Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 126 of 235
Found at i:42801429 original size:115 final size:115
Alignment explanation
Indices: 42801244--42801470 Score: 445
Period size: 115 Copynumber: 2.0 Consensus size: 115
42801234 TCACGATCGA
42801244 CATAACCATGTTACAAATTCAATACATAAAAATCTTCTTATCCAAGGCTATATTTGACCTATATG
1 CATAACCATGTTACAAATTCAATACATAAAAATCTTCTTATCCAAGGCTATATTTGACCTATATG
42801309 TATTTTCTTTACAACCATTCATCAACAATTAAGCACATGTTTAATGGCGG
66 TATTTTCTTTACAACCATTCATCAACAATTAAGCACATGTTTAATGGCGG
42801359 CATAACCATGTTACAAATTCAATACATAAAAATCTTCTTATCCAAGGCTATATTTGACCTATATG
1 CATAACCATGTTACAAATTCAATACATAAAAATCTTCTTATCCAAGGCTATATTTGACCTATATG
*
42801424 TATTTTCTTTACAACCATTCATCATCAATTAAGCACATGTTTAATGG
66 TATTTTCTTTACAACCATTCATCAACAATTAAGCACATGTTTAATGG
42801471 TCGAATGCAC
Statistics
Matches: 111, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
115 111 1.00
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.36
Consensus pattern (115 bp):
CATAACCATGTTACAAATTCAATACATAAAAATCTTCTTATCCAAGGCTATATTTGACCTATATG
TATTTTCTTTACAACCATTCATCAACAATTAAGCACATGTTTAATGGCGG
Found at i:42803844 original size:27 final size:27
Alignment explanation
Indices: 42803814--42803906 Score: 109
Period size: 27 Copynumber: 3.5 Consensus size: 27
42803804 GTGGGCCCAC
42803814 ATTACCAAAATACCCCTAGTTTGTAAA
1 ATTACCAAAATACCCCTAGTTTGTAAA
* * *
42803841 ATTACCGAAATACCACTAGTTTGTGAA
1 ATTACCAAAATACCCCTAGTTTGTAAA
* * *
42803868 ATCACC-GAATA-CCCTCAATTTGTAAA
1 ATTACCAAAATACCCCT-AGTTTGTAAA
42803894 ATTACCAAAATAC
1 ATTACCAAAATAC
42803907 TCTTGTAGGA
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
25 3 0.06
26 17 0.32
27 33 0.62
ACGTcount: A:0.41, C:0.23, G:0.09, T:0.28
Consensus pattern (27 bp):
ATTACCAAAATACCCCTAGTTTGTAAA
Found at i:42804844 original size:25 final size:25
Alignment explanation
Indices: 42804789--42804859 Score: 90
Period size: 25 Copynumber: 2.8 Consensus size: 25
42804779 AGGAAGTGCC
* *
42804789 AAAAGGGCTTCTTCCCCAGTTTACCG
1 AAAAGGGCTT-TGCCCCAGTTTACAG
*
42804815 AAAAGGGCTTTGCCCTAGTTTATCAG
1 AAAAGGGCTTTGCCCCAGTTTA-CAG
42804841 -AAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
42804860 ATTAAAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
25 28 0.70
26 12 0.30
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.28
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACAG
Found at i:42804872 original size:24 final size:23
Alignment explanation
Indices: 42804788--42804886 Score: 81
Period size: 25 Copynumber: 4.0 Consensus size: 23
42804778 GAGGAAGTGC
* *
42804788 CAAAAGGGCTTCTTCCCCAGTTTAC
1 CAAAAGGGCTT-TGCCCCAG-TTAT
*
42804813 CGAAAAGGGCTTTGCCCTAGTTTAT
1 C-AAAAGGGCTTTGCCCCAG-TTAT
42804838 CAGAAAGGGCTTTGCCCCAGTTAT
1 CA-AAAGGGCTTTGCCCCAGTTAT
* **
42804862 TAAAAGAGGCTAGGCCTCCAGTTAT
1 CAAAAG-GGCTTTGCC-CCAGTTAT
42804887 ATGATAAAGC
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
23 4 0.06
24 13 0.21
25 36 0.57
26 10 0.16
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.27
Consensus pattern (23 bp):
CAAAAGGGCTTTGCCCCAGTTAT
Found at i:42805066 original size:42 final size:42
Alignment explanation
Indices: 42805007--42805098 Score: 175
Period size: 42 Copynumber: 2.2 Consensus size: 42
42804997 TAGTCTCCCC
*
42805007 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
42805049 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
42805091 AAATGGGC
1 AAATGGGC
42805099 CTAAGGGCCA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.33
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:42805157 original size:31 final size:31
Alignment explanation
Indices: 42805122--42805267 Score: 276
Period size: 31 Copynumber: 4.7 Consensus size: 31
42805112 CGTTTACAGT
42805122 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
42805153 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
42805184 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
42805215 AAAGGCTTCGGCCCAGTGATATGATTTATGG
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
42805246 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
42805268 TCAAGACTAA
Statistics
Matches: 114, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
30 5 0.04
31 109 0.96
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:42805527 original size:78 final size:78
Alignment explanation
Indices: 42805429--42805584 Score: 294
Period size: 78 Copynumber: 2.0 Consensus size: 78
42805419 GGACTCGGAG
* *
42805429 ATGGCCACACTATTGTTTCTGTTTCTTTTAATTGCAATAAGTAGCTGATTTATTTCTTTATAAGT
1 ATGGCCACACTACTGTTTCTGTTTCTTTTAATTGCAATAAGTAGCCGATTTATTTCTTTATAAGT
42805494 TTTATCTTATTAA
66 TTTATCTTATTAA
42805507 ATGGCCACACTACTGTTTCTGTTTCTTTTAATTGCAATAAGTAGCCGATTTATTTCTTTATAAGT
1 ATGGCCACACTACTGTTTCTGTTTCTTTTAATTGCAATAAGTAGCCGATTTATTTCTTTATAAGT
42805572 TTTATCTTATTAA
66 TTTATCTTATTAA
42805585 TATTATTATT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 76 1.00
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.49
Consensus pattern (78 bp):
ATGGCCACACTACTGTTTCTGTTTCTTTTAATTGCAATAAGTAGCCGATTTATTTCTTTATAAGT
TTTATCTTATTAA
Found at i:42808172 original size:17 final size:17
Alignment explanation
Indices: 42808146--42808183 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
42808136 AAATTTATAC
*
42808146 ATAAATATTGATTTAAT
1 ATAAAAATTGATTTAAT
*
42808163 ATAAAAATTGATTTGAT
1 ATAAAAATTGATTTAAT
42808180 ATAA
1 ATAA
42808184 TTATACACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (17 bp):
ATAAAAATTGATTTAAT
Found at i:42815326 original size:30 final size:31
Alignment explanation
Indices: 42815292--42815354 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 31
42815282 ATCCAATATG
* *
42815292 TCACAAAACACATTATTAACATCTTGG-ATA
1 TCACAAAACACATTATCAACATCTAGGCATA
42815322 TCACAAAACACATTATCAACATCTAGGCATA
1 TCACAAAACACATTATCAACATCTAGGCATA
42815353 TC
1 TC
42815355 CAAGCCATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.43, C:0.24, G:0.06, T:0.27
Consensus pattern (31 bp):
TCACAAAACACATTATCAACATCTAGGCATA
Found at i:42817167 original size:20 final size:19
Alignment explanation
Indices: 42817116--42817169 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
42817106 CGTAACAAAA
*
42817116 GCACCGAAGTGTAGACAGAG
1 GCACCGAAGTGCA-ACAGAG
*
42817136 GCA-CAAATGTGCAATCAGAG
1 GCACCGAA-GTGCAA-CAGAG
42817156 GCACCGAAGTGCAA
1 GCACCGAAGTGCAA
42817170 ACTCGTACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 4 0.14
20 21 0.75
21 3 0.11
ACGTcount: A:0.37, C:0.22, G:0.30, T:0.11
Consensus pattern (19 bp):
GCACCGAAGTGCAACAGAG
Found at i:42820265 original size:14 final size:14
Alignment explanation
Indices: 42820231--42820265 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
42820221 TTTGAATCTG
42820231 TTTTATTTTATTTT
1 TTTTATTTTATTTT
**
42820245 TCGTATTTTATTTT
1 TTTTATTTTATTTT
42820259 TTTTATT
1 TTTTATT
42820266 ATCTTAACAA
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.14, C:0.03, G:0.03, T:0.80
Consensus pattern (14 bp):
TTTTATTTTATTTT
Found at i:42820891 original size:25 final size:23
Alignment explanation
Indices: 42820844--42820909 Score: 62
Period size: 25 Copynumber: 2.8 Consensus size: 23
42820834 AAAGTTTTTA
*
42820844 TTTAATATAATTTAATTTGATTT
1 TTTAATTTAATTTAATTTGATTT
*
42820867 TTAATAATTTAATTTACTTAT-ATTT
1 TT--TAATTTAATTTAATT-TGATTT
* *
42820892 TTTAATTTATTTTTATTT
1 TTTAATTTAATTTAATTT
42820910 TAAAAGAATC
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
22 1 0.03
23 14 0.40
25 19 0.54
26 1 0.03
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (23 bp):
TTTAATTTAATTTAATTTGATTT
Found at i:42820897 original size:18 final size:18
Alignment explanation
Indices: 42820874--42820910 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
42820864 TTTTTAATAA
42820874 TTTAATTTACTTATATTT
1 TTTAATTTACTTATATTT
* *
42820892 TTTAATTTATTTTTATTT
1 TTTAATTTACTTATATTT
42820910 T
1 T
42820911 AAAAGAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTAATTTACTTATATTT
Found at i:42831578 original size:22 final size:22
Alignment explanation
Indices: 42831533--42831579 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
42831523 TTTTCCCTGT
* * **
42831533 TTTTTTTAGAGTTAGGATTTGG
1 TTTTTTTAAAGTAAGGATAGGG
42831555 TTTTTTTAAAGTAAGGATAGGG
1 TTTTTTTAAAGTAAGGATAGGG
42831577 TTT
1 TTT
42831580 AGGATTTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51
Consensus pattern (22 bp):
TTTTTTTAAAGTAAGGATAGGG
Found at i:42832922 original size:25 final size:25
Alignment explanation
Indices: 42832874--42832922 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
42832864 CTATTGAAAA
*
42832874 CAAATGTTTTTTTATTTTTATTTAC
1 CAAATGTTTTTTTAATTTTATTTAC
42832899 CAAATGTGTTTTTTAATTTT-TTTA
1 CAAATGT-TTTTTTAATTTTATTTA
42832923 AATAGAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.63
Consensus pattern (25 bp):
CAAATGTTTTTTTAATTTTATTTAC
Found at i:42833771 original size:17 final size:18
Alignment explanation
Indices: 42833736--42833774 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
42833726 TTATTCACAA
* *
42833736 TTTAATATTTTTATTTAT
1 TTTAATATTTATATATAT
42833754 TTTAATA-TTATATATAT
1 TTTAATATTTATATATAT
42833771 TTTA
1 TTTA
42833775 TGTATTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTAATATTTATATATAT
Found at i:42838275 original size:38 final size:38
Alignment explanation
Indices: 42838214--42838326 Score: 136
Period size: 38 Copynumber: 2.9 Consensus size: 38
42838204 ATTTGATGTG
*
42838214 TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGTAAAA
1 TATCCGGG-TTAAA-TCCCGCAGGCTTCGTGCTGGTAAAA
***
42838254 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTGTTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAAA
* * * *
