Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 144 of 199
Found at i:42137946 original size:27 final size:27
Alignment explanation
Indices: 42137911--42138222 Score: 345
Period size: 27 Copynumber: 11.6 Consensus size: 27
42137901 CAAGACCCAT
* *
42137911 ATAGAGTAAAATGACTAAAATACCCCC
1 ATAGGGTAAAATGACCAAAATACCCCC
** * **
42137938 ATATTGTAAAATGATCAAAATACCCTT
1 ATAGGGTAAAATGACCAAAATACCCCC
* *
42137965 ATAGGGTAAAATGATCGAAATACCCCC
1 ATAGGGTAAAATGACCAAAATACCCCC
**
42137992 ATAGGGTAAAATGACTGAAATACCCCC
1 ATAGGGTAAAATGACCAAAATACCCCC
* *
42138019 ATAGGGTAAAGTGACCAAAATACCCTC
1 ATAGGGTAAAATGACCAAAATACCCCC
* * *
42138046 GTTGGGTAAAATGACCAAAATACCCTC
1 ATAGGGTAAAATGACCAAAATACCCCC
* * *
42138073 ATAAGGTAAAATGACCAAAATTCCCTC
1 ATAGGGTAAAATGACCAAAATACCCCC
*
42138100 ATAGGGTAAAATGACCAAAAGACCCCC
1 ATAGGGTAAAATGACCAAAATACCCCC
* ***
42138127 ATAGGGTAAAATGACCGAAATACCTTT
1 ATAGGGTAAAATGACCAAAATACCCCC
* * * *
42138154 ATAAGGTAGAATGACCGAAATACCCCT
1 ATAGGGTAAAATGACCAAAATACCCCC
* *
42138181 ATAGGGTAAAATGATCAAAATACCCCT
1 ATAGGGTAAAATGACCAAAATACCCCC
*
42138208 ATAAGGTAAAATGAC
1 ATAGGGTAAAATGAC
42138223 TGTTATACCC
Statistics
Matches: 242, Mismatches: 43, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 242 1.00
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.21
Consensus pattern (27 bp):
ATAGGGTAAAATGACCAAAATACCCCC
Found at i:42143392 original size:21 final size:22
Alignment explanation
Indices: 42143347--42143392 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
42143337 AGAGAAAAAT
*
42143347 AAAAGTGAAAAAGAAGAAAATG
1 AAAAGTGAAAAAGAAGAAAAGG
**
42143369 AAAA-TGAAAAAGGCGAAAAGG
1 AAAAGTGAAAAAGAAGAAAAGG
42143390 AAA
1 AAA
42143393 GCGAAAGAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.67, C:0.02, G:0.24, T:0.07
Consensus pattern (22 bp):
AAAAGTGAAAAAGAAGAAAAGG
Found at i:42146876 original size:32 final size:31
Alignment explanation
Indices: 42146822--42146898 Score: 100
Period size: 32 Copynumber: 2.5 Consensus size: 31
42146812 CAGCTACTGC
* * **
42146822 TGTTCACACCAATGGACCGTCCAATTCCTGG
1 TGTTCACACCAAAGGACCGTCCAAGTCCAAG
*
42146853 TGTTCACAACCAAAGGACTGTCCAAGTCCAAG
1 TGTTCAC-ACCAAAGGACCGTCCAAGTCCAAG
42146885 TGTTCACACCAAAG
1 TGTTCACACCAAAG
42146899 ACTCTTCAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 14 0.35
32 26 0.65
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.22
Consensus pattern (31 bp):
TGTTCACACCAAAGGACCGTCCAAGTCCAAG
Found at i:42148864 original size:12 final size:12
Alignment explanation
Indices: 42148830--42148871 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
42148820 CTGTGGCACG
*
42148830 ACCCCCTACTAT
1 ACCCCCTACTGT
*
42148842 ACCCTCT-CTGT
1 ACCCCCTACTGT
42148853 ACCCCCTACTGT
1 ACCCCCTACTGT
*
42148865 ACACCCT
1 ACCCCCT
42148872 CTGGGACCTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.19, C:0.50, G:0.05, T:0.26
Consensus pattern (12 bp):
ACCCCCTACTGT
Found at i:42151985 original size:27 final size:28
Alignment explanation
Indices: 42151926--42151979 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
42151916 AATATAACTA
*
42151926 AAATTAAATATTTTAATAATTTAAGTGC
1 AAATTAAATATTTTAATAATTAAAGTGC
*
42151954 AAATTAATTATTTTAA-AATTAAAGTG
1 AAATTAAATATTTTAATAATTAAAGTG
42151980 TGAATTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 9 0.38
28 15 0.62
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (28 bp):
AAATTAAATATTTTAATAATTAAAGTGC
Found at i:42160989 original size:23 final size:22
Alignment explanation
Indices: 42160937--42160989 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
42160927 TCCTTGTCTT
*
42160937 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
* *
42160959 CTTATTTTCTCTTCTTTCTTC-AA
1 TTTCTTTTCT-TTCTTT-TTCTAA
42160982 TTTCTTTT
1 TTTCTTTT
42160990 TCACTTTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 7 0.29
23 14 0.58
24 3 0.12
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:42161003 original size:18 final size:18
Alignment explanation
Indices: 42160982--42161021 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
42160972 CTTTCTTCAA
* * *
42160982 TTTCTTTTTCACTTTTCT
1 TTTCTATTTCACATTCCT
42161000 TTTCTATTTCACATTCCT
1 TTTCTATTTCACATTCCT
42161018 TTTC
1 TTTC
42161022 ACTCTCAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.10, C:0.25, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTCTATTTCACATTCCT
Found at i:42167101 original size:40 final size:40
Alignment explanation
Indices: 42167037--42167173 Score: 168
Period size: 40 Copynumber: 3.4 Consensus size: 40
42167027 CTATATTTTT
* * * *
42167037 ACAAGGGCACCGAAGTTTTTACAAGGGAAAAATTGTGCAA
1 ACAAGGACACCAAAGTGTTTACAAGGGCAAAATTGTGCAA
* *
42167077 ACAAGGACACCAAAGTGTTGACAAGGGCACAATTGTGCAA
1 ACAAGGACACCAAAGTGTTTACAAGGGCAAAATTGTGCAA
* * * *
42167117 ACAGGGACACCAAAGTGTTTACAGGGGCATAGTTGTGCAA
1 ACAAGGACACCAAAGTGTTTACAAGGGCAAAATTGTGCAA
42167157 AC-AGGACCACCAAAGTG
1 ACAAGGA-CACCAAAGTG
42167174 CAATCAAGGA
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
39 3 0.04
40 81 0.96
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.17
Consensus pattern (40 bp):
ACAAGGACACCAAAGTGTTTACAAGGGCAAAATTGTGCAA
Found at i:42167201 original size:20 final size:20
Alignment explanation
Indices: 42167178--42167215 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42167168 AAAGTGCAAT
42167178 CAAGGACATCGAAGTGTATA
1 CAAGGACATCGAAGTGTATA
* *
42167198 CAAGGGCATCGAGGTGTA
1 CAAGGACATCGAAGTGTA
42167216 ATGAAGGCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.16, G:0.32, T:0.18
Consensus pattern (20 bp):
CAAGGACATCGAAGTGTATA
Found at i:42170481 original size:23 final size:23
Alignment explanation
Indices: 42170455--42170507 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
42170445 TAATACATGT
42170455 TTTTAATATGTC-AAGCTACAACA
1 TTTTAATATGTCTAAGCT-CAACA
* *
42170478 TTTTAATGTGTCTTAAGCTGAACA
1 TTTTAATATGTC-TAAGCTCAACA
42170502 TTTTAA
1 TTTTAA
42170508 GTGCAGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 11 0.42
24 10 0.38
25 5 0.19
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (23 bp):
TTTTAATATGTCTAAGCTCAACA
Found at i:42170655 original size:13 final size:13
Alignment explanation
Indices: 42170637--42170661 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42170627 TCTAAAATAA
42170637 AATTTATTTGTTG
1 AATTTATTTGTTG
42170650 AATTTATTTGTT
1 AATTTATTTGTT
42170662 CCAGGTACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (13 bp):
AATTTATTTGTTG
Found at i:42174412 original size:53 final size:53
Alignment explanation
Indices: 42174332--42174436 Score: 192
Period size: 53 Copynumber: 2.0 Consensus size: 53
42174322 TTTCCCGAAC
*
42174332 GCTTTATGTTTCTGTTTTGACGTCAATGATGGGCCTTTTTATCCATTGTGAAT
1 GCTTTATGTTTCTGTTTTGACATCAATGATGGGCCTTTTTATCCATTGTGAAT
*
42174385 GCTTTATGTTTTTGTTTTGACATCAATGATGGGCCTTTTTATCCATTGTGAA
1 GCTTTATGTTTCTGTTTTGACATCAATGATGGGCCTTTTTATCCATTGTGAA
42174437 ACGGTGGAAC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.18, C:0.14, G:0.20, T:0.48
Consensus pattern (53 bp):
GCTTTATGTTTCTGTTTTGACATCAATGATGGGCCTTTTTATCCATTGTGAAT
Found at i:42180241 original size:81 final size:81
Alignment explanation
Indices: 42180106--42180287 Score: 319
Period size: 81 Copynumber: 2.2 Consensus size: 81
42180096 TACGAAATTG
* *
42180106 TAAAAAAAATTAAAAAAAAAAATTCGAAAAAATAGTTTATTTTGGATTCAAATTTTCCTTTTGCA
1 TAAAAAAATTTGAAAAAAAAAATTCGAAAAAATAGTTTATTTTGGATTCAAATTTTCCTTTTGCA
42180171 TTTAGCATTTAGTAGT
66 TTTAGCATTTAGTAGT
** *
42180187 TAAAAAAATTTGAAAAAAAAAATTCGAAAAGTTAGTTTATTTTGGATTCAAATTTTCCTTTTGTA
1 TAAAAAAATTTGAAAAAAAAAATTCGAAAAAATAGTTTATTTTGGATTCAAATTTTCCTTTTGCA
42180252 TTTAGCATTTAGTAGT
66 TTTAGCATTTAGTAGT
42180268 TAAAAAAATTTGAAAAAAAA
1 TAAAAAAATTTGAAAAAAAA
42180288 GGAAAGTGAT
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 96 1.00
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (81 bp):
TAAAAAAATTTGAAAAAAAAAATTCGAAAAAATAGTTTATTTTGGATTCAAATTTTCCTTTTGCA
TTTAGCATTTAGTAGT
Found at i:42181350 original size:12 final size:12
Alignment explanation
Indices: 42181279--42181324 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
42181269 GACAAGAAGA
*
42181279 GAAAAATGAAAGT
1 GAAAAA-GAAATT
*
42181292 GAAAAAGAGATT
1 GAAAAAGAAATT
42181304 GAAAAAGAAATT
1 GAAAAAGAAATT
*
42181316 GCAAAAGAA
1 GAAAAAGAA
42181325 GAAAAAGCGA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 23 0.79
13 6 0.21
ACGTcount: A:0.63, C:0.02, G:0.22, T:0.13
Consensus pattern (12 bp):
GAAAAAGAAATT
Found at i:42182605 original size:13 final size:13
Alignment explanation
Indices: 42182587--42182614 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
42182577 GATTATTATG
42182587 CATTCTCTATTAC
1 CATTCTCTATTAC
42182600 CATTCTCTATTAC
1 CATTCTCTATTAC
42182613 CA
1 CA
42182615 AGTATGGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.32, G:0.00, T:0.43
Consensus pattern (13 bp):
CATTCTCTATTAC
Found at i:42192238 original size:19 final size:19
Alignment explanation
Indices: 42192208--42192252 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
42192198 AAGCTCATTT
42192208 TTTAATTATTTAATATATTA
1 TTTAA-TATTTAATATATTA
42192228 TTTAATATTTAATATATTA
1 TTTAATATTTAATATATTA
*
42192247 TGTAAT
1 TTTAAT
42192253 TTACATCACA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTAATATTTAATATATTA
Found at i:42195575 original size:20 final size:21
Alignment explanation
Indices: 42195550--42195589 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
42195540 TAAAAAAGAG
42195550 AAAGAAAAGAAAAA-TGAGAA
1 AAAGAAAAGAAAAAGTGAGAA
*
42195570 AAAGAAAGGAAAAAGTGAGA
1 AAAGAAAAGAAAAAGTGAGA
42195590 GAGTTGAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.70, C:0.00, G:0.25, T:0.05
Consensus pattern (21 bp):
AAAGAAAAGAAAAAGTGAGAA
Found at i:42197598 original size:45 final size:44
Alignment explanation
Indices: 42197530--42197664 Score: 171
Period size: 45 Copynumber: 3.0 Consensus size: 44
42197520 ACTACTAGTG
42197530 TACCGGGTACCATTGATTATAAAGGTGGTTGCTGTGTGCTGATTC
1 TACCGGGTA-CATTGATTATAAAGGTGGTTGCTGTGTGCTGATTC
* * *
42197575 TACCGGTTATCATTGATTGTAAAGGTGGTTGCAGTGTGCTGATTC
1 TACCGGGTA-CATTGATTATAAAGGTGGTTGCTGTGTGCTGATTC
