Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013507.1 Kokia drynarioides strain JFW-HI SEQ_128533, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 162429
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 27 characters in sequence are not A, C, G, or T
Found at i:1882 original size:30 final size:29
Alignment explanation
Indices: 1813--2338 Score: 332
Period size: 29 Copynumber: 17.9 Consensus size: 29
1803 AAGATCCCTA
*
1813 AACTATCCAAAAATTACCA-TTTTACCCCCG
1 AACT-TCCAAAAA-TCCCATTTTTACCCCCG
* *
1843 AACTTCCAAAAATCCCATTTTTGA-TCGCG
1 AACTTCCAAAAATCCCATTTTT-ACCCCCG
*
1872 AACATTCCAAAAATTACCA-TTTTACCCCCG
1 AAC-TTCCAAAAA-TCCCATTTTTACCCCCG
* *
1902 AACTTCCAAAAATCTCATTTTTTA-CCTCG
1 AACTTCCAAAAATCCCA-TTTTTACCCCCG
** * *
1931 AACCTTCTTAAAATGACCA-TTTTACCACCG
1 AA-CTTCCAAAAAT-CCCATTTTTACCCCCG
* **
1961 AACTTCCAAAAATCCCATTTTTAACTTCG
1 AACTTCCAAAAATCCCATTTTTACCCCCG
* * *
1990 AACCTTTCAAAAATTACCA-TTTTACCCTCG
1 AA-CTTCCAAAAA-TCCCATTTTTACCCCCG
* *
2020 AACTTCTAAAAGTCCCATTTTTTA--CCCG
1 AACTTCCAAAAATCCCA-TTTTTACCCCCG
** * * *
2048 AACCTTTTTAAAATTACCA-TTTTACTCCCG
1 AA-C-TTCCAAAAATCCCATTTTTACCCCCG
*
2078 AACTTCCAAAAATCACATTTTTGA-CCCCG
1 AACTTCCAAAAATCCCATTTTT-ACCCCCG
** ** * *
2107 AACCTTCGTAAAATGACA-TTTTACCCTCA
1 AA-CTTCCAAAAATCCCATTTTTACCCCCG
*
2136 AACTTCCAAAAATCCCATTTTTAACCCCG
1 AACTTCCAAAAATCCCATTTTTACCCCCG
* * * *
2165 AACCTTCTTAAAATTACCA-TTTTA-CCCCA
1 AA-CTTC-CAAAAATCCCATTTTTACCCCCG
* * *
2194 AACTTTCAAAAATCCCATTTTTAACCTCG
1 AACTTCCAAAAATCCCATTTTTACCCCCG
* *
2223 AACCTTCCAAAAATTACCA-TTTTACCCCCA
1 AA-CTTCCAAAAA-TCCCATTTTTACCCCCG
2253 AACTTCCAAAAAT-CCATTTTTGA-CCCCG
1 AACTTCCAAAAATCCCATTTTT-ACCCCCG
*
2281 AACCTTCCAAAAATTACCA-TTTTACCCCC-
1 AA-CTTCCAAAAA-TCCCATTTTTACCCCCG
*
2310 AAGCATCCAAAAATCCCATTTTTGACCCC
1 AA-CTTCCAAAAATCCCATTTTT-ACCCC
2339 GAGGCATCCA
Statistics
Matches: 388, Mismatches: 70, Indels: 76
0.73 0.13 0.14
Matches are distributed among these distances:
27 11 0.03
28 68 0.18
29 144 0.37
30 140 0.36
31 25 0.06
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.31
Consensus pattern (29 bp):
AACTTCCAAAAATCCCATTTTTACCCCCG
Found at i:1890 original size:59 final size:59
Alignment explanation
Indices: 1818--2369 Score: 673
Period size: 59 Copynumber: 9.4 Consensus size: 59
1808 CCCTAAACTA
* * *
1818 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGATCGCGAACAT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
* * *
1877 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTTACCTCGAACCT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
** * * * **
1936 TCTTAAAATGACCATTTTACCACCGAACTTCCAAAAATCCCATTTTTAACTTCGAACCT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
* * * * *
1995 TTCAAAAATTACCATTTTACCCTCGAACTTCTAAAAGTCCCATTTTTTA-CCCGAACCT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
*** * *
2053 TTTTAAAATTACCATTTTACTCCCGAACTTCCAAAAATCACATTTTTGACCCCGAACCT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
** * * * *
2112 TCGTAAAATGA-CATTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCGAACCT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
** * * * *
2170 TCTTAAAATTACCATTTTA-CCCCAAACTTTCAAAAATCCCATTTTTAACCTCGAACCT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
*
2228 TCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAAT-CCATTTTTGACCCCGAACCT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
* ** *
2286 TCCAAAAATTACCATTTTACCCCC-AAGCATCCAAAAATCCCATTTTTGACCCCGAGGCA
1 TCCAAAAATTACCATTTTACCCCCGAA-CTTCCAAAAATCCCATTTTTGACCCCGAACCT
** *
2345 TCCAAAAATTAATATTTTACTCCCG
1 TCCAAAAATTACCATTTTACCCCCG
2370 GATGTCCAAA
Statistics
Matches: 431, Mismatches: 56, Indels: 11
0.87 0.11 0.02
Matches are distributed among these distances:
57 2 0.00
58 204 0.47
59 225 0.52
ACGTcount: A:0.34, C:0.31, G:0.05, T:0.31
Consensus pattern (59 bp):
TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
Found at i:2109 original size:117 final size:117
Alignment explanation
Indices: 1822--2364 Score: 705
Period size: 117 Copynumber: 4.6 Consensus size: 117
1812 AAACTATCCA
* * *
1822 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGATCGCGAACATTCCAAAAATT
1 AAAATTACCATTTTA-CCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATT
* * *
1887 ACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTTACCTCGAACCTTCTT
65 ACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTTACCCCGAACCTTCTT
* * ** *
1940 AAAATGACCATTTTACCACCGAACTTCCAAAAATCCCATTTTTAACTTCGAACCTTTCAAAAATT
1 AAAATTACCATTTTACC-CCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATT
* * * * *
2005 ACCATTTTACCCTCGAACTTCTAAAAGTCCCATTTTTTA-CCCGAACCTTTTT
65 ACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTTACCCCGAACCTTCTT
* ** *
2057 AAAATTACCATTTTACTCCCGAACTTCCAAAAATCACATTTTTGACCCCGAACCTTCGTAAAATG
1 AAAATTACCATTTTAC-CCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATT
* *
2122 A-CATTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCTT
65 ACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTTACCCCGAACCTTCTT
* * * *
2174 AAAATTACCATTTTACCCCAAACTTTCAAAAATCCCATTTTTAACCTCGAACCTTCCAAAAATTA
1 AAAATTACCATTTTACCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATTA
* **
2239 CCATTTTACCCCCAAACTTCCAAAAAT-CCATTTTTGACCCCGAACCTTCCA
66 CCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTTACCCCGAACCTTCTT
* * ** *
2290 AAAATTACCATTTTACCCCCAAGCATCCAAAAATCCCATTTTTGACCCCGAGGCATCCAAAAATT
1 AAAATTACCATTTTACCCCGAA-CTTCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATT
**
2355 AATATTTTAC
65 ACCATTTTAC
2365 TCCCGGATGT
Statistics
Matches: 371, Mismatches: 49, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
116 116 0.31
117 164 0.44
118 91 0.25
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.31
Consensus pattern (117 bp):
AAAATTACCATTTTACCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATTA
CCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTTACCCCGAACCTTCTT
Found at i:2378 original size:117 final size:115
Alignment explanation
Indices: 1822--2426 Score: 644
Period size: 117 Copynumber: 5.2 Consensus size: 115
1812 AAACTATCCA
* * *
1822 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGATCGCGAACATTCCAAAAATT
1 AAAATTACCATTTTACCCCC-AACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATT
* * *
1887 ACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTTACCTCGAACCTTCTT
65 ACCATTTTA-CCCCGAACTTCCAAAAATC-CATTTTTGACCCCGAACCTTCCT
* * * ** *
1940 AAAATGACCATTTTACCACCGAACTTCCAAAAATCCCATTTTTAACTTCGAACCTTTCAAAAATT
1 AAAATTACCATTTTACC-CCCAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATT
* * * **
2005 ACCATTTTACCCTCGAACTTCTAAAAGTCCCATTTTTTA-CCCGAACCTTTTT
65 ACCATTTTACCC-CGAACTTCCAAAAAT-CCATTTTTGACCCCGAACCTTCCT
* * ** *
2057 AAAATTACCATTTTACTCCCGAACTTCCAAAAATCACATTTTTGACCCCGAACCTTCGTAAAATG
1 AAAATTACCATTTTAC-CCCCAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATT
* * *
2122 A-CATTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCTT
65 ACCATTTTACCC-CGAACTTCCAAAAAT-CCATTTTTGACCCCGAACCTTCCT
* * * *
2174 AAAATTACCATTTTACCCCAAACTTTCAAAAATCCCATTTTTAACCTCGAACCTTCCAAAAATTA
1 AAAATTACCATTTTACCCCCAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATTA
* *
2239 CCATTTTACCCCCAAACTTCCAAAAATCCATTTTTGACCCCGAACCTTCCA
66 CCATTTTA-CCCCGAACTTCCAAAAATCCATTTTTGACCCCGAACCTTCCT
* ** *
2290 AAAATTACCATTTTACCCCCAAGCATCCAAAAATCCCATTTTTGACCCCGAGGCATCCAAAAATT
1 AAAATTACCATTTTACCCCCAA-CTTCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATT
** * * * * * *
2355 AATATTTTACTCCCGGA-TGTCCAAAGACTCCGTTTTCGACCTCGAAAC-T-CT
65 ACCATTTTAC-CCCGAACT-TCCAAA-AATCCATTTTTGACCCCGAACCTTCCT
2406 CAAAATTACCATTTTTACCCC
1 -AAAATTACCA-TTTTACCCC
2427 TAAATGTTTT
Statistics
Matches: 419, Mismatches: 55, Indels: 26
0.84 0.11 0.05
Matches are distributed among these distances:
116 119 0.28
117 182 0.43
118 115 0.27
119 3 0.01
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.31
Consensus pattern (115 bp):
AAAATTACCATTTTACCCCCAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATTA
CCATTTTACCCCGAACTTCCAAAAATCCATTTTTGACCCCGAACCTTCCT
Found at i:13240 original size:44 final size:43
Alignment explanation
Indices: 13151--13233 Score: 103
Period size: 44 Copynumber: 1.9 Consensus size: 43
13141 CTAAAAATAA
* * * *
13151 AAGGAGAATTGAGATGAAAACTCGCAAAGGGCGTATTAGAACC
1 AAGGAAAATTGAGATGAAAACCCGCAAAGGGCGGATCAGAACC
* *
13194 AAGGAAAATTTGAGTTGAAAACCCGCAAAGGGCGGCTCAG
1 AAGGAAAA-TTGAGATGAAAACCCGCAAAGGGCGGATCAG
13234 GTCCAAGAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
43 7 0.21
44 26 0.79
ACGTcount: A:0.40, C:0.16, G:0.29, T:0.16
Consensus pattern (43 bp):
AAGGAAAATTGAGATGAAAACCCGCAAAGGGCGGATCAGAACC
Found at i:14332 original size:206 final size:206
Alignment explanation
Indices: 13978--14461 Score: 788
Period size: 206 Copynumber: 2.3 Consensus size: 206
13968 AAACGGTTAG
* * * *
13978 CTTCCTGATAAGATACAGAGAAGTGGATTGAAACAAACGATGCAGTCATCTTCCTGATGAGATAC
1 CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAGACGACGCAGTCATCTTCCTGATGAGATAC
* * * *
14043 TGAGAAAAAGACCAAATCAAACCCACGCTCGATGTAAGCAAATCTTCCAACCCCAGCTTCTTGAT
66 TGAGAAGAAGACCAAATCAAACCCACACTCGATGTAAGCAAATCTTCCAACCACAGCTTCCTGAT
* *
14108 GAGATACTGAGAAGCAAGTCGAAGTGATAAAAAGGTTAGCTTCCTGATGAAATACGGAGAAGTGG
131 GAGATACTGAGAAGCAAGTCGAAGTGATAAAAAGGTTAACTTCCTGATGAAATACGAAGAAGTGG
14173 ACCAAATTCGT
196 ACCAAATTCGT
* * *
14184 CTTCCTGATGAGATACAGAGAAGCGGACTGAAACAGACGACGCAATCATCTTCCCGATGAGATAC
1 CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAGACGACGCAGTCATCTTCCTGATGAGATAC
* * *
14249 TGAGAAGAAGACCAAATCAAACCCACACTCGATGTGAGCAAATCTTCGAACCACGGCTTCCTGAT
66 TGAGAAGAAGACCAAATCAAACCCACACTCGATGTAAGCAAATCTTCCAACCACAGCTTCCTGAT
* *
14314 GAGATACTGAGAAGCAAGTCGAAGTGATAAAAAGGTTAACTTCCTGATTAAATACTAAGAAGTGG
131 GAGATACTGAGAAGCAAGTCGAAGTGATAAAAAGGTTAACTTCCTGATGAAATACGAAGAAGTGG
14379 ACCAAATTCGT
196 ACCAAATTCGT
* *
14390 CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAGACGACGCAGTCATCTTCCTGTTGAGATAT
1 CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAGACGACGCAGTCATCTTCCTGATGAGATAC
14455 TGAGAAG
66 TGAGAAG
14462 CAAGTCGAAG
Statistics
Matches: 255, Mismatches: 23, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
206 255 1.00
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.21
Consensus pattern (206 bp):
CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAGACGACGCAGTCATCTTCCTGATGAGATAC
TGAGAAGAAGACCAAATCAAACCCACACTCGATGTAAGCAAATCTTCCAACCACAGCTTCCTGAT
GAGATACTGAGAAGCAAGTCGAAGTGATAAAAAGGTTAACTTCCTGATGAAATACGAAGAAGTGG
ACCAAATTCGT
Found at i:14544 original size:133 final size:134
Alignment explanation
Indices: 14305--14594 Score: 510
Period size: 133 Copynumber: 2.2 Consensus size: 134
14295 CGAACCACGG
*
14305 CTTCCTGATGAGATACTGAGAAGCAAGTCGAAGTGATAAAAAGGTTAACTTCCTGATTAAATACT
1 CTTCCTGATGAGATACTGAGAAGCAAGTCGAAGTGATAAAAAGGTTAACTTCCTGATGAAATACT
*
14370 AAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAGACGACGCAG
66 AAGAAGTGGACCAAATTCGTCTTCCGGATGAGATACAGAGAAGCGGATTGAAACAGACGACGCAG
14435 TCAT
131 TCAT
* * *
14439 CTTCCTGTTGAGATATTGAGAAGCAAGTCGAAGTGATAAAAAGGTT-AGTTCCTGATGAAATACT
1 CTTCCTGATGAGATACTGAGAAGCAAGTCGAAGTGATAAAAAGGTTAACTTCCTGATGAAATACT
*
14503 GAGAAGTGGACCAAATTCGTCTTCCGGATGAGATACAGAGAAGCGGATTGAAACAGACGACGCAG
66 AAGAAGTGGACCAAATTCGTCTTCCGGATGAGATACAGAGAAGCGGATTGAAACAGACGACGCAG
14568 TCAT
131 TCAT
*
14572 CTTCCCGATGAGATACTGAGAAG
1 CTTCCTGATGAGATACTGAGAAG
14595 AAGACCAAAT
Statistics
Matches: 147, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
133 103 0.70
134 44 0.30
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (134 bp):
CTTCCTGATGAGATACTGAGAAGCAAGTCGAAGTGATAAAAAGGTTAACTTCCTGATGAAATACT
AAGAAGTGGACCAAATTCGTCTTCCGGATGAGATACAGAGAAGCGGATTGAAACAGACGACGCAG
TCAT
Found at i:14732 original size:339 final size:340
Alignment explanation
Indices: 14107--14739 Score: 959
Period size: 339 Copynumber: 1.9 Consensus size: 340
14097 AGCTTCTTGA
14107 TGAGATACTGAGAAGCAAGTCGAAGTGATAAAAAGGTTAGCTTCCTGATGAAATACGGAGAAGTG
1 TGAGATACTGAGAAGCAAGTCGAAGTGATAAAAAGGTTAGCTTCCTGATGAAATACGGAGAAGTG
*
14172 GACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGACTGAAACAGACGACGCAATCATCTTC
