Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008017.1 Hibiscus syriacus cultivar Beakdansim tig00110483_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: 3132588
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 15
Found at i:2358607 original size:17 final size:17
Alignment explanation
Indices: 2358585--2358623 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
2358575 ATTGCTTATA
2358585 TCATTTAAGTAAAGATG
1 TCATTTAAGTAAAGATG
*
2358602 TCATTTAAGTAATGATG
1 TCATTTAAGTAAAGATG
2358619 TCATT
1 TCATT
2358624 GCTTACATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (17 bp):
TCATTTAAGTAAAGATG
Found at i:2372127 original size:21 final size:21
Alignment explanation
Indices: 2372085--2372128 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2372075 ACTCCGGGAG
* *
2372085 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
2372106 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
2372127 CT
1 CT
2372129 CCCACTCCTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:2376040 original size:21 final size:21
Alignment explanation
Indices: 2376016--2376065 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
2376006 CATATTAAAT
* * *
2376016 GGTTGTGGTTCTATCTGATAC
1 GGTTGTGGTGCCATCTGAAAC
**
2376037 GGTTGCAGTGCCATCTGAAAC
1 GGTTGTGGTGCCATCTGAAAC
2376058 GGTTGTGG
1 GGTTGTGG
2376066 AATATACACC
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.16, G:0.34, T:0.34
Consensus pattern (21 bp):
GGTTGTGGTGCCATCTGAAAC
Found at i:2376628 original size:2 final size:2
Alignment explanation
Indices: 2376621--2376668 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2376611 ACTAAAACAC
2376621 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2376663 AT AT AT
1 AT AT AT
2376669 CTTATCAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2377810 original size:14 final size:15
Alignment explanation
Indices: 2377785--2377823 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
2377775 CTGTAAAAAG
2377785 TAATAAAA-AAAA-T
1 TAATAAAATAAAATT
*
2377798 TAGTAAAATAAAATT
1 TAATAAAATAAAATT
2377813 TAATAAAATAA
1 TAATAAAATAA
2377824 TAAATTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 7 0.32
14 4 0.18
15 11 0.50
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (15 bp):
TAATAAAATAAAATT
Found at i:2377819 original size:15 final size:14
Alignment explanation
Indices: 2377780--2377823 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
2377770 TATAACTGTA
*
2377780 AAAAGTAATAAAA-
1 AAAATTAATAAAAT
*
2377793 AAAATTAGTAAAAT
1 AAAATTAATAAAAT
2377807 AAAATTTAATAAAAT
1 AAAA-TTAATAAAAT
2377822 AA
1 AA
2377824 TAAATTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 11 0.42
14 4 0.15
15 11 0.42
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (14 bp):
AAAATTAATAAAAT
Found at i:2379128 original size:21 final size:20
Alignment explanation
Indices: 2379042--2379199 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
2379032 AAATGACCAA
**
2379042 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
2379061 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
2379081 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
2379101 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
2379122 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
2379143 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
2379163 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
2379184 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
2379200 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:2379280 original size:28 final size:28
Alignment explanation
Indices: 2379249--2379302 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
2379239 TATCCGTAAA
* *
2379249 TCGCAATGCGTATCCGTATATCGCAAGT
1 TCGCAACGCGTATCCGTAAATCGCAAGT
2379277 TCGCAACGCGTATCCGTAAATCGCAA
1 TCGCAACGCGTATCCGTAAATCGCAA
2379303 CGATAATCCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (28 bp):
TCGCAACGCGTATCCGTAAATCGCAAGT
Found at i:2379312 original size:48 final size:47
Alignment explanation
Indices: 2379229--2379322 Score: 145
Period size: 48 Copynumber: 2.0 Consensus size: 47
2379219 TATCCGTATA
*
2379229 TCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTATATCGCAAGT
1 TCGCAACGCGTATCCGTAAATCGCAA-GCGTATCCGTAAATCGCAAGT
2379277 TCGCAACGCGTATCCGTAAATCGCAA-CGATAATCCGTAAATCGCAA
1 TCGCAACGCGTATCCGTAAATCGCAAGCG-T-ATCCGTAAATCGCAA
2379323 CGAGAATCTG
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
46 2 0.05
47 1 0.02
48 40 0.93
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (47 bp):
TCGCAACGCGTATCCGTAAATCGCAAGCGTATCCGTAAATCGCAAGT
Found at i:2379336 original size:40 final size:40
Alignment explanation
Indices: 2379277--2379423 Score: 258
Period size: 40 Copynumber: 3.7 Consensus size: 40
2379267 TATCGCAAGT
* * *
2379277 TCGCAACGCGTATCCGTAAATCGCAACGATAATCCGTAAA
1 TCGCAACGAGAATCTGTAAATCGCAACGATAATCCGTAAA
2379317 TCGCAACGAGAATCTGTAAATCGCAACGATAATCCGTAAA
1 TCGCAACGAGAATCTGTAAATCGCAACGATAATCCGTAAA
2379357 TCGCAACGAGAATCTGTAAATCGCAACGATAATCCGTAAA
1 TCGCAACGAGAATCTGTAAATCGCAACGATAATCCGTAAA
*
2379397 TCGCAACGAGAATCTGTAAATCACAAC
1 TCGCAACGAGAATCTGTAAATCGCAAC
2379424 ACTGAAATTT
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 103 1.00
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (40 bp):
TCGCAACGAGAATCTGTAAATCGCAACGATAATCCGTAAA
Found at i:2379405 original size:20 final size:20
Alignment explanation
Indices: 2379166--2379423 Score: 221
Period size: 20 Copynumber: 12.5 Consensus size: 20
2379156 CGATTTTCCA
* ** *
2379166 AAATCGCAACGCGAATATGA
1 AAATCGCAACGAGAATCCGT
* *
2379186 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGAGAATC-CGT
* *
2379206 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGAGAATCCGT
* * *
2379226 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
* * *
2379246 AAATCGCAATGCGTATCCGTAT
1 AAATCGCAACGAGAATCCG--T
* *
2379268 ATCGCAAGTTCGCAACGCGTATCCGT
1 A----AA--TCGCAACGAGAATCCGT
*
2379294 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
2379314 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
2379334 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
2379354 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
2379374 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
2379394 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
2379414 AAATCACAAC
1 AAATCGCAAC
2379424 ACTGAAATTT
Statistics
Matches: 202, Mismatches: 26, Indels: 20
0.81 0.10 0.08
Matches are distributed among these distances:
20 178 0.88
21 1 0.00
22 4 0.02
26 4 0.02
28 15 0.07
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGAGAATCCGT
Found at i:2380145 original size:24 final size:24
Alignment explanation
Indices: 2380106--2380152 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2380096 AAATTTGGTC
2380106 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
2380130 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
2380153 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:2380344 original size:12 final size:12
Alignment explanation
Indices: 2380327--2380351 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2380317 ATATAATCCT
2380327 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2380339 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2380351 G
1 G
2380352 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2382728 original size:19 final size:19
Alignment explanation
Indices: 2382686--2382785 Score: 138
Period size: 19 Copynumber: 5.5 Consensus size: 19
2382676 GCGATTCTCC
2382686 CATTGCGATTTTCATTTCCG
1 CATTGCGATTTTCATTT-CG
2382706 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
2382725 CATTGCGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
*
2382741 --TTGTGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
2382758 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
2382777 CATTGCGAT
1 CATTGCGAT
2382786 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 4, Indels: 11
0.83 0.05 0.13
Matches are distributed among these distances:
14 5 0.07
16 7 0.10
17 7 0.10
19 35 0.49
20 17 0.24
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:2382782 original size:52 final size:53
Alignment explanation
