Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008041.1 Hibiscus syriacus cultivar Beakdansim tig00110528_pilon, whole genome shotgun sequence
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: 4970990
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 21
Found at i:2625148 original size:36 final size:37
Alignment explanation
Indices: 2625091--2625173 Score: 150
Period size: 36 Copynumber: 2.3 Consensus size: 37
2625081 AGTTTGGATC
2625091 AATTCAGTTCGGATCATTTTAGGTTGATTTGAAATCA
1 AATTCAGTTCGGATCATTTTAGGTTGATTTGAAATCA
2625128 AATTCAGTTCGGATCA-TTTAGGTTGATTTGAAATCA
1 AATTCAGTTCGGATCATTTTAGGTTGATTTGAAATCA
*
2625164 TATTCAGTTC
1 AATTCAGTTC
2625174 AAGTTTGAGT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
36 29 0.64
37 16 0.36
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (37 bp):
AATTCAGTTCGGATCATTTTAGGTTGATTTGAAATCA
Found at i:2627755 original size:14 final size:15
Alignment explanation
Indices: 2627725--2627763 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
2627715 AATAATAATT
*
2627725 ATAATTATA-ATACA
1 ATAATAATATATACA
2627739 ATAATAATATATA-A
1 ATAATAATATATACA
2627753 ATAATAATATA
1 ATAATAATATA
2627764 AATAATGACG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 20 0.87
15 3 0.13
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (15 bp):
ATAATAATATATACA
Found at i:2628178 original size:138 final size:137
Alignment explanation
Indices: 2627922--2628277 Score: 534
Period size: 138 Copynumber: 2.6 Consensus size: 137
2627912 CAAACTGTGT
*
2627922 ATGACATTGTTCCTTCGTGATGAGGGCGTCTGGCCATCTTTAAAGATATTTGAGATAACTCGGTT
1 ATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACTCGGTT
* *
2627987 CCTTCGTGATGAAGACATCTGGCTATTTAAGGATGACACTGCTCCTTCATGATGAGGAGTTCTGA
66 CCTTCGTGATGAGGACATCTGGCTATCTAAGGATGACACTGCTCCTTCATGATGAGGAGTTCTGA
2628052 TCAATGG
131 TCAATGG
* * * *
2628059 ATGACATTGTTCCTTCATGATGAGGACGTCTAGCCATCTTTAAAGATATTTTGAAATAACACGGT
1 ATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATA-TTTGAGATAACTCGGT
* * * *
2628124 TCCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATGA-TGCTTCTTCGTGATGAGGAGTTCT
65 TCCTTCGTGATGAGGACATCTGGCTATCTAAGGATGA-CACTGCTCCTTCATGATGAGGAGTTCT
*
2628188 GATCGATGG
129 GATCAATGG
* * * *
2628197 ATGACATTTTTCTTTCGTGATGAGGACGTATGGCCATCTTTAAAGATATTTGAGATAATTCGGTT
1 ATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACTCGGTT
*
2628262 CCTACGTGATGAGGAC
66 CCTTCGTGATGAGGAC
2628278 GTCTAACCAT
Statistics
Matches: 196, Mismatches: 21, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
137 74 0.38
138 121 0.62
139 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (137 bp):
ATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACTCGGTT
CCTTCGTGATGAGGACATCTGGCTATCTAAGGATGACACTGCTCCTTCATGATGAGGAGTTCTGA
TCAATGG
Found at i:2628271 original size:54 final size:54
Alignment explanation
Indices: 2628212--2628328 Score: 180
Period size: 54 Copynumber: 2.2 Consensus size: 54
2628202 ATTTTTCTTT
** **
2628212 CGTGATGAGGACGTATGGCCATCTTTAAAGATATTTGAGATAATTCGGTTCCTA
1 CGTGATGAGGACGTATAACCATCTTTAAAGATATTTGAGATAACGCGGTTCCTA
* *
2628266 CGTGATGAGGACGTCTAACCATCTTTAAAGATATTTGAGATAACGCGGTTCCTT
1 CGTGATGAGGACGTATAACCATCTTTAAAGATATTTGAGATAACGCGGTTCCTA
2628320 CGTGATGAG
1 CGTGATGAG
2628329 AACATCTAGC
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (54 bp):
CGTGATGAGGACGTATAACCATCTTTAAAGATATTTGAGATAACGCGGTTCCTA
Found at i:2628407 original size:21 final size:19
Alignment explanation
Indices: 2628365--2628408 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
2628355 TTTCCTAAAA
*
2628365 TATGAATAAATGATGCATT
1 TATGAATAAATGATCCATT
*
2628384 TATGAATATCATGATCCTATT
1 TATGAATA-AATGATCC-ATT
2628405 TATG
1 TATG
2628409 CCTAAAATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 6 0.29
21 7 0.33
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (19 bp):
TATGAATAAATGATCCATT
Found at i:2638548 original size:9 final size:8
Alignment explanation
Indices: 2638528--2638568 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 8
2638518 CCATGATATG
2638528 AAAATG-A
1 AAAATGAA
2638535 AAAATGCAA
1 AAAATG-AA
2638544 AAAATGAAA
1 AAAATG-AA
2638553 AAAATG-A
1 AAAATGAA
2638560 AAAATGAA
1 AAAATGAA
2638568 A
1 A
2638569 CATAAAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
7 13 0.43
8 2 0.07
9 15 0.50
ACGTcount: A:0.73, C:0.02, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAATGAA
Found at i:2641703 original size:22 final size:22
Alignment explanation
Indices: 2641675--2641728 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
2641665 CATAGCGGTG
*
2641675 GAGCAGTTGGGTTTAGGCGACA
1 GAGCAGTTGGGTGTAGGCGACA
* *
2641697 GAGCAGTTGGGTGTAGGCGGCG
1 GAGCAGTTGGGTGTAGGCGACA
2641719 GAGCAGTTGG
1 GAGCAGTTGG
2641729 AGGCAGCATC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.19, C:0.13, G:0.48, T:0.20
Consensus pattern (22 bp):
GAGCAGTTGGGTGTAGGCGACA
Found at i:2641994 original size:3 final size:3
Alignment explanation
Indices: 2641988--2642035 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
2641978 TATTATTTAT
* *
2641988 TAA TAA TAA TTA TAA TAA TAA T-A CAA TAA TAA TATA TAAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A T-AA TAA TAA
2642034 TA
1 TA
2642036 TAAATAATGA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 1 0.03
3 32 0.84
4 4 0.11
5 1 0.03
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2642018 original size:14 final size:13
Alignment explanation
Indices: 2641988--2642043 Score: 71
Period size: 12 Copynumber: 4.3 Consensus size: 13
2641978 TATTATTTAT
*
2641988 TAATAATAAT-TA
1 TAATAATAATAAA
2642000 TAATAATAATACAA
1 TAATAATAATA-AA
2642014 TAATAATATATAAA
1 TAATAATA-ATAAA
2642028 TAATAAT-ATAAA
1 TAATAATAATAAA
2642040 TAAT
1 TAAT
2642044 GACGGGACGA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
12 19 0.47
14 18 0.45
15 3 0.08
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (13 bp):
TAATAATAATAAA
Found at i:2642636 original size:2 final size:2
Alignment explanation
Indices: 2642629--2642667 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2642619 TGTATGATGC
2642629 AT AT AT 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
2642668 ATGCATGTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2643848 original size:22 final size:22
Alignment explanation
Indices: 2643822--2643895 Score: 86
Period size: 22 Copynumber: 3.5 Consensus size: 22
2643812 TTCAGTATTC
2643822 GTCCCGAAGGACTGCTATATAT
1 GTCCCGAAGGACTGCTATATAT
*
2643844 GTCCCGTAGGAC--C-ACTA-A-
1 GTCCCGAAGGACTGCTA-TATAT
2643862 GTCCCGAAGGACTGCTATATAT
1 GTCCCGAAGGACTGCTATATAT
*
2643884 GTCCCGTAGGAC
1 GTCCCGAAGGAC
2643896 CACTAAGTCC
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
18 11 0.26
19 2 0.05
20 6 0.14
21 2 0.05
22 22 0.51
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.23
Consensus pattern (22 bp):
GTCCCGAAGGACTGCTATATAT
Found at i:2643867 original size:18 final size:18
Alignment explanation
Indices: 2643844--2643913 Score: 70
Period size: 18 Copynumber: 3.7 Consensus size: 18
2643834 TGCTATATAT
*
2643844 GTCCCGTAGGACCACTAA
1 GTCCCGAAGGACCACTAA
2643862 GTCCCGAAGGACTGCTA-TATA
1 GTCCCGAAGGAC--C-ACTA-A
*
2643883 TGTCCCGTAGGACCACTAA
1 -GTCCCGAAGGACCACTAA
2643902 GTCCCGAAGGAC
1 GTCCCGAAGGAC
2643914 TACAATACCC
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
18 22 0.51
19 2 0.05
20 6 0.14
21 2 0.05
22 11 0.26
ACGTcount: A:0.27, C:0.30, G:0.24, T:0.19
Consensus pattern (18 bp):
GTCCCGAAGGACCACTAA
Found at i:2643877 original size:40 final size:40
Alignment explanation
Indices: 2643822--2643914 Score: 186
Period size: 40 Copynumber: 2.3 Consensus size: 40
2643812 TTCAGTATTC
2643822 GTCCCGAAGGACTGCTATATATGTCCCGTAGGACCACTAA
1 GTCCCGAAGGACTGCTATATATGTCCCGTAGGACCACTAA
2643862 GTCCCGAAGGACTGCTATATATGTCCCGTAGGACCACTAA
1 GTCCCGAAGGACTGCTATATATGTCCCGTAGGACCACTAA
2643902 GTCCCGAAGGACT
1 GTCCCGAAGGACT
2643915 ACAATACCCT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.27, C:0.28, G:0.24, T:0.22
Consensus pattern (40 bp):
GTCCCGAAGGACTGCTATATATGTCCCGTAGGACCACTAA
Found at i:2644571 original size:36 final size:37
Alignment explanation
Indices: 2644527--2644596 Score: 124
Period size: 36 Copynumber: 1.9 Consensus size: 37
2644517 ATTTAGGGGA
*
2644527 GAATCGATACCCCCCTAGG-GGGAATCTGTTCCCGGG
1 GAATCGATACCCCCCCAGGCGGGAATCTGTTCCCGGG
2644563 GAATCGATACCCCCCCAGGCGGGAATCTGTTCCC
1 GAATCGATACCCCCCCAGGCGGGAATCTGTTCCC
2644597 CCTGCACATA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 18 0.56
37 14 0.44
ACGTcount: A:0.20, C:0.34, G:0.27, T:0.19
Consensus pattern (37 bp):
GAATCGATACCCCCCCAGGCGGGAATCTGTTCCCGGG
Found at i:2645483 original size:19 final size:19
Alignment explanation
Indices: 2645459--2645497 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2645449 TCGAATGCAT
2645459 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
2645478 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
2645497 T
1 T
2645498 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:2645514 original size:65 final size:64
Alignment explanation
Indices: 2645396--2645604 Score: 212
Period size: 65 Copynumber: 3.2 Consensus size: 64
2645386 TATTCAAAGG
* *
2645396 CATGCACCGATGCA-TCAGTCCATGCATCGATGCA-TCGATGAAT-TAATT-GAACATCGAATGC
1 CATGCACCGATGCACTC--TCCATGCATCGATGCACTC--TGAATAT-TTTCAAACATCGAATGC
*
2645457 ATTC
61 ATTT
2645461 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATTT
* * *** * **
