Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 77 of 199
Found at i:23290490 original size:54 final size:54
Alignment explanation
Indices: 23290428--23290703 Score: 260
Period size: 54 Copynumber: 5.1 Consensus size: 54
23290418 GGGTATAATA
23290428 GTCATTTTACCCTATGAGGGTATTTCAGTCATTTTACCCTTCGGGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCAGTCATTTTACCCTTCGGGGGTATTTCG
* * * * * * *
23290482 GTCGTTTTACCCTCTGAGGGTTTTTAAGTTATTTTACCCTTCGAGGGTATTTTG
1 GTCATTTTACCCTATGAGGGTATTTCAGTCATTTTACCCTTCGGGGGTATTTCG
* * * * *
23290536 GTCATTTTACCCTCTGGGGGTATTTCGGTTATTTT-CCC-TCTGGGGGTATTTCA
1 GTCATTTTACCCTATGAGGGTATTTCAGTCATTTTACCCTTC-GGGGGTATTTCG
* *
23290589 GCCATTTTACCCTATTG-GGGTACTTT-GGTCATTTTACCC-TCTGGGGGTATTTCG
1 GTCATTTTACCCTA-TGAGGGTA-TTTCAGTCATTTTACCCTTC-GGGGGTATTTCG
* * * * * * *
23290643 GTCATTTTATCCT-TCAGGGGTACTTC-GTTCATTTTACACTCCGAGGGTATTTCA
1 GTCATTTTACCCTATGA-GGGTATTTCAG-TCATTTTACCCTTCGGGGGTATTTCG
23290697 GTCATTT
1 GTCATTT
23290704 GCCCACGAAT
Statistics
Matches: 186, Mismatches: 27, Indels: 18
0.81 0.12 0.08
Matches are distributed among these distances:
52 3 0.02
53 40 0.22
54 142 0.76
55 1 0.01
ACGTcount: A:0.15, C:0.20, G:0.22, T:0.43
Consensus pattern (54 bp):
GTCATTTTACCCTATGAGGGTATTTCAGTCATTTTACCCTTCGGGGGTATTTCG
Found at i:23290616 original size:80 final size:81
Alignment explanation
Indices: 23290430--23290651 Score: 292
Period size: 80 Copynumber: 2.8 Consensus size: 81
23290420 GTATAATAGT
* *
23290430 CATTTTACCCTA-TGAGGGTATTTCAGTCATTTTACCCT-TCGGGGGTATTTCGGTCGTTTTACC
1 CATTTTACCCTATTGAGGGTATTT-GGTCATTTTACCCTCT-GGGGGTATTTCGGTCATTTTACC
* *
23290493 CTCTGAGGGTTTTTAAGT
64 CTCTGAGGGTATTTAAGC
* * *
23290511 TATTTTACCCT-TCGAGGGTATTTTGGTCATTTTACCCTCTGGGGGTATTTCGGTTATTTT-CCC
1 CATTTTACCCTATTGAGGGTA-TTTGGTCATTTTACCCTCTGGGGGTATTTCGGTCATTTTACCC
* *
23290574 TCTGGGGGTATTTCAGC
65 TCTGAGGGTATTTAAGC
23290591 CATTTTACCCTATTG-GGGTACTTTGGTCATTTTACCCTCTGGGGGTATTTCGGTCATTTTA
1 CATTTTACCCTATTGAGGGTA-TTTGGTCATTTTACCCTCTGGGGGTATTTCGGTCATTTTA
23290652 TCCTTCAGGG
Statistics
Matches: 123, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
80 69 0.56
81 50 0.41
82 4 0.03
ACGTcount: A:0.14, C:0.20, G:0.23, T:0.43
Consensus pattern (81 bp):
CATTTTACCCTATTGAGGGTATTTGGTCATTTTACCCTCTGGGGGTATTTCGGTCATTTTACCCT
CTGAGGGTATTTAAGC
Found at i:23290650 original size:134 final size:135
Alignment explanation
Indices: 23290431--23290695 Score: 322
Period size: 134 Copynumber: 2.0 Consensus size: 135
23290421 TATAATAGTC
* *
23290431 ATTTTACCCTATGAGGGTATTTCAGTCATTTTACCCTTCGGGGGTATTTCGGTCGTTTTACCCTC
1 ATTTTACCCTATGAGGGTATTTCAGCCATTTTACCCTTCGGGGGTATTTCGGTCATTTTACCCTC
* * * * * * *
23290496 TGAGGGTTTTTAAGTTATTTTACCCTTC-GAGGGTATTTTGGTCATTTTACCCTCTGGGGGTATT
66 TGAGGGTATTTAAGTCATTTTACCCTTCAG-GGGTACTTCGGTCATTTTACACTCCGAGGGTATT
23290560 TCGGTT
130 TCGGTT
* * *
23290566 ATTTT-CCCTCTGGGGGTATTTCAGCCATTTTACCCTAT-TGGGGTACTTT-GGTCATTTTACCC
1 ATTTTACCCTATGAGGGTATTTCAGCCATTTTACCCT-TCGGGGGTA-TTTCGGTCATTTTACCC
* ** * *
23290628 TCTGGGGGTATTTCGGTCATTTTATCCTTCAGGGGTACTTCGTTCATTTTACACTCCGAGGGTAT
64 TCTGAGGGTATTTAAGTCATTTTACCCTTCAGGGGTACTTCGGTCATTTTACACTCCGAGGGTAT
23290693 TTC
129 TTC
23290696 AGTCATTTGC
Statistics
Matches: 110, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
134 100 0.91
135 10 0.09
ACGTcount: A:0.15, C:0.20, G:0.22, T:0.43
Consensus pattern (135 bp):
ATTTTACCCTATGAGGGTATTTCAGCCATTTTACCCTTCGGGGGTATTTCGGTCATTTTACCCTC
TGAGGGTATTTAAGTCATTTTACCCTTCAGGGGTACTTCGGTCATTTTACACTCCGAGGGTATTT
CGGTT
Found at i:23291416 original size:10 final size:10
Alignment explanation
Indices: 23291396--23291434 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
23291386 GAAGAGGGGT
23291396 AGAAGAAAAG
1 AGAAGAAAAG
* *
23291406 AAAAGAGAAG
1 AGAAGAAAAG
*
23291416 AGAAAAAAAG
1 AGAAGAAAAG
23291426 AGAAGAAAA
1 AGAAGAAAA
23291435 AAAGAGGGTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (10 bp):
AGAAGAAAAG
Found at i:23291416 original size:15 final size:14
Alignment explanation
Indices: 23291396--23291437 Score: 66
Period size: 15 Copynumber: 2.9 Consensus size: 14
23291386 GAAGAGGGGT
23291396 AGAAGAAAAGAAAAG
1 AGAAGAAAA-AAAAG
23291411 AGAAGAGAAAAAAAG
1 AGAAGA-AAAAAAAG
23291426 AGAAGAAAAAAA
1 AGAAGAAAAAAA
23291438 GAGGGTTCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.23
15 17 0.65
16 3 0.12
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (14 bp):
AGAAGAAAAAAAAG
Found at i:23291432 original size:13 final size:13
Alignment explanation
Indices: 23291396--23291440 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 13
23291386 GAAGAGGGGT
23291396 AGAAGAAAAGAAAAG
1 AGAAG-AAA-AAAAG
23291411 AGAAGAGAAAAAAAG
1 AG-A-AGAAAAAAAG
23291426 AGAAGAAAAAAAG
1 AGAAGAAAAAAAG
23291439 AG
1 AG
23291441 GGTTCAGCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 12 0.43
14 1 0.04
15 9 0.32
16 4 0.14
17 2 0.07
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (13 bp):
AGAAGAAAAAAAG
Found at i:23294759 original size:78 final size:78
Alignment explanation
Indices: 23294677--23294930 Score: 377
Period size: 78 Copynumber: 3.3 Consensus size: 78
23294667 AAAGTATATA
23294677 AATTGAATTAAAGGTATGAATTTTATATATGTATATGTGAGGTTCGAATATATATGTATATACAT
1 AATTGAATTAAAGGTATGAATTTTATATATGTATATGTGAGGTTCGAATATATATGTATATACAT
23294742 GTATAAGTTCTTG
66 GTATAAGTTCTTG
* *
23294755 AATTGAATTAAAGGTATGAATTATATATATGTATATGTGAGGTTTGAATATATATGTATATACAT
1 AATTGAATTAAAGGTATGAATTTTATATATGTATATGTGAGGTTCGAATATATATGTATATACAT
* *
23294820 GTATAAGTTTTTT
66 GTATAAGTTCTTG
* * * * *
23294833 AATTGAATTAAAGGTATGAATTTTACATATGTATGTGTGTGATTC-AA-ATAGATGTATATACAT
1 AATTGAATTAAAGGTATGAATTTTATATATGTATATGTGAGGTTCGAATATATATGTATATACAT
* * *
23294896 ATACAAGTACTTG
66 GTATAAGTTCTTG
*
23294909 AATTGAATTAAAAGTATGAATT
1 AATTGAATTAAAGGTATGAATT
23294931 GTAAATACTT
Statistics
Matches: 159, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
76 44 0.28
77 2 0.01
78 113 0.71
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.41
Consensus pattern (78 bp):
AATTGAATTAAAGGTATGAATTTTATATATGTATATGTGAGGTTCGAATATATATGTATATACAT
GTATAAGTTCTTG
Found at i:23294982 original size:154 final size:153
Alignment explanation
Indices: 23294677--23294966 Score: 347
Period size: 154 Copynumber: 1.9 Consensus size: 153
23294667 AAAGTATATA
* * *
23294677 AATTGAATTAAAGGTATGAATTTTATATATGTATATGTGAGGTTCGAATATATATGTATATACAT
1 AATTGAATTAAAGGTATGAATTTTACATATGTATATGTGAGATTCGAATATAGATGTATATACAT
* * * * * * * *
23294742 GTATAAGTTCTTGAATTGAATTAAAGGTATGAATTATATATATGTATATGTGAGGTTTGAATATA
66 ATACAAGTACTTGAATTGAATTAAAAGTATGAATTATAAATATGTATA---GAGATTCGAACATA
* * *
23294807 TATGTATATACATGTATAAGTTTTTT
128 GATGTACAAACATGTATAAGTTTTTT
* *
23294833 AATTGAATTAAAGGTATGAATTTTACATATGTATGTGTGTGATTC-AA-ATAGATGTATATACAT
1 AATTGAATTAAAGGTATGAATTTTACATATGTATATGTGAGATTCGAATATAGATGTATATACAT
* *
23294896 ATACAAGTACTTGAATTGAATTAAAAGTATGAATTGTAAATACT-TATA-AGATTCGAACATGGA
66 ATACAAGTACTTGAATTGAATTAAAAGTATGAATTATAAATA-TGTATAGAGATTCGAACATAGA
23294959 T-TACAAAC
130 TGTACAAAC
23294967 TTCTTGAGGT
Statistics
Matches: 115, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
149 5 0.04
150 11 0.10
154 55 0.48
155 3 0.03
156 41 0.36
ACGTcount: A:0.39, C:0.05, G:0.17, T:0.40
Consensus pattern (153 bp):
AATTGAATTAAAGGTATGAATTTTACATATGTATATGTGAGATTCGAATATAGATGTATATACAT
ATACAAGTACTTGAATTGAATTAAAAGTATGAATTATAAATATGTATAGAGATTCGAACATAGAT
GTACAAACATGTATAAGTTTTTT
Found at i:23295356 original size:66 final size:66
Alignment explanation
Indices: 23295276--23295438 Score: 267
Period size: 64 Copynumber: 2.5 Consensus size: 66
23295266 ATTTATATCT
*
23295276 TATTTGATAAGTATATATATGCATTCGGTTATATACCTTTGATGTGTATATGCATTCGATTATAA
1 TATTTGATAAGTATATATATGCATTCGGTTATATACATTTGATGTGTATATGCATTCGATTATAA
23295341 G
66 G
* *
23295342 TATTTGAT-AG-GTATATATGCATTCGGTTGTATACATTTGATGTGTATATGCATTCGATTATAA
1 TATTTGATAAGTATATATATGCATTCGGTTATATACATTTGATGTGTATATGCATTCGATTATAA
23295405 G
66 G
* *
23295406 TAGTTGATAAGTATATTTATGCATTCGGTTATA
1 TATTTGATAAGTATATATATGCATTCGGTTATA
23295439 AGTATTTGAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
64 58 0.66
65 4 0.05
66 26 0.30
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.44
Consensus pattern (66 bp):
TATTTGATAAGTATATATATGCATTCGGTTATATACATTTGATGTGTATATGCATTCGATTATAA
G
Found at i:23295413 original size:31 final size:31
Alignment explanation
Indices: 23295289--23295449 Score: 148
Period size: 31 Copynumber: 5.0 Consensus size: 31
23295279 TTGATAAGTA
*
23295289 TATATATGCATTCGGTTAT-A-TACCTTTGATG
1 TATATATGCATTCGATTATAAGTA--TTTGATG
*
23295320 TGTATATGCATTCGATTATAAGTATTTGATAGG
1 TATATATGCATTCGATTATAAGTATTTGAT--G
* * *
23295353 TATATATGCATTCGGTTGTATA-CATTTGATG
1 TATATATGCATTCGATTATA-AGTATTTGATG
* *
23295384 TGTATATGCATTCGATTATAAGTAGTTGATAAG
1 TATATATGCATTCGATTATAAGTATTTGAT--G
*
23295417 TATATTTATGCATTCGGTTATAAGTATTTGATG
1 TATA--TATGCATTCGATTATAAGTATTTGATG
23295450 AGTGTATACA
Statistics
Matches: 106, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
30 1 0.01
31 47 0.44
32 1 0.01
33 32 0.30
34 1 0.01
35 24 0.23
ACGTcount: A:0.29, C:0.08, G:0.19, T:0.44
Consensus pattern (31 bp):
TATATATGCATTCGATTATAAGTATTTGATG
Found at i:23295471 original size:35 final size:35
Alignment explanation
Indices: 23295392--23295473 Score: 92
Period size: 35 Copynumber: 2.3 Consensus size: 35
23295382 TGTGTATATG
* ** *
23295392 CATTCGATTATAAGTAGTTGATAAGTATATTTATG
1 CATTCGGTTATAAGTAGTTGATAAGTATATACATA
* * *
23295427 CATTCGGTTATAAGTATTTGATGAGTGTATACATA
1 CATTCGGTTATAAGTAGTTGATAAGTATATACATA
*
23295462 CATTTGGTTATA
1 CATTCGGTTATA
23295474 TACATTCAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.43
Consensus pattern (35 bp):
CATTCGGTTATAAGTAGTTGATAAGTATATACATA
Found at i:23297087 original size:14 final size:14
Alignment explanation