66 GACCAAATTCGTCTTCCGGATGAGATACAGAGAAGCGGACTGAAACAGACGACGCAATCATCTTC
*
14237 CCGATGAGATACTGAGAAGAAGACCAAATCAAACCCACACTCGATGTGAGCAAATCTTCGAACCA
131 CCGATGAGATACTGAGAAGAAGACCAAATCAAACCCACACCCGATGTGAGCAAATCTTCGAACCA
* * * * ** * * *
14302 CGGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGTGATAAAAAGGTTAACTTCCTGATTAAAT
196 CGGCTTCCTGATGAAACACTAAAAAGCAAGTCGAAGCAATAAAAAGGTTAACTCCCTGATGAAAC
* * * *
14367 ACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAGACGACG
261 ACTAAGAAGCGAACCAAATCCGTCTTCCTAATGAGATACAGAGAAGCGGATTGAAACAGACGACG
14432 CAGTCATCTTCCTGT
326 CAGTCATCTTCCTGT
* *
14447 TGAGATATTGAGAAGCAAGTCGAAGTGATAAAAAGGTTAG-TTCCTGATGAAATACTGAGAAGTG
1 TGAGATACTGAGAAGCAAGTCGAAGTGATAAAAAGGTTAGCTTCCTGATGAAATACGGAGAAGTG
* *
14511 GACCAAATTCGTCTTCCGGATGAGATACAGAGAAGCGGATTGAAACAGACGACGCAGTCATCTTC
66 GACCAAATTCGTCTTCCGGATGAGATACAGAGAAGCGGACTGAAACAGACGACGCAATCATCTTC
** *
14576 CCGATGAGATACTGAGAAGAAGACCAAATCAAACTTACGCCCGATGTGAGCAAATCTTCGAACTC
131 CCGATGAGATACTGAGAAGAAGACCAAATCAAACCCACACCCGATGTGAGCAAATCTTCGAAC-C
* ** * *
14641 A-GGCTTCCTGATGAAACACTAAAAAGCAGGTCGAAGCAATAAAGTGGTTAGC-CCCTTGATGAG
195 ACGGCTTCCTGATGAAACACTAAAAAGCAAGTCGAAGCAATAAAAAGGTTAACTCCC-TGATGAA
*
14704 ACAC-AGAGGAGCGAACCAAATCCGTCTTCCTAATGA
259 ACACTA-AGAAGCGAACCAAATCCGTCTTCCTAATGA
14740 AACACGAAGA
Statistics
Matches: 262, Mismatches: 28, Indels: 7
0.88 0.09 0.02
Matches are distributed among these distances:
338 3 0.01
339 218 0.83
340 41 0.16
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.21
Consensus pattern (340 bp):
TGAGATACTGAGAAGCAAGTCGAAGTGATAAAAAGGTTAGCTTCCTGATGAAATACGGAGAAGTG
GACCAAATTCGTCTTCCGGATGAGATACAGAGAAGCGGACTGAAACAGACGACGCAATCATCTTC
CCGATGAGATACTGAGAAGAAGACCAAATCAAACCCACACCCGATGTGAGCAAATCTTCGAACCA
CGGCTTCCTGATGAAACACTAAAAAGCAAGTCGAAGCAATAAAAAGGTTAACTCCCTGATGAAAC
ACTAAGAAGCGAACCAAATCCGTCTTCCTAATGAGATACAGAGAAGCGGATTGAAACAGACGACG
CAGTCATCTTCCTGT
Found at i:15193 original size:17 final size:17
Alignment explanation
Indices: 15154--15244 Score: 85
Period size: 17 Copynumber: 5.2 Consensus size: 17
15144 TTTAAATTCG
*
15154 TTTAAATTTATTTTTAGA
1 TTTAAATTTA-TTTTAAA
*
15172 TTTAAATTTATGTTAAA
1 TTTAAATTTATTTTAAA
15189 TTTAAATTTATCTTTTTAAA
1 TTTAAATTTA---TTTTAAA
***
15209 TTTAAATTTGCCTTAAA
1 TTTAAATTTATTTTAAA
*
15226 TTTAAATTTA-ATTAAA
1 TTTAAATTTATTTTAAA
15242 TTT
1 TTT
15245 GAATGGATTT
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
16 8 0.13
17 29 0.47
18 10 0.16
20 15 0.24
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:15213 original size:37 final size:35
Alignment explanation
Indices: 15154--15235 Score: 110
Period size: 37 Copynumber: 2.3 Consensus size: 35
15144 TTTAAATTCG
* **
15154 TTTAAATTTATTTTTAGATTTAAATTTATGTTAAA
1 TTTAAATTTATTTTTAAATTTAAATTTACCTTAAA
*
15189 TTTAAATTTATCTTTTTAAATTTAAATTTGCCTTAAA
1 TTTAAATTTA--TTTTTAAATTTAAATTTACCTTAAA
15226 TTTAAATTTA
1 TTTAAATTTA
15236 ATTAAATTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 10 0.24
37 31 0.76
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (35 bp):
TTTAAATTTATTTTTAAATTTAAATTTACCTTAAA
Found at i:15971 original size:33 final size:33
Alignment explanation
Indices: 15910--15976 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
15900 AAAATATCAT
* * *
15910 TAATAATATTATTAATTATATTAGCAATAATAA
1 TAATAATATCACTAATTATATTAACAATAATAA
*
15943 TAATAATATCACTAA-TATCATTAACAATATTAA
1 TAATAATATCACTAATTAT-ATTAACAATAATAA
15976 T
1 T
15977 GACAACAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 3 0.10
33 26 0.90
ACGTcount: A:0.51, C:0.07, G:0.01, T:0.40
Consensus pattern (33 bp):
TAATAATATCACTAATTATATTAACAATAATAA
Found at i:15989 original size:18 final size:18
Alignment explanation
Indices: 15968--16008 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
15958 TATCATTAAC
*
15968 AATATTAATGACAACAAT
1 AATAATAATGACAACAAT
*
15986 AATAATAATGACATCAAT
1 AATAATAATGACAACAAT
16004 AATAA
1 AATAA
16009 CATTTAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.59, C:0.10, G:0.05, T:0.27
Consensus pattern (18 bp):
AATAATAATGACAACAAT
Found at i:17177 original size:30 final size:28
Alignment explanation
Indices: 17106--17263 Score: 110
Period size: 28 Copynumber: 5.5 Consensus size: 28
17096 AAACTATCCA
17106 AAAATTACCATTTTACCCTCGACTTCCC
1 AAAATTACCATTTTACCCTCGACTTCCC
* **
17134 AAAA-TCCCAATTTTGACCC-CGAACCTTCTT
1 AAAATTACC-ATTTT-ACCCTCG-A-CTTCCC
17164 AAAATTACCATTTTACCCTCAGACTT-CC
1 AAAATTACCATTTTACCCTC-GACTTCCC
* * * *
17192 AAAAATCCCATTTTAATCC-CGAACCTTCCA
1 AAAATTACCATTTT-ACCCTCG-A-CTTCCC
*
17222 AAAATTATCATTTTACCCTCGGACTT-CC
1 AAAATTACCATTTTACCCTC-GACTTCCC
* *
17250 AAAAATCCCATTTT
1 AAAATTACCATTTT
17264 TGACCCCGAG
Statistics
Matches: 99, Mismatches: 18, Indels: 26
0.69 0.13 0.18
Matches are distributed among these distances:
27 4 0.04
28 37 0.37
29 24 0.24
30 29 0.29
31 5 0.05
ACGTcount: A:0.32, C:0.32, G:0.04, T:0.32
Consensus pattern (28 bp):
AAAATTACCATTTTACCCTCGACTTCCC
Found at i:17205 original size:58 final size:57
Alignment explanation
Indices: 17102--17296 Score: 264
Period size: 58 Copynumber: 3.4 Consensus size: 57
17092 CCCTAAACTA
*
17102 TCCAAAAATTACCATTTTACCCTCGACTTCCCAAAATCCCAATTTTGACCCCGAACCT
1 TCCAAAAATTACCATTTTACCCTCGACTTCCAAAAATCCC-ATTTTGACCCCGAACCT
** * *
17160 TCTTAAAATTACCATTTTACCCTCAGACTTCCAAAAATCCCATTTTAATCCCGAACCT
1 TCCAAAAATTACCATTTTACCCTC-GACTTCCAAAAATCCCATTTTGACCCCGAACCT
* ** *
17218 TCCAAAAATTATCATTTTACCCTCGGACTTCCAAAAATCCCATTTTTGACCCCGAGGCA
1 TCCAAAAATTACCATTTTACCCTC-GACTTCCAAAAATCCCA-TTTTGACCCCGAACCT
*
17277 TCCAAAAATTACTATTTTAC
1 TCCAAAAATTACCATTTTAC
17297 TCCCGGATGT
Statistics
Matches: 119, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
58 75 0.63
59 44 0.37
ACGTcount: A:0.32, C:0.31, G:0.06, T:0.31
Consensus pattern (57 bp):
TCCAAAAATTACCATTTTACCCTCGACTTCCAAAAATCCCATTTTGACCCCGAACCT
Found at i:17264 original size:29 final size:28
Alignment explanation
Indices: 17102--17263 Score: 132
Period size: 29 Copynumber: 5.6 Consensus size: 28
17092 CCCTAAACTA
17102 TCCAAAAATTACCATTTTACCCTC-GACT
1 TCCAAAAA-TACCATTTTACCCTCGGACT
* * *
17130 TCCCAAAATCCCAATTTTGACCC-CGAACCT
1 TCCAAAAATACC-ATTTT-ACCCTCGGA-CT
* * *
17160 TCTTAAAATTACCATTTTACCCTCAGACT
1 TC-CAAAAATACCATTTTACCCTCGGACT
* * *
17189 TCCAAAAATCCCATTTTAATCC-CGAACCT
1 TCCAAAAATACCATTTT-ACCCTCGGA-CT
*
17218 TCCAAAAATTATCATTTTACCCTCGGACT
1 TCCAAAAA-TACCATTTTACCCTCGGACT
*
17247 TCCAAAAATCCCATTTT
1 TCCAAAAATACCATTTT
17264 TGACCCCGAG
Statistics
Matches: 103, Mismatches: 21, Indels: 20
0.72 0.15 0.14
Matches are distributed among these distances:
27 3 0.03
28 34 0.33
29 39 0.38
30 21 0.20
31 6 0.06
ACGTcount: A:0.32, C:0.32, G:0.04, T:0.31
Consensus pattern (28 bp):
TCCAAAAATACCATTTTACCCTCGGACT
Found at i:17381 original size:29 final size:31
Alignment explanation
Indices: 17338--17409 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 31
17328 AAAACTCTCA
* *
17338 AAATTACCGTTTTTACCCCTCGAATGTT-TT-
1 AAATTACCATTTTTAACCC-CGAATGTTCTTG
*
17368 AAATT-CCATTTTTAACCCCGAATTTTCTTG
1 AAATTACCATTTTTAACCCCGAATGTTCTTG
17398 AAATTACCATTT
1 AAATTACCATTT
17410 GGCCCCCGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 7 0.19
29 13 0.36
30 10 0.28
31 6 0.17
ACGTcount: A:0.28, C:0.22, G:0.07, T:0.43
Consensus pattern (31 bp):
AAATTACCATTTTTAACCCCGAATGTTCTTG
Found at i:19017 original size:73 final size:73
Alignment explanation
Indices: 18938--19272 Score: 367
Period size: 73 Copynumber: 4.6 Consensus size: 73
18928 AAAAGAAACC
* * *
18938 TTTTTTAAAAGTTGCCTTATACAAGGTCTATCCCAACCTTTTTAAGGTTACCTTAGACGGGCCTA
1 TTTTTTAAAAGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTTAGACGGGTCTA
*
19003 TCTTAACT
66 TCTCAACT
* * * *
19011 TTTTTT-AAAGTTTGCCTCAGACAAGG-CTTATTCCAACC-TTGTAAGGTTGCCTTAGACGTGTC
1 TTTTTTAAAAG-TTGCCTTAGACAAGGTC-TATCCCAACCTTTTTAAGGTTGCCTTAGACGGGTC
19073 -AGT-TCTAACT
64 TA-TCTC-AACT
* * * * *
19083 TTTTTTAAAAGTTGCCTCAGACAAGGTCTATCCCAACCTTTTTAACGTTGCATTAGACAGGTTTA
1 TTTTTTAAAAGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTTAGACGGGTCTA
*
19148 TCTCAACC
66 TCTCAACT
* * *
19156 TTTTTTAAAAGTTGCTTTAGACAAGGTCTATCCCAACCTTTTTTAAGGTTGTCTTAGTCGGGTCT
1 TTTTTTAAAAGTTGCCTTAGACAAGGTCTATCCCAACC-TTTTTAAGGTTGCCTTAGACGGGTCT
19221 ATCTCAA-T
65 ATCTCAACT
** * * * *
19229 CTTTTTTAAGGGTTGCTTTAGAAAAGATTTATCCCAACCTTTTT
1 -TTTTTTAAAAGTTGCCTTAGACAAGGTCTATCCCAACCTTTTT
19273 TAAAGGTCAG
Statistics
Matches: 221, Mismatches: 30, Indels: 22
0.81 0.11 0.08
Matches are distributed among these distances:
71 2 0.01
72 60 0.27
73 96 0.43
74 63 0.29
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.39
Consensus pattern (73 bp):
TTTTTTAAAAGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTTAGACGGGTCTA
TCTCAACT
Found at i:19141 original size:36 final size:36
Alignment explanation
Indices: 18934--19272 Score: 174
Period size: 37 Copynumber: 9.2 Consensus size: 36
18924 TTGTAAAAGA
* * *
18934 AACCTTTTTTAAAAGTTGCCTTATACAAGGTCTATCCC
1 AACC-TTTTT-AAGGTTGCTTTAGACAAGGTCTATCCC
* * * * **
18972 AACCTTTTTAAGGTTACCTTAGAC-GGGCCTATCTT
1 AACCTTTTTAAGGTTGCTTTAGACAAGGTCTATCCC
* * * * *
19007 AACTTTTTTTAAAGTTTGCCTCAGACAAGG-CTTATTCC
1 AAC-CTTTTT-AAGGTTGCTTTAGACAAGGTC-TATCCC
* * * *
19045 AACC-TTGTAAGGTTGCCTTAGAC--GTGTC-AGTTCT
1 AACCTTTTTAAGGTTGCTTTAGACAAG-GTCTA-TCCC
* * * *
19079 AACTTTTTTTAAAAGTTGCCTCAGACAAGGTCTATCCC
1 AAC-CTTTTT-AAGGTTGCTTTAGACAAGGTCTATCCC
* * * *
19117 AACCTTTTTAACGTTGCATTAGAC-AGGTTTATCTC
1 AACCTTTTTAAGGTTGCTTTAGACAAGGTCTATCCC
*
19152 AACCTTTTTTAAAAGTTGCTTTAGACAAGGTCTATCCC
1 AACC-TTTTT-AAGGTTGCTTTAGACAAGGTCTATCCC
* * *
19190 AACCTTTTTTAAGGTTG-TCTTAGTC-GGGTCTATCTC
1 AACC-TTTTTAAGGTTGCT-TTAGACAAGGTCTATCCC
* * * *
19226 AATCTTTTTTAAGGGTTGCTTTAGAAAAGATTTATCCC
1 AA-CCTTTTTAA-GGTTGCTTTAGACAAGGTCTATCCC
19264 AACCTTTTT
1 AACCTTTTT
19273 TAAAGGTCAG
Statistics
Matches: 232, Mismatches: 48, Indels: 43
0.72 0.15 0.13
Matches are distributed among these distances:
33 2 0.01
34 7 0.03
35 37 0.16
36 59 0.25
37 76 0.33
38 49 0.21
39 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (36 bp):
AACCTTTTTAAGGTTGCTTTAGACAAGGTCTATCCC
Found at i:19577 original size:31 final size:31
Alignment explanation
Indices: 19542--19607 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
19532 TAAAAAAAAC
* *
19542 AATTCAACT-ATTTTTGAAAGATTGATAATCA
1 AATTCAACTCA-TTTTAAAAGATTGAAAATCA
*
19573 AATTCGACTCATTTTAAAAGATTGAAAATCA
1 AATTCAACTCATTTTAAAAGATTGAAAATCA
19604 AATT
1 AATT
19608 TAGCTAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (31 bp):
AATTCAACTCATTTTAAAAGATTGAAAATCA
Found at i:20377 original size:2 final size:2
Alignment explanation
Indices: 20370--20422 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
20360 AAGTAATACT
20370 TA TA TA TA TA TA 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 TA TA TA TA TA TA
20412 TA TA TA TA TA T
1 TA TA TA TA TA T
20423 GACGTATGAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22770 original size:4 final size:4
Alignment explanation
Indices: 22761--22786 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
22751 GTGGCAGGAG
22761 GGAC GGAC GGAC GGAC GGAC GGAC GG
1 GGAC GGAC GGAC GGAC GGAC GGAC GG
22787 CCCCATCGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.54, T:0.00
Consensus pattern (4 bp):
GGAC
Found at i:25253 original size:12 final size:12
Alignment explanation
Indices: 25238--25267 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
25228 AGTAACCAAT
25238 GAAGTGCCAAAG
1 GAAGTGCCAAAG
25250 GAAGTGCCAAAG
1 GAAGTGCCAAAG
*
25262 AAAGTG
1 GAAGTG
25268 GGAGTTGCCT
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:0.43, C:0.13, G:0.33, T:0.10
Consensus pattern (12 bp):
GAAGTGCCAAAG
Found at i:29983 original size:16 final size:17
Alignment explanation
Indices: 29954--29990 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
29944 TTTTATATTC
*
29954 ATATTTTTTAACATTGT
1 ATATTTTTTAACATTAT
29971 ATATTTTTT-ACATTAT
1 ATATTTTTTAACATTAT
29987 ATAT
1 ATAT
29991 ATATATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.59
Consensus pattern (17 bp):
ATATTTTTTAACATTAT
Found at i:29989 original size:2 final size:2
Alignment explanation