42838292 TATCCAGGATAAATCCCGCAGGCCTAGTGCTGGTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTA
42838327 TTATATTCGG
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
38 51 0.80
39 5 0.08
40 8 0.12
ACGTcount: A:0.22, C:0.25, G:0.27, T:0.26
Consensus pattern (38 bp):
TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAAA
Found at i:42838331 original size:38 final size:38
Alignment explanation
Indices: 42838230--42838332 Score: 143
Period size: 38 Copynumber: 2.7 Consensus size: 38
42838220 GGCTTAAAGA
** * *
42838230 CCCGCAGGCTTCGTGCTGGTAAAATATCCGGGTTAAAT
1 CCCGCAGGCTTCGTGCTGGTATTATATCCAGGATAAAT
*
42838268 CCCGCAGGCTTCGTGCTGGTGTTATATCCAGGATAAAT
1 CCCGCAGGCTTCGTGCTGGTATTATATCCAGGATAAAT
* *
42838306 CCCGCAGGCCTAGTGCTGGTATTATAT
1 CCCGCAGGCTTCGTGCTGGTATTATAT
42838333 TCGGGCCTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 57 1.00
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.28
Consensus pattern (38 bp):
CCCGCAGGCTTCGTGCTGGTATTATATCCAGGATAAAT
Found at i:42838378 original size:43 final size:42
Alignment explanation
Indices: 42838309--42838454 Score: 161
Period size: 43 Copynumber: 3.5 Consensus size: 42
42838299 GATAAATCCC
* * *
42838309 GCAGGCCTAGTGCTGGT-AT-TATATTCGGGCCTTTGTGCCTA
1 GCAGGCTTAGTGCCGGTGATATGTATTCGGGCCTTT-TGCCTA
* * *
42838350 GTAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCATGCCTA
1 GCAGGCTTAGTGCCGGTGATATGTATTCGGGCCTT-TTGCCTA
* *
42838393 GCAGGCTTCGTGCTGGTGATATGTATTCGGGCCTTCTTGCCTA
1 GCAGGCTTAGTGCCGGTGATATGTATTCGGGCCTT-TTGCCTA
* *
42838436 GCAGGCGTAATGCCGGTGA
1 GCAGGCTTAGTGCCGGTGA
42838455 AATGATATGT
Statistics
Matches: 88, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
41 14 0.16
42 2 0.02
43 72 0.82
ACGTcount: A:0.14, C:0.22, G:0.32, T:0.32
Consensus pattern (42 bp):
GCAGGCTTAGTGCCGGTGATATGTATTCGGGCCTTTTGCCTA
Found at i:42840258 original size:13 final size:13
Alignment explanation
Indices: 42840218--42840258 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
42840208 AAAGCATATA
42840218 AATATTTAAACAT
1 AATATTTAAACAT
42840231 AAT-TCTTCAAA-AT
1 AATAT-TT-AAACAT
42840244 AATATTTAAACAT
1 AATATTTAAACAT
42840257 AA
1 AA
42840259 AATAGATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
12 4 0.17
13 16 0.67
14 4 0.17
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.37
Consensus pattern (13 bp):
AATATTTAAACAT
Found at i:42847920 original size:35 final size:35
Alignment explanation
Indices: 42847876--42847949 Score: 139
Period size: 35 Copynumber: 2.1 Consensus size: 35
42847866 TTATTTGACC
*
42847876 CTTAAATTTGTATTAAAAGAAATTCTCATTAAATT
1 CTTAAATTTGTATTAAAAGAAACTCTCATTAAATT
42847911 CTTAAATTTGTATTAAAAGAAACTCTCATTAAATT
1 CTTAAATTTGTATTAAAAGAAACTCTCATTAAATT
42847946 CTTA
1 CTTA
42847950 CATGTTTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (35 bp):
CTTAAATTTGTATTAAAAGAAACTCTCATTAAATT
Found at i:42853560 original size:16 final size:16
Alignment explanation
Indices: 42853539--42853571 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
42853529 AGGATTAAGC
42853539 CCAAGGCGGAATGAGA
1 CCAAGGCGGAATGAGA
42853555 CCAAGGCGGAATGAGA
1 CCAAGGCGGAATGAGA
42853571 C
1 C
42853572 AACCGGAGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.21, G:0.36, T:0.06
Consensus pattern (16 bp):
CCAAGGCGGAATGAGA
Found at i:42859102 original size:16 final size:15
Alignment explanation
Indices: 42859047--42859103 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 15
42859037 CAACCCAATC
* *
42859047 TTTTTTTTCTTTTTC
1 TTTTTTTTATTTTTA
*
42859062 TTTTTATTATTTATTA
1 TTTTTTTTATTT-TTA
42859078 TTTTCTTTTATTTTTA
1 TTTT-TTTTATTTTTA
42859094 TTTTATTTTA
1 TTTT-TTTTA
42859104 GTTAAATATT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
15 10 0.29
16 18 0.51
17 7 0.20
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTTTTATTTTTA
Found at i:42859102 original size:21 final size:21
Alignment explanation
Indices: 42859057--42859095 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
42859047 TTTTTTTTCT
42859057 TTTTCTTTTTATTATTTATTA
1 TTTTCTTTTTATTATTTATTA
42859078 TTTTC-TTTTATT-TTTATT
1 TTTTCTTTTTATTATTTATT
42859096 TTATTTTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 7 0.39
21 5 0.28
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTTCTTTTTATTATTTATTA
Found at i:42859294 original size:43 final size:42
Alignment explanation
Indices: 42859209--42859301 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
42859199 TATCCATGCT
* * * *
42859209 GCCAAACAGTTCTATTCCAGCCCAGAATGCCATATCTCTGCA
1 GCCAAACAGTCCTATTCCAGCCCAGAATCCCAAAACTCTGCA
*
42859251 GCCAAACAGTCCTATTCCAGCCTTAGAATCCCCAAAAC-CTGCA
1 GCCAAACAGTCCTATTCCAGCC-CAGAAT-CCCAAAACTCTGCA
42859294 GCCAAACA
1 GCCAAACA
42859302 CCCCTTTTCA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
42 21 0.48
43 18 0.41
44 5 0.11
ACGTcount: A:0.32, C:0.35, G:0.13, T:0.19
Consensus pattern (42 bp):
GCCAAACAGTCCTATTCCAGCCCAGAATCCCAAAACTCTGCA
Found at i:42859993 original size:21 final size:22
Alignment explanation
Indices: 42859964--42860005 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
42859954 TATTCTTAAG
* *
42859964 TAAATAAATA-ATAATAAAATT
1 TAAAAAAATATATAAAAAAATT
42859985 TAAAAAAATATATAAAAAAAT
1 TAAAAAAATATATAAAAAAAT
42860006 CAAAAAAGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAAAAATATATAAAAAAATT
Found at i:42860010 original size:21 final size:21
Alignment explanation
Indices: 42859969--42860012 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
42859959 TTAAGTAAAT
* *
42859969 AAATAATAATAAAATTTAAAA
1 AAATAATAATAAAAATCAAAA
42859990 AAATATATAA-AAAAATCAAAA
1 AAATA-ATAATAAAAATCAAAA
42860011 AA
1 AA
42860013 GGAAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (21 bp):
AAATAATAATAAAAATCAAAA
Found at i:42862607 original size:26 final size:26
Alignment explanation
Indices: 42862578--42862629 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
42862568 TGTCTTTAGT
42862578 TTTGGACTAGATTATTAAAACTAAAA
1 TTTGGACTAGATTATTAAAACTAAAA
42862604 TTTGGACTAGATTATTAAAACTAAAA
1 TTTGGACTAGATTATTAAAACTAAAA
42862630 ACAAAGAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.35
Consensus pattern (26 bp):
TTTGGACTAGATTATTAAAACTAAAA
Found at i:42863227 original size:5 final size:5
Alignment explanation
Indices: 42863217--42863242 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
42863207 TTGATAACTT
42863217 TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA T
42863243 CTTGAATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:42864438 original size:66 final size:66
Alignment explanation
Indices: 42864321--42864451 Score: 167
Period size: 66 Copynumber: 2.0 Consensus size: 66
42864311 ATTTTGAAGT
* * *
42864321 TGTAGCTAGAGTTCGTCATATTTTCTTATTGCCTCTACTGCCCCTACTGCTGCTTCTGCTTTAAG
1 TGTAGCTAGAGTTCATCATATTTTCTTATTGCCTCTAATGCCCCTACTGCTGCTTCCGCTTTAAG
42864386 G
66 G
* * * *
42864387 TGTAGCTGGAGTTCATCATATTTTCTT-TTAGCCTCTAATTCTCTTGA-TGCTGCTTCCGCTTTA
1 TGTAGCTAGAGTTCATCATATTTTCTTATT-GCCTCTAATGCCCCT-ACTGCTGCTTCCGCTTTA
42864450 AG
64 AG
42864452 TTGAGCAATG
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
65 2 0.04
66 53 0.95
67 1 0.02
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.43
Consensus pattern (66 bp):
TGTAGCTAGAGTTCATCATATTTTCTTATTGCCTCTAATGCCCCTACTGCTGCTTCCGCTTTAAG
G
Found at i:42868601 original size:26 final size:26
Alignment explanation
Indices: 42868565--42868673 Score: 191
Period size: 26 Copynumber: 4.2 Consensus size: 26
42868555 ATGAAATGCC
*
42868565 TATCATGGAACATTTACCTAAACCAT
1 TATCATGGAACATTTACCTAACCCAT
42868591 TATCATGGAACATTTACCTAACCCAT
1 TATCATGGAACATTTACCTAACCCAT
* *
42868617 TATCATGGAATATTTACCTAATCCAT
1 TATCATGGAACATTTACCTAACCCAT
42868643 TATCATGGAACATTTACCTAACCCAT
1 TATCATGGAACATTTACCTAACCCAT
42868669 TATCA
1 TATCA
42868674 ATTTGTACCA
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.33
Consensus pattern (26 bp):
TATCATGGAACATTTACCTAACCCAT
Found at i:42875604 original size:26 final size:26
Alignment explanation
Indices: 42875574--42875629 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
42875564 AAACTGTCCG
42875574 GATTGATCTAATTGATTAGATTTCAA
1 GATTGATCTAATTGATTAGATTTCAA
42875600 GATTGATCTAATTGATTAGATTTCAA
1 GATTGATCTAATTGATTAGATTTCAA
42875626 GATT
1 GATT
42875630 TCGATTCTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.34, C:0.07, G:0.16, T:0.43
Consensus pattern (26 bp):
GATTGATCTAATTGATTAGATTTCAA
Found at i:42886049 original size:4 final size:4
Alignment explanation
Indices: 42886040--42886078 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
42886030 TGATGGTAGC
* *
42886040 TATG TATG TATG TATG TATG TTTG CATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
42886079 TACATTGTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.23, C:0.03, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:42887349 original size:98 final size:101
Alignment explanation
Indices: 42887240--42887424 Score: 263
Period size: 98 Copynumber: 1.9 Consensus size: 101
42887230 AGTTTTTTTT
*
42887240 AATTAATAACT-CTTTAATTTATA-AAATCAAA-TAATAAATAT-ATAATTATATATTAAAAA-A
1 AATTAATAACTCCTTT-ATTTATATAAAT-AAATTAATAAATATAATAATTATATAATAAAAATA
* * *
42887300 TATATTTTTTATATATATTATTATGTTAAAATATTTGA
64 TATAATTTTGATATATATCATTATGTTAAAATATTTGA
*
42887338 AATTAATAACTCCTTTATTTATATAAATAAATTAATAATTATAATAATTATATAATAAAAATATA
1 AATTAATAACTCCTTTATTTATATAAATAAATTAATAAATATAATAATTATATAATAAAAATATA
*
42887403 TAATTTTGATATTTATCATTAT
66 TAATTTTGATATATATCATTAT
42887425 ACTAAATATA
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
98 21 0.28
99 17 0.22
100 17 0.22
101 21 0.28
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.46
Consensus pattern (101 bp):
AATTAATAACTCCTTTATTTATATAAATAAATTAATAAATATAATAATTATATAATAAAAATATA
