ***
20531853 TTTTTTTATTAAGATAT
1 TTTTTTTAATATTTTAT
*
20531870 ATTTTTTAATATTTTAT
1 TTTTTTTAATATTTTAT
* *
20531887 TTTTTATACTATTTT
1 TTTTTTTAATATTTT
20531902 TGTAAAATAG
Statistics
Matches: 47, Mismatches: 16, Indels: 3
0.71 0.24 0.05
Matches are distributed among these distances:
16 16 0.34
17 31 0.66
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.72
Consensus pattern (17 bp):
TTTTTTTAATATTTTAT
Found at i:20532330 original size:3 final size:3
Alignment explanation
Indices: 20532317--20532367 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
20532307 TGCCGCCTGT
* *
20532317 TTC TCC TTC TTC TTC TTC -TC TTC TTTC TT- TTC TTC TTC TCC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC
20532361 TTTC TTC
1 -TTC TTC
20532368 CCAAAATGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
2 4 0.10
3 30 0.75
4 6 0.15
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:20532349 original size:20 final size:21
Alignment explanation
Indices: 20532326--20532366 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
20532316 TTTCTCCTTC
20532326 TTCTTCTTCT-CTTCTTTCTT
1 TTCTTCTTCTCCTTCTTTCTT
20532346 TTCTTCTTCTCCTTCTTTCTT
1 TTCTTCTTCTCCTTCTTTCTT
20532367 CCCAAAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (21 bp):
TTCTTCTTCTCCTTCTTTCTT
Found at i:20532587 original size:17 final size:17
Alignment explanation
Indices: 20532558--20532590 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20532548 TTTTGCTTCA
*
20532558 TTTTTTTTGTTTTTAAT
1 TTTTTTTTCTTTTTAAT
20532575 TTTTTTTTCTTTTTAA
1 TTTTTTTTCTTTTTAA
20532591 CAGAAAATGG
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:0.12, C:0.03, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTTTTTTCTTTTTAAT
Found at i:20547640 original size:18 final size:18
Alignment explanation
Indices: 20547617--20547669 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
20547607 GATAAATCCT
20547617 AATCAAGGATTTACTCCC
1 AATCAAGGATTTACTCCC
*
20547635 AATCAAGGATTGACTCCC
1 AATCAAGGATTTACTCCC
*
20547653 AATCAGGGATTTACTCC
1 AATCAAGGATTTACTCC
20547670 TATATTAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.26
Consensus pattern (18 bp):
AATCAAGGATTTACTCCC
Found at i:20555627 original size:16 final size:16
Alignment explanation
Indices: 20555605--20555660 Score: 87
Period size: 16 Copynumber: 3.5 Consensus size: 16
20555595 TGTTTGGTTC
20555605 ACTGTAATGGAATATG-
1 ACTGTAATGGAATA-GA
*
20555621 GCTGTAATGGAATAGA
1 ACTGTAATGGAATAGA
20555637 ACTGTAATGGAATAGA
1 ACTGTAATGGAATAGA
20555653 ACTGTAAT
1 ACTGTAAT
20555661 AAGTAATTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
15 1 0.03
16 36 0.97
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.29
Consensus pattern (16 bp):
ACTGTAATGGAATAGA
Found at i:20555695 original size:46 final size:44
Alignment explanation
Indices: 20555642--20555735 Score: 143
Period size: 44 Copynumber: 2.1 Consensus size: 44
20555632 ATAGAACTGT
20555642 AATGGAATAGAACTGTAATAAGTAATTCAACTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAAT-AGT-ATTCAACTGTTTGGTTGAATGG
***
20555688 AATGGAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGTATTCAACTGTTTGGTTGAATGG
20555732 AATG
1 AATG
20555736 ATGTTGTAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 23 0.51
45 3 0.07
46 19 0.42
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAGTATTCAACTGTTTGGTTGAATGG
Found at i:20555929 original size:17 final size:17
Alignment explanation
Indices: 20555907--20555939 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
20555897 AATTATTATT
20555907 AAATATAATTTAATAAA
1 AAATATAATTTAATAAA
20555924 AAATATAATTTAATAA
1 AAATATAATTTAATAA
20555940 CATTCATTAT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATATAATTTAATAAA
Found at i:20556468 original size:18 final size:18
Alignment explanation
Indices: 20556445--20556479 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20556435 ACGTGGTAGT
*
20556445 CCAACTAGATTTTAAGTG
1 CCAACTAGATCTTAAGTG
20556463 CCAACTAGATCTTAAGT
1 CCAACTAGATCTTAAGT
20556480 ATATCTGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (18 bp):
CCAACTAGATCTTAAGTG
Found at i:20556538 original size:40 final size:40
Alignment explanation
Indices: 20556487--20556731 Score: 373
Period size: 40 Copynumber: 6.1 Consensus size: 40
20556477 AGTATATCTG
* * * *
20556487 TTAATACATACTTCATCCGGGTAAATTATATAATTTTCTG
1 TTAATACATACTTCACCCGGGTAAATTATACAGTTTTCTA
*
20556527 TTAATACATACTTTACCCGGGTAAATTATACAGTTTTCTA
1 TTAATACATACTTCACCCGGGTAAATTATACAGTTTTCTA
* * *
20556567 TTAATACATACTTCATCCGGATAAATTATACAGTTTTCTG
1 TTAATACATACTTCACCCGGGTAAATTATACAGTTTTCTA
*
20556607 TTAATACATACTTTACCCGGGTAAATTATACAGTTTTCTA
1 TTAATACATACTTCACCCGGGTAAATTATACAGTTTTCTA
*
20556647 TTAATACATACTTTACCCGGGTAAATTATACAGTTTTCTA
1 TTAATACATACTTCACCCGGGTAAATTATACAGTTTTCTA
* * *
20556687 TTAATATATACTTCATCCGGATAAATTATACAGTTTTCTA
1 TTAATACATACTTCACCCGGGTAAATTATACAGTTTTCTA
20556727 TTAAT
1 TTAAT
20556732 GTGCTTGTGA
Statistics
Matches: 188, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 188 1.00
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.41
Consensus pattern (40 bp):
TTAATACATACTTCACCCGGGTAAATTATACAGTTTTCTA
Found at i:20556698 original size:120 final size:120
Alignment explanation
Indices: 20556483--20556731 Score: 435
Period size: 120 Copynumber: 2.1 Consensus size: 120
20556473 CTTAAGTATA
* * *
20556483 TCTGTTAATACATACTTCATCCGGGTAAATTATATAATTTTCTGTTAATACATACTTTACCCGGG
1 TCTGTTAATACATACTTCACCCGGGTAAATTATACAATTTTCTATTAATACATACTTTACCCGGG
20556548 TAAATTATACAGTTTTCTATTAATACATACTTCATCCGGATAAATTATACAGTTT
66 TAAATTATACAGTTTTCTATTAATACATACTTCATCCGGATAAATTATACAGTTT
* *
20556603 TCTGTTAATACATACTTTACCCGGGTAAATTATACAGTTTTCTATTAATACATACTTTACCCGGG
1 TCTGTTAATACATACTTCACCCGGGTAAATTATACAATTTTCTATTAATACATACTTTACCCGGG
*
20556668 TAAATTATACAGTTTTCTATTAATATATACTTCATCCGGATAAATTATACAGTTT
66 TAAATTATACAGTTTTCTATTAATACATACTTCATCCGGATAAATTATACAGTTT
*
20556723 TCTATTAAT
1 TCTGTTAAT
20556732 GTGCTTGTGA
Statistics
Matches: 122, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 122 1.00
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (120 bp):
TCTGTTAATACATACTTCACCCGGGTAAATTATACAATTTTCTATTAATACATACTTTACCCGGG
TAAATTATACAGTTTTCTATTAATACATACTTCATCCGGATAAATTATACAGTTT
Found at i:20563563 original size:11 final size:12
Alignment explanation
Indices: 20563533--20563563 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
20563523 ATAGATTAAA
20563533 AATAAAAAAAAT
1 AATAAAAAAAAT
*
20563545 TATAAAAAAAAT
1 AATAAAAAAAAT
20563557 AATAAAA
1 AATAAAA
20563564 TATTAGGTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (12 bp):
AATAAAAAAAAT
Found at i:20571636 original size:131 final size:131
Alignment explanation
Indices: 20571501--20571766 Score: 408
Period size: 131 Copynumber: 2.0 Consensus size: 131
20571491 TTTAAGTAAT
* *
20571501 TTTTAGAAGATATGAATGAAATCTTAAAGGGATACTCGATTATTTTGAGCAAACGCGAAATTGCA
1 TTTTAAAAGACATGAATGAAATCTTAAAGGGATACTCGATTATTTTGAGCAAACGCGAAATTGCA
* * *
20571566 ACCCAACGCGTTAGGGCACGATTCCGTGAATTACTC-AATATCGAATCTCGTCGTCGTTTTGAAG
66 ACCCAACACGTTAGGGCACGATTCCGCGAATTAC-CAAAAATCGAATCTCGTCGTCGTTTTGAAG
20571630 AA
130 AA
* * * * *
20571632 TTTTAAAAGACATGAATGAAATTTTGAAGTGATATTCGATTATTTTGAGCAAGCGCGAAATTGCA
1 TTTTAAAAGACATGAATGAAATCTTAAAGGGATACTCGATTATTTTGAGCAAACGCGAAATTGCA
* *
20571697 ACCCAACACGTTAGGGCACGATTCCGCGAATTGCCAAAAATCGAATCTCGTCTTCGTTTTGAAGA