Indices: 23297068--23297100 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
23297058 GAAAGCTTGT
23297068 GAACTGAGATGCT-C
1 GAACTGAGA-GCTGC
23297082 GAACTGAGAGCTGC
1 GAACTGAGAGCTGC
23297096 GAACT
1 GAACT
23297101 AGTGAAGTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 3 0.17
14 15 0.83
ACGTcount: A:0.30, C:0.21, G:0.30, T:0.18
Consensus pattern (14 bp):
GAACTGAGAGCTGC
Found at i:23297159 original size:117 final size:118
Alignment explanation
Indices: 23296951--23297173 Score: 331
Period size: 117 Copynumber: 1.9 Consensus size: 118
23296941 CTATGCATAC
** * * *
23296951 GAACTGAGATGCTTTAACTGAGAGCTGCGAACTGGTGAAGTACGAACTGTCTCCAAGTAATGCAT
1 GAACTGAGATGCTCGAACTGAGAGCTGCGAACTAGTGAAGTACGAACTATCTCCAAGCAATGCAT
* *
23297016 GCGAGCTGGTAAAGTACGAGCTATGCATGTGAACT-GAGAATAGAAAGCTTGT
66 GCGAGCTAGTAAAGTACGAGCCATGCATGTGAACTAGAGAATAGAAAGCTTGT
* *
23297068 GAACTGAGATGCTCGAACTGAGAGCTGCGAACTAGTGAAGTGCGAGCTATCTCCAAGCAATGCAT
1 GAACTGAGATGCTCGAACTGAGAGCTGCGAACTAGTGAAGTACGAACTATCTCCAAGCAATGCAT
** *
23297133 GCGAGCTAGTAAAGTGTGAGCCATGCATGTGAGCTAGAGAA
66 GCGAGCTAGTAAAGTACGAGCCATGCATGTGAACTAGAGAA
23297174 GTGCGAGCTA
Statistics
Matches: 93, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
117 88 0.95
118 5 0.05
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.22
Consensus pattern (118 bp):
GAACTGAGATGCTCGAACTGAGAGCTGCGAACTAGTGAAGTACGAACTATCTCCAAGCAATGCAT
GCGAGCTAGTAAAGTACGAGCCATGCATGTGAACTAGAGAATAGAAAGCTTGT
Found at i:23297175 original size:28 final size:28
Alignment explanation
Indices: 23297127--23297181 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
23297117 TCTCCAAGCA
*
23297127 ATGCATGCGAGCTAGTAAAGTGTGAGCC
1 ATGCATGCGAGCTAGTAAAGTGCGAGCC
*
23297155 ATGCATGTGAGCTAG-AGAAGTGCGAGC
1 ATGCATGCGAGCTAGTA-AAGTGCGAGC
23297182 TATCTCCAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 1 0.04
28 23 0.96
ACGTcount: A:0.29, C:0.16, G:0.35, T:0.20
Consensus pattern (28 bp):
ATGCATGCGAGCTAGTAAAGTGCGAGCC
Found at i:23303204 original size:6 final size:6
Alignment explanation
Indices: 23303193--23303227 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
23303183 CTGTATTAAA
23303193 ATTTGC ATTTGC ATTTGC ATTTGC ATTTGC ATTTG
1 ATTTGC ATTTGC ATTTGC ATTTGC ATTTGC ATTTG
23303228 TATCTGAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.14, G:0.17, T:0.51
Consensus pattern (6 bp):
ATTTGC
Found at i:23306137 original size:17 final size:18
Alignment explanation
Indices: 23306106--23306141 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
23306096 CTGGGCTATT
23306106 TGGGCTGTGTCGGCCACA
1 TGGGCTGTGTCGGCCACA
*
23306124 TGGGC-GTGTGGGCCACA
1 TGGGCTGTGTCGGCCACA
23306141 T
1 T
23306142 AGGTACCTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.11, C:0.25, G:0.42, T:0.22
Consensus pattern (18 bp):
TGGGCTGTGTCGGCCACA
Found at i:23306201 original size:31 final size:31
Alignment explanation
Indices: 23306163--23306223 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
23306153 AGGTCGTCTG
* * *
23306163 GGCCACACGGGTTGGCCAGTTGGGTCATGTA
1 GGCCACACGAGCTGGCCAGTTGGGCCATGTA
23306194 GGCCACACGAGCTGGCCAGTTGGGCCATGT
1 GGCCACACGAGCTGGCCAGTTGGGCCATGT
23306224 GGAGCTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.16, C:0.26, G:0.38, T:0.20
Consensus pattern (31 bp):
GGCCACACGAGCTGGCCAGTTGGGCCATGTA
Found at i:23309054 original size:35 final size:34
Alignment explanation
Indices: 23308969--23309062 Score: 91
Period size: 35 Copynumber: 2.7 Consensus size: 34
23308959 AAAGTATCAA
* ** *
23308969 AATAAATAAATAAATAACAA-AGAAGGATTAAAAT
1 AATAAATAAATAAATAA-AATAAAATAAGTAAAAT
* *
23309003 AATAAATGAATAAATAATATATAAATAAGTAAAAT
1 AATAAATAAATAAATAAAATA-AAATAAGTAAAAT
* *
23309038 AATGAATAAATGAATAAAATAAAAT
1 AATAAATAAATAAATAAAATAAAAT
23309063 GAATAATGAA
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
33 1 0.02
34 21 0.44
35 26 0.54
ACGTcount: A:0.67, C:0.01, G:0.07, T:0.24
Consensus pattern (34 bp):
AATAAATAAATAAATAAAATAAAATAAGTAAAAT
Found at i:23309077 original size:20 final size:20
Alignment explanation
Indices: 23308997--23309080 Score: 86
Period size: 20 Copynumber: 4.2 Consensus size: 20
23308987 AAAGAAGGAT
23308997 TAAAATAATAAATGAATAAA
1 TAAAATAATAAATGAATAAA
*
23309017 TAATAT-ATAAAT-AAGTAAA
1 TAAAATAATAAATGAA-TAAA
*
23309036 -ATAATGAATAAATGAATAAAA
1 TAAAAT-AATAAATGAAT-AAA
23309057 TAAAATGAAT-AATGAATAAA
1 TAAAAT-AATAAATGAATAAA
23309077 TAAA
1 TAAA
23309081 CAAGTGAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
18 5 0.09
19 10 0.19
20 19 0.35
21 12 0.22
22 8 0.15
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (20 bp):
TAAAATAATAAATGAATAAA
Found at i:23309981 original size:19 final size:18
Alignment explanation
Indices: 23309941--23309984 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
23309931 TGTAAAAAAT
*
23309941 GAAAAGAAAATGAAACGA
1 GAAAAGAAAATGAAACAA
23309959 GAAAACGAAAA-GAAACAA
1 GAAAA-GAAAATGAAACAA
23309977 GGAAAAGA
1 -GAAAAGA
23309985 TCAAAACCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.68, C:0.07, G:0.23, T:0.02
Consensus pattern (18 bp):
GAAAAGAAAATGAAACAA
Found at i:23310831 original size:49 final size:48
Alignment explanation
Indices: 23310703--23310840 Score: 203
Period size: 44 Copynumber: 2.9 Consensus size: 48
23310693 ATGAGATTCG
* *
23310703 CTATCTTCAATTTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGG
1 CTATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGC
*
23310751 C--T-TT-AATCTGCTCCACTACAACTTCAGGGAGATAAGGTTTGTAGC
1 CTATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGT-GC
*
23310796 CTATCTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGGTTTG
1 CTATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTG
23310841 ATATGATCTT
Statistics
Matches: 80, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
44 36 0.45
45 4 0.05
46 1 0.01
47 1 0.01
48 3 0.04
49 35 0.44
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.32
Consensus pattern (48 bp):
CTATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGC
Found at i:23311208 original size:44 final size:43
Alignment explanation
Indices: 23311097--23311274 Score: 178
Period size: 44 Copynumber: 4.0 Consensus size: 43
23311087 GATCTGCAAT
* * * *
23311097 TTATAGCTTCAATCTGTTCTACTGCAACTTCAGGGAAATAAGG
1 TTATAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA
* * *
23311140 TTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
1 TT--ATAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA
* * * *
23311185 CTTATATCTTCAATCTGCCCCACTGCAAATTTAGAGG-GATAAGA
1 -TTATAGCTTCAATCTGCTCCACTGCAACTTCAG-GGAGATAAGA
* * *
23311229 TTAGTGGCTTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
1 TTA-TAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA
23311273 TT
1 TT
23311275 CGTCATAATG
Statistics
Matches: 110, Mismatches: 19, Indels: 11
0.79 0.14 0.08
Matches are distributed among these distances:
43 7 0.06
44 65 0.59
45 36 0.33
46 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.31
Consensus pattern (43 bp):
TTATAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA
Found at i:23312171 original size:6 final size:6
Alignment explanation
Indices: 23312162--23312205 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
23312152 GGCCTCCCAT
23312162 TTTTTC TTTTTC -TTTTC TTTTTC --TTT- TTTTTC TTTTCTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTT-TC TTTTT
23312206 TTATATATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
4 3 0.09
5 8 0.24
6 16 0.48
7 6 0.18
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTC
Found at i:23312179 original size:11 final size:11
Alignment explanation
Indices: 23312163--23312204 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
23312153 GCCTCCCATT
23312163 TTTTCTTTTTC
1 TTTTCTTTTTC
23312174 TTTTCTTTTTC
1 TTTTCTTTTTC
23312185 -TTT-TTTTTC
1 TTTTCTTTTTC
23312194 TTTTCTCTTTT
1 TTTTCT-TTTT
23312205 TTTATATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 6 0.21
10 6 0.21
11 12 0.43
12 4 0.14
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:23312205 original size:16 final size:16
Alignment explanation
Indices: 23312163--23312207 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
23312153 GCCTCCCATT
23312163 TTTTCT-TTTTCTTTTC
1 TTTTCTCTTTT-TTTTC
23312179 TTTT-TCTTTTTTTTC
1 TTTTCTCTTTTTTTTC
23312194 TTTTCTCTTTTTTT
1 TTTTCTCTTTTTTT
23312208 ATATATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 10 0.37
16 17 0.63
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTCTCTTTTTTTTC
Found at i:23312216 original size:26 final size:26
Alignment explanation
Indices: 23312160--23312218 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
23312150 TTGGCCTCCC
* *
23312160 ATTTTTTCTTTTTCTTTTCTTTTTCT
1 ATTTTTTCTTTTTCTTTTCTTTATAT
*
23312186 TTTTTTTCTTTTCTCTTTT-TTTATAT
1 ATTTTTTCTTTT-TCTTTTCTTTATAT
23312212 ATTTTTT
1 ATTTTTT
23312219 TATGAAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 22 0.79
27 6 0.21
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (26 bp):
ATTTTTTCTTTTTCTTTTCTTTATAT
Found at i:23312322 original size:14 final size:15
Alignment explanation
Indices: 23312299--23312331 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
23312289 ATCAACGTTT
*
23312299 TTCCAGATAAGG-CC
1 TTCCACATAAGGTCC
23312313 TTCCACATAAGGTCC
1 TTCCACATAAGGTCC
23312328 TTCC
1 TTCC
23312332 CAATTTTGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.24, C:0.33, G:0.15, T:0.27
Consensus pattern (15 bp):
TTCCACATAAGGTCC
Found at i:23317378 original size:27 final size:26
Alignment explanation
Indices: 23317348--23317423 Score: 73
Period size: 27 Copynumber: 2.7 Consensus size: 26
23317338 AAAAATAAAC
23317348 AATAAAGAAAGATTAAAATAA-TAAATG
1 AATAAA-AAAGA-TAAAATAAGTAAATG
* *
23317375 AATAAATAATATATAAATAAGTAAATG
1 AATAAAAAAGATA-AAATAAGTAAATG
23317402 AATAAATAAATGAATAAAATAA
