Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 9 of 135
Found at i:2515724 original size:228 final size:228
Alignment explanation
Indices: 2515341--2515761 Score: 698
Period size: 228 Copynumber: 1.8 Consensus size: 228
2515331 TTTTGCTCCG
* *
2515341 GCTTTTGCTTCAGCCTCAGCTTTTCCTTCAGCTTTAGTTTCAGCTTCAGCTTCACCTTTAGCTCC
1 GCTTTTCCTTCAGCCTCAGCTTTACCTTCAGCTTTAGTTTCAGCTTCAGCTTCACCTTTAGCTCC
* *
2515406 GGCTTCACTAAACCCTCCTTGTCCTCCTACTTTTCCTCCAAAACCAAATTTAAAACCATCACCAC
66 AGCTTCACTAAACCCTCCTTGTCCTCCTACTTTTCCTCCAAAACCAAATTTAAAACCACCACCAC
* *
2515471 CACCAAAATGCATGTTACCACCACCACCACCACCACCACCACCTACCTTTCCTTGTCCTCCTAGT
131 CACCAAAATGCATGTGACCACCACCACCACCACCACCACCACCTACCTTTCCTTGACCTCCTAGT
2515536 TCTGCTTTTGCTCCGGCTTGTGCTCCGGCTTCA
196 TCTGCTTTTGCTCCGGCTTGTGCTCCGGCTTCA
* * * *
2515569 GCTTTTCCTTCAGCTTTAGCTTTACCTTCAGCTTTAGTTTTAGCTTCAGCTTCACCTTTAGCTCT
1 GCTTTTCCTTCAGCCTCAGCTTTACCTTCAGCTTTAGTTTCAGCTTCAGCTTCACCTTTAGCTCC
*
2515634 AGCTTCACTAAACCCTCCTTGTCCTCCTACTTTTCCTCCAAAACCAAATTTAAAACCACCACTAC
66 AGCTTCACTAAACCCTCCTTGTCCTCCTACTTTTCCTCCAAAACCAAATTTAAAACCACCACCAC
* * ***
2515699 CACCAAAATTCATGTGACTACCACCACCACCACCATTTCCACCTACCTTTCCTTGACCTCCTA
131 CACCAAAATGCATGTGACCACCACCACCACCACCACCACCACCTACCTTTCCTTGACCTCCTA
2515762 TTTTGCCTTC
Statistics
Matches: 177, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
228 177 1.00
ACGTcount: A:0.22, C:0.37, G:0.09, T:0.32
Consensus pattern (228 bp):
GCTTTTCCTTCAGCCTCAGCTTTACCTTCAGCTTTAGTTTCAGCTTCAGCTTCACCTTTAGCTCC
AGCTTCACTAAACCCTCCTTGTCCTCCTACTTTTCCTCCAAAACCAAATTTAAAACCACCACCAC
CACCAAAATGCATGTGACCACCACCACCACCACCACCACCACCTACCTTTCCTTGACCTCCTAGT
TCTGCTTTTGCTCCGGCTTGTGCTCCGGCTTCA
Found at i:2515794 original size:6 final size:6
Alignment explanation
Indices: 2515785--2516012 Score: 161
Period size: 6 Copynumber: 38.0 Consensus size: 6
2515775 TTCGACCTTT
** * ** * * * *
2515785 GCTTCA GCTTTT GCATCA GCTTCA GCTTTT CCTTCA TCTTTA GCTTTA
1 GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA
* * * * * *
2515833 GCTTTA CCTTCA GCTTCA GCTTTA CCTTCA GCTTCA GCTTTA CCTTCA
1 GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA
* * * * * *
2515881 GCTTCA GATTCA GCTTTA GCTTCA TCATTTA -CTTTA GCTTGA GCTTCA
1 GCTTCA GCTTCA GCTTCA GCTTCA GC-TTCA GCTTCA GCTTCA GCTTCA
* * * * ** *
2515929 TCTTCA GCTTTA CCTTCA TCTTCA GCTTTG GCTTCA GCATCA GCTTCA
1 GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA
* * *
2515977 GCTTTA GCTTCA GCTTTA GCTTTA GCTTCA GCTTCA
1 GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA
2516013 TCTTTACCAC
Statistics
Matches: 170, Mismatches: 50, Indels: 4
0.76 0.22 0.02
Matches are distributed among these distances:
5 4 0.02
6 163 0.96
7 3 0.02
ACGTcount: A:0.17, C:0.28, G:0.13, T:0.42
Consensus pattern (6 bp):
GCTTCA
Found at i:2515810 original size:228 final size:228
Alignment explanation
Indices: 2515347--2515868 Score: 679
Period size: 228 Copynumber: 2.3 Consensus size: 228
2515337 TCCGGCTTTT
* * * * *
2515347 GCTTCAGCCTCAGCTTTTCCTTCAGCTTTAGTTTCAGCTTCAGCTTCACCTTTAGCTCCGGCTTC
1 GCTTCAGCTTTAGCTTTACCTTCAGCTTTAGTTTTAGCTTCAGCTTCACCTTTAGCTCCAGCTTC
*
2515412 ACTAAACCCTCCTTGTCCTCCTACTTTTCCTCCAAAACCAAATTTAAAACCATCACCACCACCAA
66 ACTAAACCCTCCTTGTCCTCCTACTTTTCCTCCAAAACCAAATTTAAAACCACCACCACCACCAA
* *
2515477 AATGCATGTTACCACCACCACCACCACCACCACCACCTACCTTTCCTTGTCCTCCTAGTTCTGCT
131 AATGCATGTGACCACCACCACCACCACCACCACCACCTACCTTTCCTTGACCTCCTAGTTCTGCT
* * * * **
2515542 TTTGCTCCGGCTTGTGCTCCGGCTTCAGCTTTT
196 TCTGCTCCGCCTTGTGCTCCAGCTTCAGCATCA
* *
2515575 CCTTCAGCTTTAGCTTTACCTTCAGCTTTAGTTTTAGCTTCAGCTTCACCTTTAGCTCTAGCTTC
1 GCTTCAGCTTTAGCTTTACCTTCAGCTTTAGTTTTAGCTTCAGCTTCACCTTTAGCTCCAGCTTC
*
2515640 ACTAAACCCTCCTTGTCCTCCTACTTTTCCTCCAAAACCAAATTTAAAACCACCACTACCACCAA
66 ACTAAACCCTCCTTGTCCTCCTACTTTTCCTCCAAAACCAAATTTAAAACCACCACCACCACCAA
* * *** *
2515705 AATTCATGTGACTACCACCACCACCACCATTTCCACCTACCTTTCCTTGACCTCCTA-TTTTGCC
131 AATGCATGTGACCACCACCACCACCACCACCACCACCTACCTTTCCTTGACCTCCTAGTTCTG-C
* * **
2515769 TTCTGCTTCGACCTT-TGCTTCAGCTTTTGCATCA
195 TTCTGCTCCG-CCTTGTGCTCCAGCTTCAGCATCA
** * * * * * * * *
2515803 GCTTCAGCTTTTCCTTCATCTTTAGCTTTAGCTTTACCTTCAGCTTCAGCTTTACCTTCAGCTTC
1 GCTTCAGCTTTAGCTTTACCTTCAGCTTTAGTTTTAGCTTCAGCTTCACCTTTAGCTCCAGCTTC
2515868 A
66 A
2515869 GCTTTACCTT
Statistics
Matches: 253, Mismatches: 39, Indels: 4
0.85 0.13 0.01
Matches are distributed among these distances:
227 4 0.02
228 246 0.97
229 3 0.01
ACGTcount: A:0.20, C:0.36, G:0.09, T:0.34
Consensus pattern (228 bp):
GCTTCAGCTTTAGCTTTACCTTCAGCTTTAGTTTTAGCTTCAGCTTCACCTTTAGCTCCAGCTTC
ACTAAACCCTCCTTGTCCTCCTACTTTTCCTCCAAAACCAAATTTAAAACCACCACCACCACCAA
AATGCATGTGACCACCACCACCACCACCACCACCACCTACCTTTCCTTGACCTCCTAGTTCTGCT
TCTGCTCCGCCTTGTGCTCCAGCTTCAGCATCA
Found at i:2515849 original size:42 final size:42
Alignment explanation
Indices: 2515800--2516012 Score: 275
Period size: 42 Copynumber: 5.1 Consensus size: 42
2515790 AGCTTTTGCA
* * *
2515800 TCAGCTTCAGCTTTTCCTTCATCTTTAGCTTTAGCTTTACCT
1 TCAGCTTCAGCTTTACCTTCATCTTTAGCTTTAGCTTCAGCT
* * *
2515842 TCAGCTTCAGCTTTACCTTCAGCTTCAGCTTTACCTTCAGCT
1 TCAGCTTCAGCTTTACCTTCATCTTTAGCTTTAGCTTCAGCT
* * *
2515884 TCAGATTCAGCTTTAGCTTCATCATTTA-CTTTAGCTTGAGCT
1 TCAGCTTCAGCTTTACCTTCATC-TTTAGCTTTAGCTTCAGCT
* * * *
2515926 TCATCTTCAGCTTTACCTTCATCTTCAGCTTTGGCTTCAGCA
1 TCAGCTTCAGCTTTACCTTCATCTTTAGCTTTAGCTTCAGCT
* *
2515968 TCAGCTTCAGCTTTAGCTTCAGCTTTAGCTTTAGCTTCAGCT
1 TCAGCTTCAGCTTTACCTTCATCTTTAGCTTTAGCTTCAGCT
2516010 TCA
1 TCA
2516013 TCTTTACCAC
Statistics
Matches: 144, Mismatches: 25, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
41 3 0.02
42 138 0.96
43 3 0.02
ACGTcount: A:0.17, C:0.28, G:0.13, T:0.42
Consensus pattern (42 bp):
TCAGCTTCAGCTTTACCTTCATCTTTAGCTTTAGCTTCAGCT
Found at i:2516246 original size:54 final size:54
Alignment explanation
Indices: 2516158--2516264 Score: 162
Period size: 54 Copynumber: 2.0 Consensus size: 54
2516148 TTAGCTTCAC
**
2516158 CTTTACCATTAGCATCTATATTACCACTGTCATCTCCTCCACCTTGTCCTTTTT
1 CTTTACCATTAGCATCTATATTACCACTACCATCTCCTCCACCTTGTCCTTTTT
* *
2516212 CTTTACCACTT-GCATCTGTATTACCATTACCATCTCCTCCACCTTGTCCTTTT
1 CTTTACCA-TTAGCATCTATATTACCACTACCATCTCCTCCACCTTGTCCTTTT
2516265 ACCCCACCAG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
54 46 0.96
55 2 0.04
ACGTcount: A:0.18, C:0.35, G:0.06, T:0.42
Consensus pattern (54 bp):
CTTTACCATTAGCATCTATATTACCACTACCATCTCCTCCACCTTGTCCTTTTT
Found at i:2516431 original size:204 final size:198
Alignment explanation
Indices: 2516013--2516468 Score: 671
Period size: 198 Copynumber: 2.3 Consensus size: 198
2516003 TTCAGCTTCA
* * * * *
2516013 TCTTTACCACTTGCATCTATATTACCACTACTAGCTCCTCCACCTTTTCCTTTTTCCCCACCAGA
1 TCTTTACCACTTGCATCTGTATTACCACTACCATCTCCTCCACCTTGTCCTTTTACCCCACCAGA
*
2516078 ATCATTAGAGCTGTCACTTCCACCAACATTTCCATCAACCTTTCCTTGTCCTCCAAATTTTCCTT
66 ATCATTAGAGCTGTCACTTCCACCAACATTTCCAACAACCTTTCCTTGTCCTCCAAATTTTCCTT
* *
2516143 CAACTTTAGCTTCACCTTTACCATTAGCATCTATATTACCACTGTCATCTCCTCCACCTTGTCCT
131 CAACTTTAGCTTCACCTTTACCATTAGCATCTATATTACCAATATCATCTCCTCCACCTTGTCCT
2516208 TTT
196 TTT
*
2516211 TCTTTACCACTTGCATCTGTATTACCATTACCATCTCCTCCACCTTGTCCTTTTACCCCACCAGA
1 TCTTTACCACTTGCATCTGTATTACCACTACCATCTCCTCCACCTTGTCCTTTTACCCCACCAGA
*
2516276 ATCATTAGAGTTGTCACTTCCACCAACATTTCCAACAACCTTTCCTTGTCCTCCAAATTTTCCTT
66 ATCATTAGAGCTGTCACTTCCACCAACATTTCCAACAACCTTTCCTTGTCCTCCAAATTTTCCTT
* * * *
2516341 CAGCTTTAGCTTTAGCTTCCCCTTTACCACTT-GCATCTGTCTTACCAATATTATCTCCTCCACC
131 CA-----A-CTTTAGCTTCACCTTTACCA-TTAGCATCTATATTACCAATATCATCTCCTCCACC
2516405 TTGTCCTTTT
189 TTGTCCTTTT
* * * * *
2516415 TCTTTACCATTTGCATCTGTATTACCGCTATCATCACCACCACCTTGTCCTTTT
1 TCTTTACCACTTGCATCTGTATTACCACTACCATCTCCTCCACCTTGTCCTTTT
2516469 TCTTTACCAC
Statistics
Matches: 231, Mismatches: 20, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
198 124 0.54
203 1 0.00
204 104 0.45
205 2 0.01
ACGTcount: A:0.20, C:0.35, G:0.06, T:0.38
Consensus pattern (198 bp):
TCTTTACCACTTGCATCTGTATTACCACTACCATCTCCTCCACCTTGTCCTTTTACCCCACCAGA
ATCATTAGAGCTGTCACTTCCACCAACATTTCCAACAACCTTTCCTTGTCCTCCAAATTTTCCTT
CAACTTTAGCTTCACCTTTACCATTAGCATCTATATTACCAATATCATCTCCTCCACCTTGTCCT
TTT
Found at i:2516458 original size:54 final size:54
Alignment explanation
Indices: 2516362--2516522 Score: 241
Period size: 54 Copynumber: 3.0 Consensus size: 54
2516352 TTAGCTTCCC
* * *
2516362 CTTTACCACTTGCATCTGTCTTACCAATATTATCTCCTCCACCTTGTCCTTTTT
1 CTTTACCACTTGCATCTGTATTACCACTATCATCTCCTCCACCTTGTCCTTTTT
* * * *
2516416 CTTTACCATTTGCATCTGTATTACCGCTATCATCACCACCACCTTGTCCTTTTT
1 CTTTACCACTTGCATCTGTATTACCACTATCATCTCCTCCACCTTGTCCTTTTT
* *
2516470 CTTTACCACTTGCATCTGTATTACCACTACCATCTCCTCCACCTTGTGCTTTT
1 CTTTACCACTTGCATCTGTATTACCACTATCATCTCCTCCACCTTGTCCTTTT
2516523 ACCCCACCAG
Statistics
Matches: 94, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 94 1.00
ACGTcount: A:0.17, C:0.34, G:0.07, T:0.42
Consensus pattern (54 bp):
CTTTACCACTTGCATCTGTATTACCACTATCATCTCCTCCACCTTGTCCTTTTT
Found at i:2516700 original size:54 final size:54
Alignment explanation
Indices: 2516614--2516774 Score: 261
Period size: 54 Copynumber: 3.0 Consensus size: 54
2516604 TTAGCTTCAC
*
2516614 CTTTACCACTAGCATCTATATTACCACTACCATCTCCTCCACCTTGTCCTTTTT
1 CTTTACCACTTGCATCTATATTACCACTACCATCTCCTCCACCTTGTCCTTTTT
* **
2516668 CTTTACCACTTGCATCTATATTACCACCACCATCTCCTGTACCTTGTCC-TTTT
1 CTTTACCACTTGCATCTATATTACCACTACCATCTCCTCCACCTTGTCCTTTTT
*
2516721 CTTTTACCACTTGCATCTGTATTACCACTACCATCTCCTCCACCTTGTCCTTTT
1 C-TTTACCACTTGCATCTATATTACCACTACCATCTCCTCCACCTTGTCCTTTT
2516775 ACCCCACCAG
Statistics
Matches: 97, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
53 5 0.05
54 89 0.92
55 3 0.03
ACGTcount: A:0.19, C:0.37, G:0.05, T:0.40
Consensus pattern (54 bp):
CTTTACCACTTGCATCTATATTACCACTACCATCTCCTCCACCTTGTCCTTTTT
Found at i:2516714 original size:252 final size:251
Alignment explanation
Indices: 2516158--2516906 Score: 1149
Period size: 252 Copynumber: 2.9 Consensus size: 251
2516148 TTAGCTTCAC
*
2516158 CTTTACCATTAGCATCTATATTACCACTGTCATCTCCTCCACCTTGTCCTTTTTCTTTACCACTT
1 CTTTACCATT-GCATCTATATTACCACTATCATCTCCTCCACCTTGTCCTTTTTCTTTACCACTT
* * *
2516223 GCATCTGTATTACCATTACCATCTCCTCCACCTTGTCCTTTTACCCCACCAGAATCATTAGAGTT
65 GCATCTGTATTACCACTACCATCTCCTCCACCTTGTCCTTTTACCCCACCAGAATCACTAGAGCT
* *
2516288 GTCACTTCCACCAACATTTCCAACAACCTTTCCTTGTCCTCCAAATTTTCCTTCAGCTTTAGCTT
130 GTCACTTCCACCAATATTTCCATCAACCTTTCCTTGTCCTCCAAATTTTCCTT---C---AGCTT
* * * * * **
2516353 TAGCTTCCCCTTTACCACTTGCATCTGTCTTACCAATATTATCTCCTCCACCTTGTCCTTTTT
189 TAGCTTCACCTTTACCACTAGCATCTATATTACCACTACCATCTCCTCCACCTTGTCCTTTTT
* * * *
2516416 CTTTACCATTTGCATCTGTATTACCGCTATCATCACCACCACCTTGTCCTTTTTCTTTACCACTT
1 CTTTACCA-TTGCATCTATATTACCACTATCATCTCCTCCACCTTGTCCTTTTTCTTTACCACTT
*
2516481 GCATCTGTATTACCACTACCATCTCCTCCACCTTGTGCTTTTACCCCACCAGAATCACTAGAGCT
65 GCATCTGTATTACCACTACCATCTCCTCCACCTTGTCCTTTTACCCCACCAGAATCACTAGAGCT
* *
2516546 GTCACTTCTACCATTATTTCCATCAACCTTTCCTTGTCCTCCAAATTTTCCTTCAGCTTTAGCTT
130 GTCACTTCCACCAATATTTCCATCAACCTTTCCTTGTCCTCCAAATTTTCCTTCAGCTTTAGCTT
2516611 CACCTTTACCACTAGCATCTATATTACCACTACCATCTCCTCCACCTTGTCCTTTTT
195 CACCTTTACCACTAGCATCTATATTACCACTACCATCTCCTCCACCTTGTCCTTTTT
* * **
2516668 CTTTACCACTTGCATCTATATTACCACCACCATCTCCTGTACCTTGTCC-TTTTCTTTTACCACT
1 CTTTACCA-TTGCATCTATATTACCACTATCATCTCCTCCACCTTGTCCTTTTTC-TTTACCACT
2516732 TGCATCTGTATTACCACTACCATCTCCTCCACCTTGTCCTTTTACCCCACCAGAATCACTAGAGC
64 TGCATCTGTATTACCACTACCATCTCCTCCACCTTGTCCTTTTACCCCACCAGAATCACTAGAGC
* * *
2516797 TGTCACTTCCACCACTATTTCCATCGACCTTTCCTTTTCCTCCAAATTTTCCTTCAGCTTTAGCT
129 TGTCACTTCCACCAATATTTCCATCAACCTTTCCTTGTCCTCCAAATTTTCCTTCAGCTTTAGCT
*
2516862 TCACCTTTACCATTAGCATCTATATTACCACTACCATCTCCTCCA
194 TCACCTTTACCACTAGCATCTATATTACCACTACCATCTCCTCCA
2516907 GCCCCTCCAC
Statistics
Matches: 454, Mismatches: 35, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
251 5 0.01
252 279 0.61
255 1 0.00
258 167 0.37
259 2 0.00
ACGTcount: A:0.20, C:0.36, G:0.06, T:0.38
Consensus pattern (251 bp):
CTTTACCATTGCATCTATATTACCACTATCATCTCCTCCACCTTGTCCTTTTTCTTTACCACTTG
CATCTGTATTACCACTACCATCTCCTCCACCTTGTCCTTTTACCCCACCAGAATCACTAGAGCTG
TCACTTCCACCAATATTTCCATCAACCTTTCCTTGTCCTCCAAATTTTCCTTCAGCTTTAGCTTC
ACCTTTACCACTAGCATCTATATTACCACTACCATCTCCTCCACCTTGTCCTTTTT
Found at i:2517436 original size:144 final size:144
Alignment explanation
Indices: 2517144--2517420 Score: 353
Period size: 144 Copynumber: 1.9 Consensus size: 144
2517134 GTTAGTGCTT
* * *
2517144 CCACTTCCACCACTTTTTCCACCACCATCTCCTTTCCCTCCTACTTTACCTTCAAAACCAACTTT
1 CCACTGCCACCACTATTTCCACCAACATCTCCTTTCCCTCCTACTTTACCTTCAAAACCAACTTT
* * * * * * * * *
2517209 AGCTTCACCTTTACTAGTAGCAGTAGCTTTTCCATCACTACCTTTTTCACCATTATGAGTTCCAC
66 ACCCTCACCTTTACTAGTAGCACTAGCTTTGCCATCACTACCTTTTGCACCACTAAGACTGCCAC
2517274 TTGCATCAGTACTA
131 TTGCATCAGTACTA
* *
2517288 CCACTGCCACCACTATTTCCACCAACTTCTCCTTGT-CCTCCTACTTTACCTTCAAAACCAGCTT
1 CCACTGCCACCACTATTTCCACCAACATCTCCTT-TCCCTCCTACTTTACCTTCAAAACCAACTT
* * *
2517352 TACCCTCA-CTCTTACTAGTATCACTAGCTTTGCCATCACTA-CTCTTTGCTCCGCTAAGACTGC