** * * *
42197620 CGCCGGGTACTATTAATTATGAAGGTGGTTGCTATGTGCTGATTC
1 TACCGGGTAC-ATTGATTATAAAGGTGGTTGCTGTGTGCTGATTC
42197665 CATCGAGTAT
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
44 1 0.01
45 76 0.99
ACGTcount: A:0.20, C:0.15, G:0.29, T:0.36
Consensus pattern (44 bp):
TACCGGGTACATTGATTATAAAGGTGGTTGCTGTGTGCTGATTC
Found at i:42205928 original size:11 final size:11
Alignment explanation
Indices: 42205906--42205944 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
42205896 TATTATAATT
42205906 TAACATTAAAAA
1 TAACA-TAAAAA
42205918 TAACATAAAAA
1 TAACATAAAAA
*
42205929 T-ACAAAAAAA
1 TAACATAAAAA
42205939 TAACAT
1 TAACAT
42205945 CCACAATCCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 9 0.38
11 10 0.42
12 5 0.21
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (11 bp):
TAACATAAAAA
Found at i:42207172 original size:9 final size:9
Alignment explanation
Indices: 42207130--42207224 Score: 60
Period size: 9 Copynumber: 11.2 Consensus size: 9
42207120 TTTTTTGTAT
42207130 TATATATAA
1 TATATATAA
* *
42207139 TGTATACAA
1 TATATATAA
* * *
42207148 AAAATAGAA
1 TATATATAA
42207157 T-TA-ATAA
1 TATATATAA
42207164 TATATATAA
1 TATATATAA
42207173 TAATATATAA
1 T-ATATATAA
42207183 -A-A-ATAA
1 TATATATAA
*
42207189 TATA-AAAA
1 TATATATAA
*
42207197 TATATAAAA
1 TATATATAA
*
42207206 TAT-TAGAA
1 TATATATAA
42207214 TATATATAA
1 TATATATAA
42207223 TA
1 TA
42207225 AAATAGATAT
Statistics
Matches: 67, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
6 4 0.06
7 6 0.09
8 19 0.28
9 30 0.45
10 8 0.12
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (9 bp):
TATATATAA
Found at i:42207191 original size:21 final size:21
Alignment explanation
Indices: 42207162--42207244 Score: 82
Period size: 21 Copynumber: 4.0 Consensus size: 21
42207152 TAGAATTAAT
*
42207162 AATATATATAATAATATATAAA
1 AATA-ATAGAATAATATATAAA
* *
42207184 AATAATATAAAAATATAT-AA
1 AATAATAGAATAATATATAAA
* *
42207204 AATATTAGAAT-ATATATAAT
1 AATAATAGAATAATATATAAA
42207224 AA-AATAGATATAATATATAAA
1 AATAATAGA-ATAATATATAAA
42207245 TAAATTGATT
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
19 11 0.22
20 15 0.29
21 21 0.41
22 4 0.08
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
AATAATAGAATAATATATAAA
Found at i:42207198 original size:8 final size:9
Alignment explanation
Indices: 42207160--42207244 Score: 63
Period size: 9 Copynumber: 9.6 Consensus size: 9
42207150 AATAGAATTA
*
42207160 ATAATATAT
1 ATAAAATAT
42207169 ATAATAATAT
1 ATAA-AATAT
42207179 ATAAAAATAAT
1 AT-AAAAT-AT
42207190 ATAAAAATAT
1 AT-AAAATAT
42207200 ATAAAATAT
1 ATAAAATAT
*
42207209 -TAGAATAT
1 ATAAAATAT
42207217 AT---ATA-
1 ATAAAATAT
*
42207222 ATAAAATAG
1 ATAAAATAT
*
42207231 ATATAATAT
1 ATAAAATAT
42207240 ATAAA
1 ATAAA
42207245 TAAATTGATT
Statistics
Matches: 63, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
5 2 0.03
6 3 0.05
8 10 0.16
9 23 0.37
10 13 0.21
11 12 0.19
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (9 bp):
ATAAAATAT
Found at i:42207218 original size:19 final size:19
Alignment explanation
Indices: 42207174--42207244 Score: 58
Period size: 19 Copynumber: 3.6 Consensus size: 19
42207164 TATATATAAT
42207174 AATATATA-AAAATAATATA-
1 AATATATATAAAAT-AT-TAG
*
42207193 AAAATATATAAAATATTAG
1 AATATATATAAAATATTAG
*
42207212 AATATATATAATAA-AATAG
1 AATATATATAA-AATATTAG
42207231 ATATAATATATAAA
1 A-AT-ATATATAAA
42207245 TAAATTGATT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
18 2 0.05
19 24 0.55
20 10 0.23
21 8 0.18
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
AATATATATAAAATATTAG
Found at i:42207249 original size:21 final size:20
Alignment explanation
Indices: 42207162--42207267 Score: 65
Period size: 22 Copynumber: 5.0 Consensus size: 20
42207152 TAGAATTAAT
42207162 AATATATATAATAATATATAA-A
1 AATA-ATATAAT-ATATA-AATA
* *
42207184 AATAATATAA-AAATATATAA
1 AATAATATAATATATAAAT-A
* *
42207204 AATATTAGAATATATATAATAA
1 AATAATATAATATATA-AAT-A
42207226 AATAGATATAATATATAAATA
1 AATA-ATATAATATATAAATA
*
42207247 AATTGATTATAATAT-TAAATA
1 AA-T-AATATAATATATAAATA
42207268 TGTAAATAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
18 1 0.01
19 4 0.06
20 9 0.13
21 19 0.28
22 24 0.35
23 11 0.16
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
AATAATATAATATATAAATA
Found at i:42207961 original size:17 final size:17
Alignment explanation
Indices: 42207939--42207977 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
42207929 CTGACTCCAT
*
42207939 TTTTAT-TTTCTAGTTTA
1 TTTTATATTT-TAGTATA
42207956 TTTTATATTTTAGTATA
1 TTTTATATTTTAGTATA
42207973 TTTTA
1 TTTTA
42207978 CATCTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (17 bp):
TTTTATATTTTAGTATA
Found at i:42211051 original size:26 final size:26
Alignment explanation
Indices: 42211015--42211097 Score: 112
Period size: 26 Copynumber: 3.2 Consensus size: 26
42211005 CACGCCCGTA
*
42211015 CTGTGAAATGAGTATGCTCACACGAG
1 CTGTGAAATGAGTATGCTCACACGAC
* *
42211041 CTGTGAAATGAGTATGCTCATACGAT
1 CTGTGAAATGAGTATGCTCACACGAC
* **
42211067 CTGTGAAATGGGCCTGCTCACACGAC
1 CTGTGAAATGAGTATGCTCACACGAC
42211093 CTGTG
1 CTGTG
42211098 GGTTTGAATG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 50 1.00
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.25
Consensus pattern (26 bp):
CTGTGAAATGAGTATGCTCACACGAC
Found at i:42225422 original size:72 final size:72
Alignment explanation
Indices: 42225301--42225476 Score: 228
Period size: 72 Copynumber: 2.4 Consensus size: 72
42225291 TCAGCTTAGA
* * * *
42225301 AAAAATGCATTAGCAGCCTCCTCTTTTAATGCCATCCCAAGTCCCATGCACACATTAAA-TTCAG
1 AAAAATGCAGTAGCAACCTTCTCTTTAAATGCCATCCCAAGTCCCATGCACACATTAAAGTT-AG
* *
42225365 TAGCTTGG
65 CAACTTGG
* * *
42225373 AAAGATGCAGTAGCAACCTTCTCTTTAAATGCCGTCCCAAGTCCCATGCACACATTAAAGTTGGC
1 AAAAATGCAGTAGCAACCTTCTCTTTAAATGCCATCCCAAGTCCCATGCACACATTAAAGTTAGC
42225438 AACTTGG
66 AACTTGG
* *
42225445 AAAAATGTAGCAGCAACCTTTCTCTTTAAATG
1 AAAAATGCAGTAGCAACC-TTCTCTTTAAATG
42225477 TGGTCCATGT
Statistics
Matches: 90, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
72 75 0.83
73 15 0.17
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (72 bp):
AAAAATGCAGTAGCAACCTTCTCTTTAAATGCCATCCCAAGTCCCATGCACACATTAAAGTTAGC
AACTTGG
Found at i:42228667 original size:40 final size:40
Alignment explanation
Indices: 42228606--42228852 Score: 309
Period size: 40 Copynumber: 6.2 Consensus size: 40
42228596 CGGAATTTAG
* * * *
42228606 CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
* * * * *
42228646 CCGGGT-ACAGCAACTCGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTCTTAAC
* * *
42228686 CCGGAT-ATATCAACTCGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTCTTAAC
42228726 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
* *
42228766 CCGGATAAAATCACTAGCATAAATGCCTTCGGGTCTTAAT
1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
* * *
42228806 CCAGATAAAATCACTAGCACAAATGCCTTCGGGACTTAGC
1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
42228846 CCGGATA
1 CCGGATA
42228853 TCATTCAAAT
Statistics
Matches: 183, Mismatches: 22, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
39 2 0.01
40 177 0.97
41 4 0.02
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (40 bp):
CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
Found at i:42242854 original size:40 final size:40
Alignment explanation
Indices: 42242793--42243039 Score: 327
Period size: 40 Copynumber: 6.2 Consensus size: 40
42242783 CGGAATTTAG
* * * *
42242793 CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
* * * * *
42242833 CCGGGT-ACAGCAACTCGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTCTTAAC
* * *
42242873 CCGGAT-ATATCAACTCGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTCTTAAC
42242913 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
*
42242953 CCGGATAAAATCACTAGCATAAATGCCTTCGGGTCTTAAC
1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
* *
42242993 CCGGATAAAATCACTAGCACAAATGCCTTCGGGACTTAGC
1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
42243033 CCGGATA
1 CCGGATA
42243040 TCATTCAAAT
Statistics
Matches: 187, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 2 0.01
40 181 0.97
41 4 0.02
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (40 bp):
CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
Found at i:42250824 original size:74 final size:74
Alignment explanation
Indices: 42250703--42250847 Score: 281
Period size: 74 Copynumber: 2.0 Consensus size: 74
42250693 TCAGCCAAGG
42250703 TTGCAGCCCACACTTGCTGTACTAAGGCCAAAATGGCCTCTTTGATTTGTTTGGCCCAGGCCCGT
1 TTGCAGCCCACACTTGCTGTACTAAGGCCAAAATGGCCTCTTTGATTTGTTTGGCCCAGGCCCGT
42250768 GTGATTCGC
66 GTGATTCGC
*
42250777 TTGCAGCCCACACTTGCTGTACTAAGGCCAAAATGGCCTCTTTGATTTGTTTGGCCCTGGCCCGT
1 TTGCAGCCCACACTTGCTGTACTAAGGCCAAAATGGCCTCTTTGATTTGTTTGGCCCAGGCCCGT
42250842 GTGATT
66 GTGATT
42250848 GGCCCTTGTG
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.17, C:0.28, G:0.24, T:0.31
Consensus pattern (74 bp):
TTGCAGCCCACACTTGCTGTACTAAGGCCAAAATGGCCTCTTTGATTTGTTTGGCCCAGGCCCGT
GTGATTCGC
Found at i:42257686 original size:33 final size:33
Alignment explanation
Indices: 42257649--42257724 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
42257639 ATAACCTGGT
42257649 TATGGTCTTATCATTAGAATGCCATAGCCCAGC
1 TATGGTCTTATCATTAGAATGCCATAGCCCAGC
*
42257682 TATGGTCTTATCATTAGAATGTCATAGCCCAGC
1 TATGGTCTTATCATTAGAATGCCATAGCCCAGC
42257715 TATGGTCTTA
1 TATGGTCTTA
42257725 CATATATATA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (33 bp):
TATGGTCTTATCATTAGAATGCCATAGCCCAGC
Found at i:42263167 original size:23 final size:22
Alignment explanation
Indices: 42263115--42263167 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
42263105 TCCACATCTT
*
42263115 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
42263137 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
42263160 TTTCTTTT
1 TTTCTTTT
42263168 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:42277412 original size:45 final size:45
Alignment explanation
Indices: 42277343--42277501 Score: 173
Period size: 45 Copynumber: 3.6 Consensus size: 45
42277333 TACACGGTGG
* *
42277343 ATCAGCACACAGC-ACCACCCTTATAGTCAATAGTACTC-GGTGAA