2645526 GATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTGCAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTT-CAAACATCGAATGCATTT
*
2645590 CATGCATCGATGCAC
1 CATGCACCGATGCAC
2645605 ACTTGGTGCA
Statistics
Matches: 126, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
63 7 0.06
64 56 0.44
65 61 0.48
66 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (64 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTT
Found at i:2645622 original size:64 final size:65
Alignment explanation
Indices: 2645445--2645607 Score: 222
Period size: 65 Copynumber: 2.5 Consensus size: 65
2645435 GAATTAATTG
* * * *
2645445 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
* ** **
2645510 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTGC-
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTT-CA
2645573 A
65 A
2645574 AACATCGAATGCATTTCATGCATCGATGCACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
2645608 TGGTGCACCG
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 40 0.47
65 45 0.53
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:2651433 original size:20 final size:21
Alignment explanation
Indices: 2651404--2651459 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
2651394 TTTGTGCTTC
*
2651404 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
2651424 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
2651446 ATGCATCGATGCAT
1 ATGCATCGATGCAT
2651460 AAGACCATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGAAA
Found at i:2653026 original size:21 final size:21
Alignment explanation
Indices: 2652984--2653027 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2652974 ACCTCGGGAG
*
2652984 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
2653005 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
2653026 CT
1 CT
2653028 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:2653805 original size:21 final size:21
Alignment explanation
Indices: 2653766--2653805 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2653756 CAAATTAAGT
*
2653766 TAAATGAATTTTAAGATTTCA
1 TAAATGAATTTTAAAATTTCA
2653787 TAAATG-ATTTTACAAATTT
1 TAAATGAATTTTA-AAATTT
2653806 ATATTCGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
TAAATGAATTTTAAAATTTCA
Found at i:2654061 original size:19 final size:19
Alignment explanation
Indices: 2654037--2654075 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2654027 TCGAATGCAT
2654037 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
2654056 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
2654075 T
1 T
2654076 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:2654092 original size:65 final size:64
Alignment explanation
Indices: 2653974--2654179 Score: 206
Period size: 65 Copynumber: 3.2 Consensus size: 64
2653964 TATTCAAAGG
* *
2653974 CATGCACCGATGCA-TCAGTCCATGCATCGATGCA-TCGATGAAT-TAATT-GAACATCGAATGC
1 CATGCACCGATGCACTC--TCCATGCATCGATGCACTC--TGAATAT-TTTCAAACATCGAATGC
*
2654035 ATTC
61 ATTT
2654039 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATTT
* * *** * **
2654104 GATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTGCAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTT-CAAACATCGAATGCATTT
*
2654168 CATGCATCGATG
1 CATGCACCGATG
2654180 TACACTTGGT
Statistics
Matches: 123, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
63 7 0.06
64 53 0.43
65 61 0.50
66 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.27
Consensus pattern (64 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTT
Found at i:2654200 original size:64 final size:65
Alignment explanation
Indices: 2654023--2654185 Score: 213
Period size: 65 Copynumber: 2.5 Consensus size: 65
2654013 GAATTAATTG
* * * *
2654023 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
* ** **
2654088 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTGC-
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTT-CA
2654151 A
65 A
*
2654152 AACATCGAATGCATTTCATGCATCGATGTACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
2654186 TGGTGCACCG
Statistics
Matches: 84, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
64 39 0.46
65 45 0.54
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:2665733 original size:28 final size:28
Alignment explanation
Indices: 2665673--2665733 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
2665663 GGATTAAATT
* *
2665673 ATTTTTCTAAATTTAGAGAATTATTTAT
1 ATTTTTCTAAATTTAGAAAATTATTTAA
* *
2665701 TTTTTTTTAAATTTA-AAAATTATTTTAA
1 ATTTTTCTAAATTTAGAAAATTA-TTTAA
2665729 ATTTT
1 ATTTT
2665734 AAATTTTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 6 0.22
28 21 0.78
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (28 bp):
ATTTTTCTAAATTTAGAAAATTATTTAA
Found at i:2665767 original size:31 final size:32
Alignment explanation
Indices: 2665705--2665776 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 32
2665695 ATTTATTTTT
* *
2665705 TTTTAAATTTAAAAATTATTTTAAATTTTAAA
1 TTTTAAATATAAAAATTATTTTAAATATTAAA
2665737 TTTTAAATATAAAAA-TA-TTTAATATATTAAA
1 TTTTAAATATAAAAATTATTTTAA-ATATTAAA
**
2665768 AATTAAATA
1 TTTTAAATA
2665777 CACATATTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 5 0.14
31 16 0.46
32 14 0.40
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (32 bp):
TTTTAAATATAAAAATTATTTTAAATATTAAA
Found at i:2666893 original size:30 final size:30
Alignment explanation
Indices: 2666858--2666958 Score: 107
Period size: 30 Copynumber: 3.3 Consensus size: 30
2666848 GTTTTTACTT
2666858 TGATGAGGTTT-TGTTTCCTTTGTTTTGTTG
1 TGATGA-GTTTATGTTTCCTTTGTTTTGTTG
** * *
2666888 TGATGAGTTTCCGTTTTCC-TTGGTTTGCTG
1 TGATGAGTTTATG-TTTCCTTTGTTTTGTTG
* *
2666918 TAATGAGTTTATGTTTCCTTTGCTTTTATTG
1 TGATGAGTTTATGTTTCCTTTG-TTTTGTTG
2666949 TGATGAGTTT
1 TGATGAGTTT
2666959 TTGGTACGTT
Statistics
Matches: 57, Mismatches: 10, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
29 9 0.16
30 29 0.51
31 19 0.33
ACGTcount: A:0.11, C:0.10, G:0.24, T:0.55
Consensus pattern (30 bp):
TGATGAGTTTATGTTTCCTTTGTTTTGTTG
Found at i:2674980 original size:21 final size:22
Alignment explanation
Indices: 2674955--2674996 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
2674945 TACTGCCTTA
2674955 GGGGTTTCGAAACCA-CCTAAG
1 GGGGTTTCGAAACCATCCTAAG
*
2674976 GGGGTTTCTAAACCATCCTAA
1 GGGGTTTCGAAACCATCCTAA
2674997 AAAACTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (22 bp):
GGGGTTTCGAAACCATCCTAAG
Found at i:2675892 original size:22 final size:22
Alignment explanation
Indices: 2675844--2675897 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
2675834 TTCAGCTGTT
* *
2675844 ATAACTCCTGAAATTATATCAT
1 ATAACTCCTGAAATTAAATCAA
* * *
2675866 GTAACCCCTGGAATTAAATCAA
1 ATAACTCCTGAAATTAAATCAA
2675888 ATAACTCCTG
1 ATAACTCCTG
2675898 TAACTCCTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (22 bp):
ATAACTCCTGAAATTAAATCAA
Found at i:2676183 original size:6 final size:6
Alignment explanation
Indices: 2676172--2676214 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
2676162 GACACGTATT
*
2676172 ACCACG ACCACG ACCACG ACCTCG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
2676215 GCCGAGCCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.33, C:0.49, G:0.16, T:0.02
Consensus pattern (6 bp):
ACCACG
Found at i:2677382 original size:6 final size:6
Alignment explanation
Indices: 2677371--2677461 Score: 119
Period size: 6 Copynumber: 15.2 Consensus size: 6
2677361 GACACGTATT
*
2677371 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCTCG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
* * * * * *
2677419 ATCTCG ACCTCG ACCTCG ACCTCG ACCTCG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
2677462 GCCGAGCCGA
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 81 1.00
ACGTcount: A:0.27, C:0.48, G:0.16, T:0.08
Consensus pattern (6 bp):
ACCACG
Found at i:2678625 original size:6 final size:6
Alignment explanation
Indices: 2678614--2678704 Score: 128
Period size: 6 Copynumber: 15.2 Consensus size: 6
2678604 GACACGTATT
* *
2678614 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
* * * *
2678662 ACCTCG ACCTCG ACCTCG ACCTCG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
2678705 GCCGAGCCGA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 83 1.00
ACGTcount: A:0.27, C:0.49, G:0.16, T:0.07
Consensus pattern (6 bp):
ACCACG
Found at i:2691739 original size:65 final size:60
Alignment explanation
Indices: 2691591--2691742 Score: 196
Period size: 65 Copynumber: 2.4 Consensus size: 60
2691581 TATCAGTATC
* *
2691591 CTTTGAGTTGTTTCTCTTGAAACAAATTTTGTCTCGAGACAGTTTCTTTTGGAAAAAAAT
1 CTTTGAGTTGTTTCTCTTGAAACAAATTTTCTCTCGAGACAATTTCTTTTGGAAAAAAAT
* * *
2691651 CTTTGAGTTTGTTTATCTGGAAACAAAGTTGTCTCTCTTGAGACAATTTCTTTTGAGAAAAAAAT
1 CTTTGAG-TTGTTTCTCTTGAAACAAA-TT-T-TCTCTCGAGACAATTTCTTTTG-GAAAAAAAT
*
2691716 CTTTGAGTCTGTTTCCCTTGAAACAAA
1 CTTTGAGT-TGTTTCTCTTGAAACAAA
2691743 ATAAACATCT
Statistics
Matches: 78, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
60 7 0.09
61 17 0.22
62 2 0.03
63 1 0.01
64 20 0.26
65 31 0.40
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.40
Consensus pattern (60 bp):
CTTTGAGTTGTTTCTCTTGAAACAAATTTTCTCTCGAGACAATTTCTTTTGGAAAAAAAT
Found at i:2691913 original size:42 final size:40
Alignment explanation
Indices: 2691816--2691922 Score: 117
Period size: 42 Copynumber: 2.6 Consensus size: 40
2691806 GATGGCATGC
*
2691816 CGTCCTCATCGCGTAGGAATCGTGTCATCCCCCGACCAGA
1 CGTCCTCATCGCGTAGGAACCGTGTCATCCCCCGACCAGA
* * * * *
2691856 CCTCCTCATCACGTAGGAGCCGTGTCA-CCCCTGATAACCAGT