65 TACCCTCACCT-TTACTAGTAGCACTAGCTTTGCCATCACTACCT-TTTGCACCACTAAGACTGC
2517415 CACTTG
128 CACTTG
2517421 TACTAGTTGC
Statistics
Matches: 113, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
143 4 0.04
144 108 0.96
145 1 0.01
ACGTcount: A:0.22, C:0.37, G:0.07, T:0.34
Consensus pattern (144 bp):
CCACTGCCACCACTATTTCCACCAACATCTCCTTTCCCTCCTACTTTACCTTCAAAACCAACTTT
ACCCTCACCTTTACTAGTAGCACTAGCTTTGCCATCACTACCTTTTGCACCACTAAGACTGCCAC
TTGCATCAGTACTA
Found at i:2517605 original size:3 final size:3
Alignment explanation
Indices: 2517597--2517622 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2517587 GTCATCGTCT
2517597 CCA CCA CCA CCA CCA CCA CCA CCA CC
1 CCA CCA CCA CCA CCA CCA CCA CCA CC
2517623 TCCTCCTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.69, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:2517723 original size:18 final size:18
Alignment explanation
Indices: 2517700--2517742 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
2517690 TGTGCTCCTC
2517700 CACCAGCAACAGCCTTCG
1 CACCAGCAACAGCCTTCG
* *
2517718 CACCAGCAGCGGCCTTCG
1 CACCAGCAACAGCCTTCG
2517736 CACCAGC
1 CACCAGC
2517743 TGTTACAGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.23, C:0.47, G:0.21, T:0.09
Consensus pattern (18 bp):
CACCAGCAACAGCCTTCG
Found at i:2525173 original size:36 final size:36
Alignment explanation
Indices: 2525133--2525207 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
2525123 TCCACTTCCA
* *
2525133 CCACCATT-TCCACCAAACCCTCCTTGTCTTCCTACT
1 CCACC-TTATCCACCAAACCCTCCTTGCCCTCCTACT
*
2525169 CCACCTTATCCACCAAACTCTCCTTGCCCTCCTACT
1 CCACCTTATCCACCAAACCCTCCTTGCCCTCCTACT
2525205 CCA
1 CCA
2525208 ACAGCAACAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
35 2 0.06
36 33 0.94
ACGTcount: A:0.20, C:0.49, G:0.03, T:0.28
Consensus pattern (36 bp):
CCACCTTATCCACCAAACCCTCCTTGCCCTCCTACT
Found at i:2525279 original size:66 final size:66
Alignment explanation
Indices: 2525169--2525340 Score: 211
Period size: 66 Copynumber: 2.6 Consensus size: 66
2525159 TCTTCCTACT
* * * * **
2525169 CCACCTTATCCACCAAACTCTCCTTGCCCTCCTACTCCAACAGCAACATTACTGCTACCACTTCC
1 CCACCTTTTCCACCAAACCCTCCTTTCCCTCCTACTCCACCAGCAACATTACCACTACCACTTCC
2525234 A
66 A
* * * *
2525235 CCACCTTTTCCACCAAACCCTCCTTTTCCTCTTACTCCACCAGCAACATTGCCACTACCACTTTC
1 CCACCTTTTCCACCAAACCCTCCTTTCCCTCCTACTCCACCAGCAACATTACCACTACCACTTCC
2525300 A
66 A
* * * *
2525301 ACACCATTTCCACTAAACCCTCC-TTGCCTCCTACTCCACC
1 CCACCTTTTCCACCAAACCCTCCTTTCCCTCCTACTCCACC
2525341 TTATCCACCA
Statistics
Matches: 91, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
65 15 0.16
66 76 0.84
ACGTcount: A:0.24, C:0.47, G:0.03, T:0.26
Consensus pattern (66 bp):
CCACCTTTTCCACCAAACCCTCCTTTCCCTCCTACTCCACCAGCAACATTACCACTACCACTTCC
A
Found at i:2525353 original size:167 final size:168
Alignment explanation
Indices: 2525069--2525774 Score: 770
Period size: 167 Copynumber: 4.2 Consensus size: 168
2525059 ATCAGTTACC
* * * *
2525069 TCCACCAAACCCTCCTTGTCTTCCTACTTCACCAGTAACATTAGCATTACCACTTCCACTTCCAC
1 TCCACCAAACCCTCCTTGCCCTCCTACTCCACCAG---CA--A-CATTACCACTACCACTTCCAC
* * * **
2525134 CACCATTTCCACCAAACCCTCCTTGTCTTCCTACTCCACCTTATCCACCAAACTCTCCTTGCCCT
60 CACCATTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCTTATCCACCAAACCCTCCTTATCCT
* *
2525199 CCTACTCCAACAGCAACATTA-CTGCTACCACTTCCACCACCTTT
125 CCTACTCCAACAGCAACATTAGC-ACTACCACTTCCAACACCTTT
** * * * *
2525243 TCCACCAAACCCTCCTTTTCCTCTTACTCCACCAGCAACATTGCCACTACCACTTTCAACACCAT
1 TCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTACCACTACCACTTCCACCACCAT
* * *
2525308 TTCCACTAAACCCTCCTTG-CCTCCTACTCCACCTTATCCACCAAACCCTCCTTATACTCCTAAT
66 TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCTTATCCACCAAACCCTCCTTATCCTCCTACT
* * * *
2525372 CC-ACTAACAATATTAGCACTACTACTTCTAACACCATTT
131 CCAAC-AGCAACATTAGCACTACCACTTCCAACACC-TTT
* ** * ** *
2525411 T-CGCCAAACCCT-CTTCGCCCTCCTACTCCACCAGCAACATTACTGCCACCACTTTTACCACCT
1 TCCACCAAACCCTCCTT-GCCCTCCTACTCCACCAGCAACATTACCACTACCACTTCCACCACCA
* * * *
2525474 TTTACACCAAACCC-CCTTGCCCTCCAACTCCACCTT-TCCCACCAAATCCTCCTTGTCCTCCTA
65 TTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCTTAT-CCACCAAACCCTCCTTATCCTCCTA
* ** *
2525537 CTTCATGAGCAACATTAGCACTACCACTTCCAACACCATT
129 CTCCAACAGCAACATTAGCACTACCACTTCCAACACCTTT
* * *
2525577 TCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTATCGCTACCACTTCCACCACCTT
1 TCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTACCACTACCACTTCCACCACCAT
* * *
2525642 TTCCACCAAACCCTCCCTGCCCTACTACTCCACCTTGTCCACCAAACCCTCCTTATCCTCCTA--
66 TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCTTATCCACCAAACCCTCCTTATCCTCCTACT
* *
2525705 -C-ACTAGCAACATTAGCACTACCACGTCCAACACCATT
131 CCAAC-AGCAACATTAGCACTACCACTTCCAACACCTTT
* *
2525742 TCCGCCAAACCC-CTCTTGCCCTCCAACTCCACC
1 TCCACCAAACCCTC-CTTGCCCTCCTACTCCACC
2525775 TTTTCCACCA
Statistics
Matches: 455, Mismatches: 64, Indels: 35
0.82 0.12 0.06
Matches are distributed among these distances:
164 1 0.00
165 62 0.14
166 14 0.03
167 252 0.55
168 91 0.20
169 2 0.00
171 2 0.00
174 31 0.07
ACGTcount: A:0.25, C:0.45, G:0.04, T:0.26
Consensus pattern (168 bp):
TCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTACCACTACCACTTCCACCACCAT
TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCTTATCCACCAAACCCTCCTTATCCTCCTACT
CCAACAGCAACATTAGCACTACCACTTCCAACACCTTT
Found at i:2525410 original size:101 final size:102
Alignment explanation
Indices: 2525235--2525442 Score: 253
Period size: 101 Copynumber: 2.0 Consensus size: 102
2525225 ACCACTTCCA
* * * * * *
2525235 CCACCTTTTCCACCAAACCCTCCTTTTCCTCTTACTCCACCAGCAACATTGCCACTACCACTTTC
1 CCACCTTATCCACCAAACCCTCCTTATACTCCTAATCCACCAACAACATTGCCACTACCACTTTC
*
2525300 AACACCATTTCCACTAAACCCTCCTT-G-CCTCCTACT
66 AACACCATTTCCACCAAACCCT-CTTCGCCCTCCTACT
* * *
2525336 CCACCTTATCCACCAAACCCTCCTTATACTCCTAATCCACTAACAATATTAG-CACTACTAC-TT
1 CCACCTTATCCACCAAACCCTCCTTATACTCCTAATCCACCAACAACATT-GCCACTACCACTTT
* *
2525399 CTAACACCATTTTCGCCAAACCCTCTTCGCCCTCCTACT
65 C-AACACCATTTCCACCAAACCCTCTTCGCCCTCCTACT
2525438 CCACC
1 CCACC
2525443 AGCAACATTA
Statistics
Matches: 91, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
100 6 0.07
101 70 0.77
102 15 0.16
ACGTcount: A:0.25, C:0.44, G:0.03, T:0.28
Consensus pattern (102 bp):
CCACCTTATCCACCAAACCCTCCTTATACTCCTAATCCACCAACAACATTGCCACTACCACTTTC
AACACCATTTCCACCAAACCCTCTTCGCCCTCCTACT
Found at i:2525527 original size:18 final size:18
Alignment explanation
Indices: 2525478--2525528 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 18
2525468 CCACCTTTTA
*
2525478 CACCAAA-CCCCCTTGCC
1 CACCAAATCCACCTTGCC
* * *
2525495 CTCCAACTCCACCTTTCC
1 CACCAAATCCACCTTGCC
*
2525513 CACCAAATCCTCCTTG
1 CACCAAATCCACCTTG
2525529 TCCTCCTACT
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.22, C:0.53, G:0.04, T:0.22
Consensus pattern (18 bp):
CACCAAATCCACCTTGCC
Found at i:2525618 original size:66 final size:65
Alignment explanation
Indices: 2525504--2526067 Score: 272
Period size: 66 Copynumber: 8.5 Consensus size: 65
2525494 CCTCCAACTC
* * * **
2525504 CACCTTTCCCACCAAATCCTCCTTGTCCTCCTACTTCATGAGCAACATTAGCACTACCACTTCCA
1 CACCTTT-CCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCCA
2525569 A
65 A
* *
2525570 CACCATTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTATCGCTACCACTTCCA
1 CACC-TTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCCA
*
2525635 C
65 A
* * * * * *
2525636 CACCTTTTCCACCAAACCCTCCCTGCCCTACTACTCCACCTTGTCCACCA--AACCCT-CCTTAT
1 CACC-TTTCCACCAAACCCTCCTTGCCCTCCTACTCCACC-AG--CAACATTAGCACTACC--A-
* *
2525698 CCTCCTA
59 CTTCCAA
** * * * ** * * * * * *
2525705 CA-C-TAGCAACATTAGCACTACCACGTCCAACACC-ATTTCCGCCA--AACCCCTCTTGCCCT-
1 CACCTTTCCACCA--AACCCT-CCTTG-CC--CTCCTA-CTCCACCAGCAA--CAT-TAGCACTA
2525764 CCAAC-TCC-A
56 CC-ACTTCCAA
* * * * *
2525773 C-CTTTTCCACCAAACCCTCCTTGTCCTCCCACTCCACTAGCAACATTAGCATTACCACTTCCAA
1 CACCTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCCAA
* * ** * * *
2525837 CACCATTTCCACCAAAACCTCCTTGCCCTCTTGTTCCGCCAGCAACATTACCGCTACCACTTCCA
1 CACC-TTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCCA
*
2525902 T
65 A
* * * * * * * *
2525903 TACTTTTTCCACCAAACCCTCTTTGCCCTCCTACTCTACAAGTAACATTAGTACTACCAATTCCA
1 CAC-CTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCCA
2525968 A
65 A
* * * * * * * *
2525969 CACCATTTCCACCAAACCCTCTTTGCCCTCTTAGTCCATCAACAACATTACCGCTACCATTTCCA
1 CACC-TTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCCA
*
2526034 C
65 A
*
2526035 CACTTTTTCCACCAAACCCTCCATT-CCCTCCTA
1 CAC-CTTTCCACCAAACCCTCC-TTGCCCTCCTA
2526068 TATTACCTCC
Statistics
Matches: 367, Mismatches: 98, Indels: 66
0.69 0.18 0.12
Matches are distributed among these distances:
62 6 0.02
63 15 0.04
64 3 0.01
65 4 0.01
66 276 0.75
67 15 0.04
68 8 0.02
69 22 0.06
70 3 0.01
71 2 0.01
72 13 0.04
ACGTcount: A:0.25, C:0.44, G:0.05, T:0.26
Consensus pattern (65 bp):
CACCTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCCAA
Found at i:2525684 original size:102 final size:102
Alignment explanation
Indices: 2525577--2525865 Score: 397
Period size: 99 Copynumber: 2.9 Consensus size: 102
2525567 CAACACCATT
* * * * * *
2525577 TCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTATCGCTACCACTTCCACCACCTT
1 TCCACCAAACCCTCCTTGTCCTCCTACTCCACTAGCAACATTAGCACTACCACTTCCAACACCAT
* *
2525642 TTCCACCAAACCCTCCCTGCCCTACTACTCCACCTTG
66 TTCCACCAAACCCTCCTTGCCCTACAACTCCACCTTG
* *
2525679 TCCACCAAACCCTCCTTATCCTCCTA---CACTAGCAACATTAGCACTACCACGTCCAACACCAT
1 TCCACCAAACCCTCCTTGTCCTCCTACTCCACTAGCAACATTAGCACTACCACTTCCAACACCAT
* * *
2525741 TTCCGCCAAACCC-CTCTTGCCCTCCAACTCCACCTTT
66 TTCCACCAAACCCTC-CTTGCCCTACAACTCCACCTTG
* *
2525778 TCCACCAAACCCTCCTTGTCCTCCCACTCCACTAGCAACATTAGCATTACCACTTCCAACACCAT
1 TCCACCAAACCCTCCTTGTCCTCCTACTCCACTAGCAACATTAGCACTACCACTTCCAACACCAT
*
2525843 TTCCACCAAAACCTCCTTGCCCT
66 TTCCACCAAACCCTCCTTGCCCT
2525866 CTTGTTCCGC
Statistics
Matches: 163, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
98 1 0.01
99 84 0.52
102 77 0.47
103 1 0.01
ACGTcount: A:0.24, C:0.47, G:0.05, T:0.24
Consensus pattern (102 bp):
TCCACCAAACCCTCCTTGTCCTCCTACTCCACTAGCAACATTAGCACTACCACTTCCAACACCAT
TTCCACCAAACCCTCCTTGCCCTACAACTCCACCTTG
Found at i:2525786 original size:36 final size:36
Alignment explanation
Indices: 2525735--2525809 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
2525725 CCACGTCCAA
*
2525735 CACCATTTCCGCCAAACCC-CTCTTGCCCTCCAACTC
1 CACCATTTCCACCAAACCCTC-CTTGCCCTCCAACTC
* * *
2525771 CACCTTTTCCACCAAACCCTCCTTGTCCTCCCACTC
1 CACCATTTCCACCAAACCCTCCTTGCCCTCCAACTC
2525807 CAC
1 CAC
2525810 TAGCAACATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 33 0.97
37 1 0.03
ACGTcount: A:0.19, C:0.53, G:0.04, T:0.24
Consensus pattern (36 bp):
CACCATTTCCACCAAACCCTCCTTGCCCTCCAACTC
Found at i:2526066 original size:132 final size:132
Alignment explanation
Indices: 2525770--2526067 Score: 402
Period size: 132 Copynumber: 2.3 Consensus size: 132
2525760 CCCTCCAACT
* * * * * *
2525770 CCACCTTTTCCACCAAACCCTCCTTGTCCTCCCACTCCACTAGCAACATTAGCATTACCACTTCC
1 CCACTTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACAAGCAACATTAGCACTACCAATTCC
* *
2525835 AACACCATTTCCACCAAAACCTCCTTGCCCTCTTGTTCCGCCAGCAACATTACCGCTACCACTTC
66 AACACCATTTCCACCAAAACCTCCTTGCCCTCTTGTTCCACCAACAACATTACCGCTACCACTTC
2525900 CA
131 CA
** * * * *
2525902 TTACTTTTTCCACCAAACCCTCTTTGCCCTCCTACTCTACAAGTAACATTAGTACTACCAATTCC
1 CCACTTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACAAGCAACATTAGCACTACCAATTCC
* * * *
2525967 AACACCATTTCCACCAAACCCTCTTTGCCCTCTTAG-TCCATCAACAACATTACCGCTACCATTT
66 AACACCATTTCCACCAAAACCTCCTTGCCCTCTT-GTTCCACCAACAACATTACCGCTACCACTT
2526031 CCA
130 CCA
2526034 CCACTTTTTCCACCAAACCCTCCATT-CCCTCCTA
1 CCACTTTTTCCACCAAACCCTCC-TTGCCCTCCTA
2526068 TATTACCTCC
Statistics
Matches: 143, Mismatches: 21, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
132 140 0.98
133 3 0.02
ACGTcount: A:0.25, C:0.42, G:0.05, T:0.28
Consensus pattern (132 bp):
CCACTTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACAAGCAACATTAGCACTACCAATTCC
AACACCATTTCCACCAAAACCTCCTTGCCCTCTTGTTCCACCAACAACATTACCGCTACCACTTC
CA
Found at i:2526582 original size:14 final size:14
Alignment explanation
Indices: 2526563--2526594 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
2526553 AAAAATATGG
2526563 AGTGTGGGAGCAAC
1 AGTGTGGGAGCAAC
2526577 AGTGTGGGAGCAAC
1 AGTGTGGGAGCAAC
2526591 AGTG
1 AGTG
2526595 GTTGTTTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.28, C:0.12, G:0.44, T:0.16
Consensus pattern (14 bp):
AGTGTGGGAGCAAC
Found at i:2535143 original size:48 final size:48
Alignment explanation
Indices: 2535080--2535179 Score: 137
Period size: 48 Copynumber: 2.1 Consensus size: 48
2535070 ACCAAACCCT
* * * *
2535080 CCTTGCCCACCTACTCCACCAGCAGCATTAGCGCTACCGCTTCCACCA
1 CCTTGCCCACCTACTCCACCAGCAACATTAGCACTACCACTTACACCA
* * *
2535128 CCTTGCCCTCGTACTCCACCAGCAACATTAGCACTACCACTTAGACCA
1 CCTTGCCCACCTACTCCACCAGCAACATTAGCACTACCACTTACACCA
2535176 CCTT
1 CCTT