Indices: 2382669--2382785 Score: 200
Period size: 53 Copynumber: 2.2 Consensus size: 53
2382659 GAAATGAAAA
2382669 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
* * *
2382722 TCGCATTGCGATTCTCTCGTTGTGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
2382774 TCGCATTGCGAT
1 TCGCATTGCGAT
2382786 AGTCAATTTT
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
52 30 0.49
53 31 0.51
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:2382911 original size:14 final size:14
Alignment explanation
Indices: 2382892--2382928 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2382882 CATCAATTAC
2382892 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2382906 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2382920 ACAAATCAA
1 ACAAATCAA
2382929 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:2384929 original size:14 final size:14
Alignment explanation
Indices: 2384910--2384966 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2384900 GCGAAATGAA
*
2384910 AATCGCAACGACAG
1 AATCGCAACGAAAG
2384924 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
2384941 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
2384957 AATCGCAACG
1 AATCGCAACG
2384967 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:2384937 original size:33 final size:33
Alignment explanation
Indices: 2384891--2384983 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
2384881 GCGAAACCAA
*
2384891 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
2384924 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
2384957 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
2384984 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:2384948 original size:19 final size:19
Alignment explanation
Indices: 2384854--2384988 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
2384844 TAGTTTACTT
* *
2384854 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
2384874 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
2384893 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2384912 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
2384926 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
2384945 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
2384959 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2384978 TCGCAATGCGA
1 TCGCAACGCGA
2384989 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2385006 original size:19 final size:19
Alignment explanation
Indices: 2384984--2385112 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
2384974 AAAATCGCAA
2384984 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2385003 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
2385017 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2385036 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
2385050 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
2385069 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
2385088 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
2385108 TGCGA
1 TGCGA
2385113 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:2385026 original size:33 final size:33
Alignment explanation
Indices: 2384984--2385075 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
2384974 AAAATCGCAA
2384984 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
2385017 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
2385050 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
2385076 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:2385315 original size:93 final size:93
Alignment explanation
Indices: 2385156--2385722 Score: 1098
Period size: 93 Copynumber: 6.1 Consensus size: 93
2385146 TTGAATGGAT
2385156 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2385221 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
2385249 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2385314 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
2385342 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2385407 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
2385435 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2385500 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
2385528 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2385593 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
2385621 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATATAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
2385686 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
2385714 AAATTTACT
1 AAATTTACT
2385723 AAGCAATCTA
Statistics
Matches: 468, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 468 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:2387445 original size:14 final size:14
Alignment explanation
Indices: 2387426--2387501 Score: 53
Period size: 14 Copynumber: 4.7 Consensus size: 14
2387416 TTGAAATGAA
2387426 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2387440 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
*
2387457 ACAATCGCAACGCGAAATGAA
1 --AATCGCAA--CG--A-GAG
2387478 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2387492 AATCGCAACG
1 AATCGCAACG
2387502 CGAAATGAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
14 20 0.38
15 1 0.02
16 5 0.10
17 3 0.06
19 20 0.38
21 1 0.02
22 2 0.04
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2387464 original size:19 final size:19
Alignment explanation
Indices: 2387440--2387523 Score: 97
Period size: 19 Copynumber: 4.7 Consensus size: 19
2387430 GCAACGAGAG
* *
2387440 AATCGCAACGCGAGATGAC
1 AATCGCAACGCGAAATGAA
2387459 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2387478 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
2387492 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2387511 AATCGCAATGCGA
1 AATCGCAACGCGA
2387524 TTTTGGTTTC
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 39 0.71
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:2387480 original size:52 final size:52
Alignment explanation
Indices: 2387418--2387523 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 52
2387408 TCTTTTGGTT
* *
2387418 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAGATGACAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
*
2387470 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
2387522 GA
1 GA
2387524 TTTTGGTTTC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.10
Consensus pattern (52 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:2387554 original size:14 final size:14
Alignment explanation
Indices: 2387535--2387591 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2387525 TTTGGTTTCG
2387535 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2387549 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2387568 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2387582 CGTTGCGATT
1 CGTTGCGATT
2387592 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2387567 original size:33 final size:33
Alignment explanation
Indices: 2387519--2387599 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
2387509 AAAATCGCAA
**
2387519 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2387552 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2387585 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
2387600 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:2387602 original size:21 final size:21
Alignment explanation
Indices: 2387576--2387651 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
2387566 CGCGTTGCGA
2387576 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
2387597 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
*
2387617 TTCTCTCATTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
2387638 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
2387652 CTCTTCTGCA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.13, C:0.25, G:0.16, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:2387632 original size:41 final size:41
Alignment explanation
Indices: 2387575--2387652 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
2387565 TCGCGTTGCG
* *
2387575 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCATTGCGATTTTCATTTATCTCGTTGCGACAGTC