TAATTTTGATATATATCATTATGTTAAAATATTTGA
Found at i:42887919 original size:13 final size:13
Alignment explanation
Indices: 42887901--42887925 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42887891 CAATATATTT
42887901 ATTAATTAAAAAC
1 ATTAATTAAAAAC
42887914 ATTAATTAAAAA
1 ATTAATTAAAAA
42887926 TAAAAAATTG
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:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAC
Found at i:42900097 original size:3 final size:3
Alignment explanation
Indices: 42900091--42900122 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
42900081 AAAACTGTAT
42900091 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
42900123 GGGTTACTAC
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:42900432 original size:25 final size:23
Alignment explanation
Indices: 42900403--42900464 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
42900393 ATATGAATAT
* *
42900403 ATGATTTATAATTGATATGCTAAAA
1 ATGATATATAATTGA-ATG-AAAAA
42900428 ATGATATATAACTTGAATGAAAAA
1 ATGATATATAA-TTGAATGAAAAA
* *
42900452 ATTATGTATAATT
1 ATGATATATAATT
42900465 TAAATTGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 2 0.06
24 13 0.41
25 13 0.41
26 4 0.12
ACGTcount: A:0.47, C:0.03, G:0.11, T:0.39
Consensus pattern (23 bp):
ATGATATATAATTGAATGAAAAA
Found at i:42907276 original size:28 final size:28
Alignment explanation
Indices: 42907236--42907291 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
42907226 ATACGTCGCA
42907236 CCGTAGGCATTAATAGTGCTTCTGTTGT
1 CCGTAGGCATTAATAGTGCTTCTGTTGT
* *
42907264 CCGTAGGCATTAATGGTGTTTCTGTTGT
1 CCGTAGGCATTAATAGTGCTTCTGTTGT
42907292 TCAACTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.16, C:0.16, G:0.27, T:0.41
Consensus pattern (28 bp):
CCGTAGGCATTAATAGTGCTTCTGTTGT
Found at i:42911593 original size:20 final size:19
Alignment explanation
Indices: 42911570--42911609 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
42911560 TATGCATCAA
*
42911570 TGTTTATGTATTGTTTTGTT
1 TGTTTATCTATTG-TTTGTT
*
42911590 TGTTTGTCTATTGTTTGTT
1 TGTTTATCTATTGTTTGTT
42911609 T
1 T
42911610 TTGTGTGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.07, C:0.03, G:0.20, T:0.70
Consensus pattern (19 bp):
TGTTTATCTATTGTTTGTT
Found at i:42914908 original size:16 final size:16
Alignment explanation
Indices: 42914887--42914917 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42914877 TTATTATATT
42914887 TTTTTACTTTTTTTAC
1 TTTTTACTTTTTTTAC
*
42914903 TTTTTATTTTTTTTA
1 TTTTTACTTTTTTTA
42914918 TATTTTGTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.06, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTACTTTTTTTAC
Found at i:42915007 original size:18 final size:17
Alignment explanation
Indices: 42914956--42915003 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
42914946 TTTTTTAAGT
*
42914956 TTTATATTATTTTTATAA
1 TTTATATTATTATT-TAA
42914974 TTTAT-TTCACTTATTTAA
1 TTTATATT-A-TTATTTAA
42914992 TTTATATTATTA
1 TTTATATTATTA
42915004 ATTTTAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
17 5 0.19
18 15 0.58
19 6 0.23
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTATATTATTATTTAA
Found at i:42915859 original size:10 final size:9
Alignment explanation
Indices: 42915841--42915929 Score: 63
Period size: 10 Copynumber: 9.4 Consensus size: 9
42915831 TAAAATTTAA
42915841 AAAATATTT
1 AAAATATTT
42915850 AAAATCATTT
1 AAAAT-ATTT
*
42915860 AAAATATTAA
1 AAAATATT-T
42915870 AAAATATTT
1 AAAATATTT
*
42915879 TAAATCATTT
1 AAAAT-ATTT
* *
42915889 TAAATGTTTT
1 AAAAT-ATTT
* *
42915899 ATAATATTA
1 AAAATATTT
42915908 AAAATATATT
1 AAAATAT-TT
*
42915918 -TAATATTT
1 AAAATATTT
42915926 AAAA
1 AAAA
42915930 AATAATTTGA
Statistics
Matches: 62, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
8 2 0.03
9 27 0.44
10 33 0.53
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (9 bp):
AAAATATTT
Found at i:42915865 original size:19 final size:18
Alignment explanation
Indices: 42915841--42915929 Score: 63
Period size: 19 Copynumber: 4.7 Consensus size: 18
42915831 TAAAATTTAA
42915841 AAAATATTTAAAATCATTT
1 AAAATATTTAAAAT-ATTT
*
42915860 AAAATATTAAAAAATATTT
1 AAAATATT-TAAAATATTT
* * *
42915879 TAAATCATTTTAAATGTTTT
1 AAAAT-ATTTAAAAT-ATTT
* *
42915899 ATAATATTAAAAATATATT
1 AAAATATTTAAAATAT-TT
*
42915918 -TAATATTTAAAA
1 AAAATATTTAAAA
42915930 AATAATTTGA
Statistics
Matches: 55, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
18 12 0.22
19 29 0.53
20 14 0.25
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (18 bp):
AAAATATTTAAAATATTT
Found at i:42915869 original size:29 final size:28
Alignment explanation
Indices: 42915831--42915943 Score: 109
Period size: 29 Copynumber: 3.9 Consensus size: 28
42915821 AAATTCTATG
42915831 TAAAATTTAAAAAATATTTAAAATCATT
1 TAAAATTTAAAAAATATTTAAAATCATT
*
42915859 TAAAATATTAAAAAATATTTTAAATCATT
1 TAAAAT-TTAAAAAATATTTAAAATCATT
* ** * * *
42915888 TTAAATGTTTTATAATATTAAAAATATATT
1 TAAAAT-TTAAAAAATATTTAAAAT-CATT
*
42915918 TAATATTTAAAAAATAATTTGAAAAT
1 TAAAATTTAAAAAAT-ATTT-AAAAT
42915944 ATATTTTTAA
Statistics
Matches: 66, Mismatches: 15, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
28 6 0.09
29 45 0.68
30 10 0.15
31 5 0.08
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (28 bp):
TAAAATTTAAAAAATATTTAAAATCATT
Found at i:42915946 original size:31 final size:34
Alignment explanation
Indices: 42915899--42915987 Score: 98
Period size: 34 Copynumber: 2.7 Consensus size: 34
42915889 TAAATGTTTT
42915899 ATAATATTAAAAATATA-TTTAATATTTA-AAAA
1 ATAATATTAAAAATATATTTTAATATTTATAAAA
*
42915931 ATAAT-TTGAAAATATATTTTTAATATTTATAAAA
1 ATAATATTAAAAATATA-TTTTAATATTTATAAAA
*
42915965 A-ATATATTATAAAACAT-TTTTAA
1 ATA-ATATTA-AAAATATATTTTAA
42915988 AAAATACATT
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
31 10 0.21
32 5 0.10
33 12 0.25
34 13 0.27
35 2 0.04
36 6 0.12
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (34 bp):
ATAATATTAAAAATATATTTTAATATTTATAAAA
Found at i:42915978 original size:13 final size:13
Alignment explanation
Indices: 42915952--42915993 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 13
42915942 ATATATTTTT
42915952 AATATTTATAAAA
1 AATATTTATAAAA
42915965 AATATATTATAAAA
1 AATAT-TTATAAAA
*
42915979 CAT-TTT-TAAAA
1 AATATTTATAAAA
42915990 AATA
1 AATA
42915994 CATTTCAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 7 0.28
12 2 0.08
13 6 0.24
14 10 0.40
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (13 bp):
AATATTTATAAAA
Found at i:42918974 original size:30 final size:30
Alignment explanation
Indices: 42918938--42919090 Score: 261
Period size: 30 Copynumber: 5.1 Consensus size: 30
42918928 GGTCAAATGG
* * *
42918938 ACTCGAACCGCCTATATCCGGGTGATATGA
1 ACTCGAACCACCCATGTCCGGGTGATATGA
42918968 ACTCGAACCACCCATGTCCGGGTGATATGA
1 ACTCGAACCACCCATGTCCGGGTGATATGA
42918998 ACTCGAACCACCCATGTCCGGGTGATATGA
1 ACTCGAACCACCCATGTCCGGGTGATATGA
42919028 ACTCGAACCACCCATGTCCGGGTGATATGA
1 ACTCGAACCACCCATGTCCGGGTGATATGA
* *
42919058 ACTCGAACCACCTATGTCCGGGTTATATGA
1 ACTCGAACCACCCATGTCCGGGTGATATGA
42919088 ACT
1 ACT
42919091 GCTCTGGGAC
Statistics
Matches: 118, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 118 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (30 bp):
ACTCGAACCACCCATGTCCGGGTGATATGA
Found at i:42922107 original size:18 final size:16
Alignment explanation
Indices: 42922078--42922114 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 16
42922068 ATATTCAATA
42922078 TATATTTTTTTAAATT
1 TATATTTTTTTAAATT
42922094 TATATTTATATTTAAATT
1 TATATTT-T-TTTAAATT
42922112 TAT
1 TAT
42922115 TAATAGTCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.37
17 1 0.05
18 11 0.58
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATATTTTTTTAAATT
Found at i:42922261 original size:23 final size:21
Alignment explanation
Indices: 42922212--42922261 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
42922202 AAAAAAAGAA
42922212 TTTAAAAATAATATTTAAAAT
1 TTTAAAAATAATATTTAAAAT
*
42922233 TGTAAAAA-AATATTATAAAACAT
1 TTTAAAAATAATATT-T-AAA-AT
42922256 TTTAAA
1 TTTAAA
42922262 TATACAATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 6 0.25
21 8 0.33
22 3 0.12
23 7 0.29
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
TTTAAAAATAATATTTAAAAT
Found at i:42922444 original size:27 final size:26
Alignment explanation
Indices: 42922379--42922444 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
42922369 TTTAAAAAAA
* *
42922379 TATTTAAAATATTATGATTTCTTATAT
1 TATTTAAAA-ATTATAATTTCTTAAAT
*
42922406 TA-TTAAGAAATTATAATTTTTTAAAT
1 TATTTAA-AAATTATAATTTCTTAAAT
42922432 GTATTTAAAAATT
1 -TATTTAAAAATT
42922445 GTATTTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 18 0.55
27 11 0.33
28 4 0.12
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (26 bp):
TATTTAAAAATTATAATTTCTTAAAT
Found at i:42922950 original size:21 final size:21
Alignment explanation
Indices: 42922925--42923011 Score: 63
Period size: 22 Copynumber: 4.0 Consensus size: 21
42922915 TAAAAAATAT
42922925 TTTTAAAAATAATAATTAAAA
1 TTTTAAAAATAATAATTAAAA
*
42922946 TTTTAAAAA-AATATTATAAAACA
1 TTTTAAAAATAATA--ATTAAA-A
*
42922969 TTTTAAATAT-AT-ATTACAAA
1 TTTTAAAAATAATAATTA-AAA
*
42922989 TTTTTTAAAATTAATAATATAAA
1 --TTTTAAAAATAATAAT-TAAA
42923012 TTAAATAAGC
Statistics
Matches: 51, Mismatches: 5, Indels: 17
0.70 0.07 0.23
Matches are distributed among these distances:
20 8 0.16
21 11 0.22
22 13 0.25
23 13 0.25
24 4 0.08
25 2 0.04
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
TTTTAAAAATAATAATTAAAA
Found at i:42923012 original size:23 final size:22
Alignment explanation
Indices: 42922923--42923013 Score: 62
Period size: 23 Copynumber: 4.1 Consensus size: 22
42922913 GTTAAAAAAT