1 CGTCCTCATCGCGTAGGAACCGTGTCATCCCCCG---ACCAGA
*
2691898 CGTCCTCATCGCGTAGAAACCGTGT
1 CGTCCTCATCGCGTAGGAACCGTGT
2691923 TATCATCCTT
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
39 5 0.09
40 23 0.43
42 26 0.48
ACGTcount: A:0.21, C:0.36, G:0.21, T:0.21
Consensus pattern (40 bp):
CGTCCTCATCGCGTAGGAACCGTGTCATCCCCCGACCAGA
Found at i:2691996 original size:133 final size:133
Alignment explanation
Indices: 2691800--2692285 Score: 652
Period size: 133 Copynumber: 3.6 Consensus size: 133
2691790 AGACATTATC
* * *
2691800 CCTAAAGATGGCATGCCGTCCTCATCGCGTAGGAATCGTGTCATCCCCCGACCAGACCTCCTCAT
1 CCTAAAGATGGCATGCCATCCTCATCACGTAGGAACCGTGTCATCCCCCGACCAGACCTCCTCAT
* *
2691865 CACGTAGGAGCCGTGTCACCCCTGATAACCAGTCGTCCTCATCGCGTAGAAACCGTGTTATCATC
66 CACGTAGGAGCCGTGTCACCCCTGATAACCAGCCGTCCTCATCGCGTAGAAACCGTGTTATCACC
2691930 CTT
131 CTT
* * * * * *
2691933 CCTAAAGATGGCCTGTCATCCTCATCACGTAAGAACCGTATCATCCCCCGATCAAACCTCCTCAT
1 CCTAAAGATGGCATGCCATCCTCATCACGTAGGAACCGTGTCATCCCCCGACCAGACCTCCTCAT
* * * *
2691998 CACATAGGAGTCGTGTCACCCCTGATAACCAGCCATCCTCATCACGTAGAAACCGTGTTATCACC
66 CACGTAGGAGCCGTGTCACCCCTGATAACCAGCCGTCCTCATCGCGTAGAAACCGTGTTATCACC
*
2692063 CTC
131 CTT
* * *
2692066 CCTAAAGATGGCATGCCATCCTCATCGCGTAGGAACCGTGTCATCCCCCGACTAGACCTCCTTAT
1 CCTAAAGATGGCATGCCATCCTCATCACGTAGGAACCGTGTCATCCCCCGACCAGACCTCCTCAT
* * *
2692131 CACGTAGGAGCCGTGTCAACCCTAGATAACCAGCCGCCCTCATCGCGTAGGAACCGTGTTATCAC
66 CACGTAGGAGCCGTGTCACCCCT-GATAACCAGCCGTCCTCATCGCGTAGAAACCGTGTTATCAC
2692196 CCTT
130 CCTT
* * * * * * * *
2692200 CCTAAAGATGGCCA-G-AACTCTTCATCACGTATGAGCCGTGCCATCCACCGACCATATCTCCTC
1 CCTAAAGATGG-CATGCCA-TCCTCATCACGTAGGAACCGTGTCATCCCCCGACCAGACCTCCTC
*
2692263 ATCACGTAGGAGTCGTGTCACCC
64 ATCACGTAGGAGCCGTGTCACCC
2692286 TTAGACGACC
Statistics
Matches: 304, Mismatches: 46, Indels: 5
0.86 0.13 0.01
Matches are distributed among these distances:
133 194 0.64
134 108 0.36
135 2 0.01
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.22
Consensus pattern (133 bp):
CCTAAAGATGGCATGCCATCCTCATCACGTAGGAACCGTGTCATCCCCCGACCAGACCTCCTCAT
CACGTAGGAGCCGTGTCACCCCTGATAACCAGCCGTCCTCATCGCGTAGAAACCGTGTTATCACC
CTT
Found at i:2692055 original size:42 final size:41
Alignment explanation
Indices: 2691949--2692055 Score: 96
Period size: 40 Copynumber: 2.6 Consensus size: 41
2691939 GATGGCCTGT
*
2691949 CATCCTCATCACGTA-AGAACCGTATCATCCCCCGATCAAAC
1 CATCCTCATCACGTAGA-AACCGTGTCATCCCCCGATCAAAC
* * ** *
2691990 C-TCCTCATCACATAGGAGTCGTGTCA-CCCCTGAT-AACCAGC
1 CATCCTCATCACGTAGAAACCGTGTCATCCCCCGATCAA--A-C
2692031 CATCCTCATCACGTAGAAACCGTGT
1 CATCCTCATCACGTAGAAACCGTGT
2692056 TATCACCCTC
Statistics
Matches: 51, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
38 2 0.04
39 7 0.14
40 20 0.39
41 3 0.06
42 19 0.37
ACGTcount: A:0.28, C:0.36, G:0.14, T:0.21
Consensus pattern (41 bp):
CATCCTCATCACGTAGAAACCGTGTCATCCCCCGATCAAAC
Found at i:2692276 original size:267 final size:266
Alignment explanation
Indices: 2691798--2692285 Score: 762
Period size: 267 Copynumber: 1.8 Consensus size: 266
2691788 TGAGACATTA
* *
2691798 TCCCTAAAGATGGCATGCCGTCCTCATCGCGTAGGAATCGTGTCATCCCCCGACCAGACCTCCTC
1 TCCCTAAAGATGGCATGCCATCCTCATCGCGTAGGAACCGTGTCATCCCCCGACCAGACCTCCTC
* * *
2691863 ATCACGTAGGAGCCGTGTCACCCCTGATAACCAGTCGTCCTCATCGCGTAGAAACCGTGTTATCA
66 ATCACGTAGGAGCCGTGTCAACCCTGATAACCAGCCGCCCTCATCGCGTAGAAACCGTGTTATCA
* * * * * *
2691928 TCCTTCCTAAAGATGGCCTGTCATCCTCATCACGTAAGAACCGTATCATCCCCCGATCAAACCTC
131 CCCTTCCTAAAGATGGCCAGACATCCTCATCACGTAAGAACCGTACCATCCACCGACCAAACCTC
2691993 CTCATCACATAGGAGTCGTGTCACCCCTGATAACCAGCCATCCTCATCACGTAGAAACCGTGTTA
196 CTCATCACATAGGAGTCGTGTCACCCCTGATAACCAGCCATCCTCATCACGTAGAAACCGTGTTA
2692058 TCACCC
261 TCACCC
* *
2692064 TCCCTAAAGATGGCATGCCATCCTCATCGCGTAGGAACCGTGTCATCCCCCGACTAGACCTCCTT
1 TCCCTAAAGATGGCATGCCATCCTCATCGCGTAGGAACCGTGTCATCCCCCGACCAGACCTCCTC
*
2692129 ATCACGTAGGAGCCGTGTCAACCCTAGATAACCAGCCGCCCTCATCGCGTAGGAACCGTGTTATC
66 ATCACGTAGGAGCCGTGTCAACCCT-GATAACCAGCCGCCCTCATCGCGTAGAAACCGTGTTATC
* * * * * *
2692194 ACCCTTCCTAAAGATGGCCAGA-ACTCTTCATCACGTATGAGCCGTGCCATCCACCGACCATATC
130 ACCCTTCCTAAAGATGGCCAGACA-TCCTCATCACGTAAGAACCGTACCATCCACCGACCAAACC
*
2692258 TCCTCATCACGTAGGAGTCGTGTCACCC
194 TCCTCATCACATAGGAGTCGTGTCACCC
2692286 TTAGACGACC
Statistics
Matches: 199, Mismatches: 21, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
266 86 0.43
267 113 0.57
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.23
Consensus pattern (266 bp):
TCCCTAAAGATGGCATGCCATCCTCATCGCGTAGGAACCGTGTCATCCCCCGACCAGACCTCCTC
ATCACGTAGGAGCCGTGTCAACCCTGATAACCAGCCGCCCTCATCGCGTAGAAACCGTGTTATCA
CCCTTCCTAAAGATGGCCAGACATCCTCATCACGTAAGAACCGTACCATCCACCGACCAAACCTC
CTCATCACATAGGAGTCGTGTCACCCCTGATAACCAGCCATCCTCATCACGTAGAAACCGTGTTA
TCACCC
Found at i:2695214 original size:25 final size:28
Alignment explanation
Indices: 2695164--2695215 Score: 74
Period size: 25 Copynumber: 2.0 Consensus size: 28
2695154 ATATTTTGTG
2695164 TTTAAGTTTTGTTGATTTTGAATCGAGC
1 TTTAAGTTTTGTTGATTTTGAATCGAGC
*
2695192 TTTAA-TTTT-TT-ATTTTGAGTCGAG
1 TTTAAGTTTTGTTGATTTTGAATCGAG
2695216 TTTGAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 12 0.52
26 2 0.09
27 4 0.17
28 5 0.22
ACGTcount: A:0.21, C:0.06, G:0.19, T:0.54
Consensus pattern (28 bp):
TTTAAGTTTTGTTGATTTTGAATCGAGC
Found at i:2705704 original size:5 final size:5
Alignment explanation
Indices: 2705694--2705724 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
2705684 TTTCGCAAAG
*
2705694 ATAAA ATAAA ATAAA ATAAA ACAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
2705725 GTGAAAAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (5 bp):
ATAAA
Found at i:2708808 original size:26 final size:27
Alignment explanation
Indices: 2708769--2708835 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 27
2708759 TGGATCTGTA
* * *
2708769 AAATAGCCAA-AATACCCCTAGAATTC
1 AAATAACCAAGAATACCCATAGAATAC
*
2708795 AAATGACC-AGAATACCCATAGAATAC
1 AAATAACCAAGAATACCCATAGAATAC
2708821 AAATAACCAAGAATA
1 AAATAACCAAGAATA
2708836 TCACCAAGCT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
25 1 0.03
26 27 0.79
27 6 0.18
ACGTcount: A:0.52, C:0.22, G:0.09, T:0.16
Consensus pattern (27 bp):
AAATAACCAAGAATACCCATAGAATAC
Found at i:2710025 original size:24 final size:24
Alignment explanation
Indices: 2709998--2710051 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
2709988 TGACATGAAT
* *
2709998 TCTGATCTGGATTTTGTTCTGATA
1 TCTGATCTGAATTCTGTTCTGATA
* * *
2710022 TCTGATTTGAATTCTGTTTTGATT
1 TCTGATCTGAATTCTGTTCTGATA
2710046 TCTGAT
1 TCTGAT
2710052 ATCTCCGTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.17, C:0.11, G:0.19, T:0.54
Consensus pattern (24 bp):
TCTGATCTGAATTCTGTTCTGATA
Found at i:2710221 original size:2 final size:2
Alignment explanation
Indices: 2710214--2710311 Score: 196
Period size: 2 Copynumber: 49.0 Consensus size: 2
2710204 GGGTAGTGTT
2710214 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2710256 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2710298 CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA
2710312 TGTTTTAAAA
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 96 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2712010 original size:43 final size:40
Alignment explanation
Indices: 2711950--2712055 Score: 117
Period size: 39 Copynumber: 2.6 Consensus size: 40
2711940 AGGGACGATA
* * * *
2711950 ACACGGTTTCTATGTGATGAGGACGAT-TGGTTATCTAGGGGTG
1 ACACGGTTCCTACGTGATGAGGACGATATGG---TC-AGAGATG
*
2711993 ACACGGTTCCTACGTGATGAGGA-GGTATGGTCAGAGATG
1 ACACGGTTCCTACGTGATGAGGACGATATGGTCAGAGATG
2712032 ACACGGTTCCTACGTGATGAGGAC
1 ACACGGTTCCTACGTGATGAGGAC
2712056 AACATGCCAT
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
39 28 0.50
40 2 0.04
42 2 0.04
43 24 0.43
ACGTcount: A:0.24, C:0.16, G:0.34, T:0.26
Consensus pattern (40 bp):
ACACGGTTCCTACGTGATGAGGACGATATGGTCAGAGATG
Found at i:2712377 original size:66 final size:66
Alignment explanation
Indices: 2712304--2712450 Score: 206
Period size: 66 Copynumber: 2.2 Consensus size: 66
2712294 CTCAAAGATG
* *
2712304 TTTGTTTCAAGAGAAACAAACTCAAAGATTTCCCTTCACAAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACAAACTCAAAGATTTCCCTTCAAAAGAAACTGTCTCAAGAGAGAAAAAA
2712369 C
66 C
* * * * *
2712370 TTTGTTTCCAGAGAAGCATACTCAAAGATTTTCTTTCAAAAGAAACTGTCTCAAGAGAGAAAAAA
1 TTTGTTTCAAGAGAAACAAACTCAAAGATTTCCCTTCAAAAGAAACTGTCTCAAGAGAGAAAAAA
2712435 C
66 C
* *
2712436 -TTATTTCAAAAGAAA
1 TTTGTTTCAAGAGAAA
2712451 TAGACTCCAA
Statistics
Matches: 70, Mismatches: 11, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
65 11 0.16
66 59 0.84
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.26
Consensus pattern (66 bp):
TTTGTTTCAAGAGAAACAAACTCAAAGATTTCCCTTCAAAAGAAACTGTCTCAAGAGAGAAAAAA
C
Found at i:2712480 original size:66 final size:66
Alignment explanation
Indices: 2712308--2712488 Score: 179
Period size: 66 Copynumber: 2.8 Consensus size: 66
2712298 AAGATGTTTG
* * * * *
2712308 TTTCAAGAGAAACAAACTCAAAGATTTCCCTT-CACAAGAAACTGTCTCAAGAGAGACAAAACTT
1 TTTCAAAAGAAACAGACTCAAAGATTT-TCTTCCAAAAGAAACTGTCTCAAGAGAGAAAAAACTT
*
2712372 TG
65 TA
* * * * *
2712374 TTTCCAGAGAAGCATACTCAAAGATTTTCTTTCAAAAGAAACTGTCTCAAGAGAGAAAAAAC-TT
1 TTTCAAAAGAAACAGACTCAAAGATTTTCTTCCAAAAGAAACTGTCTCAAGAGAGAAAAAACTTT
2712438 A
66 A
* * * * *
2712439 TTTCAAAAGAAATAGACTCCAAGACTTTTGTTCCAAGAGAAA-TGACTCAA
1 TTTCAAAAGAAACAGACTCAAAGA-TTTTCTTCCAAAAGAAACTGTCTCAA
2712489 AGATGATTTA
Statistics
Matches: 96, Mismatches: 17, Indels: 5
0.81 0.14 0.04