1 AATAAA-AAA-G-ATAAAATAA
23317424 AAGGAATAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
25 2 0.05
26 9 0.22
27 18 0.45
28 2 0.05
29 6 0.15
30 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (26 bp):
AATAAAAAAGATAAAATAAGTAAATG
Found at i:23317411 original size:12 final size:12
Alignment explanation
Indices: 23317367--23317424 Score: 62
Period size: 12 Copynumber: 4.5 Consensus size: 12
23317357 AGATTAAAAT
23317367 AATAAATGAATA
1 AATAAATGAATA
*
23317379 AATAATATATAAATA
1 AAT-A-A-ATGAATA
*
23317394 AGTAAATGAATA
1 AATAAATGAATA
23317406 AATAAATGAATAA
1 AATAAATGAAT-A
23317419 AATAAA
1 AATAAA
23317425 AGGAATAATG
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
12 19 0.50
13 9 0.24
14 2 0.05
15 8 0.21
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (12 bp):
AATAAATGAATA
Found at i:23317444 original size:4 final size:4
Alignment explanation
Indices: 23317363--23317424 Score: 56
Period size: 4 Copynumber: 15.8 Consensus size: 4
23317353 AGAAAGATTA
* * * *
23317363 AAAT -AAT AAAT GAAT AAAT -AAT ATAT AAAT AAGT AAAT GAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
*
23317409 AAAT GAAT AAAAT AAA
1 AAAT AAAT -AAAT AAA
23317425 AGGAATAATG
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
3 6 0.13
4 36 0.80
5 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:23318335 original size:19 final size:18
Alignment explanation
Indices: 23318296--23318336 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
23318286 TGTAAAATAA
*
23318296 AAAATAAAAAGAAACGAG
1 AAAATAAAAAGAAACAAG
*
23318314 AAAATGAAAAGAAACAAGG
1 AAAATAAAAAGAAACAA-G
23318333 AAAA
1 AAAA
23318337 GATCAAAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.73, C:0.05, G:0.17, T:0.05
Consensus pattern (18 bp):
AAAATAAAAAGAAACAAG
Found at i:23321757 original size:15 final size:16
Alignment explanation
Indices: 23321731--23321760 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
23321721 AAATAATTAA
23321731 TTAGATAAAAAATATT
1 TTAGATAAAAAATATT
23321747 TTAGA-AAAAAATAT
1 TTAGATAAAAAATAT
23321761 ATACAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (16 bp):
TTAGATAAAAAATATT
Found at i:23321874 original size:16 final size:16
Alignment explanation
Indices: 23321849--23321886 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
23321839 TATGTTTAAT
23321849 TAAATATTTAAGTAGA
1 TAAATATTTAAGTAGA
* *
23321865 TAAATTTTTAATTAGA
1 TAAATATTTAAGTAGA
23321881 TAAATA
1 TAAATA
23321887 AAAATTTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (16 bp):
TAAATATTTAAGTAGA
Found at i:23321947 original size:24 final size:24
Alignment explanation
Indices: 23321919--23321967 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
23321909 TCCATTTAAT
*
23321919 TTAAATTAAATAATTATTTAT-TTA
1 TTAAATTAAAT-ACTATTTATATTA
*
23321943 TTAAATTATATACTATTTATATTA
1 TTAAATTAAATACTATTTATATTA
23321967 T
1 T
23321968 ATATTAGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
TTAAATTAAATACTATTTATATTA
Found at i:23321973 original size:23 final size:23
Alignment explanation
Indices: 23321933--23321990 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
23321923 ATTAAATAAT
23321933 TATTTAT-TTATTAAATTA-TATAC
1 TATTTATATTA-TAAATTAGTAT-C
* *
23321956 TATTTATATTATATATTAGTATT
1 TATTTATATTATAAATTAGTATC
*
23321979 TATTTAAATTAT
1 TATTTATATTAT
23321991 TAGCATTTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 24 0.80
24 6 0.20
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (23 bp):
TATTTATATTATAAATTAGTATC
Found at i:23321978 original size:19 final size:19
Alignment explanation
Indices: 23321937--23321999 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
23321927 AATAATTATT
*
23321937 TATTTA-TTAAATTATATAC
1 TATTTATTTAAATTAT-TAG
*
23321956 TATTTATATTATA-TATTAG
1 TATTTAT-TTAAATTATTAG
23321975 TATTTATTTAAATTATTAG
1 TATTTATTTAAATTATTAG
*
23321994 CATTTA
1 TATTTA
23322000 CTAAAATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
18 4 0.11
19 26 0.70
20 3 0.08
21 4 0.11
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (19 bp):
TATTTATTTAAATTATTAG
Found at i:23322006 original size:19 final size:19
Alignment explanation
Indices: 23321969--23322007 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
23321959 TTATATTATA
* * *
23321969 TATTAGTATTTATTTAAAT
1 TATTAGCATTTACTAAAAT
23321988 TATTAGCATTTACTAAAAT
1 TATTAGCATTTACTAAAAT
23322007 T
1 T
23322008 TATACCCTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.51
Consensus pattern (19 bp):
TATTAGCATTTACTAAAAT
Found at i:23337835 original size:11 final size:11
Alignment explanation
Indices: 23337815--23337866 Score: 61
Period size: 11 Copynumber: 4.7 Consensus size: 11
23337805 TCCTCTCTCA
23337815 AATTTCCTCTT
1 AATTTCCTCTT
* *
23337826 AATTTGCTCTC
1 AATTTCCTCTT
23337837 AATTTCCTCTT
1 AATTTCCTCTT
23337848 AAATTT-CTCTT
1 -AATTTCCTCTT
*
23337859 AAATTCCT
1 AATTTCCT
23337867 ATTTTTAACT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
10 4 0.12
11 25 0.74
12 5 0.15
ACGTcount: A:0.23, C:0.25, G:0.02, T:0.50
Consensus pattern (11 bp):
AATTTCCTCTT
Found at i:23337843 original size:22 final size:22
Alignment explanation
Indices: 23337808--23337866 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
23337798 AAACTAATCC
23337808 TCTCTCAAATTTCCTCTT-AATT
1 TCTCTC-AATTTCCTCTTAAATT
23337830 TGCTCTCAATTTCCTCTTAAATT
1 T-CTCTCAATTTCCTCTTAAATT
* *
23337853 TCTCTTAAATTCCT
1 TCTCTCAATTTCCT
23337867 ATTTTTAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 23 0.70
23 10 0.30
ACGTcount: A:0.22, C:0.27, G:0.02, T:0.49
Consensus pattern (22 bp):
TCTCTCAATTTCCTCTTAAATT
Found at i:23338936 original size:7 final size:7
Alignment explanation
Indices: 23338924--23338949 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
23338914 TAGTCGATTG
23338924 GTATTTA
1 GTATTTA
23338931 GTATTTA
1 GTATTTA
23338938 GTATTTA
1 GTATTTA
23338945 GTATT
1 GTATT
23338950 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:23339623 original size:18 final size:18
Alignment explanation
Indices: 23339600--23339639 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
23339590 CAGGTGCGTT
*
23339600 TCCTAACCCTTTTATGTA
1 TCCTAACCCTTATATGTA
*
23339618 TCCTAACCCTTATATGTT
1 TCCTAACCCTTATATGTA
23339636 TCCT
1 TCCT
23339640 TTTTCGAGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.30, G:0.05, T:0.45
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:23340204 original size:22 final size:22
Alignment explanation
Indices: 23340179--23340685 Score: 479
Period size: 21 Copynumber: 23.1 Consensus size: 22
23340169 TTTAATTGAC
23340179 AAACCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
23340201 AAACCCT-AACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
* * *
23340222 AAACCCT-AATCTTTAAATTAA
1 AAACCCTAAACCCTTAACTTAA
23340243 AAACCCTAAACCCTTAACTTAAAACCCA
1 AAACCCTAAACCCTTAACTT---A---A
*
23340271 TAAACCCTAAACCCTTAATTTAA
1 -AAACCCTAAACCCTTAACTTAA
* * * *
23340294 AAACACT-AACTCTTGACTTTA
1 AAACCCTAAACCCTTAACTTAA
23340315 AAACCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
* *
23340337 AACCCCT-AACACTTAA---AA
1 AAACCCTAAACCCTTAACTTAA
*
23340355 AAACACT-AACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
* *
23340376 AAACCCT-AACCCTTAATTTTA
1 AAACCCTAAACCCTTAACTTAA
* *
23340397 AACCCCTAAACCTTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
23340419 AAACCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
*
23340441 AAATCCT-AACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
* * *
23340462 AAA-CCTTAACCTTTAACTTTA
1 AAACCCTAAACCCTTAACTTAA
* *
23340483 AAACCCTAAACCTTTAACCT-A
1 AAACCCTAAACCCTTAACTTAA
*
23340504 AAACCCTAAACCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAA
*
23340526 AAACCCTAAACCCTTAACTTTA
1 AAACCCTAAACCCTTAACTTAA
* *
23340548 AAACCCT-AACCCTTGACTTTA
1 AAACCCTAAACCCTTAACTTAA
*
23340569 AAACCATAAACCCTTAAGC-TAA
1 AAACCCTAAACCCTTAA-CTTAA
* * *
23340591 AAACCCCAACCCCTTAACTTTA
1 AAACCCTAAACCCTTAACTTAA
*
23340613 AAACCCT-AACCCTTAACTTTA
1 AAACCCTAAACCCTTAACTTAA
* *
23340634 AAACCTTAAAACCCTAACCCTTAACTTTA
1 AAACCCT---A----AACCCTTAACTTAA
23340663 AAACCCT-AACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
23340684 AA
1 AA
23340686 GCGCATCCAT
Statistics
Matches: 407, Mismatches: 51, Indels: 55
0.79 0.10 0.11
Matches are distributed among these distances:
18 15 0.04
20 3 0.01
21 195 0.48
22 150 0.37
23 2 0.00
25 1 0.00
26 1 0.00
28 1 0.00
29 39 0.10
ACGTcount: A:0.43, C:0.31, G:0.01, T:0.26
Consensus pattern (22 bp):
AAACCCTAAACCCTTAACTTAA
Found at i:23340227 original size:43 final size:43
Alignment explanation
Indices: 23340179--23340685 Score: 512
Period size: 43 Copynumber: 11.6 Consensus size: 43
23340169 TTTAATTGAC
*
23340179 AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTTA
* * * *
23340222 AAACCCT-AATCTTTAAATTAAAAACCCTAAACCCTTAACTTAAAACCCA
1 AAACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTT------TA
* * * *
23340271 TAAACCCTAAACCCTTAATTTAAAAACACTAACTCTTGACTTTA
1 -AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTTA
* * *
23340315 AAACCCTAAACCCTTAACTTAAAACCCCTAACACTTAA---AA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTTA
* *
23340355 AAACACT-AACCCTTAACTTAAAAACCCTAACCCTTAATTTTA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTTA
* * *
23340397 AACCCCTAAACCTTTAACTTAAAAACCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTTA
* * *
23340441 AAATCCT-AACCCTTAACTTAAAAACCTTAACCTTTAACTTTA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTTA
* * * *
23340483 AAACCCTAAACCTTTAACCT-AAAACCCTAAACCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTTA
* *
23340526 AAACCCTAAACCCTTAACTTTAAAACCCTAACCCTTGACTTTA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTTA
* *
23340569 AAACCATAAACCCTTAAGC-TAAAAACCCCAACCCCTTAACTTTA