2535180 TTCCACTGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.23, C:0.45, G:0.11, T:0.21
Consensus pattern (48 bp):
CCTTGCCCACCTACTCCACCAGCAACATTAGCACTACCACTTACACCA
Found at i:2535277 original size:54 final size:54
Alignment explanation
Indices: 2535219--2535426 Score: 254
Period size: 54 Copynumber: 3.6 Consensus size: 54
2535209 ACTCCACTTT
* *
2535219 TTCCACCAAACCCTCCTTGTCCTCCTCCTCCACCAGCAACATTACCGCTACCAC
1 TTCCACCAAACCCTCCTTGTCCTCCTACTCCACCACCAACATTACCGCTACCAC
* *
2535273 TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCACCAACATTAATGCTGCCACTTCCACCACC
1 TTCCACCAAACCCTCCTTGTCCTCCTACTCCACCACCAACATT-A-----CCGC-T--ACCA-C
**
2535337 TTTTCCACCAAACCCTCCTTGTCCTCCTACTCCACCACCAACATTAGTGCTACCAC
1 --TTCCACCAAACCCTCCTTGTCCTCCTACTCCACCACCAACATTACCGCTACCAC
2535393 TTCCACCAAACCCTCCTTGTCCTCCTACTCCACC
1 TTCCACCAAACCCTCCTTGTCCTCCTACTCCACC
2535427 TCCTTGTCCT
Statistics
Matches: 134, Mismatches: 8, Indels: 24
0.81 0.05 0.14
Matches are distributed among these distances:
54 74 0.55
55 1 0.01
56 1 0.01
57 4 0.03
59 1 0.01
60 4 0.03
61 1 0.01
63 4 0.03
64 1 0.01
65 1 0.01
66 42 0.31
ACGTcount: A:0.22, C:0.49, G:0.05, T:0.24
Consensus pattern (54 bp):
TTCCACCAAACCCTCCTTGTCCTCCTACTCCACCACCAACATTACCGCTACCAC
Found at i:2535350 original size:66 final size:66
Alignment explanation
Indices: 2535273--2535475 Score: 253
Period size: 66 Copynumber: 2.9 Consensus size: 66
2535263 CCGCTACCAC
*
2535273 TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCACCAACATTAATGCTGCCACTTCCACCACCT
1 TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCACCAACATTAATGCTACCACTTCCACCACCT
2535338 T
66 T
* *
2535339 TTCCACCAAACCCTCCTTGTCCTCCTACTCCACCACCAACATTAGTGCTACCACTTCCACCAAAC
1 TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCACCAACATTAATGCTACCACTTCCACC--A-
2535404 CCTCCT
63 CCT--T
* ** * *
2535410 TGTCCTCCTACTCCACCTCCTTGTCCTCCTACTCCACCACCAACATTAGTGCTACCACTTCCACC
1 T-TCCACC-A-AAC-CCTCCTTGCCCTCCTACTCCACCACCAACATTAATGCTACCACTTCCACC
2535475 A
62 A
2535476 AACCCTCCTT
Statistics
Matches: 122, Mismatches: 6, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
66 58 0.48
68 1 0.01
69 3 0.02
71 2 0.02
72 5 0.04
73 2 0.02
74 1 0.01
75 50 0.41
ACGTcount: A:0.22, C:0.48, G:0.05, T:0.25
Consensus pattern (66 bp):
TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCACCAACATTAATGCTACCACTTCCACCACCT
T
Found at i:2535354 original size:159 final size:153
Alignment explanation
Indices: 2535065--2535365 Score: 386
Period size: 159 Copynumber: 1.9 Consensus size: 153
2535055 TCCACCATCA
* * *
2535065 TTTCCACCAAACCCTCCTTGCCCACCTACTCCACCAGCAGCATTAGCGCTACCGCTTCCACCACC
1 TTTCCACCAAACCCTCCTTGCCCACCTACTCCACCAGCAACATTACCGCTACCACTTCCACCACC
* * * * ** *
2535130 TTGCCCTCGTACTCCACCAGCAACATTAGCACTACCACTTAGACCACCTTTTCCACTGAATCCTC
66 TTGCCCTCCTACTCCACCACCAACATTAACACTACCACTTACACCACCTTTTCCACCAAACCCTC
2535195 CTTGACCTCCTAGTACTCCACTT
131 CTTGACCTCCTAGTACTCCACTT
* * *
2535218 TTTCCACCAAACCCTCCTTGTCCTCCTCCTCCACCAGCAACATTACCGCTACCACTTCCACCAAA
1 TTTCCACCAAACCCTCCTTGCCCACCTACTCCACCAGCAACATTACCGCTACCACTTCCACC--A
** * *
2535283 CCCTCCTTGCCCTCCTACTCCACCACCAACATTAATGCTGCCACTTCCACCACCTTTTCCACCAA
64 ----CCTTGCCCTCCTACTCCACCACCAACATTAACACTACCACTTACACCACCTTTTCCACCAA
*
2535348 ACCCTCCTTGTCCTCCTA
125 ACCCTCCTTGACCTCCTA
2535366 CTCCACCACC
Statistics
Matches: 124, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
153 56 0.45
155 1 0.01
159 67 0.54
ACGTcount: A:0.22, C:0.46, G:0.07, T:0.25
Consensus pattern (153 bp):
TTTCCACCAAACCCTCCTTGCCCACCTACTCCACCAGCAACATTACCGCTACCACTTCCACCACC
TTGCCCTCCTACTCCACCACCAACATTAACACTACCACTTACACCACCTTTTCCACCAAACCCTC
CTTGACCTCCTAGTACTCCACTT
Found at i:2535430 original size:21 final size:21
Alignment explanation
Indices: 2535404--2535447 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
2535394 TCCACCAAAC
2535404 CCTCCTTGTCCTCCTACTCCA
1 CCTCCTTGTCCTCCTACTCCA
2535425 CCTCCTTGTCCTCCTACTCCA
1 CCTCCTTGTCCTCCTACTCCA
2535446 CC
1 CC
2535448 ACCAACATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.09, C:0.55, G:0.05, T:0.32
Consensus pattern (21 bp):
CCTCCTTGTCCTCCTACTCCA
Found at i:2535438 original size:75 final size:75
Alignment explanation
Indices: 2535350--2535501 Score: 295
Period size: 75 Copynumber: 2.0 Consensus size: 75
2535340 TCCACCAAAC
*
2535350 CCTCCTTGTCCTCCTACTCCACCACCAACATTAGTGCTACCACTTCCACCAAACCCTCCTTGTCC
1 CCTCCTTGTCCTCCTACTCCACCACCAACATTAGTGCTACCACTTCCACCAAACCCTCCTTGCCC
2535415 TCCTACTCCA
66 TCCTACTCCA
2535425 CCTCCTTGTCCTCCTACTCCACCACCAACATTAGTGCTACCACTTCCACCAAACCCTCCTTGCCC
1 CCTCCTTGTCCTCCTACTCCACCACCAACATTAGTGCTACCACTTCCACCAAACCCTCCTTGCCC
2535490 TCCTACTCCA
66 TCCTACTCCA
2535500 CC
1 CC
2535502 CCCAACATTA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 76 1.00
ACGTcount: A:0.20, C:0.49, G:0.05, T:0.26
Consensus pattern (75 bp):
CCTCCTTGTCCTCCTACTCCACCACCAACATTAGTGCTACCACTTCCACCAAACCCTCCTTGCCC
TCCTACTCCA
Found at i:2535535 original size:36 final size:36
Alignment explanation
Indices: 2535488--2535561 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
2535478 CCCTCCTTGC
* * *
2535488 CCTCCTACTCCACCCCCAACATTAGTGCTACCCCTT
1 CCTCCTACTCCACCACCAACATTAGAGCTACCACTT
2535524 CCTCCTACTCCACCACCAACATTAGAGCTACCACTT
1 CCTCCTACTCCACCACCAACATTAGAGCTACCACTT
2535560 CC
1 CC
2535562 ACCAAACCCT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.23, C:0.49, G:0.05, T:0.23
Consensus pattern (36 bp):
CCTCCTACTCCACCACCAACATTAGAGCTACCACTT
Found at i:2535541 original size:90 final size:90
Alignment explanation
Indices: 2535433--2535615 Score: 321
Period size: 90 Copynumber: 2.0 Consensus size: 90
2535423 CACCTCCTTG
*
2535433 TCCTCCTACTCCACCACCAACATTAGTGCTACCACTTCCACCAAACCCTCCTTGCCCTCCTACTC
1 TCCTCCTACTCCACCACCAACATTAGAGCTACCACTTCCACCAAACCCTCCTTGCCCTCCTACTC
* * *
2535498 CACCCCCAACATTAGTGCTACCCCT
66 CACCACCAACATTAGCGCTACCACT
2535523 TCCTCCTACTCCACCACCAACATTAGAGCTACCACTTCCACCAAACCCTCCTTGCCCTCCTACTC
1 TCCTCCTACTCCACCACCAACATTAGAGCTACCACTTCCACCAAACCCTCCTTGCCCTCCTACTC
*
2535588 CACCACCAATATTAGCGCTACCACT
66 CACCACCAACATTAGCGCTACCACT
2535613 TCC
1 TCC
2535616 ACCACCTTTT
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 88 1.00
ACGTcount: A:0.23, C:0.48, G:0.05, T:0.23
Consensus pattern (90 bp):
TCCTCCTACTCCACCACCAACATTAGAGCTACCACTTCCACCAAACCCTCCTTGCCCTCCTACTC
CACCACCAACATTAGCGCTACCACT
Found at i:2535706 original size:93 final size:93
Alignment explanation
Indices: 2535587--2535880 Score: 331
Period size: 93 Copynumber: 3.0 Consensus size: 93
2535577 CCCTCCTACT
* *
2535587 CCACCACCAATATTAGCGCTACCACTTCCACCACCTTTTCCACCAAACCCTCCAGTCCCTCCTAT
1 CCACCACCAACATTAGCGCTACCACTTCCACCACCTCTTCCACCAAACCCTCCAGTCCCTCCTAT
* *
2535652 ATTTCCTCCATTTCCAATACCTCTACCA
66 ATTACCTCCAATTCCAATACCTCTACCA
* * *
2535680 CCACCAGCAACATTAGTGCTATCACTTCCACCACCTCTTCCACCAAACCCTCCAGTCCCTCCTAT
1 CCACCACCAACATTAGCGCTACCACTTCCACCACCTCTTCCACCAAACCCTCCAGTCCCTCCTAT
*
2535745 ATTACCTCCAATTCCAATACCTTTACCACCA
66 ATTACCTCCAATTCCAATACC--T-CTACCA
* * *
2535776 CCTCCTAATCCACCTGCAATATTAGCGCTACCACTTCCACCACCTTTTCCACCTAACCCTCCTAG
1 ---CC--A-CCA-C--CAACATTAGCGCTACCACTTCCACCACCTCTTCCACCAAACCCTCC-AG
* *
2535841 T-CCTCCTATATTACCACCCAA-TCCAATACCTCCACCA
56 TCCCTCCTATATTACC-TCCAATTCCAATACCTCTACCA
2535878 CCA
1 CCA
2535881 ACTCCTGCTC
Statistics
Matches: 172, Mismatches: 15, Indels: 24
0.82 0.07 0.11
Matches are distributed among these distances:
93 79 0.46
95 1 0.01
96 5 0.03
97 1 0.01
99 4 0.02
101 1 0.01
102 9 0.05
103 1 0.01
105 64 0.37
106 7 0.04
ACGTcount: A:0.26, C:0.45, G:0.04, T:0.26
Consensus pattern (93 bp):
CCACCACCAACATTAGCGCTACCACTTCCACCACCTCTTCCACCAAACCCTCCAGTCCCTCCTAT
ATTACCTCCAATTCCAATACCTCTACCA
Found at i:2535893 original size:105 final size:105
Alignment explanation
Indices: 2535680--2535886 Score: 292
Period size: 105 Copynumber: 2.0 Consensus size: 105
2535670 ACCTCTACCA
* *
2535680 CCACCAGCAACATTAGTGCTATCACTTCCACCACCTCTTCCACCAAACCCTCCAGTCCCTCCTAT
1 CCACCAGCAACATTAGCGCTACCACTTCCACCACCTCTTCCACCAAACCCTCCAGTCCCTCCTAT
* ** *
2535745 ATTACCTCCAATTCCAATACCTTTACCACCACCTCCTAAT
66 ATTACCCCCAATTCCAATACCTCCACCACCAACTCCTAAT
* * * *
2535785 CCACCTGCAATATTAGCGCTACCACTTCCACCACCTTTTCCACCTAACCCTCCTAGT-CCTCCTA
1 CCACCAGCAACATTAGCGCTACCACTTCCACCACCTCTTCCACCAAACCCTCC-AGTCCCTCCTA
2535849 TATTACCACCCAA-TCCAATACCTCCACCACCAACTCCT
65 TATTACC-CCCAATTCCAATACCTCCACCACCAACTCCT
2535887 GCTCCACGAT
Statistics
Matches: 90, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
105 83 0.92
106 7 0.08
ACGTcount: A:0.26, C:0.45, G:0.04, T:0.25
Consensus pattern (105 bp):
CCACCAGCAACATTAGCGCTACCACTTCCACCACCTCTTCCACCAAACCCTCCAGTCCCTCCTAT
ATTACCCCCAATTCCAATACCTCCACCACCAACTCCTAAT
Found at i:2535957 original size:15 final size:15
Alignment explanation
Indices: 2535937--2535966 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2535927 CACCTTTTAA
2535937 AGCAGCAGCACCAGC
1 AGCAGCAGCACCAGC
2535952 AGCAGCAGCACCAGC
1 AGCAGCAGCACCAGC
2535967 TGCTTTAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.40, G:0.27, T:0.00
Consensus pattern (15 bp):
AGCAGCAGCACCAGC
Found at i:2537072 original size:29 final size:30
Alignment explanation
Indices: 2537017--2537075 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
2537007 ATCTCAAAAT
*
2537017 TATACATGAACTTTAATTTAATGTGCAATTC
1 TATACATGAACTTTAATTT-AGGTGCAATTC
*
2537048 TATACATGAATTTTAATTT-GGTGCAATT
1 TATACATGAACTTTAATTTAGGTGCAATT
2537076 ATACACGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
31 18 0.69
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (30 bp):
TATACATGAACTTTAATTTAGGTGCAATTC
Found at i:2537086 original size:29 final size:29
Alignment explanation
Indices: 2537014--2537086 Score: 71
Period size: 31 Copynumber: 2.5 Consensus size: 29
2537004 TAAATCTCAA
*
2537014 AATTATACA-TGAACTTTAATTTAATGTGC
1 AATTATACACTGAACTTTAATTT-AGGTGC
*
2537043 AATTCTATACA-TGAATTTTAATTT-GGTGC
1 AA-T-TATACACTGAACTTTAATTTAGGTGC
2537072 AATTATACACGTGAA
1 AATTATACAC-TGAA
2537087 ACTCTGATTG
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
27 6 0.16
28 1 0.03
29 12 0.32
30 1 0.03
31 18 0.47
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (29 bp):
AATTATACACTGAACTTTAATTTAGGTGC
Found at i:2537294 original size:30 final size:29
Alignment explanation
Indices: 2537260--2537323 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
2537250 AATTTACAAG
2537260 AATTGAATC-AAATCAAAATTTCATGTATAC
1 AATTGAA-CAAAATCAAAA-TTCATGTATAC
*
2537290 AATTGCACAAAATCAAAATTCATGTATAC
1 AATTGAACAAAATCAAAATTCATGTATAC
2537319 AATTG
1 AATTG
2537324 CACATTAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 17 0.53
30 15 0.47
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.31
Consensus pattern (29 bp):
AATTGAACAAAATCAAAATTCATGTATAC
Found at i:2537312 original size:29 final size:30
Alignment explanation
Indices: 2537269--2537327 Score: 111
Period size: 29 Copynumber: 2.0 Consensus size: 30
2537259 GAATTGAATC
2537269 AAATCAAAATTTCATGTATACAATTGCACA
1 AAATCAAAATTTCATGTATACAATTGCACA
2537299 AAATCAAAA-TTCATGTATACAATTGCACA
1 AAATCAAAATTTCATGTATACAATTGCACA
2537328 TTAAACCATA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 20 0.69
30 9 0.31
ACGTcount: A:0.47, C:0.17, G:0.07, T:0.29
Consensus pattern (30 bp):
AAATCAAAATTTCATGTATACAATTGCACA
Found at i:2541834 original size:66 final size:65
Alignment explanation
Indices: 2541755--2541966 Score: 239
Period size: 66 Copynumber: 3.2 Consensus size: 65
2541745 ACCACCTTGC
* * * * * *
2541755 CCTCCTACCCCACCAGCAACCTCAGTGCTACCACTTCCACTACCTTCTCCACCAAATCCTCCATG
1 CCTCCTACTCCACCAGCAACCTTAGCGCTACCACTTCCACCACCTTTTCCACCAAACCCTCCATG
* *
2541820 TCCTCCTACTCCACCAGC-ACCATTAGCGCTACCACTTCCACCACCTTTTGCACTAAACCCTCCA
1 -CCTCCTACTCCACCAGCAACC-TTAGCGCTACCACTTCCACCACCTTTTCCACCAAACCCTCCA
2541884 TG
64 TG
* * * * * *
2541886 CCATCTTACAT-CACCAGCAACATTACCACTACCACTTCCACCACCTTTTCCACCAACCCCTCCT
1 CC-TCCTAC-TCCACCAGCAACCTTAGCGCTACCACTTCCACCACCTTTTCCACCAAACCCTCCA
2541950 TG
64 TG
2541952 ACCTCCTACTCCACC
1 -CCTCCTACTCCACC
2541967 TTTTCCACCA
Statistics
Matches: 123, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
65 6 0.05
66 112 0.91
67 5 0.04
ACGTcount: A:0.24, C:0.48, G:0.05, T:0.23
Consensus pattern (65 bp):
CCTCCTACTCCACCAGCAACCTTAGCGCTACCACTTCCACCACCTTTTCCACCAAACCCTCCATG
Found at i:2541968 original size:18 final size:18
Alignment explanation
Indices: 2541947--2542002 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
2541937 ACCAACCCCT
*
2541947 CCTTGACCTCCTACTCCA
1 CCTTGTCCTCCTACTCCA
* * * * *
2541965 CCTTTTCCACCAAATCCT
1 CCTTGTCCTCCTACTCCA
2541983 CCTTGTCCTCCTACTCCA
1 CCTTGTCCTCCTACTCCA
2542001 CC
1 CC
2542003 AGCAACATTA
Statistics
Matches: 27, Mismatches: 11, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.16, C:0.50, G:0.04, T:0.30
Consensus pattern (18 bp):
CCTTGTCCTCCTACTCCA
Found at i:2541972 original size:36 final size:36
Alignment explanation
Indices: 2541926--2542002 Score: 127
Period size: 36 Copynumber: 2.1 Consensus size: 36
2541916 ACCACTTCCA
*