Matches are distributed among these distances:
65 30 0.31
66 66 0.69
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.25
Consensus pattern (66 bp):
TTTCAAAAGAAACAGACTCAAAGATTTTCTTCCAAAAGAAACTGTCTCAAGAGAGAAAAAACTTT
A
Found at i:2712905 original size:25 final size:23
Alignment explanation
Indices: 2712874--2712924 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 23
2712864 CAAAAGTATG
2712874 AAAATG-TTAATTAAAAGAGTTTTGA
1 AAAATGTTTAA-TAAAAGA--TTTGA
2712899 AAAATGTTTAATAAAAGATTTGA
1 AAAATGTTTAATAAAAGATTTGA
2712922 AAA
1 AAA
2712925 TATTGCCTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 8 0.32
25 13 0.52
26 4 0.16
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (23 bp):
AAAATGTTTAATAAAAGATTTGA
Found at i:2713902 original size:15 final size:13
Alignment explanation
Indices: 2713874--2713911 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
2713864 CATTTATCTT
2713874 TCTTTGCTTTTTC
1 TCTTTGCTTTTTC
2713887 TCTTTGCTTCTTTTC
1 TCTTTGC-T-TTTTC
2713902 TCTTTG-TTTT
1 TCTTTGCTTTT
2713912 GATTTGATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 3 0.13
13 8 0.35
14 1 0.04
15 11 0.48
ACGTcount: A:0.00, C:0.21, G:0.08, T:0.71
Consensus pattern (13 bp):
TCTTTGCTTTTTC
Found at i:2715854 original size:16 final size:16
Alignment explanation
Indices: 2715833--2715869 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
2715823 TTTGATCGTT
2715833 GACATTAACATCTGTC
1 GACATTAACATCTGTC
2715849 GACATTAACATCTGTC
1 GACATTAACATCTGTC
2715865 GACAT
1 GACAT
2715870 ATGTGATATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (16 bp):
GACATTAACATCTGTC
Found at i:2721993 original size:3 final size:3
Alignment explanation
Indices: 2721987--2722038 Score: 58
Period size: 3 Copynumber: 18.3 Consensus size: 3
2721977 CGTTAAATAA
*
2721987 TAT TAT TA- TAT TAT TAT T-T TCAT TGT TAT TAT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
2722030 TAT T-T TAT T
1 TAT TAT TAT T
2722039 TTCTGTAGGC
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
2 8 0.19
3 32 0.76
4 2 0.05
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2725215 original size:31 final size:31
Alignment explanation
Indices: 2725177--2725252 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 31
2725167 TAAGGCAACC
* * *
2725177 CTTGGGTAGGCTCTGCGGCCGT-GATATTTTT
1 CTTGGGTAGGCTCTACGGCC-TCGAGAATTTT
*
2725208 CTTGGGTAGGCCTCTATGGCCTCGAGAATTTT
1 CTTGGGTAGG-CTCTACGGCCTCGAGAATTTT
2725240 CTTGGGTAGGCTC
1 CTTGGGTAGGCTC
2725253 GCAGGCCCCA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
31 14 0.36
32 25 0.64
ACGTcount: A:0.12, C:0.21, G:0.32, T:0.36
Consensus pattern (31 bp):
CTTGGGTAGGCTCTACGGCCTCGAGAATTTT
Found at i:2726763 original size:9 final size:9
Alignment explanation
Indices: 2726749--2726774 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2726739 AGCTTACCCT
2726749 AATTTTCCC
1 AATTTTCCC
2726758 AATTTTCCC
1 AATTTTCCC
2726767 AATTTTCC
1 AATTTTCC
2726775 TTCCTCGTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (9 bp):
AATTTTCCC
Found at i:2730841 original size:13 final size:13
Alignment explanation
Indices: 2730792--2730840 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
2730782 TGGACCAGTT
*
2730792 GAGCCGAGCCACC
1 GAGCCAAGCCACC
*
2730805 GAGCCGAGCCACTC
1 GAGCCAAGCCAC-C
*
2730819 -AGCCAAGCCGCC
1 GAGCCAAGCCACC
2730831 GAGCCAAGCC
1 GAGCCAAGCC
2730841 GACTGATCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 1 0.03
13 30 0.94
14 1 0.03
ACGTcount: A:0.24, C:0.45, G:0.29, T:0.02
Consensus pattern (13 bp):
GAGCCAAGCCACC
Found at i:2734352 original size:2 final size:2
Alignment explanation
Indices: 2734345--2734376 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2734335 TTTCGAAAGG
2734345 TA TA TA TA TA TA TA TA -A 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 T
2734377 GTGGTGTGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2734366 original size:13 final size:13
Alignment explanation
Indices: 2734348--2734373 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2734338 CGAAAGGTAT
2734348 ATATATATATATA
1 ATATATATATATA
2734361 ATATATATATATA
1 ATATATATATATA
2734374 TATGTGGTGT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATATATA
Found at i:2734366 original size:15 final size:15
Alignment explanation
Indices: 2734346--2734375 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2734336 TTCGAAAGGT
2734346 ATATATATATATATA
1 ATATATATATATATA
2734361 ATATATATATATATA
1 ATATATATATATATA
2734376 TGTGGTGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:2734385 original size:2 final size:2
Alignment explanation
Indices: 2734376--2734414 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2734366 TATATATATA
2734376 TG TG -G TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2734415 CGTGCGCTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (2 bp):
TG
Found at i:2735118 original size:53 final size:53
Alignment explanation
Indices: 2735056--2735161 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
2735046 GTAATTTACC
*
2735056 AACTATTATGTATGTTATATATTTTTATGGTTATTTTTCGTATAGTCCCTCTA
1 AACTATTATGCATGTTATATATTTTTATGGTTATTTTTCGTATAGTCCCTCTA
2735109 AACTATTATGCATGTTATATATTTTTATGGTTATTTTTCGTATAGTCCCTCTA
1 AACTATTATGCATGTTATATATTTTTATGGTTATTTTTCGTATAGTCCCTCTA
2735162 TGTTTAGTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.25, C:0.12, G:0.11, T:0.52
Consensus pattern (53 bp):
AACTATTATGCATGTTATATATTTTTATGGTTATTTTTCGTATAGTCCCTCTA
Found at i:2736307 original size:132 final size:130
Alignment explanation
Indices: 2736009--2736373 Score: 340
Period size: 132 Copynumber: 2.8 Consensus size: 130
2735999 AGATAAAGAG
* *
2736009 AATAGTAATATATTTTCATTTCTG-TTGGAGTAATAAATGATTGC-TCTAAGGCATGAGAGGTCA
1 AATAGTAATATCTCTTCATTT-TGATTGGAGTAATAAATGATTGCTTC-AAGGCATGAGAGGTCA
* * * * * * * * *
2736072 TTTATTCTCGATTGGAAATAATACGATATTATCGTTCTCTCTCGAATTAATATTGATTTTTAGGA
64 TTTATTCTCGATTGAAAATATTA-GATATTATCGTTTTCACTAGAATCAATATCGAATTTTAAGA
* *
2736137 TAG
128 CAA
* * * *** * * *
2736140 AATAATGATATCTCTTCATTTCGATCATAGCAATAAAAAGATTGCTTCAAGGTATGAGAGGTCAT
1 AATAGTAATATCTCTTCATTTTGATTGGAGTAAT-AAATGATTGCTTCAAGGCATGAGAGGTCAT
* * * *
2736205 TTATTCTTGATTGAAAATCATTAGATATTATTGTTTTCACTATAATCGATATCGAATTTTAAGAC
65 TTATTCTCGATTGAAAAT-ATTAGATATTATCGTTTTCACTAGAATCAATATCGAATTTTAAGAC
2736270 AA
129 AA
* * * * * * *
2736272 AATAGTAATATCTCTTCATTTTGATTGGATTAATAATTGACTGTTTTAAGGCATGAAAGGTAATT
1 AATAGTAATATCTCTTCATTTTGATTGGAGTAATAAATGATTGCTTCAAGGCATGAGAGGTCATT
*
2736337 TATTCTCGA-TGAAAAATAATTATATATTATCGTTTTC
66 TATTCTCGATTG-AAAAT-ATTAGATATTATCGTTTTC
2736374 TCTCTTAAAA
Statistics
Matches: 183, Mismatches: 46, Indels: 10
0.77 0.19 0.04
Matches are distributed among these distances:
130 3 0.02
131 76 0.42
132 99 0.54
133 5 0.03
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (130 bp):
AATAGTAATATCTCTTCATTTTGATTGGAGTAATAAATGATTGCTTCAAGGCATGAGAGGTCATT
TATTCTCGATTGAAAATATTAGATATTATCGTTTTCACTAGAATCAATATCGAATTTTAAGACAA
Found at i:2741530 original size:84 final size:83
Alignment explanation
Indices: 2741388--2741554 Score: 298
Period size: 84 Copynumber: 2.0 Consensus size: 83
2741378 TCCTCCTTAC
* *
2741388 CCAAAGTGGTTTGCGCCAGTGCCTGATGCGAATATCACGTAGGTACTTCAGGAAATTCAATATAA
1 CCAAAGTAGTTTGCGCCAGTGCCCGATGCGAATATCACGTAGGTACTTCAGGAAATTCAATATAA
2741453 AATTGTATTGCCTTCAAA
66 AATTGTATTGCCTTCAAA
*
2741471 CCAAAGTAGTTTGACGCCAGTGCCCGATGCGAATATCACGTAGGTACTTCAGGACATTCAATATA
1 CCAAAGTAGTTTG-CGCCAGTGCCCGATGCGAATATCACGTAGGTACTTCAGGAAATTCAATATA
2741536 AAATTGTATTGCCTTCAAA
65 AAATTGTATTGCCTTCAAA
2741555 AAGACTGTAC
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
83 12 0.15
84 68 0.85
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (83 bp):
CCAAAGTAGTTTGCGCCAGTGCCCGATGCGAATATCACGTAGGTACTTCAGGAAATTCAATATAA
AATTGTATTGCCTTCAAA
Found at i:2747183 original size:13 final size:13
Alignment explanation
Indices: 2747165--2747207 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
2747155 GTACTTCGCC
2747165 TGAAAAAAAAGAA
1 TGAAAAAAAAGAA
*
2747178 TGAAAACAAAGAA
1 TGAAAAAAAAGAA
*
2747191 TAAAAAAAAAGAA
1 TGAAAAAAAAGAA
2747204 TGAA
1 TGAA
2747208 TGAATGAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.74, C:0.02, G:0.14, T:0.09
Consensus pattern (13 bp):
TGAAAAAAAAGAA
Found at i:2747240 original size:35 final size:34
Alignment explanation
Indices: 2747175--2747246 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 34
2747165 TGAAAAAAAA
2747175 GAATGAAAACAAAGAATAAAAAAAAAGAATGAAT
1 GAATGAAAACAAAGAATAAAAAAAAAGAATGAAT
* *
2747209 GAATGAAAAGAGAA-AATGAAAAAAAATGAATGAAT
1 GAATGAAAACA-AAGAAT-AAAAAAAAAGAATGAAT
2747244 GAA
1 GAA
2747247 AAAAGAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
34 13 0.38
35 21 0.62
ACGTcount: A:0.68, C:0.01, G:0.18, T:0.12
Consensus pattern (34 bp):
GAATGAAAACAAAGAATAAAAAAAAAGAATGAAT
Found at i:2747264 original size:31 final size:31
Alignment explanation
Indices: 2747165--2747254 Score: 107
Period size: 31 Copynumber: 3.0 Consensus size: 31
2747155 GTACTTCGCC
*
2747165 TGAAAAAAAA-GAATGAA--AACAAAGAATAA
1 TGAAAAAAAATGAATGAATGAAAAAAGAA-AA
* *
2747194 -AAAAAAAGAATGAATGAATGAAAAGAGAAAA
1 TGAAAAAA-AATGAATGAATGAAAAAAGAAAA
2747225 TGAAAAAAAATGAATGAATGAAAAAAGAAA
1 TGAAAAAAAATGAATGAATGAAAAAAGAAA
2747255 TAAGGAAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
28 6 0.12
29 2 0.04
30 7 0.14
31 23 0.45
32 13 0.25
ACGTcount: A:0.71, C:0.01, G:0.17, T:0.11
Consensus pattern (31 bp):
TGAAAAAAAATGAATGAATGAAAAAAGAAAA