Indices: 29984--30018 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
29974 TTTTTTACAT
*
29984 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30019 TTTTATACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:30025 original size:16 final size:16
Alignment explanation
Indices: 29988--30029 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
29978 TTACATTATA
* *
29988 TATATATATATATATA
1 TATATACATATATATT
30004 TATATACATATATATT
1 TATATACATATATATT
*
30020 TTTATACATA
1 TATATACATA
30030 GATTAGTACA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (16 bp):
TATATACATATATATT
Found at i:30137 original size:12 final size:12
Alignment explanation
Indices: 30120--30150 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
30110 ATATATACTG
30120 ACACACAGACAC
1 ACACACAGACAC
*
30132 ACACACATACAC
1 ACACACAGACAC
30144 ACACACA
1 ACACACA
30151 CATATATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.52, C:0.42, G:0.03, T:0.03
Consensus pattern (12 bp):
ACACACAGACAC
Found at i:30145 original size:14 final size:14
Alignment explanation
Indices: 30128--30154 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
30118 TGACACACAG
30128 ACACACACACATAC
1 ACACACACACATAC
30142 ACACACACACATA
1 ACACACACACATA
30155 TATATATAAT
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:0.52, C:0.41, G:0.00, T:0.07
Consensus pattern (14 bp):
ACACACACACATAC
Found at i:35044 original size:31 final size:31
Alignment explanation
Indices: 35006--35066 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
34996 AACGTCTTGG
35006 TGACTTAAATAAAAACTTTTGAATAGTTCAA
1 TGACTTAAATAAAAACTTTTGAATAGTTCAA
*
35037 TGACTTAAATGAAAACTTTTGAATAGTTCA
1 TGACTTAAATAAAAACTTTTGAATAGTTCA
35067 GTAACCAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.36
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTTGAATAGTTCAA
Found at i:36737 original size:17 final size:18
Alignment explanation
Indices: 36715--36748 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
36705 CCCAAATAAA
36715 ATTTTAAATTTA-AATTT
1 ATTTTAAATTTAGAATTT
36732 ATTTTAAATTTAGAATT
1 ATTTTAAATTTAGAATT
36749 AAAATGTCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
ATTTTAAATTTAGAATTT
Found at i:37873 original size:29 final size:29
Alignment explanation
Indices: 37830--38129 Score: 175
Period size: 30 Copynumber: 10.2 Consensus size: 29
37820 TTGAATTATC
* * *
37830 CAAAAATCATGTTTTGACCTCGAACTTTT
1 CAAAAATTATATTTTGACCTCAAACTTTT
37859 CAAAAATTATATTTTGATCCT-AAACTTTT
1 CAAAAATTATATTTTGA-CCTCAAACTTTT
* * * * * * *
37888 TAAAAATCATGTTTTCACCCCTGAAC-TCT
1 CAAAAATTATATTTTGACCTC-AAACTTTT
* * *
37917 CTAAAAATTATATTTTAACCCTTAAACTTTC
1 C-AAAAATTATATTTTGA-CCTCAAACTTTT
* * * *
37948 CAAAAACTACATTTTAACC-CTAAACTTCT
1 CAAAAATTATATTTTGACCTC-AAACTTTT
* *
37977 CAAAAATTACATTTTGACCCTCGAAC-TTT
1 CAAAAATTATATTTTGA-CCTCAAACTTTT
* *
38006 CTAAAAATTATGTTTTGACCCTTAAACTTTT
1 C-AAAAATTATATTTTGA-CCTCAAACTTTT
* * *
38037 CAAAAATTACATTTT-TCCCCAAACTTTT
1 CAAAAATTATATTTTGACCTCAAACTTTT
* * *
38065 CAAAAATTATCATTTT-ACCCCCAAGA-TGTC
1 CAAAAATTAT-ATTTTGA-CCTCAA-ACTTTT
* *
38095 CAAAAATTACATTTTTGACCTCGAAC-TTT
1 CAAAAATTATA-TTTTGACCTCAAACTTTT
38124 CAAAAA
1 CAAAAA
38130 AACACATTTT
Statistics
Matches: 208, Mismatches: 46, Indels: 34
0.72 0.16 0.12
Matches are distributed among these distances:
28 21 0.10
29 77 0.37
30 99 0.48
31 11 0.05
ACGTcount: A:0.36, C:0.22, G:0.05, T:0.37
Consensus pattern (29 bp):
CAAAAATTATATTTTGACCTCAAACTTTT
Found at i:37927 original size:59 final size:59
Alignment explanation
Indices: 37831--38051 Score: 218
Period size: 59 Copynumber: 3.7 Consensus size: 59
37821 TGAATTATCC
* * * *
37831 AAAAATCATGTTTTGACCTC-GAACTTTTCAAAAATTATATTTTGATCCTAAACTTTTT
1 AAAAATCATGTTTTGACCCCTGAACTTCTCAAAAATTATATTTTGACCCTAAACTTTCT
* * *
37889 AAAAATCATGTTTTCACCCCTGAAC-TCTCTAAAAATTATATTTTAACCCTTAAACTTTCC
1 AAAAATCATGTTTTGACCCCTGAACTTCTC-AAAAATTATATTTTGACCC-TAAACTTTCT
* * * *
37949 AAAAACTACA--TTTT-AACCCTAAACTTCTCAAAAATTACATTTTGACCCTCGAACTTTCT
1 AAAAA-T-CATGTTTTGACCCCTGAACTTCTCAAAAATTATATTTTGACCCT-AAACTTTCT
* * * * *
38008 AAAAATTATGTTTTGACCCTTAAACTTTTCAAAAATTACATTTT
1 AAAAATCATGTTTTGACCCCTGAACTTCTCAAAAATTATATTTT
38052 TCCCCAAACT
Statistics
Matches: 136, Mismatches: 17, Indels: 18
0.80 0.10 0.11
Matches are distributed among these distances:
57 1 0.01
58 23 0.17
59 62 0.46
60 47 0.35
61 1 0.01
62 2 0.01
ACGTcount: A:0.36, C:0.20, G:0.05, T:0.39
Consensus pattern (59 bp):
AAAAATCATGTTTTGACCCCTGAACTTCTCAAAAATTATATTTTGACCCTAAACTTTCT
Found at i:37953 original size:30 final size:29
Alignment explanation
Indices: 37852--38109 Score: 180
Period size: 30 Copynumber: 8.8 Consensus size: 29
37842 TTTGACCTCG
* * *
37852 AACTTTTCAAAAATTATATTTTGATCCTA
1 AACTTTCCAAAAATTATATTTTAACCCTA
** * * * *
37881 AACTTTTTAAAAATCATGTTTTCACCCCTG
1 AACTTTCCAAAAATTATATTTT-AACCCTA
* *
37911 AACTCTCTAAAAATTATATTTTAACCCTTA
1 AACTTTCCAAAAATTATATTTTAACCC-TA
* *
37941 AACTTTCCAAAAACTACATTTTAACCCTA
1 AACTTTCCAAAAATTATATTTTAACCCTA
* * *
37970 AAC-TTCTCAAAAATTACATTTTGACCCTCG
1 AACTTTC-CAAAAATTATATTTTAACCCT-A
* * *
38000 AACTTTCTAAAAATTATGTTTTGACCCTTA
1 AACTTTCCAAAAATTATATTTTAACCC-TA
* * * *
38030 AACTTTTCAAAAATTACATTTT-TCCCCA
1 AACTTTCCAAAAATTATATTTTAACCCTA
* * *
38058 AACTTTTCAAAAATTATCATTTTACCCCCA
1 AACTTTCCAAAAATTAT-ATTTTAACCCTA
* *
38088 AGA-TGTCCAAAAATTACATTTT
1 A-ACTTTCCAAAAATTATATTTT
38110 TGACCTCGAA
Statistics
Matches: 185, Mismatches: 35, Indels: 18
0.78 0.15 0.08
Matches are distributed among these distances:
28 20 0.11
29 60 0.32
30 100 0.54
31 5 0.03
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.38
Consensus pattern (29 bp):
AACTTTCCAAAAATTATATTTTAACCCTA
Found at i:38003 original size:89 final size:87
Alignment explanation
Indices: 37899--38346 Score: 301
Period size: 87 Copynumber: 5.1 Consensus size: 87
37889 AAAAATCATG
*
37899 TTTTCACCCCTGAACTCTCTAAAAATTATATTTTAACCCTTAAACTTTCCAAAAACTACATTTTA
1 TTTT-ACCCC-GAACTCTCTAAAAATTATATTTTGACCCTTAAACTTTCCAAAAACTACATTTT-
*
37964 ACCCTAAACTTCTCAAAAATTA-CA
63 ACCCCAAACTTCTCAAAAATTACCA
* * * * *
37988 TTTTGACCCTCGAACTTTCTAAAAATTATGTTTTGACCCTTAAACTTTTCAAAAATTACATTTTT
1 TTTT-ACCC-CGAACTCTCTAAAAATTATATTTTGACCCTTAAACTTTCCAAAAACTACATTTTA
* *
38053 CCCCAAACTTTTCAAAAATTATCA
64 CCCCAAACTTCTCAAAAATTACCA
* * * * * ** *
38077 TTTTACCCCCAAGATGTCCAAAAATTACATTTTTGA-CCTCGAACTTTCAAAAAAAC-ACATTTT
1 TTTTACCCCGAA-CTCTCTAAAAATTATA-TTTTGACCCTTAAACTTTC-CAAAAACTACATTTT
38140 ACCCCAAAC-TCTCAAAAATTACCA
63 ACCCCAAACTTCTCAAAAATTACCA
* * * * * * *
38164 TTTTCCCCCCGAA-TATAC-AAAAATTACCATTTT-A-CTTCTGAA-TGTCCAAAAATTACATTT
1 TTTT-ACCCCGAACTCT-CTAAAAATTA-TATTTTGACCCT-TAAACTTTCCAAAAACTACA-TT
* * *
38224 TTGCCCTCGAATTTC-CAAAAATTACCA
61 TTACCC-CAAACTTCTCAAAAATTACCA
* * * ** * * * **
38251 TTTTACCCTCGAA-TATCTAAAAATTACATTTTCACCC-CCAAGTGTCCAAAAATTATTGTTTTA
1 TTTTACCC-CGAACTCTCTAAAAATTATATTTTGACCCTTAAACTTTCCAAAAACTA-CATTTTA
* *
38314 CCCTCGAACCTC-CAAAAATTACCA
64 CCC-CAAACTTCTCAAAAATTACCA
38338 TTTTACCCC
1 TTTTACCCC
38347 CGAGCATCCA
Statistics
Matches: 297, Mismatches: 43, Indels: 41
0.78 0.11 0.11
Matches are distributed among these distances:
84 5 0.02
85 9 0.03
86 37 0.12
87 105 0.35
88 67 0.23
89 73 0.25
90 1 0.00
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.34
Consensus pattern (87 bp):
TTTTACCCCGAACTCTCTAAAAATTATATTTTGACCCTTAAACTTTCCAAAAACTACATTTTACC
CCAAACTTCTCAAAAATTACCA
Found at i:38099 original size:58 final size:57
Alignment explanation
Indices: 38037--38282 Score: 230
Period size: 58 Copynumber: 4.3 Consensus size: 57
38027 TTAAACTTTT
* *
38037 CAAAAATTACATTTTT-CCCCAAACTTTTCAAAAATTATCATTTTACCCCCAAGATGTC
1 CAAAAATTACATTTTTGCCCCGAA-TTTTCAAAAATTACCATTTTACCCCCAA-ATGTC
* * * *
38095 CAAAAATTACATTTTTGACCTCGAACTTTCAAAAA-AACACATTTTA-CCCCAAA-CTC
1 CAAAAATTACATTTTTG-CCCCGAATTTTCAAAAATTAC-CATTTTACCCCCAAATGTC
** * * ** **
38151 TCAAAAATTACCATTTTCCCCCCGAATATACAAAAATTACCATTTTACTTCTGAATGTC
1 -CAAAAATTA-CATTTTTGCCCCGAATTTTCAAAAATTACCATTTTACCCCCAAATGTC
* * * *
38210 CAAAAATTACATTTTTGCCCTCGAATTTCCAAAAATTACCATTTTACCCTCGAATATC
1 CAAAAATTACATTTTTGCCC-CGAATTTTCAAAAATTACCATTTTACCCCCAAATGTC
*
38268 TAAAAATTACATTTT
1 CAAAAATTACATTTT
38283 CACCCCCAAG
Statistics
Matches: 151, Mismatches: 28, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
56 2 0.01
57 39 0.26
58 87 0.58
59 18 0.12
60 5 0.03
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.34
Consensus pattern (57 bp):
CAAAAATTACATTTTTGCCCCGAATTTTCAAAAATTACCATTTTACCCCCAAATGTC
Found at i:38130 original size:30 final size:28
Alignment explanation
Indices: 37841--38282 Score: 186
Period size: 29 Copynumber: 15.1 Consensus size: 28
37831 AAAAATCATG
*
37841 TTTTGACCTCGAACTTTTCAAAAATTATA
1 TTTTGACCTCGAAC-TTTCAAAAATTACA
* * * **
37870 TTTTGATCCT-AAACTTTTTAAAAATCATG
1 TTTTGA-CCTCGAAC-TTTCAAAAATTACA
* * * *
37899 TTTTCACCCCTGAACTCTCTAAAAATTATA
1 TTTTGACCTC-GAACTTTC-AAAAATTACA
* ** *
37929 TTTTAACCCTTAAACTTTCCAAAAACTACA
1 TTTTGA-CCTCGAACTTT-CAAAAATTACA
* *
37959 TTTTAACC-CTAAACTTCTCAAAAATTACA
1 TTTTGACCTC-GAACTT-TCAAAAATTACA
**
37988 TTTTGACCCTCGAACTTTCTAAAAATTATG
1 TTTTGA-CCTCGAACTTTC-AAAAATTACA
**
38018 TTTTGACCCTTAAACTTTTCAAAAATTACA
1 TTTTGA-CCTCGAAC-TTTCAAAAATTACA
* * *
38048 TTTT-TCCCCAAACTTTTCAAAAATTATCA
1 TTTTGACCTCGAAC-TTTCAAAAATTA-CA
* * * *
38077 TTTT-ACCCCCAAGATGTCCAAAAATTACA
1 TTTTGACCTCGAA-CT-TTCAAAAATTACA
**
38106 TTTTTGACCTCGAACTTTCAAAAAAACACA
1 -TTTTGACCTCGAACTTTC-AAAAATTACA
* * *
38136 TTTT-ACCCCAAACTCTCAAAAATTACCA
1 TTTTGACCTCGAACTTTCAAAAATTA-CA
** * *
38164 TTTTCCCCCCGAA-TATACAAAAATTACCA
1 TTTTGACCTCGAACT-TTCAAAAATTA-CA
* *
38193 TTTT-ACTTCTGAA-TGTCCAAAAATTACA
1 TTTTGACCTC-GAACT-TTCAAAAATTACA
*
38221 TTTTTGCCCTCGAA-TTTCCAAAAATTACCA
1 -TTTTGACCTCGAACTTT-CAAAAATTA-CA
*
38251 TTTT-ACCCTCGAA-TATCTAAAAATTACA
1 TTTTGA-CCTCGAACTTTC-AAAAATTACA
38279 TTTT
1 TTTT
38283 CACCCCCAAG
Statistics
Matches: 325, Mismatches: 60, Indels: 57
0.74 0.14 0.13
Matches are distributed among these distances:
27 6 0.02
28 50 0.15
29 148 0.46
30 107 0.33
31 14 0.04
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.36
Consensus pattern (28 bp):
TTTTGACCTCGAACTTTCAAAAATTACA
Found at i:38184 original size:29 final size:29
Alignment explanation
Indices: 38065--38361 Score: 200
Period size: 29 Copynumber: 10.2 Consensus size: 29
38055 CCAAACTTTT
* * *
38065 CAAAAATTATCATTTTACCCCCAAGATGTC
1 CAAAAATTACCATTTTACCCCCGA-ATATC
* *
38095 CAAAAATTA-CATTTTTGA-CCTCGAACT-TT
1 CAAAAATTACCA-TTTT-ACCCCCGAA-TATC
*
38124 CAAAAA-AACACATTTTA-CCCC-AA-ACTC
1 CAAAAATTAC-CATTTTACCCCCGAATA-TC
* *
38151 TCAAAAATTACCATTTTCCCCCCGAATATA
1 -CAAAAATTACCATTTTACCCCCGAATATC
** * *
38181 CAAAAATTACCATTTTACTTCTGAATGTC
1 CAAAAATTACCATTTTACCCCCGAATATC
* * *
38210 CAAAAATTA-CATTTTTGCCCTCGAATTTC
1 CAAAAATTACCA-TTTTACCCCCGAATATC
*
38239 CAAAAATTACCATTTTACCCTCGAATATC
1 CAAAAATTACCATTTTACCCCCGAATATC
* *
38268 TAAAAATTA-CATTTTCACCCCC-AAGTGTC
1 CAAAAATTACCATTTT-ACCCCCGAA-TATC
*** * **
38297 CAAAAATTATTGTTTTACCCTCGAACCTC
1 CAAAAATTACCATTTTACCCCCGAATATC
**
38326 CAAAAATTACCATTTTACCCCCGAGCATC
1 CAAAAATTACCATTTTACCCCCGAATATC
38355 CAAAAAT
1 CAAAAAT
38362 CGTATTTTTG
Statistics
Matches: 211, Mismatches: 38, Indels: 37
0.74 0.13 0.13
Matches are distributed among these distances:
27 3 0.01
28 27 0.13
29 148 0.70
30 31 0.15
31 2 0.01
ACGTcount: A:0.37, C:0.27, G:0.05, T:0.31
Consensus pattern (29 bp):
CAAAAATTACCATTTTACCCCCGAATATC
Found at i:42645 original size:21 final size:19
Alignment explanation
Indices: 42616--42663 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
42606 CGAAGTGCTT
*
42616 AAAATAAAAGAAAGAAAAAGA
1 AAAAAAAAAG-AAGAAAAA-A
42637 AAAAAAAAAGAAGAAAAAA
1 AAAAAAAAAGAAGAAAAAA
42656 AAACAAAA
1 AAA-AAAA
42664 TAAATAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 4 0.16
20 12 0.48
21 9 0.36
ACGTcount: A:0.85, C:0.02, G:0.10, T:0.02
Consensus pattern (19 bp):
AAAAAAAAAGAAGAAAAAA
Found at i:43609 original size:11 final size:10
Alignment explanation
Indices: 43593--43626 Score: 52
Period size: 11 Copynumber: 3.4 Consensus size: 10
43583 TGCAATATAG
43593 AAAAATAAATA
1 AAAAATAAA-A
43604 AAAAATAAAA
1 AAAAATAAAA
43614 AAAAA-AAAA
1 AAAAATAAAA
43623 AAAA
1 AAAA