1 ATCAGCACATAGCAACCACCTTTATA-TCAATAGTACTCGGGTGAA
* *
42277387 ATCAGCACATAGCAACCACTTTTATACTCAATGGTAC-CGGGTGAA
1 ATCAGCACATAGCAACCACCTTTATA-TCAATAGTACTCGGGTGAA
* * * * *
42277432 ATCAGCACATAGCAACCACCTATATAACCATTGCTA-TCTGGTGAA
1 ATCAGCACATAGCAACCACCTTTATATCAATAG-TACTCGGGTGAA
*
42277477 ATTAGCACATAGCAACCACCTTTAT
1 ATCAGCACATAGCAACCACCTTTAT
42277502 TTTCATTAAT
Statistics
Matches: 98, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
44 17 0.17
45 81 0.83
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (45 bp):
ATCAGCACATAGCAACCACCTTTATATCAATAGTACTCGGGTGAA
Found at i:42281367 original size:30 final size:30
Alignment explanation
Indices: 42281333--42281429 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
42281323 AGCTCACTCC
42281333 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
42281363 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
42281393 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
42281423 TAGCTCA
1 TAGCTCA
42281430 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:42283189 original size:11 final size:12
Alignment explanation
Indices: 42283163--42283188 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42283153 AAAGGAGAAG
42283163 AAATTCAAAAAA
1 AAATTCAAAAAA
42283175 AAATTCAAAAAA
1 AAATTCAAAAAA
42283187 AA
1 AA
42283189 TCGAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:42284206 original size:21 final size:22
Alignment explanation
Indices: 42284155--42284215 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
42284145 AAGAGAAAAT
42284155 AAAGAAA-AGAAAAGAAAAAGAA
1 AAAGAAATA-AAAAGAAAAAGAA
* *
42284177 AAAGCAAT-AGAAGAAAAAGAA
1 AAAGAAATAAAAAGAAAAAGAA
*
42284198 AATGAAATAAAAAGAAAA
1 AAAGAAATAAAAAGAAAA
42284216 GAGAGGCAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 18 0.56
22 14 0.44
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.05
Consensus pattern (22 bp):
AAAGAAATAAAAAGAAAAAGAA
Found at i:42284215 original size:6 final size:6
Alignment explanation
Indices: 42284155--42284204 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
42284145 AAGAGAAAAT
*
42284155 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA TAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
42284204 A
1 A
42284205 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.04
Consensus pattern (6 bp):
AAAGAA
Found at i:42284297 original size:11 final size:12
Alignment explanation
Indices: 42284265--42284295 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
42284255 TTGAGAGAAC
42284265 TTGAAAAAGCCT
1 TTGAAAAAGCCT
42284277 TTGAAAAAGCCT
1 TTGAAAAAGCCT
42284289 TTGAAAA
1 TTGAAAA
42284296 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:42286483 original size:30 final size:30
Alignment explanation
Indices: 42286449--42286544 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
42286439 AGCTCACTCC
42286449 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
42286479 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
*
42286509 CAGCTCAACTTTAGCTCACGAGCTAAA-CT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
42286538 TAGCTCA
1 TAGCTCA
42286545 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
29 9 0.18
30 42 0.82
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:42303498 original size:39 final size:40
Alignment explanation
Indices: 42303414--42303514 Score: 125
Period size: 40 Copynumber: 2.5 Consensus size: 40
42303404 AGATACTAAT
* *
42303414 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTACGAGTTCTAAAA
* *
42303454 TCCGGGTTAAGTCCCGAAGGCATT-GTATGAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTACGAGTT-CTAAAA
* *
42303494 -CCGGGCTATGTCCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCA
42303515 CTTGAACGAG
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
39 26 0.48
40 28 0.52
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTACGAGTTCTAAAA
Found at i:42320161 original size:15 final size:14
Alignment explanation
Indices: 42320141--42320171 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
42320131 TGTCGAATCC
42320141 TCCCTTTTCTCTCTT
1 TCCCTTTTCTCT-TT
42320156 TCCCTTTTCTCTTT
1 TCCCTTTTCTCTTT
42320170 TC
1 TC
42320172 TACTAGCCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (14 bp):
TCCCTTTTCTCTTT
Found at i:42320892 original size:27 final size:27
Alignment explanation
Indices: 42320849--42321091 Score: 244
Period size: 27 Copynumber: 9.0 Consensus size: 27
42320839 CTCTAAGGAT
* *
42320849 AAAATTACCCTCAAAGGTTAAAATGACC
1 AAAA-TACCCTCGAAGGGTAAAATGACC
42320877 AAAATACCCTCGAAGGGTAAAATGACC
1 AAAATACCCTCGAAGGGTAAAATGACC
* * *
42320904 GAAATACCCCCGAAGGGTAAAATGATC
1 AAAATACCCTCGAAGGGTAAAATGACC
* *
42320931 GAAATACCC-CTGGAGGGTAAAATGACC
1 AAAATACCCTC-GAAGGGTAAAATGACC
* *
42320958 AAAATAACCTTGAAGGGTAAAATGACC
1 AAAATACCCTCGAAGGGTAAAATGACC
* *
42320985 AAAATAGCCC-C-AGAGGGTAAAATAATC
1 AAAATA-CCCTCGA-AGGGTAAAATGACC
* * *
42321012 AAAATACCATCGAACGGTAAAATGATC
1 AAAATACCCTCGAAGGGTAAAATGACC
* * * *
42321039 GAAATACCCCCAAAGGGTAAAATGACT
1 AAAATACCCTCGAAGGGTAAAATGACC
42321066 AAAATACCC-C-ATAGGGTAAAATGACC
1 AAAATACCCTCGA-AGGGTAAAATGACC
42321092 GTTATACCCC
Statistics
Matches: 181, Mismatches: 27, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
25 1 0.01
26 18 0.10
27 155 0.86
28 7 0.04
ACGTcount: A:0.45, C:0.21, G:0.18, T:0.16
Consensus pattern (27 bp):
AAAATACCCTCGAAGGGTAAAATGACC
Found at i:42320990 original size:81 final size:81
Alignment explanation
Indices: 42320867--42321107 Score: 279
Period size: 81 Copynumber: 3.0 Consensus size: 81
42320857 CCTCAAAGGT
* *
42320867 TAAAATGACCAAAATACCCTCGAAGGGTAAAATGACCGAAATACCCCCGAAGGGTAAAATGATCG
1 TAAAATGACCAAAATACCCTCGAAGGGTAAAATGACCAAAATACCCCAG-AGGGTAAAATGATCG
42320932 AAATACCCCT-GGAGGG
65 AAATACCCCTAGGAGGG
* * * *
42320948 TAAAATGACCAAAATAACCTTGAAGGGTAAAATGACCAAAATAGCCCCAGAGGGTAAAATAATCA
1 TAAAATGACCAAAATACCCTCGAAGGGTAAAATGACCAAAATA-CCCCAGAGGGTAAAATGATCG
* * * *
42321013 AAATA-CCATCGAACGG
65 AAATACCCCTAGGAGGG
* * * * * * * *
42321029 TAAAATGATCGAAATACCCCCAAAGGGTAAAATGACTAAAATACCCCATAGGGTAAAATGACCGT
1 TAAAATGACCAAAATACCCTCGAAGGGTAAAATGACCAAAATACCCCAGAGGGTAAAATGATCGA
*
42321094 TATACCCCTAGGAG
66 AATACCCCTAGGAG
42321108 ATGAAATGAC
Statistics
Matches: 131, Mismatches: 26, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
80 23 0.18
81 103 0.79
82 5 0.04
ACGTcount: A:0.44, C:0.21, G:0.19, T:0.17
Consensus pattern (81 bp):
TAAAATGACCAAAATACCCTCGAAGGGTAAAATGACCAAAATACCCCAGAGGGTAAAATGATCGA
AATACCCCTAGGAGGG
Found at i:42321452 original size:28 final size:28
Alignment explanation
Indices: 42321412--42321534 Score: 131
Period size: 28 Copynumber: 4.4 Consensus size: 28
42321402 TACTGCACTG
* **
42321412 CACTGTTACTGTATTGGTTTAAGGCCCA
1 CACTGCTACTGTATTGGGCTAAGGCCCA
*
42321440 CACTGCTACTGTATTGGGCTAAGGCTCA
1 CACTGCTACTGTATTGGGCTAAGGCCCA
*
42321468 CACTGCTACTTTATTGGGCTAAGGCCCA
1 CACTGCTACTGTATTGGGCTAAGGCCCA
** * *
42321496 CACTAATACTGCT-TAGGGCTCAGGCCCA
1 CACTGCTACTG-TATTGGGCTAAGGCCCA
* *
42321524 GACTGTTACTG
1 CACTGCTACTG
42321535 CCTGTCGTAT
Statistics
Matches: 80, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
28 79 0.99
29 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (28 bp):
CACTGCTACTGTATTGGGCTAAGGCCCA
Found at i:42326239 original size:13 final size:13
Alignment explanation
Indices: 42326221--42326248 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
42326211 TAAGGTGTTG
42326221 TGTAATGGATTTT
1 TGTAATGGATTTT
42326234 TGTAATGGATTTT
1 TGTAATGGATTTT
42326247 TG
1 TG
42326249 AGGCAACTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.25, T:0.54
Consensus pattern (13 bp):
TGTAATGGATTTT
Found at i:42327578 original size:27 final size:27
Alignment explanation
Indices: 42327540--42327767 Score: 246
Period size: 27 Copynumber: 8.4 Consensus size: 27
42327530 TATGATTCAT
42327540 GGGTAAAATGACCGAAATACCCTCAAA
1 GGGTAAAATGACCGAAATACCCTCAAA
*
42327567 GGGTAAAATGACCGAAATACCCTCGAA
1 GGGTAAAATGACCGAAATACCCTCAAA
* * **
42327594 GGATAAAATGACCGGAATACCCCTGTAA
1 GGGTAAAATGACCGAAATA-CCCTCAAA
*
42327622 -GGTAAAATGACCGTAATACCCTCAAA
1 GGGTAAAATGACCGAAATACCCTCAAA
** * *
42327648 GGGTAAAATGACTTAAATACCCCCGACA
1 GGGTAAAATGACCGAAATACCCTC-AAA
* * *
42327676 -GGTAAAATAACTGAAATACCCT-AGA
1 GGGTAAAATGACCGAAATACCCTCAAA
* *
42327701 GGGTAAAATAACCGAAATATCCTCAAA
1 GGGTAAAATGACCGAAATACCCTCAAA
* * *
42327728 GGGTAAAATGACCAAAATATCCCCCATA
1 GGGTAAAATGACCGAAATA-CCCTCAAA
42327756 GGGTAAAATGAC
1 GGGTAAAATGAC
42327768 TGTTATACCC
Statistics
Matches: 169, Mismatches: 26, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
25 2 0.01
26 26 0.15
27 116 0.69
28 25 0.15
ACGTcount: A:0.43, C:0.21, G:0.18, T:0.18
Consensus pattern (27 bp):
GGGTAAAATGACCGAAATACCCTCAAA
Found at i:42327682 original size:81 final size:79
Alignment explanation
Indices: 42327541--42327767 Score: 278
Period size: 81 Copynumber: 2.8 Consensus size: 79
42327531 ATGATTCATG
* *
42327541 GGTAAAATGACCGAAATACCCTCAAAGGGTAAAATGACCGAAATACCCTCGAAGGATAAAATGAC
1 GGTAAAATGACCGAAATACCCTCAAAGGGTAAAATGACCAAAATACCCCCGAAGG-TAAAATGAC
*
42327606 CGGAATACCCCT-GTAA
65 CGAAATA-CCCTAG-AA
* ** *
42327622 GGTAAAATGACCGTAATACCCTCAAAGGGTAAAATGACTTAAATACCCCCGACAGGTAAAATAAC
1 GGTAAAATGACCGAAATACCCTCAAAGGGTAAAATGACCAAAATACCCCCGA-AGGTAAAATGAC
* *
42327687 TGAAATACCCTAGAG
65 CGAAATACCCTAGAA
* *
42327702 GGTAAAATAACCGAAATATCCTCAAAGGGTAAAATGACCAAAATATCCCCC-ATAGGGTAAAATG
1 GGTAAAATGACCGAAATACCCTCAAAGGGTAAAATGACCAAAATA-CCCCCGA-A-GGTAAAATG
42327766 AC
63 AC
42327768 TGTTATACCC
Statistics
Matches: 127, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
80 47 0.37
81 77 0.61
82 3 0.02
ACGTcount: A:0.43, C:0.21, G:0.18, T:0.18
Consensus pattern (79 bp):
GGTAAAATGACCGAAATACCCTCAAAGGGTAAAATGACCAAAATACCCCCGAAGGTAAAATGACC
GAAATACCCTAGAA
Found at i:42327960 original size:26 final size:26
Alignment explanation
Indices: 42327925--42327975 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
42327915 GCCACATATA
42327925 CTGTTACTGGCAGCTTCGCTGCGATT
1 CTGTTACTGGCAGCTTCGCTGCGATT
* *
42327951 CTGTTACTGGCAGCTTTGTTGCGAT
1 CTGTTACTGGCAGCTTCGCTGCGAT