66 ACCCAACACGTTAGGGCACGATTCCGCGAATTACCAAAAATCGAATCTCGTCGTCGTTTTGAAGA
20571762 A
131 A
20571763 TTTT
1 TTTT
20571767 TAAATGAATG
Statistics
Matches: 122, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
130 1 0.01
131 121 0.99
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (131 bp):
TTTTAAAAGACATGAATGAAATCTTAAAGGGATACTCGATTATTTTGAGCAAACGCGAAATTGCA
ACCCAACACGTTAGGGCACGATTCCGCGAATTACCAAAAATCGAATCTCGTCGTCGTTTTGAAGA
A
Found at i:20578130 original size:21 final size:21
Alignment explanation
Indices: 20578105--20578148 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
20578095 ATTAGTGTAG
*
20578105 TTTACCCTTATAA-TTATTATA
1 TTTACCCTAATAATTTATT-TA
*
20578126 TTTACTCTAATAATTTATTTA
1 TTTACCCTAATAATTTATTTA
20578147 TT
1 TT
20578149 AGTATATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTACCCTAATAATTTATTTA
Found at i:20581859 original size:3 final size:3
Alignment explanation
Indices: 20581851--20581878 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
20581841 CTGTAAATAC
20581851 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
20581879 TCCTTGATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:20584716 original size:12 final size:11
Alignment explanation
Indices: 20584699--20584745 Score: 51
Period size: 12 Copynumber: 4.2 Consensus size: 11
20584689 AAACTTGTTA
20584699 TTTGTTTATTTG
1 TTTGTTT-TTTG
20584711 TTTGTTTGTTTG
1 TTTGTTT-TTTG
*
20584723 TTT-TTTTTTT
1 TTTGTTTTTTG
*
20584733 TTTTTTTTTTG
1 TTTGTTTTTTG
20584744 TT
1 TT
20584746 CTTTAGCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
10 6 0.19
11 11 0.35
12 14 0.45
ACGTcount: A:0.02, C:0.00, G:0.13, T:0.85
Consensus pattern (11 bp):
TTTGTTTTTTG
Found at i:20600283 original size:51 final size:51
Alignment explanation
Indices: 20600212--20600371 Score: 234
Period size: 51 Copynumber: 3.2 Consensus size: 51
20600202 CTGATCACAT
*
20600212 TTATCACTTGTCACTGATCAGATAAGTGTAGCTTTAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTTAAGCTACCACTTATCAC
* *
20600263 TTATCACTTGTCACTGATCAGATAAGAGTAGC-TAAGCTACCACTTATCAT
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTTAAGCTACCACTTATCAC
* * *
20600313 TTGTCACTTATCACTGATCAGATAAGTGTAG-TTGAGGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTT-AAGCTACCACTTATCAC
*
20600364 TTGTCACT
1 TTATCACT
20600372 GATCAGAAGT
Statistics
Matches: 99, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
50 45 0.45
51 54 0.55
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (51 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTTAAGCTACCACTTATCAC
Found at i:20611683 original size:3 final size:3
Alignment explanation
Indices: 20611670--20611700 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
20611660 AAAAGTAAAT
20611670 TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
20611701 ATTAAATTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:20612836 original size:13 final size:13
Alignment explanation
Indices: 20612818--20612844 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20612808 GCTCAATAGG
20612818 GACACGCCCGTGT
1 GACACGCCCGTGT
20612831 GACACGCCCGTGT
1 GACACGCCCGTGT
20612844 G
1 G
20612845 CGATTACTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.37, G:0.33, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:20613475 original size:19 final size:19
Alignment explanation
Indices: 20613451--20613497 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
20613441 AATGCCTCTT
*
20613451 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTGCAT-CA
20613470 TTTGCATTACATTGCATCA
1 TTTGCATTACATTGCATCA
*
20613489 TATGCATTA
1 TTTGCATTA
20613498 AATTTCATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTGCATCA
Found at i:20621816 original size:130 final size:130
Alignment explanation
Indices: 20621633--20621911 Score: 373
Period size: 130 Copynumber: 2.1 Consensus size: 130
20621623 TATTATCGCG
* * * * * *
20621633 AATCTTATCTCCTTGAAGTTGCAGTAGAGTAGATTGAAGCCACTAATCTTATCTCCCTGAAGATG
1 AATCTTATCTCTTTGAAATTGCAGTAGAGCAGATTAAAGCCACTAACCTTATCTCCCTAAAGATG
* * * *
20621698 TAGTGGAG-GTTGAAGTTACAAGTCTTATCTCCTTGAAGTTGCAGTGGAACAGATTGAAGATAGC
66 CAGTGGAGAGTTGAAGTTACAAGTCTTATCTCCCTGAAG-AGCAGTGGAACAAATTGAAGATAGC
20621762 A
130 A
* * *
20621763 AATCTTATCTCTTTGAAATTGCAGTAGAGCATATTAAAGCTA-TAAACCTTATCTCCCTAAAGTT
1 AATCTTATCTCTTTGAAATTGCAGTAGAGCAGATTAAAGCCACT-AACCTTATCTCCCTAAAGAT
*
20621827 GCAGTGGAGCAAGTTGAAGTTACAAGTCTTATCTCCCTGAAGAGCAGTGGAACAAATTTAAGATA
65 GCAGTGGAG--AGTTGAAGTTACAAGTCTTATCTCCCTGAAGAGCAGTGGAACAAATTGAAGATA
20621892 GCA
128 GCA
*
20621895 AATCTTATCTCTCTGAA
1 AATCTTATCTCTTTGAA
20621912 GTTACAACAA
Statistics
Matches: 130, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
129 1 0.01
130 61 0.47
132 39 0.30
133 29 0.22
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (130 bp):
AATCTTATCTCTTTGAAATTGCAGTAGAGCAGATTAAAGCCACTAACCTTATCTCCCTAAAGATG
CAGTGGAGAGTTGAAGTTACAAGTCTTATCTCCCTGAAGAGCAGTGGAACAAATTGAAGATAGCA
Found at i:20621858 original size:44 final size:44
Alignment explanation
Indices: 20621633--20622246 Score: 289
Period size: 44 Copynumber: 13.6 Consensus size: 44
20621623 TATTATCGCG
* * * ** *
20621633 AATCTTATCTCCTTGAAGTTGCAGTAGAG-TAGATTGAAGCCACT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAG-TTGAAGATACA
* * *
20621677 AATCTTATCTCCCTGAAGATGTAGTGGAG---GTTGAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGTTGAAGATACA
* * *
20621718 AGTCTTATCTCCTTGAAGTTGCAGTGGAAC-AGATTGAAGATAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAG-TTGAAGATA-CA
** * * * * *
20621763 AATCTTATCTCTTTGAAATTGCAGTAGAGCATA-TTAAAGCTATA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCA-AGTTGAAGATACA
* * *
20621807 AACCTTATCTCCCTAAAGTTGCAGTGGAGCAAGTTGAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGTTGAAGATACA
* * * * *
20621851 AGTCTTATCTCCCTGAAG-AGCAGTGGAACAAATTTAAGATAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGTTGAAGATA-CA
* * **** ***
20621895 AATCTTATCTCTCTGAAGTTACAACAAAGC-AGATTGAAGTCATTGTGGTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAG-TTGAAG--A---T-ACA
* * **
20621945 AATCTTATCTCCTTGAAGTTGCAGTGGAGC-AGATTAAAGCCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAG-TTGAAGATACA
* * * * * *
20621989 AATCTTATCTTCTTGAAGTTGTAGTGGAGTAAATTGAAGATAACG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGTTGAAGAT-ACA
** *
20622034 AATCTTATCTCCCTGAAGTTATAGTGGAGC-AGATTGAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAG-TTGAAGATACA
* * * * * **
20622078 AATCCTATTTCCCTGAAGTTGCAATAGAGC-AGATTGAAAATAGTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAG-TTGAAGATA-CA
* * * * * * *
20622123 AATCTTATTTCCTTTAAGTTACAGTGGAACAAATTAAAGCTACAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGTT---G----AAGATACA
* * * *
20622174 AATCTCATCTCCGTGAAGTTGCAGTAGAGCATA-TTGAAGATAACG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCA-AGTTGAAGAT-ACA
* *
20622219 AATCTTATTTCCCTGAAGTTGTAGTGGA
1 AATCTTATCTCCCTGAAGTTGCAGTGGA
20622247 ACAGATTAAA
Statistics
Matches: 424, Mismatches: 116, Indels: 59
0.71 0.19 0.10
Matches are distributed among these distances:
41 32 0.08
42 1 0.00
43 20 0.05
44 174 0.41
45 129 0.30
46 1 0.00
47 2 0.00
48 2 0.00
50 32 0.08
51 26 0.06
52 5 0.01
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGTTGAAGATACA
Found at i:20622061 original size:89 final size:89
Alignment explanation