2541926 CCACCTTTTCCACCAACCCCTCCTTGACCTCCTACT
1 CCACCTTTTCCACCAAACCCTCCTTGACCTCCTACT
* *
2541962 CCACCTTTTCCACCAAATCCTCCTTGTCCTCCTACT
1 CCACCTTTTCCACCAAACCCTCCTTGACCTCCTACT
2541998 CCACC
1 CCACC
2542003 AGCAACATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.17, C:0.52, G:0.03, T:0.29
Consensus pattern (36 bp):
CCACCTTTTCCACCAAACCCTCCTTGACCTCCTACT
Found at i:2541993 original size:168 final size:168
Alignment explanation
Indices: 2541796--2542134 Score: 524
Period size: 168 Copynumber: 2.0 Consensus size: 168
2541786 CACTTCCACT
* *
2541796 ACCTTCTCCACCAAATCCTCCATGTCCTCCTACTCCACCAGCACCATTAGCGCTACCACTTCCAC
1 ACCTTCTCCACCAAATCCTCCATGTCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCCAC
* *
2541861 CACCTTTTGCA-CTAAACCCTCCATG-CCATCTTACAT-CACCAGCAACATTACCACTACCACTT
66 CACCTTTTCCAGC-AAACCCTCCATGTCC-TCCTAC-TCCACCAGCAACATTACCACTACCACTT
2541923 CCACCACCTTTTCCACC-AACCCCTCCTTGACCTCCTACTCC
128 CCACCACCTTTTCCACCGAA-CCCTCCTTGACCTCCTACTCC
* *
2541964 ACCTTTTCCACCAAATCCTCCTTGTCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCCAC
1 ACCTTCTCCACCAAATCCTCCATGTCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCCAC
* *
2542029 CACCTTTTCCAGCAAACCCTCCTTGTCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCCA
66 CACCTTTTCCAGCAAACCCTCCATGTCCTCCTACTCCACCAGCAACATTACCACTACCACTTCCA
* *
2542094 CCACCTTTTCCACCGAACCCTCCTTGCCCTCCTACTTC
131 CCACCTTTTCCACCGAACCCTCCTTGACCTCCTACTCC
2542132 ACC
1 ACC
2542135 AGCAACATTA
Statistics
Matches: 157, Mismatches: 10, Indels: 8
0.90 0.06 0.05
Matches are distributed among these distances:
167 1 0.01
168 151 0.96
169 5 0.03
ACGTcount: A:0.23, C:0.47, G:0.05, T:0.25
Consensus pattern (168 bp):
ACCTTCTCCACCAAATCCTCCATGTCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCCAC
CACCTTTTCCAGCAAACCCTCCATGTCCTCCTACTCCACCAGCAACATTACCACTACCACTTCCA
CCACCTTTTCCACCGAACCCTCCTTGACCTCCTACTCC
Found at i:2542028 original size:234 final size:234
Alignment explanation
Indices: 2541749--2542200 Score: 663
Period size: 234 Copynumber: 1.9 Consensus size: 234
2541739 ACTTCCACCA
* ** * *
2541749 CCTTGCCCTCCTACCCCACCAGCAACCTCAGTGCTACCACTTCCACTACCTTCTCCACCAAATCC
1 CCTTGCCCTCCTACCCCACCAGCAACATCAGCACTACCACTTCCACCACCTTCTCCACCAAACCC
* * * *
2541814 TCCATGTCCTCCTACTCCACCAGCACCATTAGCGCTACCACTTCCACCACCTTTTGCACTAAACC
66 TCCATGTCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCCACCACCTTTTCCACCAAACC
* *
2541879 CTCCATGCCATCTTACATCACCAGCAACATTACCACTACCACTTCCACCACCTTTTCCACC-AAC
131 CTCCATGCCATCCTACATCACCAGCAACATTACCACTACCACTTCCACCACCTTTTCCACCAAAA
2541943 CCCTCCTTGACCTCCTACTCCACCTTTTCCACCAAATCCT
196 CCC-CCTTGACCTCCTACTCCACCTTTTCCACCAAATCCT
* * * * *
2541983 CCTTGTCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCCACCACCTTTTCCAGCAAACCC
1 CCTTGCCCTCCTACCCCACCAGCAACATCAGCACTACCACTTCCACCACCTTCTCCACCAAACCC
* *
2542048 TCCTTGTCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCCACCACCTTTTCCACCGAACC
66 TCCATGTCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCCACCACCTTTTCCACCAAACC
* * * * *
2542113 CTCCTTGCCCTCCTACTTCACCAGCAACATTAGCGCTACCACTTCCACCACCTTTTCCACCAAAA
131 CTCCATGCCATCCTACATCACCAGCAACATTACCACTACCACTTCCACCACCTTTTCCACCAAAA
* *
2542178 CCCCCTTGTCCTCCTATTCCACC
196 CCCCCTTGACCTCCTACTCCACC
2542201 AGCAACATCA
Statistics
Matches: 192, Mismatches: 25, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
234 187 0.97
235 5 0.03
ACGTcount: A:0.23, C:0.47, G:0.06, T:0.25
Consensus pattern (234 bp):
CCTTGCCCTCCTACCCCACCAGCAACATCAGCACTACCACTTCCACCACCTTCTCCACCAAACCC
TCCATGTCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCCACCACCTTTTCCACCAAACC
CTCCATGCCATCCTACATCACCAGCAACATTACCACTACCACTTCCACCACCTTTTCCACCAAAA
CCCCCTTGACCTCCTACTCCACCTTTTCCACCAAATCCT
Found at i:2542050 original size:66 final size:66
Alignment explanation
Indices: 2541962--2542914 Score: 1020
Period size: 66 Copynumber: 14.1 Consensus size: 66
2541952 ACCTCCTACT
* * *
2541962 CCACCTTTTCCACCAAATCCTCCTTGTCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCC
1 CCACCTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCC
2542027 A
66 A
* * *
2542028 CCACCTTTTCCAGCAAACCCTCCTTGTCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCC
1 CCACCTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCC
2542093 A
66 A
* *
2542094 CCACCTTTTCCACCGAACCCTCCTTGCCCTCCTACTTCACCAGCAACATTAGCGCTACCACTTCC
1 CCACCTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCC
2542159 A
66 A
* * * * *
2542160 CCACCTTTTCCACCAAAACCC-CCTTGTCCTCCTATTCCACCAGCAACATCAACGTTACCACTTC
1 CCACCTTTTCCACC-AAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTC
2542224 CA
65 CA
** * * ** * * * ** ** *
2542226 CCACCACTTCCACC-ACCTTTTCCACCTAACTCTCCTTGC-CCTCCTA-CTCCACCAGCAACATT
1 CCACCTTTTCCACCAAAC----CCTCCTTGCCCTCC-TACTCCACC-AGCAACATTAGC-GC--T
* * *
2542288 AGCGCTACCA
57 ACCACTTCCA
* *
2542298 CTTCCACCACCTTTCCCACCAAACCCTCCTTGTCCTCCTACTCCACCAGCAACATTAGCGCTACC
1 ------CCACCTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACC
2542363 ACTTCCA
60 ACTTCCA
* *
2542370 CCACCTTTTCCACCAAACTCTCCTTGCCCTCCTACTCCACCAGCAACATTAACGCTACCACTTCC
1 CCACCTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCC
2542435 A
66 A
* * *
2542436 CCACCTTTTCCACCAAACCCTCCATGCCCTCCTACTCCACCAGCAATATTAGCGCCACCACTTCC
1 CCACCTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCC
2542501 A
66 A
* * * *
2542502 CCACCTTTTCCACCAAAACCC-CCTTGTCCTCCTATTCCACCAGCAACATCAACATTACCACTTC
1 CCACCTTTTCCACC-AAACCCTCCTTGCCCTCCTACTCCACCAG------CAACATTAGCGC-T-
2542566 CACCACCACTTCCA
57 ----ACCACTTCCA
* *
2542580 CCACCTTTCCCACCAAACCCTCCTTGCCCTCCTACTCCACTAGCAACATTAGCGCTACCACTTCC
1 CCACCTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCC
2542645 A
66 A
* *
2542646 CCACCTTTCCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGTGCTACCACTTCC
1 CCACCTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCC
2542711 A
66 A
* * * *** *
2542712 CCACCTTTTCCACCAAACGCTCCTTGCCCTCCTACTCCACCTGCAGCATTAATACTACCACCTCC
1 CCACCTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCC
2542777 A
66 A
* * * *
2542778 CCACCTTTTCCACCAAACCCTCCTTGCCCTCCTACACCCCCAGCAACATTAGTGCTACCAATAT-
1 CCACCTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACT-TC
2542842 CA
65 CA
* * * * * *
2542844 CCACCTTTTCCACCAAAACCC-CCTTGTCCTCCTATTCCACCAGTAACATCAACGTTACCACTTC
1 CCACCTTTTCCACC-AAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTC
2542908 CA
65 CA
2542910 CCACC
1 CCACC
2542915 ACTTCCACTG
Statistics
Matches: 748, Mismatches: 102, Indels: 74
0.81 0.11 0.08
Matches are distributed among these distances:
64 2 0.00
65 1 0.00
66 586 0.78
67 18 0.02
68 2 0.00
69 17 0.02
70 2 0.00
71 1 0.00
72 35 0.05
74 4 0.01
75 19 0.03
77 6 0.01
78 53 0.07
79 2 0.00
ACGTcount: A:0.24, C:0.47, G:0.05, T:0.24
Consensus pattern (66 bp):
CCACCTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCC
A
Found at i:2542251 original size:12 final size:12
Alignment explanation
Indices: 2542216--2542242 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2542206 CATCAACGTT
2542216 ACCACTTCCACC
1 ACCACTTCCACC
2542228 ACCACTTCCACC
1 ACCACTTCCACC
2542240 ACC
1 ACC
2542243 TTTTCCACCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.59, G:0.00, T:0.15
Consensus pattern (12 bp):
ACCACTTCCACC
Found at i:2542356 original size:342 final size:342
Alignment explanation
Indices: 2541962--2542963 Score: 1700
Period size: 342 Copynumber: 2.9 Consensus size: 342
2541952 ACCTCCTACT
* * *
2541962 CCACCTTTTCCACCAAATCCTCCTTGTCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCC
1 CCACCTTTCCCACCAAACCCTCCTTGTCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCC
* * *
2542027 ACCACCTTTTCCAGCAAACCCTCCTTGTCCTCCTACTCCACCAGCAACATTAGCACTACCACTTC
66 ACCACCTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAACACTACCACTTC
* *
2542092 CACCACCTTTTCCACCGAACCCTCCTTGCCCTCCTACTTCACCAGCAACATTAGCGCTACCACTT
131 CACCACCTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTT
2542157 CCACCACCTTTTCCACCAAAACCCCCTTGTCCTCCTATTCCACCAGCAACATCAACGTTACCACT
196 CCACCACCTTTTCCACCAAAACCCCCTTGTCCTCCTATTCCACCAGCAACATCAACGTTACCACT
* *
2542222 TCCACCACCACTTCCACCACCTTTTCCACCTAACTCTCCTTGCCCTCCTACTCCACCAGCAACAT
261 TCCACCACCACTTCCACCACCTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACAT
2542287 TAGCGCTACCACTTCCA
326 TAGCGCTACCACTTCCA
2542304 CCACCTTTCCCACCAAACCCTCCTTGTCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCC
1 CCACCTTTCCCACCAAACCCTCCTTGTCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCC
* *
2542369 ACCACCTTTTCCACCAAACTCTCCTTGCCCTCCTACTCCACCAGCAACATTAACGCTACCACTTC
66 ACCACCTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAACACTACCACTTC
* * *
2542434 CACCACCTTTTCCACCAAACCCTCCATGCCCTCCTACTCCACCAGCAATATTAGCGCCACCACTT
131 CACCACCTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTT
*
2542499 CCACCACCTTTTCCACCAAAACCCCCTTGTCCTCCTATTCCACCAGCAACATCAACATTACCACT
196 CCACCACCTTTTCCACCAAAACCCCCTTGTCCTCCTATTCCACCAGCAACATCAACGTTACCACT
* *
2542564 TCCACCACCACTTCCACCACCTTTCCCACCAAACCCTCCTTGCCCTCCTACTCCACTAGCAACAT
261 TCCACCACCACTTCCACCACCTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACAT
2542629 TAGCGCTACCACTTCCA
326 TAGCGCTACCACTTCCA
* *
2542646 CCACCTTTCCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGTGCTACCACTTCC
1 CCACCTTTCCCACCAAACCCTCCTTGTCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCC
* * * * *
2542711 ACCACCTTTTCCACCAAACGCTCCTTGCCCTCCTACTCCACCTGCAGCATTAATACTACCACCTC
66 ACCACCTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAACACTACCACTTC
* * * *
2542776 CACCACCTTTTCCACCAAACCCTCCTTGCCCTCCTACACCCCCAGCAACATTAGTGCTACCAATA
131 CACCACCTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACT-
*
2542841 T-CACCACCTTTTCCACCAAAACCCCCTTGTCCTCCTATTCCACCAGTAACATCAACGTTACCAC
195 TCCACCACCTTTTCCACCAAAACCCCCTTGTCCTCCTATTCCACCAGCAACATCAACGTTACCAC
**
2542905 TTCCACCACCACTTCCACTGCCTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCA
260 TTCCACCACCACTTCCACCACCTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCA
2542964 CCACTTCCAC
Statistics
Matches: 620, Mismatches: 39, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
342 619 1.00
343 1 0.00
ACGTcount: A:0.24, C:0.47, G:0.05, T:0.24
Consensus pattern (342 bp):
CCACCTTTCCCACCAAACCCTCCTTGTCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCC
ACCACCTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAACACTACCACTTC
CACCACCTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTT
CCACCACCTTTTCCACCAAAACCCCCTTGTCCTCCTATTCCACCAGCAACATCAACGTTACCACT
TCCACCACCACTTCCACCACCTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACAT
TAGCGCTACCACTTCCA
Found at i:2542575 original size:12 final size:12
Alignment explanation
Indices: 2542558--2542584 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2542548 CATCAACATT
2542558 ACCACTTCCACC
1 ACCACTTCCACC
2542570 ACCACTTCCACC
1 ACCACTTCCACC
2542582 ACC
1 ACC
2542585 TTTCCCACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.59, G:0.00, T:0.15
Consensus pattern (12 bp):
ACCACTTCCACC
Found at i:2542922 original size:276 final size:263
Alignment explanation
Indices: 2541962--2542914 Score: 1192
Period size: 276 Copynumber: 3.5 Consensus size: 263
2541952 ACCTCCTACT
* * * * *
2541962 CCACCTTTTCCACCAAATCCTCCTTGTCCTCCTACTCCACCAGCAACATTAGCACTACCACTTCC
1 CCACCTTTTCCACCAAACCCTCCTTGCCCTCCTACACCACCAGCAACATTAGCGCTACCAATTCC
* *
2542027 ACCACCTTTTCCAGCAAACCCTCCTTGTCCTCCTACTCCACCAGCAACATTAGCACTACCACTTC
66 ACCACCTTTCCCACCAAACCCTCCTTGTCCTCCTACTCCACCAGCAACATTAGCACTACCACTTC
* *
2542092 CACCACCTTTTCCACCGAACCCTCCTTGCCCTCCTACTTCACCAGCAACATTAGCGCTACCACTT
131 CACCACCTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTT
* * * *
2542157 CCACCACCTTTTCCACCAAAACCCCCTTGTCCTCCTATTCCACCAGCAACATCAACGTTACCACT
196 CCACCACCTTTTCCACC-AAACCTCCTTGCCCTCCTACTCCACCAGCAACATTAA---T---AC-
2542222 TCCACCACCACTTCCA
253 T--ACCA-C-C-TCCA
* * * *
2542238 CCACCTTTTCCACCTAACTCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCC
1 CCACCTTTTCCACCAAACCCTCCTTGCCCTCCTACACCACCAGCAACATTAGCGCTACCAATTCC
*
2542303 ACCACCTTTCCCACCAAACCCTCCTTGTCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTC
66 ACCACCTTTCCCACCAAACCCTCCTTGTCCTCCTACTCCACCAGCAACATTAGCACTACCACTTC
* *
2542368 CACCACCTTTTCCACCAAACTCTCCTTGCCCTCCTACTCCACCAGCAACATTAACGCTACCACTT
131 CACCACCTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTT
* * *** * *
2542433 CCACCACCTTTTCCACCAAACCCTCCATGCCCTCCTACTCCACCAGCAATATTAGCGCCACCACT
196 CCACCACCTTTTCCACCAAA-CCTCCTTGCCCTCCTACTCCACCAGCAACATTAATACTACCACC
2542498 TCCA
260 TCCA
* * * *
2542502 CCACCTTTTCCACCAAAACCC-CCTTGTCCTCCTATTCCACCAGCAACATCAACATTACCACTTC
1 CCACCTTTTCCACC-AAACCCTCCTTGCCCTCCTA---CACCA-C--CAGCAACATTAGCGC-T-
* *
2542566 CACCACCACTTCCACCACCTTTCCCACCAAACCCTCCTTGCCCTCCTACTCCACTAGCAACATTA
57 -ACCA--A-TTCCACCACCTTTCCCACCAAACCCTCCTTGTCCTCCTACTCCACCAGCAACATTA
* *
2542631 GCGCTACCACTTCCACCACCTTTCCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATT
118 GCACTACCACTTCCACCACCTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATT
* * *
2542696 AGTGCTACCACTTCCACCACCTTTTCCACCAAACGCTCCTTGCCCTCCTACTCCACCTGCAGCAT
183 AGCGCTACCACTTCCACCACCTTTTCCACCAAAC-CTCCTTGCCCTCCTACTCCACCAGCAACAT
2542761 TAATACTACCACCTCCA
247 TAATACTACCACCTCCA
* *
2542778 CCACCTTTTCCACCAAACCCTCCTTGCCCTCCTACACCCCCAGCAACATTAGTGCTACCAATAT-
1 CCACCTTTTCCACCAAACCCTCCTTGCCCTCCTACACCACCAGCAACATTAGCGCTACCAAT-TC
* * * * * **
2542842 CACCACCTTTTCCACCAAAACCC-CCTTGTCCTCCTATTCCACCAGTAACATCAACGTTACCACT
65 CACCACCTTTCCCACC-AAACCCTCCTTGTCCTCCTACTCCACCAGCAACATTAGCACTACCACT
2542906 TCCACCACC
129 TCCACCACC
2542915 ACTTCCACTG
Statistics
Matches: 599, Mismatches: 60, Indels: 48
0.85 0.08 0.07
Matches are distributed among these distances:
264 89 0.15
265 12 0.02
266 1 0.00
267 12 0.02
268 1 0.00
269 1 0.00
270 24 0.04
271 1 0.00
272 1 0.00
273 8 0.01
275 10 0.02
276 439 0.73
ACGTcount: A:0.24, C:0.47, G:0.05, T:0.24
Consensus pattern (263 bp):
CCACCTTTTCCACCAAACCCTCCTTGCCCTCCTACACCACCAGCAACATTAGCGCTACCAATTCC
ACCACCTTTCCCACCAAACCCTCCTTGTCCTCCTACTCCACCAGCAACATTAGCACTACCACTTC
CACCACCTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTT
CCACCACCTTTTCCACCAAACCTCCTTGCCCTCCTACTCCACCAGCAACATTAATACTACCACCT
CCA
Found at i:2548287 original size:28 final size:29
Alignment explanation
Indices: 2548254--2548311 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
2548244 TAATATATTT
* * *
2548254 TTTAATGATTATATTA-TTAAATTACATA
1 TTTAATCATTATATAACATAAATTACATA
*
2548282 TTTAATCTTTATATAACATAAATTACATA
1 TTTAATCATTATATAACATAAATTACATA
2548311 T
1 T
2548312 CGCATCATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (29 bp):
TTTAATCATTATATAACATAAATTACATA
Found at i:2555207 original size:146 final size:147
Alignment explanation
Indices: 2554980--2555275 Score: 386
Period size: 146 Copynumber: 2.0 Consensus size: 147
2554970 GGGTCCAAAT
* * * * *
2554980 ATGCTATCAACCCCAAGACTGCTTTTGCCTATTTAAACACAATTCAATCATTCAACATTAGAATA
1 ATGCTATCAACCCCAAGACTGCTGTTGCCTAATGAAACACAATTCAATCATTCAACATTACAACA
** * *
2555045 CTTGATTTCGACTT-AAAATCCAGCAACAATACAAGCACAGAAGTAGAAAAATTCATCCCTCCAC
66 CTCAATTTCGACTTAAAAATCCAGCAACAATACAAGCACAAAAGTA-AAAAATTCATCCCTACA-
*
2555109 AA-GAACAAATTCAAACAA
129 AACCAACAAATTCAAACAA
**
2555127 ATGCTATCAACCCCAAGACTGCTGTT-CC-AATGAAA-ACAATTTTCAATCATTCAGTATTACAA
1 ATGCTATCAACCCCAAGACTGCTGTTGCCTAATGAAACACAA--TTCAATCATTCAACATTACAA
* **
2555189 CACTCAATTTCTACTTAAAAATCCAGCAACAATACAAGCACAAAAGTAAATTATTCATCCCTACA
64 CACTCAATTTCGACTTAAAAATCCAGCAACAATACAAGCACAAAAGTAAAAAATTCATCCCTACA
2555254 AACCAACAAATTCAAACAA
129 AACCAACAAATTCAAACAA
2555273 ATG
1 ATG
2555276 AGAATAATAA
Statistics
Matches: 130, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
144 4 0.03
145 7 0.05
146 64 0.49
147 55 0.42
ACGTcount: A:0.43, C:0.25, G:0.08, T:0.25
Consensus pattern (147 bp):
ATGCTATCAACCCCAAGACTGCTGTTGCCTAATGAAACACAATTCAATCATTCAACATTACAACA
CTCAATTTCGACTTAAAAATCCAGCAACAATACAAGCACAAAAGTAAAAAATTCATCCCTACAAA
CCAACAAATTCAAACAA
Found at i:2557874 original size:18 final size:18
Alignment explanation
Indices: 2557851--2557888 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
2557841 ACAAGAATTT
*
2557851 TTATTTGAGTTATTCAAA
1 TTATTTGAGTTAATCAAA
2557869 TTATTTGAGTTAATCAAA
1 TTATTTGAGTTAATCAAA
2557887 TT
1 TT
2557889 GTAAAATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.05, G:0.11, T:0.50
Consensus pattern (18 bp):
TTATTTGAGTTAATCAAA
Found at i:2560343 original size:16 final size:16
Alignment explanation
Indices: 2560322--2560375 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 16
2560312 TTTTTATACA
2560322 AATTTTATATATTTTT
1 AATTTTATATATTTTT
*
2560338 AA-TTT-TATATTTAT
1 AATTTTATATATTTTT
2560352 -ATTTTATAGT-TTTTAT
1 AATTTTATA-TATTTT-T
2560368 AATTTTAT
1 AATTTTAT
2560376 TTTATTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
13 1 0.03
14 11 0.35
15 8 0.26
16 4 0.13
17 7 0.23
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (16 bp):
AATTTTATATATTTTT
Found at i:2560355 original size:29 final size:29
Alignment explanation
Indices: 2560323--2560380 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
2560313 TTTTATACAA
2560323 ATTTTATA-TATTTT-TAATTTTATATTTAT
1 ATTTTATAGT-TTTTATAATTTTAT-TTTAT
2560352 ATTTTATAGTTTTTATAATTTTATTTTAT
1 ATTTTATAGTTTTTATAATTTTATTTTAT
2560381 TTAATAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 17 0.63
30 10 0.37
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (29 bp):
ATTTTATAGTTTTTATAATTTTATTTTAT
Found at i:2560451 original size:16 final size:18
Alignment explanation
Indices: 2560406--2560452 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
2560396 GATTGTTTTA
* *
2560406 TTTTCATAATTCTATAAT
1 TTTTCAAAATTATATAAT
*
2560424 TTTTCAATATTATATAA-
1 TTTTCAAAATTATATAAT
2560441 TTTT-AAAATTAT
1 TTTTCAAAATTAT
2560453 GAATATTTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 7 0.28
17 4 0.16
18 14 0.56
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTTCAAAATTATATAAT
Found at i:2560563 original size:17 final size:15
Alignment explanation
Indices: 2560543--2560597 Score: 53
Period size: 17 Copynumber: 3.6 Consensus size: 15
2560533 TTTATTTTGG
2560543 ATTTAAATTTGTATACA
1 ATTTAAATTT-TATA-A
2560560 ATTTAAATCTATTATAA
1 ATTTAAAT-T-TTATAA
2560577 ATTTAAA-TTTA-AA
1 ATTTAAATTTTATAA
2560590 A-TTAAATT
1 ATTTAAATT
2560598 AAATGTCCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
12 5 0.14
13 4 0.11
14 3 0.09
15 1 0.03
17 16 0.46
18 5 0.14
19 1 0.03
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (15 bp):
ATTTAAATTTTATAA
Found at i:2561246 original size:29 final size:28
Alignment explanation
Indices: 2561214--2561422 Score: 117
Period size: 30 Copynumber: 7.1 Consensus size: 28
2561204 AAAATTACCA
2561214 TTTTACTCCCAAACTTTCCAAAATCCCAT
1 TTTTAC-CCCAAACTTTCCAAAATCCCAT
* ** *
2561243 TTTTAACCCTGA-TTTCACCAAAAATTACCA-
1 TTTTACCCCAAACTTT--CC-AAAA-TCCCAT
2561273 TTTTACCCCTAAACTTTCCAAAATCCCAT
1 TTTTACCCC-AAACTTTCCAAAATCCCAT
*
2561302 TTTTAACCCC-AA-TTTCACTAAAAATTACCA-
1 TTTT-ACCCCAAACTTTC-C--AAAA-TCCCAT
2561332 TTTTACCCCTAAACTTTCCAAAATCCCAT
1 TTTTACCCC-AAACTTTCCAAAATCCCAT
* * * *
2561361 TTTTAACCTC-GATTTTACCAAAAATTACCA-
1 TTTT-ACCCCAAACTTT-CC-AAAA-TCCCAT
* * *
2561391 TTTTACCTCGAACTTTCCAAAATCTCAT
1 TTTTACCCCAAACTTTCCAAAATCCCAT
2561419 TTTT
1 TTTT
2561423 TAACCCTAAT
Statistics
Matches: 140, Mismatches: 18, Indels: 45
0.69 0.09 0.22
Matches are distributed among these distances:
27 10 0.07
28 27 0.19
29 37 0.26
30 43 0.31
31 16 0.11
32 7 0.05
ACGTcount: A:0.33, C:0.29, G:0.01, T:0.36
Consensus pattern (28 bp):
TTTTACCCCAAACTTTCCAAAATCCCAT
Found at i:2561443 original size:58 final size:58
Alignment explanation
Indices: 2561202--2561632 Score: 484
Period size: 59 Copynumber: 7.4 Consensus size: 58
2561192 CTAAACCATT
*
2561202 CAAAAATTACCATTTTACTCCCAAACTTTCCAAAATCCCATTTTTAACCCTGATTTCAC
1 CAAAAATTACCATTTTAC-CCCGAACTTTCCAAAATCCCATTTTTAACCCTGATTTCAC
* **
2561261 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCCCAATTTCAC
1 CAAAAATTACCATTTTACCCC-GAACTTTCCAAAATCCCATTTTTAACCCTGATTTCAC
* * *
2561320 TAAAAATTACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTAA-CCTCGATTTTAC
1 CAAAAATTACCATTTTACCCC-GAACTTTCCAAAATCCCATTTTTAACCCT-GATTTCAC
* * * *
2561379 CAAAAATTACCATTTTACCTCGAACTTTCCAAAATCTCATTTTTTAACCCTAATTTTAC
1 CAAAAATTACCATTTTACCCCGAACTTTCCAAAATCCCA-TTTTTAACCCTGATTTCAC
* * * * * *
2561438 C-AAAATTATCATTTTACCCCCGAAC-TTCCTAAAATCTCGTTTTTAACCCCGATTTTAT
1 CAAAAATTACCATTTTA-CCCCGAACTTTCC-AAAATCCCATTTTTAACCCTGATTTCAC
* *
2561496 C-AAAATTACCGTTTTACCCCCGAA-TTTCCCAAAATCCCATTTTCAA-CCTCGATTTCAC
1 CAAAAATTACCATTTTA-CCCCGAACTTT-CCAAAATCCCATTTTTAACCCT-GATTTCAC
* * *
2561554 CAAAAATTACCATTTTACCCCTGAACATTCCAAAATCCCATTTTTAA-TCTCGGTTTCAC
1 CAAAAATTACCATTTTACCCC-GAACTTTCCAAAATCCCATTTTTAACCCT-GATTTCAC
2561613 C-AAAATTA-CATTTTTACCCC
1 CAAAAATTACCA-TTTTACCCC
2561633 CGAAAGTTAA
Statistics
Matches: 329, Mismatches: 30, Indels: 27
0.85 0.08 0.07
Matches are distributed among these distances:
57 4 0.01
58 119 0.36
59 201 0.61
60 5 0.02
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (58 bp):
CAAAAATTACCATTTTACCCCGAACTTTCCAAAATCCCATTTTTAACCCTGATTTCAC
Found at i:2561528 original size:29 final size:29
Alignment explanation
Indices: 2561204--2561574 Score: 144
Period size: 29 Copynumber: 12.7 Consensus size: 29
2561194 AAACCATTCA
* *
2561204 AAAATTACCATTTTACTCCCAAACTTT-CC
1 AAAATTACCATTTTACCCCCGAA-TTTCCC
* * *
2561233 AAAA-TCCCATTTTTAACCCTG-ATTTCACC
1 AAAATTACCA-TTTTACCCCCGAATTTC-CC
**
2561262 AAAAATTACCATTTTACCCCTAAACTTT-CC
1 -AAAATTACCATTTTACCCCCGAA-TTTCCC
* * *
2561292 AAAA-TCCCATTTTTAACCCC-AATTTCACTA
1 AAAATTACCA-TTTTACCCCCGAATTTC-C-C
**
2561322 AAAATTACCATTTTACCCCTAAACTTT-CC
1 AAAATTACCATTTTACCCCCGAA-TTTCCC
* * * * *
2561351 AAAA-TCCCATTTTTAACCTCGATTTTACCA
1 AAAATTACCA-TTTTACCCCCGAATTT-CCC
*
2561381 AAAATTACCATTTTA-CCTCGAACTTT-CC
1 AAAATTACCATTTTACCCCCGAA-TTTCCC
* * *
2561409 AAAA-T-CTCATTTTTTA-ACCCTAATTTTACC
1 AAAATTAC-CA--TTTTACCCCCGAA-TTTCCC
* * *
2561439 AAAATTATCATTTTACCCCCGAACTTCCT
1 AAAATTACCATTTTACCCCCGAATTTCCC
** * * **
2561468 AAAATCT-CGTTTTTAACCCCGATTTTATC
1 AAAAT-TACCATTTTACCCCCGAATTTCCC
*
2561497 AAAATTACCGTTTTACCCCCGAATTTCCC
1 AAAATTACCATTTTACCCCCGAATTTCCC
* * *
2561526 AAAA-TCCCATTTTCAACCTCG-ATTTCACC
1 AAAATTACCATTTT-ACCCCCGAATTTC-CC
2561555 AAAAATTACCATTTTACCCC
1 -AAAATTACCATTTTACCCC
2561575 TGAACATTCC
Statistics
Matches: 252, Mismatches: 58, Indels: 63
0.68 0.16 0.17
Matches are distributed among these distances:
26 1 0.00
27 9 0.04
28 36 0.14
29 114 0.45
30 60 0.24
31 26 0.10
32 6 0.02
ACGTcount: A:0.33, C:0.30, G:0.02, T:0.35
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCCGAATTTCCC
Found at i:2561633 original size:117 final size:117
Alignment explanation
Indices: 2561202--2561636 Score: 526
Period size: 117 Copynumber: 3.7 Consensus size: 117
2561192 CTAAACCATT
*
2561202 CAAAAATTACCATTTTACTCCC-AAACTTTCCAAAATCCCATTTTTAACCCTGATTTCACCAAAA
1 CAAAAATTACCATTTTAC-CCCTAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAA
**
2561266 ATTACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCCCAATTTCAC
65 ATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAA-CCCAATTTCAC
* * *
2561320 TAAAAATTACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCTCGATTTTACCAAAAA
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAA
* * *
2561385 TTACCATTTTA-CCTCGAACTTTCCAAAATCTCATTTTTTAACCCTAATTTTAC
66 TTACCATTTTACCCCCGAACTTTCCAAAATCCCA-TTTTTAACCC-AATTTCAC
* ** * * * *
2561438 C-AAAATTATCATTTTACCCCCGAAC-TTCCTAAAATCTCGTTTTTAACCCCGATTTTATC-AAA
1 CAAAAATTACCATTTTACCCCTAAACTTTCC-AAAATCCCATTTTTAACCCCGATTTCACCAAAA
* * *
2561500 ATTACCGTTTTACCCCCGAA-TTTCCCAAAATCCCATTTTCAACCTCGATTTCAC
65 ATTACCATTTTACCCCCGAACTTT-CCAAAATCCCATTTTTAACC-CAATTTCAC
* * * * *
2561554 CAAAAATTACCATTTTACCCCTGAACATTCCAAAATCCCATTTTTAATCTCGGTTTCACC-AAAA
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAA
2561618 TTA-CATTTTTACCCCCGAA
66 TTACCA-TTTTACCCCCGAA
2561637 AGTTAAAAAT
Statistics
Matches: 274, Mismatches: 33, Indels: 21
0.84 0.10 0.06
Matches are distributed among these distances:
116 37 0.14
117 151 0.55
118 86 0.31
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (117 bp):
CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAA
TTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCAATTTCAC
Found at i:2563884 original size:17 final size:18
Alignment explanation
Indices: 2563856--2563889 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2563846 AAAAATTGTT
*
2563856 TTTAATTTTTATTATTTC
1 TTTAATTTTTATGATTTC
2563874 TTTAA-TTTTATGATTT
1 TTTAATTTTTATGATTT
2563890 TTTTTGAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTAATTTTTATGATTTC
Found at i:2566688 original size:25 final size:25
Alignment explanation
Indices: 2566635--2566689 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
2566625 ATAGCATATT
* *
2566635 ATATTTAAATATATATAATATTAAT
1 ATATTTAAATATATATAATAATAAA
*
2566660 ATATTTTAATATA-ATAATACATAAA
1 ATATTTAAATATATATAATA-ATAAA
2566685 ATATT
1 ATATT
2566690 ATATTTCTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 6 0.23
25 20 0.77
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATTTAAATATATATAATAATAAA
Found at i:2566780 original size:24 final size:25
Alignment explanation
Indices: 2566748--2566804 Score: 107
Period size: 24 Copynumber: 2.3 Consensus size: 25
2566738 CATGAAACAT
2566748 ATTATGAAGCATCTTAAAG-TTTTC
1 ATTATGAAGCATCTTAAAGTTTTTC
2566772 ATTATGAAGCATCTTAAAGTTTTTC
1 ATTATGAAGCATCTTAAAGTTTTTC
2566797 ATTATGAA
1 ATTATGAA
2566805 ACATAATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 19 0.59
25 13 0.41
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (25 bp):
ATTATGAAGCATCTTAAAGTTTTTC
Found at i:2569126 original size:18 final size:17
Alignment explanation
Indices: 2569105--2569138 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2569095 TTAAGGTTTA
*
2569105 AATTAATTTTAATTTTTT
1 AATTAAATTT-ATTTTTT
2569123 AATTAAATTTATTTTT
1 AATTAAATTTATTTTT