42327976 ATTGGTGTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.12, C:0.24, G:0.27, T:0.37
Consensus pattern (26 bp):
CTGTTACTGGCAGCTTCGCTGCGATT
Found at i:42328120 original size:28 final size:28
Alignment explanation
Indices: 42328079--42328137 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
42328069 ACTGCACTGT
* * *
42328079 ACTGTTACTGTATTGGGCTACGGCCCAC
1 ACTGCTACTGTATTGGGCTAAGGCCAAC
*
42328107 ACTGCTACTTTATTGGGCTAAGGCCAAC
1 ACTGCTACTGTATTGGGCTAAGGCCAAC
42328135 ACT
1 ACT
42328138 AATACTGCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (28 bp):
ACTGCTACTGTATTGGGCTAAGGCCAAC
Found at i:42328143 original size:28 final size:28
Alignment explanation
Indices: 42328084--42328144 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
42328074 ACTGTACTGT
* * **
42328084 TACTGTATTGGGCTACGGCCCACACTGC
1 TACTGTATTGGGCTAAGGCCAACACTAA
*
42328112 TACTTTATTGGGCTAAGGCCAACACTAA
1 TACTGTATTGGGCTAAGGCCAACACTAA
42328140 TACTG
1 TACTG
42328145 CTTAGGGCTC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (28 bp):
TACTGTATTGGGCTAAGGCCAACACTAA
Found at i:42356351 original size:9 final size:9
Alignment explanation
Indices: 42356325--42356358 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
42356315 TAATGCTAAT
*
42356325 GCTGGCATG
1 GCTGGCTTG
42356334 GCATGGCTTG
1 GC-TGGCTTG
42356344 GCTGGCTTG
1 GCTGGCTTG
42356353 GCTGGC
1 GCTGGC
42356359 ATGGAGTGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.06, C:0.24, G:0.44, T:0.26
Consensus pattern (9 bp):
GCTGGCTTG
Found at i:42364092 original size:33 final size:33
Alignment explanation
Indices: 42364050--42364114 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
42364040 GTATTATTAT
*
42364050 GTTTAGTTGGTGCTTGGGTTAGCTTTAGATGAA
1 GTTTAGTTGGTGCATGGGTTAGCTTTAGATGAA
42364083 GTTTAGTTGGTGCATGGGTTAGCTTTAGATGA
1 GTTTAGTTGGTGCATGGGTTAGCTTTAGATGA
42364115 TATATATTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.18, C:0.06, G:0.34, T:0.42
Consensus pattern (33 bp):
GTTTAGTTGGTGCATGGGTTAGCTTTAGATGAA
Found at i:42369179 original size:24 final size:24
Alignment explanation
Indices: 42369100--42369180 Score: 78
Period size: 24 Copynumber: 3.4 Consensus size: 24
42369090 TAACACCTAT
*
42369100 TTGGACAACATTAATATGCTAAAAA
1 TTGGACAGCA-TAATATGCTAAAAA
* * * *
42369125 -TGGACAGCAT-TTAAGC-ACTAAT
1 TTGGACAGCATAATATGCTA-AAAA
42369147 TTGGACAGCATAATATGCTAAAAA
1 TTGGACAGCATAATATGCTAAAAA
42369171 TTGGACAGCA
1 TTGGACAGCA
42369181 ATAAACACCA
Statistics
Matches: 43, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
21 1 0.02
22 6 0.14
23 11 0.26
24 24 0.56
25 1 0.02
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (24 bp):
TTGGACAGCATAATATGCTAAAAA
Found at i:42369194 original size:46 final size:48
Alignment explanation
Indices: 42369001--42369200 Score: 202
Period size: 47 Copynumber: 4.2 Consensus size: 48
42368991 AGGCTTAGCA
* *
42369001 CAATTTGGACAGCATTAATATACTAAAAAATGGACAGCAATTAAGCATC
1 CAATTTGGACAGCATTAATATGCTAAAAAATGGACAGCAATTAAACA-C
*
42369050 C--TTTGGA-AGCATT-ATATTGCCTAAAAAAAATGGAC-G-AATTTAACAC
1 CAATTTGGACAGCATTAATA-TG-CT--AAAAAATGGACAGCAATTAAACAC
* * * *
42369096 CTATTTGGACAACATTAATATGCT-AAAAATGGACAGCATTTAAGCAC
1 CAATTTGGACAGCATTAATATGCTAAAAAATGGACAGCAATTAAACAC
* *
42369143 TAATTTGGACAGCA-TAATATGCTAAAAATTGGACAGCAA-TAAACAC
1 CAATTTGGACAGCATTAATATGCTAAAAAATGGACAGCAATTAAACAC
*
42369189 CAATTTAGACAG
1 CAATTTGGACAG
42369201 ATCTTTCATC
Statistics
Matches: 125, Mismatches: 15, Indels: 25
0.76 0.09 0.15
Matches are distributed among these distances:
45 13 0.10
46 35 0.28
47 46 0.37
48 9 0.07
49 19 0.15
50 3 0.02
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.26
Consensus pattern (48 bp):
CAATTTGGACAGCATTAATATGCTAAAAAATGGACAGCAATTAAACAC
Found at i:42373934 original size:40 final size:39
Alignment explanation
Indices: 42373801--42374022 Score: 203
Period size: 40 Copynumber: 5.6 Consensus size: 39
42373791 TCCTCGTTCA
* * * * *
42373801 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
* * *
42373840 CATGCCTTCGGGACGTAACCCGGATTTAACAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
*
42373879 AATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
* * *
42373918 GAATGCCCTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
* ** * * ** *
42373958 AAAGGCCTTC-GGATCTTAGTCCGGATATATTCGCTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCAC
* *
42373999 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
42374023 CAGCATTCAA
Statistics
Matches: 152, Mismatches: 27, Indels: 7
0.82 0.15 0.04
Matches are distributed among these distances:
39 70 0.46
40 74 0.49
41 8 0.05
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
Found at i:42373940 original size:79 final size:79
Alignment explanation
Indices: 42373799--42373969 Score: 218
Period size: 78 Copynumber: 2.2 Consensus size: 79
42373789 GCTCCTCGTT
* * * * *
42373799 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACCATGCCTTCGGGACGTAACCCGGA
1 CAAATGCCTTCGGGACATAACCCGGCTTTAATAACTCACACAATGCCCTCGGGACGTAACCCGGA
42373864 TTTAACAACTCGCA
66 TTTAACAACTCGCA
* * *
42373878 C-AATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACGAATGCCCTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAACCCGGCTTTAATAACTCACAC-AATGCCCTCGGGACGTAACCCGG
** *
42373942 ATTTAGTATCTCGCA
65 ATTTAACAACTCGCA
*
42373957 CAAAGGCCTTCGG
1 CAAATGCCTTCGG
42373970 ATCTTAGTCC
Statistics
Matches: 78, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
78 34 0.44
79 34 0.44
80 10 0.13
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.23
Consensus pattern (79 bp):
CAAATGCCTTCGGGACATAACCCGGCTTTAATAACTCACACAATGCCCTCGGGACGTAACCCGGA
TTTAACAACTCGCA
Found at i:42381793 original size:40 final size:40
Alignment explanation
Indices: 42381702--42381871 Score: 207
Period size: 40 Copynumber: 4.3 Consensus size: 40
42381692 TCCTCGTTCA
* * * * *
42381702 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
42381741 CATGCCTTCGGGACGTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
42381781 AATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * *
42381821 AATGCCCTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
42381861 AAGGCCTTCGG
1 AATGCCTTCGG
42381872 ATCTTAGTCC
Statistics
Matches: 112, Mismatches: 18, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
39 32 0.29
40 80 0.71
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:42385631 original size:10 final size:10
Alignment explanation
Indices: 42385616--42385664 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
42385606 GGGTTAAGAC
42385616 TGAGCTGAAT
1 TGAGCTGAAT
42385626 TGAGCTCGAA-
1 TGAGCT-GAAT
*
42385636 TGAGCTGACT
1 TGAGCTGAAT
* *
42385646 TGAGCTCAAG
1 TGAGCTGAAT
42385656 TGAGCTGAA
1 TGAGCTGAA
42385665 CTAAGTTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 2 0.06
10 27 0.84
11 3 0.09
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (10 bp):
TGAGCTGAAT
Found at i:42385639 original size:20 final size:20
Alignment explanation
Indices: 42385616--42385664 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
42385606 GGGTTAAGAC
42385616 TGAGCTGAATTGAGCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
42385636 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
42385656 TGAGCTGAA
1 TGAGCTGAA
42385665 CTAAGTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:42386596 original size:33 final size:33
Alignment explanation
Indices: 42386528--42386599 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
42386518 TTCAGGAGGC
* * **
42386528 TTACCTTTAGGAGCAGGAAAATAAAGTTCTTTT
1 TTACCTTTAGGAGCAGGAAAACAAAGCTCAGTT
* *
42386561 TTACCTTTTGGAGCAGGGAAACAAAGCTCAGTT
1 TTACCTTTAGGAGCAGGAAAACAAAGCTCAGTT
42386594 TTACCT
1 TTACCT
42386600 GGCTCGATCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (33 bp):
TTACCTTTAGGAGCAGGAAAACAAAGCTCAGTT
Found at i:42390130 original size:20 final size:20
Alignment explanation
Indices: 42390107--42390155 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
42390097 GGGTTAAGAT
*
42390107 TGAGCTGAATTGTGCTCGAA
1 TGAGCTGAATTGAGCTCGAA
* * * *
42390127 TGAGATGACTTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAA
42390147 TGAGCTGAA
1 TGAGCTGAA
42390156 ATAATTTAAA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.27, C:0.12, G:0.33, T:0.29
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:42396029 original size:16 final size:16
Alignment explanation
Indices: 42396008--42396039 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
42395998 CTTTTGTTGC
*
42396008 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
42396024 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
42396040 GTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:42396332 original size:51 final size:51
Alignment explanation
Indices: 42396267--42396457 Score: 217
Period size: 51 Copynumber: 3.8 Consensus size: 51
42396257 CTGGTTCACA
* * *
42396267 TAGTAGCTTGCACATAGTACTACACTCGTGACCATCACTATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGGTACACG
* * * * *
42396318 TAGTAGCCTTCACATAGTACTACACACGTGATCA-AAGCTATCCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCA-CTATCCGGTACACG
*** *
42396369 TAGTAGCCTGCACATAGTACTACACATACGACCTATCATTAT--GGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATCCGGTACACG
* *
42396419 TAGTAGCCTGCATATAATACTACACACGTGACCATCACT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
42396458 TTCACTTTCA
Statistics
Matches: 114, Mismatches: 23, Indels: 8
0.79 0.16 0.06
Matches are distributed among these distances:
49 5 0.04
50 35 0.31
51 69 0.61
52 4 0.04
53 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGGTACACG
Found at i:42396446 original size:101 final size:100
Alignment explanation
Indices: 42396265--42396449 Score: 257
Period size: 101 Copynumber: 1.8 Consensus size: 100
42396255 TACTGGTTCA
* *
42396265 CATAGTAGCTTGCACATAGTACTACACTCGTGACCATCACTATCCGATACACGTAGTAGCCTTCA
1 CATAGTAGCCTGCACATAGTACTACACTCG-GACCATCACTAT-CGATACACGTAGTAGCCTGCA
*
42396330 CATAGTACTACACACGTGATCAAAGCTATCCGGTACG
64 CATAATACTACACACGTGATCAAAGCTATCCGGTACG
* *
42396367 CATAGTAGCCTGCACATAGTACTACACATAC-GACCTATCATTAT-GGTACACGTAGTAGCCTGC
1 CATAGTAGCCTGCACATAGTACTACAC-T-CGGACC-ATCACTATCGATACACGTAGTAGCCTGC