*
42922923 ATTTTTAAAAATAATAAT-TAA
1 ATTTTTTAAAATAATAATATAA
* * *
42922944 A-ATTTTAAAAAAATATTATAAA
1 ATTTTTTAAAATAATAATAT-AA
** * *
42922966 ACATTTT-AAATATATATTACAA
1 ATTTTTTAAAATA-ATAATATAA
42922988 ATTTTTTAAAATTAATAATATAA
1 ATTTTTTAAAA-TAATAATATAA
42923011 ATT
1 ATT
42923014 AAATAAGCAA
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
20 12 0.22
21 2 0.04
22 14 0.26
23 24 0.44
24 2 0.04
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTTTTTAAAATAATAATATAA
Found at i:42923041 original size:36 final size:37
Alignment explanation
Indices: 42923001--42923074 Score: 100
Period size: 37 Copynumber: 2.0 Consensus size: 37
42922991 TTTTAAAATT
*
42923001 AATAATAT-AAA-TTAAATAAGCAAAATAAAT-TAAGAA
1 AATAATATAAAACTTAAAAAAG-AAAA-AAATCTAAGAA
42923037 AATAATATAAAACTTAAAAAAGAAAAAAATCTAAGAA
1 AATAATATAAAACTTAAAAAAGAAAAAAATCTAAGAA
42923074 A
1 A
42923075 GAGACAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
36 12 0.35
37 14 0.41
38 8 0.24
ACGTcount: A:0.69, C:0.04, G:0.05, T:0.22
Consensus pattern (37 bp):
AATAATATAAAACTTAAAAAAGAAAAAAATCTAAGAA
Found at i:42923046 original size:18 final size:18
Alignment explanation
Indices: 42922996--42923047 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
42922986 AAATTTTTTA
*
42922996 AAATTAATAATATAAATT
1 AAATAAATAATATAAATT
** *
42923014 AAATAAGCAAAATAAATT
1 AAATAAATAATATAAATT
42923032 AAGA-AAATAATATAAA
1 AA-ATAAATAATATAAA
42923048 ACTTAAAAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
18 25 0.96
19 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (18 bp):
AAATAAATAATATAAATT
Found at i:42929088 original size:10 final size:10
Alignment explanation
Indices: 42929075--42929178 Score: 66
Period size: 10 Copynumber: 9.5 Consensus size: 10
42929065 AAAAATTACA
42929075 AAAAAAATTT
1 AAAAAAATTT
*
42929085 AAAATAATTT
1 AAAAAAATTT
**
42929095 TTAAAAATTAT
1 AAAAAAATT-T
*
42929106 AAAACTTATATTTT
1 AAAA---A-AATTT
42929120 TAAAAAAATTAT
1 -AAAAAAATT-T
42929132 AATAAAAATTCT
1 AA-AAAAATT-T
*
42929144 AAAAAATATGT
1 AAAAAA-ATTT
42929155 AAAAAAATTT
1 AAAAAAATTT
42929165 -AAAAAATTT
1 AAAAAAATTT
42929174 AAAAA
1 AAAAA
42929179 TTTCTAAAAC
Statistics
Matches: 73, Mismatches: 11, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
9 9 0.12
10 22 0.30
11 19 0.26
12 14 0.19
14 2 0.03
15 7 0.10
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (10 bp):
AAAAAAATTT
Found at i:42929118 original size:24 final size:20
Alignment explanation
Indices: 42929077--42929125 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 20
42929067 AAATTACAAA
42929077 AAAAATTTAAAATAATTTTT
1 AAAAATTTAAAATAATTTTT
42929097 AAAAATTATAAAACTTATATTTTT
1 AAAAATT-TAAAA--TA-ATTTTT
42929121 AAAAA
1 AAAAA
42929126 AATTATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.28
21 5 0.20
23 2 0.08
24 11 0.44
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAAATTTAAAATAATTTTT
Found at i:42929159 original size:12 final size:10
Alignment explanation
Indices: 42929118--42929178 Score: 70
Period size: 11 Copynumber: 5.8 Consensus size: 10
42929108 AACTTATATT
42929118 TTTAAAAAAA
1 TTTAAAAAAA
42929128 TTATAATAAAAA
1 TT-TAA-AAAAA
42929140 TTCTAAAAAATA
1 TT-TAAAAAA-A
*
42929152 TGTAAAAAAA
1 TTTAAAAAAA
42929162 TTT-AAAAAA
1 TTTAAAAAAA
42929171 TTTAAAAA
1 TTTAAAAA
42929179 TTTCTAAAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
9 9 0.20
10 9 0.20
11 14 0.32
12 12 0.27
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (10 bp):
TTTAAAAAAA
Found at i:42929187 original size:10 final size:9
Alignment explanation
Indices: 42929135--42929178 Score: 52
Period size: 9 Copynumber: 4.4 Consensus size: 9
42929125 AAATTATAAT
42929135 AAAAATTCTA
1 AAAAATT-TA
42929145 AAAAATATGTAA
1 AAAAAT-T-T-A
42929157 AAAAATTTA
1 AAAAATTTA
42929166 AAAAATTTA
1 AAAAATTTA
42929175 AAAA
1 AAAA
42929179 TTTCTAAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
9 14 0.45
10 7 0.23
11 3 0.10
12 7 0.23
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (9 bp):
AAAAATTTA
Found at i:42930185 original size:23 final size:22
Alignment explanation
Indices: 42930155--42930203 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
42930145 ATTTAATCAA
*
42930155 AATTAATTTTAAT-GATTAATTT
1 AATTAA-TTTAATCGATTAATTC
42930177 AATTCAATTTAATCGATTAATTC
1 AATT-AATTTAATCGATTAATTC
42930200 AATT
1 AATT
42930204 TAAACCTCGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (22 bp):
AATTAATTTAATCGATTAATTC
Found at i:42942816 original size:20 final size:19
Alignment explanation
Indices: 42942786--42942824 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
42942776 TAATATTTTA
42942786 TAAAAAATCAACAAATTAT
1 TAAAAAATCAACAAATTAT
42942805 TAAAAAATTCAACAAATTAT
1 TAAAAAA-TCAACAAATTAT
42942825 AAAGAAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (19 bp):
TAAAAAATCAACAAATTAT
Found at i:42942827 original size:19 final size:18
Alignment explanation
Indices: 42942783--42942827 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 18
42942773 ACATAATATT
42942783 TTATAAAAAATCAACAAA
1 TTATAAAAAATCAACAAA
42942801 TTATTAAAAAATTCAACAAA
1 TTA-TAAAAAA-TCAACAAA
42942821 TTATAAA
1 TTATAAA
42942828 GAAAAAGTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.12
19 11 0.44
20 11 0.44
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (18 bp):
TTATAAAAAATCAACAAA
Found at i:42943646 original size:20 final size:20
Alignment explanation
Indices: 42943590--42943651 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
42943580 TTTAGTGATA
*
42943590 TAATAAATTA-TTAATATAAT
1 TAATAAATTATTTAATAT-TT
* *
42943610 AAATAAA--ATTTATTATTT
1 TAATAAATTATTTAATATTT
42943628 TAATAAATTATTTAATATTT
1 TAATAAATTATTTAATATTT
42943648 TAAT
1 TAAT
42943652 TTTATTTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
18 8 0.24
19 6 0.18
20 20 0.59
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TAATAAATTATTTAATATTT
Found at i:42943748 original size:15 final size:15
Alignment explanation
Indices: 42943714--42943782 Score: 61
Period size: 15 Copynumber: 4.5 Consensus size: 15
42943704 ATATTATTGA
42943714 AAATA-TTTAAT-AT
1 AAATATTTTAATAAT
*
42943727 TAATATTTTAATAAT
1 AAATATTTTAATAAT
*
42943742 AAATATTTATTACAATTAT
1 AAATA-TT-TT--AATAAT
*
42943761 AAATATATTAATAAT
1 AAATATTTTAATAAT
42943776 AAATATT
1 AAATATT
42943783 CATAAGTCCA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
13 4 0.09
14 6 0.14
15 17 0.39
16 2 0.05
17 4 0.09
18 1 0.02
19 10 0.23
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (15 bp):
AAATATTTTAATAAT
Found at i:42946287 original size:3 final size:3
Alignment explanation
Indices: 42946279--42946324 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
42946269 AAATCATAAG
42946279 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
42946325 TAAACGAACT
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:42955150 original size:27 final size:27
Alignment explanation
Indices: 42955119--42955270 Score: 189
Period size: 27 Copynumber: 5.6 Consensus size: 27
42955109 TAAATTGTAC
42955119 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
42955146 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42955172 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
42955200 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
42955228 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
42955255 AGCACTAAGTGTGCGA
1 AGCACTAAGTGTGCGA
42955271 GTGGAAAGTT
Statistics
Matches: 107, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
27 84 0.79
28 23 0.21
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:42955233 original size:82 final size:81
Alignment explanation
Indices: 42955120--42955270 Score: 232
Period size: 82 Copynumber: 1.9 Consensus size: 81
42955110 AAATTGTACA
* *
42955120 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
42955184 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
42955201 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
42955266 TGCGA
65 TGCGA
42955271 GTGGAAAGTT
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 15 0.24
82 47 0.75
83 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:42955260 original size:55 final size:54
Alignment explanation
Indices: 42955119--42955272 Score: 193
Period size: 55 Copynumber: 2.8 Consensus size: 54
42955109 TAAATTGTAC
* *
42955119 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGA-AATGAATATG
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTATGAATATG
* * ** * *
42955172 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTTGACTATG
1 A-GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTATGAATATG
* *
42955227 TAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGTGCGAGT
1 -AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGT
42955273 GGAAAGTTAG
Statistics
Matches: 85, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
53 1 0.01
54 38 0.45
55 45 0.53
56 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (54 bp):
AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTATGAATATG
Found at i:42956018 original size:12 final size:13
Alignment explanation
Indices: 42955995--42956019 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42955985 ACCTTAGGCC
42955995 AATACAAAAAAAG
1 AATACAAAAAAAG
42956008 AATACAAAAAAA
1 AATACAAAAAAA
42956020 CTTATGGCTA
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:0.80, C:0.08, G:0.04, T:0.08
Consensus pattern (13 bp):
AATACAAAAAAAG
Found at i:42957969 original size:25 final size:23
Alignment explanation
Indices: 42957927--42957979 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 23
42957917 AAATTTATTT
*
42957927 TTATTATTAGTTCTATTATTGCTA
1 TTATTATTAGTTCCATTATT-CTA
42957951 CTTATTATTA-TTGCCATTATTCTA