43627 GGGAAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 8 0.35
10 6 0.26
11 9 0.39
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:43633 original size:27 final size:26
Alignment explanation
Indices: 43603--43696 Score: 91
Period size: 27 Copynumber: 3.4 Consensus size: 26
43593 AAAAATAAAT
*
43603 AAAAAATAAAAAAAAAAAAAAAAAGGG
1 AAAAAAGAAAAAAAAAAAAAAAAA-GG
* *
43630 AAAAAAGAAAAAAAGAAGAAAAAAGG
1 AAAAAAGAAAAAAAAAAAAAAAAAGG
*
43656 -AAAAAGAAAATAGAGAAAACGAAAAAAAGA
1 AAAAAAGAAAA-A-A-AAAA--AAAAAAAGG
43686 AAAAAAGAAAA
1 AAAAAAGAAAA
43697 GGAGAGGTTG
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
25 10 0.18
26 3 0.05
27 22 0.40
28 3 0.05
30 7 0.13
31 10 0.18
ACGTcount: A:0.82, C:0.01, G:0.15, T:0.02
Consensus pattern (26 bp):
AAAAAAGAAAAAAAAAAAAAAAAAGG
Found at i:43639 original size:7 final size:7
Alignment explanation
Indices: 43603--43696 Score: 63
Period size: 7 Copynumber: 13.6 Consensus size: 7
43593 AAAAATAAAT
*
43603 AAAAAAT
1 AAAAAAG
43610 AAAAAA-
1 AAAAAAG
43616 AAAAAA-
1 AAAAAAG
*
43622 AAAAAGGG
1 AAAAA-AG
43630 AAAAAAG
1 AAAAAAG
43637 --AAAA-
1 AAAAAAG
*
43641 AAAGAAG
1 AAAAAAG
43648 AAAAAAG
1 AAAAAAG
*
43655 GAAAAAG
1 AAAAAAG
*
43662 AAAATAG
1 AAAAAAG
*
43669 AGAAAACG
1 A-AAAAAG
43677 AAAAAAAG
1 -AAAAAAG
43685 AAAAAAAG
1 -AAAAAAG
43693 AAAA
1 AAAA
43697 GGAGAGGTTG
Statistics
Matches: 70, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
5 4 0.06
6 14 0.20
7 29 0.41
8 22 0.31
9 1 0.01
ACGTcount: A:0.82, C:0.01, G:0.15, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:43641 original size:8 final size:8
Alignment explanation
Indices: 43612--43696 Score: 75
Period size: 8 Copynumber: 10.5 Consensus size: 8
43602 TAAAAAATAA
*
43612 AAAAAAAA
1 AAAAAAAG
43620 AAAAAAAGG
1 AAAAAAA-G
*
43629 GAAAAAAG
1 AAAAAAAG
43637 AAAAAAAG
1 AAAAAAAG
43645 AAGAAAAA-
1 AA-AAAAAG
*
43653 AGGAAAAAG
1 A-AAAAAAG
*
43662 -AAAATAG
1 AAAAAAAG
* *
43669 AGAAAACG
1 AAAAAAAG
43677 AAAAAAAG
1 AAAAAAAG
43685 AAAAAAAG
1 AAAAAAAG
43693 AAAA
1 AAAA
43697 GGAGAGGTTG
Statistics
Matches: 61, Mismatches: 11, Indels: 10
0.74 0.13 0.12
Matches are distributed among these distances:
7 5 0.08
8 45 0.74
9 11 0.18
ACGTcount: A:0.81, C:0.01, G:0.16, T:0.01
Consensus pattern (8 bp):
AAAAAAAG
Found at i:44761 original size:49 final size:48
Alignment explanation
Indices: 44634--44805 Score: 182
Period size: 49 Copynumber: 3.5 Consensus size: 48
44624 CTGAGAAAAA
* *
44634 CATGAAGATTTAAAGGGGAAGGTTGAGGCCATAACGGCGAACCTGATAC
1 CATGAAGATTTAAA-GGGAAGGTTGAGGCCACAACGGCGAACCCGATAC
** * * * * *
44683 CTAAAAAGATATGATGGGAAAGGTTGAGGCCGCAACGGCAAACCCGATAC
1 C-ATGAAGATTTAAAGGG-AAGGTTGAGGCCACAACGGCGAACCCGATAC
* * *
44733 CATGAAGATTTGAAGGGAAGGATCGAGGCCACAACGGCGAACCCGGTAC
1 CATGAAGATTTAAAGGGAAGG-TTGAGGCCACAACGGCGAACCCGATAC
*
44782 CATGAAGATGTAAAGGGAAAGGTT
1 CATGAAGATTTAAAGGG-AAGGTT
44806 AAGACCGTAA
Statistics
Matches: 99, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
48 4 0.04
49 55 0.56
50 40 0.40
ACGTcount: A:0.36, C:0.17, G:0.31, T:0.16
Consensus pattern (48 bp):
CATGAAGATTTAAAGGGAAGGTTGAGGCCACAACGGCGAACCCGATAC
Found at i:44834 original size:98 final size:99
Alignment explanation
Indices: 44634--44924 Score: 223
Period size: 99 Copynumber: 2.9 Consensus size: 99
44624 CTGAGAAAAA
* * * * *
44634 CATGAAGATTTAAAGGGGAAGGTTGAGGCCATAACGGCGAACCTGATACCTAAAAAGATATGATG
1 CATGAAGATTTAAAGGGGAAGGTCGAGGCCACAACGGCGAACCCGATACCTAAAAAGATATAAAG
* * *
44699 GGAAAGGTTGAGGCCGCAACGGCAAACCCGATAC
66 GGAAAGGTTAAGACCGCAACGACAAACCCGATAC
* * ** *
44733 CATGAAGATTTGAA-GGGAAGGATCGAGGCCACAACGGCGAACCCGGTACC-ATGAAGATGTAAA
1 CATGAAGATTTAAAGGGGAAGG-TCGAGGCCACAACGGCGAACCCGATACCTAAAAAGATATAAA
* **
44796 GGGAAAGGTTAAGACCGTAACGATGAACCC-AGTAC
65 GGGAAAGGTTAAGACCGCAACGACAAACCCGA-TAC
* * * * * * * ** *
44831 CATGAATAGA-TGATAGGAG-TGGACTGAGGCCGCAACGGCAAATACGATACCTTAAAAAGATGT
1 CATG-A-AGATTTAAAGGGGAAGGTC-GAGGCCACAACGGCGAACCCGATACC-TAAAAAGATAT
* * * *
44894 AAAGGGAAAGGTTGAGTCCACAACGATAAAC
62 AAAGGGAAAGGTTAAGACCGCAACGACAAAC
44925 ATGATACCTA
Statistics
Matches: 150, Mismatches: 34, Indels: 14
0.76 0.17 0.07
Matches are distributed among these distances:
97 1 0.01
98 47 0.31
99 63 0.42
100 5 0.03
101 34 0.23
ACGTcount: A:0.38, C:0.18, G:0.29, T:0.16
Consensus pattern (99 bp):
CATGAAGATTTAAAGGGGAAGGTCGAGGCCACAACGGCGAACCCGATACCTAAAAAGATATAAAG
GGAAAGGTTAAGACCGCAACGACAAACCCGATAC
Found at i:45438 original size:39 final size:39
Alignment explanation
Indices: 45395--45483 Score: 106
Period size: 39 Copynumber: 2.3 Consensus size: 39
45385 CCGAGACAGG
* * **
45395 GGCAGATTGCAACCATCCGATCTTTTACCTTGACCATGA
1 GGCAGATTGCAACCATCCAATCTCTTACCCCGACCATGA
** * *
45434 GGCAGATCACAGCCATCCAATCTCTTACCCCGATCATGA
1 GGCAGATTGCAACCATCCAATCTCTTACCCCGACCATGA
45473 GGCAGATTGCA
1 GGCAGATTGCA
45484 GTTATTCAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (39 bp):
GGCAGATTGCAACCATCCAATCTCTTACCCCGACCATGA
Found at i:46075 original size:209 final size:209
Alignment explanation
Indices: 45502--46457 Score: 1353
Period size: 209 Copynumber: 4.6 Consensus size: 209
45492 AAACAATGAG
* * * * * *
45502 GCGGTCATCTTCTTGATGAGATACTGAGAAGTAGACTAAATAAATGAAATC-AGGCTCAAAGTGA
1 GCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAAGCTCAATGTGA
* *
45566 GC-AAATTTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGT
66 GCGAAA-CTTCGAA-CCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGT
* * * * * * *
45630 TAGCTTCTTGATGAGATACTGAAAAGTGGACCAAATTCGTCTTTCTGATGAGATACAGAAAAACG
129 CAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGCG
45695 GATTAAAACATGTGAT
194 GATTAAAACATGTGAT
* * *
45711 GTGGTCATCTTCCTAATGAGATACTGAGAAGTAGACCAAATCAACGAAACCAAAGCTCAATGTGA
1 GCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAAGCTCAATGTGA
* * *
45776 GCGAAACTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGATCGAAGCAATAAAATAGTC
66 GCGAAACTTCGAA-CCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTC
* *
45841 AGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCGG
130 AGCTTCCTGATGAGATACTGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGCGG
45906 ATTAAAACATGTGAT
195 ATTAAAACATGTGAT
*
45921 GCGGTCATCTTCCTGATAAGATACTGAGAAGTAGACCAAATCAATGAAA-CAAAGCTCAATGTGA
1 GCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAAGCTCAATGTGA
** * * * *
45985 GAAAAACTTCGAACACCAGCTTCCTGGTAAGATACTAAGAAGCAGGTCGAAGCAATAAAATGGTT
66 GCGAAACTTCGAAC-CCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTC
* * *
46050 AGCTTCCTGATGAGATATTGAGAAGTGGACCAAATCCGTCTTCTTGATGAGATACAAAGAAGCGG
130 AGCTTCCTGATGAGATACTGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGCGG
46115 ATTAAAACATGTGAT
195 ATTAAAACATGTGAT
* * * *
46130 GCAGTCATCTTTCTGATGAGATATTGAGAAGTAGACCAAATCAATGAAA-CAAAACTCAATGTGA
1 GCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAAGCTCAATGTGA
* * *
46194 ACGAAACTTCGAACCTCAGCTTCCTGATGAGATTCTAAGAAGCAGGTCGAAGCAATAAAATGGTC
66 GCGAAACTTCGAACC-CAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTC
* *
46259 AGTTTCCTGATGAGATACTGAGAAGTGGACCAAATCCGTCTTCCTGATAAGATACAGAGAAGCGG
130 AGCTTCCTGATGAGATACTGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGCGG
* * *
46324 ATCAAAATAAGTGAT
195 ATTAAAACATGTGAT
* * * * *
46339 GCAGTCGTCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAACGCTCGATGTGT
1 GCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAAGCTCAATGTGA
* * *
46404 GCGAAACTTCGAACCTCAGCTTCCCGATGAGAAACGGAGAAGCAGGTCGAAGCA
66 GCGAAACTTCGAACC-CAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
46458 GGTCGAAGCA
Statistics
Matches: 670, Mismatches: 72, Indels: 9
0.89 0.10 0.01
Matches are distributed among these distances:
208 2 0.00
209 421 0.63
210 244 0.36
211 3 0.00
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (209 bp):
GCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAAGCTCAATGTGA
GCGAAACTTCGAACCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTCA
GCTTCCTGATGAGATACTGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGCGGA
TTAAAACATGTGAT
Found at i:46413 original size:419 final size:417
Alignment explanation
Indices: 45489--46457 Score: 1381
Period size: 419 Copynumber: 2.3 Consensus size: 417
45479 TTGCAGTTAT
* * * * *
45489 TCAAAACAA-TGAGGCGGTCATCTTCTTGATGAGATACTGAGAAGTAGACTAAATAAATGAAATC
1 TCAAAACAAGTGATGCAGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAA-C
* * * *
45553 -AGGCTCAAAGTGAGCAAATTTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAA
65 AAAGCTCAATGTGAGCAAA-CTTCGAA-CCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAA
* *
45617 GCAATAAAATGGTTAGCTTCTTGATGAGATACTGAAAAGTGGACCAAATTCGTCTTTCTGATGAG
128 GCAATAAAATGGTTAGCTTCCTGATGAGATACTGAAAAGTGGACCAAATCCGTCTTTCTGATGAG
**
45682 ATACAGAAAAACGGATTAAAACATGTGATGTGGTCATCTTCCTAATGAGATACTGAGAAGTAGAC
193 ATACAGAAAAACGGATTAAAACATGTGATGCAGTCATCTTCCTAATGAGATACTGAGAAGTAGAC
* *
45747 CAAATCAACGAAACCAAAGCTCAATGTGAGCGAAACTTCGAACCCCAACTTCCTGATGAGATACT
258 CAAATCAACGAAACCAAAACTCAATGTGAACGAAACTTCGAACCCCAACTTCCTGATGAGATACT
* *
45812 GAGAAGCAGATCGAAGCAATAAAATAGTCAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATT
323 AAGAAGCAGATCGAAGCAATAAAATAGTCAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATC
*
45877 CGTCTTCCTAATGAGATACAGAGAAGCGGA
388 CGTCTTCCTAATAAGATACAGAGAAGCGGA
* * * *
45907 TTAAAACATGTGATGCGGTCATCTTCCTGATAAGATACTGAGAAGTAGACCAAATCAATGAAACA
1 TCAAAACAAGTGATGCAGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACA
* * * *
45972 AAGCTCAATGTGAGAAAAACTTCGAACACCAGCTTCCTGGTAAGATACTAAGAAGCAGGTCGAAG
66 AAGCTCAATGTGAG-CAAACTTCGAAC-CCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAG
* *
46037 CAATAAAATGGTTAGCTTCCTGATGAGATATTGAGAAGTGGACCAAATCCGTC-TTCTTGATGAG
129 CAATAAAATGGTTAGCTTCCTGATGAGATACTGAAAAGTGGACCAAATCCGTCTTTC-TGATGAG
* * * *
46101 ATACA-AAGAAGCGGATTAAAACATGTGATGCAGTCATCTTTCTGATGAGATATTGAGAAGTAGA
193 ATACAGAA-AAACGGATTAAAACATGTGATGCAGTCATCTTCCTAATGAGATACTGAGAAGTAGA
* * * *
46165 CCAAATCAATGAAA-CAAAACTCAATGTGAACGAAACTTCGAACCTCAGCTTCCTGATGAGATTC
257 CCAAATCAACGAAACCAAAACTCAATGTGAACGAAACTTCGAACCCCAACTTCCTGATGAGATAC
* * *
46229 TAAGAAGCAGGTCGAAGCAATAAAATGGTCAGTTTCCTGATGAGATACTGAGAAGTGGACCAAAT
322 TAAGAAGCAGATCGAAGCAATAAAATAGTCAGCTTCCTGATGAGATACTGAGAAGTGGACCAAAT
*
46294 CCGTCTTCCTGATAAGATACAGAGAAGCGGA
387 CCGTCTTCCTAATAAGATACAGAGAAGCGGA
* *
46325 TCAAAATAAGTGATGCAGTCGTCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACC
1 TCAAAACAAGTGATGCAGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAA-C
* * * * * *
46390 AACGCTCGATGTGTGCGAAACTTCGAACCTCAGCTTCCCGATGAGAAACGGAGAAGCAGGTCGAA
65 AAAGCTCAATGTGAGC-AAACTTCGAACC-CAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAA
46455 GCA
128 GCA
46458 GGTCGAAGCA
Statistics
Matches: 488, Mismatches: 54, Indels: 17
0.87 0.10 0.03
Matches are distributed among these distances:
418 206 0.42
419 279 0.57
420 3 0.01
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (417 bp):
TCAAAACAAGTGATGCAGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACA
AAGCTCAATGTGAGCAAACTTCGAACCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
ATAAAATGGTTAGCTTCCTGATGAGATACTGAAAAGTGGACCAAATCCGTCTTTCTGATGAGATA
CAGAAAAACGGATTAAAACATGTGATGCAGTCATCTTCCTAATGAGATACTGAGAAGTAGACCAA
ATCAACGAAACCAAAACTCAATGTGAACGAAACTTCGAACCCCAACTTCCTGATGAGATACTAAG
AAGCAGATCGAAGCAATAAAATAGTCAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATCCGT
CTTCCTAATAAGATACAGAGAAGCGGA
Found at i:46457 original size:10 final size:10
Alignment explanation
Indices: 46442--46467 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
46432 GAGAAACGGA
46442 GAAGCAGGTC
1 GAAGCAGGTC
46452 GAAGCAGGTC
1 GAAGCAGGTC
46462 GAAGCA
1 GAAGCA
46468 ATAAAATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.35, C:0.19, G:0.38, T:0.08
Consensus pattern (10 bp):
GAAGCAGGTC
Found at i:46941 original size:17 final size:18
Alignment explanation
Indices: 46919--46952 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
46909 CCCAAATAAA
46919 ATTTTAAATTTA-AATTT
1 ATTTTAAATTTAGAATTT
46936 ATTTTAAATTTAGAATT
1 ATTTTAAATTTAGAATT
46953 AAAATGTCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
ATTTTAAATTTAGAATTT
Found at i:48396 original size:30 final size:29