2569139 ATTTAATTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
AATTAAATTTATTTTTT
Found at i:2569401 original size:30 final size:31
Alignment explanation
Indices: 2569344--2569402 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2569334 GTAGTAAAAG
*
2569344 TAAAATTATATTTTAATCTCGTTAAAAATGA
1 TAAAATTATAATTTAATCTCGTTAAAAATGA
* *
2569375 TAAAATTTTAATTTAAT-TCTTTAAAAAT
1 TAAAATTATAATTTAATCTCGTTAAAAAT
2569403 TATATTATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (31 bp):
TAAAATTATAATTTAATCTCGTTAAAAATGA
Found at i:2570093 original size:23 final size:23
Alignment explanation
Indices: 2570067--2570111 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2570057 AGTTAAATCT
* *
2570067 AAAATTTAAAATCTAAAAAATAA
1 AAAAATTAAAATCCAAAAAATAA
*
2570090 AAAAATTAAATTCCAAAAAATA
1 AAAAATTAAAATCCAAAAAATA
2570112 CAAGTACAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (23 bp):
AAAAATTAAAATCCAAAAAATAA
Found at i:2577346 original size:16 final size:16
Alignment explanation
Indices: 2577325--2577355 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2577315 AATTTTTGTT
*
2577325 TCTTAATTCGATTGAG
1 TCTTAACTCGATTGAG
2577341 TCTTAACTCGATTGA
1 TCTTAACTCGATTGA
2577356 CATGAACATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (16 bp):
TCTTAACTCGATTGAG
Found at i:2579096 original size:15 final size:16
Alignment explanation
Indices: 2579070--2579111 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
2579060 ATTCATTATG
*
2579070 TTAAATTAAAATTAAA
1 TTAAACTAAAATTAAA
2579086 TTAAA-TAAAATTAAA
1 TTAAACTAAAATTAAA
*
2579101 CTAAACTAAAA
1 TTAAACTAAAA
2579112 GTGATTGAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (16 bp):
TTAAACTAAAATTAAA
Found at i:2598443 original size:21 final size:23
Alignment explanation
Indices: 2598400--2598446 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
2598390 TTGATTTCTT
*
2598400 TTCCTATTGTGTATTAGATGTTTC
1 TTCCTATTATGTATTAGA-GTTTC
2598424 TTCCTATTATGTATT-G-GTTTC
1 TTCCTATTATGTATTAGAGTTTC
2598445 TT
1 TT
2598447 AATTCTGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 7 0.32
23 1 0.05
24 14 0.64
ACGTcount: A:0.15, C:0.13, G:0.15, T:0.57
Consensus pattern (23 bp):
TTCCTATTATGTATTAGAGTTTC
Found at i:2602544 original size:4 final size:5
Alignment explanation
Indices: 2602516--2602547 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
2602506 TTGTTATCTT
2602516 TTGCC TTGCC TTGCC TTGCC TTG-C TTG-C TTGC
1 TTGCC TTGCC TTGCC TTGCC TTGCC TTGCC TTGC
2602548 AGATTTGACT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 8 0.31
5 18 0.69
ACGTcount: A:0.00, C:0.34, G:0.22, T:0.44
Consensus pattern (5 bp):
TTGCC
Found at i:2610584 original size:24 final size:24
Alignment explanation
Indices: 2610557--2610619 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
2610547 AAAAAAATAT
2610557 TAAATATTTTAAAAATTA-ATTATA
1 TAAATATTTTAAAAATTATATT-TA
*
2610581 TAAACT-TATT-AAAATTATATTTA
1 TAAA-TATTTTAAAAATTATATTTA
*
2610604 TAAATATTATAAAAAT
1 TAAATATTTTAAAAAT
2610620 ATAAAAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
22 1 0.03
23 15 0.47
24 15 0.47
25 1 0.03
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
TAAATATTTTAAAAATTATATTTA
Found at i:2611336 original size:17 final size:18
Alignment explanation
Indices: 2611314--2611413 Score: 53
Period size: 18 Copynumber: 5.3 Consensus size: 18
2611304 TATTAGAATT
2611314 TTTATAT-TTTTATAATA
1 TTTATATATTTTATAATA
*
2611331 TTTATA-AGTTTATATCAATT
1 TTTATATA-TTT-TAT-AATA
*
2611351 TTCATATATTAATTTTTTAATA
1 TT--TATA-T-ATTTTATAATA
* * *
2611373 TTTA-ATGTTTTTTATATG
1 TTTATATATTTTATA-ATA
*
2611391 TTTATATATTTTATAATT
1 TTTATATATTTTATAATA
2611409 TTTAT
1 TTTAT
2611414 GATTTTTAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 21
0.69 0.09 0.23
Matches are distributed among these distances:
17 13 0.20
18 17 0.27
19 12 0.19
20 7 0.11
22 9 0.14
23 2 0.03
24 3 0.05
25 1 0.02
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (18 bp):
TTTATATATTTTATAATA
Found at i:2614003 original size:7 final size:7
Alignment explanation
Indices: 2613991--2614015 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2613981 ATAGAAAATG
2613991 AATTTAA
1 AATTTAA
2613998 AATTTAA
1 AATTTAA
2614005 AATTTAA
1 AATTTAA
2614012 AATT
1 AATT
2614016 AATTTACGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
AATTTAA
Found at i:2617420 original size:11 final size:11
Alignment explanation
Indices: 2617406--2617431 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2617396 ATTTTTTTCT
2617406 TGTTTTTATAG
1 TGTTTTTATAG
2617417 TGTTTTTATAG
1 TGTTTTTATAG
2617428 TGTT
1 TGTT
2617432 AATCGCCTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.19, T:0.65
Consensus pattern (11 bp):
TGTTTTTATAG
Found at i:2629630 original size:21 final size:21
Alignment explanation
Indices: 2629604--2629672 Score: 66
Period size: 26 Copynumber: 3.0 Consensus size: 21
2629594 ATAAACAATA
2629604 TAATGATTTTGCCTTTTAACT
1 TAATGATTTTGCCTTTTAACT
*
2629625 TAATGACATAATTTTACCTTTTAACT
1 TAATG-----ATTTTGCCTTTTAACT
* *
2629651 TAATGGTTTTGACTTTTAACT
1 TAATGATTTTGCCTTTTAACT
2629672 T
1 T
2629673 TAGAAAGTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
21 19 0.49
26 20 0.51
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.51
Consensus pattern (21 bp):
TAATGATTTTGCCTTTTAACT
Found at i:2643429 original size:16 final size:16
Alignment explanation
Indices: 2643408--2643439 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2643398 TAATTAATTC
*
2643408 ATATTTGTTATATATA
1 ATATTTGCTATATATA
2643424 ATATTTGCTATATATA
1 ATATTTGCTATATATA
2643440 CTTATTAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (16 bp):
ATATTTGCTATATATA
Found at i:2644243 original size:14 final size:14
Alignment explanation
Indices: 2644226--2644252 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2644216 TTAAATTAAA
2644226 ATTATTAAAATTTC
1 ATTATTAAAATTTC
2644240 ATTATTAAAATTT
1 ATTATTAAAATTT
2644253 AAAGTTAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTATTAAAATTTC
Found at i:2645326 original size:18 final size:17
Alignment explanation
Indices: 2645287--2645325 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2645277 GTTTCAACTA
*
2645287 TAAAACATTTATCTTTT
1 TAAAACAATTATCTTTT
*
2645304 TAAAACAATTATTTTTT
1 TAAAACAATTATCTTTT
2645321 TAAAA
1 TAAAA
2645326 AAAATGATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.49
Consensus pattern (17 bp):
TAAAACAATTATCTTTT
Found at i:2646816 original size:57 final size:56
Alignment explanation
Indices: 2646718--2646826 Score: 146
Period size: 57 Copynumber: 1.9 Consensus size: 56
2646708 AGACAATTCA
* * * *
2646718 TTGTTGAACCTGTCTTTGATATTGGTGAATGGAAGGCTTTAATGGCTGAAGACCCT
1 TTGTTGAACCAGTCTCTGATATTGATGAATGGAAGGCTTTAATGGCTAAAGACCCT
* * *
2646774 TTGTTGAACTCAGTCTCTGATATTGATGAGTGGAGGGTTTTAATGGCTAAAGA
1 TTGTTGAAC-CAGTCTCTGATATTGATGAATGGAAGGCTTTAATGGCTAAAGA
2646827 TCGGAAACTA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
56 9 0.20
57 36 0.80
ACGTcount: A:0.25, C:0.12, G:0.28, T:0.36
Consensus pattern (56 bp):
TTGTTGAACCAGTCTCTGATATTGATGAATGGAAGGCTTTAATGGCTAAAGACCCT
Found at i:2649129 original size:61 final size:59
Alignment explanation
Indices: 2649055--2649229 Score: 190
Period size: 60 Copynumber: 2.9 Consensus size: 59
2649045 TCGAACTTGA
* * *
2649055 CATTTTTTT-TAATTTGGTATCTAAACTTTTTGTTGATCCAATTTGATACCTGAACATGG
1 CATTTTTTTCTAATTTGGTACCTAAACTTTTT-TTAATCCAATTTGATACCTAAACATGG
* * * **
2649114 CATTCTTTTTCTAATTTGGCACCTCAACTTTTTTTAATCCAATTTGGTACCTAAATTTGG
1 CATT-TTTTTCTAATTTGGTACCTAAACTTTTTTTAATCCAATTTGATACCTAAACATGG
* * * * *
2649174 CATTTTATCCTAATTTTGTACCTAAGCTTTTTTTTATATTCAATTTGATACCTAAA
1 CATTTTTTTCTAATTTGGTACCTAAAC-TTTTTTTA-ATCCAATTTGATACCTAAA
2649230 TTTATTAGAT
Statistics
Matches: 96, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
59 21 0.22
60 39 0.41
61 36 0.38
ACGTcount: A:0.26, C:0.17, G:0.10, T:0.48
Consensus pattern (59 bp):
CATTTTTTTCTAATTTGGTACCTAAACTTTTTTTAATCCAATTTGATACCTAAACATGG
Found at i:2649230 original size:61 final size:60
Alignment explanation
Indices: 2649064--2649232 Score: 171
Period size: 61 Copynumber: 2.8 Consensus size: 60
2649054 ACATTTTTTT
* * * * * ** * *
2649064 TAATTTGGTATCTAAACTTTTTGTTGATCCAATTTGATACCTGAACATGGCATTCTTTTTC
1 TAATTTGGCACCTCAACTTTTT-TTAATCCAATTTGATACCTAAATTTGGCATTCTTATCC
*
2649125 TAATTTGGCACCTCAACTTTTTTTAATCCAATTTGGTACCTAAATTTGGCATT-TTATCC
1 TAATTTGGCACCTCAACTTTTTTTAATCCAATTTGATACCTAAATTTGGCATTCTTATCC
* * *
2649184 TAATTTTGTACCT-AAGCTTTTTTTTATATTCAATTTGATACCTAAATTT
1 TAATTTGGCACCTCAA-C-TTTTTTTA-ATCCAATTTGATACCTAAATTT
2649233 ATTAGATATT
Statistics
Matches: 91, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
58 2 0.02
59 16 0.18
60 34 0.37
61 39 0.43
ACGTcount: A:0.26, C:0.17, G:0.10, T:0.47
Consensus pattern (60 bp):
TAATTTGGCACCTCAACTTTTTTTAATCCAATTTGATACCTAAATTTGGCATTCTTATCC
Found at i:2649497 original size:31 final size:30
Alignment explanation
Indices: 2649462--2649567 Score: 98
Period size: 28 Copynumber: 3.6 Consensus size: 30
2649452 AAAAAAAAAA
2649462 TCAAGTTTAGGTACCAAATTAGGAAAAAGT
1 TCAAGTTTAGGTACCAAATTAGGAAAAAGT
2649492 GTCAAGTTT-GAGTACCAAATT-GGACAAAA--
1 -TCAAGTTTAG-GTACCAAATTAGGA-AAAAGT
**
2649521 AAAAGTTTAGGTACCAAATTA-GAAAAAG-
1 TCAAGTTTAGGTACCAAATTAGGAAAAAGT
* * *
2649549 TCAGGTTCAGATACCAAAT
1 TCAAGTTTAGGTACCAAAT
2649568 ATTATATTAA
Statistics
Matches: 63, Mismatches: 7, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
27 4 0.06
28 32 0.51
29 1 0.02
30 4 0.06
31 22 0.35
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (30 bp):
TCAAGTTTAGGTACCAAATTAGGAAAAAGT
Found at i:2649534 original size:28 final size:29
Alignment explanation
Indices: 2649464--2649548 Score: 88
Period size: 31 Copynumber: 2.9 Consensus size: 29
2649454 AAAAAAAATC
**
2649464 AAGTTTAGGTACCAAATTAGGAAAAAGTGTC
1 AAGTTTAGGTACCAAATTAGGAAAAA--GAA
2649495 AAGTTT-GAGTACCAAATT-GGACAAAA-AA
1 AAGTTTAG-GTACCAAATTAGGA-AAAAGAA
2649523 AAGTTTAGGTACCAAATTA-GAAAAAG
1 AAGTTTAGGTACCAAATTAGGAAAAAG
2649549 TCAGGTTCAG
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
27 4 0.09
28 18 0.38
29 1 0.02
30 4 0.09
31 20 0.43
ACGTcount: A:0.47, C:0.09, G:0.20, T:0.24
Consensus pattern (29 bp):
AAGTTTAGGTACCAAATTAGGAAAAAGAA
Found at i:2649547 original size:92 final size:92
Alignment explanation
Indices: 2649376--2649547 Score: 213
Period size: 92 Copynumber: 1.9 Consensus size: 92
2649366 TAAAAAAAAA
***
2649376 TTAGGTACCAAATTAAGAAAAAAAGCTAAGTTCAAGTACCAAATTGGACCCCAAAAAGTTTGAAG
1 TTAGGTACCAAATTAAGAAAAAAAGCTAAGTTCAAGTACCAAATTGGACAAAAAAAAGTTTGAAG
* *
2649441 TACCAACTTTAAAAAAAAAAATCAAGT
66 TACCAAATTGAAAAAAAAAAATCAAGT
* ** ** *
2649468 TTAGGTACCAAATTAGGAAAAAGTG-TCAAGTTTGAGTACCAAATTGGACAAAAAAAAGTTT-AG
1 TTAGGTACCAAATTAAGAAAAAAAGCT-AAGTTCAAGTACCAAATTGGACAAAAAAAAGTTTGAA
2649531 GTACCAAATTAGAAAAA
65 GTACCAAATT-GAAAAA
2649548 GTCAGGTTCA
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
91 11 0.16
92 56 0.84
ACGTcount: A:0.49, C:0.13, G:0.16, T:0.23
Consensus pattern (92 bp):
TTAGGTACCAAATTAAGAAAAAAAGCTAAGTTCAAGTACCAAATTGGACAAAAAAAAGTTTGAAG
TACCAAATTGAAAAAAAAAAATCAAGT
Found at i:2660158 original size:16 final size:18
Alignment explanation
Indices: 2660119--2660160 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
2660109 AATTTATGTA
2660119 ATATTT-TATATTATAAT
1 ATATTTATATATTATAAT
*
2660136 ATTTTTATATATTA-AAT
1 ATATTTATATATTATAAT
2660153 A-ATTTATA
1 ATATTTATA
2660161 ACATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 9 0.41
18 7 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATATTTATATATTATAAT
Found at i:2672078 original size:16 final size:15
Alignment explanation
Indices: 2672053--2672109 Score: 50
Period size: 16 Copynumber: 3.9 Consensus size: 15
2672043 TTGAACCTTA
*
2672053 TTTTTAATTATATAT
1 TTTTTAATTATAAAT
2672068 TTTTATAATTATAAA-
1 TTTT-TAATTATAAAT
2672083 --TTTAATTA-AAAT
1 TTTTTAATTATAAAT
*
2672095 ATTTTAATTGATAAA
1 TTTTTAATT-ATAAA
2672110 CAATTATTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
11 3 0.09
12 6 0.17
13 2 0.06
14 7 0.20
15 5 0.14
16 12 0.34
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TTTTTAATTATAAAT
Found at i:2676031 original size:30 final size:31
Alignment explanation
Indices: 2675962--2676031 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 31
2675952 CTAAAATTTC
* *
2675962 AAAAATAT-AAAAATTAAAATTAATTAACTG
1 AAAAATATAAAAAAATAAAATTAATCAACTG
** *
2675992 AGCAA-ATAAAAAAATGAAATTAATCAACT-
1 AAAAATATAAAAAAATAAAATTAATCAACTG
2676021 AAAAATATAAA
1 AAAAATATAAA
2676032 TTATTAAAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
29 5 0.16
30 26 0.84
ACGTcount: A:0.66, C:0.06, G:0.04, T:0.24
Consensus pattern (31 bp):
AAAAATATAAAAAAATAAAATTAATCAACTG
Found at i:2676596 original size:3 final size:3
Alignment explanation
Indices: 2676583--2676613 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2676573 TACCAAGCAA
*
2676583 AAG AGG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