Found at i:2747284 original size:21 final size:20
Alignment explanation
Indices: 2747246--2747286 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
2747236 GAATGAATGA
**
2747246 AAAAAGAAATAAGGAAAAAG
1 AAAAAGAAATAAACAAAAAG
2747266 AAAAAGAGAATAAACAAAAAG
1 AAAAAGA-AATAAACAAAAAG
2747287 GAGGGTTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.76, C:0.02, G:0.17, T:0.05
Consensus pattern (20 bp):
AAAAAGAAATAAACAAAAAG
Found at i:2748850 original size:3 final size:3
Alignment explanation
Indices: 2748838--2748882 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
2748828 ATCCCATTAA
2748838 ATT A-T ATT ATT A-T ATT ATT A-T ATT AATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT
2748881 AT
1 AT
2748883 AAATACATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 6 0.16
3 29 0.76
4 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:2748851 original size:8 final size:8
Alignment explanation
Indices: 2748838--2748883 Score: 67
Period size: 8 Copynumber: 5.8 Consensus size: 8
2748828 ATCCCATTAA
2748838 ATTATATT
1 ATTATATT
2748846 ATTATATT
1 ATTATATT
2748854 ATTATATT
1 ATTATATT
*
2748862 AAT-TATT
1 ATTATATT
2748869 ATTATTATT
1 ATTA-TATT
2748878 ATTATA
1 ATTATA
2748884 AATACATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
7 6 0.18
8 20 0.59
9 8 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
ATTATATT
Found at i:2750103 original size:29 final size:30
Alignment explanation
Indices: 2750033--2750092 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
2750023 CAATTTAAGG
*
2750033 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTAAATTTA
2750064 CAAAATGTTTTTGGACTT-AATTAAATTTA
1 CAAAATGTTTTTGGACTTGAATTAAATTTA
2750093 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 10 0.36
30 12 0.43
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTAAATTTA
Found at i:2750240 original size:20 final size:18
Alignment explanation
Indices: 2750215--2750304 Score: 60
Period size: 20 Copynumber: 4.9 Consensus size: 18
2750205 CACCTGCACT
2750215 AATGCATCGATGCATCATGC
1 AATGCATCGATGCATC-T-C
*
2750235 AATGCATCCATGCA-CTC
1 AATGCATCGATGCATCTC
* *
2750252 AA-ACATCGAATGCA-CTT
1 AATGCATCG-ATGCATCTC
*
2750269 AGTGCATCGATGCATCCTGC
1 AATGCATCGATGCAT-CT-C
* *
2750289 CATGCATCCATGCATC
1 AATGCATCGATGCATC
2750305 AAGGCTGCAA
Statistics
Matches: 55, Mismatches: 10, Indels: 11
0.72 0.13 0.14
Matches are distributed among these distances:
16 4 0.07
17 16 0.29
18 6 0.11
19 4 0.07
20 25 0.45
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (18 bp):
AATGCATCGATGCATCTC
Found at i:2750453 original size:20 final size:22
Alignment explanation
Indices: 2750415--2750454 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
2750405 TTTGAGTAGA
2750415 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
2750437 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
2750455 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:2751583 original size:5 final size:6
Alignment explanation
Indices: 2751566--2751590 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2751556 GTTTTAGTCC
2751566 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
2751591 GCATGTTGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:2755557 original size:18 final size:18
Alignment explanation
Indices: 2755531--2755569 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2755521 CATATATACC
2755531 TTTTTATTTAATTTTT-A
1 TTTTTATTTAATTTTTCA
2755548 TTTTTAATTTAATTTTTCA
1 TTTTT-ATTTAATTTTTCA
2755567 TTT
1 TTT
2755570 CATTTCACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTATTTAATTTTTCA
Found at i:2757285 original size:30 final size:31
Alignment explanation
Indices: 2757230--2757287 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
2757220 CAACCATTCA
* *
2757230 CAACTTTTCCAAAATTGCCAAAATGGTCCCC
1 CAACTTTTCAAAAATTGACAAAATGGTCCCC
*
2757261 CAACTTTTCAAAAATT-ACATAATGGTC
1 CAACTTTTCAAAAATTGACAAAATGGTC
2757288 TCCAAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 9 0.38
31 15 0.62
ACGTcount: A:0.36, C:0.26, G:0.09, T:0.29
Consensus pattern (31 bp):
CAACTTTTCAAAAATTGACAAAATGGTCCCC
Found at i:2763216 original size:16 final size:16
Alignment explanation
Indices: 2763178--2763221 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 16
2763168 TGCATGCTTC
* *
2763178 CCCTTCTTCTATTTTT
1 CCCTTTTTCTCTTTTT
2763194 CCC--TTTCTCTTTTT
1 CCCTTTTTCTCTTTTT
2763208 CCCTTTTTCTCTTT
1 CCCTTTTTCTCTTT
2763222 GCATCAGTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 12 0.50
16 12 0.50
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (16 bp):
CCCTTTTTCTCTTTTT
Found at i:2766022 original size:21 final size:21
Alignment explanation
Indices: 2765996--2766060 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
2765986 ATGACTAATC
*
2765996 GTTTATTGTAAACTGTTTGTA
1 GTTTATTGTAAAATGTTTGTA
** *
2766017 GTTTATTGTAATTTGTTTGCA
1 GTTTATTGTAAAATGTTTGTA
2766038 GTTTATTGTAAAATGTTTGTA
1 GTTTATTGTAAAATGTTTGTA
2766059 GT
1 GT
2766061 GTCCCCCGTC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.23, C:0.03, G:0.20, T:0.54
Consensus pattern (21 bp):
GTTTATTGTAAAATGTTTGTA
Found at i:2766730 original size:2 final size:2
Alignment explanation
Indices: 2766723--2766757 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2766713 TCAATCTACA
2766723 AT 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 A
2766758 ATTTACGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2767389 original size:30 final size:30
Alignment explanation
Indices: 2767350--2767414 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
2767340 CATTCATAAC
* * *
2767350 TTTTCCAAAATTTTCAAAATGGTATCCC-AA
1 TTTTTCAAAAATTACAAAATGGT-TCCCAAA
*
2767380 TTTTTCAAAAATTACATAATGGTTCCCAAA
1 TTTTTCAAAAATTACAAAATGGTTCCCAAA
2767410 TTTTT
1 TTTTT
2767415 ATAAGGATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 4 0.13
30 26 0.87
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.42
Consensus pattern (30 bp):
TTTTTCAAAAATTACAAAATGGTTCCCAAA
Found at i:2772056 original size:187 final size:187
Alignment explanation
Indices: 2771741--2772113 Score: 737
Period size: 187 Copynumber: 2.0 Consensus size: 187
2771731 GAAACCACCA
*
2771741 TGATCAGCAATTTTCCTGCATGTGATCAACCATCATTGAGAAAAAGGGAAATAATTTCCAGCTCT
1 TGATCAGCAATTTTCCTGCATGTGATCAACCATCATTGAGAAAAAGGGAAATAATCTCCAGCTCT
2771806 TATTAGCATTTAAACAATTTCAAGGGTTCAAAGATATAGGGATAATGAATTCAAGAATAACTCAG
66 TATTAGCATTTAAACAATTTCAAGGGTTCAAAGATATAGGGATAATGAATTCAAGAATAACTCAG
2771871 GGAACAGTGGATAGTTGTACGGACTACTCCCAGCTTCTACATACAAGTTCATACATG
131 GGAACAGTGGATAGTTGTACGGACTACTCCCAGCTTCTACATACAAGTTCATACATG
2771928 TGATCAGCAATTTTCCTGCATGTGATCAACCATCATTGAGAAAAAGGGAAATAATCTCCAGCTCT
1 TGATCAGCAATTTTCCTGCATGTGATCAACCATCATTGAGAAAAAGGGAAATAATCTCCAGCTCT
2771993 TATTAGCATTTAAACAATTTCAAGGGTTCAAAGATATAGGGATAATGAATTCAAGAATAACTCAG
66 TATTAGCATTTAAACAATTTCAAGGGTTCAAAGATATAGGGATAATGAATTCAAGAATAACTCAG
2772058 GGAACAGTGGATAGTTGTACGGACTACTCCCAGCTTCTACATACAAGTTCATACAT
131 GGAACAGTGGATAGTTGTACGGACTACTCCCAGCTTCTACATACAAGTTCATACAT
2772114 CTAGGTCCAT
Statistics
Matches: 185, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
187 185 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (187 bp):
TGATCAGCAATTTTCCTGCATGTGATCAACCATCATTGAGAAAAAGGGAAATAATCTCCAGCTCT
TATTAGCATTTAAACAATTTCAAGGGTTCAAAGATATAGGGATAATGAATTCAAGAATAACTCAG
GGAACAGTGGATAGTTGTACGGACTACTCCCAGCTTCTACATACAAGTTCATACATG
Found at i:2780273 original size:20 final size:20
Alignment explanation
Indices: 2780248--2780300 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
2780238 AATTTTCCAG
* *
2780248 AATCGCAACTCGAAGATGA-A
1 AATCGCAACGCGAACAT-ATA
2780268 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAACATATA
2780288 AATCGCAACGCGA
1 AATCGCAACGCGA
2780301 TTCTGACTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.43, C:0.25, G:0.19, T:0.13
Consensus pattern (20 bp):
AATCGCAACGCGAACATATA
Found at i:2780357 original size:20 final size:20
Alignment explanation
Indices: 2780267--2780499 Score: 211
Period size: 20 Copynumber: 11.6 Consensus size: 20
2780257 TCGAAGATGA
**
2780267 AAATCGCAACGCGAA-CATAT
1 AAATCGCAACGCGAATC-CGT
* *
2780287 AAATCGCAACGCGATTCTG-
1 AAATCGCAACGCGAATCCGT
* * *
2780306 ACTATCGCAACGAGTATCCGT
1 A-AATCGCAACGCGAATCCGT
* *
2780327 AAAATCACAACGCGTATCCGT
1 -AAATCGCAACGCGAATCCGT
*
2780348 AAATCGCAACGAC-AATACGT
1 AAATCGCAACG-CGAATCCGT
*
2780368 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGAATCCGT
* *
2780389 AAATCGCAACGAGAATACGT
1 AAATCGCAACGCGAATCCGT
* *
2780409 AAATCGCAACGCGTATCTGT
1 AAATCGCAACGCGAATCCGT
* *
2780429 AAATCGCAACGAGAATACGT
1 AAATCGCAACGCGAATCCGT
* *
2780449 AAATCGCAATGCGAATACGT
1 AAATCGCAACGCGAATCCGT
* *
2780469 AAATCGCAATGCGAATCTGT
1 AAATCGCAACGCGAATCCGT
2780489 AAATCGCAACG
1 AAATCGCAACG
2780500 AGATTCTGAC
Statistics
Matches: 175, Mismatches: 31, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
19 1 0.01
20 139 0.79
21 34 0.19
22 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:2780424 original size:40 final size:40
Alignment explanation
Indices: 2780309--2780499 Score: 258
Period size: 40 Copynumber: 4.7 Consensus size: 40
2780299 GATTCTGACT
* * *
2780309 ATCGCAACGAGTATCCGTAAAATCACAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCCGTAA
*
2780350 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCCGTAA
*
2780391 ATCGCAACGAGAATACGTAAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTAA
* * *
2780431 ATCGCAACGAGAATACGTAAATCGCAATGCGAATACGTAA