Indices: 20621633--20622482 Score: 337
Period size: 89 Copynumber: 9.3 Consensus size: 89
20621623 TATTATCGCG
* * ** * *
20621633 AATCTTATC-TCCTTGAAGTTGCAGTAGAGTAGATTGAAG-CCACTAATCTTATCTCCCTGAAGA
1 AATCTTATCTTCC-TGAAGTTGCAGTAGAGCAAATTGAAGATAACGAATCTTATCTCCCTGAAGT
** * * **
20621696 TGTAGTGG---AGGTTGAAGTTACA
65 TACAGTGGAACAGATTAAAGCCACA
* * * * * * ** *
20621718 AGTCTTATC-TCCTTGAAGTTGCAGTGGAACAGATTGAAGATAGCAAATCTTATCTCTTTGAAAT
1 AATCTTATCTTCC-TGAAGTTGCAGTAGAGCAAATTGAAGATAACGAATCTTATCTCCCTGAAGT
* * * * * *
20621782 TGCAGTAGAGCATATTAAAGCTATA
65 TACAGTGGAACAGATTAAAGCCACA
* * * * * *
20621807 AACCTTATCTCCCTAAAGTTGCAGTGGAGCAAGTTGAAG-TTAC-AAGTCTTATCTCCCTGAAG-
1 AATCTTATCTTCCTGAAGTTGCAGTAGAGCAAATTGAAGATAACGAA-TCTTATCTCCCTGAAGT
* * **
20621869 -AGCAGTGGAACAAATTTAAGATAGCA
65 TA-CAGTGGAACAGATTAAAGCCA-CA
* ** * * *** *
20621895 AATCTTATC-TCTCTGAAGTTACAACAAAGCAGATTGAAGTCATTGTGGTGAATCTTATCTCCTT
1 AATCTTATCTTC-CTGAAGTTGCAGTAGAGCAAATTGAAG--A---TAACGAATCTTATCTCCCT
* *
20621959 GAAGTTGCAGTGGAGCAGATTAAAGCCACA
60 GAAGTTACAGTGGAACAGATTAAAGCCACA
* * * *
20621989 AATCTTATCTTCTTGAAGTTGTAGTGGAGTAAATTGAAGATAACGAATCTTATCTCCCTGAAGTT
1 AATCTTATCTTCCTGAAGTTGCAGTAGAGCAAATTGAAGATAACGAATCTTATCTCCCTGAAGTT
* * * **
20622054 ATAGTGGAGCAGATTGAAGTTACA
66 ACAGTGGAACAGATTAAAGCCACA
* * * * ** * * *
20622078 AATCCTAT-TTCCCTGAAGTTGCAATAGAGCAGATTGAAAATAGTGAATCTTATTTCCTTTAAGT
1 AATCTTATCTT-CCTGAAGTTGCAGTAGAGCAAATTGAAGATAACGAATCTTATCTCCCTGAAGT
*
20622142 TACAGTGGAACAAATTAAAGCTACAAGTTACA
65 TACAGTGGAACAGATTAAAGC--C-----ACA
* * *
20622174 AATCTCATC-TCCGTGAAGTTGCAGTAGAGCATATTGAAGATAACGAATCTTATTTCCCTGAAGT
1 AATCTTATCTTCC-TGAAGTTGCAGTAGAGCAAATTGAAGATAACGAATCTTATCTCCCTGAAGT
** *
20622238 TGTAGTGGAACAGATTAAAACTACAAATTGCA
65 TACAGTGGAACAGATTAAAGC--C--A---CA
** * * * * * * *
20622270 AATCTTATCCCCCTGAAGTTGCAGTGGAGCAGATTGAAGAATAGCAAATCTCATTTCCCTAAAGT
1 AATCTTATCTTCCTGAAGTTGCAGTAGAGCAAATTGAAG-ATAACGAATCTTATCTCCCTGAAGT
* *
20622335 TGC-GATAGAACAGATTAAAGCTACAAGTTACA
65 TACAG-TGGAACAGATTAAAGC--C-----ACA
* * * * * * * * * * * *
20622367 AATTTTAGCTCCCTGAAGTTACAGTAAAGCAATTTAAAGCT-ACAAATATTATCTCCCTAAATTT
1 AATCTTATCTTCCTGAAGTTGCAGTAGAGCAAATTGAAGATAACGAATCTTATCTCCCTGAAGTT
* ** * *
20622431 GCAGTGGGTCAGATTTAAGCTACA
66 ACAGTGGAACAGATTAAAGCCACA
*
20622455 AATCTTAT-TTCCCTGAAGTTACAGTAGA
1 AATCTTATCTT-CCTGAAGTTGCAGTAGA
20622483 ACAGATGAAA
Statistics
Matches: 578, Mismatches: 147, Indels: 77
0.72 0.18 0.10
Matches are distributed among these distances:
85 35 0.06
86 22 0.04
87 20 0.03
88 70 0.12
89 142 0.25
90 2 0.00
92 1 0.00
93 1 0.00
94 45 0.08
95 54 0.09
96 111 0.19
97 74 0.13
100 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (89 bp):
AATCTTATCTTCCTGAAGTTGCAGTAGAGCAAATTGAAGATAACGAATCTTATCTCCCTGAAGTT
ACAGTGGAACAGATTAAAGCCACA
Found at i:20622204 original size:96 final size:96
Alignment explanation
Indices: 20622070--20622455 Score: 384
Period size: 96 Copynumber: 4.0 Consensus size: 96
20622060 GAGCAGATTG
* * *
20622070 AAGTTACAAATC-CTATTTCCCTGAAGTTGCAATAGAGCAGATTGAAAATAGTGAATCTTATTTC
1 AAGTTACAAATCTC-ATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAAATAGCGAATCTTATTTC
* * * *
20622134 CTTTAAGTTACAGTGGAACAAATTAAAGCTAC
65 CCTAAAGTTGCAGTGGAACAGATTAAAGCTAC
* * * *
20622166 AAGTTACAAATCTCATCTCCGTGAAGTTGCAGTAGAGCATATTGAAGATAACGAATCTTATTTCC
1 AAGTTACAAATCTCATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAAATAGCGAATCTTATTTCC
* * *
20622231 CTGAAGTTGTAGTGGAACAGATTAAAACTAC
66 CTAAAGTTGCAGTGGAACAGATTAAAGCTAC
* * * * * * *
20622262 AAATTGCAAATCTTATCCCCCTGAAGTTGCAGTGGAGCAGATTGAAGAATAGCAAATCTCATTTC
1 AAGTTACAAATCTCATCTCCCTGAAGTTGCAGTAGAGCAGATTGAA-AATAGCGAATCTTATTTC
*
20622327 CCTAAAGTTGC-GATAGAACAGATTAAAGCTAC
65 CCTAAAGTTGCAG-TGGAACAGATTAAAGCTAC
* * * * * * * * * *
20622359 AAGTTACAAATTTTAGCTCCCTGAAGTTACAGTAAAGCA-ATTTAAAGCTA-CAAATATTATCTC
1 AAGTTACAAATCTCATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAA-ATAGCGAATCTTATTTC
* ** *
20622422 CCTAAATTTGCAGTGGGTCAGATTTAAGCTAC
65 CCTAAAGTTGCAGTGGAACAGATTAAAGCTAC
20622454 AA
1 AA
20622456 ATCTTATTTC
Statistics
Matches: 239, Mismatches: 46, Indels: 11
0.81 0.16 0.04
Matches are distributed among these distances:
95 38 0.16
96 129 0.54
97 72 0.30
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (96 bp):
AAGTTACAAATCTCATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAAATAGCGAATCTTATTTCC
CTAAAGTTGCAGTGGAACAGATTAAAGCTAC
Found at i:20622488 original size:44 final size:45
Alignment explanation
Indices: 20622363--20622496 Score: 132
Period size: 44 Copynumber: 3.0 Consensus size: 45
20622353 AGCTACAAGT
* *
20622363 TACAAATTTTAGCTCCCTGAAGTTACAGTA-AAGCA-ATTTAAAGC
1 TACAAATATTATCTCCCTGAAGTTACAGTAGAA-CAGATTTAAAGC
* * * * **
20622407 TACAAATATTATCTCCCTAAATTTGCAGTGGGTCAGATTT-AAGC
1 TACAAATATTATCTCCCTGAAGTTACAGTAGAACAGATTTAAAGC
* * *
20622451 TACAAATCTTATTTCCCTGAAGTTACAGTAGAACAGA-TGAAAGC
1 TACAAATATTATCTCCCTGAAGTTACAGTAGAACAGATTTAAAGC
20622495 TA
1 TA
20622497 TAAGTTACGA
Statistics
Matches: 70, Mismatches: 17, Indels: 6
0.75 0.18 0.06
Matches are distributed among these distances:
43 1 0.01
44 65 0.93
45 4 0.06
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.31
Consensus pattern (45 bp):
TACAAATATTATCTCCCTGAAGTTACAGTAGAACAGATTTAAAGC
Found at i:20622522 original size:139 final size:141
Alignment explanation
Indices: 20622268--20622522 Score: 320
Period size: 139 Copynumber: 1.8 Consensus size: 141
20622258 CTACAAATTG
* *
20622268 CAAATCTTATCCCCCTGAAGTTGCAGTGGAGCAGATTGAAGAATAGCAAATCTCATTTCCCTAAA
1 CAAATATTATCCCCCTAAAGTTGCAGTGGAGCAGATTGAAGAATAGCAAATCTCATTTCCCTAAA
* * * *
20622333 GTTGCGATAGAACAGATTAAAGCTACAAGTTACAAATTTTAGCTCCCTGAAGTTACAGTAAAGCA
66 GTTACGATAGAACAGATGAAAGCTACAAGTTACAAATCTTAGCTCACTGAAGTTACAGTAAAGCA
20622398 ATTTAAAGCTA
131 ATTTAAAGCTA
* * * * * *
20622409 CAAATATTATCTCCCTAAATTTGCAGTGG-GTCAGATTTAAG-CTA-CAAATCTTATTTCCCTGA
1 CAAATATTATCCCCCTAAAGTTGCAGTGGAG-CAGATTGAAGAATAGCAAATCTCATTTCCCTAA
* * **
20622471 AGTTAC-AGTAGAACAGATGAAAGCTATAAGTTACGAATCTTATTTCACTGAA
65 AGTTACGA-TAGAACAGATGAAAGCTACAAGTTACAAATCTTAGCTCACTGAA
20622523 ATAGTAGTGG
Statistics
Matches: 96, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
138 1 0.01
139 58 0.60
140 3 0.03
141 34 0.35
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.29
Consensus pattern (141 bp):
CAAATATTATCCCCCTAAAGTTGCAGTGGAGCAGATTGAAGAATAGCAAATCTCATTTCCCTAAA
GTTACGATAGAACAGATGAAAGCTACAAGTTACAAATCTTAGCTCACTGAAGTTACAGTAAAGCA
ATTTAAAGCTA
Found at i:20629281 original size:38 final size:38
Alignment explanation
Indices: 20629182--20629291 Score: 116
Period size: 38 Copynumber: 2.9 Consensus size: 38
20629172 ACAATTAATT
* * *
20629182 ATTTTTTAAAATT-TAAAAATTCAAAATATATGTTATA
1 ATTTTTTAAAATTATTAAATTTAAAAATATATGTTATA
* * *
20629219 AGTTTTTTAAAA-AATTATATTTTAAAAATATATGTTTTA
1 A-TTTTTTAAAATTATTA-AATTTAAAAATATATGTTATA
* *
20629258 ATTTTTTAAAATTATTAAATTTAATAATCTATGT
1 ATTTTTTAAAATTATTAAATTTAAAAATATATGT
20629292 GGCATTCCAC
Statistics
Matches: 59, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
37 1 0.02
38 36 0.61
39 22 0.37
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.50
Consensus pattern (38 bp):
ATTTTTTAAAATTATTAAATTTAAAAATATATGTTATA
Found at i:20630222 original size:22 final size:22
Alignment explanation
Indices: 20630197--20630239 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