2676614 GATGGTTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2686225 original size:23 final size:23
Alignment explanation
Indices: 2686199--2686387 Score: 178
Period size: 23 Copynumber: 8.4 Consensus size: 23
2686189 AGTGCTGGGC
2686199 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
2686222 AACAGAGAGTACACAAA--G-T-
1 AACAGAGAGCACACAAAGTGCTA
*
2686241 -AC--TGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
2686261 ATCAGAGAGCACACGAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* * *
2686284 ATCAGAGAGTACACGAAGTGCTAA
1 AACAGAGAGCACACAAAGTGCT-A
* *
2686308 TAACAGAGAGCACGA-GACGTGCTA
1 -AACAGAGAGCAC-ACAAAGTGCTA
* *
2686332 AACAGAGAGCACACACAGTGCTG
1 AACAGAGAGCACACAAAGTGCTA
*
2686355 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
2686378 ATCAGAGAGC
1 AACAGAGAGC
2686388 GCGCTAGTGT
Statistics
Matches: 139, Mismatches: 16, Indels: 22
0.79 0.09 0.12
Matches are distributed among these distances:
16 10 0.07
18 3 0.02
19 1 0.01
20 1 0.01
21 2 0.01
22 1 0.01
23 101 0.73
24 2 0.01
25 17 0.12
26 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:2686259 original size:39 final size:39
Alignment explanation
Indices: 2686205--2686279 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
2686195 GGGCAACAGA
*
2686205 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
* *
2686244 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT
2686280 GCTAATCAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
Found at i:2686361 original size:71 final size:69
Alignment explanation
Indices: 2686255--2686387 Score: 182
Period size: 71 Copynumber: 1.9 Consensus size: 69
2686245 AGCACACAAA
* *
2686255 GTGCTAATCAGAGAGCACACGAAGTGCTAATCAGAGAGTACACGA-AGTGCTAATAACAGAGAGC
1 GTGCTAAACAGAGAGCACACGAAGTGCTAATCAGAGAGCACAC-ACAGTGCTAAT--CAGAGAGC
2686319 ACGAGAC
63 ACGAGAC
2686326 GTGCTAAACAGAGAGCACAC-ACAGTGCTGAA-CAGAGAGCACACACAGTGCTAATCAGAGAGC
1 GTGCTAAACAGAGAGCACACGA-AGTGCT-AATCAGAGAGCACACACAGTGCTAATCAGAGAGC
2686388 GCGCTAGTGT
Statistics
Matches: 57, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
69 8 0.14
70 2 0.04
71 45 0.79
72 2 0.04
ACGTcount: A:0.39, C:0.22, G:0.26, T:0.13
Consensus pattern (69 bp):
GTGCTAAACAGAGAGCACACGAAGTGCTAATCAGAGAGCACACACAGTGCTAATCAGAGAGCACG
AGAC
Found at i:2695250 original size:92 final size:92
Alignment explanation
Indices: 2695075--2695253 Score: 209
Period size: 92 Copynumber: 2.0 Consensus size: 92
2695065 AATTGTTTTT
* * * * * *
2695075 TCAATTGGATATGTGAATTTTCAAAATGCATCAAAAAGATATTCAAACTTTTTCAAATAACGCAA
1 TCAATTGGATATGTGAACTTTCAAAATGCATCAAAAAAACACTCAAAATTTTTCAAAAAACGCAA
* *
2695140 TTAAACCCCTTTTCTTTTTTTTTTTAC
66 TTAAACCCATGTTCTTTTTTTTTTTAC
* * *
2695167 TCAATT-GAGTATTTGAACTTTCAAAATGCATCAAAAAAACCCTCAAAATTTTTCAAAAAATGCA
1 TCAATTGGA-TATGTGAACTTTCAAAATGCATCAAAAAAACACTCAAAATTTTTCAAAAAACGCA
* * *
2695231 ATTAAGCCTATGGT-TTTTTTTTT
65 ATTAAACCCATGTTCTTTTTTTTT
2695254 GGATTGTGTA
Statistics
Matches: 72, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
91 11 0.15
92 61 0.85
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (92 bp):
TCAATTGGATATGTGAACTTTCAAAATGCATCAAAAAAACACTCAAAATTTTTCAAAAAACGCAA
TTAAACCCATGTTCTTTTTTTTTTTAC
Found at i:2695469 original size:28 final size:27
Alignment explanation
Indices: 2695397--2695493 Score: 115
Period size: 28 Copynumber: 3.5 Consensus size: 27
2695387 TGTGACAAAT
** *
2695397 AAAATTATAAAAAA-TAAAAATCAATA
1 AAAATTATAAAAAATTAAATTTTAATA
2695423 AAAATTATAAAAATTATTAAATTTTAATA
1 AAAATTATAAAAA--ATTAAATTTTAATA
*
2695452 AAAATATATAAAAAATTAAATTTTATTA
1 AAAAT-TATAAAAAATTAAATTTTAATA
*
2695480 AAAATTAGAAAAAA
1 AAAATTATAAAAAA
2695494 AATTGTAAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
26 13 0.21
27 8 0.13
28 19 0.31
29 14 0.23
30 8 0.13
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (27 bp):
AAAATTATAAAAAATTAAATTTTAATA
Found at i:2695726 original size:19 final size:18
Alignment explanation
Indices: 2695702--2695746 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
2695692 TTTATAATTT
2695702 TTTTCTATATTTCTATATA
1 TTTTCTATATTTCTATA-A
*
2695721 TTTTCTATATTTTTATAA
1 TTTTCTATATTTCTATAA
2695739 TTTT-TATA
1 TTTTCTATA
2695747 AAAATTTTCG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 4 0.16
18 5 0.20
19 16 0.64
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTCTATATTTCTATAA
Found at i:2695747 original size:9 final size:9
Alignment explanation
Indices: 2695691--2695877 Score: 78
Period size: 9 Copynumber: 19.4 Consensus size: 9
2695681 GATATGAAAA
2695691 TTTTATAATTT
1 TTTTATAA--T
*
2695702 TTTTCTATAT
1 TTTTATA-AT
*
2695712 TTCTATATAT
1 TTTTATA-AT
2695722 TTTCTAT-AT
1 TTT-TATAAT
2695731 TTTTATAAT
1 TTTTATAAT
2695740 TTTTATAAAAAT
1 TTTTAT---AAT
**
2695752 TTTCGTAAT
1 TTTTATAAT
2695761 TTTT-TAAAT
1 TTTTAT-AAT
*
2695770 TTTTATATTTT
1 TTTTATA--AT
*
2695781 TTTTCTAAT
1 TTTTATAAT
*
2695790 TTTTAATAAA
1 TTTT-ATAAT
2695800 TTTTA-AATT
1 TTTTATAA-T
2695809 TTTTATAATT
1 TTTTATAA-T
*
2695819 TTTTATTAAAA
1 TTTTA-T-AAT
*
2695830 TTTAATAAT
1 TTTTATAAT
*
2695839 TTTTATAAC
1 TTTTATAAT
*
2695848 TTTTATTGA-
1 TTTTA-TAAT
*
2695857 TTTTAT-TT
1 TTTTATAAT
2695865 TTTTATAAT
1 TTTTATAAT
2695874 TTTT
1 TTTT
2695878 TACCACATGC
Statistics
Matches: 137, Mismatches: 21, Indels: 38
0.70 0.11 0.19
Matches are distributed among these distances:
8 13 0.09
9 62 0.45
10 31 0.23
11 21 0.15
12 10 0.07
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.65
Consensus pattern (9 bp):
TTTTATAAT
Found at i:2695834 original size:39 final size:38
Alignment explanation
Indices: 2695720--2695853 Score: 119
Period size: 39 Copynumber: 3.4 Consensus size: 38
2695710 ATTTCTATAT
* * **
2695720 ATTTTCTATATTTTTATAA-TTTTTATAAAAATTTTCGTA
1 ATTTT-TAAATTTTTATAATTTTTTATTAAAA-TTTAATA
* **
2695759 ATTTTTTAAATTTTTAT-ATTTTTTTTCTAATTTTTAATA
1 A-TTTTTAAATTTTTATAATTTTTTAT-TAAAATTTAATA
*
2695798 AATTTTAAATTTTTTATAATTTTTTATTAAAATTTAATA
1 ATTTTTAAA-TTTTTATAATTTTTTATTAAAATTTAATA
*
2695837 ATTTTTATAACTTTTAT
1 ATTTTTA-AATTTTTAT
2695854 TGATTTTATT
Statistics
Matches: 76, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
38 8 0.11
39 52 0.68
40 16 0.21
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.63
Consensus pattern (38 bp):
ATTTTTAAATTTTTATAATTTTTTATTAAAATTTAATA
Found at i:2695878 original size:10 final size:10
Alignment explanation
Indices: 2695691--2695879 Score: 80
Period size: 10 Copynumber: 19.5 Consensus size: 10
2695681 GATATGAAAA
2695691 TTTTATAATT
1 TTTTATAATT
*
2695701 TTTT-TCTATAT
1 TTTTAT-AAT-T
*
2695712 TTCTATATATT
1 TTTTATA-ATT
*
2695723 TTCTAT-A-T
1 TTTTATAATT
2695731 TTTTATAATT
1 TTTTATAATT
* *
2695741 TTTATAAAAAT
1 TTT-TATAATT
**
2695752 TTTCGTAATT
1 TTTTATAATT
2695762 TTTTA-AA-T
1 TTTTATAATT
*
2695770 TTTTATATTTT
1 TTTTATA-ATT
*
2695781 TTTTCTAATT
1 TTTTATAATT
* *
2695791 TTTAATAA-A
1 TTTTATAATT
2695800 TTTTA-AATT
1 TTTTATAATT
2695809 TTTTATAATT
1 TTTTATAATT
**
2695819 TTTTATTAAAA
1 TTTTA-TAATT
*
2695830 TTTAATAA-T
1 TTTTATAATT
*
2695839 TTTTATAA-C
1 TTTTATAATT
*
2695848 TTTTAT--TGA
1 TTTTATAAT-T
2695857 TTTTAT--TT
1 TTTTATAATT
2695865 TTTTATAATT
1 TTTTATAATT
2695875 TTTTA
1 TTTTA
2695880 CCACATGCCA
Statistics
Matches: 134, Mismatches: 28, Indels: 34
0.68 0.14 0.17
Matches are distributed among these distances:
8 20 0.15
9 35 0.26
10 43 0.32
11 33 0.25
12 3 0.02
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (10 bp):
TTTTATAATT
Found at i:2699709 original size:17 final size:16
Alignment explanation
Indices: 2699661--2699709 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
2699651 ATTAAATTTT
*
2699661 AATAAAAAGTATAAAA
1 AATAAAAATTATAAAA
* *
2699677 AATAAAATTTATTAAAG
1 AATAAAAATTA-TAAAA
2699694 AATAAAAAATTATAAA
1 AAT-AAAAATTATAAA
2699710 TGCATCAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 9 0.33
17 11 0.41
18 7 0.26
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (16 bp):
AATAAAAATTATAAAA
Found at i:2700892 original size:27 final size:27
Alignment explanation
Indices: 2700843--2700894 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
2700833 ATTTTTTTTT
* * * *
2700843 AATTTGGTATTTAATTTTTTTAAATTC
1 AATTTGATATCTAAATTTATTAAATTC
2700870 AATTTGATATCTAAATTTATTAAAT
1 AATTTGATATCTAAATTTATTAAAT
2700895 GTTATATAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.54
Consensus pattern (27 bp):
AATTTGATATCTAAATTTATTAAATTC
Found at i:2709213 original size:19 final size:20
Alignment explanation
Indices: 2709163--2709218 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
2709153 CACTCACTGT
2709163 TTAAAAAATATTTATTAAAAA
1 TTAAAAAAT-TTTATTAAAAA
* **
2709184 TTTAATTATTTT-TTAAAAA
1 TTAAAAAATTTTATTAAAAA
*
2709203 TTAAAAAATTTAATTA
1 TTAAAAAATTTTATTA
2709219 TTACATATGA
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
19 15 0.56
20 6 0.22
21 6 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTAAAAAATTTTATTAAAAA
Found at i:2709287 original size:10 final size:9
Alignment explanation
Indices: 2709243--2709435 Score: 81
Period size: 9 Copynumber: 20.6 Consensus size: 9
2709233 TTCTTCTATT
*
2709243 AAATGATAA
1 AAATTATAA
*
2709252 AAA-AATAA
1 AAATTATAA
*
2709260 AAA-TAAAA
1 AAATTATAA
2709268 AAATTATAA
1 AAATTATAA
2709277 AAATTATTAA
1 AAATTA-TAA
**
2709287 ATTTTACTAA
1 AAATTA-TAA
*
2709297 AAAATATAGA
1 AAATTATA-A
2709307 AACTATT-TAA
1 AA--ATTATAA
* *
2709317 AATTTATTAG
1 AAATTA-TAA
*
2709327 AAATTAAAA
1 AAATTATAA
2709336 AAATTATAA
1 AAATTATAA
*
2709345 AAATCATAA
1 AAATTATAA
2709354 AAATT-TATA
1 AAATTATA-A
*
2709363 AAATTTTATA
1 AAATTATA-A
* *
2709373 AAGTCATAAGA
1 AAATTAT-A-A
2709384 AAATTATAA
1 AAATTATAA
* *
2709393 AAAATGTAA
1 AAATTATAA
*
2709402 AGAAATATAA
1 A-AATTATAA
*
2709412 AACTCGTA-AA
1 AAAT--TATAA
2709422 AAATTATAA
1 AAATTATAA
2709431 AAATT
1 AAATT
2709436 GTCGTAATAA
Statistics
Matches: 139, Mismatches: 31, Indels: 28
0.70 0.16 0.14
Matches are distributed among these distances:
8 19 0.14
9 59 0.42
10 48 0.35
11 11 0.08
12 2 0.01
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (9 bp):
AAATTATAA
Found at i:2709299 original size:30 final size:29
Alignment explanation
Indices: 2709265--2709395 Score: 99
Period size: 30 Copynumber: 4.5 Consensus size: 29
2709255 AATAAAAATA
*
2709265 AAAAAATTATAAAAATTATTAAATTTTACT
1 AAAAAATTATAAAAATTATTAAAATTTA-T
* *
2709295 AAAAAA-TATAGAAACTATTTAAAATTTAT
1 AAAAAATTATAAAAATTA-TTAAAATTTAT
* * * * *
2709324 TAGAAATTAAAAAAATTA-TAAAAATCAT
1 AAAAAATTATAAAAATTATTAAAATTTAT
* * *
2709352 AAAAATTTAT-AAAATT-TTATAAAGTCAT
1 AAAAAATTATAAAAATTATTA-AAATTTAT
2709380 AAGAAAATTATAAAAA
1 AA-AAAATTATAAAAA
2709396 ATGTAAAGAA
Statistics
Matches: 79, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
27 8 0.10
28 23 0.29
29 21 0.27
30 27 0.34
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAAAATTATAAAAATTATTAAAATTTAT
Found at i:2709337 original size:19 final size:20
Alignment explanation
Indices: 2709315--2709365 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 20
2709305 GAAACTATTT
* *
2709315 AAAATTTATTAGAAATTA-A
1 AAAATTTATTAAAAATCATA
*
2709334 AAAAATTA-TAAAAATCATA
1 AAAATTTATTAAAAATCATA
2709353 AAAATTTA-TAAAA
1 AAAATTTATTAAAA
2709366 TTTTATAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 7 0.26
19 20 0.74
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (20 bp):
AAAATTTATTAAAAATCATA
Found at i:2709373 original size:20 final size:19
Alignment explanation
Indices: 2709256--2709374 Score: 77
Period size: 20 Copynumber: 6.3 Consensus size: 19
2709246 TGATAAAAAA
*
2709256 ATAAAAA-TA-AAAAAATT
1 ATAAAAATTATAAAATATT
* *
2709273 ATAAAAATTATTAAATTTT
1 ATAAAAATTATAAAATATT
*
2709292 ACTAAAAAATATAGAAACTATT
1 A-TAAAAATTATA-AAA-TATT
* *
2709314 -TAAAATTTATTAGAA-ATT
1 ATAAAAATTA-TAAAATATT
* *
2709332 AAAAAAATTATAAAA-ATC
1 ATAAAAATTATAAAATATT
*
2709350 ATAAAAATTTATAAAATTTT
1 ATAAAAA-TTATAAAATATT
2709370 ATAAA
1 ATAAA
2709375 GTCATAAGAA
Statistics
Matches: 77, Mismatches: 16, Indels: 15
0.71 0.15 0.14
Matches are distributed among these distances:
17 7 0.09
18 17 0.22
19 21 0.27
20 24 0.31
21 5 0.06
22 3 0.04
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (19 bp):
ATAAAAATTATAAAATATT
Found at i:2709500 original size:12 final size:11
Alignment explanation
Indices: 2709454--2709505 Score: 70
Period size: 11 Copynumber: 4.7 Consensus size: 11
2709444 AAAAAAAGCA
2709454 TTTTATAATTT
1 TTTTATAATTT
2709465 TTTTATAATTT
1 TTTTATAATTT
* *
2709476 TTAT-TGATTT
1 TTTTATAATTT
2709486 TTTTATAATTGT
1 TTTTATAATT-T
2709498 TTTTATAA
1 TTTTATAA
2709506 CTTTAATTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
10 8 0.23
11 18 0.51
12 9 0.26
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (11 bp):
TTTTATAATTT
Found at i:2709515 original size:33 final size:32
Alignment explanation
Indices: 2709454--2709515 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 32
2709444 AAAAAAAGCA
* *
2709454 TTTTATAATTTTTTTATAATTTTTATTGATTT
1 TTTTATAATTTTTTTATAACTTTAATTGATTT
2709486 TTTTATAATTGTTTTTATAACTTTAATTGA
1 TTTTATAATT-TTTTTATAACTTTAATTGA