2387616 ATTCTCTCATTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCATTGCGATTTTCATTTATCTCGTTGCGAC
2387653 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.14, C:0.26, G:0.15, T:0.45
Consensus pattern (41 bp):
ATTCTCTCATTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:2387637 original size:20 final size:20
Alignment explanation
Indices: 2387542--2387651 Score: 99
Period size: 21 Copynumber: 5.8 Consensus size: 20
2387532 TCGCGTTGCG
2387542 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
2387562 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
2387575 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
***
2387595 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGATTTTC
*
2387616 ATTCTCTCATTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
2387636 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
2387652 CTCTTCTGCA
Statistics
Matches: 70, Mismatches: 11, Indels: 17
0.71 0.11 0.17
Matches are distributed among these distances:
13 3 0.04
14 9 0.13
19 9 0.13
20 20 0.29
21 29 0.41
ACGTcount: A:0.13, C:0.25, G:0.17, T:0.45
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:2387778 original size:33 final size:33
Alignment explanation
Indices: 2387731--2387801 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
2387721 AATACTAACT
* *
2387731 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
2387764 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
2387797 TGAAA
1 TGAAA
2387802 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:2388035 original size:22 final size:22
Alignment explanation
Indices: 2387983--2388037 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
2387973 TGGTTGTGAG
**
2387983 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
2388005 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
2388027 GGATTTCTTCG
1 GGATTTCTTCG
2388038 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:2388209 original size:20 final size:20
Alignment explanation
Indices: 2388184--2388377 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
2388174 CTTTAAATAT
2388184 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2388204 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
2388226 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2388245 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
2388265 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
2388285 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2388305 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
2388325 CGTGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
2388345 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
2388365 CGCGTTGCGATTT
1 CGCGTTGCGATTT
2388378 TTGAAAATCG
Statistics
Matches: 145, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:2388371 original size:60 final size:60
Alignment explanation
Indices: 2388184--2388377 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
2388174 CTTTAAATAT
**
2388184 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
2388245 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * * ** *
2388305 CACGTTGCGATTTACGGATACGTGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
2388365 CGCGTTGCGATTT
1 CGCGTTGCGATTT
2388378 TTGAAAATCG
Statistics
Matches: 111, Mismatches: 22, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:2388388 original size:21 final size:20
Alignment explanation
Indices: 2388344--2388501 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
2388334 ATTTATGTGT
* * *
2388344 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTGAAAA
2388364 TCGCGTTGCGATTTTTGAAAA
1 TCGCGTTGCGA-TTTTGAAAA
** * **
2388385 TCGCAATGCGAATTTGTACTA
1 TCGCGTTGCGATTTTG-AAAA
* *
2388406 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTGAA-AA
*
2388427 TCGCGTTGCGATTTTGGAAA
1 TCGCGTTGCGATTTTGAAAA
** * ***
2388447 -CTGATTTGCGATTCTGGGGA
1 TC-GCGTTGCGATTTTGAAAA
* **
2388467 TCGCGTTGCGATTTT-TATT
1 TCGCGTTGCGATTTTGAAAA
2388486 TCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTG
2388502 TTGGTCATTT
Statistics
Matches: 104, Mismatches: 28, Indels: 12
0.72 0.19 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTTGAAAA
Found at i:2388437 original size:42 final size:43
Alignment explanation
Indices: 2388344--2388442 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
2388334 ATTTATGTGT
* *
2388344 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTTGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTTCAAAA
**
2388385 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGA-TTTTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTTCAA-AA
*
2388427 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
2388443 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 14 0.30
42 30 0.64
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.38
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTTCAAAA
Found at i:2390846 original size:24 final size:23
Alignment explanation
Indices: 2390819--2390865 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
2390809 GGGTTCTACA
*
2390819 CGGTCCTTCGGGACAAATTCTATG
1 CGGTCCTTCAGGACAAA-TCTATG
*
2390843 CGGTCTTTCAGGACAAATCTATG
1 CGGTCCTTCAGGACAAATCTATG
2390866 TGGCACTTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (23 bp):
CGGTCCTTCAGGACAAATCTATG
Found at i:2390892 original size:24 final size:24
Alignment explanation
Indices: 2390867--2390948 Score: 128
Period size: 24 Copynumber: 3.4 Consensus size: 24
2390857 AAATCTATGT
* *
2390867 GGCACTTCGGTGCATATTCTACGT
1 GGCACTTCGGTGCAAATTCTACGC
*
2390891 GGCACTTCGGTGTAAATTCTACGC
1 GGCACTTCGGTGCAAATTCTACGC
2390915 GGCACTTCGGTGCAAATTCTACGC
1 GGCACTTCGGTGCAAATTCTACGC
2390939 GGCAGCTTCG
1 GGCA-CTTCG
2390949 ACTGCAATTA
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
24 48 0.91
25 5 0.09
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.28
Consensus pattern (24 bp):
GGCACTTCGGTGCAAATTCTACGC
Found at i:2397371 original size:21 final size:20
Alignment explanation
Indices: 2397345--2397403 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 20
2397335 ATTATCCAAT
2397345 AAACTTGACATCCATAACAAC
1 AAACTTGA-ATCCATAACAAC
2397366 AAACTTGAAATCCATAACAAC
1 AAACTTG-AATCCATAACAAC
* *
2397387 CAACCTGAACTCCATAA
1 AAACTTGAA-TCCATAA
2397404 TAATAAATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.06
21 31 0.91
22 1 0.03
ACGTcount: A:0.47, C:0.29, G:0.05, T:0.19
Consensus pattern (20 bp):
AAACTTGAATCCATAACAAC
Found at i:2398492 original size:11 final size:11
Alignment explanation
Indices: 2398476--2398507 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
2398466 ACATTTGCTC
2398476 GCTTATGGAGG
1 GCTTATGGAGG
2398487 GCTTATGGAGG
1 GCTTATGGAGG
2398498 GCTTATGGAG
1 GCTTATGGAG
2398508 TGACCTGAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.19, C:0.09, G:0.44, T:0.28
Consensus pattern (11 bp):
GCTTATGGAGG
Found at i:2399816 original size:21 final size:20
Alignment explanation
Indices: 2399749--2399846 Score: 85
Period size: 21 Copynumber: 4.8 Consensus size: 20
2399739 CGCAACACGA
2399749 ACTAT-GCAATGCGA-ACTGG
1 ACTATCGCAATGCGATA-TGG
*
2399768 ACTATCGCAATGCGAATATGT
1 ACTATCGCAATGCG-ATATGG
** *
2399789 AAAATCGCAATGCGATAGTCG
1 ACTATCGCAATGCGATA-TGG
*
2399810 ACTATCGCAATGAGA-ACTTGG
1 ACTATCGCAATGCGATA--TGG
2399831 ACTATCGCAATGCGAT
1 ACTATCGCAATGCGAT
2399847 TTGCGATTTA
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 5 0.08
20 12 0.19
21 44 0.71
22 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.23
Consensus pattern (20 bp):
ACTATCGCAATGCGATATGG
Found at i:2399838 original size:42 final size:42
Alignment explanation
Indices: 2399749--2399846 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 42
2399739 CGCAACACGA
* * *
2399749 ACTAT-GCAATGCGA-ACTGGACTATCGCAATGCGAATATGT
1 ACTATCGCAATGCGATACTCGACTATCGCAATGAGAATATGG
** *
2399789 AAAATCGCAATGCGATAGTCGACTATCGCAATGAGAACT-TGG
1 ACTATCGCAATGCGATACTCGACTATCGCAATGAGAA-TATGG
2399831 ACTATCGCAATGCGAT
1 ACTATCGCAATGCGAT
2399847 TTGCGATTTA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
40 3 0.06
41 9 0.19
42 34 0.72
43 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.23
Consensus pattern (42 bp):
ACTATCGCAATGCGATACTCGACTATCGCAATGAGAATATGG