*
42396430 ATATAATACTACACACGTGA
63 ACATAATACTACACACGTGA
42396450 CCATCACTTT
Statistics
Matches: 74, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
101 35 0.47
102 30 0.41
103 8 0.11
104 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (100 bp):
CATAGTAGCCTGCACATAGTACTACACTCGGACCATCACTATCGATACACGTAGTAGCCTGCACA
TAATACTACACACGTGATCAAAGCTATCCGGTACG
Found at i:42402291 original size:11 final size:12
Alignment explanation
Indices: 42402275--42402303 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
42402265 TTTGCATCAA
42402275 AGTTTTT-TAAT
1 AGTTTTTCTAAT
42402286 AGTTTTTCTAAT
1 AGTTTTTCTAAT
42402298 AGTTTT
1 AGTTTT
42402304 AAATGTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.24, C:0.03, G:0.10, T:0.62
Consensus pattern (12 bp):
AGTTTTTCTAAT
Found at i:42403144 original size:36 final size:36
Alignment explanation
Indices: 42403076--42403151 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
42403066 ATGATGGCTA
* *
42403076 ATGTGAAAGTGAAAATGAGGGTGTGTTGTTCATGCC
1 ATGTGAAAGTGAAAATGAGGGTATGTTATTCATGCC
* *
42403112 ATGTGACAGT-AAATATGTGGGTATGTTATTCATGCC
1 ATGTGAAAGTGAAA-ATGAGGGTATGTTATTCATGCC
42403148 ATGT
1 ATGT
42403152 AATAGAGATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 3 0.09
36 32 0.91
ACGTcount: A:0.28, C:0.09, G:0.29, T:0.34
Consensus pattern (36 bp):
ATGTGAAAGTGAAAATGAGGGTATGTTATTCATGCC
Found at i:42423172 original size:21 final size:21
Alignment explanation
Indices: 42423147--42423190 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
42423137 AAAGTGGTTA
42423147 AATTATATTATTTGGTCCTTT
1 AATTATATTATTTGGTCCTTT
42423168 AATTATATTATTTGGTCCTTT
1 AATTATATTATTTGGTCCTTT
42423189 AA
1 AA
42423191 ACTATCTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.09, G:0.09, T:0.55
Consensus pattern (21 bp):
AATTATATTATTTGGTCCTTT
Found at i:42426081 original size:59 final size:58
Alignment explanation
Indices: 42426010--42426216 Score: 206
Period size: 59 Copynumber: 3.5 Consensus size: 58
42426000 TTAATAGAGG
* * *
42426010 TCGCCACGAAGGCTTTCCCTTCAAGGATTTGCAGCAAAGGCATCATTTTCTTTTAGTAC
1 TCGCCACAAAGGCTTTCCCTTCAAAGATTT-TAGCAAAGGCATCATTTTCTTTTAGTAC
* * * *
42426069 TTGCCACAAAGGCTTT-CCTATTAAAGATTTTA-TATGAAGGCATCCTTTTCTTTTAGTAC
1 TCGCCACAAAGGCTTTCCCT-TCAAAGATTTTAGCA--AAGGCATCATTTTCTTTTAGTAC
* * * * *
42426128 TCACTACAAAGGCTTTCCTTTCAGAGATTTTAGACAAAGGCATCATTTTCTTTCAGTAC
1 TCGCCACAAAGGCTTTCCCTTCAAAGATTTTAG-CAAAGGCATCATTTTCTTTTAGTAC
* *
42426187 TGGCCA-AACA-GCTTTCCTTTCAAAGATTTT
1 TCGCCACAA-AGGCTTTCCCTTCAAAGATTTT
42426217 CCACAAAGGC
Statistics
Matches: 121, Mismatches: 20, Indels: 15
0.78 0.13 0.10
Matches are distributed among these distances:
57 1 0.01
58 25 0.21
59 92 0.76
60 2 0.02
61 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (58 bp):
TCGCCACAAAGGCTTTCCCTTCAAAGATTTTAGCAAAGGCATCATTTTCTTTTAGTAC
Found at i:42429909 original size:16 final size:16
Alignment explanation
Indices: 42429888--42429919 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
42429878 GAAGGTTCTA
42429888 CAAATTCCCATAACTT
1 CAAATTCCCATAACTT
*
42429904 CAAATTGCCATAACTT
1 CAAATTCCCATAACTT
42429920 TAATGCTGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.28, G:0.03, T:0.31
Consensus pattern (16 bp):
CAAATTCCCATAACTT
Found at i:42432193 original size:30 final size:32
Alignment explanation
Indices: 42432126--42432210 Score: 97
Period size: 33 Copynumber: 2.7 Consensus size: 32
42432116 AGTAAAAGTC
* *
42432126 TGGGCCTGAGCCCTATT-CAGTAGCAGTACAGTG
1 TGGGCCTTAGCCC-ATTACAGTAACAGTACA-TG
42432159 TGGGCCTTAGCCCATTACAGTAACAGT-C-TG
1 TGGGCCTTAGCCCATTACAGTAACAGTACATG
*
42432189 TGGGCCTTA-CCCAATACAGTAA
1 TGGGCCTTAGCCCATTACAGTAA
42432211 TCAGAACAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
29 12 0.25
30 11 0.23
32 4 0.08
33 21 0.44
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.25
Consensus pattern (32 bp):
TGGGCCTTAGCCCATTACAGTAACAGTACATG
Found at i:42432375 original size:26 final size:26
Alignment explanation
Indices: 42432346--42432397 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
42432336 AGTAATAATG
*
42432346 ACGCAGCAAAGCTGCCAATAACAGTA
1 ACGCAACAAAGCTGCCAATAACAGTA
*
42432372 ACGCAACAAAGCTGCCAGTAACAGTA
1 ACGCAACAAAGCTGCCAATAACAGTA
42432398 TATGTGGCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.42, C:0.27, G:0.19, T:0.12
Consensus pattern (26 bp):
ACGCAACAAAGCTGCCAATAACAGTA
Found at i:42432591 original size:27 final size:26
Alignment explanation
Indices: 42432557--42432928 Score: 183
Period size: 27 Copynumber: 13.9 Consensus size: 26
42432547 CATTTCCACT
**
42432557 CCTT-GGGGTATAACAATCATTTTAC
1 CCTTGGGGGTATTTCAATCATTTTAC
* *
42432582 CCTATGGGGGTATTTTAGTCATTTTAC
1 CCT-TGGGGGTATTTCAATCATTTTAC
* * *
42432609 CATTTAGGGGTATTTCGATCATTTTAC
1 C-CTTGGGGGTATTTCAATCATTTTAC
*
42432636 CCTTCGGGGGTATTTCGATCATTTTAC
1 CCTT-GGGGGTATTTCAATCATTTTAC
* * *
42432663 CCTTCGAGAGTATTTCAACCATTTTAC
1 CCTT-GGGGGTATTTCAATCATTTTAC
** * *
42432690 CCTTCAAGGGTATTTTAGTCA-TTTAC
1 CCTT-GGGGGTATTTCAATCATTTTAC
*** *
42432716 CCATCAAGGGTATTTCGATCATTTTAC
1 CC-TTGGGGGTATTTCAATCATTTTAC
**** *
42432743 CCATCAAAGGTATTTCGATCATTTTAC
1 CC-TTGGGGGTATTTCAATCATTTTAC
* * ***
42432770 CCTTCAGGGGCATTTTGGTCATTTTAC
1 CCTT-GGGGGTATTTCAATCATTTTAC
* * * *
42432797 CCTTCAGGGGTATTTCGATCACTTTGC
1 CCTT-GGGGGTATTTCAATCATTTTAC
* * *
42432824 CCTTCGGGGGTATTTTATTTATTTTAC
1 CCTT-GGGGGTATTTCAATCATTTTAC
* * * **
42432851 CTTTCAGGTGTATTTCGGTCATTTTAC
1 CCTT-GGGGGTATTTCAATCATTTTAC
** *
42432878 CCTGTGGGGGTAATTT-GGTCATTTTAT
1 CCT-TGGGGGT-ATTTCAATCATTTTAC
* *
42432905 CCTATGGGGGTAATTCGATCATTT
1 CCT-TGGGGGTATTTCAATCATTT
42432929 ATTGGCCTCG
Statistics
Matches: 280, Mismatches: 57, Indels: 18
0.79 0.16 0.05
Matches are distributed among these distances:
25 3 0.01
26 27 0.10
27 244 0.87
28 6 0.02
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.41
Consensus pattern (26 bp):
CCTTGGGGGTATTTCAATCATTTTAC
Found at i:42432722 original size:26 final size:28
Alignment explanation
Indices: 42432572--42432880 Score: 243
Period size: 27 Copynumber: 11.5 Consensus size: 28
42432562 GGGTATAACA
** *
42432572 ATCATTTTACCCTAT-GGGGGTATTTTAG
1 ATCATTTTACCCT-TCAAGGGTATTTTCG
* * *
42432600 -TCATTTTACCATTTAGGGGTA-TTTCG
1 ATCATTTTACCCTTCAAGGGTATTTTCG
**
42432626 ATCATTTTACCCTTCGGGGGTA-TTTCG
1 ATCATTTTACCCTTCAAGGGTATTTTCG
* * *
42432653 ATCATTTTACCCTTCGAGAGTA-TTTCA
1 ATCATTTTACCCTTCAAGGGTATTTTCG
* *
42432680 ACCATTTTACCCTTCAAGGGTATTTTAG
1 ATCATTTTACCCTTCAAGGGTATTTTCG
*
42432708 -TCA-TTTACCCATCAAGGGTA-TTTCG
1 ATCATTTTACCCTTCAAGGGTATTTTCG
* *
42432733 ATCATTTTACCCATCAAAGGTA-TTTCG
1 ATCATTTTACCCTTCAAGGGTATTTTCG
* *
42432760 ATCATTTTACCCTTCAGGGGCATTTT-G
1 ATCATTTTACCCTTCAAGGGTATTTTCG
* *
42432787 GTCATTTTACCCTTCAGGGGTA-TTTCG
1 ATCATTTTACCCTTCAAGGGTATTTTCG
* * **
42432814 ATCACTTTGCCCTTCGGGGGTATTTT--
1 ATCATTTTACCCTTCAAGGGTATTTTCG
* *
42432840 ATTTATTTTACCTTTC-AGGTGTA-TTTCG
1 A-TCATTTTACCCTTCAAGG-GTATTTTCG
*
42432868 GTCATTTTACCCT
1 ATCATTTTACCCT
42432881 GTGGGGGTAA
Statistics
Matches: 233, Mismatches: 36, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
25 4 0.02
26 33 0.14
27 187 0.80
28 9 0.04
ACGTcount: A:0.20, C:0.21, G:0.17, T:0.42
Consensus pattern (28 bp):
ATCATTTTACCCTTCAAGGGTATTTTCG
Found at i:42432756 original size:80 final size:81
Alignment explanation
Indices: 42432627--42432817 Score: 251
Period size: 80 Copynumber: 2.4 Consensus size: 81
42432617 GGTATTTCGA
* ** * *
42432627 TCATTTTACCCTTCGGGGGTATTTCGATCATTTTACCCTTCGAGAGTATTTCAACCATTTTACCC
1 TCATTTTACCCATCAAGGGTATTTCGATCATTTTACCCATCAAGAGTATTTCAACCATTTTACCC
*
42432692 TTCAAGGGTATTTTAG
66 TTCAAGGGCATTTTAG
* *
42432708 TCA-TTTACCCATCAAGGGTATTTCGATCATTTTACCCATCAA-AGGTATTTCGATCATTTTACC
1 TCATTTTACCCATCAAGGGTATTTCGATCATTTTACCCATCAAGA-GTATTTCAACCATTTTACC
* *
42432771 CTTCAGGGGCATTTTGG
65 CTTCAAGGGCATTTTAG
* *
42432788 TCATTTTACCCTTCAGGGGTATTTCGATCA
1 TCATTTTACCCATCAAGGGTATTTCGATCA
42432818 CTTTGCCCTT
Statistics
Matches: 96, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
79 1 0.01
80 68 0.71
81 27 0.28
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.39
Consensus pattern (81 bp):
TCATTTTACCCATCAAGGGTATTTCGATCATTTTACCCATCAAGAGTATTTCAACCATTTTACCC
TTCAAGGGCATTTTAG
Found at i:42432793 original size:107 final size:108
Alignment explanation
Indices: 42432589--42432811 Score: 290
Period size: 107 Copynumber: 2.1 Consensus size: 108
42432579 TACCCTATGG
* * * ***
42432589 GGGTATTTTAGTCATTTTACCATTTAGGGGTATTTCGATCATTTTACCCTTCGGGGGTATTTCGA
1 GGGTATTTTAGTCATTTTACCATTCAAGGGTATTTCGATCATTTTACCCATCAAAGGTATTTCGA
*
42432654 TCATTTTACCCTTCGAGAGTATTTCAACCATTTTACCCTTCAA
66 TCATTTTACCCTTCGAGAGCATTTCAACCATTTTACCCTTCAA
42432697 GGGTATTTTAGTCA-TTTACCCA-TCAAGGGTATTTCGATCATTTTACCCATCAAAGGTATTTCG
1 GGGTATTTTAGTCATTTTA-CCATTCAAGGGTATTTCGATCATTTTACCCATCAAAGGTATTTCG
* **** *
42432760 ATCATTTTACCCTTC-AGGGGCATTTTGGTCATTTTACCCTTCAG
65 ATCATTTTACCCTTCGA-GAGCATTTCAACCATTTTACCCTTCAA
42432804 GGGTATTT
1 GGGTATTT
42432812 CGATCACTTT
Statistics
Matches: 100, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
106 1 0.01
107 82 0.82
108 17 0.17
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.41
Consensus pattern (108 bp):
GGGTATTTTAGTCATTTTACCATTCAAGGGTATTTCGATCATTTTACCCATCAAAGGTATTTCGA
TCATTTTACCCTTCGAGAGCATTTCAACCATTTTACCCTTCAA
Found at i:42432812 original size:54 final size:54
Alignment explanation
Indices: 42432572--42432928 Score: 300
Period size: 54 Copynumber: 6.6 Consensus size: 54
42432562 GGGTATAACA
* * * *
42432572 ATCATTTTACCCTAT-GGGGGTATTT-TAGTCATTTTACCATTTAGGGGTATTTCG
1 ATCATTTTACCCT-TCAGGGGTATTTCGA-TCATTTTACCCTTCAGGGGTATTTCG
* * *
42432626 ATCATTTTACCCTTCGGGGGTATTTCGATCATTTTACCCTTC-GAGAGTATTTCA
1 ATCATTTTACCCTTCAGGGGTATTTCGATCATTTTACCCTTCAG-GGGTATTTCG
* * * * *
42432680 ACCATTTTACCCTTCAAGGGTATTT-TAGTCA-TTTACCCATCAAGGGTATTTCG
1 ATCATTTTACCCTTCAGGGGTATTTCGA-TCATTTTACCCTTCAGGGGTATTTCG
* ** * *
42432733 ATCATTTTACCCATCAAAGGTATTTCGATCATTTTACCCTTCAGGGGCATTTTG
1 ATCATTTTACCCTTCAGGGGTATTTCGATCATTTTACCCTTCAGGGGTATTTCG
* * * * *
42432787 GTCATTTTACCCTTCAGGGGTATTTCGATCACTTTGCCCTTCGGGGGTATTT-T