1 -TTATTATTAGTT-CCATTATTCTA
42957975 TTATT
1 TTATT
42957980 TCTTATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 5 0.19
24 5 0.19
25 16 0.62
ACGTcount: A:0.25, C:0.11, G:0.06, T:0.58
Consensus pattern (23 bp):
TTATTATTAGTTCCATTATTCTA
Found at i:42960986 original size:19 final size:19
Alignment explanation
Indices: 42960962--42961008 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
42960952 AACGTCTCTT
*
42960962 TTTGCATT-CATTTCATACA
1 TTTGCATTACATTGCAT-CA
42960981 TTTGCATTACATTGCATCA
1 TTTGCATTACATTGCATCA
*
42961000 TATGCATTA
1 TTTGCATTA
42961009 GATTTTCACG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTGCATCA
Found at i:42965278 original size:86 final size:86
Alignment explanation
Indices: 42965133--42965396 Score: 402
Period size: 86 Copynumber: 3.1 Consensus size: 86
42965123 AGTAAAAATT
* * * * *
42965133 GAAGATAAACCTTGCCTCTCTCGGTCGTAGCAGAGCTGGTTGAAGTTATCAGATTTTGCCTTCCT
1 GAAGACAAACCTTGCCTCTCTCGTTTGTAGCAGAGCTGGTTGAAGATATCAGATCTTGCCTTCCT
42965198 GCATTGACAGCGAAGCAGATC
66 GCATTGACAGCGAAGCAGATC
* * *
42965219 GAAGACAAACCTTGCCACTCTCGTTTGTAGTAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
1 GAAGACAAACCTTGCCTCTCTCGTTTGTAGCAGAGCTGGTTGAAGATATCAGATCTTGCCTTCCT
*
42965284 GCACTGACAGCGAAGCAGATC
66 GCATTGACAGCGAAGCAGATC
* *
42965305 GAAGACAAACCTTGCCTCTCTCGTTTGTAGCAGAGCTGGTTGAAGATATCAGATCTTGCTTTTCT
1 GAAGACAAACCTTGCCTCTCTCGTTTGTAGCAGAGCTGGTTGAAGATATCAGATCTTGCCTTCCT
* *
42965370 GTATTTGGCAGCGAAGCAGATC
66 GCA-TTGACAGCGAAGCAGATC
42965392 GAAGA
1 GAAGA
42965397 TGGCAGATTT
Statistics
Matches: 160, Mismatches: 17, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
86 139 0.87
87 21 0.13
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.27
Consensus pattern (86 bp):
GAAGACAAACCTTGCCTCTCTCGTTTGTAGCAGAGCTGGTTGAAGATATCAGATCTTGCCTTCCT
GCATTGACAGCGAAGCAGATC
Found at i:42965585 original size:134 final size:134
Alignment explanation
Indices: 42965344--42965619 Score: 482
Period size: 134 Copynumber: 2.1 Consensus size: 134
42965334 GCAGAGCTGG
* * *
42965344 TTGAAGATATCAGATCTTGCTTTTCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTA
1 TTGAAGATATCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTA
* *
42965409 CCTCCCTGACAACAGTGGAGTACATTGAAGCCGATAATTCTATCTCCCTGTATTTGGCAGTGGAA
66 CCTCCCTGACAACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGAAA
42965474 TAGA
131 TAGA
42965478 TTGAAGAT-TGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTT
1 TTGAAGATAT-CAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTT
*
42965542 ACCTCCCTGACCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGAA
65 ACCTCCCTGACAACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGAA
42965607 ATAGA
130 ATAGA
42965612 TTGAAGAT
1 TTGAAGAT
42965620 CAAGGATGGC
Statistics
Matches: 135, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
133 1 0.01
134 134 0.99
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.30
Consensus pattern (134 bp):
TTGAAGATATCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTA
CCTCCCTGACAACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGAAA
TAGA
Found at i:42965635 original size:95 final size:96
Alignment explanation
Indices: 42965521--42965715 Score: 320
Period size: 97 Copynumber: 2.0 Consensus size: 96
42965511 GCAGCGAAGC
42965521 AGATCAAAGATGGCAGATTTTACCTCC-CTGACCACAGTGGAGTACATTGAAGCCGATAACTCTA
1 AGATCAAAGATGGCAGATTTTACCTCCACTGACCACAGTGGAGTACATTGAAGCCGATAACTCTA
42965585 TCTCCCTGTATTTGGCAGTGAAATAGATTGA
66 TCTCCCTGTATTTGGCAGTGAAATAGATTGA
* * * * *
42965616 AGATCAAGGATGGCAGATTTTACCTCCATGTGACTACAGTGGAGTATATTGAAGCCGATAATTCT
1 AGATCAAAGATGGCAGATTTTACCTCCA-CTGACCACAGTGGAGTACATTGAAGCCGATAACTCT
*
42965681 ATCTCCCTGTATTTGGCAGTGGAATAGATTGA
65 ATCTCCCTGTATTTGGCAGTGAAATAGATTGA
42965713 AGA
1 AGA
42965716 AAGCAGATCT
Statistics
Matches: 92, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
95 26 0.28
97 66 0.72
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (96 bp):
AGATCAAAGATGGCAGATTTTACCTCCACTGACCACAGTGGAGTACATTGAAGCCGATAACTCTA
TCTCCCTGTATTTGGCAGTGAAATAGATTGA
Found at i:42965759 original size:44 final size:44
Alignment explanation
Indices: 42965705--42966261 Score: 403
Period size: 44 Copynumber: 12.7 Consensus size: 44
42965695 GGCAGTGGAA
* * *
42965705 TAGATTGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAG
1 TAGATCGAAGAAAGCAGATCTTGTCTTCCTATATTGGCGTGAAG
* * * * * **
42965749 TAGATCGAAGATAGTAGGTCCTATCTTCCTATATTGATAG-GAAG
1 TAGATCGAAGAAAGCAGATCTTGTCTTCCTATATTG-GCGTGAAG
* * * * *
42965793 TGGATCGAAG-ATGCAGATCTTGTCTTCCCATATTGGTGGCGAAG
1 TAGATCGAAGAAAGCAGATCTTGTCTTCCTATATTGG-CGTGAAG
* * * *
42965837 TAGATCGAAGAAAGTAAATCTTGTCTTCATGTATTGGCGTGAAG
1 TAGATCGAAGAAAGCAGATCTTGTCTTCCTATATTGGCGTGAAG
* * * * *
42965881 TAGATCGAAGATAGCAGGTCCTATCTTCCTATATTGGTAG-GAAG
1 TAGATCGAAGAAAGCAGATCTTGTCTTCCTATATTGG-CGTGAAG
* * * * * * *
42965925 TGGATCAAAG-ATGCAGATCTTGTCTTCCCATACTGGTGGCGAAG
1 TAGATCGAAGAAAGCAGATCTTGTCTTCCTATATTGG-CGTGAAG
* * * *
42965969 TAGATCGCAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAG
1 TAGATCGAAGAAAGCAGATCTTGTCTTCCTATATTGGCGTGAAG
* * * * **
42966013 TAGATCGAAGATAGCAGGTCCTATCTTCCTATATTGATAG-GAAG
1 TAGATCGAAGAAAGCAGATCTTGTCTTCCTATATTG-GCGTGAAG
* * * * * *
42966057 TGGATCCAAGATA-CAGATCTTGTCTTCCCATATTGGTGGCGAAG
1 TAGATCGAAGAAAGCAGATCTTGTCTTCCTATATTGG-CGTGAAG
* **
42966101 TAGATCGAAG-ATGCAGATCTTGTCTTCCTATATTGATAG-GAAG
1 TAGATCGAAGAAAGCAGATCTTGTCTTCCTATATTG-GCGTGAAG
* * * * * *
42966144 TGGATCGAAG-ATGCAGATCTTGTCTTCCCATTTTGGTGGCGAAG
1 TAGATCGAAGAAAGCAGATCTTGTCTTCCTATATTGG-CGTGAAG
* * * *
42966188 TAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTAAAG
1 TAGATCGAAGAAAGCAGATCTTGTCTTCCTATATTGGCGTGAAG
** * *
42966232 TAGATCGAAGATTGTAGATCTTGCCTTCCT
1 TAGATCGAAGAAAGCAGATCTTGTCTTCCT
42966262 GAAGTTGACA
Statistics
Matches: 393, Mismatches: 105, Indels: 30
0.74 0.20 0.06
Matches are distributed among these distances:
43 96 0.24
44 233 0.59
45 64 0.16
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (44 bp):
TAGATCGAAGAAAGCAGATCTTGTCTTCCTATATTGGCGTGAAG
Found at i:42965942 original size:132 final size:132
Alignment explanation
Indices: 42965705--42966127 Score: 731
Period size: 132 Copynumber: 3.2 Consensus size: 132
42965695 GGCAGTGGAA
* *
42965705 TAGATTGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGTAGGTCC
1 TAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCC
*
42965770 TATCTTCCTATATTGATAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGA
66 TATCTTCCTATATTGATAGGAAGTGGATCAAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGA
42965835 AG
131 AG
* *
42965837 TAGATCGAAGAAAGTAAATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCC
1 TAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCC
* *
42965902 TATCTTCCTATATTGGTAGGAAGTGGATCAAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGA
66 TATCTTCCTATATTGATAGGAAGTGGATCAAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGA
42965967 AG
131 AG
* *
42965969 TAGATCGCAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCC
1 TAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCC
* *
42966034 TATCTTCCTATATTGATAGGAAGTGGATCCAAGATACAGATCTTGTCTTCCCATATTGGTGGCGA
66 TATCTTCCTATATTGATAGGAAGTGGATCAAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGA
42966099 AG
131 AG
*
42966101 TAGATCGAAG-ATGCAGATCTTGTCTTC
1 TAGATCGAAGAAAGCAGATCTTGTCTTC
42966128 CTATATTGAT
Statistics
Matches: 273, Mismatches: 18, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
131 15 0.05
132 258 0.95
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.30
Consensus pattern (132 bp):
TAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCC
TATCTTCCTATATTGATAGGAAGTGGATCAAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGA
AG
Found at i:42966206 original size:132 final size:132
Alignment explanation
Indices: 42965705--42966215 Score: 633
Period size: 132 Copynumber: 3.9 Consensus size: 132
42965695 GGCAGTGGAA
* * * * *
42965705 TAGATTGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGTAGGTCC
1 TAGATCGAAGAAAGCAGATCTTGTCTTCATATATTGGAGTGAAGTAGATCGAAGATAGCAGATCC
*
42965770 TATCTTCCTATATTGATAGGAAGTGGAT-C-GAAGATGCAGATCTTGTCTTCCCATATTGGTGGC
66 TATCTTCCTATATTGGTAGGAAGTGGATCCAGAA-A-GCAGATCTTGTCTTCCCATATTGGTGGC
42965833 GAAG
129 GAAG
* * * * *
42965837 TAGATCGAAGAAAGTAAATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCC
1 TAGATCGAAGAAAGCAGATCTTGTCTTCATATATTGGAGTGAAGTAGATCGAAGATAGCAGATCC
*
42965902 TATCTTCCTATATTGGTAGGAAGTGGAT-CA-AAGATGCAGATCTTGTCTTCCCATACTGGTGGC
66 TATCTTCCTATATTGGTAGGAAGTGGATCCAGAA-A-GCAGATCTTGTCTTCCCATATTGGTGGC
42965965 GAAG
129 GAAG
* * * * *
42965969 TAGATCGCAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCC
1 TAGATCGAAGAAAGCAGATCTTGTCTTCATATATTGGAGTGAAGTAGATCGAAGATAGCAGATCC
* *
42966034 TATCTTCCTATATTGATAGGAAGTGGATCCAAGATA-CAGATCTTGTCTTCCCATATTGGTGGCG
66 TATCTTCCTATATTGGTAGGAAGTGGATCC-AGAAAGCAGATCTTGTCTTCCCATATTGGTGGCG
42966098 AAG
130 AAG
* * * *
42966101 TAGATCGAAG-ATGCAGATCTTGTCTTCCTATATTGATAG-GAAGTGGATCGAAGAT-GCAGATC
1 TAGATCGAAGAAAGCAGATCTTGTCTTCATATATTG-GAGTGAAGTAGATCGAAGATAGCAGATC
* * * * * *
42966163 TTGTCTTCCCATTTTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTC
65 CTATCTTCCTATATTGGTAG-GAAGTGGATC-CAGAAAGCAGATCTTGTCTTC
42966216 ATGTATTGGC
Statistics
Matches: 341, Mismatches: 30, Indels: 16
0.88 0.08 0.04
Matches are distributed among these distances:
130 20 0.06
131 49 0.14
132 268 0.79
133 1 0.00
134 2 0.01
135 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.30
Consensus pattern (132 bp):
TAGATCGAAGAAAGCAGATCTTGTCTTCATATATTGGAGTGAAGTAGATCGAAGATAGCAGATCC
TATCTTCCTATATTGGTAGGAAGTGGATCCAGAAAGCAGATCTTGTCTTCCCATATTGGTGGCGA