1 AAACCCTAAACCCTTAA-CTTAAAAACCCTAA-CCCTTAACTTTA
23340613 AAACCCT-AACCCTTAACTTTAAAACCTTAAAACCCTAACCCTTAACTTTA
1 AAACCCTAAACCCTTAAC-TT---A----AAAACCCTAACCCTTAACTTTA
23340663 AAACCCT-AACCCTTAACTTAAAA
1 AAACCCTAAACCCTTAACTTAAAA
23340686 GCGCATCCAT
Statistics
Matches: 386, Mismatches: 50, Indels: 57
0.78 0.10 0.12
Matches are distributed among these distances:
39 28 0.07
40 7 0.02
42 53 0.14
43 176 0.46
44 45 0.12
46 1 0.00
47 1 0.00
49 3 0.01
50 46 0.12
51 26 0.07
ACGTcount: A:0.43, C:0.31, G:0.01, T:0.26
Consensus pattern (43 bp):
AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTTA
Found at i:23340296 original size:72 final size:71
Alignment explanation
Indices: 23340201--23340463 Score: 231
Period size: 72 Copynumber: 3.9 Consensus size: 71
23340191 CTTAACTTAA
*
23340201 AAACCCTAACCCTTAACTTAAAAACCCTAA-TCTTTAAATTAAAAACCCTAAACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAAAAACACTAACTC-TTAAATTAAAAACCCTAAACCCTTAACTTAA
23340265 AACCCAT
65 AACCCAT
* * * *
23340272 AAACCCTAAACCCTTAATTTAAAAACACTAACTCTTGACTTTAAAACCCTAAACCCTTAACTTAA
1 AAACCCT-AACCCTTAACTTAAAAACACTAACTCTTAAATTAAAAACCCTAAACCCTTAACTTAA
23340337 AA--C--
65 AACCCAT
* * * * *
23340340 ---CCCTAACACTTAA---AAAAACACTAACCCTTAACTTAAAAACCCT-AACCCTTAATTTTAA
1 AAACCCTAACCCTTAACTTAAAAACACTAACTCTTAAATTAAAAACCCTAAACCCTTAACTTAAA
*
23340398 ACCCCT
66 ACCCAT
* * * *
23340404 AAA-CCT-----TTAACTTAAAAACCCTAAACCCTTAACTTAAAAATCCT-AACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAAAAACACT-AACTCTTAAATTAAAAACCCTAAACCCTTAACTTAA
23340462 AA
65 AA
23340464 ACCTTAACCT
Statistics
Matches: 164, Mismatches: 15, Indels: 32
0.78 0.07 0.15
Matches are distributed among these distances:
60 14 0.09
61 31 0.19
62 1 0.01
64 16 0.10
65 38 0.23
66 3 0.02
70 1 0.01
71 7 0.04
72 51 0.31
73 2 0.01
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.26
Consensus pattern (71 bp):
AAACCCTAACCCTTAACTTAAAAACACTAACTCTTAAATTAAAAACCCTAAACCCTTAACTTAAA
ACCCAT
Found at i:23340344 original size:65 final size:65
Alignment explanation
Indices: 23340275--23340648 Score: 408
Period size: 65 Copynumber: 5.8 Consensus size: 65
23340265 AACCCATAAA
* * *
23340275 CCCTAAACCCTTAA-TTTAAAAACACTAACTCTTGACTTTAAAACCCTAAACCCTTAACTTAAAA
1 CCCTAAACCCTTAACTTT-AAAACCCTAACCCTTAACTTTAAAACCCTAAACCCTTAACTTAAAA
23340339 C
65 C
* * * * * *
23340340 CCCT-AACACTTAA---AAAAACACTAACCCTTAACTTAAAAACCCT-AACCCTTAATTTTAAAC
1 CCCTAAACCCTTAACTTTAAAACCCTAACCCTTAACTTTAAAACCCTAAACCCTTAACTTAAAAC
* * * *
23340400 CCCTAAACCTTTAACTTAAAAACCCTAAACCCTTAACTTAAAAATCCT-AACCCTTAACTTAAAA
1 CCCTAAACCCTTAACTTTAAAACCCT-AACCCTTAACTTTAAAACCCTAAACCCTTAACTTAAAA
23340464 -
65 C
* * * * * *
23340464 ACCTTAACCTTTAACTTTAAAACCCTAAACCTTTAAC-CTAAAACCCTAAACCCTTAACCTAAAA
1 CCCTAAACCCTTAACTTTAAAACCCT-AACCCTTAACTTTAAAACCCTAAACCCTTAACTTAAAA
*
23340528 A
65 C
* * *
23340529 CCCTAAACCCTTAACTTTAAAACCCTAACCCTTGACTTTAAAACCATAAACCCTTAAGCTAAAAA
1 CCCTAAACCCTTAACTTTAAAACCCTAACCCTTAACTTTAAAACCCTAAACCCTTAA-CTTAAAA
23340594 C
65 C
* *
23340595 CCC-AACCCCTTAACTTTAAAACCCTAACCCTTAACTTTAAAACCTTAAAACCCT
1 CCCTAAACCCTTAACTTTAAAACCCTAACCCTTAACTTTAAAACCCT-AAACCCT
23340649 AACCCTTAAC
Statistics
Matches: 265, Mismatches: 34, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
60 19 0.07
61 33 0.12
63 7 0.03
64 72 0.27
65 119 0.45
66 15 0.06
ACGTcount: A:0.42, C:0.31, G:0.01, T:0.26
Consensus pattern (65 bp):
CCCTAAACCCTTAACTTTAAAACCCTAACCCTTAACTTTAAAACCCTAAACCCTTAACTTAAAAC
Found at i:23340643 original size:29 final size:29
Alignment explanation
Indices: 23340610--23340667 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
23340600 CCCCTTAACT
23340610 TTAAAACCCTAACCCTTAACTTTAAAACC
1 TTAAAACCCTAACCCTTAACTTTAAAACC
23340639 TTAAAACCCTAACCCTTAACTTTAAAACC
1 TTAAAACCCTAACCCTTAACTTTAAAACC
23340668 CTAACCCTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.31, G:0.00, T:0.28
Consensus pattern (29 bp):
TTAAAACCCTAACCCTTAACTTTAAAACC
Found at i:23340969 original size:125 final size:128
Alignment explanation
Indices: 23340707--23340992 Score: 368
Period size: 125 Copynumber: 2.2 Consensus size: 128
23340697 AGGGCGCGAT
*
23340707 TTCACAAATTCTTCTCA-AATAGCATCCTGCTTCAAGCATTTTTTTTTAAAACTATTTGCTCAGA
1 TTCAAAAATTCTTCTCATAA-AGCATCCTGCTTCAAGCA--TTTTTTTAAAACTATTTGCTCAGA
* * * * *
23340771 AACATCAACTCGAAATTATTTCTTCCAGGACCTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGA
63 AACATCAACTCAAAATTATTTCTTCCAGGACCTACTATAGCAAAAGCGCGTACACGAGGACGCAA
*
23340836 T
128 C
* *
23340837 TTC-AAAATTCTTCTCATAAAGCATCCTGCTTGAAGCA-TTTTTT-ATACTATTTGCTCAGAAA-
1 TTCAAAAATTCTTCTCATAAAGCATCCTGCTTCAAGCATTTTTTTAAAACTATTTGCTCAGAAAC
* * *
23340898 AGTCAAGTCAAAATTATTT-TTTCAGGACCTACTATAGCAAAAGCGCGTACACGTGGACGCAAC
66 A-TCAACTCAAAATTATTTCTTCCAGGACCTACTATAGCAAAAGCGCGTACACGAGGACGCAAC
* *
23340961 TTCAAAAATCCTTCTGATAAAGCATCCTGCTT
1 TTCAAAAATTCTTCTCATAAAGCATCCTGCTT
23340993 TGATTTTATC
Statistics
Matches: 139, Mismatches: 14, Indels: 11
0.85 0.09 0.07
Matches are distributed among these distances:
124 41 0.29
125 58 0.42
126 6 0.04
129 29 0.21
130 5 0.04
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.31
Consensus pattern (128 bp):
TTCAAAAATTCTTCTCATAAAGCATCCTGCTTCAAGCATTTTTTTAAAACTATTTGCTCAGAAAC
ATCAACTCAAAATTATTTCTTCCAGGACCTACTATAGCAAAAGCGCGTACACGAGGACGCAAC
Found at i:23342355 original size:6 final size:6
Alignment explanation
Indices: 23342344--23342370 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
23342334 TAATTTACTC
23342344 TTTCTT TTTCTT TTTCTT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTT
23342371 GTATAGGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTCTT
Found at i:23347314 original size:19 final size:19
Alignment explanation
Indices: 23347277--23347315 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
23347267 TACATCACAT
*
23347277 TAAATTACAAAAGTCGTTA
1 TAAATTACAAAAGTAGTTA
*
23347296 TAAATTACAAATGTAGTTA
1 TAAATTACAAAAGTAGTTA
23347315 T
1 T
23347316 TTTTTAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (19 bp):
TAAATTACAAAAGTAGTTA
Found at i:23349479 original size:34 final size:34
Alignment explanation
Indices: 23349436--23349507 Score: 135
Period size: 34 Copynumber: 2.1 Consensus size: 34
23349426 TACATCTCTC
*
23349436 TCAATTACAAATTCAGAAGAGAAATTGGGCAAGG
1 TCAATTACAAATTCAAAAGAGAAATTGGGCAAGG
23349470 TCAATTACAAATTCAAAAGAGAAATTGGGCAAGG
1 TCAATTACAAATTCAAAAGAGAAATTGGGCAAGG
23349504 TCAA
1 TCAA
23349508 GTCTGAGGGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.46, C:0.12, G:0.21, T:0.21
Consensus pattern (34 bp):
TCAATTACAAATTCAAAAGAGAAATTGGGCAAGG
Found at i:23354866 original size:3 final size:3
Alignment explanation
Indices: 23354860--23354891 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
23354850 TAATTAGCTT
23354860 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
23354892 GTATTTGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:23357413 original size:14 final size:14
Alignment explanation
Indices: 23357394--23357420 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
23357384 ATATTAAACT
23357394 CTTTTTCTTTTTTC
1 CTTTTTCTTTTTTC
23357408 CTTTTTCTTTTTT
1 CTTTTTCTTTTTT
23357421 TTTTCTCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (14 bp):
CTTTTTCTTTTTTC
Found at i:23358038 original size:15 final size:15
Alignment explanation
Indices: 23358018--23358047 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
23358008 AACATAAATT
23358018 TATTCCTTCCCCATC
1 TATTCCTTCCCCATC
23358033 TATTCCTTCCCCATC
1 TATTCCTTCCCCATC
23358048 AACATCTTTA
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:0.13, C:0.47, G:0.00, T:0.40
Consensus pattern (15 bp):
TATTCCTTCCCCATC
Found at i:23371965 original size:24 final size:22
Alignment explanation
Indices: 23371938--23372002 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
23371928 CCCTTTATTT
23371938 TTTCACAAACAAATATTCTCTCAA
1 TTTC-CAAACAAA-ATTCTCTCAA
***
23371962 TTTCCTTCCAAAATTCTCTCAA
1 TTTCCAAACAAAATTCTCTCAA
***
23371984 TTTCCTTCCAAAATTCTCT
1 TTTCCAAACAAAATTCTCT
23372003 TAAACTCTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 29 0.76
23 5 0.13
24 4 0.11
ACGTcount: A:0.31, C:0.29, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTCCAAACAAAATTCTCTCAA
Found at i:23371980 original size:22 final size:22
Alignment explanation
Indices: 23371947--23372002 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
23371937 TTTTCACAAA
23371947 CAAATATTCTCTCAATTTCCTTC
1 CAAA-ATTCTCTCAATTTCCTTC
23371970 CAAAATTCTCTCAATTTCCTTC
1 CAAAATTCTCTCAATTTCCTTC
23371992 CAAAATTCTCT
1 CAAAATTCTCT
23372003 TAAACTCTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.29, C:0.30, G:0.00, T:0.41
Consensus pattern (22 bp):
CAAAATTCTCTCAATTTCCTTC
Found at i:23372033 original size:52 final size:52
Alignment explanation
Indices: 23371955--23372054 Score: 164
Period size: 52 Copynumber: 1.9 Consensus size: 52
23371945 AACAAATATT
* * * *
23371955 CTCTCAATTTCCTTCCAAAATTCTCTCAATTTCCTTCCAAAATTCTCTTAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCTTAAA
23372007 CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCT
1 CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCT
23372055 CAAATCCATA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.30, C:0.32, G:0.00, T:0.38
Consensus pattern (52 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCTTAAA
Found at i:23372046 original size:21 final size:22
Alignment explanation
Indices: 23372007--23372059 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
23371997 TTCTCTTAAA
23372007 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
23372029 CTCTCAATTTCCTTCAAAAAAT-
1 CTCTCAAATTCCTTC-CAAAATC
23372051 CTCTCAAAT
1 CTCTCAAAT
23372060 CCATATTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 22 0.81
23 5 0.19