20630187 TATCCAAACA
20630197 ATAACAATAAAATAGTAGCAAC
1 ATAACAATAAAATAGTAGCAAC
* * *
20630219 ATAATAGTAAAATGGTAGCAA
1 ATAACAATAAAATAGTAGCAA
20630240 AACAAGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.09, G:0.14, T:0.21
Consensus pattern (22 bp):
ATAACAATAAAATAGTAGCAAC
Found at i:20631041 original size:32 final size:34
Alignment explanation
Indices: 20630995--20631059 Score: 82
Period size: 35 Copynumber: 2.0 Consensus size: 34
20630985 ATAAAAAATG
*
20630995 TATAAAATTATT-AAAGA-TT-AAAATAATATAA
1 TATAAAATTATTAAAAAATTTAAAAATAATATAA
*
20631026 TATAAATATTTTTAAAAAATTTAAAAATAATATA
1 TATAAA-ATTATTAAAAAATTTAAAAATAATATA
20631060 GACAGGCCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 6 0.21
32 5 0.18
33 4 0.14
34 2 0.07
35 11 0.39
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (34 bp):
TATAAAATTATTAAAAAATTTAAAAATAATATAA
Found at i:20631743 original size:24 final size:24
Alignment explanation
Indices: 20631683--20631736 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
20631673 AATGTTATTG
20631683 TTAAAAATATTAATTTTCGGTTGA
1 TTAAAAATATTAATTTTCGGTTGA
20631707 TTAAAAATATTAATTTTCGGTTGA
1 TTAAAAATATTAATTTTCGGTTGA
20631731 TTAAAA
1 TTAAAA
20631737 TTTTTAACAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.41, C:0.04, G:0.11, T:0.44
Consensus pattern (24 bp):
TTAAAAATATTAATTTTCGGTTGA
Found at i:20633765 original size:3 final size:3
Alignment explanation
Indices: 20633757--20633805 Score: 55
Period size: 3 Copynumber: 16.0 Consensus size: 3
20633747 ATGGTTTAAA
* *
20633757 AAT AAT AAT AAT AAT AAT GAT AAT AAT ATT AAT -AT AAAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT -AAT
20633803 AAT
1 AAT
20633806 CTAAAGTTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 2 0.05
3 32 0.82
4 5 0.13
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:20635531 original size:44 final size:44
Alignment explanation
Indices: 20635464--20635962 Score: 245
Period size: 44 Copynumber: 11.0 Consensus size: 44
20635454 CAACTTGTCG
*
20635464 CTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTGCTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTGCTAT
* *
20635508 CTTCAATCTGCTCCACTGTAACTTCAGGGAAATAAGGTTTGCTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAAATAA-GATTGCTAT
* ** * * *
20635553 CTTCAATCTGCTCCACTACAACTTCATAGAGATAAAGTTTG-TAG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAAAT-AAGATTGCTAT
* * * ** *
20635597 CTTTAATCTGCTCTACTGCAACTTTAAAGAGATAAGATTCGCTATAAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATT-GC--T-AT
* ** * *
20635645 AACTTCAATCCG-TCACACTGCAACTTCAGGGGTATGAGATTTG-TAA
1 --CTTCAATCTGCTC-CACTGCAACTTCAGGGAAATAAGA-TTGCTAT
* * * * * * *
20635691 CTTCAATCTACTCTACTGTAATTTCAAGGAGATAAGATTTGTTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGA-TTGCTAT
* * * * *
20635736 TTTTAACCTGCTCCACTGCGACTTCAGGGAAATAAGGTTTGTAATTTG-TAG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAAATAA-----G--A-TTGCTAT
* * * * * **
20635787 CTTTAATCTGATCTACTACAACTTCAGAGAAATAAGATTTTTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTGCTAT
* ** * * * * * *
20635831 CTTTAATCTATTCTACTACAACTTTAGAGAGATAAGATTTTCTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGA-TTGCTAT
* * * * * *
20635876 CTTCGATCTACTCCAATGCGAA-TTCAGGGAGATAAGATT-ATAA
1 CTTCAATCTGCTCCACTGC-AACTTCAGGGAAATAAGATTGCTAT
* **
20635919 CTTCAATCTACTCCACTGCAACTTCAGGGAGGTAAGACTTGCTA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGA-TTGCTA
20635963 CACTAACTTT
Statistics
Matches: 354, Mismatches: 75, Indels: 51
0.74 0.16 0.11
Matches are distributed among these distances:
42 2 0.01
43 40 0.11
44 133 0.38
45 104 0.29
46 6 0.02
47 2 0.01
48 1 0.00
49 2 0.01
50 27 0.08
51 32 0.09
52 5 0.01
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (44 bp):
CTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTGCTAT
Found at i:20635632 original size:89 final size:89
Alignment explanation
Indices: 20635464--20635641 Score: 196
Period size: 89 Copynumber: 2.0 Consensus size: 89
20635454 CAACTTGTCG
* * * * *
20635464 CTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTGCTATCTTCAATCTGCTCCACTGTAA
1 CTTCAATCTGCTCCACTACAACTTCAGAGAAATAAGATTGCTAGCTTCAATCTGCTCCACTGCAA
** * *
20635529 CTTCAGGGAAATAAGGTTTGCTAT
66 CTTCAAAGAAATAAGATTCGCTAT
* * * * *
20635553 CTTCAATCTGCTCCACTACAACTTCATAGAGATAAAGTTTG-TAGCTTTAATCTGCTCTACTGCA
1 CTTCAATCTGCTCCACTACAACTTCAGAGAAAT-AAGATTGCTAGCTTCAATCTGCTCCACTGCA
* *
20635617 ACTTTAAAGAGATAAGATTCGCTAT
65 ACTTCAAAGAAATAAGATTCGCTAT
20635642 AATAACTTCA
Statistics
Matches: 72, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
89 66 0.92
90 6 0.08
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (89 bp):
CTTCAATCTGCTCCACTACAACTTCAGAGAAATAAGATTGCTAGCTTCAATCTGCTCCACTGCAA
CTTCAAAGAAATAAGATTCGCTAT
Found at i:20635945 original size:43 final size:44
Alignment explanation
Indices: 20635805--20635955 Score: 144
Period size: 43 Copynumber: 3.4 Consensus size: 44
20635795 TGATCTACTA
* * * * * *
20635805 CAACTTCAGAGAAATAAGATTTTTATCTTTAATCTATTCTACTA
1 CAACTTCAGAGAGATAAGATTTATATCTTCAATCTACTCCACTG
* * * *
20635849 CAACTTTAGAGAGATAAGATTTTCTATCTTCGATCTACTCCAATG
1 CAACTTCAGAGAGATAAGA-TTTATATCTTCAATCTACTCCACTG
* *
20635894 CGAA-TTCAGGGAGATAAGA-TTATAACTTCAATCTACTCCACTG
1 C-AACTTCAGAGAGATAAGATTTATATCTTCAATCTACTCCACTG
* *
20635937 CAACTTCAGGGAGGTAAGA
1 CAACTTCAGAGAGATAAGA
20635956 CTTGCTACAC
Statistics
Matches: 88, Mismatches: 16, Indels: 7
0.79 0.14 0.06
Matches are distributed among these distances:
42 2 0.02
43 35 0.40
44 17 0.19
45 32 0.36
46 2 0.02
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (44 bp):
CAACTTCAGAGAGATAAGATTTATATCTTCAATCTACTCCACTG
Found at i:20636158 original size:15 final size:15
Alignment explanation
Indices: 20636138--20636176 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
20636128 TAACTAGATA
20636138 TGCATGAATGATATT
1 TGCATGAATGATATT
20636153 TGCATGAATGATATT
1 TGCATGAATGATATT
20636168 TGCATGAAT
1 TGCATGAAT
20636177 ACAGAATGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (15 bp):
TGCATGAATGATATT
Found at i:20636645 original size:14 final size:14
Alignment explanation
Indices: 20636626--20636658 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
20636616 GCAGCATGAG
*
20636626 CTTCTCTGCACAAA
1 CTTCTCTACACAAA
20636640 CTTCTCTACACAAA
1 CTTCTCTACACAAA
20636654 CTTCT
1 CTTCT
20636659 TGATGACCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.27, C:0.36, G:0.03, T:0.33
Consensus pattern (14 bp):
CTTCTCTACACAAA
Found at i:20647810 original size:23 final size:22
Alignment explanation
Indices: 20647784--20647840 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
20647774 TATAAAAAGA
*
20647784 AAAATAATAGGTAAAAACCAAAT
1 AAAATAATAGATAAAAA-CAAAT
*
20647807 AAAATAAGATA-ATAAAAATAAAT
1 AAAAT-A-ATAGATAAAAACAAAT
20647830 AAAATAATAGA
1 AAAATAATAGA
20647841 ACGTAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
21 3 0.10
22 2 0.07
23 14 0.48
24 7 0.24
25 3 0.10
ACGTcount: A:0.70, C:0.04, G:0.07, T:0.19
Consensus pattern (22 bp):
AAAATAATAGATAAAAACAAAT
Found at i:20647831 original size:18 final size:19
Alignment explanation
Indices: 20647803--20647838 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
20647793 GGTAAAAACC
*
20647803 AAATAAAATAAGATAATAA
1 AAATAAAATAAAATAATAA
20647822 AAAT-AAATAAAATAATA
1 AAATAAAATAAAATAATA