Alignment explanation
Indices: 48360--48863 Score: 287
Period size: 30 Copynumber: 17.1 Consensus size: 29
48350 CCCAAAAAGT
* *
48360 CCCTAAACTATCCAAAAATCACATTTTCAC
1 CCCTAAACTTTCCAAAAATTACATTTT-AC
* *
48390 CCCTAAACTTTCCAAAAATTATATTTTAA
1 CCCTAAACTTTCCAAAAATTACATTTTAC
* *
48419 CCCTCGAACTTTCTAAAAATTACATTTTGAC
1 CCCT-AAACTTTCCAAAAATTACATTTT-AC
* * * *
48450 CCATGAACTCTCCAAAAATTATATTTTAAC
1 CCCTAAACTTTCCAAAAATTACATTTT-AC
* **
48480 CCCTAACCTTTCCAAAAAGCA-ATTTTTTGAC
1 CCCTAAACTTTCCAAAAATTACA--TTTT-AC
*
48511 CCCTGAA-TTTCTCAAAAATTACATTTTGA-
1 CCCTAAACTTTC-CAAAAATTACATTTT-AC
* ** *
48540 CCCTCAAATTTTCCAAAAATTATGTTTTAA
1 CCCT-AAACTTTCCAAAAATTACATTTTAC
* * * **
48570 CCCTCGAACTTTCCAAAAGTTACTTTTTTG
1 CCCT-AAACTTTCCAAAAATTACATTTTAC
*
48600 CTC-AAACTTTCCAAAAATTACCATTTTAC
1 CCCTAAACTTTCCAAAAATTA-CATTTTAC
** *
48629 CCCCGAA-TGTCCAAAAATTACATTTTTTAC
1 CCCTAAACTTTCCAAAAATTACA--TTTTAC
*
48659 CCC-GAACTTTCCAAAAATTACATTTTTAC
1 CCCTAAACTTTCCAAAAATTACA-TTTTAC
* * *
48688 CCCCAAACTCT-CAAAAAATACTATTTTA-
1 CCCTAAACTTTCCAAAAATTAC-ATTTTAC
* * * **
48716 CCCTCGAA-TGTCTAAAAATTACATTTTTTG
1 CCCT-AAACTTTCCAAAAATTACA-TTTTAC
* * * *
48746 TCCTCGAACTTCCCAAATATTACTATTTTAC
1 CCCT-AAACTTTCCAAAAATTAC-ATTTTAC
** * *
48777 CTTTGAA-TATCCAAAAA-TACCATTTTAC
1 CCCTAAACTTTCCAAAAATTA-CATTTTAC
* *
48805 CCCTAAA-TGTCCAAAAATTACATTTTGC
1 CCCTAAACTTTCCAAAAATTACATTTTAC
**
48833 CCCCGAA-TTTCCAAAAATTACCATTTTAC
1 CCCTAAACTTTCCAAAAATTA-CATTTTAC
48862 CC
1 CC
48864 TCGGATGTCT
Statistics
Matches: 374, Mismatches: 75, Indels: 51
0.75 0.15 0.10
Matches are distributed among these distances:
28 69 0.18
29 90 0.24
30 172 0.46
31 41 0.11
32 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (29 bp):
CCCTAAACTTTCCAAAAATTACATTTTAC
Found at i:48466 original size:60 final size:59
Alignment explanation
Indices: 48365--48863 Score: 332
Period size: 60 Copynumber: 8.5 Consensus size: 59
48355 AAAGTCCCTA
* * * *
48365 AACTATCCAAAAATCACATTTTCACCCCTAAACTTTCCAAAAATTATATTTTAACCCTCG
1 AACTTTCCAAAAATTACATTTTGACCCCTGAACTTTCCAAAAATTATATTTT-ACCCTCG
* * * *
48425 AACTTTCTAAAAATTACATTTTGACCCATGAACTCTCCAAAAATTATATTTTAACCC-CT
1 AACTTTCCAAAAATTACATTTTGACCCCTGAACTTTCCAAAAATTATATTTT-ACCCTCG
** * *
48484 AACCTTTCCAAAAAGCA-ATTTTTTGACCCCTGAA-TTTCTCAAAAATTACATTTTGACCCTCA
1 AA-CTTTCCAAAAATTACA--TTTTGACCCCTGAACTTTC-CAAAAATTATATTTT-ACCCTCG
* ** * * ** *
48546 AATTTTCCAAAAATTATGTTTT-AACCCTCGAACTTTCCAAAAGTTACT-TTTT-TGCTCA
1 AACTTTCCAAAAATTACATTTTGACCCCT-GAACTTTCCAAAAATTA-TATTTTACCCTCG
* * *
48604 AACTTTCCAAAAATTACCATTTT-ACCCCCGAA-TGTCCAAAAATTACATTTTTTACCC-CG
1 AACTTTCCAAAAATTA-CATTTTGACCCCTGAACTTTCCAAAAATT--ATATTTTACCCTCG
* ** * *
48663 AACTTTCCAAAAATTACATTTTTACCCCCAAACTCT-CAAAAAATACTATTTTACCCTCG
1 AACTTTCCAAAAATTACATTTTGACCCCTGAACTTTCCAAAAATTA-TATTTTACCCTCG
* * * * * * * *
48722 AA-TGTCTAAAAATTACATTTTTTGTCCTC-GAACTTCCCAAATATTACTATTTTACCTTTG
1 AACTTTCCAAAAATTACA--TTTTGACCCCTGAACTTTCCAAAAATTA-TATTTTACCCTCG
* * * * * *
48782 AA-TATCCAAAAA-TACCATTTT-ACCCCT-AAATGTCCAAAAATTACATTTTGCCCCCG
1 AACTTTCCAAAAATTA-CATTTTGACCCCTGAACTTTCCAAAAATTATATTTTACCCTCG
48838 AA-TTTCCAAAAATTACCATTTT-ACCC
1 AACTTTCCAAAAATTA-CATTTTGACCC
48864 TCGGATGTCT
Statistics
Matches: 350, Mismatches: 65, Indels: 51
0.75 0.14 0.11
Matches are distributed among these distances:
56 19 0.05
57 39 0.11
58 55 0.16
59 64 0.18
60 124 0.35
61 46 0.13
62 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (59 bp):
AACTTTCCAAAAATTACATTTTGACCCCTGAACTTTCCAAAAATTATATTTTACCCTCG
Found at i:48560 original size:91 final size:89
Alignment explanation
Indices: 48363--48587 Score: 249
Period size: 91 Copynumber: 2.5 Consensus size: 89
48353 AAAAAGTCCC
* * * * **
48363 TAAACTATCCAAAAATCACATTTTCACCCCTAAACTTTCCAAAAATTATATTTTAACCCTCGAAC
1 TAAACTCTCCAAAAATTATATTTTAACCCCT-AACTTTCCAAAAACAATATTTTAACCCTCGAAC
48428 TTTCTAAAAATTACATTTTGACCCA
65 TTTCTAAAAATTACATTTTGACCCA
* * *
48453 TGAACTCTCCAAAAATTATATTTTAACCCCTAACCTTTCCAAAAAGCAATTTTTTGACCC-CTGA
1 TAAACTCTCCAAAAATTATATTTTAACCCCTAA-CTTTCCAAAAA-CAATATTTTAACCCTC-GA
48517 A-TTTCTCAAAAATTACATTTTGACCC-
63 ACTTTCT-AAAAATTACATTTTGACCCA
* * * *
48543 TCAAATTTTCCAAAAATTATGTTTTAACCCTCGAACTTTCCAAAA
1 T-AAACTCTCCAAAAATTATATTTTAACCC-CTAACTTTCCAAAA
48588 GTTACTTTTT
Statistics
Matches: 115, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
89 2 0.02
90 44 0.38
91 66 0.57
92 3 0.03
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.34
Consensus pattern (89 bp):
TAAACTCTCCAAAAATTATATTTTAACCCCTAACTTTCCAAAAACAATATTTTAACCCTCGAACT
TTCTAAAAATTACATTTTGACCCA
Found at i:48641 original size:29 final size:29
Alignment explanation
Indices: 48609--48949 Score: 252
Period size: 29 Copynumber: 11.8 Consensus size: 29
48599 GCTCAAACTT
48609 TCCAAAAATTACCATTTTACCCCCGAATG
1 TCCAAAAATTACCATTTTACCCCCGAATG
*
48638 TCCAAAAATTA-CATTTTTTA-CCCCGAACTT
1 TCCAAAAATTACCA--TTTTACCCCCGAA-TG
**
48668 TCCAAAAATTA-CATTTTTACCCCC-AAAC
1 TCCAAAAATTACCA-TTTTACCCCCGAATG
* * *
48696 TCTCAAAAAATACTATTTTACCCTCGAATG
1 TC-CAAAAATTACCATTTTACCCCCGAATG
* ** *
48726 TCTAAAAATTA-CATTTTTTGTCCTCGAACT-
1 TCCAAAAATTACCA--TTTTACCCCCGAA-TG
* * *** *
48756 TCCCAAATATTACTATTTTACCTTTGAATA
1 T-CCAAAAATTACCATTTTACCCCCGAATG
**
48786 TCCAAAAA-TACCATTTTACCCCTAAATG
1 TCCAAAAATTACCATTTTACCCCCGAATG
* *
48814 TCCAAAAATTA-CATTTTGCCCCCGAATT
1 TCCAAAAATTACCATTTTACCCCCGAATG
* *
48842 TCCAAAAATTACCATTTTACCCTCGGATG
1 TCCAAAAATTACCATTTTACCCCCGAATG
* *
48871 TCTAAAAATTA-CATTTTGCCCCC-AAGTG
1 TCCAAAAATTACCATTTTACCCCCGAA-TG
* * * **
48899 TCCAAAAATTATCGTTTTACGCCCGAACC
1 TCCAAAAATTACCATTTTACCCCCGAATG
*
48928 TCCAAAAGTTACCATTTTACCC
1 TCCAAAAATTACCATTTTACCC
48950 TCGGGCATCC
Statistics
Matches: 246, Mismatches: 48, Indels: 36
0.75 0.15 0.11
Matches are distributed among these distances:
27 1 0.00
28 74 0.30
29 109 0.44
30 52 0.21
31 9 0.04
32 1 0.00
ACGTcount: A:0.34, C:0.27, G:0.06, T:0.33
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTACCCCCGAATG
Found at i:50389 original size:14 final size:13
Alignment explanation
Indices: 50367--50405 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
50357 CCAGAAAAGT
50367 AAATCATTTTCCA
1 AAATCATTTTCCA
*
50380 AAATTCATTTTTCTA
1 AAA-TCA-TTTTCCA
50395 AAATCATTTTC
1 AAATCATTTTC
50406 AATGAAACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 8 0.35
14 6 0.26
15 9 0.39
ACGTcount: A:0.36, C:0.18, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATCATTTTCCA
Found at i:50397 original size:15 final size:14
Alignment explanation
Indices: 50367--50404 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
50357 CCAGAAAAGT
50367 AAATCA-TTTTCCA
1 AAATCATTTTTCCA
*
50380 AAATTCATTTTTCTA
1 AAA-TCATTTTTCCA
50395 AAATCATTTT
1 AAATCATTTT
50405 CAATGAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 3 0.14
14 10 0.45
15 9 0.41
ACGTcount: A:0.37, C:0.16, G:0.00, T:0.47
Consensus pattern (14 bp):
AAATCATTTTTCCA
Found at i:52510 original size:30 final size:32
Alignment explanation
Indices: 52476--52542 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 32
52466 AAATTACCCC
52476 TTAAATAA-CACATTAATATTTAATT-AATTT
1 TTAAATAACCACATTAATATTTAATTAAATTT
* * **
52506 TTAAA-AACCACTTTTATATTTTTTTAAATTT
1 TTAAATAACCACATTAATATTTAATTAAATTT
52537 TTAAAT
1 TTAAAT
52543 TTTTAAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
29 2 0.07
30 18 0.60
31 10 0.33
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (32 bp):
TTAAATAACCACATTAATATTTAATTAAATTT
Found at i:56002 original size:47 final size:47
Alignment explanation
Indices: 55933--56031 Score: 180
Period size: 47 Copynumber: 2.1 Consensus size: 47
55923 TCAAAGACAA
* *
55933 CGAGCTCGCAGACATAGCTCGCAAGGCGAGTTCATAGATGGGGTCCG
1 CGAGCTCACAAACATAGCTCGCAAGGCGAGTTCATAGATGGGGTCCG
55980 CGAGCTCACAAACATAGCTCGCAAGGCGAGTTCATAGATGGGGTCCG
1 CGAGCTCACAAACATAGCTCGCAAGGCGAGTTCATAGATGGGGTCCG
56027 CGAGC
1 CGAGC
56032 ACATCTCGCA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.25, C:0.26, G:0.32, T:0.16
Consensus pattern (47 bp):
CGAGCTCACAAACATAGCTCGCAAGGCGAGTTCATAGATGGGGTCCG
Found at i:64646 original size:2 final size:2
Alignment explanation
Indices: 64637--64683 Score: 60
Period size: 2 Copynumber: 23.5 Consensus size: 2
64627 GTGTTTTTTT
* *
64637 TA TA -A TA TA TA TA TA TA TA TA TA TA TT TCA TT TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
64679 TA TA T
1 TA TA T
64684 GTATTTTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
1 1 0.03
2 37 0.95
3 1 0.03
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:67652 original size:27 final size:27
Alignment explanation
Indices: 67622--67673 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
67612 TGGCATGTCC
67622 AACTTCATTAACCCTACTTGTCATTCA
1 AACTTCATTAACCCTACTTGTCATTCA
67649 AACTTCATTAACCCTACTTGTCATT
1 AACTTCATTAACCCTACTTGTCATT
67674 TTTGAATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.29, C:0.29, G:0.04, T:0.38
Consensus pattern (27 bp):
AACTTCATTAACCCTACTTGTCATTCA
Found at i:68004 original size:17 final size:18
Alignment explanation
Indices: 67982--68015 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
67972 ACTTTAGTTT
67982 TAAAAAA-AACCTTAATG
1 TAAAAAATAACCTTAATG
67999 TAAAAAATAACCTTAAT
1 TAAAAAATAACCTTAAT
68016 ATTTGATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.59, C:0.12, G:0.03, T:0.26
Consensus pattern (18 bp):
TAAAAAATAACCTTAATG
Found at i:68264 original size:21 final size:23
Alignment explanation
Indices: 68224--68268 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
68214 CAGCAAATGA
68224 TTTTAAAAATAATTTAAAATTATT
1 TTTTAAAAATAA-TTAAAATTATT
68248 TTTTAAAAAT-A-TAAAATTATT
1 TTTTAAAAATAATTAAAATTATT
68269 ATAATTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.48
23 1 0.05
24 10 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTTAAAAATAATTAAAATTATT
Found at i:69656 original size:31 final size:31
Alignment explanation
Indices: 69603--69687 Score: 77
Period size: 31 Copynumber: 2.8 Consensus size: 31
69593 TTAGTTACTA
* *
69603 AATTATTCGAAA-GTTTTCATTTAAATCACTG
1 AATTATTC-AAATATTTTTATTTAAATCACTG
* *
69634 AATTATTCAAATATTTTTATTTAAGTTACTG
1 AATTATTCAAATATTTTTATTTAAATCACTG
* *
69665 AGTTATT-AAGTTATTTTT-TTTAA
1 AATTATTCAA-ATATTTTTATTTAA
69688 GTTTTGCCAT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
30 10 0.22
31 36 0.78
ACGTcount: A:0.34, C:0.07, G:0.08, T:0.51
Consensus pattern (31 bp):
AATTATTCAAATATTTTTATTTAAATCACTG
Found at i:70548 original size:62 final size:62
Alignment explanation
Indices: 70471--70595 Score: 157
Period size: 62 Copynumber: 2.0 Consensus size: 62
70461 TTAATTTGTA
* * *
70471 TTAAATATTATAATTATCT-AATTTTATTGTTTATCTA-ATTAATATTTAGATACTA-TTTATAT
1 TTAAATATTACAATTAT-TAAACTTTATT-TTTA-CCAGATTAATATTTAGATACTACTTTATAT
* *
70533 TTAAATATTGCAATTATTAAACTTTATTTTTACCAGATTAATATTTAGGTACTACTTTATAT
1 TTAAATATTACAATTATTAAACTTTATTTTTACCAGATTAATATTTAGATACTACTTTATAT
70595 T
1 T
70596 AGTTTACAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
60 2 0.04
61 22 0.40
62 31 0.56
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (62 bp):
TTAAATATTACAATTATTAAACTTTATTTTTACCAGATTAATATTTAGATACTACTTTATAT
Found at i:74397 original size:29 final size:28
Alignment explanation
Indices: 74356--74421 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
74346 AAGATGGTAT
74356 TTTTTTTATTTAA-AAATAAATAAATTAA
1 TTTTTTTATTTAATAAA-AAATAAATTAA
* *
74384 TTTTTTTATATTAATTAAAAATAAATTAG
1 TTTTTTTAT-TTAATAAAAAATAAATTAA
74413 TATTTTTTA
1 T-TTTTTTA
74422 AATTTCATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 9 0.27
29 15 0.45
30 9 0.27
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (28 bp):
TTTTTTTATTTAATAAAAAATAAATTAA
Found at i:79059 original size:14 final size:14
Alignment explanation
Indices: 79040--79080 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
79030 AATTTTACAT
79040 TATTTTTTACTTAA
1 TATTTTTTACTTAA
* *
79054 TCTTTTTGA--TAA
1 TATTTTTTACTTAA
79066 TATTTTTTACTTAA
1 TATTTTTTACTTAA
79080 T
1 T
79081 TGATAAATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 4
0.72 0.14 0.14
Matches are distributed among these distances:
12 10 0.48
14 11 0.52
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.63