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:23372129 original size:29 final size:28
Alignment explanation
Indices: 23372091--23372148 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 28
23372081 ATTCAATTTC
23372091 ATTTTTTTAAGAA-AATTTTAAATATTTTT
1 ATTTTTTTAA-AATAATTTT-AATATTTTT
23372120 ATTTTTTTAAAATAATTTTAATATTTTT
1 ATTTTTTTAAAATAATTTTAATATTTTT
23372148 A
1 A
23372149 ATATTTTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 12 0.43
29 16 0.57
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (28 bp):
ATTTTTTTAAAATAATTTTAATATTTTT
Found at i:23372138 original size:19 final size:20
Alignment explanation
Indices: 23372106--23372149 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
23372096 TTTAAGAAAA
* *
23372106 TTTT-AAAT-ATTTTTATTT
1 TTTTAAAATAATTTTAATAT
23372124 TTTTAAAATAATTTTAATAT
1 TTTTAAAATAATTTTAATAT
23372144 TTTTAA
1 TTTTAA
23372150 TATTTTCAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 4 0.18
19 4 0.18
20 14 0.64
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTAAAATAATTTTAATAT
Found at i:23372155 original size:28 final size:29
Alignment explanation
Indices: 23372095--23372155 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 29
23372085 AATTTCATTT
* *
23372095 TTTTAAGAAAATTTTAAATATTTTTATTT
1 TTTTAAGAAAATTTTAAATATTTTTAATA
23372124 TTTTAA-AATAATTTT-AATATTTTTAATA
1 TTTTAAGAA-AATTTTAAATATTTTTAATA
23372152 TTTT
1 TTTT
23372156 CAACAATGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 17 0.59
29 12 0.41
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (29 bp):
TTTTAAGAAAATTTTAAATATTTTTAATA
Found at i:23372155 original size:29 final size:29
Alignment explanation
Indices: 23372094--23372155 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
23372084 CAATTTCATT
*
23372094 TTTTTAAGAAAATTTTAAATATTTTTATT
1 TTTTTAAGAAAATTTTAAATATTTTTATA
23372123 TTTTTAA-AATAATTTT-AATATTTTTAATA
1 TTTTTAAGAA-AATTTTAAATATTTTT-ATA
23372152 TTTT
1 TTTT
23372156 CAACAATGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 11 0.37
29 19 0.63
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (29 bp):
TTTTTAAGAAAATTTTAAATATTTTTATA
Found at i:23372275 original size:14 final size:15
Alignment explanation
Indices: 23372246--23372279 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
23372236 AAATTTTAAA
23372246 TTTTATTTAAGATAT
1 TTTTATTTAAGATAT
*
23372261 TTTTATTTATG-TAT
1 TTTTATTTAAGATAT
23372275 TTTTA
1 TTTTA
23372280 GATAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTTAAGATAT
Found at i:23373249 original size:7 final size:7
Alignment explanation
Indices: 23373237--23373261 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
23373227 AGTGGATTGA
23373237 TATTTAG
1 TATTTAG
23373244 TATTTAG
1 TATTTAG
23373251 TATTTAG
1 TATTTAG
23373258 TATT
1 TATT
23373262 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:23374137 original size:24 final size:24
Alignment explanation
Indices: 23374110--23374165 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
23374100 GCATGGCTTT
*
23374110 CAAACTCCGTCGCCGTTCATGATG
1 CAAACACCGTCGCCGTTCATGATG
23374134 CAAACACCGTCGCCGTTCATGATG
1 CAAACACCGTCGCCGTTCATGATG
23374158 CAAACACC
1 CAAACACC
23374166 TCCACATACA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.27, C:0.36, G:0.18, T:0.20
Consensus pattern (24 bp):
CAAACACCGTCGCCGTTCATGATG
Found at i:23375956 original size:124 final size:124
Alignment explanation
Indices: 23375735--23376015 Score: 424
Period size: 124 Copynumber: 2.3 Consensus size: 124
23375725 CCACGAGGGC
* * *
23375735 GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAATAATTATTTCCTACATGACCAACTGTAGC
1 GCGATTTTATACTATTTGCTCAGAAACGTC-AAAAATAATTATTTCCTACATGACCAACTGTACC
* * **
23375800 GAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTC-ATATAGCATCCTGGTATCA
65 GAAATCGCGTCCACGAAGGCACGATTTCACAATTTCTTCTCTA-ATAGCATCCTGGTAGAA
*
23375860 GCGATTTTATACTATTTGCTCAGAAAACGTCAAAAA-AATTATTTCTTACATGACCAACTGTACC
1 GCGATTTTATACTATTTGCTCAG-AAACGTCAAAAATAATTATTTCCTACATGACCAACTGTACC
*
23375924 GAAATCGCGTCCACGAAGGCACGATTTTACAATTTCTTCTCTAATAGCATCCTGGTAGAA
65 GAAATCGCGTCCACGAAGGCACGATTTCACAATTTCTTCTCTAATAGCATCCTGGTAGAA
23375984 GCGATTTTATACTATTTGAC-CAGAAACGTCAA
1 GCGATTTTATACTATTTG-CTCAGAAACGTCAA
23376016 CTCAAAATAA
Statistics
Matches: 144, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
123 9 0.06
124 100 0.69
125 28 0.19
126 7 0.05
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (124 bp):
GCGATTTTATACTATTTGCTCAGAAACGTCAAAAATAATTATTTCCTACATGACCAACTGTACCG
AAATCGCGTCCACGAAGGCACGATTTCACAATTTCTTCTCTAATAGCATCCTGGTAGAA
Found at i:23376799 original size:14 final size:15
Alignment explanation
Indices: 23376779--23376819 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
23376769 TTTGATTGCC
23376779 AGTAAAATGTTTTC-
1 AGTAAAATGTTTTCT
* *
23376793 CGTAAAATGATTTCT
1 AGTAAAATGTTTTCT
23376808 AG-AAAATGTTTT
1 AGTAAAATGTTTT
23376820 ACTTTTCTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 21 0.95
15 1 0.05
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (15 bp):
AGTAAAATGTTTTCT
Found at i:23376828 original size:20 final size:20
Alignment explanation
Indices: 23376803--23376842 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
23376793 CGTAAAATGA
*
23376803 TTTCTAGAAAATGTTTTACT
1 TTTCTAGAAAATGATTTACT
*
23376823 TTTCTATAAAATGATTTACT
1 TTTCTAGAAAATGATTTACT
23376843 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (20 bp):
TTTCTAGAAAATGATTTACT
Found at i:23376966 original size:20 final size:20
Alignment explanation
Indices: 23376941--23376979 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
23376931 GTTTTTACAT
23376941 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
23376961 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
23376980 TTTTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:23377602 original size:19 final size:19
Alignment explanation
Indices: 23377578--23377631 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
23377568 ACAACCTATA
23377578 AAATTGTTATGAGTATCCT
1 AAATTGTTATGAGTATCCT
23377597 AAATTGTTATGAGTATCCT
1 AAATTGTTATGAGTATCCT
*
23377616 AAATTGTTATCAGTAT
1 AAATTGTTATGAGTAT
23377632 GTTGTGCAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.43
Consensus pattern (19 bp):
AAATTGTTATGAGTATCCT
Found at i:23386449 original size:58 final size:59
Alignment explanation
Indices: 23386368--23386483 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 59
23386358 TTAAACTTAA
* * *
23386368 TATTAAGTTAATATAATACTTATC-AAGATAAATATTATATTAAATTTAATATTAAACC
1 TATTAAATTAATAGAATACTTATCTAAGATAAATATTAAATTAAATTTAATATTAAACC
* *
23386426 TATTAAATTAATAGAATATTTATCTATAAGATAAATATTAAATTTAATTTAATATTAA
1 TATTAAATTAATAGAATACTTATC--TAAGATAAATATTAAATTAAATTTAATATTAA
23386484 GATAAATACT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
58 21 0.42
61 29 0.58
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.43
Consensus pattern (59 bp):
TATTAAATTAATAGAATACTTATCTAAGATAAATATTAAATTAAATTTAATATTAAACC
Found at i:23386497 original size:25 final size:25
Alignment explanation
Indices: 23386468--23386518 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
23386458 AAATATTAAA
*
23386468 TTTAAT-TTAATATTAAGATAAATAC
1 TTTAATATTAA-ATTAAGAAAAATAC
*
23386493 TTTAATATTAAATTAATAAAAATAC
1 TTTAATATTAAATTAAGAAAAATAC
23386518 T
1 T
23386519 ATCAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (25 bp):
TTTAATATTAAATTAAGAAAAATAC
Found at i:23389912 original size:155 final size:154
Alignment explanation
Indices: 23389622--23389923 Score: 448
Period size: 155 Copynumber: 2.0 Consensus size: 154
23389612 TTCTTTTAAA
*
23389622 AAAAAATCACTACTTTTCTTAAATATCAAAACTTTATTTCGAAATAATTGAAAAAGATCAAAACT
1 AAAAAATCACTACTTTTCTTAAAGATCAAAACTTTATTTCGAAATAATTGAAAAAGATCAAAACT
*
23389687 TTGTTTTAAAATTTTAAACTTTTCCTTTAAAATGACTAAAAAAATAGATTTTTAAGAATAAAAAT
66 TTGTTTTAAAATTTTAAACATTTCCTTTAAAATGACTAAAAAAATAGATTTTTAAGAATAAAAAT
*
23389752 CTAAACTTTCTCTCTTTTTTCTTTT
131 ATAAACTTTCTCT-TTTTTTCTTTT
* *
23389777 AAAAAATCACTACTTTTCTTAAAGATCAAAACTTTAATTTCTAAATAGTTGACAAAA-ATCAAAA
1 AAAAAATCACTACTTTTCTTAAAGATCAAAACTTT-ATTTCGAAATAATTGA-AAAAGATCAAAA
* *** * *
23389841 TTTTGTTTTAAAATTTTAAA-ATTTCCTTTAAAATGACTCAAAAAAATAGATTTTT-ATTTTTAC
64 CTTTGTTTTAAAATTTTAAACATTTCCTTTAAAATGACT-AAAAAAATAGATTTTTAAGAATAAA
23389904 AATATAAACTTTCTCTTTTT
128 AATATAAACTTTCTCTTTTT
23389924 AAAAAAAATC
Statistics
Matches: 133, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
154 4 0.03
155 69 0.52
156 56 0.42
157 4 0.03
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.42
Consensus pattern (154 bp):
AAAAAATCACTACTTTTCTTAAAGATCAAAACTTTATTTCGAAATAATTGAAAAAGATCAAAACT
TTGTTTTAAAATTTTAAACATTTCCTTTAAAATGACTAAAAAAATAGATTTTTAAGAATAAAAAT
ATAAACTTTCTCTTTTTTTCTTTT
Found at i:23390129 original size:18 final size:18
Alignment explanation
Indices: 23390102--23390137 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
23390092 TATAGCAAAA
23390102 AAAAAAAAAAAGATAGAAG
1 AAAAAAAAAAA-ATAGAAG
*
23390121 AAAAGAAAAAAATAGAA
1 AAAAAAAAAAAATAGAA
23390138 TGCTTGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.06
Consensus pattern (18 bp):
AAAAAAAAAAAATAGAAG
Found at i:23395277 original size:42 final size:41
Alignment explanation
Indices: 23395212--23395452 Score: 227
Period size: 43 Copynumber: 5.7 Consensus size: 41
23395202 ACCGGAAAAC
** ** *
23395212 ATTGAATAAAAAGGGGTTGCTAAGTTATGATTCCCCGAATT
1 ATTGAATTTAAAGGGGTTGCTAAGTGCTGATTCCCCGTATT
* * *
23395253 ATTGACTTTAAAGGTGGTTGCTAAGTGCCGATTCCACTGTATCT
1 ATTGAATTTAAAGG-GGTTGCTAAGTGCTGATTCC-CCGTAT-T
* *
23395297 -TTGATTGTTAAAGGGGTTGCTATGTGCTGATTCCCCGTATT
1 ATTGAAT-TTAAAGGGGTTGCTAAGTGCTGATTCCCCGTATT
* *
23395338 ACTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCT
1 ATTGAATTTAAAGG-GGTTGCTAAGTGCTGATTCC-CCGTAT-T
* * * *
23395382 -TTGACTGTGAAAGGGGTTGCTATGTGCTGATTCCCCGTATC