20647839 GAACGTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (19 bp):
AAATAAAATAAAATAATAA
Found at i:20650953 original size:31 final size:31
Alignment explanation
Indices: 20650915--20650976 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
20650905 ACTCCTTGTA
20650915 ATCATTCGAATTCGACATAGTGAATTTTCTT
1 ATCATTCGAATTCGACATAGTGAATTTTCTT
*
20650946 ATCATTCGAATTTGACATAGTGAATTTTCTT
1 ATCATTCGAATTCGACATAGTGAATTTTCTT
20650977 CTCCTCTACC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.44
Consensus pattern (31 bp):
ATCATTCGAATTCGACATAGTGAATTTTCTT
Found at i:20652454 original size:105 final size:104
Alignment explanation
Indices: 20652236--20652483 Score: 289
Period size: 105 Copynumber: 2.4 Consensus size: 104
20652226 GTGTAAGGTT
* ** *
20652236 CACATGGGCAAAGGACACAGATGTGTGTCTAGGCCGTGTAACTCACTATTTGTGATTTAAAACCA
1 CACACGGGC-AAGGACACAGGCGTGTGTCTAGGCCGTGTAACTCACTATTTATGATTTAAAACCA
* * * * *
20652301 GATGGACAAGGACATAGGCGTGTGCCCAGGCCGTGTGAGT
65 CACGGACAAGGACATAGGCATGTGCCCAGGCCGTATGAGC
* * * * * *
20652341 CACACGGGCAGGGACACAGGCGTGTGTTTAGGCCGTGTAACTCACTGTTTATGCTTTAAAGCTAC
1 CACACGGGCAAGGACACAGGCGTGTGTCTAGGCCGTGTAACTCACTATTTATGATTTAAAACCAC
* *
20652406 ACGGGCAGAGGACATAGGCATGTGCCTAGGCCGTATGAGC
66 ACGGACA-AGGACATAGGCATGTGCCCAGGCCGTATGAGC
* ** *
20652446 CACACGGGCAAGAACATGGGCATGTGTCTAGGCCGTGT
1 CACACGGGCAAGGACACAGGCGTGTGTCTAGGCCGTGT
20652484 GACATATAAA
Statistics
Matches: 119, Mismatches: 23, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
104 51 0.43
105 68 0.57
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.22
Consensus pattern (104 bp):
CACACGGGCAAGGACACAGGCGTGTGTCTAGGCCGTGTAACTCACTATTTATGATTTAAAACCAC
ACGGACAAGGACATAGGCATGTGCCCAGGCCGTATGAGC
Found at i:20653677 original size:27 final size:27
Alignment explanation
Indices: 20653628--20653679 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
20653618 AAGAAAAATT
* *
20653628 ACAATCCTTACTTTATAGGGGTTAACC
1 ACAATCCTAACTTTATAGAGGTTAACC
* *
20653655 ACAATCCTAATTTTCTAGAGGTTAA
1 ACAATCCTAACTTTATAGAGGTTAA
20653680 TTAATAAAGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (27 bp):
ACAATCCTAACTTTATAGAGGTTAACC
Found at i:20655764 original size:11 final size:11
Alignment explanation
Indices: 20655744--20655786 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
20655734 TTAGAATATA
*
20655744 CCCATTCCTTG
1 CCCATACCTTG
*
20655755 CCCATACCTTT
1 CCCATACCTTG
*
20655766 CCCATACC-TA
1 CCCATACCTTG
20655776 CCCATACCTTG
1 CCCATACCTTG
20655787 GAAAGGTCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.19, C:0.47, G:0.05, T:0.30
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:20656345 original size:18 final size:18
Alignment explanation
Indices: 20656324--20656373 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
20656314 GTTTACGGTG
20656324 CTATTCACGTATACGACA
1 CTATTCACGTATACGACA
* * **
20656342 CTATTTATGTATACGGTA
1 CTATTCACGTATACGACA
20656360 CTATTCACGTATAC
1 CTATTCACGTATAC
20656374 AGTAGTTGGG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (18 bp):
CTATTCACGTATACGACA
Found at i:20660439 original size:11 final size:11
Alignment explanation
Indices: 20660419--20660472 Score: 65
Period size: 11 Copynumber: 5.0 Consensus size: 11
20660409 TTAGAATATA
*
20660419 CCCATTCCTTG
1 CCCATACCTTG
20660430 CCCATACCTTG
1 CCCATACCTTG
* *
20660441 CCCATACATTT
1 CCCATACCTTG
*
20660452 CCCATACC-TA
1 CCCATACCTTG
20660462 CCCATACCTTG
1 CCCATACCTTG
20660473 GAAAGGTCAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
10 9 0.25
11 27 0.75
ACGTcount: A:0.20, C:0.44, G:0.06, T:0.30
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:20661564 original size:24 final size:23
Alignment explanation
Indices: 20661506--20661587 Score: 112
Period size: 24 Copynumber: 3.6 Consensus size: 23
20661496 ACAACTTTGG
*
20661506 CCCATTTACA-TAAACCCTAAAA
1 CCCATTTACATTAAACCCCAAAA
* *
20661528 TCCATTTACATTAAACCCCCAAA
1 CCCATTTACATTAAACCCCAAAA
20661551 CCCATTTTACATTAAACCCCAAAA
1 CCCA-TTTACATTAAACCCCAAAA
*
20661575 CCCAATTACATTA
1 CCCATTTACATTA
20661588 GCCCAACTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
22 9 0.17
23 21 0.40
24 22 0.42
ACGTcount: A:0.41, C:0.33, G:0.00, T:0.26
Consensus pattern (23 bp):
CCCATTTACATTAAACCCCAAAA
Found at i:20662722 original size:15 final size:15
Alignment explanation
Indices: 20662698--20662729 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
20662688 TAATTAATTT
*
20662698 TTATATTTTCTATTA
1 TTATACTTTCTATTA
20662713 TTATACTTTCTATTA
1 TTATACTTTCTATTA
20662728 TT
1 TT
20662730 TATTGTTATT
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:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (15 bp):
TTATACTTTCTATTA
Found at i:20662729 original size:3 final size:3
Alignment explanation
Indices: 20662723--20662765 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
20662713 TTATACTTTC
* **
20662723 TAT TATT TAT TGT TAT TGG TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
20662766 ATACATATAG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:20663434 original size:22 final size:22
Alignment explanation
Indices: 20663409--20663503 Score: 70
Period size: 22 Copynumber: 4.2 Consensus size: 22
20663399 TACTTATTAT
20663409 TTTATTTTAATATTATTATGTA
1 TTTATTTTAATATTATTATGTA
*
20663431 TTTATTTTAA-AATA-TATGTA
1 TTTATTTTAATATTATTATGTA
* *
20663451 TATATTTGTGTAGTATTATTAATGTA
1 TTTA-TT-T-TAATATTATT-ATGTA
* * *
20663477 TATAATTTTTATGTTATTA-GTA
1 T-TTATTTTAATATTATTATGTA
20663499 TTTAT
1 TTTAT
20663504 AATGTATCTT
Statistics
Matches: 56, Mismatches: 10, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
20 9 0.16
21 8 0.14
22 15 0.27
23 3 0.05
24 10 0.18
25 2 0.04
26 8 0.14
27 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (22 bp):
TTTATTTTAATATTATTATGTA
Found at i:20663450 original size:20 final size:22
Alignment explanation
Indices: 20663409--20663457 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
20663399 TACTTATTAT
*
20663409 TTTATTTTAATATTATTATGTA
1 TTTATTTTAATAATATTATGTA
20663431 TTTATTTTAA-AATA-TATGTA
1 TTTATTTTAATAATATTATGTA
*
20663451 TATATTT
1 TTTATTT
20663458 GTGTAGTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 12 0.48
21 3 0.12
22 10 0.40
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (22 bp):
TTTATTTTAATAATATTATGTA
Found at i:20663456 original size:24 final size:22
Alignment explanation
Indices: 20663385--20663457 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
20663375 CATATATCCT
* *
20663385 TATATTTATTATTATACTTA-T-
1 TATATTTATT-TTAAAATTATTA
*
20663406 TAT-TTTATTTTAATATTATTA
1 TATATTTATTTTAAAATTATTA
*
20663427 TGTATTTATTTTAAAATATATGTA
1 TATATTTATTTTAAAAT-TAT-TA
20663451 TATATTT
1 TATATTT
20663458 GTGTAGTATT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
19 6 0.15
20 7 0.17
21 5 0.12
22 12 0.29
23 3 0.07
24 8 0.20
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (22 bp):
TATATTTATTTTAAAATTATTA
Found at i:20665395 original size:59 final size:59
Alignment explanation
Indices: 20665293--20665438 Score: 229
Period size: 59 Copynumber: 2.4 Consensus size: 59
20665283 CATAGTCAGT
*
20665293 AATATATTTGTACAAAAATATTCAAAAGAACTTCTATTTTATTAAATGAAACAATATTAA
1 AATA-ATTTGTACAAAAATATTCAAAAGAACTTCTATTTTATTAAATGAAACAATATAAA
* *
20665353 AATAATTTTTACAAAAATATTCAAAAGAACTTTTATTTTATTAAATGAAACAATATAAA
1 AATAATTTGTACAAAAATATTCAAAAGAACTTCTATTTTATTAAATGAAACAATATAAA