Found at i:2399932 original size:21 final size:19
Alignment explanation
Indices: 2399906--2399961 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 19
2399896 TACATTCTCA
*
2399906 TGCGATAGTCCAAGTTCGCGT
1 TGCGATAGTCCAAATT--CGT
*
2399927 TGCGATTTATTCCAAATTCGT
1 TGCGA--TAGTCCAAATTCGT
2399948 TGCGATAGTCCAAA
1 TGCGATAGTCCAAA
2399962 ATCGCAACGA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 8 0.27
21 13 0.43
23 9 0.30
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.32
Consensus pattern (19 bp):
TGCGATAGTCCAAATTCGT
Found at i:2400061 original size:6 final size:6
Alignment explanation
Indices: 2400052--2400100 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
2400042 CGACCACGAC
*
2400052 CGGAGA CGGAGA CGGAGA CGGAGA C-GAGA CGGAGA C-GAGA CGGCGA
1 CGGAGA CGGAGA CGGAGA CGGAGA CGGAGA CGGAGA CGGAGA CGGAGA
2400098 CGG
1 CGG
2400101 CGGCGGCGCG
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
5 10 0.25
6 30 0.75
ACGTcount: A:0.31, C:0.20, G:0.49, T:0.00
Consensus pattern (6 bp):
CGGAGA
Found at i:2400082 original size:11 final size:11
Alignment explanation
Indices: 2400054--2400099 Score: 74
Period size: 11 Copynumber: 4.1 Consensus size: 11
2400044 ACCACGACCG
2400054 GAGACGGAGAC
1 GAGACGGAGAC
2400065 GGAGACGGAGAC
1 -GAGACGGAGAC
2400077 GAGACGGAGAC
1 GAGACGGAGAC
*
2400088 GAGACGGCGAC
1 GAGACGGAGAC
2400099 G
1 G
2400100 GCGGCGGCGC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 22 0.67
12 11 0.33
ACGTcount: A:0.33, C:0.20, G:0.48, T:0.00
Consensus pattern (11 bp):
GAGACGGAGAC
Found at i:2400082 original size:17 final size:18
Alignment explanation
Indices: 2400052--2400100 Score: 75
Period size: 17 Copynumber: 2.8 Consensus size: 18
2400042 CGACCACGAC
2400052 CGGAGACGGAGACGGAGA
1 CGGAGACGGAGACGGAGA
2400070 CGGAGAC-GAGACGGAGA
1 CGGAGACGGAGACGGAGA
*
2400087 C-GAGACGGCGACGG
1 CGGAGACGGAGACGG
2400101 CGGCGGCGCG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 5 0.17
17 17 0.59
18 7 0.24
ACGTcount: A:0.31, C:0.20, G:0.49, T:0.00
Consensus pattern (18 bp):
CGGAGACGGAGACGGAGA
Found at i:2403684 original size:5 final size:5
Alignment explanation
Indices: 2403674--2403701 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
2403664 TCTCATATCA
2403674 CATAT CATAT CATAT CATAT CATAT CAT
1 CATAT CATAT CATAT CATAT CATAT CAT
2403702 GAACATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (5 bp):
CATAT
Found at i:2403713 original size:15 final size:15
Alignment explanation
Indices: 2403673--2403713 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
2403663 TTCTCATATC
2403673 ACATATCATATCATA
1 ACATATCATATCATA
*
2403688 TCATATCATATCATGA
1 ACATATCATATCAT-A
2403704 ACATAT-ATAT
1 ACATATCATAT
2403714 GTCTTATGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 17 0.74
16 6 0.26
ACGTcount: A:0.44, C:0.17, G:0.02, T:0.37
Consensus pattern (15 bp):
ACATATCATATCATA
Found at i:2410321 original size:15 final size:15
Alignment explanation
Indices: 2410301--2410333 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
2410291 CGTAGGACCC
2410301 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
2410316 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
2410331 CTA
1 CTA
2410334 TTATACCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.18, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:2410482 original size:23 final size:26
Alignment explanation
Indices: 2410445--2410513 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
2410435 TTCTCTTGTG
2410445 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
2410469 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
* *
2410494 ATCA--CATATCATATCACATG
1 ATCATGTATCTCATATCACATG
2410514 AACATATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 21 0.52
25 8 0.20
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:2410495 original size:12 final size:12
Alignment explanation
Indices: 2410478--2410513 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
2410468 TATCATGTTC
2410478 TCATATCACATG
1 TCATATCACATG
*
2410490 TCATATCACATA
1 TCATATCACATG
2410502 TCATATCACATG
1 TCATATCACATG
2410514 AACATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:2410929 original size:64 final size:63
Alignment explanation
Indices: 2410821--2411004 Score: 226
Period size: 64 Copynumber: 2.9 Consensus size: 63
2410811 TAATGAAGGT
* * ** * **
2410821 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTATTATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT-TTATTATTAATGGG
* **
2410885 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTT-ATTATTAATGGG
* * *
2410949 ATGCATTGATGCACTACTTATGCATCGATGCATGAATTACATTCGATGTTT-TTATT
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTATTATT
2411005 TTAAAAGAGT
Statistics
Matches: 104, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
62 5 0.05
63 2 0.02
64 97 0.93
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTATTATTAATGGG
Found at i:2411018 original size:64 final size:64
Alignment explanation
Indices: 2410884--2411046 Score: 179
Period size: 64 Copynumber: 2.5 Consensus size: 64
2410874 TTATTGCTGG
* * * * *
2410884 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGG
1 GATGCATTGATGCACTACTTATGCATCGATGCACCAATTACATTCGATGTTTCATTATTAAAGA
** *
2410948 GATGCATTGATGCACTACTTATGCATCGATGCATGAATTACATTCGATGTTTTTATT-TTAAA-A
1 GATGCATTGATGCACTACTTATGCATCGATGCACCAATTACATTCGATG-TTTCATTATTAAAGA
** *
2411011 GAGTGCATCT-ATGCACTACCAATGCATCGATACACC
1 GA-TGCAT-TGATGCACTACTTATGCATCGATGCACC
2411047 TTCAAACAAT
Statistics
Matches: 83, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
63 2 0.02
64 74 0.89
65 7 0.08
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (64 bp):
GATGCATTGATGCACTACTTATGCATCGATGCACCAATTACATTCGATGTTTCATTATTAAAGA
Found at i:2419191 original size:20 final size:20
Alignment explanation
Indices: 2419139--2419183 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
2419129 GAATATGTAG
2419139 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
2419159 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
2419179 ATCGC
1 ATCGC
2419184 GTTGCGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:2419418 original size:26 final size:22
Alignment explanation
Indices: 2419351--2419407 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
2419341 CACTCTCTAT
* * *
2419351 GGCGACATCCATCCCCATCTCT
1 GGCGAAATCCGTCCCCATCTCC
2419373 GGCGAAATCCGTCCCCATCTCC
1 GGCGAAATCCGTCCCCATCTCC
2419395 GGCGAAATCCGTC
1 GGCGAAATCCGTC
2419408 TATCTCCATC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.19, C:0.42, G:0.19, T:0.19
Consensus pattern (22 bp):
GGCGAAATCCGTCCCCATCTCC
Found at i:2419867 original size:20 final size:20
Alignment explanation
Indices: 2419764--2419869 Score: 101
Period size: 20 Copynumber: 5.4 Consensus size: 20
2419754 GGATCGCAAC
*
2419764 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
*
2419783 GCTATTTTCA-TTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
** *
2419802 GCGATAATCAAATTT-GCGTT
1 GCGATTTTC-ATTTTCGCGTT
** *
2419822 GCGATAGTCATTTTCGTGTT
1 GCGATTTTCATTTTCGCGTT
*
2419842 GCGATTTTCATTTTCGTGTT
1 GCGATTTTCATTTTCGCGTT
2419862 GCGATTTT
1 GCGATTTT
2419870 AAGTTTCAGA
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
19 26 0.35
20 45 0.61
21 3 0.04
ACGTcount: A:0.15, C:0.16, G:0.22, T:0.47
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Found at i:2419876 original size:20 final size:20
Alignment explanation
Indices: 2419833--2419876 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
2419823 CGATAGTCAT
* *
2419833 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
2419853 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
2419873 TTTC
1 TTTC
2419877 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:2421789 original size:20 final size:20
Alignment explanation
Indices: 2421764--2421829 Score: 87
Period size: 20 Copynumber: 3.3 Consensus size: 20
2421754 AACAAAAATT
*
2421764 GCAACGCCAAAATGACTATC
1 GCAACGCGAAAATGACTATC
*
2421784 GCAACGCGGAAATGACTATC
1 GCAACGCGAAAATGACTATC
* **
2421804 GCAAAGCGAATTTGACTATC
1 GCAACGCGAAAATGACTATC
2421824 GCAACG
1 GCAACG
2421830 GGATAATCGC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (20 bp):