1 ATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTAA
* *
2780471 ATCGCAATGCGAAT-CTGTAAATCGCAACG
1 ATCGCAACGAGAATAC-GTAAATCGCAACG
2780500 AGATTCTGAC
Statistics
Matches: 136, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 81 0.60
41 54 0.40
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (40 bp):
ATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTAA
Found at i:2781386 original size:24 final size:24
Alignment explanation
Indices: 2781359--2781412 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2781349 GTATTCGAAA
2781359 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
2781383 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
2781407 TTTGAT
1 TTTGAT
2781413 GATTTTTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:2784035 original size:19 final size:19
Alignment explanation
Indices: 2783988--2784071 Score: 61
Period size: 19 Copynumber: 4.6 Consensus size: 19
2783978 AATCACAACG
* *
2783988 TGAAAATTGCAACGCGAAAA
1 TGAAAATCGCAATGC-AAAA
**
2784008 TGACTATCGCAATGCAAAA
1 TGAAAATCGCAATGCAAAA
*
2784027 TGAAAATCGCAA--C--GA
1 TGAAAATCGCAATGCAAAA
* *
2784042 -GAGAATCGCAATGCGAAA
1 TGAAAATCGCAATGCAAAA
2784060 TGAAAATCGCAA
1 TGAAAATCGCAA
2784072 CGAGGGAAAG
Statistics
Matches: 49, Mismatches: 10, Indels: 11
0.70 0.14 0.16
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 1 0.02
17 1 0.02
18 1 0.02
19 24 0.49
20 11 0.22
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.15
Consensus pattern (19 bp):
TGAAAATCGCAATGCAAAA
Found at i:2784050 original size:33 final size:33
Alignment explanation
Indices: 2784013--2784075 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
2784003 GAAAATGACT
2784013 ATCGCAATGCAAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCAAAATGAAAATCGCAACGAGAGA
*
2784046 ATCGCAATGCGAAATGAAAATCGCAACGAG
1 ATCGCAATGCAAAATGAAAATCGCAACGAG
2784076 GGAAAGCGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCAAAATGAAAATCGCAACGAGAGA
Found at i:2784428 original size:33 final size:33
Alignment explanation
Indices: 2784389--2784535 Score: 204
Period size: 33 Copynumber: 4.3 Consensus size: 33
2784379 GGAAATTACC
*
2784389 ATCGCAACGAGAGAATCGCAATGCAAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
* *
2784422 ATCGCAACGCGAAAATGACTATCACAATGCGAAATGAAA
1 ATCGCAA--CG-AGA-GA--ATCGCAATGCGAAATGAAA
2784461 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
*
2784494 ATCGCAACGAGGGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
2784527 ATCGCAACG
1 ATCGCAACG
2784536 CGAATTTAGT
Statistics
Matches: 102, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
33 66 0.65
35 4 0.04
36 4 0.04
37 4 0.04
39 24 0.24
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
Found at i:2784570 original size:19 final size:19
Alignment explanation
Indices: 2784535--2784597 Score: 99
Period size: 19 Copynumber: 3.3 Consensus size: 19
2784525 AAATCGCAAC
*
2784535 GCGAATTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
2784554 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
* *
2784573 GCGATTTTAATTTCGCATT
1 GCGATTTTAGTTTCGCGTT
2784592 GCGATT
1 GCGATT
2784598 CTCTCGTTGC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.16, C:0.16, G:0.24, T:0.44
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:2784628 original size:19 final size:19
Alignment explanation
Indices: 2784545--2784629 Score: 83
Period size: 19 Copynumber: 4.7 Consensus size: 19
2784535 GCGAATTTAG
*
2784545 TTTCGCGTTGCGATTTT-A
1 TTTCGCATTGCGATTTTCA
* *
2784563 GTTTCGCGTTGCGATTTTAA
1 -TTTCGCATTGCGATTTTCA
2784583 TTTCGCATTGCGA--TTC-
1 TTTCGCATTGCGATTTTCA
*
2784599 TCTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
2784616 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
2784630 AGTCATTTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
14 6 0.11
16 7 0.12
17 6 0.11
19 36 0.64
20 1 0.02
ACGTcount: A:0.13, C:0.20, G:0.21, T:0.46
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:2784755 original size:14 final size:14
Alignment explanation
Indices: 2784736--2784772 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2784726 CATCAATTAA
2784736 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2784750 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2784764 ACAAATCAA
1 ACAAATCAA
2784773 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2786210 original size:42 final size:42
Alignment explanation
Indices: 2786164--2786248 Score: 100
Period size: 42 Copynumber: 2.0 Consensus size: 42
2786154 GATGACAATG
* * *
2786164 GCCTCTTGAACGGT-GGTAGGGGACTCTCGAGGAATGATAGGA
1 GCCTCTTCAACGATAGG-AGGGGACTCTCGAGGAATGACAGGA
* * *
2786206 GCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGGA
1 GCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGACAGGA
2786248 G
1 G
2786249 AGTCGGGCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
42 34 0.94
43 2 0.06
ACGTcount: A:0.25, C:0.18, G:0.36, T:0.21
Consensus pattern (42 bp):
GCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGACAGGA
Found at i:2788212 original size:20 final size:20
Alignment explanation
Indices: 2788189--2788270 Score: 87
Period size: 20 Copynumber: 4.2 Consensus size: 20
2788179 TTTTGGTTGA
*
2788189 AATGAAAATCGCAAAGAGAG
1 AATGAAAATCGCAACGAGAG
* *
2788209 AATGAAAATCGCAATGCG-G
1 AATGAAAATCGCAACGAGAG
** *
2788228 ATATGACTATCGCAACGCGA-
1 A-ATGAAAATCGCAACGAGAG
2788248 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
2788268 AAT
1 AAT
2788271 CACAACGCGA
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
19 17 0.33
20 34 0.67
ACGTcount: A:0.46, C:0.16, G:0.23, T:0.15
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:2788258 original size:19 final size:19
Alignment explanation
Indices: 2788187--2788332 Score: 96
Period size: 19 Copynumber: 8.1 Consensus size: 19
2788177 TCTTTTGGTT
* *
2788187 GAAATGAAAATCGCAAAGA
1 GAAATGAAAATCGCAACGC
*
2788206 GAGAATGAAAATCGCAATGC
1 GA-AATGAAAATCGCAACGC
* **
2788226 GGATATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
2788246 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
* *
2788263 G--A-GAGAATCACAACGC
1 GAAATGAAAATCGCAACGC
* *
2788279 GAAATTAAAATCGCAA--T
1 GAAATGAAAATCGCAACGC
*
2788296 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
2788312 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
2788331 GA
1 GA
2788333 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 20, Indels: 24
0.68 0.14 0.17
Matches are distributed among these distances:
14 18 0.19
15 2 0.02
16 3 0.03
17 3 0.03
18 2 0.02
19 37 0.39
20 28 0.29
21 2 0.02
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:2788328 original size:33 final size:33
Alignment explanation
Indices: 2788236--2788329 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
2788226 GGATATGACT
*
2788236 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAATGAGAGA
* *
2788269 ATCACAACGCGAAATTAAAATCGCAATGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAATGAGAGA
2788302 ATCGCAACGCGAAATGAAAATCGCAATG
1 ATCGCAACGCGAAATGAAAATCGCAATG
2788330 CGATTTTGGT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.13
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAATGAGAGA
Found at i:2788352 original size:19 final size:19
Alignment explanation
Indices: 2788328--2788449 Score: 83
Period size: 20 Copynumber: 6.5 Consensus size: 19
2788318 AAAATCGCAA
**
2788328 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
2788347 TTCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
2788366 TGCGA--TTC---TCTCGT
1 TGCGATTTTCATTTCGCGT
*
2788380 TGCGATTTTCATTTCTCTCGT
1 TGCGATTTTCA-TT-TCGCGT
** *
2788401 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCA-TTTCGCGT
**
2788421 TGCGATTTTCATTTTCATGT
1 TGCGATTTTCA-TTTCGCGT
2788441 TGCGATTTT
1 TGCGATTTT
2788450 AAGTTTAGAA
Statistics
Matches: 84, Mismatches: 12, Indels: 13
0.77 0.11 0.12
Matches are distributed among these distances:
14 10 0.12
16 3 0.04
17 3 0.04
19 20 0.24
20 30 0.36
21 18 0.21
ACGTcount: A:0.11, C:0.19, G:0.20, T:0.50
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:2788397 original size:21 final size:20
Alignment explanation
Indices: 2788378--2788449 Score: 92
Period size: 20 Copynumber: 3.5 Consensus size: 20
2788368 CGATTCTCTC
2788378 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCAT
** *
2788398 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCAT
2788419 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
2788439 GTTGCGATTTT
1 GTTGCGATTTT
2788450 AAGTTTAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
20 30 0.67
21 15 0.33
ACGTcount: A:0.12, C:0.17, G:0.19, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:2789043 original size:20 final size:20
Alignment explanation
Indices: 2789015--2789183 Score: 178
Period size: 20 Copynumber: 8.3 Consensus size: 20
2789005 AAAAATCGCT
2789015 TTGCGATTTACGGATACGCG
1 TTGCGATTTACGGATACGCG
* * *
2789035 TTACGATTTTACGTAT-TGTCG
1 TTGCGA-TTTACGGATACG-CG
*
2789056 TTGCGATTTACGGATACGCA
1 TTGCGATTTACGGATACGCG
* * *
2789076 TTGCGATTTACGTATTCTCG
1 TTGCGATTTACGGATACGCG
*
2789096 TTGCGATTTACAGATACGCG
1 TTGCGATTTACGGATACGCG
* * * *
2789116 TTGCAATTTACGTATTCTCG
1 TTGCGATTTACGGATACGCG
*
2789136 TTGCGATTTACGGATACGTG
1 TTGCGATTTACGGATACGCG
*
2789156 TTGCGATTTTACGGATACTCG
1 TTGCGA-TTTACGGATACGCG
2789177 TTGCGAT
1 TTGCGAT
2789184 AGTCAGAATC
Statistics
Matches: 118, Mismatches: 27, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
20 84 0.71
21 34 0.29
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (20 bp):