* *
20665412 AACAATTTGTACAAAAAAAATTCAAAA
1 AATAATTTGTAC-AAAAATATTCAAAA
20665439 ATAAATCAAT
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
59 62 0.78
60 17 0.22
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.34
Consensus pattern (59 bp):
AATAATTTGTACAAAAATATTCAAAAGAACTTCTATTTTATTAAATGAAACAATATAAA
Found at i:20668671 original size:31 final size:31
Alignment explanation
Indices: 20668635--20668758 Score: 182
Period size: 31 Copynumber: 4.0 Consensus size: 31
20668625 AGGATTGGAT
20668635 AAAATAAAAATTTATGTATAAAATTTATAAA
1 AAAATAAAAATTTATGTATAAAATTTATAAA
** *
20668666 AAAATAAAAATTTATGTATAGGATTGGAT---
1 AAAATAAAAATTTATGTATAAAATT-TATAAA
20668695 AAAATAAAAATTTATGTATAAAATTTATAAA
1 AAAATAAAAATTTATGTATAAAATTTATAAA
20668726 AAAATAAAAATTTATGTATAAAATTTAGTAAA
1 AAAATAAAAATTTATGTATAAAATTTA-TAAA
20668758 A
1 A
20668759 TTCCATAATT
Statistics
Matches: 82, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
28 2 0.02
29 23 0.28
31 50 0.61
32 7 0.09
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (31 bp):
AAAATAAAAATTTATGTATAAAATTTATAAA
Found at i:20668695 original size:60 final size:60
Alignment explanation
Indices: 20668625--20668745 Score: 242
Period size: 60 Copynumber: 2.0 Consensus size: 60
20668615 ATAATTTGTG
20668625 AGGATTGGATAAAATAAAAATTTATGTATAAAATTTATAAAAAAATAAAAATTTATGTAT
1 AGGATTGGATAAAATAAAAATTTATGTATAAAATTTATAAAAAAATAAAAATTTATGTAT
20668685 AGGATTGGATAAAATAAAAATTTATGTATAAAATTTATAAAAAAATAAAAATTTATGTAT
1 AGGATTGGATAAAATAAAAATTTATGTATAAAATTTATAAAAAAATAAAAATTTATGTAT
20668745 A
1 A
20668746 AAATTTAGTA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (60 bp):
AGGATTGGATAAAATAAAAATTTATGTATAAAATTTATAAAAAAATAAAAATTTATGTAT
Found at i:20668758 original size:60 final size:60
Alignment explanation
Indices: 20668632--20668759 Score: 213
Period size: 60 Copynumber: 2.1 Consensus size: 60
20668622 GTGAGGATTG
** *
20668632 GATAAAATAAAAATTTATGTATAAAATTTATAAAAAAATAAAAATTTATGTATAGGATTG
1 GATAAAATAAAAATTTATGTATAAAATTTATAAAAAAATAAAAATTTATGTATAAAATTA
20668692 GATAAAATAAAAATTTATGTATAAAATTTATAAAAAAATAAAAATTTATGTATAAAATTTA
1 GATAAAATAAAAATTTATGTATAAAATTTATAAAAAAATAAAAATTTATGTATAAAA-TTA
20668753 G-TAAAAT
1 GATAAAAT
20668760 TCCATAATTA
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
60 61 0.95
61 3 0.05
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (60 bp):
GATAAAATAAAAATTTATGTATAAAATTTATAAAAAAATAAAAATTTATGTATAAAATTA
Found at i:20669996 original size:23 final size:24
Alignment explanation
Indices: 20669936--20669997 Score: 60
Period size: 23 Copynumber: 2.7 Consensus size: 24
20669926 AGTTATTATA
*
20669936 ATTATAATTATAATTTAATAAAAGT
1 ATTATAATT-TAATTTAATAAAAAT
*
20669961 A--ATAA-TTACATTT-TTAAAAAT
1 ATTATAATTTA-ATTTAATAAAAAT
20669982 ATTATAATTTAATTTA
1 ATTATAATTTAATTTA
20669998 TAATTATGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 11
0.70 0.05 0.26
Matches are distributed among these distances:
21 9 0.30
22 5 0.17
23 12 0.40
24 3 0.10
25 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (24 bp):
ATTATAATTTAATTTAATAAAAAT
Found at i:20670255 original size:31 final size:30
Alignment explanation
Indices: 20670190--20670284 Score: 102
Period size: 31 Copynumber: 3.1 Consensus size: 30
20670180 GGAATTTGAT
* *
20670190 ACATG-AATTTTGATTTGATGCAATTATAC
1 ACATGAAATTTTAATTTGATTCAATTATAC
* *
20670219 ACATGAAATTTTAATTATGATTCAAATATAT
1 ACATGAAATTTTAATT-TGATTCAATTATAC
***
20670250 ACATGAAACTTTCCTTTTGATTCAATTATAC
1 ACATGAAA-TTTTAATTTGATTCAATTATAC
20670281 ACAT
1 ACAT
20670285 TTAAAGAAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
29 5 0.09
30 9 0.17
31 35 0.65
32 5 0.09
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (30 bp):
ACATGAAATTTTAATTTGATTCAATTATAC
Found at i:20704689 original size:58 final size:61
Alignment explanation
Indices: 20704627--20704776 Score: 168
Period size: 61 Copynumber: 2.5 Consensus size: 61
20704617 GGATACGACA
* * * *
20704627 TAATAATTCTTGAAAGCAAGCAAGATTGAAA-TGTTCATCCC-TTCATAAAGTTAT-TAAG
1 TAATAATTCTTGAAAGTAAGCAAGATTCAAAGCGCTCATCCCTTTCATAAAGTTATATAAG
* * *
20704685 TAATAACTCTTGAAAGTAAGCATA-A-TCAAAGCGCTCATCCCTTTTATAAGGTTATGATAAG
1 TAATAATTCTTGAAAGTAAGCA-AGATTCAAAGCGCTCATCCCTTTCATAAAGTTAT-ATAAG
*
20704746 TAATAATTCTAGAAAGTAAGCAAGA-TCAAAG
1 TAATAATTCTTGAAAGTAAGCAAGATTCAAAG
20704777 TGTTAGAGGT
Statistics
Matches: 77, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
57 4 0.05
58 29 0.38
59 12 0.16
60 1 0.01
61 31 0.40
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (61 bp):
TAATAATTCTTGAAAGTAAGCAAGATTCAAAGCGCTCATCCCTTTCATAAAGTTATATAAG
Found at i:20705976 original size:14 final size:14
Alignment explanation
Indices: 20705957--20705987 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
20705947 ATACTTCCAA
20705957 TCAATATTGACATT
1 TCAATATTGACATT
20705971 TCAATATTGACATT
1 TCAATATTGACATT
20705985 TCA
1 TCA
20705988 GCCATGCACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.42
Consensus pattern (14 bp):
TCAATATTGACATT
Found at i:20711522 original size:21 final size:20
Alignment explanation
Indices: 20711497--20711553 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 20
20711487 TTAGTTATTG
20711497 AAGTTTATATTTTTGTTAATT
1 AAGTTTATATTTTT-TTAATT
*
20711518 TAGTTCT-TATTTTCTTTAATT
1 AAGTT-TATATTTT-TTTAATT
*
20711539 AAATTTACTATTTTT
1 AAGTTTA-TATTTTT
20711554 AAAAATAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
20 1 0.03
21 20 0.69
22 8 0.28
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.63
Consensus pattern (20 bp):
AAGTTTATATTTTTTTAATT
Found at i:20711693 original size:16 final size:16
Alignment explanation
Indices: 20711674--20711706 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
20711664 TTGTATAATT
*
20711674 TTTTTGAGTATTTTTA
1 TTTTTGAATATTTTTA
20711690 TTTTTGAATATTTTTA
1 TTTTTGAATATTTTTA
20711706 T
1 T
20711707 ACTTTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.70
Consensus pattern (16 bp):
TTTTTGAATATTTTTA
Found at i:20716661 original size:29 final size:29
Alignment explanation
Indices: 20716629--20716690 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
20716619 AAGCACTATA
* * *
20716629 GTGCCATTTTGTTCTGATATTGCACTTCT
1 GTGCCACTATGTTCTGATATTGCACTTCG
* * *
20716658 GTGCTACTATGTTTTGTTATTGCACTTCG
1 GTGCCACTATGTTCTGATATTGCACTTCG
20716687 GTGC
1 GTGC
20716691 ATCTCTGTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (29 bp):
GTGCCACTATGTTCTGATATTGCACTTCG
Found at i:20721898 original size:18 final size:19
Alignment explanation
Indices: 20721875--20721916 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
20721865 TAATAAGTTT
20721875 TTAATTTAATAAA-TTT-AA
1 TTAATTTAA-AAATTTTAAA
20721893 TTAA-TTAAAAATTTTAAA
1 TTAATTTAAAAATTTTAAA
20721911 TTAATT
1 TTAATT
20721917 ACACATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 3 0.14
17 7 0.33
18 10 0.48
19 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTAATTTAAAAATTTTAAA
Found at i:20722443 original size:32 final size:30
Alignment explanation
Indices: 20722407--20722512 Score: 94
Period size: 32 Copynumber: 3.5 Consensus size: 30
20722397 CTATGTATCA
*
20722407 TTAAAATTCGAAAACATCATTTATAATTATAT
1 TTAAAATTCTAAAA-ATCATTTAT-ATTATAT
*
20722439 TTAAAATTAT-AAAAT-ATTTCATA-TATCA-
1 TTAAAATTCTAAAAATCATTT-ATATTAT-AT
* *
20722467 TTAAAATTTTAAAGTATCATTTATTATTATAT
1 TTAAAATTCTAAA-AATCATTTA-TATTATAT