Consensus pattern (14 bp):
TATTTTTTACTTAA
Found at i:79143 original size:15 final size:16
Alignment explanation
Indices: 79108--79145 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
79098 GGATATAACT
*
79108 TAAATTAAGTTTTTATC
1 TAAATTAAG-TTTTATA
79125 TAAATTAAG-TTTATA
1 TAAATTAAGTTTTATA
79140 TAAATT
1 TAAATT
79146 TTTATAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 11 0.55
17 9 0.45
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (16 bp):
TAAATTAAGTTTTATA
Found at i:82999 original size:117 final size:117
Alignment explanation
Indices: 82793--83019 Score: 411
Period size: 117 Copynumber: 1.9 Consensus size: 117
82783 TTGATTAGGG
*
82793 AAGTAATTTCAAACAAGTTGACTCTTGGTTACCAAATAAGTAATGAGAGATTAGTTGCTCGACAT
1 AAGTAATTTCAAACAAGTTGACTCTTGGTTACCAAATAAGTAAGGAGAGATTAGTTGCTCGACAT
82858 TGAGTCAACAACTAAAACTAATTTATTAAGATCATTGTAGACATCGTTAGAA
66 TGAGTCAACAACTAAAACTAATTTATTAAGATCATTGTAGACATCGTTAGAA
*
82910 AAGTAATTTCAAACAAGTTGACTCTTGGTTATCAAATGAA-TAAGGAGAGATTAGTTGCTCGACA
1 AAGTAATTTCAAACAAGTTGACTCTTGGTTACCAAAT-AAGTAAGGAGAGATTAGTTGCTCGACA
*
82974 TTGAGTCAACAACTAGAACTAATTTATTAAGATCATTGTAGACATC
65 TTGAGTCAACAACTAAAACTAATTTATTAAGATCATTGTAGACATC
83020 CTTGTGTCGA
Statistics
Matches: 106, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
117 104 0.98
118 2 0.02
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.31
Consensus pattern (117 bp):
AAGTAATTTCAAACAAGTTGACTCTTGGTTACCAAATAAGTAAGGAGAGATTAGTTGCTCGACAT
TGAGTCAACAACTAAAACTAATTTATTAAGATCATTGTAGACATCGTTAGAA
Found at i:91544 original size:12 final size:12
Alignment explanation
Indices: 91527--91571 Score: 67
Period size: 11 Copynumber: 3.9 Consensus size: 12
91517 AAGGTTTGAA
91527 AAGAAAAAAAAG
1 AAGAAAAAAAAG
91539 AAGAAAAAAAAG
1 AAGAAAAAAAAG
*
91551 GAG-AAAAAAA-
1 AAGAAAAAAAAG
91561 AAGAAAAAAAA
1 AAGAAAAAAAA
91572 CATGGCTGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
10 2 0.07
11 14 0.47
12 14 0.47
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAAAG
Found at i:97148 original size:18 final size:18
Alignment explanation
Indices: 97114--97147 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
97104 TATCTAAAAA
97114 TAATATAAAATATTATAT
1 TAATATAAAATATTATAT
97132 TAATA-AAAATA-TATAT
1 TAATATAAAATATTATAT
97148 AAAAAACCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 6 0.38
18 5 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TAATATAAAATATTATAT
Found at i:99524 original size:14 final size:13
Alignment explanation
Indices: 99494--99543 Score: 57
Period size: 14 Copynumber: 3.8 Consensus size: 13
99484 TTTAGTTTAC
99494 AATTTTTTAAAAT
1 AATTTTTTAAAAT
*
99507 -ATTTTTTATAACT
1 AATTTTTTA-AAAT
*
99520 AATTTTTAAAAATT
1 AATTTTTTAAAA-T
99534 AATTTTTTAA
1 AATTTTTTAA
99544 GTAAACAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
12 8 0.27
13 5 0.17
14 17 0.57
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (13 bp):
AATTTTTTAAAAT
Found at i:106565 original size:30 final size:29
Alignment explanation
Indices: 106533--106778 Score: 153
Period size: 29 Copynumber: 8.4 Consensus size: 29
106523 AATCGGGATA
*
106533 AAAAATGGAATTTTTGGACATTCAAGGGT
1 AAAAATGGAATTTTTGGAGATTCAAGGGT
* * *
106562 -AAAATGGTAATTTATGAGAGTTTCGA-GGT
1 AAAAATGG-AATTTTTG-GAGATTCAAGGGT
* * * * *
106591 CAAAATGGAGTTTTTAGACATTCGAGGGT
1 AAAAATGGAATTTTTGGAGATTCAAGGGT
* * * *
106620 -AAAATGAAATTTTTAGAGGTTCGAGGGT
1 AAAAATGGAATTTTTGGAGATTCAAGGGT
* * *
106648 AAAAATGTAATTTTTGAAAGTTTCAA-GGT
1 AAAAATGGAATTTTTG-GAGATTCAAGGGT
* *
106677 CAAAAATGGAATTTTTGGAGGTTCGAGGGT
1 -AAAAATGGAATTTTTGGAGATTCAAGGGT
** * *
106707 AAAAATATAATTTTTTGAAAGTTTCAA-GGT
1 AAAAATGGAA-TTTTTG-GAGATTCAAGGGT
* *
106737 CAAAAATGAAATTTTTGGA-AGTTCAAGGAT
1 -AAAAATGGAATTTTTGGAGA-TTCAAGGGT
*
106767 AAAAATGTAATT
1 AAAAATGGAATT
106779 ATTGAACAGT
Statistics
Matches: 171, Mismatches: 33, Indels: 26
0.74 0.14 0.11
Matches are distributed among these distances:
28 38 0.22
29 65 0.38
30 54 0.32
31 14 0.08
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.33
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAGATTCAAGGGT
Found at i:106596 original size:58 final size:57
Alignment explanation
Indices: 106533--106778 Score: 180
Period size: 60 Copynumber: 4.2 Consensus size: 57
106523 AATCGGGATA
* *
106533 AAAAATGGAATTTTTGGACATTCAAGGGTAAAATGGTAATTTATGAGAGTTTCGA-GGT
1 AAAAATGGAATTTTTGGACATTCAAGGGTAAAAT-GAAATTT-TGAGAGGTTCGAGGGT
* * * * *
106591 CAAAATGGAGTTTTTAGACATTCGAGGGTAAAATGAAATTTTTAGAGGTTCGAGGGT
1 AAAAATGGAATTTTTGGACATTCAAGGGTAAAATGAAATTTTGAGAGGTTCGAGGGT
* * *
106648 AAAAATGTAATTTTT-GAAAGTTTCAA-GGTCAAAAATGGAATTTTTG-GAGGTTCGAGGGT
1 AAAAATGGAATTTTTGGACA--TTCAAGGGT--AAAAT-GAAATTTTGAGAGGTTCGAGGGT
** * * * * *
106707 AAAAATATAATTTTTTGAAAGTTTCAA-GGTCAAAAATGAAATTTTTG-GAAGTTCAAGGAT
1 AAAAATGGAATTTTTGGACA--TTCAAGGGT--AAAATGAAA-TTTTGAGAGGTTCGAGGGT
*
106767 AAAAATGTAATT
1 AAAAATGGAATT
106779 ATTGAACAGT
Statistics
Matches: 160, Mismatches: 20, Indels: 14
0.82 0.10 0.07
Matches are distributed among these distances:
56 13 0.08
57 24 0.15
58 34 0.21
59 35 0.22
60 54 0.34
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.33
Consensus pattern (57 bp):
AAAAATGGAATTTTTGGACATTCAAGGGTAAAATGAAATTTTGAGAGGTTCGAGGGT
Found at i:106617 original size:28 final size:28
Alignment explanation
Indices: 106534--106710 Score: 126
Period size: 28 Copynumber: 6.1 Consensus size: 28
106524 ATCGGGATAA
* *
106534 AAAATGGAATTTTTGGACATTCAAGGGT
1 AAAATGGAATTTTTAGACATTCGAGGGT
* **
106562 AAAATGGTAATTTATGAGAGTTTCGA-GGT
1 AAAATGG-AATTT-TTAGACATTCGAGGGT
*
106591 CAAAATGGAGTTTTTAGACATTCGAGGGT
1 -AAAATGGAATTTTTAGACATTCGAGGGT
* **
106620 AAAATGAAATTTTTAGAGGTTCGAGGGT
1 AAAATGGAATTTTTAGACATTCGAGGGT
* * *
106648 AAAAATGTAATTTTT-GAAAGTTTC-AAGGT
1 -AAAATGGAATTTTTAGACA--TTCGAGGGT
* **
106677 CAAAAATGGAATTTTTGGAGGTTCGAGGGT
1 --AAAATGGAATTTTTAGACATTCGAGGGT
106707 AAAA
1 AAAA
106711 ATATAATTTT
Statistics
Matches: 118, Mismatches: 21, Indels: 20
0.74 0.13 0.13
Matches are distributed among these distances:
28 46 0.39
29 35 0.30
30 35 0.30
31 2 0.02
ACGTcount: A:0.36, C:0.06, G:0.26, T:0.32
Consensus pattern (28 bp):
AAAATGGAATTTTTAGACATTCGAGGGT
Found at i:106631 original size:86 final size:87
Alignment explanation
Indices: 106534--106778 Score: 223
Period size: 86 Copynumber: 2.8 Consensus size: 87
106524 ATCGGGATAA
* * * *
106534 AAAATGGAATTTTTGGACATTCAAGGGT-AAAATGGTAATTTATGAGAGTTTCGAGGTC-AAAAT
1 AAAATGAAATTTTTAGACATTCAAGGGTAAAAAT-GTAATTTATGAAAGTTTCAAGGTCAAAAAT
*
106597 GGAGTTTTTAGACATTCGAGGGT
65 GGAATTTTTAGACATTCGAGGGT
** * *
106620 AAAATGAAATTTTTAGAGGTTCGAGGGTAAAAATGTAATTTTTGAAAGTTTCAAGGTCAAAAATG
1 AAAATGAAATTTTTAGACATTCAAGGGTAAAAATGTAATTTATGAAAGTTTCAAGGTCAAAAATG
* **
106685 GAATTTTTGGAGGTTCGAGGGT
66 GAATTTTTAGACATTCGAGGGT
* * * * *
106707 AAAAAT-ATAATTTTTTGAAAGTTTCAA-GGTCAAAAATGAAATTTTTGGAAG-TTCAAGGAT-A
1 -AAAATGA-AATTTTTAGACA--TTCAAGGGT-AAAAATGTAATTTATGAAAGTTTCAAGG-TCA
*
106768 AAAATGTAATT
60 AAAATGGAATT
106779 ATTGAACAGT
Statistics
Matches: 132, Mismatches: 19, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
86 44 0.33
87 30 0.23
88 14 0.11
89 21 0.16
90 23 0.17
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.33
Consensus pattern (87 bp):
AAAATGAAATTTTTAGACATTCAAGGGTAAAAATGTAATTTATGAAAGTTTCAAGGTCAAAAATG
GAATTTTTAGACATTCGAGGGT
Found at i:106690 original size:59 final size:59
Alignment explanation
Indices: 106620--106784 Score: 258
Period size: 60 Copynumber: 2.8 Consensus size: 59
106610 ATTCGAGGGT
*
106620 AAAATGAAATTTTTAGAGGTTCGAGGGTAAAAATGTAATTTTTGAAAGTTTCAAGGTCA
1 AAAATGAAATTTTTGGAGGTTCGAGGGTAAAAATGTAATTTTTGAAAGTTTCAAGGTCA
* *
106679 AAAATGGAATTTTTGGAGGTTCGAGGGTAAAAATATAATTTTTTGAAAGTTTCAAGGTCA
1 AAAATGAAATTTTTGGAGGTTCGAGGGTAAAAATGTAA-TTTTTGAAAGTTTCAAGGTCA
* * * *
106739 AAAATGAAATTTTTGGAAGTTCAAGGATAAAAATGTAATTATTGAA
1 AAAATGAAATTTTTGGAGGTTCGAGGGTAAAAATGTAATTTTTGAA
106785 CAGTCTAGGG
Statistics
Matches: 96, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
59 42 0.44
60 54 0.56
ACGTcount: A:0.41, C:0.04, G:0.21, T:0.34
Consensus pattern (59 bp):
AAAATGAAATTTTTGGAGGTTCGAGGGTAAAAATGTAATTTTTGAAAGTTTCAAGGTCA
Found at i:108479 original size:445 final size:446
Alignment explanation
Indices: 107641--108980 Score: 2337
Period size: 445 Copynumber: 3.0 Consensus size: 446
107631 ATTGGTTTTC
*
107641 CTTTTAAAAAAATCTACCTTTGCTTTCTTCTTTTGAACCGATGAAATCGTTTTGCCTACAATTCT
1 CTTTTAAAAAAATCTACCTTTGCTTTCTTCTTTTGAACCGATGAAATCGTTTTGCCTACGATTCT
*
107706 GTTGTTTCTTATTTTGAGATTATTTTTAAAACTTTTCCCTTGCTTCCTTGCAGAGCTGTACGCGA
66 GTTGTTTCTTGTTTTGAGATTATTTTTAAAACTTTTCCCTTGCTTCCTTGCAGAGCTGTACGCGA
* * * *
107771 CGAAGAACAGACGATGATCGGAGGCGAGTTAGACGTGATTCCAGCGGCGGCAACAGTCAAGGAGT
131 CGAAGAACGGACGATGATCGGAGGCGAGTTCGACGTGATT-C-GCGGCGACAGCAGTCAAGGAGT
*
107836 TACTTAATCCTTTCGTTTTCCTTTTTTGTTTTTT-AAAAGTTATTATTGTTATTATTAATTATTA
194 TACTTAATCCTTTCGTTTTCCTTTTTTATTTTTTAAAAAGTTATTATTGTTATTATTAATTATTA
107900 TAATTACTATCATTAATTAATGCCATTAATATTATCCTATTATTAATATTATTATTATTAAGGCT
259 TAATTACTATCATTAATTAATGCCATTAATATTATCCTATTATTAATATTATTATTATTAAGGCT
107965 ATTTATTAACAAAAAAAGGGGTAATAAATATTGACCGAATGTATTAAATATAAGCACTAATGTAT
324 ATTTATTAACAAAAAAAGGGGTAATAAATATTGACCGAATGTATTAAATATAAGCACTAATGTAT
108030 ATTGGCAACTAATGAGTTAGAGATTTAAAGTCTAAACGGCAGTAAACATGCATTGAAT
389 ATTGGCAACTAATGAGTTAGAGATTTAAAGTCTAAACGGCAGTAAACATGCATTGAAT
* *
108088 CTTTAAAAAAAATCTTCCTTTGCTTTCTTCTTTTGAACCGATGAAATCGTTTTGCCTACGATTCT
1 CTTTTAAAAAAATCTACCTTTGCTTTCTTCTTTTGAACCGATGAAATCGTTTTGCCTACGATTCT
* *
108153 GTAGTTTCTTGTTTTGAGATTATTTTTAAAACTTTTTCCTTGCTTCCTTGCAGAGCTGTACGCGA
66 GTTGTTTCTTGTTTTGAGATTATTTTTAAAACTTTTCCCTTGCTTCCTTGCAGAGCTGTACGCGA
* * *
108218 TGAAGAACGGGCGATGATCGGAGGCGAGTTCGACCTGATTC-CGGCGACAGCAGTCAAGGAGTTA
131 CGAAGAACGGACGATGATCGGAGGCGAGTTCGACGTGATTCGCGGCGACAGCAGTCAAGGAGTTA
* *
108282 CTTAGTCCTTTCGTTTTCCTTTTTTATTTTTTAAAAAGTTATTATTATTATTATTAATTATTATA
196 CTTAATCCTTTCGTTTTCCTTTTTTATTTTTTAAAAAGTTATTATTGTTATTATTAATTATTATA
* *
108347 ATTACTATCATTAATGAATGCCATTAATATTATCCTATTATTAATATTATTATTATTAAGGTTGA
261 ATTACTATCATTAATTAATGCCATTAATATTATCCTATTATTAATATTATTATTATTAAGGCT-A
*
108412 -TTATTAAC-AAAAAAGGGGATAATAAATATTGATCGAATGTATTAAATATAAGCACTAATGTAT
325 TTTATTAACAAAAAAAGGGG-TAATAAATATTGACCGAATGTATTAAATATAAGCACTAATGTAT
108475 ATTGGCAACTAATGAGTTAGAGATTTAAAGTCTAAACGGCAGTAAACATGCATTGAAT
389 ATTGGCAACTAATGAGTTAGAGATTTAAAGTCTAAACGGCAGTAAACATGCATTGAAT
*
108533 CTTTTAAAAAAATCTGCCTTTGCTTTCTTCTTTTGAACCGATGAAATCGTTTTGCCTACGATTCT
1 CTTTTAAAAAAATCTACCTTTGCTTTCTTCTTTTGAACCGATGAAATCGTTTTGCCTACGATTCT
*
108598 GTTGTTTCTTGTTTTGAGATTATTTTTAAAACTTTTCCCTTGCTTCCTTGCAGAGTTGTACGCGA
66 GTTGTTTCTTGTTTTGAGATTATTTTTAAAACTTTTCCCTTGCTTCCTTGCAGAGCTGTACGCGA
* * *
108663 CGAAGAACGGACGATGATCGGAGGCGAGTTCGATGTGATTTCGGCGACGACAGCAGTCAGGGAGT
131 CGAAGAACGGACGATGATCGGAGGCGAGTTCGACGTGA-TTC-GCGGCGACAGCAGTCAAGGAGT
108728 TACTTAATCCTTTCGTTTTCCTTTTTTATTTTTTAAAAAGTTATTATTGTTATTATTAATTATTA
194 TACTTAATCCTTTCGTTTTCCTTTTTTATTTTTTAAAAAGTTATTATTGTTATTATTAATTATTA
*
108793 TAATTACTATCATTAATTAATGCCACTAATATTATCCTATTATTAATATTATTATTATTAAGGCT
259 TAATTACTATCATTAATTAATGCCATTAATATTATCCTATTATTAATATTATTATTATTAAGGCT
108858 ATTTATTAACAAAAAAAGGGGTAATAAATATTGACCGAATGTATTAAATATAAGCACTAATGTAT
324 ATTTATTAACAAAAAAAGGGGTAATAAATATTGACCGAATGTATTAAATATAAGCACTAATGTAT
* * * *
108923 ATTGACAACTAATGAGTTAGAGATTTAAAATCTAAACGGTAATAAACATGCATTGAAT
389 ATTGGCAACTAATGAGTTAGAGATTTAAAGTCTAAACGGCAGTAAACATGCATTGAAT
108981 AGTACTTGGC
Statistics
Matches: 845, Mismatches: 40, Indels: 15
0.94 0.04 0.02
Matches are distributed among these distances:
444 61 0.07
445 360 0.43
446 5 0.01
447 160 0.19
448 249 0.29
449 10 0.01
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (446 bp):
CTTTTAAAAAAATCTACCTTTGCTTTCTTCTTTTGAACCGATGAAATCGTTTTGCCTACGATTCT
GTTGTTTCTTGTTTTGAGATTATTTTTAAAACTTTTCCCTTGCTTCCTTGCAGAGCTGTACGCGA
CGAAGAACGGACGATGATCGGAGGCGAGTTCGACGTGATTCGCGGCGACAGCAGTCAAGGAGTTA
CTTAATCCTTTCGTTTTCCTTTTTTATTTTTTAAAAAGTTATTATTGTTATTATTAATTATTATA
ATTACTATCATTAATTAATGCCATTAATATTATCCTATTATTAATATTATTATTATTAAGGCTAT
TTATTAACAAAAAAAGGGGTAATAAATATTGACCGAATGTATTAAATATAAGCACTAATGTATAT
TGGCAACTAATGAGTTAGAGATTTAAAGTCTAAACGGCAGTAAACATGCATTGAAT