1 ATTGAAT-TTAAAGGGGTTGCTAAGTGCTGATTCCCCGTATT
*
23395423 ACTGAATTT-AAGGTGGTTGCTAAGTGCTGA
1 ATTGAATTTAAAGG-GGTTGCTAAGTGCTGA
23395453 ATCCACCGAG
Statistics
Matches: 163, Mismatches: 26, Indels: 22
0.77 0.12 0.10
Matches are distributed among these distances:
40 4 0.02
41 34 0.21
42 55 0.34
43 56 0.34
44 14 0.09
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (41 bp):
ATTGAATTTAAAGGGGTTGCTAAGTGCTGATTCCCCGTATT
Found at i:23395329 original size:43 final size:43
Alignment explanation
Indices: 23395221--23395460 Score: 228
Period size: 42 Copynumber: 5.7 Consensus size: 43
23395211 CATTGAATAA
** * * *
23395221 AAAGG-GGTTGCTAAGTTATGATTCC-CCGAAT-TATTGACTTT
1 AAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCT-CTGAATTT
* * * *
23395262 AAAGGTGGTTGCTAAGTGCCGATTCCACTGTATCTTTGATTGTT
1 AAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCTCTGAAT-TT
* *
23395306 AAAGG-GGTTGCTATGTGCTGATTCC-CCGTAT-TACTGAATAT
1 AAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCT-CTGAATTT
* * *
23395347 AAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTTGACTGTG
1 AAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCTCTGAAT-TT
* *
23395391 AAAGG-GGTTGCTATGTGCTGATTCC-CCGTATCACTGAATTT
1 AAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCTCTGAATTT
*
23395432 -AAGGTGGTTGCTAAGTGCTGAATCCACCG
1 AAAGGTGGTTGCTAAGTGCTGATTCCACCG
23395461 AGTAACGAAT
Statistics
Matches: 164, Mismatches: 24, Indels: 21
0.78 0.11 0.10
Matches are distributed among these distances:
40 4 0.02
41 31 0.19
42 59 0.36
43 56 0.34
44 14 0.09
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.34
Consensus pattern (43 bp):
AAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCTCTGAATTT
Found at i:23395364 original size:85 final size:84
Alignment explanation
Indices: 23395221--23395460 Score: 345
Period size: 85 Copynumber: 2.8 Consensus size: 84
23395211 CATTGAATAA
* ** * * * *
23395221 AAAGGGGTTGCTAAGTTATGATTCCCCGAATTATTGACTTTAAAGGTGGTTGCTAAGTGCCGATT
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATTACTGA-ATTAAAGGTGGTTGCTAAGTGCTGATT
* * *
23395286 CCACTGTATCTTTGATTGTT
65 CCACCGTATCTTTGACTGTG
23395306 AAAGGGGTTGCTATGTGCTGATTCCCCGTATTACTGAATATAAAGGTGGTTGCTAAGTGCTGATT
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATTACTGAAT-TAAAGGTGGTTGCTAAGTGCTGATT
23395371 CCACCGTATCTTTGACTGTG
65 CCACCGTATCTTTGACTGTG
* * *
23395391 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCACTGAATTTAAGGTGGTTGCTAAGTGCTGAATC
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATTACTGAATTAAAGGTGGTTGCTAAGTGCTGATTC
23395456 CACCG
66 CACCG
23395461 AGTAACGAAT
Statistics
Matches: 141, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
84 30 0.21
85 111 0.79
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.34
Consensus pattern (84 bp):
AAAGGGGTTGCTATGTGCTGATTCCCCGTATTACTGAATTAAAGGTGGTTGCTAAGTGCTGATTC
CACCGTATCTTTGACTGTG
Found at i:23401031 original size:22 final size:21
Alignment explanation
Indices: 23400998--23401039 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
23400988 ACATATTACC
23400998 ATTTAGTCATTTAAACTTTAAG
1 ATTTAGTCATTTAAA-TTTAAG
*
23401020 ATTTA-TCAATTTTAATTTAA
1 ATTTAGTC-ATTTAAATTTAA
23401040 CAAAGCAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (21 bp):
ATTTAGTCATTTAAATTTAAG
Found at i:23401775 original size:11 final size:11
Alignment explanation
Indices: 23401759--23401785 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
23401749 ATTTTTTTAA
23401759 TTTTAAAATAC
1 TTTTAAAATAC
23401770 TTTTAAAATAC
1 TTTTAAAATAC
23401781 TTTTA
1 TTTTA
23401786 TTAAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:23401795 original size:40 final size:39
Alignment explanation
Indices: 23401746--23401881 Score: 179
Period size: 40 Copynumber: 3.5 Consensus size: 39
23401736 TTATTATTTA
* *
23401746 TTAATTTTTTTAATTTTAAAATACTTTTAAAATACTTTT
1 TTAAATTTTTTAATTTTAAAATATTTTTAAAATACTTTT
*
23401785 ATTAAATTTTTTAAATTTT-AAATTTTTTTAAAATACTTTT
1 -TTAAATTTTTT-AATTTTAAAATATTTTTAAAATACTTTT
*
23401825 TTAATTTTTTTTAATTTTAAAATATTTTTAAAATACTTTT
1 TTAA-ATTTTTTAATTTTAAAATATTTTTAAAATACTTTT
*
23401865 TTTAA-TTTTT-ATTTTAA
1 TTAAATTTTTTAATTTTAA
23401882 TTTTTAAAAT
Statistics
Matches: 86, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
37 7 0.08
38 5 0.06
39 10 0.12
40 58 0.67
41 6 0.07
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (39 bp):
TTAAATTTTTTAATTTTAAAATATTTTTAAAATACTTTT
Found at i:23403633 original size:27 final size:28
Alignment explanation
Indices: 23403601--23403653 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
23403591 TTCTATTCCA
*
23403601 AAATTTAATTAATTA-ATTAATTAAAAT
1 AAATTTAATCAATTATATTAATTAAAAT
*
23403628 AAATTTAATCAATTATTTTAATTAAA
1 AAATTTAATCAATTATATTAATTAAA
23403654 TTATTTTCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (28 bp):
AAATTTAATCAATTATATTAATTAAAAT
Found at i:23408182 original size:129 final size:129
Alignment explanation
Indices: 23407952--23408209 Score: 489
Period size: 129 Copynumber: 2.0 Consensus size: 129
23407942 CTACAAAACC
**
23407952 AAAAGGCGAGAGAGTGATACTATCAAAAGATATTTGAAAACAGTAACTGCAGAAACATATTTGTC
1 AAAAGGCGAGAGAGTGATACTATCAAAAGATACGTGAAAACAGTAACTGCAGAAACATATTTGTC
*
23408017 ACCCTCATAGATGCCTAATGCCAGCAATATAAAGAAATTCATTATGACTATGATAACTTCAGGA
66 ACCCTCATAGATGCCTAATGCCAGCAATACAAAGAAATTCATTATGACTATGATAACTTCAGGA
23408081 AAAAGGCGAGAGAGTGATACTATCAAAAGATACGTGAAAACAGTAACTGCAGAAACATATTTGTC
1 AAAAGGCGAGAGAGTGATACTATCAAAAGATACGTGAAAACAGTAACTGCAGAAACATATTTGTC
23408146 ACCCTCATAGATGCCTAATGCCAGCAATACAAAGAAATTCATTATGACTATGATAACTTCAGGA
66 ACCCTCATAGATGCCTAATGCCAGCAATACAAAGAAATTCATTATGACTATGATAACTTCAGGA
23408210 GTAGTGAGAG
Statistics
Matches: 126, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
129 126 1.00
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.24
Consensus pattern (129 bp):
AAAAGGCGAGAGAGTGATACTATCAAAAGATACGTGAAAACAGTAACTGCAGAAACATATTTGTC
ACCCTCATAGATGCCTAATGCCAGCAATACAAAGAAATTCATTATGACTATGATAACTTCAGGA
Found at i:23415552 original size:18 final size:18
Alignment explanation
Indices: 23415506--23415556 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
23415496 AGCTCTCAGG
23415506 CATTCTTCTCCCTTCATC
1 CATTCTTCTCCCTTCATC
* ***
23415524 CAGTAAGCTCCCTTCATC
1 CATTCTTCTCCCTTCATC
23415542 CATTCTTCTCCCTTC
1 CATTCTTCTCCCTTC
23415557 CTTCATTCCT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.14, C:0.43, G:0.04, T:0.39
Consensus pattern (18 bp):
CATTCTTCTCCCTTCATC
Found at i:23418367 original size:14 final size:15
Alignment explanation
Indices: 23418345--23418425 Score: 53
Period size: 15 Copynumber: 5.3 Consensus size: 15
23418335 CAATCAAACA
23418345 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
23418359 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
23418374 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
23418394 CCAG-AAATCA-TTT
1 CCAGAAAATCATTTT
*
23418407 CACGGAAAA-CATTTT
1 C-CAGAAAATCATTTT
23418422 CCAG
1 CCAG
23418426 TGTTTGTTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 18
0.68 0.08 0.24
Matches are distributed among these distances:
13 4 0.08
14 16 0.31
15 18 0.35
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.17
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.30
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:23418386 original size:20 final size:20
Alignment explanation
Indices: 23418361--23418400 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
23418351 AATATTTTCC
*
23418361 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
23418381 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
23418401 TCATTTCACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:23418406 original size:34 final size:35
Alignment explanation
Indices: 23418349--23418415 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
23418339 CAAACACCAG
* *
23418349 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTCACAGAAAAGT
*
23418384 AAAACATTTTCCAG-AAATCATTTCACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTCACAGAAAA
23418416 CATTTTCCAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.30
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTCACAGAAAAGT
Found at i:23418466 original size:18 final size:18
Alignment explanation
Indices: 23418439--23418485 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
23418429 TTGTTTAACT
*
23418439 GAAAACATTTTACATTTG
1 GAAAATATTTTACATTTG
23418457 GAAAATATTTTACATTTG
1 GAAAATATTTTACATTTG
23418475 GAAAATATTTT
1 GAAAATATTTT
23418486 TCAATAAACG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (18 bp):
GAAAATATTTTACATTTG
Found at i:23418643 original size:25 final size:25
Alignment explanation
Indices: 23418615--23418664 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
23418605 CAGGTAAGGC
**
23418615 TCCTTCTCCTTCTTCTGTTCTTCAT
1 TCCTTCTCCTTCTTCCATTCTTCAT
*
23418640 TCCTTTTCCTTCTTCCATTCTTCAT
1 TCCTTCTCCTTCTTCCATTCTTCAT
23418665 CTTCTCTTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.06, C:0.36, G:0.02, T:0.56
Consensus pattern (25 bp):
TCCTTCTCCTTCTTCCATTCTTCAT
Found at i:23423768 original size:25 final size:23
Alignment explanation
Indices: 23423740--23423787 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
23423730 ATTACATACA
*
23423740 TATTCAACCTTAATATACTATAACT
1 TATTCAA-CTTAATA-ACAATAACT
*
23423765 TATTCAATTTAATAACAATAACT
1 TATTCAACTTAATAACAATAACT
23423788 CAATTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 8 0.38
24 6 0.29
25 7 0.33
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.40
Consensus pattern (23 bp):
TATTCAACTTAATAACAATAACT
Found at i:23427121 original size:19 final size:19
Alignment explanation
Indices: 23427097--23427134 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
23427087 TGGGCCACGT