20722499 TTAAAATTCTAAAA
1 TTAAAATTCTAAAA
20722513 TATTTTATGT
Statistics
Matches: 60, Mismatches: 6, Indels: 17
0.72 0.07 0.20
Matches are distributed among these distances:
28 12 0.20
29 8 0.13
30 7 0.12
31 10 0.17
32 23 0.38
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (30 bp):
TTAAAATTCTAAAAATCATTTATATTATAT
Found at i:20722471 original size:28 final size:27
Alignment explanation
Indices: 20722439--20722539 Score: 78
Period size: 28 Copynumber: 3.5 Consensus size: 27
20722429 ATAATTATAT
20722439 TTAAAATTATAAAATATTTCATATATCA
1 TTAAAATTATAAAATATTT-ATATATCA
*
20722467 TTAAAATTTTAAAGTATCATTTATTATTAT-A
1 TTAAAATTATAAA--AT-ATTTA-TA-TATCA
* *
20722498 TTTAAAATTCTAAAATATTTTATGTATCA
1 -TTAAAATTATAAAATA-TTTATATATCA
* *
20722527 TTAGATTTATAAA
1 TTAAAATTATAAA
20722540 TAATTTTTTA
Statistics
Matches: 59, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
28 25 0.42
29 3 0.05
30 9 0.15
31 7 0.12
32 15 0.25
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.48
Consensus pattern (27 bp):
TTAAAATTATAAAATATTTATATATCA
Found at i:20722473 original size:60 final size:60
Alignment explanation
Indices: 20722402--20722529 Score: 184
Period size: 60 Copynumber: 2.1 Consensus size: 60
20722392 TAACACTATG
20722402 TATCATTAAAATTCGAAAACATCATTTATAATTATATTTAAAATTATAAAATATTTCATA
1 TATCATTAAAATTCGAAAACATCATTTATAATTATATTTAAAATTATAAAATATTTCATA
** ** * * * *
20722462 TATCATTAAAATTTTAAAGTATCATTTATTATTATATTTAAAATTCTAAAATATTTTATG
1 TATCATTAAAATTCGAAAACATCATTTATAATTATATTTAAAATTATAAAATATTTCATA
20722522 TATCATTA
1 TATCATTA
20722530 GATTTATAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.46
Consensus pattern (60 bp):
TATCATTAAAATTCGAAAACATCATTTATAATTATATTTAAAATTATAAAATATTTCATA
Found at i:20723456 original size:7 final size:7
Alignment explanation
Indices: 20723444--20723468 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
20723434 ATAGCCTAAT
20723444 ATATATA
1 ATATATA
20723451 ATATATA
1 ATATATA
20723458 ATATATA
1 ATATATA
20723465 ATAT
1 ATAT
20723469 TATTTATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
ATATATA
Found at i:20724164 original size:30 final size:30
Alignment explanation
Indices: 20724130--20724189 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
20724120 ACTTAACAAG
20724130 TAAATGCCTCTAAAATAATAACAAAATTAA
1 TAAATGCCTCTAAAATAATAACAAAATTAA
* *
20724160 TAAATTCCTTTAAAATAATAACAAAATTAA
1 TAAATGCCTCTAAAATAATAACAAAATTAA
20724190 CAATAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.30
Consensus pattern (30 bp):
TAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:20738693 original size:5 final size:5
Alignment explanation
Indices: 20738677--20738709 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
20738667 TATAAAGTTG
*
20738677 ATATA ATGTA ATATA ATATA ATATA ATATA ATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATA
20738710 ATGCAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:20742113 original size:6 final size:6
Alignment explanation
Indices: 20742102--20742140 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
20742092 CCAAAAGGAA
20742102 TTTGCT TTTGCT TTTGCT TTT-CT TTT-C- TTTGC- TTTGCT T
1 TTTGCT TTTGCT TTTGCT TTTGCT TTTGCT TTTGCT TTTGCT T
20742141 GCAAACAGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 3 0.10
5 12 0.39
6 16 0.52
ACGTcount: A:0.00, C:0.18, G:0.13, T:0.69
Consensus pattern (6 bp):
TTTGCT
Found at i:20742595 original size:25 final size:25
Alignment explanation
Indices: 20742567--20742620 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
20742557 TTTCTTTATA
*
20742567 TTATTAAT-TTTATATTTAAAAATCT
1 TTATTAATATTTA-ATTTAAAAATAT
*
20742592 TTA-TAATATTTAATTTAAAATTAT
1 TTATTAATATTTAATTTAAAAATAT
20742616 TTATT
1 TTATT
20742621 TAAATAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 17 0.68
25 8 0.32
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
TTATTAATATTTAATTTAAAAATAT
Found at i:20742728 original size:21 final size:23
Alignment explanation
Indices: 20742687--20742738 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
20742677 TCATTTGTTG
20742687 AATATGTTAAAATTGTTTTATT-T
1 AATAT-TTAAAATTGTTTTATTAT
*
20742710 ATTATTTAAAATT-TTTTATTAT
1 AATATTTAAAATTGTTTTATTAT
20742732 AATATTT
1 AATATTT
20742739 GAATGGATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 7 0.27
22 15 0.58
23 4 0.15
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (23 bp):
AATATTTAAAATTGTTTTATTAT
Found at i:20746232 original size:29 final size:29
Alignment explanation
Indices: 20746199--20746265 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
20746189 TGTGTGTACC
** *
20746199 ATGTGAAAAGGGATAACTTCGTTTATCTA
1 ATGTGAAAAGGGATAACTTCGGCTATCGA
*
20746228 ATGTGAAAAGGGATAACTTTGGCTATCGA
1 ATGTGAAAAGGGATAACTTCGGCTATCGA
20746257 ATGTGAAAA
1 ATGTGAAAA
20746266 AGAAAGGTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.37, C:0.09, G:0.24, T:0.30
Consensus pattern (29 bp):
ATGTGAAAAGGGATAACTTCGGCTATCGA
Found at i:20746457 original size:32 final size:31
Alignment explanation
Indices: 20746293--20746534 Score: 126
Period size: 33 Copynumber: 7.3 Consensus size: 31
20746283 GTATACCACA
*
20746293 TGAAAAGGCTATGTGCACTTTGTGTGTACACT
1 TGAAAAGG-TATGTACACTTTGTGTGTACACT
* * * *
20746325 TGGAAAGGTTAGGTATACTTTGTGTATAC-CAT
1 TGAAAAGG-TATGTACACTTTGTGTGTACAC-T
** *
20746357 ATGGAAAGGAAGGGTATACACAACTTTGTGTATACCACT
1 -T-G-AA--AA-GGTATGTAC-ACTTTGTGTGTA-CACT
* * * * *
20746396 TGAAAAGGAAAGATACACTATATGAGTACACT
1 TGAAAAGGTATG-TACACTTTGTGTGTACACT
* *
20746428 TGAAAAGGTTATGTGCACTTTGTGTGTACAAAT
1 TGAAAAGG-TATGTACACTTTGTGTGTAC-ACT
* *
20746461 TGGAAAGAGTATGTACACTTCGTGTGTACCACT
1 TGAAAAG-GTATGTACACTTTGTGTGTA-CACT
* * *
20746494 TGAAAAGGGAATGTACACCTTGAGTGTACAACT
1 TGAAAA-GGTATGTACACTTTGTGTGTAC-ACT
*
20746527 AGAAAAGG
1 TGAAAAGG
20746535 AAAGGTCCAT
Statistics
Matches: 157, Mismatches: 36, Indels: 34
0.69 0.16 0.15
Matches are distributed among these distances:
31 1 0.01
32 51 0.32
33 70 0.45
34 8 0.05
35 1 0.01
36 2 0.01
37 6 0.04
38 15 0.10
39 2 0.01
40 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (31 bp):
TGAAAAGGTATGTACACTTTGTGTGTACACT
Found at i:20750059 original size:22 final size:20
Alignment explanation
Indices: 20750026--20750071 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 20
20750016 ATTTAGGTTA
20750026 TATT-TAAATATTATATATAAC
1 TATTATAAATATTA-AT-TAAC
*
20750047 TATTATAATTATTAATTAAC
1 TATTATAAATATTAATTAAC
20750067 -ATTAT
1 TATTAT
20750072 GGTTTTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 5 0.22
20 4 0.17
21 6 0.26
22 8 0.35
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (20 bp):
TATTATAAATATTAATTAAC
Found at i:20750665 original size:12 final size:12
Alignment explanation
Indices: 20750648--20750678 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
20750638 GAAGTAGGGG
20750648 AGAAAAAGAGAA
1 AGAAAAAGAGAA
*
20750660 AGAAAAAGGGAA
1 AGAAAAAGAGAA
20750672 AGAAAAA
1 AGAAAAA
20750679 TAAAAGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAGAA
Found at i:20755688 original size:13 final size:13
Alignment explanation
Indices: 20755670--20755695 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20755660 AATATTGCAT
20755670 GAAAAATTTTATC
1 GAAAAATTTTATC
20755683 GAAAAATTTTATC
1 GAAAAATTTTATC
20755696 AATTATGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
GAAAAATTTTATC