Found at i:109623 original size:15 final size:14
Alignment explanation
Indices: 109588--109642 Score: 58
Period size: 17 Copynumber: 3.7 Consensus size: 14
109578 TGATTAAATT
109588 TAAATTTAAAGAAAA
1 TAAATTTAAA-AAAA
109603 TTTAAATTTAAAAAAGA
1 --TAAATTTAAAAAA-A
*
109620 TAAATTT-TAAAAA
1 TAAATTTAAAAAAA
109633 TAAATTTAAA
1 TAAATTTAAA
109643 CCAATTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
13 8 0.24
14 5 0.15
15 7 0.21
16 3 0.09
17 11 0.32
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (14 bp):
TAAATTTAAAAAAA
Found at i:110566 original size:206 final size:206
Alignment explanation
Indices: 110200--110998 Score: 1105
Period size: 206 Copynumber: 3.9 Consensus size: 206
110190 AGTTGGTATA
* * * *
110200 CTTCTCTGTATCTCATCAGGAACATGATCGCCTCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
* *
110265 CAGGAAGACGAATTTGGTCCACTTCTT-ATTATCTCATCAGGAAGCTAACCTTTTTATTGCTTC-
66 CAGGAAGACGAATTTGGTCCACTT-TTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCG
* ** *
110328 ACCCTGCTTCTCAGTATCTTATCAGGAAGCTGGGGTTCGAAGATTTGCTCGTATTGAGCGTGGGT
130 A-CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGGT
110393 TTGATTTTGTCTT
194 TTGATTTTGTCTT
* * * *
110406 CTTCTCAGTATCTCATCAAGAAGGTGACCGCATCGCTTATTTCAATCCGCTTCTCTGTATCTCAT
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
* * *
110471 CAGGGAGACGAATTTGGTTCACTTTTCAGTATCTTATCAGGAAGCTAACCATTTTATTGCTTCGA
66 CAGGAAGACGAATTTGGTCCACTTTTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
* ** * *
110536 CCTGCTTCTTAGTATCTCATCAAAAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCCCTGAG-T
131 CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAG-CGTGGGTT
* *
110600 TG-GTAT-TCTT
195 TGATTTTGTCTT
** * * *
110610 CTT-T--GTATCTCATCAGGAAGATGATTGCCTTACTTGTTTCAATCCGCTTCTCTGTACCTCAT
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
*
110672 CAGGAAGACGAATTTGGTCCA-TTTCTCAGTATCTCATCAGGAAGCTAACC-TTTTATTGCTTTG
66 CAGGAAGACGAATTTGGTCCACTTT-TCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCG
* *
110735 CCCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCACATCGAGCGTGGGTT
130 ACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTT
*
110800 TGATTTGGTCTT
195 TGATTTTGTCTT
* * * * *
110812 CTTCTCAGTATCTTATCAGGACGATAACCGCATCATTTGTTTCAATCCGCTTCTTTGTATCTCAT
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
* * * *
110877 TAGTAAGACAAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
66 CAGGAAGACGAATTTGGTCCACTTTTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
*
110942 CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCAAAGATTTGCTCACATCGAGC
131 CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGC
110999 CGTGAGTTGG
Statistics
Matches: 516, Mismatches: 65, Indels: 24
0.85 0.11 0.04
Matches are distributed among these distances:
199 4 0.01
200 70 0.14
201 93 0.18
202 7 0.01
203 2 0.00
204 7 0.01
205 95 0.18
206 233 0.45
207 5 0.01
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.36
Consensus pattern (206 bp):
CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
CAGGAAGACGAATTTGGTCCACTTTTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTT
GATTTTGTCTT
Found at i:110857 original size:406 final size:407
Alignment explanation
Indices: 109993--111035 Score: 1519
Period size: 406 Copynumber: 2.6 Consensus size: 407
109983 TCTGGTTTCA
* * * ** ** *
109993 TTGACTTGGCCTTCTTCTCAGTATCTCATTAGGAAGATGACCATATCACTTGTTTTGATCCACTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTT
* * * *
110058 CTCTGTGTTTCATTAGGAAGACGAATTTGGTTCACTTCTCCGTATCTCATCAGGAAGCTAACCCT
66 CTCTGTATCTCATTAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* * *
110123 TTTATTGCTTC-ACCCTGCTTCTCAATATCTCATCAGGAAGTTGGGGGTCAAAGATTTG-T----
131 TTTATTGCTTCGA-CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCAAAGATTTGCTCACA
* * *
110182 TCGTG--TTGAGTTGGTATACTTCTCTGTATCTCATCAGGAACATGATCGCCTCACTTGTTTCAA
195 TCGAGCCCTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGATCGCCTCACTTGTTTCAA
* * *
110245 TCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTTATTATCTCATCAGGAAGC
260 TCCGCTTCTCTGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGC
* *
110310 TAACCTTTTTATTGCTTCACCCTGCTTCTCAGTATCTTATCAGGAAGCTGGGGTTCGAAGATTTG
325 TAACCTTTTTATTGCTTCACCCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTG
** *
110375 CTCGTATTGAGCGTGGGT
390 CTCACATCGAGCGTGGGT
* * * * *
110393 TTGATTTTGTCTTCTTCTCAGTATCTCATCAAGAAGGTGACCGCATCGCTTATTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTT
* * * *
110458 CTCTGTATCTCATCAGGGAGACGAATTTGGTTCACTTTTCAGTATCTTATCAGGAAGCTAACCAT
66 CTCTGTATCTCATTAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* ** *
110523 TTTATTGCTTCGACCTGCTTCTTAGTATCTCATCAAAAAGCTGGGGTTCGAAGATTTGCTCACAT
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCAAAGATTTGCTCACAT
* * * *
110588 CGAGCCCTGAGTTGGTATTCTTCTTTGTATCTCATCAGGAAGATGATTGCCTTACTTGTTTCAAT
196 CGAGCCCTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGATCGCCTCACTTGTTTCAAT
*
110653 CCGCTTCTCTGTACCTCATCAGGAAGACGAATTTGGTCCATTTCTCAGTATCTCATCAGGAAGCT
261 CCGCTTCTCTGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCT
**
110718 AACC-TTTTATTGCTTTGCCCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGC
326 AACCTTTTTATTGCTTCACCCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGC
110782 TCACATCGAGCGTGGGT
391 TCACATCGAGCGTGGGT
* * * *
110799 TTGATTTGGTCTTCTTCTCAGTATCTTATCAGGACGATAACCGCATCATTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTT
* * * *
110864 CTTTGTATCTCATTAGTAAGACAAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
66 CTCTGTATCTCATTAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
110929 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCAAAGATTTGCTCACAT
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCAAAGATTTGCTCACAT
*
110994 CGAGCCGTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAG
196 CGAGCCCTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAG
111036 CTGAAGGTCG
Statistics
Matches: 565, Mismatches: 70, Indels: 10
0.88 0.11 0.02
Matches are distributed among these distances:
400 158 0.28
401 2 0.00
405 4 0.01
406 283 0.50
407 118 0.21
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (407 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTT
CTCTGTATCTCATTAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCAAAGATTTGCTCACAT
CGAGCCCTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGATCGCCTCACTTGTTTCAAT
CCGCTTCTCTGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCT
AACCTTTTTATTGCTTCACCCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGC
TCACATCGAGCGTGGGT
Found at i:112343 original size:29 final size:29
Alignment explanation
Indices: 112311--112623 Score: 167
Period size: 29 Copynumber: 10.7 Consensus size: 29
112301 AAAATCGATA
* *
112311 TAAAAATGGAATTTTTGGACATTCGGGGG
1 TAAAAATGGAATTTTTGGAAATTCGAGGG
* **
112340 T-AAAATGGTAATTTTTTAGAGTTTCGA-GG
1 TAAAAATGG-AA-TTTTTGGAAATTCGAGGG
* * *
112369 TCAAAAATAGAGTTTTTGGACATTCGAGGG
1 T-AAAAATGGAATTTTTGGAAATTCGAGGG
*
112399 T-AAAATGGTAATTTTT-GAAAGTTTTG-GGG
1 TAAAAATGG-AATTTTTGGAAA--TTCGAGGG
* ** *
112428 TTATAAATGGAATTTTTGGAGGTT-TAGGGG
1 -TAAAAATGGAATTTTTGGAAATTCGA-GGG
* **
112458 TAAAAATGTAATTTTT-GAAAGTTTTAGGG
1 TAAAAATGGAATTTTTGGAAA-TTCGAGGG
* **
112487 TCAAAATGGAATTTTTGGAGGTTCGAGGG
1 TAAAAATGGAATTTTTGGAAATTCGAGGG
* * ** *
112516 TTAAAATGTAATTTTT-GAAAGTTTTAAGGT
1 TAAAAATGGAATTTTTGGAAA--TTCGAGGG
* ** *
112546 TAAAAATGGAGTTTTTGGATGTTCGTGGG
1 TAAAAATGGAATTTTTGGAAATTCGAGGG
* **
112575 TAAAAATGTAATTTTT-GAAAGTTTCGAGAT
1 TAAAAATGGAATTTTTGGAAA--TTCGAGGG
112605 TAAAAATGGAATTTTTGGA
1 TAAAAATGGAATTTTTGGA
112624 TAGTTTAGGG
Statistics
Matches: 211, Mismatches: 51, Indels: 42
0.69 0.17 0.14
Matches are distributed among these distances:
28 22 0.10
29 100 0.47
30 71 0.34
31 18 0.09
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.38
Consensus pattern (29 bp):
TAAAAATGGAATTTTTGGAAATTCGAGGG
Found at i:112529 original size:176 final size:177
Alignment explanation
Indices: 112313--112633 Score: 450
Period size: 176 Copynumber: 1.8 Consensus size: 177
112303 AATCGATATA
* * *
112313 AAAATGGAATTTTTGGACATTCGGGGGTAAAATGGTAATTTTTTAGAGTTTCGAGGTCAAAAATA
1 AAAATGGAATTTTTGGACATTCGGGGGTAAAATGGTAATTTTTGAAAGTTTCAAGGTCAAAAATA
* * * *
112378 GAGTTTTTGGACATTCGAGGGT-AAAATGGTAATTTTTGAAAGTTTTGGGGTTATAAATGGAATT
66 GAGTTTTTGGACATTCGAGGGTAAAAAT-GTAATTTTTGAAAGTTTCGAGATTAAAAATGGAATT
*
112442 TTTGGA-GGTTTAGGGGTAAAAATGTAATTTTTGAAAGTTTTAGGGTC
130 TTTGGATAGTTTAGGGGTAAAAATGTAATTTTTGAAAGTTTTAGGGTC
** * * *
112489 AAAATGGAATTTTTGGAGGTTCGAGGGTTAAAAT-GTAATTTTTGAAAGTTTTAAGGTTAAAAAT
1 AAAATGGAATTTTTGGACATTCG-GGGGTAAAATGGTAATTTTTGAAAGTTTCAAGGTCAAAAAT
* ** *
112553 GGAGTTTTTGGATGTTCGTGGGTAAAAATGTAATTTTTGAAAGTTTCGAGATTAAAAATGGAATT
65 AGAGTTTTTGGACATTCGAGGGTAAAAATGTAATTTTTGAAAGTTTCGAGATTAAAAATGGAATT
112618 TTTGGATAGTTTAGGG
130 TTTGGATAGTTTAGGG
112634 ATCTCCAAGG
Statistics
Matches: 125, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
176 103 0.82
177 22 0.18
ACGTcount: A:0.32, C:0.03, G:0.27, T:0.38
Consensus pattern (177 bp):
AAAATGGAATTTTTGGACATTCGGGGGTAAAATGGTAATTTTTGAAAGTTTCAAGGTCAAAAATA
GAGTTTTTGGACATTCGAGGGTAAAAATGTAATTTTTGAAAGTTTCGAGATTAAAAATGGAATTT
TTGGATAGTTTAGGGGTAAAAATGTAATTTTTGAAAGTTTTAGGGTC
Found at i:112553 original size:117 final size:117
Alignment explanation
Indices: 112311--112623 Score: 355
Period size: 117 Copynumber: 2.7 Consensus size: 117
112301 AAAATCGATA
* ** * * *
112311 TAAAAATGGAATTTTTGGACATTCGGGGGT-AAAATGGTAATTTTTTAGAG-TTTCGAGGTCAAA
1 TAAAAATGGAATTTTTGGACGTTTAGGGGTAAAAAT-GTAATTTTTGAAAGTTTTAG-GGTC-AA
* * **
112374 AATAGAGTTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAGTTTTGGGGT
63 AATGGAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAGTTTTAAGGT
* *
112429 TATAAATGGAATTTTTGGAGGTTTAGGGGTAAAAATGTAATTTTTGAAAGTTTTAGGGTCAAAAT
1 TAAAAATGGAATTTTTGGACGTTTAGGGGTAAAAATGTAATTTTTGAAAGTTTTAGGGTCAAAAT
**
112494 GGAATTTTTGGAGGTTCGAGGGTTAAAAT-GTAATTTTTGAAAGTTTTAAGGT
66 GGAATTTTTGGACATTCGAGGG-TAAAATGGTAATTTTTGAAAGTTTTAAGGT
* * * * ** *
112546 TAAAAATGGAGTTTTTGGATG-TTCGTGGGTAAAAATGTAATTTTTGAAAGTTTCGAGATTAAAA
1 TAAAAATGGAATTTTTGGACGTTTAG-GGGTAAAAATGTAATTTTTGAAAGTTT-TAGGGTCAAA
112610 ATGGAATTTTTGGA
64 ATGGAATTTTTGGA
112624 TAGTTTAGGG
Statistics
Matches: 168, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
116 3 0.02
117 89 0.53
118 67 0.40
119 9 0.05
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.38
Consensus pattern (117 bp):
TAAAAATGGAATTTTTGGACGTTTAGGGGTAAAAATGTAATTTTTGAAAGTTTTAGGGTCAAAAT
GGAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAGTTTTAAGGT
Found at i:112624 original size:59 final size:58
Alignment explanation
Indices: 112311--112623 Score: 351
Period size: 59 Copynumber: 5.3 Consensus size: 58
112301 AAAATCGATA
* * * *
112311 TAAAAATGGAATTTTTGGACATTCGGGGGTAAAATGGTAATTTTTTAGAGTTTCGAGGT
1 TAAAAATGGAATTTTTGGACGTTCGAGGGTAAAAT-GTAATTTTTGAAAGTTTCGAGGT
* * * * * *
112370 CAAAAATAGAGTTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAGTTTTGGGGT
1 TAAAAATGGAATTTTTGGACGTTCGAGGGTAAAAT-GTAATTTTTGAAAGTTTCGAGGT
* * * * *
112429 TATAAATGGAATTTTTGGAGGTT-TAGGGGTAAAAATGTAATTTTTGAAAGTTT-TAGGG
1 TAAAAATGGAATTTTTGGACGTTCGA-GGGT-AAAATGTAATTTTTGAAAGTTTCGAGGT
* * **
112487 TCAAAATGGAATTTTTGGAGGTTCGAGGGTTAAAATGTAATTTTTGAAAGTTTTAAGGT
1 TAAAAATGGAATTTTTGGACGTTCGAGGG-TAAAATGTAATTTTTGAAAGTTTCGAGGT
* * * *
112546 TAAAAATGGAGTTTTTGGATGTTCGTGGGTAAAAATGTAATTTTTGAAAGTTTCGAGAT
1 TAAAAATGGAATTTTTGGACGTTCGAGGGT-AAAATGTAATTTTTGAAAGTTTCGAGGT
112605 TAAAAATGGAATTTTTGGA
1 TAAAAATGGAATTTTTGGA
112624 TAGTTTAGGG
Statistics
Matches: 217, Mismatches: 31, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
58 50 0.23
59 162 0.75
60 5 0.02
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.38
Consensus pattern (58 bp):
TAAAAATGGAATTTTTGGACGTTCGAGGGTAAAATGTAATTTTTGAAAGTTTCGAGGT
Found at i:113682 original size:3 final size:3
Alignment explanation
Indices: 113676--113764 Score: 52
Period size: 3 Copynumber: 28.3 Consensus size: 3
113666 TTTTAAAAAA
* * * * *
113676 ATT ATT ATT GTT ATT ATT AATT ATT ATA ATT ACT ATC ATT AATT AAT