1 ATCATTTTACCCTTCAGGGGTATTTCGATCATTTTACCCTTCAGGGGTATTTCG
* * * * *
42432840 ATTTATTTTACCTTTCAGGTGTATTTCGGTCATTTTACCCTGT-GGGGGTAATTT-G
1 A-TCATTTTACCCTTCAGGGGTATTTCGATCATTTTACCCT-TCAGGGGT-ATTTCG
* * * *
42432895 GTCATTTTATCCTAT-GGGGGTAATTCGATCATTT
1 ATCATTTTACCCT-TCAGGGGTATTTCGATCATTT
42432929 ATTGGCCTCG
Statistics
Matches: 246, Mismatches: 46, Indels: 22
0.78 0.15 0.07
Matches are distributed among these distances:
53 45 0.18
54 194 0.79
55 7 0.03
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.42
Consensus pattern (54 bp):
ATCATTTTACCCTTCAGGGGTATTTCGATCATTTTACCCTTCAGGGGTATTTCG
Found at i:42432889 original size:81 final size:80
Alignment explanation
Indices: 42432572--42432880 Score: 334
Period size: 81 Copynumber: 3.8 Consensus size: 80
42432562 GGGTATAACA
* * * *
42432572 ATCATTTTACCCTAT-GGGGGTATTTTAGTCATTTTACCATTTAGGGGTATTTCGATCATTTTAC
1 ATCATTTTACCCT-TCGAGGGTATTTTA-TCATTTTACCCTTCAGGGGTATTTCGGTCATTTTAC
*
42432636 CCTTCGGGGGTATTTCG
64 CCTTCAGGGGTATTTCG
* * * * **
42432653 ATCATTTTACCCTTCGAGAGTATTTCAACCATTTTACCCTTCAAGGGTATTTTAGTCA-TTTACC
1 ATCATTTTACCCTTCGAGGGTATTT-TATCATTTTACCCTTCAGGGGTATTTCGGTCATTTTACC
* *
42432717 CATCAAGGGTATTTCG
65 CTTCAGGGGTATTTCG
* * * * * *
42432733 ATCATTTTACCCATCAAAGGTATTTCGATCATTTTACCCTTCAGGGGCATTTTGGTCATTTTACC
1 ATCATTTTACCCTTCGAGGGTATTT-TATCATTTTACCCTTCAGGGGTATTTCGGTCATTTTACC
42432798 CTTCAGGGGTATTTCG
65 CTTCAGGGGTATTTCG
* * * * * *
42432814 ATCACTTTGCCCTTCGGGGGTATTTTATTTATTTTACCTTTCAGGTGTATTTCGGTCATTTTACC
1 ATCATTTTACCCTTCGAGGGTATTTTA-TCATTTTACCCTTCAGGGGTATTTCGGTCATTTTACC
42432879 CT
65 CT
42432881 GTGGGGGTAA
Statistics
Matches: 188, Mismatches: 36, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
80 70 0.37
81 117 0.62
82 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.17, T:0.42
Consensus pattern (80 bp):
ATCATTTTACCCTTCGAGGGTATTTTATCATTTTACCCTTCAGGGGTATTTCGGTCATTTTACCC
TTCAGGGGTATTTCG
Found at i:42435245 original size:28 final size:28
Alignment explanation
Indices: 42435167--42435262 Score: 113
Period size: 28 Copynumber: 3.4 Consensus size: 28
42435157 TATTCAGTAG
* * *
42435167 CAGT-ACAATGTGGGCCTTAGCACATTA
1 CAGTAACAGTGTGGGCCTTAGCCCAATA
* *
42435194 CAGCAATAGTCTGTGGGCCTTAGCCCAATA
1 CAGTAACAG--TGTGGGCCTTAGCCCAATA
42435224 CAGTAACAGTGTGGGCCTTAGCCCAATA
1 CAGTAACAGTGTGGGCCTTAGCCCAATA
42435252 CAGTAATCAGT
1 CAGTAA-CAGT
42435263 ACAATGCAGT
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
27 3 0.05
28 27 0.47
29 4 0.07
30 24 0.41
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (28 bp):
CAGTAACAGTGTGGGCCTTAGCCCAATA
Found at i:42435402 original size:26 final size:26
Alignment explanation
Indices: 42435373--42435440 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 26
42435363 ATATCGCAAT
* *
42435373 AAAGCTACAAGTAATAATGACGCAGC
1 AAAGCTACAAGTAACAATAACGCAGC
* * *
42435399 AAAGCTGCCAGTAACAGTAACGCAGC
1 AAAGCTACAAGTAACAATAACGCAGC
* *
42435425 AAAGCTGCTAGTAACA
1 AAAGCTACAAGTAACA
42435441 GTATATGTGG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.43, C:0.22, G:0.21, T:0.15
Consensus pattern (26 bp):
AAAGCTACAAGTAACAATAACGCAGC
Found at i:42435441 original size:26 final size:26
Alignment explanation
Indices: 42435392--42435443 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
42435382 AGTAATAATG
42435392 ACGCAGCAAAGCTGCCAGTAACAGTA
1 ACGCAGCAAAGCTGCCAGTAACAGTA
*
42435418 ACGCAGCAAAGCTGCTAGTAACAGTA
1 ACGCAGCAAAGCTGCCAGTAACAGTA
42435444 TATGTGGCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.25, G:0.23, T:0.13
Consensus pattern (26 bp):
ACGCAGCAAAGCTGCCAGTAACAGTA
Found at i:42435606 original size:27 final size:27
Alignment explanation
Indices: 42435576--42435635 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
42435566 CCACTCCTAA
*
42435576 GGGTATAACAATCATTTTACCCTATGG
1 GGGTATAACAATCATTTTACCCTATAG
*** * *
42435603 GGGTATTTTAGTCATTTTACCCTTTAG
1 GGGTATAACAATCATTTTACCCTATAG
42435630 GGGTAT
1 GGGTAT
42435636 TTCGATCATT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.40
Consensus pattern (27 bp):
GGGTATAACAATCATTTTACCCTATAG
Found at i:42435636 original size:27 final size:27
Alignment explanation
Indices: 42435586--42435700 Score: 119
Period size: 27 Copynumber: 4.3 Consensus size: 27
42435576 GGGTATAACA
* * *
42435586 ATCATTTTACCCTATGGGGGTATTT-T
1 ATCATTTTACCCTTTAGGGGTATTTCG
42435612 AGTCATTTTACCCTTTAGGGGTATTTCG
1 A-TCATTTTACCCTTTAGGGGTATTTCG
*
42435640 ATCATTTTA-TCTTTCAGGGGTATTTCG
1 ATCATTTTACCCTTT-AGGGGTATTTCG
* *
42435667 ATAATTTTACCCTTT-GGTAGTATTTCG
1 ATCATTTTACCCTTTAGG-GGTATTTCG
*
42435694 GTCATTT
1 ATCATTT
42435701 AAATTTGACC
Statistics
Matches: 75, Mismatches: 9, Indels: 9
0.81 0.10 0.10
Matches are distributed among these distances:
26 7 0.09
27 63 0.84
28 5 0.07
ACGTcount: A:0.19, C:0.16, G:0.18, T:0.47
Consensus pattern (27 bp):
ATCATTTTACCCTTTAGGGGTATTTCG
Found at i:42436290 original size:41 final size:41
Alignment explanation
Indices: 42436233--42436516 Score: 304
Period size: 41 Copynumber: 7.0 Consensus size: 41
42436223 GTACATCCAG
* *
42436233 GGGTACCGAAGTACAAACAGGGGCACGTCTGTGCATTTCAA
1 GGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATTCAA
* * * * *
42436274 GGGTATCGGAGTACAAACAGGGGCACCTAAGTGCATTTCAA
1 GGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATTCAA
* * *
42436315 GGGTATCGAAGTACAAACAGGGGCAGGTATGTGTAATTCAA
1 GGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATTCAA
* * * *
42436356 GGGTACCAAAATACAAACAGGGGCATGTATGTGCAATTCAG
1 GGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATTCAA
* * * * *
42436397 GGGTACTGAAGTACAAACAAGGGCATGTATGTGTAATTCAG
1 GGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATTCAA
* * * *
42436438 GGGTACCAAAGTTC-AACAGGGGCACGTATGTGCAATGCAG
1 GGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATTCAA
* * *
42436478 GGGTACTGAAGTGCAATA-A-GGGCACGTATGTGTAATTCA
1 GGGTACCGAAGTACAA-ACAGGGGCACGTATGTGCAATTCA
42436517 TCATTATTCG
Statistics
Matches: 207, Mismatches: 34, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
40 51 0.25
41 155 0.75
42 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.21
Consensus pattern (41 bp):
GGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATTCAA
Found at i:42436371 original size:82 final size:82
Alignment explanation
Indices: 42436230--42436516 Score: 348
Period size: 82 Copynumber: 3.5 Consensus size: 82
42436220 AATGTACATC
* * * * * **
42436230 CAGGGGTACCGAAGTACAAACAGGGGCACGTCTGTGCATTTCAAGGGTATCGGAGTACAAACAGG
1 CAGGGGTACTGAAGTACAAACAGGGGCACGTATGTGTAATTCAAGGGTACCAAAGTACAAACAGG
* * *
42436295 GGCACCTAAGTGCATTT
66 GGCACGTATGTGCAATT
* * *
42436312 CAAGGGTA-TCGAAGTACAAACAGGGGCAGGTATGTGTAATTCAAGGGTACCAAAATACAAACAG
1 CAGGGGTACT-GAAGTACAAACAGGGGCACGTATGTGTAATTCAAGGGTACCAAAGTACAAACAG
*
42436376 GGGCATGTATGTGCAATT
65 GGGCACGTATGTGCAATT
* * * *
42436394 CAGGGGTACTGAAGTACAAACAAGGGCATGTATGTGTAATTCAGGGGTACCAAAGTTC-AACAGG
1 CAGGGGTACTGAAGTACAAACAGGGGCACGTATGTGTAATTCAAGGGTACCAAAGTACAAACAGG
*
42436458 GGCACGTATGTGCAATG
66 GGCACGTATGTGCAATT
*
42436475 CAGGGGTACTGAAGTGCAATA-A-GGGCACGTATGTGTAATTCA
1 CAGGGGTACTGAAGTACAA-ACAGGGGCACGTATGTGTAATTCA
42436517 TCATTATTCG
Statistics
Matches: 178, Mismatches: 24, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
80 19 0.11
81 40 0.22
82 118 0.66
83 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.21
Consensus pattern (82 bp):
CAGGGGTACTGAAGTACAAACAGGGGCACGTATGTGTAATTCAAGGGTACCAAAGTACAAACAGG
GGCACGTATGTGCAATT
Found at i:42436399 original size:21 final size:21
Alignment explanation
Indices: 42436373--42436440 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
42436363 AAAATACAAA
42436373 CAGGGGCATGTATGTGCAATT
1 CAGGGGCATGTATGTGCAATT
* * * *
42436394 CAGGGGTACTG-AAGTACAA-A
1 CAGGGGCA-TGTATGTGCAATT
* *
42436414 CAAGGGCATGTATGTGTAATT
1 CAGGGGCATGTATGTGCAATT
42436435 CAGGGG
1 CAGGGG
42436441 TACCAAAGTT
Statistics
Matches: 33, Mismatches: 11, Indels: 6
0.66 0.22 0.12
Matches are distributed among these distances:
19 2 0.06
20 11 0.33
21 18 0.55
22 2 0.06
ACGTcount: A:0.29, C:0.13, G:0.34, T:0.24
Consensus pattern (21 bp):
CAGGGGCATGTATGTGCAATT
Found at i:42436480 original size:21 final size:20
Alignment explanation
Indices: 42436373--42436509 Score: 57
Period size: 21 Copynumber: 6.8 Consensus size: 20
42436363 AAAATACAAA
*
42436373 CAGGGGCATGTATGTGCAATT
1 CAGGGGCACGTATGTGCAA-T
* * * *
42436394 CAGGGGTAC-TGAAGTACAAA
1 CAGGGGCACGT-ATGTGCAAT
* * *
42436414 CAAGGGCATGTATGTGTAATT
1 CAGGGGCACGTATGTGCAA-T
* ** * *
42436435 CAGGGGTACCAAAGTTCAA-
1 CAGGGGCACGTATGTGCAAT
42436454 CAGGGGCACGTATGTGCAAT
1 CAGGGGCACGTATGTGCAAT
* *
42436474 GCAGGGGTAC-TGAAGTGCAAT
1 -CAGGGGCACGT-ATGTGCAAT
*
42436495 -AAGGGCACGTATGTG
1 CAGGGGCACGTATGTG
42436510 TAATTCATCA
Statistics
Matches: 79, Mismatches: 30, Indels: 16
0.63 0.24 0.13
Matches are distributed among these distances:
19 24 0.30
20 14 0.18
21 41 0.52
ACGTcount: A:0.30, C:0.15, G:0.33, T:0.22
Consensus pattern (20 bp):
CAGGGGCACGTATGTGCAAT
Found at i:42440078 original size:20 final size:20
Alignment explanation
Indices: 42439984--42440085 Score: 89
Period size: 20 Copynumber: 5.1 Consensus size: 20
42439974 TTGTACGGGA
* *
42439984 TTTGCACTTCGGTGCCTCTG
1 TTTGCACTTTGGTGCCCCTG
*
42440004 TTTGCACTTTGGTGCCCCTA
1 TTTGCACTTTGGTGCCCCTG
* * * *
42440024 TATACATTTTGGTGTCCCTG
1 TTTGCACTTTGGTGCCCCTG
**
42440044 TTTATACATTT-GTGCCCCTG
1 TTTGCAC-TTTGGTGCCCCTG
* *
42440064 TCTGCACTTTGGTGCCACTG
1 TTTGCACTTTGGTGCCCCTG
42440084 TT
1 TT
42440086 ATACATCTAT
Statistics
Matches: 63, Mismatches: 17, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
19 3 0.05
20 57 0.90
21 3 0.05
ACGTcount: A:0.11, C:0.26, G:0.21, T:0.42
Consensus pattern (20 bp):
TTTGCACTTTGGTGCCCCTG
Found at i:42458022 original size:91 final size:90
Alignment explanation
Indices: 42457847--42458040 Score: 264
Period size: 91 Copynumber: 2.1 Consensus size: 90
42457837 GATGGCTGAG
*
42457847 GTCGCGACATCGAGGTACGATGTCGCAACGCACCTTGCATTTTCAAATTCCTGGAAAACTATCTA
1 GTCGCGACATCGAGGTACGATGTCGCAACACACCTTGCATTTTCAAATTCCTGGAAAACTATCTA
* *
42457912 CCATGTCGCGACATAGGATAGTGGT
66 CCACGTCGCGACACAGGATAGTGGT
* ** * * *