Found at i:20756176 original size:20 final size:21
Alignment explanation
Indices: 20756148--20756188 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
20756138 GAATATGCTG
* *
20756148 TAAATTGAAA-GTTTTTGATA
1 TAAAATGAAAGGTTATTGATA
20756168 TAAAATGAAAGGTTATTGATA
1 TAAAATGAAAGGTTATTGATA
20756189 GATAAATCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.17, T:0.39
Consensus pattern (21 bp):
TAAAATGAAAGGTTATTGATA
Found at i:20756884 original size:29 final size:29
Alignment explanation
Indices: 20756851--20756919 Score: 120
Period size: 29 Copynumber: 2.4 Consensus size: 29
20756841 TGTGTGTACC
*
20756851 ATGTGAAAAGGGATAGCTTCGGCTATCTA
1 ATGTGAAAAGGGATAGCTTCGGCTATCGA
*
20756880 ATGTGAAAAGGGATAGCTTTGGCTATCGA
1 ATGTGAAAAGGGATAGCTTCGGCTATCGA
20756909 ATGTGAAAAGG
1 ATGTGAAAAGG
20756920 AAAGGTATAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.33, C:0.10, G:0.30, T:0.26
Consensus pattern (29 bp):
ATGTGAAAAGGGATAGCTTCGGCTATCGA
Found at i:20756949 original size:33 final size:33
Alignment explanation
Indices: 20756912--20757095 Score: 140
Period size: 33 Copynumber: 5.5 Consensus size: 33
20756902 CTATCGAATG
*
20756912 TGAAAAGGAAAGGTATACCTTGTGTATACCACA
1 TGAAAAGGAAAGGTATACTTTGTGTATACCACA
* * ** * *
20756945 TGAAAA-GACTATGTGCACTTTGTGTGTA-CACT
1 TGAAAAGGA-AAGGTATACTTTGTGTATACCACA
** *
20756977 TGGAAAA-GTTAGGTATACTTTGTGTATACCATA
1 T-GAAAAGGAAAGGTATACTTTGTGTATACCACA
* * *
20757010 TGGAAAGGAAGGGTATACACAACTTTGTGTATACCATA
1 TGAAAAGGAAAGGTAT-----ACTTTGTGTATACCACA
* * *
20757048 CGAAAAGGAATGGTATACTTTGTGTATACCACT
1 TGAAAAGGAAAGGTATACTTTGTGTATACCACA
20757081 TGAAAAGGAAAGGTA
1 TGAAAAGGAAAGGTA
20757096 CACTATATGA
Statistics
Matches: 117, Mismatches: 25, Indels: 18
0.73 0.16 0.11
Matches are distributed among these distances:
32 25 0.21
33 62 0.53
38 30 0.26
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (33 bp):
TGAAAAGGAAAGGTATACTTTGTGTATACCACA
Found at i:20757044 original size:38 final size:38
Alignment explanation
Indices: 20756993--20757065 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
20756983 AGTTAGGTAT
* *
20756993 ACTTTGTGTATACCATATGGAAAGGAAGGGTATACACA
1 ACTTTGTGTATACCATACGAAAAGGAAGGGTATACACA
*
20757031 ACTTTGTGTATACCATACGAAAAGGAATGGTATAC
1 ACTTTGTGTATACCATACGAAAAGGAAGGGTATAC
20757066 TTTGTGTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (38 bp):
ACTTTGTGTATACCATACGAAAAGGAAGGGTATACACA
Found at i:20757153 original size:33 final size:33
Alignment explanation
Indices: 20757112--20757219 Score: 117
Period size: 33 Copynumber: 3.3 Consensus size: 33
20757102 ATGAGTACAC
*
20757112 TTGAAAAGGTTATGTGCACTTTGTGTGTACAAA
1 TTGAAAAGGGTATGTGCACTTTGTGTGTACAAA
* * * * *
20757145 TTGGAAAGGGTATGTACACTTCGTGTGTACCAC
1 TTGAAAAGGGTATGTGCACTTTGTGTGTACAAA
* * * *
20757178 TTGAAAAGGGAATGTGCACCTTGAGTGTACAAC
1 TTGAAAAGGGTATGTGCACTTTGTGTGTACAAA
*
20757211 TAGAAAAGG
1 TTGAAAAGG
20757220 AAAGGTCCAT
Statistics
Matches: 61, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (33 bp):
TTGAAAAGGGTATGTGCACTTTGTGTGTACAAA
Found at i:20757153 original size:65 final size:66
Alignment explanation
Indices: 20757064--20757225 Score: 175
Period size: 66 Copynumber: 2.5 Consensus size: 66
20757054 GGAATGGTAT
* * **
20757064 ACTTTGTGTATACCACTTGAAAAGGAAAGGTACACTAT-ATGAGTA-CACTTGAAAAGGTTATGT
1 ACTTTGTGTGTACAACTTGAAAAGGAAAGGTACACT-TCATGAGTACCACTTGAAAAGGGAATGT
20757127 GC
65 GC
* * ** * * *
20757129 ACTTTGTGTGTACAAATTGGAAAGGGTATGTACACTTCGTGTGTACCACTTGAAAAGGGAATGTG
1 ACTTTGTGTGTACAACTTGAAAAGGAAAGGTACACTTCATGAGTACCACTTGAAAAGGGAATGTG
20757194 C
66 C
* * *
20757195 ACCTTGAGTGTACAACTAGAAAAGGAAAGGT
1 ACTTTGTGTGTACAACTTGAAAAGGAAAGGT
20757226 CCATCGGAAA
Statistics
Matches: 76, Mismatches: 19, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
64 1 0.01
65 34 0.45
66 41 0.54
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.28
Consensus pattern (66 bp):
ACTTTGTGTGTACAACTTGAAAAGGAAAGGTACACTTCATGAGTACCACTTGAAAAGGGAATGTG
C
Found at i:20760521 original size:46 final size:46
Alignment explanation
Indices: 20760469--20760604 Score: 175
Period size: 46 Copynumber: 3.0 Consensus size: 46
20760459 GCTCTCTGAT
* *
20760469 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCGTGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
20760515 ATGAAATGTGTAAGACCATGGTTGAAAAATACGATGGCAACATGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * * *
20760561 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATG
20760605 TCAAAGATAA
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
45 1 0.01
46 78 0.99
ACGTcount: A:0.40, C:0.14, G:0.25, T:0.21
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:20760914 original size:17 final size:16
Alignment explanation
Indices: 20760886--20760918 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
20760876 TGATGGTGCA
20760886 TGAAATATTGATATAT
1 TGAAATATTGATATAT
20760902 TGAAATGATTGATATAT
1 TGAAAT-ATTGATATAT
20760919 ACTTATGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (16 bp):
TGAAATATTGATATAT
Found at i:20766837 original size:13 final size:13
Alignment explanation
Indices: 20766801--20766838 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
20766791 TATATATATT
*
20766801 TAAAAAATTTATA
1 TAAAAAATTAATA
*
20766814 TAATAAA-TAATA
1 TAAAAAATTAATA
20766826 TAAAAAATTAATA
1 TAAAAAATTAATA
20766839 CGGACTGGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
TAAAAAATTAATA
Found at i:20769481 original size:29 final size:31
Alignment explanation
Indices: 20769427--20769492 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
20769417 AAATTTACCG
*
20769427 TATATTTTTTAATATAATATAAAAAA-TATT
1 TATAATTTTTAATATAATATAAAAAATTATT
* **
20769457 TGTAATTTTT-ATATAATATTTAAAATTATT
1 TATAATTTTTAATATAATATAAAAAATTATT
20769487 TATAAT
1 TATAAT
20769493 CTTTCTCAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 13 0.43
30 17 0.57
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (31 bp):
TATAATTTTTAATATAATATAAAAAATTATT
Found at i:20775129 original size:16 final size:16
Alignment explanation
Indices: 20775108--20775142 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
20775098 TGCCATGCTA
20775108 CATATATTACAGAATT
1 CATATATTACAGAATT
20775124 CATATATTACAGAATT
1 CATATATTACAGAATT
20775140 CAT
1 CAT
20775143 GTGAATCGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (16 bp):
CATATATTACAGAATT
Found at i:20781734 original size:21 final size:21
Alignment explanation
Indices: 20781710--20781752 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
20781700 ACCTTTTCTA
**
20781710 AAGTTAAAAGTTAAAACCATT
1 AAGTTAAAAGGCAAAACCATT
20781731 AAGTTAAAAGGCAAAACCATT
1 AAGTTAAAAGGCAAAACCATT
20781752 A
1 A
20781753 TATTGTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.23
Consensus pattern (21 bp):
AAGTTAAAAGGCAAAACCATT
Found at i:20782446 original size:20 final size:20
Alignment explanation
Indices: 20782421--20782485 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
20782411 AAAGATTACA
*
20782421 AAAAATTCAAAATAAATTTT
1 AAAAATTCAAAATATATTTT
20782441 AAAAA-T-AAAA-ATATTTAT
1 AAAAATTCAAAATATATTT-T
*
20782459 AAAAAATCCAAAATATATATTT
1 -AAAAATTCAAAATATAT-TTT
20782481 AAAAA
1 AAAAA
20782486 ATTATAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
17 5 0.14
18 5 0.14
19 6 0.16
20 5 0.14
21 9 0.24
22 5 0.14
23 2 0.05
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAAATTCAAAATATATTTT
Done.