23427097 TGGGCCAAAATGGGC-CGTG
1 TGGGCC-AAATGGGCTCGTG
*
23427116 TGGGCCCAATGGGCTCGTG
1 TGGGCCAAATGGGCTCGTG
23427135 GGCCCCATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.16, C:0.24, G:0.42, T:0.18
Consensus pattern (19 bp):
TGGGCCAAATGGGCTCGTG
Found at i:23427375 original size:27 final size:27
Alignment explanation
Indices: 23427345--23427483 Score: 138
Period size: 27 Copynumber: 5.2 Consensus size: 27
23427335 GTGGGGTCAA
* * *
23427345 TAAAATGACCGAAATACCTTCGAAGGG
1 TAAAATAACCGAAATACCCTCAAAGGG
* *
23427372 TAAAATAATCGAAATACCCCCAAAGGG
1 TAAAATAACCGAAATACCCTCAAAGGG
* * * *
23427399 CAAAATAATCGAAATA-CCTCAAAAGA
1 TAAAATAACCGAAATACCCTCAAAGGG
* * *
23427425 TAAAATGACCGAAATCCCCT-AAAGGA
1 TAAAATAACCGAAATACCCTCAAAGGG
* *
23427451 TAAAATAACCAAAATACCCTCATAGGG
1 TAAAATAACCGAAATACCCTCAAAGGG
23427478 TAAAAT
1 TAAAAT
23427484 GACTGTTATA
Statistics
Matches: 91, Mismatches: 19, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
26 41 0.45
27 50 0.55
ACGTcount: A:0.49, C:0.20, G:0.14, T:0.17
Consensus pattern (27 bp):
TAAAATAACCGAAATACCCTCAAAGGG
Found at i:23427472 original size:53 final size:54
Alignment explanation
Indices: 23427344--23427486 Score: 155
Period size: 53 Copynumber: 2.7 Consensus size: 54
23427334 CGTGGGGTCA
* * * * *
23427344 ATAAAATGACCGAAATACCTTCGAAGGGTAAAATAATCGAAATACCCCCAAAGG
1 ATAAAATAACCGAAATACCCTCAAAGGGTAAAATGACCGAAATACCCCCAAAGG
** * * * *
23427398 GCAAAATAATCGAAATA-CCTCAAAAGATAAAATGACCGAAAT-CCCCTAAAGG
1 ATAAAATAACCGAAATACCCTCAAAGGGTAAAATGACCGAAATACCCCCAAAGG
* *
23427450 ATAAAATAACCAAAATACCCTCATAGGGTAAAATGAC
1 ATAAAATAACCGAAATACCCTCAAAGGGTAAAATGAC
23427487 TGTTATACCC
Statistics
Matches: 70, Mismatches: 18, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
52 22 0.31
53 35 0.50
54 13 0.19
ACGTcount: A:0.49, C:0.20, G:0.14, T:0.17
Consensus pattern (54 bp):
ATAAAATAACCGAAATACCCTCAAAGGGTAAAATGACCGAAATACCCCCAAAGG
Found at i:23427820 original size:58 final size:58
Alignment explanation
Indices: 23427730--23427860 Score: 262
Period size: 58 Copynumber: 2.3 Consensus size: 58
23427720 GCTGCAATAT
23427730 TGGTGTGTTGGCTGGGTGGGTCGATTTTATCCCCACATGGTGTGATGGTGGTATGGAG
1 TGGTGTGTTGGCTGGGTGGGTCGATTTTATCCCCACATGGTGTGATGGTGGTATGGAG
23427788 TGGTGTGTTGGCTGGGTGGGTCGATTTTATCCCCACATGGTGTGATGGTGGTATGGAG
1 TGGTGTGTTGGCTGGGTGGGTCGATTTTATCCCCACATGGTGTGATGGTGGTATGGAG
23427846 TGGTGTGTTGGCTGG
1 TGGTGTGTTGGCTGG
23427861 ATTGGAATGG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 73 1.00
ACGTcount: A:0.11, C:0.11, G:0.43, T:0.35
Consensus pattern (58 bp):
TGGTGTGTTGGCTGGGTGGGTCGATTTTATCCCCACATGGTGTGATGGTGGTATGGAG
Found at i:23427912 original size:28 final size:28
Alignment explanation
Indices: 23427880--23427944 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
23427870 GGTTGCATTA
*
23427880 CCACACTGTTACTGTATTGGGCTAAGGC
1 CCACACTGTTACTGTATCGGGCTAAGGC
23427908 CCACACTGTTACTGTATCGGGCTAAGGC
1 CCACACTGTTACTGTATCGGGCTAAGGC
23427936 CCACACTGT
1 CCACACTGT
23427945 ACTATCACTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.22, C:0.29, G:0.23, T:0.26
Consensus pattern (28 bp):
CCACACTGTTACTGTATCGGGCTAAGGC
Found at i:23445971 original size:44 final size:42
Alignment explanation
Indices: 23445880--23446083 Score: 169
Period size: 44 Copynumber: 4.7 Consensus size: 42
23445870 TTTTGATCCA
* * *
23445880 CTCCACTGCAACTTCAGGGAGATAGGATTTGCGGTTCTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAGGA-TTG-GTTTCTTATCTG
*
23445924 CTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTGTGTCTG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGGTTTC-T-TATCTG
* * * * * * *
23445968 CTCCACTGTAAATTTAGGGAGATAAGACTGGTTGC-GATCTG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTATCTG
* * * * *
23446009 CTCTACTGCAACTTCAGAGAGATAAGATCT-GTATTTTTAATCTA
1 CTCCACTGCAACTTCAGGGAGATAGGAT-TGGT-TTCTT-ATCTG
* *
23446053 TTCCACTGCAACTTTAGGGAGATAGGATTGG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGG
23446084 GGTCTTCGAT
Statistics
Matches: 126, Mismatches: 27, Indels: 14
0.75 0.16 0.08
Matches are distributed among these distances:
41 28 0.22
42 6 0.05
43 5 0.04
44 87 0.69
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (42 bp):
CTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTATCTG
Found at i:23446461 original size:24 final size:24
Alignment explanation
Indices: 23446434--23446490 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
23446424 CGGATTGCCC
**
23446434 CCACTGTAATTTTCAAGGTTCAAT
1 CCACTGTAATCCTCAAGGTTCAAT
23446458 CCACTGTAATCCTCAAGGTTCAAT
1 CCACTGTAATCCTCAAGGTTCAAT
23446482 CCACTGTAA
1 CCACTGTAA
23446491 CCTTTGGGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (24 bp):
CCACTGTAATCCTCAAGGTTCAAT
Found at i:23451841 original size:45 final size:45
Alignment explanation
Indices: 23451778--23451913 Score: 188
Period size: 44 Copynumber: 3.1 Consensus size: 45
23451768 TCTGGCGCGC
*
23451778 TTTCAT-ATGATGCCATAATGTCTTTCAACTATGGTCTTACAT-AT
1 TTTCATCATGATGCCATAATATCTTTCAACTATGGTCTTAC-TCAT
*
23451822 TTTCATCATGATGCCATAATATCTTTC-AGTATGGTCTTACTCAT
1 TTTCATCATGATGCCATAATATCTTTCAACTATGGTCTTACTCAT
* * * *
23451866 TTTCATCATGATTCCATAACATCTTTTAGCTATGGTCTTACTCAT
1 TTTCATCATGATGCCATAATATCTTTCAACTATGGTCTTACTCAT
23451911 TTT
1 TTT
23451914 TGGCGTATAA
Statistics
Matches: 82, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
43 1 0.01
44 44 0.54
45 37 0.45
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.45
Consensus pattern (45 bp):
TTTCATCATGATGCCATAATATCTTTCAACTATGGTCTTACTCAT
Found at i:23453983 original size:45 final size:45
Alignment explanation
Indices: 23453932--23454046 Score: 117
Period size: 45 Copynumber: 2.6 Consensus size: 45
23453922 GGACTACTAG
* * * *
23453932 GATGCCATAGCATCTTTCAGCTATGGTCTTAGTC-TTATTTACCAT
1 GATGCCATAGCATCTTTCAGCTATGGTCGTACTCATT-TATACCAC
** * * *
23453977 GATGCCATAGTGTCTTTCAACCATGGTCGTACTCATTTATATCAC
1 GATGCCATAGCATCTTTCAGCTATGGTCGTACTCATTTATACCAC
23454022 GATGCCAT-GACATCTTTCAGCTATG
1 GATGCCATAG-CATCTTTCAGCTATG
23454047 ACCTTAATCA
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
44 1 0.02
45 52 0.95
46 2 0.04
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (45 bp):
GATGCCATAGCATCTTTCAGCTATGGTCGTACTCATTTATACCAC
Found at i:23458587 original size:25 final size:25
Alignment explanation
Indices: 23458553--23458607 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
23458543 AATTCTTGTC
23458553 TTTCTAAATATCACTGACTGATGTA
1 TTTCTAAATATCACTGACTGATGTA
23458578 TTTCTAAATATCACTGACTGATGTA
1 TTTCTAAATATCACTGACTGATGTA
23458603 TTTCT
1 TTTCT
23458608 TGTCTAAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44
Consensus pattern (25 bp):
TTTCTAAATATCACTGACTGATGTA
Found at i:23460325 original size:50 final size:50
Alignment explanation
Indices: 23460250--23460492 Score: 308
Period size: 50 Copynumber: 4.9 Consensus size: 50
23460240 CATTTGGGTA
*
23460250 AAGAGGTCCCATGTAAGA-TCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACT-ATGTCTGGGACATGGCATTGGCACCGAGAT
*
23460300 AAGAGGTCCCATGTAAGACTATGTCTGGGACATGGCGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACTATGTCTGGGACATGGCATTGGCACCGAGAT
* * *
23460350 AAGAGGTCCCATGTAAGACTATGTTTGGGACATGGCATTGACATCGAGAT
1 AAGAGGTCCCATGTAAGACTATGTCTGGGACATGGCATTGGCACCGAGAT
* ** * * * *
23460400 GAGAGGTCCCCCGTAAGACCATGTCTGGGATATGGCATGGGCACCGATAT
1 AAGAGGTCCCATGTAAGACTATGTCTGGGACATGGCATTGGCACCGAGAT
* ** * * *
23460450 GAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 AAGAGGTCCCATGTAAGACTATGTCTGGGACATGGCATTGGCA
23460493 GTACAGAAAA
Statistics
Matches: 172, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
50 171 0.99
51 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (50 bp):
AAGAGGTCCCATGTAAGACTATGTCTGGGACATGGCATTGGCACCGAGAT
Found at i:23463440 original size:12 final size:10
Alignment explanation
Indices: 23463410--23463443 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
23463400 GGCTAAGTGA
23463410 TTTGGGTGTG
1 TTTGGGTGTG
23463420 TTTGGGTGTG
1 TTTGGGTGTG
*
23463430 TTTGGGAGTG
1 TTTGGGTGTG
23463440 TTTG
1 TTTG
23463444 ACACAAATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.03, C:0.00, G:0.47, T:0.50
Consensus pattern (10 bp):
TTTGGGTGTG
Found at i:23464917 original size:27 final size:27
Alignment explanation
Indices: 23464849--23464948 Score: 112
Period size: 27 Copynumber: 3.7 Consensus size: 27
23464839 GCTTGGGCCA
*
23464849 TAAAATTACCGAAATAACCTCGAAGGG
1 TAAAATTACCGAAATACCCTCGAAGGG
*
23464876 TAAAATGACCGAAATACCCTCGAAGGG
1 TAAAATTACCGAAATACCCTCGAAGGG
* * * *
23464903 TAAAATTATCAAAATACCCCCAAAAGGG
1 TAAAATTACCGAAATACCCTC-GAAGGG
* *
23464931 -AAAATGACTGAAATACCC
1 TAAAATTACCGAAATACCC
23464949 CTATGGGGTA
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
27 56 0.92
28 5 0.08
ACGTcount: A:0.46, C:0.21, G:0.16, T:0.17
Consensus pattern (27 bp):
TAAAATTACCGAAATACCCTCGAAGGG
Found at i:23464949 original size:27 final size:27
Alignment explanation
Indices: 23464871--23464967 Score: 90
Period size: 27 Copynumber: 3.6 Consensus size: 27
23464861 AATAACCTCG
* * *
23464871 AAGGGTAAAATGACCGAAATACCCTCG
1 AAGGGTAAAATGACTGAAATACCCCCA
* *
23464898 AAGGGTAAAATTA-TCAAAATACCCCCAA
1 AAGGGTAAAATGACT-GAAATACCCCC-A
*
23464926 AAGGG-AAAATGACTGAAATACCCCTA
1 AAGGGTAAAATGACTGAAATACCCCCA
**
23464952 TGGGGTAAAATGACTG
1 AAGGGTAAAATGACTG
23464968 TTATGCCCCT
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
26 4 0.07
27 46 0.82
28 6 0.11
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.18
Consensus pattern (27 bp):
AAGGGTAAAATGACTGAAATACCCCCA
Found at i:23464976 original size:27 final size:27
Alignment explanation
Indices: 23464931--23464997 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
23464921 CCCAAAAGGG
** *
23464931 AAAATGACTGAAATACCCCTATGG-GGT
1 AAAATGACTGTTATACCCCTA-GGAGAT
*