TTGCGATTTACGGATACGCG
Found at i:2789097 original size:40 final size:41
Alignment explanation
Indices: 2789015--2789183 Score: 252
Period size: 40 Copynumber: 4.2 Consensus size: 41
2789005 AAAAATCGCT
* *
2789015 TTGCGATTTACGGATACGCGTTACGATTTTACGTATTGTCG
1 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTCG
*
2789056 TTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCTCG
1 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTCG
* *
2789096 TTGCGATTTACAGATACGCGTTGC-AATTTACGTATTCTCG
1 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTCG
* * *
2789136 TTGCGATTTACGGATACGTGTTGCGATTTTACGGATACTCG
1 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTCG
2789177 TTGCGAT
1 TTGCGAT
2789184 AGTCAGAATC
Statistics
Matches: 116, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
39 1 0.01
40 71 0.61
41 44 0.38
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (41 bp):
TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTCG
Found at i:2789197 original size:81 final size:80
Alignment explanation
Indices: 2789015--2789224 Score: 235
Period size: 81 Copynumber: 2.6 Consensus size: 80
2789005 AAAAATCGCT
* * * * *
2789015 TTGCGATTTACGGATACGCGTTACGATTTTACGTATTGTCGTTGCGATTTACGGATACGCATTGC
1 TTGCGATGTACAGATACGCGTTGC-AATTTACGTATTCTCGTTGCGATTTACGGATACGCATTGC
* *
2789080 GATTTACGTATTCTCG
65 GATTTACGGATACTCG
* **
2789096 TTGCGATTTACAGATACGCGTTGCAATTTACGTATTCTCGTTGCGATTTACGGATACGTGTTGCG
1 TTGCGATGTACAGATACGCGTTGCAATTTACGTATTCTCGTTGCGATTTACGGATACGCATTGCG
2789161 ATTTTACGGATACTCG
66 A-TTTACGGATACTCG
* ** * *
2789177 TTGCGATAGT-CAGA-ATCGCGTTGCGATTTATATGTTCGCGTTGCGATT
1 TTGCGAT-GTACAGATA-CGCGTTGCAATTTACGTATTCTCGTTGCGATT
2789225 ATGGCAACTG
Statistics
Matches: 112, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
80 39 0.35
81 72 0.64
82 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (80 bp):
TTGCGATGTACAGATACGCGTTGCAATTTACGTATTCTCGTTGCGATTTACGGATACGCATTGCG
ATTTACGGATACTCG
Found at i:2801644 original size:23 final size:23
Alignment explanation
Indices: 2801618--2801693 Score: 73
Period size: 23 Copynumber: 3.1 Consensus size: 23
2801608 CTCCCAAATT
2801618 TTTAACTTTTTCTTTTCTCTTTC
1 TTTAACTTTTTCTTTTCTCTTTC
* *
2801641 TTTATTCATTTT-TTTTCTCTTTC
1 TTTA-ACTTTTTCTTTTCTCTTTC
*
2801664 ATGTTAACTTTTTACTTTTTCTCTCTC
1 -T-TTAACTTTTT-C-TTTTCTCTTTC
2801691 TTT
1 TTT
2801694 TACTCATCTT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
23 15 0.36
24 11 0.26
25 5 0.12
26 1 0.02
27 10 0.24
ACGTcount: A:0.11, C:0.20, G:0.01, T:0.68
Consensus pattern (23 bp):
TTTAACTTTTTCTTTTCTCTTTC
Found at i:2808953 original size:17 final size:19
Alignment explanation
Indices: 2808928--2808966 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
2808918 ATATCTGTAT
2808928 TATTAATATTT-TGTTCTA
1 TATTAATATTTATGTTCTA
2808946 TATT-ATATTTAATGTTCTA
1 TATTAATATTT-ATGTTCTA
2808965 TA
1 TA
2808967 AGTTGTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 9 0.47
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TATTAATATTTATGTTCTA
Found at i:2811027 original size:29 final size:29
Alignment explanation
Indices: 2810982--2811060 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 29
2810972 CCCCTTCTCG
* * **
2810982 AATTAATTACCAAAATAGCACCCATTTTA
1 AATTAATTCCCAAAATAGCACCAAAATTA
* * *
2811011 AATTAATTCCCATAATAACACCAAAATTG
1 AATTAATTCCCAAAATAGCACCAAAATTA
* *
2811040 AATAAATTCCCAGAATAGCAC
1 AATTAATTCCCAAAATAGCAC
2811061 TGGTCAACGG
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.47, C:0.22, G:0.05, T:0.27
Consensus pattern (29 bp):
AATTAATTCCCAAAATAGCACCAAAATTA
Found at i:2818238 original size:30 final size:29
Alignment explanation
Indices: 2818202--2818271 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 29
2818192 CATTTTACAG
*
2818202 AAATAGCACCCCTTTTCGAATTAATTACCA
1 AAATAGCACCCATTTT-GAATTAATTACCA
* *
2818232 AAATAGCAACACATTTTGAATTAATTCCCA
1 AAATAGC-ACCCATTTTGAATTAATTACCA
*
2818262 TAATAGCACC
1 AAATAGCACC
2818272 AAAATCGAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 2 0.06
30 25 0.74
31 7 0.21
ACGTcount: A:0.40, C:0.24, G:0.07, T:0.29
Consensus pattern (29 bp):
AAATAGCACCCATTTTGAATTAATTACCA
Found at i:2819304 original size:23 final size:23
Alignment explanation
Indices: 2819278--2819323 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2819268 TCATATCTAC
2819278 AGATCATAACTCCATAAATCACT
1 AGATCATAACTCCATAAATCACT
2819301 AGATCATAACTCCATAAATCACT
1 AGATCATAACTCCATAAATCACT
2819324 CTCAGATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.26, G:0.04, T:0.26
Consensus pattern (23 bp):
AGATCATAACTCCATAAATCACT
Found at i:2821377 original size:5 final size:5
Alignment explanation
Indices: 2821367--2821420 Score: 55
Period size: 5 Copynumber: 11.8 Consensus size: 5
2821357 ATGCTGCTTA
* *
2821367 TTTTC TTTTC TTTT- TTCTC TCTT- TTTT- TTTTC TTTTC -TTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
2821413 -TTTC TTTT
1 TTTTC TTTT
2821421 TTTCAGTCTC
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
4 18 0.44
5 23 0.56
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:2821395 original size:13 final size:13
Alignment explanation
Indices: 2821367--2821423 Score: 62
Period size: 13 Copynumber: 4.2 Consensus size: 13
2821357 ATGCTGCTTA
2821367 TTTTCTTTTCTTTT
1 TTTTC-TTTCTTTT
*
2821381 TTCTCTCTT-TTTT
1 TTTTCT-TTCTTTT
*
2821394 TTTTCTTTTCTTTC
1 TTTTC-TTTCTTTT
2821408 TTTTCTTTCTTTT
1 TTTTCTTTCTTTT
2821421 TTT
1 TTT
2821424 CAGTCTCTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
13 21 0.58
14 15 0.42
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTCTTTCTTTT
Found at i:2821402 original size:9 final size:9
Alignment explanation
Indices: 2821367--2821423 Score: 51
Period size: 9 Copynumber: 5.8 Consensus size: 9
2821357 ATGCTGCTTA
2821367 TTTTCTTTTC
1 TTTT-TTTTC
2821377 TTTTTTCTCTC
1 TTTTTT-T-TC
2821388 TTTTTTTTTTC
1 --TTTTTTTTC
*
2821399 TTTTCTTTC
1 TTTTTTTTC
*
2821408 TTTTCTTTC
1 TTTTTTTTC
2821417 TTTTTTT
1 TTTTTTT
2821424 CAGTCTCTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
9 25 0.61
10 5 0.12
11 4 0.10
12 1 0.02
13 6 0.15
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:2821402 original size:27 final size:29
Alignment explanation
Indices: 2821367--2821423 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
2821357 ATGCTGCTTA
2821367 TTTTCTTTTC-TT-TTTTCTCTCTTTTTT
1 TTTTCTTTTCTTTCTTTTCTCTCTTTTTT
*
2821394 TTTTCTTTTCTTTCTTTTCTTTCTTTTTT
1 TTTTCTTTTCTTTCTTTTCTCTCTTTTTT
2821423 T
1 T
2821424 CAGTCTCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 10 0.37
28 2 0.07
29 15 0.56
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (29 bp):
TTTTCTTTTCTTTCTTTTCTCTCTTTTTT
Found at i:2826191 original size:21 final size:21
Alignment explanation
Indices: 2826149--2826191 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2826139 TTTCTGGGCT
*
2826149 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
2826170 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
2826191 A
1 A
2826192 ACGAATATGA
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:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:2826915 original size:104 final size:103
Alignment explanation
Indices: 2826730--2826948 Score: 375
Period size: 104 Copynumber: 2.1 Consensus size: 103
2826720 GTAGAGGGTC
* *
2826730 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTATGAGGTTTGGTAAGACACCTAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTATGAGGTCTGGTAAGACACATAC
*
2826795 TTGATCCTTGGTATATGTATATGATTCTTAAGGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAA-GGAATGA
* * *
2826834 TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTATGAGGTCTGGTAAGACACATAC
2826899 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
2826937 TATGTGGTCCTT
1 TATGTGGTCCTT
2826949 ATAGACATTA
Statistics
Matches: 108, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
103 18 0.17
104 90 0.83
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTATGAGGTCTGGTAAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:2833103 original size:21 final size:21
Alignment explanation
Indices: 2833061--2833103 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2833051 TTTCTGGGCT
*
2833061 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
2833082 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
2833103 A
1 A
2833104 ACGAATATGA
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:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:2833156 original size:20 final size:20
Alignment explanation
Indices: 2833131--2833168 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2833121 GAACGCTAGA
*
2833131 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
2833151 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
2833169 TAATAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:2833874 original size:103 final size:103
Alignment explanation
Indices: 2833649--2833866 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
2833639 GTAGAGGGTC
* *
2833649 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAATATGTGTGAGGTCTGGTAAGACACCTAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTAAGACACATAC
*
2833714 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
2833752 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTAAGACACATAC
2833817 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
2833855 TATGTGGTCCTT
1 TATGTGGTCCTT
2833867 ATAGACATTA