AG
Found at i:42966207 original size:264 final size:264
Alignment explanation
Indices: 42965713--42966215 Score: 760
Period size: 264 Copynumber: 1.9 Consensus size: 264
42965703 AATAGATTGA
* *
42965713 AGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGTAGGTCCTATCTTCC
1 AGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCC
* *
42965778 TATATTGATAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATC
66 TATATTGATAGGAAGTGGATCCAAGATACAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATC
* * * *
42965843 GAAGAAAGTAAATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTT
131 GAAGAAAGCAAATCTTGTCTTCATATATTGGAGTGAAGTAGATCGAAGATAGCAGATCCTATCTT
* * *
42965908 CCTATATTGGTAGGAAGTGGATCAAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGA
196 CCCATATTGGTAGGAAGTAGATCAAAGAAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGA
42965973 TCGC
261 TCGC
42965977 AGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCC
1 AGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCC
42966042 TATATTGATAGGAAGTGGATCCAAGATACAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATC
66 TATATTGATAGGAAGTGGATCCAAGATACAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATC
* * * * * * *
42966107 GAAG-ATGCAGATCTTGTCTTCCTATATTGATAG-GAAGTGGATCGAAGAT-GCAGATCTTGTCT
131 GAAGAAAGCAAATCTTGTCTTCATATATTG-GAGTGAAGTAGATCGAAGATAGCAGATCCTATCT
* * **
42966169 TCCCATTTTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTC
195 TCCCATATTGGTAG-GAAGTAGATCAAAG-AAGCAGATCTTGTCTTC
42966216 ATGTATTGGC
Statistics
Matches: 214, Mismatches: 22, Indels: 6
0.88 0.09 0.02
Matches are distributed among these distances:
262 21 0.10
263 46 0.21
264 147 0.69
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (264 bp):
AGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCC
TATATTGATAGGAAGTGGATCCAAGATACAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATC
GAAGAAAGCAAATCTTGTCTTCATATATTGGAGTGAAGTAGATCGAAGATAGCAGATCCTATCTT
CCCATATTGGTAGGAAGTAGATCAAAGAAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGA
TCGC
Found at i:42968030 original size:25 final size:23
Alignment explanation
Indices: 42967988--42968040 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 23
42967978 AAATTTATTT
*
42967988 TTATTATTAGTTCTATTATTGCTA
1 TTATTATTAGTTCCATTATT-CTA
42968012 CTTATTATTA-TTGCCATTATTCTA
1 -TTATTATTAGTT-CCATTATTCTA
42968036 TTATT
1 TTATT
42968041 TCTTATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 5 0.19
24 5 0.19
25 16 0.62
ACGTcount: A:0.25, C:0.11, G:0.06, T:0.58
Consensus pattern (23 bp):
TTATTATTAGTTCCATTATTCTA
Found at i:42970679 original size:19 final size:19
Alignment explanation
Indices: 42970655--42970701 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
42970645 AACGTCTCTT
*
42970655 TTTGCATT-CATTTCATACA
1 TTTGCATTACATTGCAT-CA
42970674 TTTGCATTACATTGCATCA
1 TTTGCATTACATTGCATCA
*
42970693 TATGCATTA
1 TTTGCATTA
42970702 GATTTTCACG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTGCATCA
Found at i:42976184 original size:18 final size:18
Alignment explanation
Indices: 42976161--42976198 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
42976151 TGGTAATTTA
42976161 TTTATTATTTTATTTTGT
1 TTTATTATTTTATTTTGT
* *
42976179 TTTATTGTTTTGTTTTGT
1 TTTATTATTTTATTTTGT
42976197 TT
1 TT
42976199 GGATGCTGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.79
Consensus pattern (18 bp):
TTTATTATTTTATTTTGT
Found at i:42983168 original size:28 final size:28
Alignment explanation
Indices: 42983135--42983190 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
42983125 ATGATGTTTC
42983135 AACTCAAAACTTACTAGGAATATGTTCA
1 AACTCAAAACTTACTAGGAATATGTTCA
42983163 AACTCAAAACTTACTAGGAATATGTTCA
1 AACTCAAAACTTACTAGGAATATGTTCA
42983191 TTCTTTTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.29
Consensus pattern (28 bp):
AACTCAAAACTTACTAGGAATATGTTCA
Found at i:42988468 original size:26 final size:26
Alignment explanation
Indices: 42988439--42988542 Score: 156
Period size: 26 Copynumber: 4.0 Consensus size: 26
42988429 TGGTACAAAT
42988439 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
42988465 TGATAAT-GGATTAGGTAAATATTCCA
1 TGATAATAGG-TTAGGTAAATGTTCCA
* *
42988491 TGATAATGGGTTAGATAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
42988517 TGATAATAGTTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
42988543 CGATGGGCAT
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
25 2 0.03
26 66 0.94
27 2 0.03
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:42988617 original size:17 final size:17
Alignment explanation
Indices: 42988595--42988643 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
42988585 TGAAATATGA
42988595 ATGTGGGCATGTCTAGG
1 ATGTGGGCATGTCTAGG
*
42988612 ATGTGGGCA---AT-GG
1 ATGTGGGCATGTCTAGG
42988625 ATGTGGGCATGTCTAGG
1 ATGTGGGCATGTCTAGG
42988642 AT
1 AT
42988644 TGGATCCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
13 11 0.42
14 1 0.04
16 1 0.04
17 13 0.50
ACGTcount: A:0.20, C:0.10, G:0.41, T:0.29
Consensus pattern (17 bp):
ATGTGGGCATGTCTAGG
Found at i:42992446 original size:20 final size:20
Alignment explanation
Indices: 42992421--42992460 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
42992411 ACAGCATTGA
*
42992421 ATAGCTAATCTTTAGGGATT
1 ATAGCTAATCTTTAGAGATT
* *
42992441 ATAGCTGATTTTTAGAGATT
1 ATAGCTAATCTTTAGAGATT
42992461 CTAATTAGAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.42
Consensus pattern (20 bp):
ATAGCTAATCTTTAGAGATT
Found at i:43002055 original size:28 final size:29
Alignment explanation
Indices: 43002023--43002138 Score: 112
Period size: 28 Copynumber: 4.0 Consensus size: 29
43002013 TACCTGTATC
* *
43002023 TGGCCCATTAAGCCC-AATCATATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
* *
43002051 TGGCCCATTAGGCCCAAACCACCTGT-ATA
1 TGGCCCATTAGGCCCAAATCACAT-TCATA
* *
43002080 TGGCCCATTAGGCCCAAAATCACATTTACA
1 TGGCCCATTAGGCCC-AAATCACATTCATA
* * *
43002110 TGGCCCATTATGTCC-AGTCACATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
43002138 T
1 T
43002139 TCATGTTCAC
Statistics
Matches: 72, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
28 25 0.35
29 24 0.33
30 23 0.32
ACGTcount: A:0.29, C:0.30, G:0.14, T:0.27
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTCATA
Found at i:43002088 original size:29 final size:29
Alignment explanation
Indices: 43002014--43002097 Score: 100
Period size: 29 Copynumber: 2.9 Consensus size: 29
43002004 AATTTCACAT
* * *
43002014 ACCTGTATCTGGCCCATTAAGCCC-AATC
1 ACCTGTATATGGCCCATTAGGCCCAAACC
**
43002042 ATAT-TCATATGGCCCATTAGGCCCAAACC
1 ACCTGT-ATATGGCCCATTAGGCCCAAACC
43002071 ACCTGTATATGGCCCATTAGGCCCAAA
1 ACCTGTATATGGCCCATTAGGCCCAAA
43002098 ATCACATTTA
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
27 1 0.02
28 18 0.39
29 26 0.57
30 1 0.02
ACGTcount: A:0.29, C:0.32, G:0.15, T:0.24
Consensus pattern (29 bp):
ACCTGTATATGGCCCATTAGGCCCAAACC
Found at i:43003686 original size:17 final size:17
Alignment explanation
Indices: 43003651--43003934 Score: 74
Period size: 19 Copynumber: 14.8 Consensus size: 17
43003641 TATTCTTTTT
43003651 AATTAAATTCTATTTTTTAA
1 AATTAAATT-TA--TTTTAA
43003671 AATTAAATTTATTTTAAA
1 AATTAAATTTATTTT-AA
* *
43003689 CTTTAATTAATTTTGATTTTTTA
1 ----AATTAAATTT-A-TTTTAA
* *
43003712 AATTAAATTAAATTTTTTA
1 AATTAAATT-TA-TTTTAA
43003731 AATTAAATTTATTTTAA
1 AATTAAATTTATTTTAA
*
43003748 ACTTTAATTCATTTATTTTCAA
1 A-ATTAA---ATTTATTTT-AA
*
43003770 CTTTAATTAATTTTGATTTTTAA
1 ----AATTAAATTT-A-TTTTAA
* *
43003793 AATTTTATTTTATTTTTTAA
1 AA-TTAAATTTA--TTTTAA
43003813 AATTAAATTTATTTTAA
1 AATTAAATTTATTTTAA
* *
43003830 AATTTAATTAATTTATTTCATT
1 AA-TT-A--AATTTATTTTA-A
*
43003852 AATTAATTTTTATTGTT--
1 AATTAA-ATTTATT-TTAA
*
43003869 --TTAAATAT-TTTTAA
1 AATTAAATTTATTTTAA
43003883 AATTAAATTTATTTTAA
1 AATTAAATTTATTTTAA
*
43003900 ACTTTAATTAATTTATTTTAA
1 A-ATT-A--AATTTATTTTAA
*
43003921 AATTTAATTTATTT
1 AATTAAATTTATTT
43003935 ATTTATTTAT
Statistics
Matches: 205, Mismatches: 22, Indels: 77
0.67 0.07 0.25
Matches are distributed among these distances:
12 2 0.01
13 2 0.01
14 2 0.01
15 4 0.02
16 7 0.03
17 34 0.17
18 12 0.06
19 45 0.22
20 29 0.14
21 34 0.17
22 16 0.08
23 5 0.02
24 8 0.04
25 4 0.02
26 1 0.00
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (17 bp):
AATTAAATTTATTTTAA
Found at i:43003731 original size:14 final size:14
Alignment explanation
Indices: 43003714--43003740 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
43003704 ATTTTTTAAA
43003714 TTAAATTAAATTTT
1 TTAAATTAAATTTT
43003728 TTAAATTAAATTT
1 TTAAATTAAATTT
43003741 ATTTTAAACT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTAAATTAAATTTT
Found at i:43003738 original size:60 final size:60
Alignment explanation
Indices: 43003646--43003761 Score: 189
Period size: 60 Copynumber: 1.9 Consensus size: 60
43003636 TTAATTATTC
**
43003646 TTTTTAATTAAATTCTATTTTTTAAAATTAAATTTATTTTAAACTTTAATTAATTTTGAT
1 TTTTTAATTAAATTAAATTTTTTAAAATTAAATTTATTTTAAACTTTAATTAATTTTGAT
*
43003706 TTTTTAAATTAAATTAAATTTTTT-AAATTAAATTTATTTTAAACTTTAATTCATTT
1 TTTTT-AATTAAATTAAATTTTTTAAAATTAAATTTATTTTAAACTTTAATTAATTT
43003762 ATTTTCAACT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
60 36 0.69
61 16 0.31
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (60 bp):
TTTTTAATTAAATTAAATTTTTTAAAATTAAATTTATTTTAAACTTTAATTAATTTTGAT
Found at i:43003763 original size:21 final size:21
Alignment explanation
Indices: 43003731--43004029 Score: 166
Period size: 21 Copynumber: 13.6 Consensus size: 21
43003721 AAATTTTTTA
*
43003731 AATTAAATTTATTTTAAACTTT
1 AATT-AATTTATTTTAAAATTT
* * *
43003753 AATTCATTTATTTTCAACTTT
1 AATTAATTTATTTTAAAATTT
43003774 AATTAATTTTGATTTTTAAAATTT