42457937 GTCGTGACATC-AGGGTACGATGTTTCAACACACCTTGCATTTTTCAAATTCTTGGGAAACTGTC
1 GTCGCGACATCGA-GGTACGATGTCGCAACACACCTTGCA-TTTTCAAATTCCTGGAAAACTATC
*
42458001 TACCACGTCGTGACACAGGATAGTGGT
64 TACCACGTCGCGACACAGGATAGTGGT
*
42458028 GTTGCGACATCGA
1 GTCGCGACATCGA
42458041 TGTGATTTTG
Statistics
Matches: 89, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
89 1 0.01
90 33 0.37
91 54 0.61
92 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (90 bp):
GTCGCGACATCGAGGTACGATGTCGCAACACACCTTGCATTTTCAAATTCCTGGAAAACTATCTA
CCACGTCGCGACACAGGATAGTGGT
Found at i:42464267 original size:20 final size:21
Alignment explanation
Indices: 42464239--42464277 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
42464229 TAAATTCCAA
42464239 TTTAACCAAAAA-TATTTATT
1 TTTAACCAAAAATTATTTATT
*
42464259 TTTACCCAAAAATTATTTA
1 TTTAACCAAAAATTATTTA
42464278 AAACCATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.44
Consensus pattern (21 bp):
TTTAACCAAAAATTATTTATT
Found at i:42468970 original size:56 final size:56
Alignment explanation
Indices: 42468884--42469003 Score: 222
Period size: 56 Copynumber: 2.1 Consensus size: 56
42468874 ACAAGGGATG
42468884 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
* *
42468940 ATGGGTAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
42468996 ATGGGCAA
1 ATGGGCAA
42469004 TAAACTAATA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 61 1.00
ACGTcount: A:0.45, C:0.08, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:42480941 original size:27 final size:27
Alignment explanation
Indices: 42480911--42481088 Score: 171
Period size: 27 Copynumber: 6.6 Consensus size: 27
42480901 ATATTGAGCC
* *
42480911 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
42480938 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
42480965 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
42480993 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* * **
42481020 TGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
42481047 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
42481074 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42481089 GTACAATTTA
Statistics
Matches: 127, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
27 102 0.80
28 25 0.20
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:42489063 original size:27 final size:27
Alignment explanation
Indices: 42489033--42489210 Score: 171
Period size: 27 Copynumber: 6.6 Consensus size: 27
42489023 ATATTGAGCC
* *
42489033 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
42489060 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
42489087 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
42489115 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* * **
42489142 TGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
42489169 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
42489196 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42489211 GTACAATTTA
Statistics
Matches: 127, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
27 102 0.80
28 25 0.20
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:42518045 original size:25 final size:26
Alignment explanation
Indices: 42518017--42518085 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 26
42518007 GCTATAAACG
42518017 GTAAGCC-CATACAAGCTGAACATCA
1 GTAAGCCTCATACAAGCTGAACATCA
* * *
42518042 GTAA-CCTCATGCGAGCTGAACATCG
1 GTAAGCCTCATACAAGCTGAACATCA
42518067 GTAAGCTCTC-T-CAAGCTGA
1 GTAAGC-CTCATACAAGCTGA
42518086 GAATAGGTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
24 2 0.05
25 30 0.81
26 2 0.05
27 3 0.08
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.20
Consensus pattern (26 bp):
GTAAGCCTCATACAAGCTGAACATCA
Found at i:42525173 original size:25 final size:25
Alignment explanation
Indices: 42525114--42525177 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 25
42525104 AAATGATAAA
*
42525114 CTCATTCGAGCTGAATATCAGTAAG
1 CTCATTCGAGCTAAATATCAGTAAG
*
42525139 CTCATGCGAGCTAAATATCAGTAAG
1 CTCATTCGAGCTAAATATCAGTAAG
42525164 CTC-TCTCGAGCTAA
1 CTCAT-TCGAGCTAA
42525178 GAATCGGTAC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
24 1 0.03
25 34 0.97
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (25 bp):
CTCATTCGAGCTAAATATCAGTAAG
Found at i:42539163 original size:4 final size:4
Alignment explanation
Indices: 42539156--42539184 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
42539146 AAAAATTAAA
42539156 AAAG AAAG AAAG AAAG AAA- AAAG AAAG AA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AA
42539185 GAACGCACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:42544809 original size:39 final size:38
Alignment explanation
Indices: 42544734--42544811 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 38
42544724 CTAACACTCA
* * *
42544734 CGCCAACTAGTTAGTAACTAACATACCCTGCTAGTGGC
1 CGCCAACTAGTTAATAACTAACATACCCTACAAGTGGC
* **
42544772 CGCCAAACTATTTAATAACTAACATGTCCTACAAGTGGC
1 CGCC-AACTAGTTAATAACTAACATACCCTACAAGTGGC
42544811 C
1 C
42544812 CATCATATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
38 4 0.12
39 29 0.88
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.24
Consensus pattern (38 bp):
CGCCAACTAGTTAATAACTAACATACCCTACAAGTGGC
Found at i:42544901 original size:14 final size:14
Alignment explanation
Indices: 42544882--42544910 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
42544872 GATACCGAGC
42544882 ACATACCCCTAAGT
1 ACATACCCCTAAGT
42544896 ACATACCCCTAAGT
1 ACATACCCCTAAGT
42544910 A
1 A
42544911 AATCATATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.34, G:0.07, T:0.21
Consensus pattern (14 bp):
ACATACCCCTAAGT
Found at i:42549765 original size:25 final size:25
Alignment explanation
Indices: 42549731--42549822 Score: 89
Period size: 25 Copynumber: 3.7 Consensus size: 25
42549721 TCCTGTACAT
*
42549731 GTATTCTCACACGAGCTATGAAA-CG
1 GTATGCTCACACGAGCTAT-AAATCG
* *
42549756 GTATGCTCACACGAGCTGTAAATTG
1 GTATGCTCACACGAGCTATAAATCG
* * *
42549781 GTTTGCTCACACGAGCTGTAAATCA
1 GTATGCTCACACGAGCTATAAATCG
*
42549806 GT-TAGCTCACATGAGCT
1 GTAT-GCTCACACGAGCT
42549823 GTGGAAATGG
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
24 4 0.07
25 54 0.93
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (25 bp):
GTATGCTCACACGAGCTATAAATCG
Found at i:42549823 original size:25 final size:25
Alignment explanation
Indices: 42549760--42549824 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 25
42549750 GAAACGGTAT
** *
42549760 GCTCACACGAGCTGTAAATTGGTTT
1 GCTCACACGAGCTGTAAATCAGTTA
42549785 GCTCACACGAGCTGTAAATCAGTTA
1 GCTCACACGAGCTGTAAATCAGTTA
*
42549810 GCTCACATGAGCTGT
1 GCTCACACGAGCTGT
42549825 GGAAATGGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (25 bp):
GCTCACACGAGCTGTAAATCAGTTA
Found at i:42551090 original size:25 final size:25
Alignment explanation
Indices: 42551059--42551116 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
42551049 GCTGTAAACA
* *
42551059 GTAAGCTCATACGAGCTAAATATCG
1 GTAAGCTCATACAAGCTAAATACCG
*
42551084 GTAAGCTCATGCAAGCTAAATACCG
1 GTAAGCTCATACAAGCTAAATACCG
*
42551109 ATAAGCTC
1 GTAAGCTC
42551117 TCTCGAGTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.22
Consensus pattern (25 bp):
GTAAGCTCATACAAGCTAAATACCG
Found at i:42551545 original size:8 final size:8
Alignment explanation
Indices: 42551532--42551557 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
42551522 ACCCATATTT
42551532 TTCACAAA
1 TTCACAAA
42551540 TTCACAAA
1 TTCACAAA
42551548 TTCACAAA
1 TTCACAAA
42551556 TT
1 TT
42551558 TACCACATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (8 bp):
TTCACAAA
Found at i:42555881 original size:29 final size:29
Alignment explanation
Indices: 42555837--42555893 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
42555827 AGCCCCATGA
* * *
42555837 CAAGTGGTATCCGAGTTGTTGGTTCGAAC
1 CAAGTGATATCCGAGTTATTGATTCGAAC
*
42555866 CAAGTGATATCTGAGTTATTGATTCGAA
1 CAAGTGATATCCGAGTTATTGATTCGAA
42555894 TGCACAGTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.33
Consensus pattern (29 bp):
CAAGTGATATCCGAGTTATTGATTCGAAC
Found at i:42560054 original size:14 final size:14
Alignment explanation
Indices: 42560033--42560068 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
42560023 TCCAACAAAG
42560033 AACA-TCCTACAAT
1 AACATTCCTACAAT
*
42560046 AACATTCCTCCAAT
1 AACATTCCTACAAT
42560060 AACATTCCT
1 AACATTCCT
42560069 GGGCACCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.39, C:0.33, G:0.00, T:0.28
Consensus pattern (14 bp):
AACATTCCTACAAT
Found at i:42563712 original size:39 final size:38
Alignment explanation
Indices: 42563663--42563762 Score: 128
Period size: 39 Copynumber: 2.6 Consensus size: 38
42563653 CGAATATAAT
* *
42563663 AATTATAATTACCATAATTATAATAACGCTTGACCGAAA
1 AATTATAATTACAATAATTATAATAACACTTGACCG-AA
* * * * *
42563702 AATTACAATTACAATAATTATAATAATATTTGATCGTA
1 AATTATAATTACAATAATTATAATAACACTTGACCGAA
42563740 AATTATAATTACAATAATTATAA
1 AATTATAATTACAATAATTATAA
42563763 CAAGGATTTC
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
38 23 0.43
39 30 0.57
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.36
Consensus pattern (38 bp):
AATTATAATTACAATAATTATAATAACACTTGACCGAA
Found at i:42570772 original size:23 final size:22
Alignment explanation
Indices: 42570721--42570772 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
42570711 CCTCGTCTTT
*
42570721 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
42570743 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
42570766 TTCTTTT
1 TTCTTTT
42570773 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:42572593 original size:40 final size:40
Alignment explanation
Indices: 42572548--42573212 Score: 1093
Period size: 40 Copynumber: 16.6 Consensus size: 40
42572538 CAAGCTCAAT
* * * * *
42572548 TGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACGAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
*
42572588 TGCCTTCGGGTCTTAGCCCGGATATATCAACTT-GCACAAT
1 TGCCTTCGGGTCTTAGCCCGGATATATCAA-TTCGCACAAA
42572628 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
* * *
42572668 CGCCGTCGGGTCTTAGCCCGGATATATCAGTTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