23464958 AAAATGACTGTTATGCCCCTAGGAGAT
1 AAAATGACTGTTATACCCCTAGGAGAT
*
23464985 GAAATGACTGTTA
1 AAAATGACTGTTA
23464998 AGGCATTGTG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 2 0.06
27 32 0.94
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.25
Consensus pattern (27 bp):
AAAATGACTGTTATACCCCTAGGAGAT
Found at i:23465186 original size:26 final size:26
Alignment explanation
Indices: 23465157--23465258 Score: 123
Period size: 26 Copynumber: 3.9 Consensus size: 26
23465147 TTTGCCACAA
*
23465157 ATACTGTTAGTGGCAGCTTTGCTGTG
1 ATACTGTTACTGGCAGCTTTGCTGTG
* * *
23465183 ATACTGATACTGGCAGCTCTACTGTG
1 ATACTGTTACTGGCAGCTTTGCTGTG
* * *
23465209 TTACTGTTACTAGCAGCTTTGCTGCG
1 ATACTGTTACTGGCAGCTTTGCTGTG
* *
23465235 TTACTATTACTGGCAGCTTTGCTG
1 ATACTGTTACTGGCAGCTTTGCTG
23465259 CAATATTGGT
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 64 1.00
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.37
Consensus pattern (26 bp):
ATACTGTTACTGGCAGCTTTGCTGTG
Found at i:23475248 original size:20 final size:20
Alignment explanation
Indices: 23475223--23475261 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
23475213 GCTACTCATA
23475223 TTTTTA-AAAACTTATCAGAG
1 TTTTTAGAAAACTTA-CAGAG
*
23475243 TTTTTAGAACACTTACAGA
1 TTTTTAGAAAACTTACAGA
23475262 ATCGGTGCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.38
Consensus pattern (20 bp):
TTTTTAGAAAACTTACAGAG
Found at i:23482121 original size:42 final size:42
Alignment explanation
Indices: 23482062--23482146 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
23482052 ACCTTCCTTG
23482062 TACAATCATCTGATGATGTCTTATCTGACTGCTTTTCCACTT
1 TACAATCATCTGATGATGTCTTATCTGACTGCTTTTCCACTT
23482104 TACAATCATCTGATGATGTCTTATCTGACTGCTTTTCCACTT
1 TACAATCATCTGATGATGTCTTATCTGACTGCTTTTCCACTT
23482146 T
1 T
23482147 CACCGTTTAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.44
Consensus pattern (42 bp):
TACAATCATCTGATGATGTCTTATCTGACTGCTTTTCCACTT
Found at i:23486615 original size:24 final size:24
Alignment explanation
Indices: 23486567--23486613 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
23486557 ACTGGTCATA
*
23486567 GAGAGAATTGAGGAGGGATATTTG
1 GAGAGAATTGAGGAGGAATATTTG
*
23486591 GAGAGATTTGAGGAGAGAATATT
1 GAGAGAATTGAGGAG-GAATATT
23486614 GGGATTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.38, T:0.26
Consensus pattern (24 bp):
GAGAGAATTGAGGAGGAATATTTG
Found at i:23487465 original size:20 final size:19
Alignment explanation
Indices: 23487432--23487473 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
23487422 CATGGGCTTA
*
23487432 GGCCGTAATGGGCCACGTTG
1 GGCCGAAATGGGCCACG-TG
*
23487452 GGCCGAAATTGGCCACGTG
1 GGCCGAAATGGGCCACGTG
23487471 GGC
1 GGC
23487474 TTAATGGGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.17, C:0.26, G:0.40, T:0.17
Consensus pattern (19 bp):
GGCCGAAATGGGCCACGTG
Found at i:23487764 original size:27 final size:27
Alignment explanation
Indices: 23487723--23488079 Score: 396
Period size: 27 Copynumber: 13.3 Consensus size: 27
23487713 TCTGAATAGT
* *
23487723 TAAAATGACCAAAATACCCCCACAGGG
1 TAAAATGACCGAAATACCCCCATAGGG
* * *
23487750 TTAAATGACCGAAATAGCCCTATAGGG
1 TAAAATGACCGAAATACCCCCATAGGG
*
23487777 TAAAATGACCGAAATACCCCCATAGGA
1 TAAAATGACCGAAATACCCCCATAGGG
** * *
23487804 TAAAATGATTGAAACACCCTCATAGGG
1 TAAAATGACCGAAATACCCCCATAGGG
* * *
23487831 TAAAATGACCGAAGTACCCCTATCGGG
1 TAAAATGACCGAAATACCCCCATAGGG
*
23487858 TAAAATGACCGAAATA--CCCATAGTG
1 TAAAATGACCGAAATACCCCCATAGGG
**
23487883 TAAAATGAATGAAATACCCCCATAGGG
1 TAAAATGACCGAAATACCCCCATAGGG
* * * *
23487910 TAAAATAACCAAAATACCTCTATAGGG
1 TAAAATGACCGAAATACCCCCATAGGG
* * *
23487937 TAAAATGATCGAAATACCCCTATAAGG
1 TAAAATGACCGAAATACCCCCATAGGG
* *
23487964 TAAAATGATCGAAATACCCCCACAGGG
1 TAAAATGACCGAAATACCCCCATAGGG
* * * *
23487991 TAAAATGACTGAAATACTCTCATAAGG
1 TAAAATGACCGAAATACCCCCATAGGG
* **
23488018 TAAAATGACCAAAATACCCTTATAGGG
1 TAAAATGACCGAAATACCCCCATAGGG
*
23488045 TAAAATGACCAAAATA-CCCCATAGGG
1 TAAAATGACCGAAATACCCCCATAGGG
23488071 TAAAATGAC
1 TAAAATGAC
23488080 TGGTATACCT
Statistics
Matches: 273, Mismatches: 55, Indels: 5
0.82 0.17 0.02
Matches are distributed among these distances:
25 20 0.07
26 17 0.06
27 236 0.86
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (27 bp):
TAAAATGACCGAAATACCCCCATAGGG
Found at i:23491342 original size:51 final size:51
Alignment explanation
Indices: 23491262--23491364 Score: 179
Period size: 51 Copynumber: 2.0 Consensus size: 51
23491252 AAGGAGAATG
* *
23491262 GCAACGAGACTTGGGTACTAATTTGCCTATAACGTTTCCTCCATCGAGCAT
1 GCAACGAGACTTGGGTACTAATTTGCCTATAACATTTCATCCATCGAGCAT
*
23491313 GCAACGAGACTTGGGTACTAATTTTCCTATAACATTTCATCCATCGAGCAT
1 GCAACGAGACTTGGGTACTAATTTGCCTATAACATTTCATCCATCGAGCAT
23491364 G
1 G
23491365 ATCCCTATAG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.30
Consensus pattern (51 bp):
GCAACGAGACTTGGGTACTAATTTGCCTATAACATTTCATCCATCGAGCAT
Found at i:23510635 original size:27 final size:27
Alignment explanation
Indices: 23510605--23510659 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
23510595 GCCCTTAGGT
23510605 ATGTCCTTTTACAAACTTGTGTATGGA
1 ATGTCCTTTTACAAACTTGTGTATGGA
23510632 ATGTCCTTTTACAAACTTGTGTATGGA
1 ATGTCCTTTTACAAACTTGTGTATGGA
23510659 A
1 A
23510660 AAATAACCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (27 bp):
ATGTCCTTTTACAAACTTGTGTATGGA
Found at i:23516028 original size:17 final size:16
Alignment explanation
Indices: 23515978--23516035 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 16
23515968 GGGTGAGAAG
23515978 TAAAAGTTTAGGGGAAAAA
1 TAAAAGTTTA-GGG--AAA
*
23515997 TAAAAAGTTTTGGGAAA
1 T-AAAAGTTTAGGGAAA
23516014 TAAAAGTTTGAGGGAAA
1 TAAAAGTTT-AGGGAAA
23516031 GTAAA
1 -TAAA
23516036 TAAGGGGAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
16 8 0.24
17 10 0.29
18 4 0.12
19 4 0.12
20 8 0.24
ACGTcount: A:0.50, C:0.00, G:0.26, T:0.24
Consensus pattern (16 bp):
TAAAAGTTTAGGGAAA
Found at i:23516322 original size:30 final size:30
Alignment explanation
Indices: 23516286--23516370 Score: 152
Period size: 30 Copynumber: 2.8 Consensus size: 30
23516276 GGAGGGGAGG
23516286 GGAGTAAAAGTTTTGGGGGGAAAGTGGGAA
1 GGAGTAAAAGTTTTGGGGGGAAAGTGGGAA
23516316 GGAGTAAAAGTTTTGGGGGGAAAGTGGGAA
1 GGAGTAAAAGTTTTGGGGGGAAAGTGGGAA
* *
23516346 GGAGTAAAAGTTTTGAGGGAAAAGT
1 GGAGTAAAAGTTTTGGGGGGAAAGT
23516371 AAAAAGGTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.35, C:0.00, G:0.44, T:0.21
Consensus pattern (30 bp):
GGAGTAAAAGTTTTGGGGGGAAAGTGGGAA
Found at i:23516442 original size:18 final size:18
Alignment explanation
Indices: 23516419--23516455 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
23516409 TATAGTTTGA
23516419 TATTTGAATTATTCGAAT
1 TATTTGAATTATTCGAAT
*
23516437 TATTTGAGTTATTCGAAT
1 TATTTGAATTATTCGAAT
23516455 T
1 T
23516456 CGAAAACTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.51
Consensus pattern (18 bp):
TATTTGAATTATTCGAAT
Found at i:23519426 original size:22 final size:22
Alignment explanation
Indices: 23519381--23519427 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
23519371 ACCAGTGACT
* *
23519381 ATGTCGCAACATGGAATGCTTA
1 ATGTCGCAACATAGAATGCATA
23519403 ATGTCGCAACATAGAGA-GCATA
1 ATGTCGCAACATAGA-ATGCATA
23519425 ATG
1 ATG
23519428 GAGAAATCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.23
Consensus pattern (22 bp):
ATGTCGCAACATAGAATGCATA
Found at i:23522585 original size:2 final size:2
Alignment explanation
Indices: 23522578--23522609 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
23522568 CCTATAGAGC
23522578 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
23522610 CTTTCGAGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23525062 original size:37 final size:37
Alignment explanation
Indices: 23525016--23525119 Score: 165
Period size: 37 Copynumber: 2.8 Consensus size: 37
23525006 ATCCAACCCA
*
23525016 AACATGCCAAATGCTCATAAGAGCTAATACAACCGAT
1 AACACGCCAAATGCTCATAAGAGCTAATACAACCGAT
* * *
23525053 AACACGCCAAATGCTCATAAGAGTTAATCCAACTGAT
1 AACACGCCAAATGCTCATAAGAGCTAATACAACCGAT
23525090 AACACGCCAAATGCTCATAAGAGCT-ATACA
1 AACACGCCAAATGCTCATAAGAGCTAATACA
23525120 TCTGCCCCTA
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
36 4 0.07
37 57 0.93
ACGTcount: A:0.42, C:0.25, G:0.13, T:0.19
Consensus pattern (37 bp):
AACACGCCAAATGCTCATAAGAGCTAATACAACCGAT
Found at i:23531248 original size:17 final size:18
Alignment explanation
Indices: 23531226--23531259 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
23531216 CTTAATGTCT
23531226 GTTCTA-GAACTCACTAA
1 GTTCTATGAACTCACTAA
*
23531243 GTTCTATGAACTTACTA
1 GTTCTATGAACTCACTA
23531260 CATTACCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (18 bp):
GTTCTATGAACTCACTAA
Found at i:23534287 original size:27 final size:26
Alignment explanation
Indices: 23534241--23534298 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
23534231 TTGACACACT
* *
23534241 TTAAATATGTAGGAAATTAAACAAAC
1 TTAAAGATGTACGAAATTAAACAAAC
* *
23534267 ATTAAAGATGTACGAATTTAAACATAC
1 -TTAAAGATGTACGAAATTAAACAAAC
23534294 TTAAA
1 TTAAA
23534299 ACATGTATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 5 0.19
27 22 0.81
ACGTcount: A:0.52, C:0.09, G:0.10, T:0.29
Consensus pattern (26 bp):
TTAAAGATGTACGAAATTAAACAAAC
Found at i:23534304 original size:27 final size:26
Alignment explanation
Indices: 23534241--23534305 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 26
23534231 TTGACACACT
* *
23534241 TTAAATATGTAGGAAATTAAACAAAC
1 TTAAACATGTACGAAATTAAACAAAC
* * *
23534267 ATTAAAGATGTACGAATTTAAACATAC
1 -TTAAACATGTACGAAATTAAACAAAC
23534294 TTAAAACATGTA
1 TT-AAACATGTA
23534306 TTAAAGATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 2 0.06
27 30 0.94
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.29
Consensus pattern (26 bp):
TTAAACATGTACGAAATTAAACAAAC
Done.