1 AATTAA-TTT-A-TTTTAAAATTT
* *
43003798 TATT--TTATTTTTTAAAA-TT
1 AATTAATT-TATTTTAAAATTT
43003817 -A--AATTTATTTTAAAATTT
1 AATTAATTTATTTTAAAATTT
* *
43003835 AATTAATTTATTTCATTAA-TT
1 AATTAATTTATTTTA-AAATTT
** *
43003856 AATTTTTATTGTTTTAAATATTTTT
1 AATTAAT-TTATTTTAAA-A--TTT
*
43003881 AAAATTAAATTTATTTTAAACTTT
1 --AATT-AATTTATTTTAAAATTT
43003905 AATTAATTTATTTTAAAATTT
1 AATTAATTTATTTTAAAATTT
* **
43003926 AATTTATTTA-TTTATTTATTT
1 AATTAATTTATTTTA-AAATTT
* *
43003947 AATT-TTGATTGTTTTAAATATTTTT
1 AATTAAT--TTATTTTAAA-A--TTT
*
43003972 AAAATTAAATTTATTTTAAACTTT
1 --AATT-AATTTATTTTAAAATTT
43003996 AATTAATTTATTTTAAAATTT
1 AATTAATTTATTTTAAAATTT
*
43004017 AATTTATTTATTT
1 AATTAATTTATTT
43004030 CTTTAATTAA
Statistics
Matches: 215, Mismatches: 32, Indels: 61
0.70 0.10 0.20
Matches are distributed among these distances:
17 9 0.04
18 5 0.02
19 3 0.01
20 13 0.06
21 101 0.47
22 27 0.13
23 6 0.03
24 18 0.08
25 5 0.02
27 26 0.12
28 1 0.00
29 1 0.00
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (21 bp):
AATTAATTTATTTTAAAATTT
Found at i:43003949 original size:38 final size:39
Alignment explanation
Indices: 43003877--43004042 Score: 140
Period size: 38 Copynumber: 4.0 Consensus size: 39
43003867 TTTTAAATAT
* **
43003877 TTTTAAAATTAAATTTATTT-TAAACTTTAATTAATTTA
1 TTTTAAAATTTAATTTATTTATTTACTTTAATTAATTTA
*
43003915 TTTTAAAATTTAATTTATTTATTTA-TTTATTTAATTTTGA
1 TTTTAAAATTTAATTTATTTATTTACTTTAATTAA-TTT-A
*
43003955 TTGTTTTAAATATTTTTAAAATTAAATTTATTTTAAACTTTAATTAATTTA
1 ---TTTTAAA-A--TTT--AATT-TATTTA-TTT--ACTTTAATTAATTTA
43004006 TTTTAAAATTTAATTTATTTATTT-CTTTAATTAATTT
1 TTTTAAAATTTAATTTATTTATTTACTTTAATTAATTT
43004043 TGATTGTTTT
Statistics
Matches: 105, Mismatches: 7, Indels: 32
0.73 0.05 0.22
Matches are distributed among these distances:
38 40 0.38
39 5 0.05
40 1 0.01
41 3 0.03
42 5 0.05
43 11 0.10
44 1 0.01
45 3 0.03
46 3 0.03
47 1 0.01
48 11 0.10
49 5 0.05
50 3 0.03
51 1 0.01
52 4 0.04
53 8 0.08
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (39 bp):
TTTTAAAATTTAATTTATTTATTTACTTTAATTAATTTA
Found at i:43003977 original size:53 final size:51
Alignment explanation
Indices: 43003915--43004079 Score: 142
Period size: 53 Copynumber: 3.4 Consensus size: 51
43003905 AATTAATTTA
*
43003915 TTTTAAAATTTAATTTATTTATTTATTTATTTAATTTTGATTGTTTTAAATAT
1 TTTTAAAATTAAATTTATTT-TTTATTTA-TTAATTTTGATTGTTTTAAATAT
**
43003968 TTTTAAAATTAAATTTATTTTAAACTTTAATTAA-TTT-A---TTTTAAA-A-
1 TTTTAAAATTAAATTTATTTTTTA-TTT-ATTAATTTTGATTGTTTTAAATAT
* *
43004014 -TTT--AATT-TATTTATTTCTTTA--A-TTAATTTTGATTGTTTTAAATAT
1 TTTTAAAATTAAATTTATTT-TTTATTTATTAATTTTGATTGTTTTAAATAT
43004059 TTTTAAAATTAAATTTATTTT
1 TTTTAAAATTAAATTTATTTT
43004080 AAACTTCAAT
Statistics
Matches: 90, Mismatches: 8, Indels: 33
0.69 0.06 0.25
Matches are distributed among these distances:
38 4 0.04
39 3 0.03
40 1 0.01
42 8 0.09
43 13 0.14
44 1 0.01
45 3 0.03
46 3 0.03
47 1 0.01
48 12 0.13
49 8 0.09
51 1 0.01
52 5 0.06
53 26 0.29
54 1 0.01
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.61
Consensus pattern (51 bp):
TTTTAAAATTAAATTTATTTTTTATTTATTAATTTTGATTGTTTTAAATAT
Found at i:43004082 original size:17 final size:17
Alignment explanation
Indices: 43003968--43004025 Score: 62
Period size: 17 Copynumber: 3.2 Consensus size: 17
43003958 TTTTAAATAT
43003968 TTTTAAAATTAAATTTA
1 TTTTAAAATTAAATTTA
*
43003985 TTTTAAACTTTAATTAATTTA
1 TTTTAAA-ATT-A--AATTTA
*
43004006 TTTTAAAATTTAATTTA
1 TTTTAAAATTAAATTTA
43004023 TTT
1 TTT
43004026 ATTTCTTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
17 16 0.47
18 2 0.06
19 1 0.03
20 2 0.06
21 13 0.38
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTAAAATTAAATTTA
Found at i:43004134 original size:91 final size:91
Alignment explanation
Indices: 43003813--43004096 Score: 498
Period size: 91 Copynumber: 3.1 Consensus size: 91
43003803 TATTTTTTAA
* *
43003813 AATTAAATTTATTTTAAAATTTAATTAATTTATTTCA-TTAATTAATTTTTATTGTTTTAAATAT
1 AATT-AATTTATTTTAAAATTTAATTTATTTATTT-ATTTAATTAATTTTGATTGTTTTAAATAT
43003877 TTTTAAAATTAAATTTATTTTAAACTTT
64 TTTTAAAATTAAATTTATTTTAAACTTT
*
43003905 AATTAATTTATTTTAAAATTTAATTTATTTATTTATTTATTTAATTTTGATTGTTTTAAATATTT
1 AATTAATTTATTTTAAAATTTAATTTATTTATTTATTTAATTAATTTTGATTGTTTTAAATATTT
43003970 TTAAAATTAAATTTATTTTAAACTTT
66 TTAAAATTAAATTTATTTTAAACTTT
*
43003996 AATTAATTTATTTTAAAATTTAATTTATTTATTTCTTTAATTAATTTTGATTGTTTTAAATATTT
1 AATTAATTTATTTTAAAATTTAATTTATTTATTTATTTAATTAATTTTGATTGTTTTAAATATTT
*
43004061 TTAAAATTAAATTTATTTTAAACTTC
66 TTAAAATTAAATTTATTTTAAACTTT
43004087 AATTAATTTA
1 AATTAATTTA
43004097 CTTCTTTAAT
Statistics
Matches: 185, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
90 1 0.01
91 180 0.97
92 4 0.02
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (91 bp):
AATTAATTTATTTTAAAATTTAATTTATTTATTTATTTAATTAATTTTGATTGTTTTAAATATTT
TTAAAATTAAATTTATTTTAAACTTT
Found at i:43004288 original size:19 final size:19
Alignment explanation
Indices: 43004250--43004288 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
43004240 TTATCATTAG
* *
43004250 ATACAAAATTGATTTGCAA
1 ATACAAAATTGATCTACAA
*
43004269 ATACAATATTGATCTACAA
1 ATACAAAATTGATCTACAA
43004288 A
1 A
43004289 GATAAATTAT
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:0.49, C:0.13, G:0.08, T:0.31
Consensus pattern (19 bp):
ATACAAAATTGATCTACAA
Found at i:43004828 original size:72 final size:72
Alignment explanation
Indices: 43004711--43004854 Score: 252
Period size: 72 Copynumber: 2.0 Consensus size: 72
43004701 CGGTCCAAGT
*
43004711 TAAAACTGTAACACCCCTTGCCCGCATCCGACGCCGGGACGGGGTTCAAGGTGCTACCTGACTTT
1 TAAAACTGTAACACCCCTCGCCCGCATCCGACGCCGGGACGGGGTTCAAGGTGCTACCTGACTTT
43004776 TACTAAC
66 TACTAAC
* * *
43004783 TAAAACTGTAACACCTCTCGCCCGCATCCGACGTCGGGACGGGGTTCGAGGTGCTACCTGACTTT
1 TAAAACTGTAACACCCCTCGCCCGCATCCGACGCCGGGACGGGGTTCAAGGTGCTACCTGACTTT
43004848 TACTAAC
66 TACTAAC
43004855 ACTTCCATAC
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.23, C:0.31, G:0.23, T:0.23
Consensus pattern (72 bp):
TAAAACTGTAACACCCCTCGCCCGCATCCGACGCCGGGACGGGGTTCAAGGTGCTACCTGACTTT
TACTAAC
Found at i:43006765 original size:46 final size:46
Alignment explanation
Indices: 43006698--43006872 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
43006688 TGTAACCCAC
43006698 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
43006744 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCGCAT
* * * ** *
43006794 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
43006837 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
43006873 ATGCTCAACC
Statistics
Matches: 109, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 63 0.58
47 26 0.24
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
Found at i:43006818 original size:93 final size:93
Alignment explanation
Indices: 43006706--43006876 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
43006696 ACCCATAAGT
** *
43006706 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
43006771 CGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
*
43006799 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
43006864 CGAGTTCGGATGC
66 CGAGCTCGGATGC
43006877 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:43008336 original size:21 final size:21
Alignment explanation
Indices: 43008303--43008356 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
43008293 AAAATAGGGC
* *
43008303 ACACGCCCATGTGGAATGGTA
1 ACACGCCCGTGTGGAAGGGTA
*
43008324 ACACTCCCGTGTGGAAGGGTA
1 ACACGCCCGTGTGGAAGGGTA
43008345 ACACGCCCGTGT
1 ACACGCCCGTGT
43008357 CCCACACCCG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.24, C:0.28, G:0.30, T:0.19
Consensus pattern (21 bp):
ACACGCCCGTGTGGAAGGGTA
Found at i:43011682 original size:39 final size:38
Alignment explanation
Indices: 43011599--43011682 Score: 87
Period size: 39 Copynumber: 2.2 Consensus size: 38
43011589 TCAAAGACAA
*
43011599 TTTAAAAAAATACAAAATGATAAATCTTGAAAAAATAT
1 TTTAAAAAAATACAAAATGATAAATCTTGAAAAAAGAT
* * * * * * *
43011637 TATAAAAAATATACAAACTGATGATTTTTTAAAATAGAT
1 TTTAAAAAA-ATACAAAATGATAAATCTTGAAAAAAGAT
43011676 TTTAAAA
1 TTTAAAA
43011683 TTTATGCACC
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
38 8 0.22
39 28 0.78
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.33
Consensus pattern (38 bp):
TTTAAAAAAATACAAAATGATAAATCTTGAAAAAAGAT
Found at i:43014656 original size:14 final size:15
Alignment explanation
Indices: 43014626--43014672 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
43014616 ATAACTTAAA
43014626 TTTAATATTTAAATT
1 TTTAATATTTAAATT
43014641 TTTAATATTT-AATT
1 TTTAATATTTAAATT
**
43014655 TTTCAGCATTTAAATT
1 TTT-AATATTTAAATT
43014671 TT
1 TT
43014673 CAATTTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 7 0.25
15 15 0.54
16 6 0.21
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (15 bp):
TTTAATATTTAAATT
Found at i:43014718 original size:13 final size:13
Alignment explanation
Indices: 43014700--43014725 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43014690 TAATATTTTT
43014700 ACTTTTATAATAG
1 ACTTTTATAATAG
43014713 ACTTTTATAATAG
1 ACTTTTATAATAG
43014726 GTAGAAACTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
ACTTTTATAATAG
Found at i:43018780 original size:6 final size:6
Alignment explanation
Indices: 43018771--43018911 Score: 60
Period size: 6 Copynumber: 23.0 Consensus size: 6
43018761 CATCAACTAT
** *
43018771 ATTATA ATTATA ATTATA ACCATA ATTAATA TATTAATA A--ATA A-AATA
1 ATTATA ATTATA ATTATA ATTATA ATT-ATA -ATT-ATA ATTATA ATTATA
* * *
43018819 ATTATA ATTAT- ATTGT- ATGATCA ACTAT- ATTATA ATTATA ATTATA
1 ATTATA ATTATA ATTATA ATTAT-A ATTATA ATTATA ATTATA ATTATA
** * * *
43018865 ACCATA ATTAATA TATTAATA AATAAA ATAAAATA ATTATA ATTATA