*
42572708 TGCCTTCGGGTCTTATCCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
* *
42572748 TGCCTTCGGGTCTTATCCCGGATATATCAAATCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
42572788 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
* *
42572828 TGCCTTCAGGTCTTAGCCCGGATATATCAACTT-GCACAAT
1 TGCCTTCGGGTCTTAGCCCGGATATATCAA-TTCGCACAAA
42572868 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
* * *
42572908 CGCCGTCGGGTCTTAGCCCGGATATATCAGTTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
*
42572948 TGCCTTCGGGTCTTATCCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
*
42572988 TGCCTTCGGGTCTTATCCCGGATATATCCAA-TCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATAT-CAATTCGCACAAA
42573028 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
*
42573068 TGCCTTCAGGTCTTAGCCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
*
42573108 TGCCTTCGGGTCTTATCCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
42573148 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
42573188 TGCCTTCGGGTCTTAGCCCGGATAT
1 TGCCTTCGGGTCTTAGCCCGGATAT
42573213 CATTCAAATG
Statistics
Matches: 586, Mismatches: 33, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
39 7 0.01
40 573 0.98
41 6 0.01
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (40 bp):
TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
Found at i:42576424 original size:9 final size:9
Alignment explanation
Indices: 42576410--42576435 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
42576400 AAATTTCGTA
42576410 TTTTTTGAT
1 TTTTTTGAT
42576419 TTTTTTGAT
1 TTTTTTGAT
42576428 TTTTTTGA
1 TTTTTTGA
42576436 CTGATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.77
Consensus pattern (9 bp):
TTTTTTGAT
Found at i:42578143 original size:20 final size:20
Alignment explanation
Indices: 42578115--42578169 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
42578105 ATGGGATTGG
*
42578115 ACTTCGGTGCCTCTGTTTTC
1 ACTTTGGTGCCTCTGTTTTC
*
42578135 ACTTTGGTGTCTCTGTTTTC
1 ACTTTGGTGCCTCTGTTTTC
42578155 ACTTTGGTGCCTCTG
1 ACTTTGGTGCCTCTG
42578170 ATTGCACAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.05, C:0.25, G:0.22, T:0.47
Consensus pattern (20 bp):
ACTTTGGTGCCTCTGTTTTC
Found at i:42587404 original size:47 final size:47
Alignment explanation
Indices: 42587341--42587661 Score: 484
Period size: 47 Copynumber: 6.7 Consensus size: 47
42587331 CCCTTCGGGA
* * *
42587341 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
42587388 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
42587435 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGTCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
42587482 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
42587529 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
42587578 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
42587625 CTTATCACATATATATACACTTTCACATTCATCACAT
1 CTTATCAC--ATATATACACTTTCACATTCATCACAT
42587662 CATGTACAGA
Statistics
Matches: 253, Mismatches: 15, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
46 1 0.00
47 181 0.72
49 70 0.28
50 1 0.00
ACGTcount: A:0.28, C:0.30, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:42587575 original size:96 final size:96
Alignment explanation
Indices: 42587341--42587661 Score: 501
Period size: 96 Copynumber: 3.4 Consensus size: 96
42587331 CCCTTCGGGA
* *
42587341 CTTATCACAT-T-TATACACTTCCACATCCATCACATTGGCCATTCGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
42587404 ACTTTCACATTCATCACATTGGCCATTCGGC
66 ACTTTCACATTCATCACATTGGCCATTCGGC
* * * * *
42587435 CTTATCTC--ATATATGCA-TGTTCACATTCATCACATTGGTCATTCGGCCTTATCACACATACA
1 CTTATCACATATATATACACT-TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATA
42587497 CA-TGTTCACATTCATCACATTGGCCATTCGGC
65 CACT-TTCACATTCATCACATTGGCCATTCGGC
42587529 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
* *
42587594 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATTGGCCATTCGGC
42587625 CTTATCACATATATATACACTTTCACATTCATCACAT
1 CTTATCACATATATATACACTTTCACATTCATCACAT
42587662 CATGTACAGA
Statistics
Matches: 205, Mismatches: 14, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
93 3 0.01
94 87 0.42
96 113 0.55
97 2 0.01
ACGTcount: A:0.28, C:0.30, G:0.08, T:0.34
Consensus pattern (96 bp):
CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
ACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:42587601 original size:143 final size:142
Alignment explanation
Indices: 42587355--42587661 Score: 467
Period size: 143 Copynumber: 2.1 Consensus size: 142
42587345 TCACATTTAT
* *
42587355 ACACTTCCACATCCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCA
1 ACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCA
* * * * *
42587420 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCACATTGGTCATTCGGCCTT
66 CATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCACATCGGCCATTAGGCCTT
42587485 ATCAC-ACATAC
131 ATCACAACATAC
42587496 ACA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATACACTTTCACATTCA
1 ACACT-TTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATATATACACTTTCACATTCA
42587560 TCACATTGGCCATTCGGCCTTATCACATATATACACT-TTCACATTCATCACATCGGCCATTAGG
63 TCACATTGGCCATTCGGCCTTATCACATATATACA-TGTTCACATTCATCACATCGGCCATTAGG
* *
42587624 CCTTATCACATATATAT
127 CCTTATCACA-ACATAC
42587641 ACACTTTCACATTCATCACAT
1 ACACTTTCACATTCATCACAT
42587662 CATGTACAGA
Statistics
Matches: 150, Mismatches: 9, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
140 1 0.01
141 37 0.25
143 87 0.58
144 1 0.01
145 23 0.15
146 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (142 bp):
ACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCA
CATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCACATCGGCCATTAGGCCTT
ATCACAACATAC
Found at i:42595656 original size:19 final size:19
Alignment explanation
Indices: 42595632--42595669 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
42595622 AAAGTTAATA
42595632 AAAAATTTGATTACGGTGG
1 AAAAATTTGATTACGGTGG
*
42595651 AAAAATTTTATTACGGTGG
1 AAAAATTTGATTACGGTGG
42595670 GTGATAATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (19 bp):
AAAAATTTGATTACGGTGG
Found at i:42597985 original size:2 final size:2
Alignment explanation
Indices: 42597978--42598007 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
42597968 TAATATGCAT
42597978 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42598008 GGCTACTCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42601191 original size:16 final size:17
Alignment explanation
Indices: 42601156--42601191 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
42601146 TTAACTAACC
42601156 AAACAAATCAATTTTCA
1 AAACAAATCAATTTTCA
*
42601173 AAACCAATCAA-TTTCA
1 AAACAAATCAATTTTCA
42601189 AAA
1 AAA
42601192 GTGAATAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.56, C:0.19, G:0.00, T:0.25
Consensus pattern (17 bp):
AAACAAATCAATTTTCA
Found at i:42607283 original size:43 final size:43
Alignment explanation
Indices: 42607222--42607310 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
42607212 CAACAATCCA
*
42607222 TTATTTTTGGTTCATTCTCGGTCTTAGCCAATTATCCATTATT
1 TTATTGTTGGTTCATTCTCGGTCTTAGCCAATTATCCATTATT
42607265 TTATTGTTGGTTCATTCTCGGTCTTAGCCAATTATCCATTATT
1 TTATTGTTGGTTCATTCTCGGTCTTAGCCAATTATCCATTATT
42607308 TTA
1 TTA
42607311 CTTAACCATT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.19, C:0.18, G:0.12, T:0.51
Consensus pattern (43 bp):
TTATTGTTGGTTCATTCTCGGTCTTAGCCAATTATCCATTATT
Found at i:42610237 original size:41 final size:41
Alignment explanation
Indices: 42610177--42610259 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 41
42610167 TTGCTCAGAT
* *
42610177 AATGGATAGGTGCTTGAATTAATTAACAACAAGTCAACAAA
1 AATGGATAGGTGATTGAATTAATTAACAACAAATCAACAAA
42610218 AATGGATAGGT-ATTAGAATTAATTAACAACAAATCAACAAA
1 AATGGATAGGTGATT-GAATTAATTAACAACAAATCAACAAA
42610259 A
1 A
42610260 TAAAAAGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
40 2 0.05
41 37 0.95
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.24
Consensus pattern (41 bp):
AATGGATAGGTGATTGAATTAATTAACAACAAATCAACAAA
Found at i:42615209 original size:20 final size:18
Alignment explanation
Indices: 42615184--42615223 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
42615174 ACTTCAAAAT
42615184 CTTGCATTGCAAAAATTTTC
1 CTTGCATT--AAAAATTTTC
*
42615204 CTTGCATTAGAAATTTTC
1 CTTGCATTAAAAATTTTC
42615222 CT
1 CT
42615224 ATTATTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
20 8 0.42
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.42
Consensus pattern (18 bp):
CTTGCATTAAAAATTTTC
Found at i:42615231 original size:3 final size:3
Alignment explanation
Indices: 42615223--42615268 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
42615213 GAAATTTTCC
42615223 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
42615269 TTCCTTCTCC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:42616035 original size:15 final size:17
Alignment explanation
Indices: 42616001--42616038 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
42615991 TAATTTATTT
42616001 ATTTTTATTATTTTAGA
1 ATTTTTATTATTTTAGA
*
42616018 ATTTTTA-TA-TTTATA
1 ATTTTTATTATTTTAGA
42616033 ATTTTT
1 ATTTTT
42616039 TTTCCTTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 11 0.55
16 2 0.10
17 7 0.35
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
ATTTTTATTATTTTAGA
Found at i:42617390 original size:43 final size:43
Alignment explanation
Indices: 42617337--42617458 Score: 147
Period size: 43 Copynumber: 2.8 Consensus size: 43
42617327 TTTTTGTGAG
* * * * *
42617337 AAGCGTCGCTAAAAGT-TTTTTCTATAGTGGCGTTTGTGATAAA
1 AAGCGCCGCTAAAAGTCATTGTCTATAGCGGCGTTTGTG-GAAA
*
42617380 AAGCGCCGCTAAAAGTCATTGTCTTTAGCGGCGTTTGTGGAAA
1 AAGCGCCGCTAAAAGTCATTGTCTATAGCGGCGTTTGTGGAAA
* * *
42617423 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTT
1 AAGCGCCGCTAAAAGTCATTGTCTATAGCGGCGTTT
42617459 ATTTCGAAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
43 52 0.74
44 18 0.26
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (43 bp):
AAGCGCCGCTAAAAGTCATTGTCTATAGCGGCGTTTGTGGAAA
Done.