GCAACGCGAAAATGACTATC
Found at i:2421884 original size:19 final size:19
Alignment explanation
Indices: 2421862--2421904 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
2421852 AAATCGCAAC
2421862 GCGA-ATTTAGTTTCGCATT
1 GCGATATTTA-TTTCGCATT
*
2421881 GCGATTTTTATTTCGCATT
1 GCGATATTTATTTCGCATT
2421900 GCGAT
1 GCGAT
2421905 TATCTTGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (19 bp):
GCGATATTTATTTCGCATT
Found at i:2421905 original size:19 final size:20
Alignment explanation
Indices: 2421867--2421905 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
2421857 GCAACGCGAA
2421867 TTTAGTTTCGCATTGCGATT
1 TTTAGTTTCGCATTGCGATT
2421887 TTTA-TTTCGCATTGCGATT
1 TTTAGTTTCGCATTGCGATT
2421906 ATCTTGTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.15, C:0.15, G:0.18, T:0.51
Consensus pattern (20 bp):
TTTAGTTTCGCATTGCGATT
Found at i:2421936 original size:20 final size:20
Alignment explanation
Indices: 2421911--2421958 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
2421901 CGATTATCTT
2421911 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCAAATTCGC
**
2421931 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCAAATTCGC
2421951 GTTGCGAT
1 GTTGCGAT
2421959 TTTAAGTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
GTTGCGATAGTCAAATTCGC
Found at i:2421968 original size:20 final size:20
Alignment explanation
Indices: 2421911--2421968 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
2421901 CGATTATCTT
*
2421911 GTTGCGATAGTCAA-ATTCGC
1 GTTGCGATAGT-AAGTTTCGC
* *
2421931 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTAAGTTTCGC
**
2421951 GTTGCGATTTTAAGTTTC
1 GTTGCGATAGTAAGTTTC
2421969 AGAAACTATT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.40
Consensus pattern (20 bp):
GTTGCGATAGTAAGTTTCGC
Found at i:2422549 original size:42 final size:42
Alignment explanation
Indices: 2422444--2422565 Score: 133
Period size: 42 Copynumber: 2.9 Consensus size: 42
2422434 GCCCGACTCA
*
2422444 CCTGTCATCATTCAAGAGG-CCTCTCCTATCGTTCAAGAGGAC
1 CCTGTCATCATTCAAGAGGTCC-CTCCTATCATTCAAGAGGAC
* ** *
2422486 CCTATCATCCCTCAAGA-GTCCCATCCCATCATTCAAGAGG-C
1 CCTGTCATCATTCAAGAGGTCCC-TCCTATCATTCAAGAGGAC
* * *
2422527 CCTGTCATCGTTGAAGAGGTCCCTCCTACCATTCAAGAG
1 CCTGTCATCATTCAAGAGGTCCCTCCTATCATTCAAGAG
2422566 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
41 30 0.45
42 36 0.55
ACGTcount: A:0.25, C:0.34, G:0.17, T:0.25
Consensus pattern (42 bp):
CCTGTCATCATTCAAGAGGTCCCTCCTATCATTCAAGAGGAC
Found at i:2424083 original size:20 final size:20
Alignment explanation
Indices: 2424058--2424135 Score: 95
Period size: 20 Copynumber: 3.9 Consensus size: 20
2424048 AGGTACACTT
*
2424058 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCTAAAGTCAAAA
*
2424078 TCGCAATG-TGAAAGTCAAAA
1 TCGCAACGCT-AAAGTCAAAA
* *
2424098 TCGCAATGCGAAAGTCAAAA
1 TCGCAACGCTAAAGTCAAAA
*
2424118 TCGCAACGCGAAAGTCAA
1 TCGCAACGCTAAAGTCAA
2424136 TTCGCGTTGC
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
19 1 0.02
20 51 0.98
ACGTcount: A:0.44, C:0.23, G:0.18, T:0.15
Consensus pattern (20 bp):
TCGCAACGCTAAAGTCAAAA
Found at i:2424102 original size:40 final size:40
Alignment explanation
Indices: 2424058--2424135 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
2424048 AGGTACACTT
* * *
2424058 TCGCAACGCTAAACTCAAAATCGCAATGTGAAAGTCAAAA
1 TCGCAACGCGAAACTCAAAATCGCAACGCGAAAGTCAAAA
* *
2424098 TCGCAATGCGAAAGTCAAAATCGCAACGCGAAAGTCAA
1 TCGCAACGCGAAACTCAAAATCGCAACGCGAAAGTCAA
2424136 TTCGCGTTGC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.44, C:0.23, G:0.18, T:0.15
Consensus pattern (40 bp):
TCGCAACGCGAAACTCAAAATCGCAACGCGAAAGTCAAAA
Found at i:2424199 original size:20 final size:20
Alignment explanation
Indices: 2424174--2424324 Score: 170
Period size: 20 Copynumber: 7.8 Consensus size: 20
2424164 GCAATTTTCT
*
2424174 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
*
2424194 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
2424214 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* **
2424234 CGTTACGAT--T----TTTT
1 CGTTGCGATAGTCAAATTCG
*
2424248 CGTTGTGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
2424268 TGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
2424288 CGTTGAGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
2424308 CATTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
2424325 GAATGTGTAA
Statistics
Matches: 108, Mismatches: 17, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
14 9 0.08
16 1 0.01
18 1 0.01
20 97 0.90
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:2424305 original size:74 final size:74
Alignment explanation
Indices: 2424125--2424308 Score: 244
Period size: 74 Copynumber: 2.5 Consensus size: 74
2424115 AAATCGCAAC
* * ** * *
2424125 GCGAAAGTC-AATTCGCGTTGCGATAGTCTAATAAGCTTTGCAATTTTCTCGTTGCGATAGTCAA
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTACAATTTTCTCGTTGCGATAGTCAA
2424189 ATTCCCGTT
66 ATTCCCGTT
* * * *
2424198 GCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTACGATTTTTTCGTTGTGATAGTCAA
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTACAATTTTCTCGTTGCGATAGTCAA
**
2424263 ATTCGTGTT
66 ATTCCCGTT
*
2424272 GCGATAGTCAAATTCGCGTTGAGATAGTCAAATTCGC
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGC
2424309 ATTGCGATAT
Statistics
Matches: 96, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
73 7 0.07
74 89 0.93
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (74 bp):
GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTACAATTTTCTCGTTGCGATAGTCAA
ATTCCCGTT
Found at i:2425185 original size:13 final size:13
Alignment explanation
Indices: 2425167--2425207 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
2425157 TGACTTTTTT
2425167 GGTCAAAGTCAAC
1 GGTCAAAGTCAAC
* *
2425180 GGTCAAAGACGAC
1 GGTCAAAGTCAAC
*
2425193 GGTCACAGTCAAC
1 GGTCAAAGTCAAC
2425206 GG
1 GG
2425208 GCTAGGTCAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.34, C:0.24, G:0.29, T:0.12
Consensus pattern (13 bp):
GGTCAAAGTCAAC
Found at i:2427265 original size:35 final size:35
Alignment explanation
Indices: 2427223--2427323 Score: 175
Period size: 35 Copynumber: 2.9 Consensus size: 35
2427213 CGTCAAGTCC
2427223 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCAGTA
1 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCAGTA
*
2427258 AGTAAGGCCCTGAGCACAAAGCCAAGGAGCCAGTA
1 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCAGTA
* *
2427293 AGTAAGGCACTGAGCACAAAGCCGGGGAGCC
1 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCC
2427324 TTCAGGTATA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 62 1.00
ACGTcount: A:0.35, C:0.26, G:0.32, T:0.08
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCAGTA
Found at i:2427444 original size:24 final size:24
Alignment explanation
Indices: 2427394--2427454 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
2427384 TATATAAAAA
* **
2427394 ATCAAAACATAATTCAGTTCAGAT
1 ATCAAAACAGAATTCAGGCCAGAT
*
2427418 ATCAAAACAGAATTCAGGCCAGGT
1 ATCAAAACAGAATTCAGGCCAGAT
* *
2427442 ATCATATCAGAAT
1 ATCAAAACAGAAT
2427455 CCATGTCAGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.25
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGGCCAGAT
Found at i:2430044 original size:11 final size:11
Alignment explanation
Indices: 2430019--2430048 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
2430009 GGTTTTGTTC
2430019 AAAATGAGTTA
1 AAAATGAGTTA
2430030 AAAATTGAGTTA
1 AAAA-TGAGTTA
2430042 AAAATGA
1 AAAATGA
2430049 TGATACTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.57, C:0.00, G:0.17, T:0.27
Consensus pattern (11 bp):
AAAATGAGTTA
Found at i:2433396 original size:12 final size:12
Alignment explanation
Indices: 2433379--2433403 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2433369 AAATACGTTG
2433379 TCGGTTTTGTTA
1 TCGGTTTTGTTA
2433391 TCGGTTTTGTTA
1 TCGGTTTTGTTA
2433403 T
1 T
2433404 TATTTAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.24, T:0.60
Consensus pattern (12 bp):
TCGGTTTTGTTA
Found at i:2433814 original size:14 final size:14
Alignment explanation
Indices: 2433783--2433830 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