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTAAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:2836686 original size:44 final size:44
Alignment explanation
Indices: 2836635--2837117 Score: 567
Period size: 44 Copynumber: 11.0 Consensus size: 44
2836625 CTATTTTAAA
* * * *
2836635 ATAAATGAAAATGCATAATGGTGCATTATTGGAAAAAAGGTGCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
* * *
2836679 ATAAATGAAAATGCATAACAATGCATTATTGGTAGAAAGGTGAC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
* * *
2836723 ATAAATGAAAATGCATAATGGTGCATTATTGGCAGAAAGGTGTC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
*
2836767 ATAAATGAAAATGCATAAC-AGTGCATTATTGGCAGAATGGTGCC
1 ATAAATGAAAATGCATAACGA-TGCATTATTGGCAGAAAGGTGCC
* * * * *
2836811 ATAAATG-AAATGCATAACAATACATT-TTTGCAGAAAGATGAC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
** * * *
2836853 ATAAATGAAAATGCATAACGATTTATTTTTGGTAGAAAGATGCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
* * * * *
2836897 CTAAATGAAAATGCATAATGGTGCATTATTGGCAGAAAAGTGCT
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
* * * *
2836941 ATAAATGAAAATGCATAACGATGTATTATTGGCAAAAATGTTCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
* * *
2836985 ATAAATGAAAATTCATAACGATGCGTTATTGGCAGAAATGTGCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
* * * * *
2837029 ATAAATGAAAATGCATAATGGTGCATTATTGGTAGCAAGTTGCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
* **
2837073 ATAAATGAAAATGCATAATGACACATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
2837117 A
1 A
2837118 CTCATGGTAT
Statistics
Matches: 372, Mismatches: 63, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
42 19 0.05
43 32 0.09
44 321 0.86
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.27
Consensus pattern (44 bp):
ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
Found at i:2836887 original size:174 final size:176
Alignment explanation
Indices: 2836635--2837115 Score: 596
Period size: 174 Copynumber: 2.7 Consensus size: 176
2836625 CTATTTTAAA
*** * * * * * *
2836635 ATAAATGAAAATGCATAATGGTGCATTATTGGAAAAAAGGTGCCATAAATGAAAATGCATAACAA
1 ATAAATGAAAATGCATAACAATACATTATTGGCAGAAATGTGACATAAATGAAAATGCATAACGA
* *
2836700 TGCATTATTGGTAGAAAGGTGACATAAATGAAAATGCATAATGGTGCATTATTGGCAGAAAGGTG
66 TGCATTATTGGTAGAAAGATGCCATAAATGAAAATGCATAATGGTGCATTATTGGCAGAAAGGTG
*
2836765 -TCATAAATGAAAATGCATAAC-AGTGCATTATTGGC-AGAATGGTGCC
131 CT-ATAAATGAAAATGCATAACGA-TGCATTATTGGCAAAAAT-GTGCC
*
2836811 ATAAATG-AAATGCATAACAATACATT-TTTGCAGAAA-GATGACATAAATGAAAATGCATAACG
1 ATAAATGAAAATGCATAACAATACATTATTGGCAGAAATG-TGACATAAATGAAAATGCATAACG
** * * *
2836873 ATTTATTTTTGGTAGAAAGATGCCCTAAATGAAAATGCATAATGGTGCATTATTGGCAGAAAAGT
65 ATGCATTATTGGTAGAAAGATGCCATAAATGAAAATGCATAATGGTGCATTATTGGCAGAAAGGT
* *
2836938 GCTATAAATGAAAATGCATAACGATGTATTATTGGCAAAAATGTTCC
130 GCTATAAATGAAAATGCATAACGATGCATTATTGGCAAAAATGTGCC
* * * * * * *
2836985 ATAAATGAAAATTCATAACGATGCGTTATTGGCAGAAATGTGCCATAAATGAAAATGCATAATGG
1 ATAAATGAAAATGCATAACAATACATTATTGGCAGAAATGTGACATAAATGAAAATGCATAACGA
* * ***
2837050 TGCATTATTGGTAGCAAGTTGCCATAAATGAAAATGCATAATGACACATTATTGGCAGAAAGGTG
66 TGCATTATTGGTAGAAAGATGCCATAAATGAAAATGCATAATGGTGCATTATTGGCAGAAAGGTG
2837115 C
131 C
2837116 CACTCATGGT
Statistics
Matches: 261, Mismatches: 37, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
173 1 0.00
174 129 0.49
175 36 0.14
176 94 0.36
177 1 0.00
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.27
Consensus pattern (176 bp):
ATAAATGAAAATGCATAACAATACATTATTGGCAGAAATGTGACATAAATGAAAATGCATAACGA
TGCATTATTGGTAGAAAGATGCCATAAATGAAAATGCATAATGGTGCATTATTGGCAGAAAGGTG
CTATAAATGAAAATGCATAACGATGCATTATTGGCAAAAATGTGCC
Found at i:2837016 original size:218 final size:219
Alignment explanation
Indices: 2836635--2837046 Score: 564
Period size: 218 Copynumber: 1.9 Consensus size: 219
2836625 CTATTTTAAA
* * *
2836635 ATAAATGAAAATGCATAATGGTGCATTATTGGAAAAAAGGTGCCATAAATGAAAATGCATAACAA
1 ATAAATGAAAATGCATAACGATGCATTATTGGAAAAAAGATGCCATAAATGAAAATGCATAACAA
* * * * *
2836700 TGCATTATTGGTAGAAAGGTGACATAAATGAAAATGCATAATGGTGCATTATTGGCAGAAAGGTG
66 TGCATTATTGGCAGAAAAGTGACATAAATGAAAATGCATAACGATGCATTATTGGCAAAAAGGTG
2836765 TCATAAATGAAAATGCATAACAGTGCATTATTGGCAG-AATGGTGCCATAAATG-AAATGCATAA
131 TCATAAATGAAAATGCATAACAGTGCATTATTGGCAGAAAT-GTGCCATAAATGAAAATGCATAA
2836828 CAATACATTTTTGCAGAAAGATGAC
195 CAATACATTTTTGCAGAAAGATGAC
** * * * * ***
2836853 ATAAATGAAAATGCATAACGATTTATTTTTGGTAGAAAGATGCCCTAAATGAAAATGCATAATGG
1 ATAAATGAAAATGCATAACGATGCATTATTGGAAAAAAGATGCCATAAATGAAAATGCATAACAA
* *
2836918 TGCATTATTGGCAGAAAAGTG-CTATAAATGAAAATGCATAACGATGTATTATTGGCAAAAATGT
66 TGCATTATTGGCAGAAAAGTGAC-ATAAATGAAAATGCATAACGATGCATTATTGGCAAAAAGGT
* *
2836982 -TCCATAAATGAAAATTCATAAC-GATGCGTTATTGGCAGAAATGTGCCATAAATGAAAATGCAT
130 GT-CATAAATGAAAATGCATAACAG-TGCATTATTGGCAGAAATGTGCCATAAATGAAAATGCAT
2837045 AA
193 AA
2837047 TGGTGCATTA
Statistics
Matches: 168, Mismatches: 21, Indels: 9
0.85 0.11 0.05
Matches are distributed among these distances:
217 3 0.02
218 152 0.90
219 13 0.08
ACGTcount: A:0.42, C:0.11, G:0.20, T:0.27
Consensus pattern (219 bp):
ATAAATGAAAATGCATAACGATGCATTATTGGAAAAAAGATGCCATAAATGAAAATGCATAACAA
TGCATTATTGGCAGAAAAGTGACATAAATGAAAATGCATAACGATGCATTATTGGCAAAAAGGTG
TCATAAATGAAAATGCATAACAGTGCATTATTGGCAGAAATGTGCCATAAATGAAAATGCATAAC
AATACATTTTTGCAGAAAGATGAC
Found at i:2837993 original size:15 final size:15
Alignment explanation
Indices: 2837973--2838002 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2837963 ATTTTACGAA
2837973 TGATTTTCTAAGTAT
1 TGATTTTCTAAGTAT
2837988 TGATTTTCTAAGTAT
1 TGATTTTCTAAGTAT
2838003 ATTCGATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53
Consensus pattern (15 bp):
TGATTTTCTAAGTAT
Found at i:2843989 original size:22 final size:21
Alignment explanation
Indices: 2843959--2844017 Score: 73
Period size: 23 Copynumber: 2.7 Consensus size: 21
2843949 CGCTAGGAAT
* *
2843959 CGATACCCCCTTGCATGGGTAA
1 CGATTCCCCCTTGAATGGGT-A
2843981 CGATTCCCCCTTTGAATGGGTA
1 CGATTCCCCC-TTGAATGGGTA
2844003 CTGATTCCCCCTTGA
1 C-GATTCCCCCTTGA
2844018 GGTAACTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 15 0.45
23 18 0.55
ACGTcount: A:0.19, C:0.32, G:0.20, T:0.29
Consensus pattern (21 bp):
CGATTCCCCCTTGAATGGGTA
Found at i:2844027 original size:20 final size:23
Alignment explanation
Indices: 2843975--2844027 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
2843965 CCCCTTGCAT
2843975 GGGTAAC-GATTCCCCCTTTGAA
1 GGGTAACTGATTCCCCCTTTGAA
2843997 TGGGT-ACTGATTCCCCC-TTG-A
1 -GGGTAACTGATTCCCCCTTTGAA
2844018 -GGTAACTGAT
1 GGGTAACTGAT
2844028 ACCCTCCAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
19 3 0.11
20 6 0.21
21 1 0.04
22 5 0.18
23 13 0.46
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.30
Consensus pattern (23 bp):
GGGTAACTGATTCCCCCTTTGAA
Found at i:2844326 original size:20 final size:20
Alignment explanation
Indices: 2844301--2844338 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2844291 GATTTTAGGA
2844301 CTAGTTTTAATTAGTTCTGT
1 CTAGTTTTAATTAGTTCTGT
2844321 CTAGTTTTAATTAGTTCT
1 CTAGTTTTAATTAGTTCT
2844339 AGGATGAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.11, G:0.13, T:0.55
Consensus pattern (20 bp):
CTAGTTTTAATTAGTTCTGT
Found at i:2846463 original size:15 final size:15
Alignment explanation
Indices: 2846443--2846472 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2846433 ATTTTACGAA
2846443 TGATTTTCTAAGTAT
1 TGATTTTCTAAGTAT
2846458 TGATTTTCTAAGTAT
1 TGATTTTCTAAGTAT
2846473 ATTCGTTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53
Consensus pattern (15 bp):
TGATTTTCTAAGTAT
Found at i:2846483 original size:16 final size:16
Alignment explanation
Indices: 2846462--2846493 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2846452 AAGTATTGAT
2846462 TTTCTAAGTATATTCG
1 TTTCTAAGTATATTCG
2846478 TTTCTAAGTATATTCG
1 TTTCTAAGTATATTCG
2846494 ATATAACTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.50
Consensus pattern (16 bp):
TTTCTAAGTATATTCG
Found at i:2851053 original size:20 final size:20
Alignment explanation
Indices: 2851016--2851054 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2851006 AGATTGAGTG
* * *
2851016 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
2851036 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
2851055 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:2851231 original size:21 final size:21
Alignment explanation
Indices: 2851205--2851284 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
2851195 CAGAACCCCA
*
2851205 GGGGGGTATCGATTCCCCTAT
1 GGGGGGAATCGATTCCCCTAT
* *
2851226 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGATTCCCC-T-AT
* *
2851249 AGGGGGAATCGGTT-CCCTCA-
1 GGGGGGAATCGATTCCCCT-AT
2851269 GGGGGG-ATCGATTCCC
1 GGGGGGAATCGATTCCC
2851285 TCTGCACCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
19 6 0.12
20 7 0.14
21 19 0.38
22 4 0.08
23 14 0.28
ACGTcount: A:0.16, C:0.25, G:0.36, T:0.23
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTAT
Found at i:2851273 original size:19 final size:20
Alignment explanation
Indices: 2851227--2851286 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 20
2851217 TTCCCCTATG
2851227 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TC-AA
2851250 GGGGGAATCGGTTCCCTC-A
1 GGGGGAATCGGTTCCCTCAA
* *
2851269 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
2851287 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.17, C:0.27, G:0.35, T:0.22
Consensus pattern (20 bp):
GGGGGAATCGGTTCCCTCAA
Done.