1 ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT -ATT ATT
** * * *
113723 GCT ATG AAT ATT ATCCT ATT ATT AAT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT AT--T ATT ATT ATT ATT ATT ATT ATT ATT A
113765 AGGCTATTTA
Statistics
Matches: 63, Mismatches: 19, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
3 54 0.86
4 6 0.10
5 3 0.05
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (3 bp):
ATT
Found at i:114490 original size:6 final size:6
Alignment explanation
Indices: 114479--114562 Score: 63
Period size: 6 Copynumber: 14.8 Consensus size: 6
114469 TCAAATTTGA
** * *
114479 TTAAAT TTAAAT TTAAA- GCAAAT TTAAAT TTAAA- --AAAG ATAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
114523 TTAAAT TTAAGA- -TAAAT TTAAAT TTAAAA ATAAAT TTAAA
1 TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
114563 CCAATTTAAG
Statistics
Matches: 61, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
3 3 0.05
4 1 0.02
5 6 0.10
6 50 0.82
7 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (6 bp):
TTAAAT
Found at i:114503 original size:17 final size:18
Alignment explanation
Indices: 114480--114562 Score: 107
Period size: 17 Copynumber: 4.6 Consensus size: 18
114470 CAAATTTGAT
114480 TAAATTTAAATTTAAAG-
1 TAAATTTAAATTTAAAGA
*
114497 CAAATTTAAATTTAAAAAAGA
1 TAAATTTAAATTT---AAAGA
114518 TAAATTTAAATTT-AAGA
1 TAAATTTAAATTTAAAGA
*
114535 TAAATTTAAATTTAAAAA
1 TAAATTTAAATTTAAAGA
114553 TAAATTTAAA
1 TAAATTTAAA
114563 CCAATTTAAG
Statistics
Matches: 58, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
17 29 0.50
18 13 0.22
20 4 0.07
21 12 0.21
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (18 bp):
TAAATTTAAATTTAAAGA
Found at i:114522 original size:38 final size:38
Alignment explanation
Indices: 114480--114552 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
114470 CAAATTTGAT
114480 TAAATTTAAATTTAA-AGCAAATTTAAATTTAAAAAAGA
1 TAAATTTAAATTTAAGA-CAAATTTAAATTTAAAAAAGA
*
114518 TAAATTTAAATTTAAGATAAATTTAAATTTAAAAA
1 TAAATTTAAATTTAAGACAAATTTAAATTTAAAAA
114553 TAAATTTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
38 32 0.97
39 1 0.03
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (38 bp):
TAAATTTAAATTTAAGACAAATTTAAATTTAAAAAAGA
Found at i:117412 original size:21 final size:20
Alignment explanation
Indices: 117387--117437 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
117377 GGATTATATA
*
117387 ATTTGGATTTATAAATTTTAT
1 ATTTGGATTT-TAAACTTTAT
* *
117408 CTTTGGATCGTTAAACTTTAT
1 ATTTGGAT-TTTAAACTTTAT
117429 ATTTGGATT
1 ATTTGGATT
117438 ATGCTATTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.27, C:0.06, G:0.14, T:0.53
Consensus pattern (20 bp):
ATTTGGATTTTAAACTTTAT
Found at i:118006 original size:21 final size:22
Alignment explanation
Indices: 117982--118033 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
117972 CGTCCGCCAA
117982 TTTGTTTGATTTATTTT-CT-TT
1 TTTGTTTGATTT-TTTTACTCTT
118003 TTTGTTTGATTTTTTTGACTCTT
1 TTTGTTTGATTTTTTT-ACTCTT
118026 TTTGTTTG
1 TTTGTTTG
118034 GAGTATGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.14
21 12 0.43
22 2 0.07
23 10 0.36
ACGTcount: A:0.08, C:0.06, G:0.13, T:0.73
Consensus pattern (22 bp):
TTTGTTTGATTTTTTTACTCTT
Found at i:122500 original size:26 final size:26
Alignment explanation
Indices: 122455--122513 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
122445 TATTTTCTCG
* * *
122455 AAATTTTACTAGGGGCAAAATTGTCA
1 AAATTTTACCAAGGGCAAAATCGTCA
*
122481 AAATTTTACCAAGGGTAAAATCGTCA
1 AAATTTTACCAAGGGCAAAATCGTCA
*
122507 ATATTTT
1 AAATTTT
122514 GCTAGGAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (26 bp):
AAATTTTACCAAGGGCAAAATCGTCA
Found at i:123515 original size:11 final size:11
Alignment explanation
Indices: 123478--123571 Score: 57
Period size: 12 Copynumber: 8.4 Consensus size: 11
123468 CCAAGCAGCA
123478 AAAATAACAAC
1 AAAATAACAAC
* *
123489 AAGACAACAAC
1 AAAATAACAAC
*
123500 AAAAATAACAGC
1 -AAAATAACAAC
* *
123512 AAAATAGCACC
1 AAAATAACAAC
* *
123523 AAAACAA-TA-
1 AAAATAACAAC
*
123532 AAAATCAACATC
1 AAAAT-AACAAC
123544 AAAATAACAACC
1 AAAATAACAA-C
*
123556 AAAATAGCAATC
1 AAAATAACAA-C
123568 AAAA
1 AAAA
123572 CAGTAAAAAA
Statistics
Matches: 61, Mismatches: 17, Indels: 9
0.70 0.20 0.10
Matches are distributed among these distances:
9 4 0.07
10 2 0.03
11 27 0.44
12 28 0.46
ACGTcount: A:0.66, C:0.20, G:0.04, T:0.10
Consensus pattern (11 bp):
AAAATAACAAC
Found at i:123525 original size:23 final size:23
Alignment explanation
Indices: 123471--123526 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
123461 ACAACATCCA
* *
123471 AGCAGCAAAAATAACAACAAGAC
1 AGCAACAAAAATAACAACAAAAC
* * *
123494 AACAACAAAAATAACAGCAAAAT
1 AGCAACAAAAATAACAACAAAAC
*
123517 AGCACCAAAA
1 AGCAACAAAA
123527 CAATAAAAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.64, C:0.21, G:0.09, T:0.05
Consensus pattern (23 bp):
AGCAACAAAAATAACAACAAAAC
Found at i:123541 original size:44 final size:45
Alignment explanation
Indices: 123493--123580 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 45
123483 AACAACAAGA
*
123493 CAACAACAAAAATAAC-AGCAAAATAGC-ACCAAAACAATAAAAAT
1 CAACAAC-AAAATAACAACCAAAATAGCAACCAAAACAATAAAAAT
* * *
123537 CAACATCAAAATAACAACCAAAATAGCAATCAAAACAGTAAAAA
1 CAACAACAAAATAACAACCAAAATAGCAACCAAAACAATAAAAA
123581 AGCACAAAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
43 8 0.21
44 16 0.42
45 14 0.37
ACGTcount: A:0.65, C:0.20, G:0.05, T:0.10
Consensus pattern (45 bp):
CAACAACAAAATAACAACCAAAATAGCAACCAAAACAATAAAAAT
Found at i:132911 original size:19 final size:19
Alignment explanation
Indices: 132887--132932 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
132877 ATAAATTTTG
*
132887 GAATTTTTATAATTAATTT
1 GAATTTTTAAAATTAATTT
* **
132906 GAATTTTAAAAATTGTTTT
1 GAATTTTTAAAATTAATTT
132925 GAATTTTT
1 GAATTTTT
132933 TTTGTAATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.57
Consensus pattern (19 bp):
GAATTTTTAAAATTAATTT
Found at i:134707 original size:31 final size:29
Alignment explanation
Indices: 134623--134707 Score: 91
Period size: 32 Copynumber: 2.8 Consensus size: 29
134613 AGGGTCCCAG
* *
134623 AAAATTTTTT-ATCTTTTAAGGGCTCAAA
1 AAAATTTTTTCAACTTTTAAGGACTCAAA
*
134651 AAAACTTTTTATCAACTTTTAAAGGACTTTAAA
1 AAAA-TTTTT-TCAACTTTT-AAGGAC-TCAAA
134684 AAAATTTTCTTCAACTTTTAAGGA
1 AAAATTTT-TTCAACTTTTAAGGA
134708 ACCTAAAACC
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
28 4 0.08
29 5 0.10
30 1 0.02
31 11 0.23
32 18 0.38
33 9 0.19
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (29 bp):
AAAATTTTTTCAACTTTTAAGGACTCAAA
Found at i:135197 original size:18 final size:18
Alignment explanation
Indices: 135176--135210 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
135166 TTAATTAATT
135176 AAAAATATTTAATGGTTA
1 AAAAATATTTAATGGTTA
*
135194 AAAAATGTTTAATGGTT
1 AAAAATATTTAATGGTT
135211 TCGAGAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.40
Consensus pattern (18 bp):
AAAAATATTTAATGGTTA
Found at i:135600 original size:18 final size:19
Alignment explanation
Indices: 135564--135605 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
135554 GTTAAAATTT
135564 ATAAAAATATTTAATAAAA
1 ATAAAAATATTTAATAAAA
*
135583 TTAAAAAT-TTTCAA-AAAA
1 ATAAAAATATTT-AATAAAA
135601 ATAAA
1 ATAAA
135606 TAAATTAACG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
ATAAAAATATTTAATAAAA
Found at i:135601 original size:19 final size:19
Alignment explanation
Indices: 135565--135602 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
135555 TTAAAATTTA
*
135565 TAAAAATATTTAATAAAAT
1 TAAAAATATTTAAAAAAAT
135584 TAAAAAT-TTTCAAAAAAAT
1 TAAAAATATTT-AAAAAAAT
135603 AAATAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (19 bp):
TAAAAATATTTAAAAAAAT
Found at i:137515 original size:51 final size:51
Alignment explanation
Indices: 137439--137540 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
137429 TACTGTATTT
* *
137439 AACTCTTTTAAGACTGTTTGATTTGTGGAGATTGTGAATGAATATGGCTCC
1 AACTCTTTTAAGACTGTTTGATTTGTGCAGATTGAGAATGAATATGGCTCC
137490 AACTCTTTTAAGACTGTTTGATTTGTGCAGATTGAGAATGAATATGGCTCC
1 AACTCTTTTAAGACTGTTTGATTTGTGCAGATTGAGAATGAATATGGCTCC
137541 GAGAGCAAGG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (51 bp):
AACTCTTTTAAGACTGTTTGATTTGTGCAGATTGAGAATGAATATGGCTCC
Found at i:140849 original size:42 final size:42
Alignment explanation
Indices: 140791--140966 Score: 138
Period size: 43 Copynumber: 4.1 Consensus size: 42
140781 TTTTGAGGAA
* * * * *
140791 AAACGTTGCTATAGAACATGATCTTTAGTGGGGCTTTGCCAA
1 AAACGTCGCTAAAGAACATGATCTTTAGCGGGGCTTTCCCAC
** **
140833 AAACACCGCTAAAGAACATTG-TCTTTAGCGGTGTTTTTCCCAC
1 AAACGTCGCTAAAGAACA-TGATCTTTAGCGG-GGCTTTCCCAC
* * * * * *
140876 AAACGTAGCTAAAGAACATGGTCTTTAACAGTGCTTTTCACAC
1 AAACGTCGCTAAAGAACATGATCTTTAGCGGGGC-TTTCCCAC
* * * *
140919 AAATGTCGCTAAAGAACATGATCTTTAGTGGCGCTTTTCTCAC
1 AAACGTCGCTAAAGAACATGATCTTTAGCGGGGC-TTTCCCAC
140962 AAACG
1 AAACG
140967 CCACCATAAA
Statistics
Matches: 103, Mismatches: 27, Indels: 7
0.75 0.20 0.05
Matches are distributed among these distances:
42 25 0.24
43 78 0.76
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.30
Consensus pattern (42 bp):
AAACGTCGCTAAAGAACATGATCTTTAGCGGGGCTTTCCCAC
Found at i:140893 original size:43 final size:43
Alignment explanation
Indices: 140840--140966 Score: 148
Period size: 43 Copynumber: 3.0 Consensus size: 43
140830 CAAAAACACC
* *
140840 GCTAAAGAACATTGTCTTTAGCGGTGTTTTTCCCACAAACGTA
1 GCTAAAGAACATTGTCTTTAGCGGTGCTTTTCACACAAACGTA
* * * * *
140883 GCTAAAGAACATGGTCTTTAACAGTGCTTTTCACACAAATGTC
1 GCTAAAGAACATTGTCTTTAGCGGTGCTTTTCACACAAACGTA
* * *
140926 GCTAAAGAACA-TGATCTTTAGTGGCGCTTTTCTCACAAACG
1 GCTAAAGAACATTG-TCTTTAGCGGTGCTTTTCACACAAACG
140967 CCACCATAAA
Statistics
Matches: 69, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
42 1 0.01
43 68 0.99
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (43 bp):
GCTAAAGAACATTGTCTTTAGCGGTGCTTTTCACACAAACGTA
Found at i:141102 original size:15 final size:15
Alignment explanation
Indices: 141082--141110 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
141072 TTTTTTCTGT
141082 CAATTCAAATCTAAC
1 CAATTCAAATCTAAC
141097 CAATTCAAATCTAA
1 CAATTCAAATCTAA
141111 ATTATACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (15 bp):
CAATTCAAATCTAAC
Found at i:142380 original size:2 final size:2
Alignment explanation
Indices: 142373--142409 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
142363 TCACTCAAAA
*
142373 CT CT CT CT CT CT TT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
142410 ATGTTATTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:147268 original size:2 final size:2
Alignment explanation
Indices: 147261--147288 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
147251 TCACTCAAAA
147261 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
147289 TTTGTGTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:152007 original size:29 final size:29
Alignment explanation
Indices: 151974--152035 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
151964 AGTGTATGTG
*
151974 CAAAACCTAAACCATTTT-AACCCAATACC
1 CAAAACCCAAACCATTTTGAA-CCAATACC
* *
152003 CAAAACCCAAACCCTTTTGAACCAATACT
1 CAAAACCCAAACCATTTTGAACCAATACC
152032 CAAA
1 CAAA
152036 CCAAACGACT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 27 0.93
30 2 0.07
ACGTcount: A:0.45, C:0.34, G:0.02, T:0.19
Consensus pattern (29 bp):
CAAAACCCAAACCATTTTGAACCAATACC
Found at i:152769 original size:2 final size:2
Alignment explanation
Indices: 152762--152790 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
152752 TCGCATTGAA
152762 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
152791 AGAAATACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:158558 original size:21 final size:22
Alignment explanation
Indices: 158518--158560 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
158508 TGAGCCATTC
158518 TTATAAGTTTTTAAACCCTTTT
1 TTATAAGTTTTTAAACCCTTTT
158540 TTATAA-TTTTCTAAA-CCTTTT
1 TTATAAGTTTT-TAAACCCTTTT
158561 AGCCTCTCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.28, C:0.14, G:0.02, T:0.56
Consensus pattern (22 bp):
TTATAAGTTTTTAAACCCTTTT
Done.