2433773 CACTTTTGTA
2433783 AATATTTCATTATAT
1 AATATTT-ATTATAT
*
2433798 AATATTTATTATTT
1 AATATTTATTATAT
* *
2433812 AATATATATT-TAC
1 AATATTTATTATAT
2433825 AATATT
1 AATATT
2433831 ATTTTAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
13 6 0.21
14 15 0.54
15 7 0.25
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (14 bp):
AATATTTATTATAT
Found at i:2435832 original size:14 final size:14
Alignment explanation
Indices: 2435804--2435843 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
2435794 AGAGGTAAGT
*
2435804 TTTATTTC-TTTTA
1 TTTATTTCGATTTA
*
2435817 TTTATTTTGATTTA
1 TTTATTTCGATTTA
2435831 TTTATTTCGATTT
1 TTTATTTCGATTT
2435844 GATAAGTCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 7 0.30
14 16 0.70
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.72
Consensus pattern (14 bp):
TTTATTTCGATTTA
Found at i:2438199 original size:36 final size:37
Alignment explanation
Indices: 2438133--2438209 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 37
2438123 AAAGCCTGAG
* * * * *
2438133 TGCACCGATGCATAGTTTTGTGCATTGATGCATCAAA
1 TGCACCAATGCATAGGTATGTGCATCGATGCATAAAA
2438170 TGCACCAATGCAT-GGTATGTGCATCGATGCATAAAA
1 TGCACCAATGCATAGGTATGTGCATCGATGCATAAAA
2438206 TGCA
1 TGCA
2438210 TTCGATGTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
36 23 0.66
37 12 0.34
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (37 bp):
TGCACCAATGCATAGGTATGTGCATCGATGCATAAAA
Found at i:2438257 original size:20 final size:20
Alignment explanation
Indices: 2438229--2438267 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2438219 CAAGAAATTA
2438229 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
* *
2438249 ATTGGTGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
2438268 CCCTTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:2440988 original size:21 final size:20
Alignment explanation
Indices: 2440958--2441024 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 20
2440948 CGAGCATCAG
*
2440958 TGCACCTTCATGGTGTATCGA
1 TGCACATTCA-GGTGTATCGA
*
2440979 TGCACATTCAAGGATGCATCGA
1 TGCACATTC-AGG-TGTATCGA
2441001 TGCA-ATGGT-AGGTGTATCGA
1 TGCACAT--TCAGGTGTATCGA
2441021 TGCA
1 TGCA
2441025 TGAAGCACAA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
20 11 0.28
21 15 0.38
22 12 0.31
23 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.28
Consensus pattern (20 bp):
TGCACATTCAGGTGTATCGA
Found at i:2446938 original size:45 final size:46
Alignment explanation
Indices: 2446858--2446948 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 46
2446848 TTGAAAAAGT
* * *
2446858 CTGAGTGCATCGATGCATAGTCTTGTGCATCGATGCATCAAATGCA
1 CTGAATGCATCGATGCATAGTCATGTGCATCGATGCATAAAATGCA
*
2446904 CTGAATGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 CTGAATGCATCGATGCATAGTCATGTGCATCGATGCATAAAATGCA
2446949 TTCGATTTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 22 0.54
46 19 0.46
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (46 bp):
CTGAATGCATCGATGCATAGTCATGTGCATCGATGCATAAAATGCA
Found at i:2446996 original size:20 final size:20
Alignment explanation
Indices: 2446968--2447006 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2446958 CAAGAAATTA
2446968 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
* *
2446988 ATTGGTGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
2447007 CCCTTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:2451310 original size:5 final size:5
Alignment explanation
Indices: 2451300--2451339 Score: 80
Period size: 5 Copynumber: 8.0 Consensus size: 5
2451290 TGGAAGCCCT
2451300 AGTTG AGTTG AGTTG AGTTG AGTTG AGTTG AGTTG AGTTG
1 AGTTG AGTTG AGTTG AGTTG AGTTG AGTTG AGTTG AGTTG
2451340 GACTTCTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (5 bp):
AGTTG
Found at i:2452052 original size:20 final size:21
Alignment explanation
Indices: 2452027--2452078 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
2452017 TTTTCCCAAT
*
2452027 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* *
2452047 TCGCAACGCGAATTGAGAAAA
1 TCGCAATGCGAATTAAGAAAA
2452068 TCGCAATGCGA
1 TCGCAATGCGA
2452079 TACTGACTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:2452091 original size:41 final size:41
Alignment explanation
Indices: 2452046--2452140 Score: 111
Period size: 41 Copynumber: 2.3 Consensus size: 41
2452036 GAATAAGTAA
* * * *
2452046 ATCGCAACGCGA-ATTGAGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGATAAT-ACAAAATCGCAACGAGATACTGACT
* *
2452087 ATCGCAATGCTATAATACAAAATCGCAACGAGATACTGACT
1 ATCGCAACGCGATAATACAAAATCGCAACGAGATACTGACT
*
2452128 TTCGCAACGCGAT
1 ATCGCAACGCGAT
2452141 TCTGACTTTC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 42 0.95
42 2 0.05
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGATAATACAAAATCGCAACGAGATACTGACT
Found at i:2452092 original size:20 final size:20
Alignment explanation
Indices: 2452067--2452161 Score: 84
Period size: 20 Copynumber: 4.7 Consensus size: 20
2452057 AATTGAGAAA
*
2452067 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * *
2452087 ATCGCAATGCTATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
2452108 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
2452128 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
2452148 TTCGCAACGCGATA
1 ATCGCAACGCGATA
2452162 ATACATAATC
Statistics
Matches: 60, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
19 2 0.03
20 44 0.73
21 12 0.20
22 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:2452376 original size:22 final size:22
Alignment explanation
Indices: 2452348--2452391 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2452338 CACTCTCTCA
2452348 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
2452370 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
2452392 TATCTCCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:2452708 original size:20 final size:20
Alignment explanation
Indices: 2452654--2452712 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
2452644 GCGATTCTCT
**
2452654 CGTTGCGATTGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
*
2452674 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
2452694 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
2452713 AGAAACTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:2452903 original size:25 final size:24
Alignment explanation
Indices: 2452849--2452903 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
2452839 TGTTTATTAT
* *
2452849 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
2452873 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
2452899 TGTTT
1 TGTTT
2452904 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:2454052 original size:18 final size:18
Alignment explanation
Indices: 2454031--2454075 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
2454021 TCCACTTTGG
*
2454031 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
2454049 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
2454067 GAGCCATCA
1 GAGCCATCA
2454076 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:2454582 original size:20 final size:20
Alignment explanation
Indices: 2454557--2454609 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
2454547 TAGTTTACTT
2454557 TCGCAACACGAAAATAACTA
1 TCGCAACACGAAAATAACTA
* * **
2454577 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATAACTA
*
2454597 TCGCAATACGAAA
1 TCGCAACACGAAA
2454610 TGAAAATCGC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.42, C:0.25, G:0.19, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATAACTA
Found at i:2454631 original size:14 final size:14
Alignment explanation
Indices: 2454612--2454669 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
2454602 ATACGAAATG
2454612 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2454626 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
2454642 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
2454658 AAAATCGCAACG
1 AAAATCGCAACG
2454670 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2454654 original size:32 final size:33
Alignment explanation
Indices: 2454596--2454686 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
2454586 GGAAATGGCT
*