1 ATTATA ATT-ATA -ATT-ATA ATTATA AT--TATA ATTATA ATTATA
43018912 TTGTATGACA
Statistics
Matches: 103, Mismatches: 21, Indels: 22
0.71 0.14 0.15
Matches are distributed among these distances:
4 4 0.04
5 15 0.15
6 54 0.52
7 12 0.12
8 18 0.17
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.41
Consensus pattern (6 bp):
ATTATA
Found at i:43018855 original size:76 final size:75
Alignment explanation
Indices: 43018762--43018905 Score: 270
Period size: 76 Copynumber: 1.9 Consensus size: 75
43018752 TGATTGCAAC
*
43018762 ATCAACTATATTATAATTATAATTATAACCATAATTAATATATTAATAAATAAAATAATTATAAT
1 ATCAACTATATTATAATTATAATTATAACCATAATTAATATATTAATAAATAAAATAA-AATAAT
43018827 TATATTGTATG
65 TATATTGTATG
43018838 ATCAACTATATTATAATTATAATTATAACCATAATTAATATATTAATAAATAAAATAAAATAATT
1 ATCAACTATATTATAATTATAATTATAACCATAATTAATATATTAATAAATAAAATAAAATAATT
43018903 ATA
66 ATA
43018906 ATTATATTGT
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
75 9 0.13
76 58 0.87
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.40
Consensus pattern (75 bp):
ATCAACTATATTATAATTATAATTATAACCATAATTAATATATTAATAAATAAAATAAAATAATT
ATATTGTATG
Found at i:43019209 original size:26 final size:26
Alignment explanation
Indices: 43019169--43019221 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
43019159 AATTAAAAAA
*
43019169 TTAATTTAATAATTTATCTATTTGAT
1 TTAATTTAATAATTTATCTAATTGAT
*
43019195 TTAATTTAA-ACATTTATTTAATTGAT
1 TTAATTTAATA-ATTTATCTAATTGAT
43019221 T
1 T
43019222 ATATGTTATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.57
Consensus pattern (26 bp):
TTAATTTAATAATTTATCTAATTGAT
Found at i:43024527 original size:66 final size:66
Alignment explanation
Indices: 43024453--43024587 Score: 252
Period size: 66 Copynumber: 2.0 Consensus size: 66
43024443 TATTATATGA
*
43024453 GTTTGATTTGAATTTGCATCATTGCATACACATATCTAATATATATTAAATCTACATCTGCATTG
1 GTTTGATTTGAATTTGCATCATTACATACACATATCTAATATATATTAAATCTACATCTGCATTG
43024518 G
66 G
*
43024519 GTTTGATTTGAATTTGCATCATTACATACTCATATCTAATATATATTAAATCTACATCTGCATTG
1 GTTTGATTTGAATTTGCATCATTACATACACATATCTAATATATATTAAATCTACATCTGCATTG
43024584 G
66 G
43024585 GTT
1 GTT
43024588 GGGATTATGT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (66 bp):
GTTTGATTTGAATTTGCATCATTACATACACATATCTAATATATATTAAATCTACATCTGCATTG
G
Found at i:43033985 original size:36 final size:37
Alignment explanation
Indices: 43033896--43033985 Score: 121
Period size: 37 Copynumber: 2.5 Consensus size: 37
43033886 TGTCGTGGTG
* *
43033896 TGTTATCAGTTGGATTAGCTTTTTGGAACATTTGGCA
1 TGTTATCGGTTGGATTAGCTTTATGGAACATTTGGCA
* *
43033933 TGTTATCGGTTGGATTAGCTCTTAT-GAGCGTTTGGCA
1 TGTTATCGGTTGGATTAGCT-TTATGGAACATTTGGCA
43033970 TGTT-TCGGTTGGATTA
1 TGTTATCGGTTGGATTA
43033986 CTTGTGTACT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
36 12 0.25
37 33 0.69
38 3 0.06
ACGTcount: A:0.18, C:0.11, G:0.28, T:0.43
Consensus pattern (37 bp):
TGTTATCGGTTGGATTAGCTTTATGGAACATTTGGCA
Found at i:43037457 original size:33 final size:31
Alignment explanation
Indices: 43037432--43037519 Score: 101
Period size: 31 Copynumber: 2.9 Consensus size: 31
43037422 GAGGATTTGC
43037432 TTGAAAAAGTTTGGCCCTTATTTGAGCATTT
1 TTGAAAAAGTTTGGCCCTTATTTGAGCATTT
* ** *
43037463 TTTAAAAAGTTTGGTTCTTATTTGACCA-TT
1 TTGAAAAAGTTTGGCCCTTATTTGAGCATTT
*
43037493 TTG-AAAAGTTT-GACCTTCATTTGAGCA
1 TTGAAAAAGTTTGGCCCTT-ATTTGAGCA
43037520 CATTTATAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
28 4 0.08
29 16 0.33
30 4 0.08
31 24 0.50
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.43
Consensus pattern (31 bp):
TTGAAAAAGTTTGGCCCTTATTTGAGCATTT
Found at i:43037515 original size:60 final size:59
Alignment explanation
Indices: 43037436--43037569 Score: 146
Period size: 60 Copynumber: 2.2 Consensus size: 59
43037426 ATTTGCTTGA
* * * * * *
43037436 AAAAGTTTGGCCCTTATTTGAGCA-TTTTTTAAAAAGTTTGGTTCTTAT-TTGACCATTTTG
1 AAAAGTTT-GACCTTATTTGAGCACATTTAT-AAAAGTTAGGTCCATATATT-ACCATTTTG
*
43037496 AAAAGTTTGACCTTCATTTGAGCACATTTATAAATGTTAGGTCCATATATTACCATTTTG
1 AAAAGTTTGACCTT-ATTTGAGCACATTTATAAAAGTTAGGTCCATATATTACCATTTTG
*
43037556 AAAACTTTGACCTT
1 AAAAGTTTGACCTT
43037570 TATGTTAGCA
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
59 5 0.08
60 52 0.83
61 6 0.10
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (59 bp):
AAAAGTTTGACCTTATTTGAGCACATTTATAAAAGTTAGGTCCATATATTACCATTTTG
Found at i:43037524 original size:31 final size:31
Alignment explanation
Indices: 43037435--43037529 Score: 97
Period size: 31 Copynumber: 3.1 Consensus size: 31
43037425 GATTTGCTTG
* **
43037435 AAAAAGTTTGGCCCTTATTTGAGCATTTTTT
1 AAAAAGTTTGGACCTTATTTGAGCACATTTT
**
43037466 AAAAAGTTTGGTTCTTATTTGA-C-CATTTT
1 AAAAAGTTTGGACCTTATTTGAGCACATTTT
*
43037495 GAAAAGTTT-GACCTTCATTTGAGCACATTTAT
1 AAAAAGTTTGGACCTT-ATTTGAGCACATTT-T
43037527 AAA
1 AAA
43037530 TGTTAGGTCC
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
28 4 0.08
29 18 0.35
30 2 0.04
31 25 0.48
32 3 0.06
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.42
Consensus pattern (31 bp):
AAAAAGTTTGGACCTTATTTGAGCACATTTT
Found at i:43037929 original size:17 final size:17
Alignment explanation
Indices: 43037899--43037942 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
43037889 ATAAAAATTC
*
43037899 AAAAATATATATAATCTAG
1 AAAAAAATATA-AAT-TAG
*
43037918 AAAAAAATATAAATTAT
1 AAAAAAATATAAATTAG
43037935 AAAAAAAT
1 AAAAAAAT
43037943 TTACAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 10 0.43
18 3 0.13
19 10 0.43
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (17 bp):
AAAAAAATATAAATTAG
Found at i:43038039 original size:9 final size:9
Alignment explanation
Indices: 43037997--43038039 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
43037987 TATTATTACA
*
43037997 AAAAAAAGT
1 AAAAAATGT
*
43038006 AAAAAGTGT
1 AAAAAATGT
* *
43038015 AAAAATTAT
1 AAAAAATGT
43038024 AAAAAATGT
1 AAAAAATGT
43038033 AAAAAAT
1 AAAAAAT
43038040 ATTTAAAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (9 bp):
AAAAAATGT
Found at i:43038047 original size:18 final size:19
Alignment explanation
Indices: 43038006--43038041 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
43037996 AAAAAAAAGT
*
43038006 AAAAAGTGTAAAAATTATA
1 AAAAAGTGTAAAAAATATA
43038025 AAAAA-TGTAAAAAATAT
1 AAAAAGTGTAAAAAATAT
43038042 TTAAAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (19 bp):
AAAAAGTGTAAAAAATATA
Found at i:43038130 original size:9 final size:9
Alignment explanation
Indices: 43038116--43038150 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
43038106 CTTGAAATTT
43038116 AATTTTTTA
1 AATTTTTTA
43038125 AATTTTTATA
1 AATTTTT-TA
*
43038135 AATTTTTTC
1 AATTTTTTA
43038144 AATTTTT
1 AATTTTT
43038151 ATATATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (9 bp):
AATTTTTTA
Found at i:43038140 original size:19 final size:19
Alignment explanation
Indices: 43038116--43038153 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
43038106 CTTGAAATTT
43038116 AATTTTTTAAATTTTTATA
1 AATTTTTTAAATTTTTATA
*
43038135 AATTTTTTCAATTTTTATA
1 AATTTTTTAAATTTTTATA
43038154 TATTAATTTG
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:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (19 bp):
AATTTTTTAAATTTTTATA
Found at i:43041501 original size:39 final size:39
Alignment explanation
Indices: 43041466--43041544 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
43041456 AAATTTAATT
43041466 TGAATTTGCCACATAGAACATCCAAGTTGGTATTTAAAA
1 TGAATTTGCCACATAGAACATCCAAGTTGGTATTTAAAA
* * *
43041505 TGGATTTGCCATATAGGACATCCAAGTTGGTATTTAAAA
1 TGAATTTGCCACATAGAACATCCAAGTTGGTATTTAAAA
43041544 T
1 T
43041545 TGCTATGGAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (39 bp):
TGAATTTGCCACATAGAACATCCAAGTTGGTATTTAAAA
Found at i:43049644 original size:12 final size:12
Alignment explanation
Indices: 43049627--43049652 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
43049617 CAATAAAAAA
43049627 TACCACACATCT
1 TACCACACATCT
43049639 TACCACACATCT
1 TACCACACATCT
43049651 TA
1 TA
43049653 ACTTCGAATA
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:0.35, C:0.38, G:0.00, T:0.27
Consensus pattern (12 bp):
TACCACACATCT
Found at i:43058260 original size:13 final size:12
Alignment explanation
Indices: 43058222--43058251 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
43058212 TCCCAGAATT
*
43058222 AAAAAAAAAGGA
1 AAAAAAAAAAGA
43058234 AAAAAAAAAAGA
1 AAAAAAAAAAGA
43058246 AAAAAA
1 AAAAAA
43058252 GAAATGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:43058524 original size:11 final size:11
Alignment explanation
Indices: 43058508--43058533 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
43058498 CCCGGCGACA
43058508 TGATTTTATTT
1 TGATTTTATTT
43058519 TGATTTTATTT
1 TGATTTTATTT
43058530 TGAT
1 TGAT
43058534 AATTTTAGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.12, T:0.69
Consensus pattern (11 bp):
TGATTTTATTT
Found at i:43058589 original size:81 final size:81
Alignment explanation
Indices: 43058454--43058614 Score: 322
Period size: 81 Copynumber: 2.0 Consensus size: 81
43058444 AAAAATTATT
43058454 ATTTTAGTCACTCTTGTTAGTTAAATTTCTTATTTTAGCTACTCCCCGGCGACATGATTTTATTT
1 ATTTTAGTCACTCTTGTTAGTTAAATTTCTTATTTTAGCTACTCCCCGGCGACATGATTTTATTT
43058519 TGATTTTATTTTGATA
66 TGATTTTATTTTGATA
43058535 ATTTTAGTCACTCTTGTTAGTTAAATTTCTTATTTTAGCTACTCCCCGGCGACATGATTTTATTT
1 ATTTTAGTCACTCTTGTTAGTTAAATTTCTTATTTTAGCTACTCCCCGGCGACATGATTTTATTT
43058600 TGATTTTATTTTGAT
66 TGATTTTATTTTGAT
43058615 TGATATAATA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.22, C:0.15, G:0.12, T:0.51
Consensus pattern (81 bp):
ATTTTAGTCACTCTTGTTAGTTAAATTTCTTATTTTAGCTACTCCCCGGCGACATGATTTTATTT
TGATTTTATTTTGATA
Done.