2454596 ATCGCAATACGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
2454629 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
2454661 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
2454687 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:2454793 original size:33 final size:33
Alignment explanation
Indices: 2454703--2454795 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
2454693 TTGTGTTTCG
* *
2454703 CGTTGCGA-TTTCATTTCGCGTTGCAATTTTGT
1 CGTTGCGATTTTCATTTCGCATTGCGATTTTGT
2454735 CGTTGCGATTTTCATTTCGCATTGCGATTTTGT
1 CGTTGCGATTTTCATTTCGCATTGCGATTTTGT
*
2454768 TGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
2454796 AGCCATTTCC
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 8 0.14
33 49 0.86
ACGTcount: A:0.13, C:0.18, G:0.22, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTTTGT
Found at i:2454814 original size:20 final size:19
Alignment explanation
Indices: 2454780--2454835 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
2454770 TTGCGATTTT
*
2454780 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
2454799 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
2454819 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
2454836 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:2455296 original size:41 final size:41
Alignment explanation
Indices: 2455200--2455287 Score: 122
Period size: 41 Copynumber: 2.1 Consensus size: 41
2455190 GACTCACCTG
* * *
2455200 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCACTA
* *
2455242 TCCTCCCTCAAGAGTCCCCCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCCCCACCGTTCAAGAGGCCACTA
2455283 TCATC
1 TCATC
2455288 GTTGAAGAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 22 0.55
42 18 0.45
ACGTcount: A:0.22, C:0.43, G:0.15, T:0.20
Consensus pattern (41 bp):
TCATCCCTCAAGAGTCCCCCCCACCGTTCAAGAGGCCACTA
Found at i:2456721 original size:14 final size:14
Alignment explanation
Indices: 2456702--2456737 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2456692 ATTGTTTAAT
2456702 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
2456716 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
2456730 TGATTTGT
1 TGATTTGT
2456738 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2456898 original size:19 final size:19
Alignment explanation
Indices: 2456874--2456941 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
2456864 ATCGCAACTA
2456874 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
2456893 GAAAATCGTAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
2456912 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
2456926 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
2456942 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 2 0.05
17 2 0.05
19 28 0.64
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.15
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:2456985 original size:20 final size:20
Alignment explanation
Indices: 2456968--2457055 Score: 115
Period size: 20 Copynumber: 4.4 Consensus size: 20
2456958 CGATTTTCTA
2456968 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
*** *
2456988 GTTGCGATTTTTCA-TTTCGA
1 GTTGCGA-TAGCCATTTTCGC
*
2457008 ATTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
2457028 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
2457048 GTTGCGAT
1 GTTGCGAT
2457056 TTCCCCGTTG
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
19 3 0.05
20 50 0.89
21 3 0.05
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.39
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGC
Found at i:2456993 original size:34 final size:36
Alignment explanation
Indices: 2456948--2457035 Score: 108
Period size: 40 Copynumber: 2.4 Consensus size: 36
2456938 GCGATTTTCA
* *
2456948 TTTCGCATTGCGATTTTC-T-AGTTGCGATAGCCAT
1 TTTCGCGTTGCGATTTTCTTCAATTGCGATAGCCAT
2456982 TTTCGCGTTGCGATTTTTCATTTCGAATTGCGATAGCCAT
1 TTTCGCGTTGCGA-TTTTC--TTC-AATTGCGATAGCCAT
2457022 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
2457036 AGCCATTTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
34 12 0.26
35 5 0.11
38 1 0.02
39 1 0.02
40 27 0.59
ACGTcount: A:0.16, C:0.20, G:0.22, T:0.42
Consensus pattern (36 bp):
TTTCGCGTTGCGATTTTCTTCAATTGCGATAGCCAT
Found at i:2457294 original size:20 final size:20
Alignment explanation
Indices: 2457269--2457318 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
2457259 TTGAAGATGA
2457269 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
2457289 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
2457309 TTGCGATTTT
1 TTGCGATTTT
2457319 GTATTATCTC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:2457389 original size:20 final size:21
Alignment explanation
Indices: 2457345--2457396 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
2457335 ATAGTCAGTA
*
2457345 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
2457366 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
2457386 TCGCATTGCGA
1 TCGCATTGCGA
2457397 ATTAGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:2458426 original size:12 final size:12
Alignment explanation
Indices: 2458409--2458433 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2458399 ATATATTCCT
2458409 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2458421 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2458433 G
1 G
2458434 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2460745 original size:19 final size:18
Alignment explanation
Indices: 2460723--2460814 Score: 74
Period size: 19 Copynumber: 5.4 Consensus size: 18
2460713 AGAAATTACT
2460723 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
2460742 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
2460756 ATCGCAACGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
**
2460775 ATCGCAA-CG--A-GGGA
1 ATCGCAAGCGAAATGAAA
2460789 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
2460808 ATCGCAA
1 ATCGCAA
2460815 CGTGAATTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 19 0.33
15 2 0.04
16 4 0.07
17 4 0.07
18 2 0.04
19 26 0.46
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.12
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:2460768 original size:33 final size:33
Alignment explanation
Indices: 2460723--2460816 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
2460713 AGAAATTACT
2460723 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
2460756 ATCGCAACGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
2460789 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
2460817 TGAATTTAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2460847 original size:19 final size:19
Alignment explanation
Indices: 2460825--2460891 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 19
2460815 CGTGAATTTA
2460825 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
2460844 ATTTCGCGTTGCGA--TTC
1 ATTTCGCGTTGCGATTTTC
*
2460861 ---TCTCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
*
2460877 ATTTCGCATTGCGAT
1 ATTTCGCGTTGCGAT
2460892 AGTACTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 10 0.25
16 3 0.08
17 3 0.08
19 24 0.60
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTTTC
Found at i:2461017 original size:14 final size:14
Alignment explanation
Indices: 2460998--2461034 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2460988 CATCAATTAA
2460998 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2461012 ACAAATCACCTTTT
1 ACAAATCAACTTTT
2461026 ACAAATCAA
1 ACAAATCAA
2461035 TTAAACAATA
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:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2462449 original size:42 final size:41
Alignment explanation
Indices: 2462390--2462594 Score: 155
Period size: 42 Copynumber: 4.9 Consensus size: 41
2462380 GTGAATCGGG
* *
2462390 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTCTTCAAGGATGACAGTGGC
* * *
2462432 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * *
2462474 CTCTTCAACGATAGGAGTGGACTCTT-AAGGGATGACATTGGC
1 CTCTTGAACGGTGGGAG-GGACTCTTCAA-GGATGACAGTGGC
* * *
2462516 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* ** * * *
2462558 CTCTTCAACAATAGGAGTGGACTCTTGAGGGATGACA
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACA
2462595 TGCGAGTCGG
Statistics
Matches: 126, Mismatches: 27, Indels: 20
0.73 0.16 0.12
Matches are distributed among these distances:
41 9 0.07
42 106 0.84
43 11 0.09
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTCTTCAAGGATGACAGTGGC
Found at i:2462456 original size:21 final size:21
Alignment explanation
Indices: 2462390--2462456 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2462380 GTGAATCGGG
*
2462390 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
2462410 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
2462432 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
2462453 CTCT
1 CTCT
2462457 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:2462531 original size:84 final size:84
Alignment explanation
Indices: 2462420--2462595 Score: 325
Period size: 84 Copynumber: 2.1 Consensus size: 84
2462410 CCTCTTCAAC
* *
2462420 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACATTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACAA
2462485 TAGGAGTGGACTCTTAAGG
66 TAGGAGTGGACTCTTAAGG
2462504 GATGACATTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACAA
1 GATGACATTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACAA
*
2462569 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTAAGG
2462588 GATGACAT
1 GATGACAT
2462596 GCGAGTCGGG
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 89 1.00
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.22
Consensus pattern (84 bp):
GATGACATTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACAA
TAGGAGTGGACTCTTAAGG
Found at i:2462990 original size:91 final size:90
Alignment explanation
Indices: 2462814--2462998 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 90
2462804 ATTTCAAACT
*
2462814 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
2462879 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
2462907 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
* *
2462971 GTATTGGCAGCAACTGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
2462998 T
1 T
2462999 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 41 0.47
93 19 0.22
95 27 0.31
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:2464748 original size:14 final size:14
Alignment explanation
Indices: 2464729--2464784 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
2464719 CGAAATGACT
2464729 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
2464743 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
2464762 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
2464776 ATCGCAACG
1 ATCGCAACG
2464785 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.43, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:2464752 original size:33 final size:33
Alignment explanation
Indices: 2464710--2464801 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
2464700 GGAAATGACT
**
2464710 ATCGCAACGCGAAATGACTATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
2464743 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
2464776 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
2464802 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.43, C:0.23, G:0.23, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:2464799 original size:19 final size:19
Alignment explanation
Indices: 2464681--2464806 Score: 110
Period size: 19 Copynumber: 7.1 Consensus size: 19
2464671 TCTTTTGGTT
2464681 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
**
2464700 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
**
2464720 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
2464737 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
2464753 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
2464770 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
2464786 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
2464805 GA
1 GA
2464807 TTTTGATTTC
Statistics
Matches: 88, Mismatches: 8, Indels: 21
0.75 0.07 0.18
Matches are distributed among these distances:
14 19 0.22
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 40 0.45
20 17 0.19
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:2464818 original size:19 final size:19
Alignment explanation
Indices: 2464796--2464837 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2464786 GAAATGAAAA
2464796 TCGCAATGCGATTTTGATT
1 TCGCAATGCGATTTTGATT
** *
2464815 TCGCGTTGCGATTTTTATT
1 TCGCAATGCGATTTTGATT
2464834 TCGC
1 TCGC
2464838 GTTGCGATAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.14, C:0.19, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCAATGCGATTTTGATT
Found at i:2464838 original size:19 final size:19
Alignment explanation
Indices: 2464802--2464868 Score: 98
Period size: 19 Copynumber: 3.5 Consensus size: 19
2464792 AAAATCGCAA
*
2464802 TGCGATTTTGATTTCGCGT
1 TGCGATTTTTATTTCGCGT
2464821 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
2464840 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
2464860 TGCGATTTT
1 TGCGATTTT
2464869 CATTCTCGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 30 0.71
20 12 0.29
ACGTcount: A:0.12, C:0.16, G:0.24, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:2465410 original size:20 final size:20
Alignment explanation
Indices: 2465385--2465437 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
2465375 GCGCTATGTA
2465385 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
2465405 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
2465425 TATCTCGTTGCGA
1 AATCGCGTTGCGA
2465438 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:2465475 original size:20 final size:20
Alignment explanation
Indices: 2465450--2465496 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
2465440 TTGTATTATT
2465450 GCATTGCGATAGTAAGTATC
1 GCATTGCGATAGTAAGTATC
*
2465470 GCATTGCGATAGTCAGTATC
1 GCATTGCGATAGTAAGTATC
2465490 GCATTGC
1 GCATTGC
2465497 AATTTTCCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (20 bp):
GCATTGCGATAGTAAGTATC
Found at i:2465610 original size:21 final size:21
Alignment explanation
Indices: 2465570--2465610 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2465560 ACTGTAGACC
**
2465570 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
2465591 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
2465611 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:2466715 original size:28 final size:29
Alignment explanation
Indices: 2466661--2466716 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
2466651 TTAAGTTTTT
* **
2466661 AAAAAAATTGAAAGTTTAGGTGCTAAAAC
1 AAAAAAATTGAAAGTTTAGCTAATAAAAC
*
2466690 AAAAAAA-TGATAGTTTAGCTAATAAAA
1 AAAAAAATTGAAAGTTTAGCTAATAAAA
2466717 ACACTTTAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.55, C:0.05, G:0.14, T:0.25
Consensus pattern (29 bp):
AAAAAAATTGAAAGTTTAGCTAATAAAAC
Found at i:2467888 original size:22 final size:22
Alignment explanation
Indices: 2467863--2467927 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
2467853 CGTCGTCCGG
*
2467863 TTCTTCCGACCGGTCGAACCGA
1 TTCTTCCGACCGGTCGGACCGA
2467885 TTCTTCCGACCGGTCGGACCGA
1 TTCTTCCGACCGGTCGGACCGA
2467907 TTCTTCCGACCGGTCGGACCG
1 TTCTTCCGACCGGTCGGACCG
2467928 GTTCATCCTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.14, C:0.37, G:0.26, T:0.23
Consensus pattern (22 bp):
TTCTTCCGACCGGTCGGACCGA
Found at i:2470659 original size:24 final size:24
Alignment explanation
Indices: 2470632--2470683 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
2470622 GGGTTTTGAA
* *
2470632 CTTGCTCAGTAGAGGCAGAATGTT
1 CTTGCTCAGCAGAGGCAGAATATT
*
2470656 CTTGCTCAGCAGAGGCAGACTATT
1 CTTGCTCAGCAGAGGCAGAATATT
2470680 CTTG
1 CTTG
2470684 TTGAGAAGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (24 bp):
CTTGCTCAGCAGAGGCAGAATATT
Found at i:2470693 original size:24 final size:24
Alignment explanation
Indices: 2470632--2470693 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
2470622 GGGTTTTGAA
* *
2470632 CTTGCTCAGTAGAGGCAGAATGTT
1 CTTGCTCAGAAGAGGCAGAATATT
* *
2470656 CTTGCTCAGCAGAGGCAGACTATT
1 CTTGCTCAGAAGAGGCAGAATATT
* *
2470680 CTTGTTGAGAAGAG
1 CTTGCTCAGAAGAG
2470694 ACATCAACAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (24 bp):
CTTGCTCAGAAGAGGCAGAATATT
Done.