2709516 AAAACATGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 10 0.37
33 17 0.63
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (32 bp):
TTTTATAATTTTTTTATAACTTTAATTGATTT
Found at i:2709598 original size:11 final size:10
Alignment explanation
Indices: 2709583--2709682 Score: 76
Period size: 10 Copynumber: 9.7 Consensus size: 10
2709573 CTTTTCGATG
2709583 TTTTTTATAA
1 TTTTTTATAA
2709593 TATTTTTATTAA
1 T-TTTTTA-TAA
2709605 TTTTTTATAA
1 TTTTTTATAA
** *
2709615 AATTTTACAA
1 TTTTTTATAA
2709625 TTTTTCTAATAA
1 TTTTT-T-ATAA
**
2709637 TTTTTTACGA
1 TTTTTTATAA
2709647 TTTTTTAT-A
1 TTTTTTATAA
*
2709656 TTTTTTCTAA
1 TTTTTTATAA
* *
2709666 CTTTTAATAA
1 TTTTTTATAA
*
2709676 TATTTTA
1 TTTTTTA
2709683 ATATTTTTAT
Statistics
Matches: 69, Mismatches: 16, Indels: 10
0.73 0.17 0.11
Matches are distributed among these distances:
9 8 0.12
10 35 0.51
11 14 0.20
12 12 0.17
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.63
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:2709608 original size:22 final size:21
Alignment explanation
Indices: 2709583--2709681 Score: 82
Period size: 22 Copynumber: 4.8 Consensus size: 21
2709573 CTTTTCGATG
*
2709583 TTTTTTATAATATTTTTATTAA
1 TTTTTTATAATATTTTTA-CAA
*
2709605 TTTTTTATAA-AATTTTACAA
1 TTTTTTATAATATTTTTACAA
*
2709625 TTTTTCTAATAAT-TTTTTACGA
1 TTTTT-T-ATAATATTTTTACAA
2709647 TTTTTTAT-AT-TTTTT-CTAA
1 TTTTTTATAATATTTTTAC-AA
* *
2709666 CTTTTAATAATATTTT
1 TTTTTTATAATATTTT
2709682 AATATTTTTA
Statistics
Matches: 64, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
18 1 0.02
19 14 0.22
20 11 0.17
21 12 0.19
22 26 0.41
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.64
Consensus pattern (21 bp):
TTTTTTATAATATTTTTACAA
Found at i:2709719 original size:10 final size:10
Alignment explanation
Indices: 2709585--2709719 Score: 57
Period size: 10 Copynumber: 13.6 Consensus size: 10
2709575 TTTCGATGTT
2709585 TTTTATAAT-A
1 TTTT-TAATAA
*
2709595 TTTTTATTAA
1 TTTTTAATAA
*
2709605 TTTTTTATAAA
1 TTTTTAAT-AA
* *
2709616 ATTTTACA-AT
1 TTTTTA-ATAA
2709626 TTTTCTAATAA
1 TTTT-TAATAA
* **
2709637 TTTTTTACGA
1 TTTTTAATAA
*
2709647 TTTTTTAT-A
1 TTTTTAATAA
**
2709656 TTTTTTCTAA
1 TTTTTAATAA
*
2709666 CTTTTAATAA
1 TTTTTAATAA
2709676 TATTTTAAT-A
1 T-TTTTAATAA
*
2709686 TTTTTATTAA
1 TTTTTAATAA
**
2709696 AATTTAATAA
1 TTTTTAATAA
2709706 --TTTAATAA
1 TTTTTAATAA
2709714 TTTTTA
1 TTTTTA
2709720 TTGGTTTTTA
Statistics
Matches: 94, Mismatches: 21, Indels: 20
0.70 0.16 0.15
Matches are distributed among these distances:
8 8 0.09
9 17 0.18
10 48 0.51
11 20 0.21
12 1 0.01
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.61
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:2722334 original size:11 final size:11
Alignment explanation
Indices: 2722318--2722342 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2722308 AGAAGTCAAA
2722318 GAGAGTAGAAT
1 GAGAGTAGAAT
2722329 GAGAGTAGAAT
1 GAGAGTAGAAT
2722340 GAG
1 GAG
2722343 TGTGCTTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.40, T:0.16
Consensus pattern (11 bp):
GAGAGTAGAAT
Found at i:2732411 original size:7 final size:7
Alignment explanation
Indices: 2732387--2732436 Score: 68
Period size: 7 Copynumber: 7.4 Consensus size: 7
2732377 TGGTTGTTGT
2732387 AAGATGG
1 AAGATGG
* *
2732394 AAGACGA
1 AAGATGG
2732401 AAGATGG
1 AAGATGG
2732408 AAGATGG
1 AAGATGG
2732415 AAGATGG
1 AAGATGG
2732422 AAGAT-G
1 AAGATGG
2732428 -AGATGG
1 AAGATGG
2732434 AAG
1 AAG
2732437 GTGAGATTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
5 4 0.11
6 2 0.05
7 31 0.84
ACGTcount: A:0.46, C:0.02, G:0.40, T:0.12
Consensus pattern (7 bp):
AAGATGG
Found at i:2732668 original size:14 final size:14
Alignment explanation
Indices: 2732649--2732676 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2732639 CTGCTTTGAT
2732649 ACAAGCATGCAGGC
1 ACAAGCATGCAGGC
2732663 ACAAGCATGCAGGC
1 ACAAGCATGCAGGC
2732677 GTCGGAAGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.29, T:0.07
Consensus pattern (14 bp):
ACAAGCATGCAGGC
Found at i:2732963 original size:14 final size:14
Alignment explanation
Indices: 2732944--2732985 Score: 84
Period size: 14 Copynumber: 3.0 Consensus size: 14
2732934 CTGCTTTGAT
2732944 ACAAGCATGCAGGC
1 ACAAGCATGCAGGC
2732958 ACAAGCATGCAGGC
1 ACAAGCATGCAGGC
2732972 ACAAGCATGCAGGC
1 ACAAGCATGCAGGC
2732986 GTCGGAAGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.36, C:0.29, G:0.29, T:0.07
Consensus pattern (14 bp):
ACAAGCATGCAGGC
Found at i:2733208 original size:309 final size:309
Alignment explanation
Indices: 2732649--2733561 Score: 1593
Period size: 309 Copynumber: 3.0 Consensus size: 309
2732639 CTGCTTTGAT
2732649 ACAAGCATGCAGGCACAAGCATGCAGGCGTCGGAAGCTATCAGCTTTGATAAACTTAAATCCCAC
1 ACAAGCATGCAGGCACAAGCATGCAGGCGTCGGAAGCTATCAGCTTTGATAAACTTAAATCCCAC
2732714 CAGCTGTCCCATAGTCGCCAACATATGAATAACCATTCATAAACTTTTGGAAGTGCGTGTTATTG
66 CAGCTGTCCCATAGTCGCCAACATATGAATAACCATTCATAAACTTTTGGAAGTGCGTGTTATTG
*
2732779 GGTTCGTCTGTTAAACTGTTTTAATAAACAAACATATGAATTCATAATCTCAAAATACAAAGGAG
131 GGTTCGTCTGTTAAACTGCTTTAATAAACAAACATATGAATTCATAATCTCAAAATACAAAGGAG
* * * *
2732844 AATGAACATTTCTGCTTTCTACCCTTTCACATCCATTTTTTTGACTTAAGTAAAAAGCCCTCTAA
196 AATGAACATCTCTGCTTTCTACCTTTTCACATCCATTTTTTTGGCTTAAGTAAAAAGCCCTCAAA
2732909 CTTTTAAAAAGAAACAATTAAGCCACTGCTTTGATACAAGCATGCAGGC
261 CTTTTAAAAAGAAACAATTAAGCCACTGCTTTGATACAAGCATGCAGGC
2732958 ACAAGCATGCAGGCACAAGCATGCAGGCGTCGGAAGCTATCAGCTTTGATAAACTTAAATCCCAC
1 ACAAGCATGCAGGCACAAGCATGCAGGCGTCGGAAGCTATCAGCTTTGATAAACTTAAATCCCAC
**
2733023 CAGCTGTCCCATAACCGCCAACATATGAATAACCATTCATAAACTTTTGGAAGTGCGTGTTATTG
66 CAGCTGTCCCATAGTCGCCAACATATGAATAACCATTCATAAACTTTTGGAAGTGCGTGTTATTG
2733088 GGTTCGTCTGTTAAACTGCTTTAATAAACAAACATATGAATTCATAATCTCAAAATACAAAGGAG
131 GGTTCGTCTGTTAAACTGCTTTAATAAACAAACATATGAATTCATAATCTCAAAATACAAAGGAG
* *
2733153 AATGAATATCTCTGCTTTCTACCTTTTCACATCCATTTTTTTGGCTTAAGTAAAAAGCTCTCAAA
196 AATGAACATCTCTGCTTTCTACCTTTTCACATCCATTTTTTTGGCTTAAGTAAAAAGCCCTCAAA
*
2733218 CTTTAAAAAAGAAACAATTAAGCCACTGCTTTGATACAAGCAT------
261 CTTTTAAAAAGAAACAATTAAGCCACTGCTTTGATACAAGCATGCAGGC
2733261 ----G--T--AGGCACAAGCATGCAGGCGTCGGAAGCTATCAGCTTTGATAAACTTAAATCCCAC
1 ACAAGCATGCAGGCACAAGCATGCAGGCGTCGGAAGCTATCAGCTTTGATAAACTTAAATCCCAC
*
2733318 CAACTGTCCCATAGTCGCCAACATATGAATAACCATTCATAAACTTTTGGAAGTGCGTGTTATTG
66 CAGCTGTCCCATAGTCGCCAACATATGAATAACCATTCATAAACTTTTGGAAGTGCGTGTTATTG
* * *
2733383 GGTTCGTCTATTAAACTGCTTTAATAAACAAACATATGAATTCATAATATCAAAATACAAAGAAG
131 GGTTCGTCTGTTAAACTGCTTTAATAAACAAACATATGAATTCATAATCTCAAAATACAAAGGAG
*
2733448 AATGAACATCTCTGCTTTCTACCTTTTCACATCCATTTTTTTGGCTTAAGTAAAAAGCCCTCCAA
196 AATGAACATCTCTGCTTTCTACCTTTTCACATCCATTTTTTTGGCTTAAGTAAAAAGCCCTCAAA
2733513 CTTTTAAAAAGAAACAATTAAGCCACTGCTTTGATACAAGCATGCAGGC
261 CTTTTAAAAAGAAACAATTAAGCCACTGCTTTGATACAAGCATGCAGGC
2733562 GTCGGAAGCT
Statistics
Matches: 578, Mismatches: 20, Indels: 20
0.94 0.03 0.03
Matches are distributed among these distances:
295 283 0.49
297 1 0.00
299 1 0.00
309 293 0.51
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (309 bp):
ACAAGCATGCAGGCACAAGCATGCAGGCGTCGGAAGCTATCAGCTTTGATAAACTTAAATCCCAC
CAGCTGTCCCATAGTCGCCAACATATGAATAACCATTCATAAACTTTTGGAAGTGCGTGTTATTG
GGTTCGTCTGTTAAACTGCTTTAATAAACAAACATATGAATTCATAATCTCAAAATACAAAGGAG
AATGAACATCTCTGCTTTCTACCTTTTCACATCCATTTTTTTGGCTTAAGTAAAAAGCCCTCAAA
CTTTTAAAAAGAAACAATTAAGCCACTGCTTTGATACAAGCATGCAGGC
Found at i:2733488 original size:295 final size:295
Alignment explanation
Indices: 2732455--2734111 Score: 2804
Period size: 295 Copynumber: 5.6 Consensus size: 295
2732445 GAGATGATAA
2732455 TCATAAACTTTTGGAAGTGCGTGTTATTGGGTTCGTCTGTTAAACTGCTTTAATAAACAAACATA
1 TCATAAACTTTTGGAAGTGCGTGTTATTGGGTTCGTCTGTTAAACTGCTTTAATAAACAAACATA
*
2732520 TGAATTCATAATCTCAAAATACAAAGGAGAATGAACATCTCTGCTTTCTACCTTTTCACATCTAT
66 TGAATTCATAATCTCAAAATACAAAGGAGAATGAACATCTCTGCTTTCTACCTTTTCACATCCAT
*
2732585 TTTTTTGGCTTAAGTAAAAAGTTCTCAAACTTTAAAAAAGAAACAATTAAGCCACTGCTTTGATA
131 TTTTTTGGCTTAAGTAAAAAGCTCTCAAACTTTAAAAAAGAAACAATTAAGCCACTGCTTTGATA
*
2732650 CAAGCATGCAGGCACAAGCATGCAGGCGTCGGAAGCTATCAGCTTTGATAAACTTAAATCCCACC
196 CAAGCATGTAGGCACAAGCATGCAGGCGTCGGAAGCTATCAGCTTTGATAAACTTAAATCCCACC
*
2732715 AGCTGTCCCATAGTCGCCAACATATGAATAACCAT
261 AGCTGTCCCATAGCCGCCAACATATGAATAACCAT
*
2732750 TCATAAACTTTTGGAAGTGCGTGTTATTGGGTTCGTCTGTTAAACTGTTTTAATAAACAAACATA
1 TCATAAACTTTTGGAAGTGCGTGTTATTGGGTTCGTCTGTTAAACTGCTTTAATAAACAAACATA
* *
2732815 TGAATTCATAATCTCAAAATACAAAGGAGAATGAACATTTCTGCTTTCTACCCTTTCACATCCAT
66 TGAATTCATAATCTCAAAATACAAAGGAGAATGAACATCTCTGCTTTCTACCTTTTCACATCCAT
* * * *
2732880 TTTTTTGACTTAAGTAAAAAGCCCTCTAACTTTTAAAAAGAAACAATTAAGCCACTGCTTTGATA
131 TTTTTTGGCTTAAGTAAAAAGCTCTCAAACTTTAAAAAAGAAACAATTAAGCCACTGCTTTGATA
2732945 CAAGCATGCAGGCACAAGCATGCAGGCACAAGCATGCAGGCGTCGGAAGCTATCAGCTTTGATAA
196 CAAGCAT----------G--T--AGGCACAAGCATGCAGGCGTCGGAAGCTATCAGCTTTGATAA
*
2733010 ACTTAAATCCCACCAGCTGTCCCATAACCGCCAACATATGAATAACCAT
247 ACTTAAATCCCACCAGCTGTCCCATAGCCGCCAACATATGAATAACCAT
2733059 TCATAAACTTTTGGAAGTGCGTGTTATTGGGTTCGTCTGTTAAACTGCTTTAATAAACAAACATA
1 TCATAAACTTTTGGAAGTGCGTGTTATTGGGTTCGTCTGTTAAACTGCTTTAATAAACAAACATA
*
2733124 TGAATTCATAATCTCAAAATACAAAGGAGAATGAATATCTCTGCTTTCTACCTTTTCACATCCAT
66 TGAATTCATAATCTCAAAATACAAAGGAGAATGAACATCTCTGCTTTCTACCTTTTCACATCCAT
2733189 TTTTTTGGCTTAAGTAAAAAGCTCTCAAACTTTAAAAAAGAAACAATTAAGCCACTGCTTTGATA
131 TTTTTTGGCTTAAGTAAAAAGCTCTCAAACTTTAAAAAAGAAACAATTAAGCCACTGCTTTGATA
2733254 CAAGCATGTAGGCACAAGCATGCAGGCGTCGGAAGCTATCAGCTTTGATAAACTTAAATCCCACC
196 CAAGCATGTAGGCACAAGCATGCAGGCGTCGGAAGCTATCAGCTTTGATAAACTTAAATCCCACC
* *
2733319 AACTGTCCCATAGTCGCCAACATATGAATAACCAT
261 AGCTGTCCCATAGCCGCCAACATATGAATAACCAT
*
2733354 TCATAAACTTTTGGAAGTGCGTGTTATTGGGTTCGTCTATTAAACTGCTTTAATAAACAAACATA
1 TCATAAACTTTTGGAAGTGCGTGTTATTGGGTTCGTCTGTTAAACTGCTTTAATAAACAAACATA
* *
2733419 TGAATTCATAATATCAAAATACAAAGAAGAATGAACATCTCTGCTTTCTACCTTTTCACATCCAT
66 TGAATTCATAATCTCAAAATACAAAGGAGAATGAACATCTCTGCTTTCTACCTTTTCACATCCAT
* * *
2733484 TTTTTTGGCTTAAGTAAAAAGCCCTCCAACTTTTAAAAAGAAACAATTAAGCCACTGC-TT--T-
131 TTTTTTGGCTTAAGTAAAAAGCTCTCAAACTTTAAAAAAGAAACAATTAAGCCACTGCTTTGATA
*
2733545 ---G-A--T----ACAAGCATGCAGGCGTCGGAAGCTATCAACTTTGATAAACTTAAATCCCACC
196 CAAGCATGTAGGCACAAGCATGCAGGCGTCGGAAGCTATCAGCTTTGATAAACTTAAATCCCACC
2733600 AGCTGTCCCATAGCCGCCAACATATGAATAACCAT
261 AGCTGTCCCATAGCCGCCAACATATGAATAACCAT
2733635 TCATAAACTTTTGGAAGTGCGTGTTATTGGGTTCGTCTGTTAAACTGCTTTAATAAACAAACATA
1 TCATAAACTTTTGGAAGTGCGTGTTATTGGGTTCGTCTGTTAAACTGCTTTAATAAACAAACATA
* *
2733700 TGAATTCATAATCTCAAAATACAAAGGAGAATGAACATCTCTGCTTGCTACCTTTTCACATCTAT
66 TGAATTCATAATCTCAAAATACAAAGGAGAATGAACATCTCTGCTTTCTACCTTTTCACATCCAT
2733765 TTTTTTGGCTTAAGTAAAAAGCTCTCAAACTTTAAAAAAGAAACAATTAAGCCACTGCTTTGATA
131 TTTTTTGGCTTAAGTAAAAAGCTCTCAAACTTTAAAAAAGAAACAATTAAGCCACTGCTTTGATA
* *
2733830 CAAGCATGCAGGCATAAGCATGCAGGCGTCGGAAGCTATCAGCTTTGATAAACTTAAATCCCACC
196 CAAGCATGTAGGCACAAGCATGCAGGCGTCGGAAGCTATCAGCTTTGATAAACTTAAATCCCACC
2733895 AGCTGTCCCATAGCCGCCAACATATGAATAACCAT
261 AGCTGTCCCATAGCCGCCAACATATGAATAACCAT
*
2733930 TCATAAACTTTTGGAAGTGCGTGTTATTGGGTTCGTCTATTAAACTGCTTTAATAAACAAACATA
1 TCATAAACTTTTGGAAGTGCGTGTTATTGGGTTCGTCTGTTAAACTGCTTTAATAAACAAACATA
*
2733995 TGAATTCATAATCTCAAAATACAAAGGAGAATGAACATCTCTGCTTTCTACCTTTTCACATCTA-
66 TGAATTCATAATCTCAAAATACAAAGGAGAATGAACATCTCTGCTTTCTACCTTTTCACATCCAT
* * *
2734059 TTTTTTGGCTTAAGTAAAAAGCTCTCCAACTTTTAAAAATAAACAATTAAGCC
131 TTTTTTGGCTTAAGTAAAAAGCTCTCAAACTTTAAAAAAGAAACAATTAAGCC
2734112 GCTACAATTA
Statistics
Matches: 1285, Mismatches: 49, Indels: 57
0.92 0.04 0.04
Matches are distributed among these distances:
281 264 0.21
282 2 0.00
284 1 0.00
285 1 0.00
287 1 0.00
288 2 0.00
289 1 0.00
292 1 0.00
294 52 0.04
295 674 0.52
297 1 0.00
299 1 0.00
305 1 0.00
309 283 0.22
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.30
Consensus pattern (295 bp):
TCATAAACTTTTGGAAGTGCGTGTTATTGGGTTCGTCTGTTAAACTGCTTTAATAAACAAACATA
TGAATTCATAATCTCAAAATACAAAGGAGAATGAACATCTCTGCTTTCTACCTTTTCACATCCAT
TTTTTTGGCTTAAGTAAAAAGCTCTCAAACTTTAAAAAAGAAACAATTAAGCCACTGCTTTGATA
CAAGCATGTAGGCACAAGCATGCAGGCGTCGGAAGCTATCAGCTTTGATAAACTTAAATCCCACC
AGCTGTCCCATAGCCGCCAACATATGAATAACCAT
Found at i:2734064 original size:576 final size:589
Alignment explanation
Indices: 2732455--2734111 Score: 2901
Period size: 604 Copynumber: 2.8 Consensus size: 589
2732445 GAGATGATAA
2732455 TCATAAACTTTTGGAAGTGCGTGTTATTGGGTTCGTCTGTTAAACTGCTTTAATAAACAAACATA
1 TCATAAACTTTTGGAAGTGCGTGTTATTGGGTTCGTCTGTTAAACTGCTTTAATAAACAAACATA
2732520 TGAATTCATAATCTCAAAATACAAAGGAGAATGAACATCTCTGCTTTCTACCTTTTCACATCTAT
66 TGAATTCATAATCTCAAAATACAAAGGAGAATGAACATCTCTGCTTTCTACCTTTTCACATCTAT
*
2732585 TTTTTTGGCTTAAGTAAAAAGTTCTCAAACTTTAAAAAAGAAACAATTAAGCCACTGCTTTGATA
131 TTTTTTGGCTTAAGTAAAAAGCTCTCAAACTTTAAAAAAGAAACAATTAAGCCACTGCTTTGATA
2732650 CAAGCATGCAGGCACAAGCATGCAGGCGTCGGAAGCTATCAGCTTTGATAAACTTAAATCCCACC
196 CAAGCATGCAGGCACAAGCATGCAGGCGTCGGAAGCTATCAGCTTTGATAAACTTAAATCCCACC
2732715 AGCTGTCCCATAGTCGCCAACATATGAATAACCATTCATAAACTTTTGGAAGTGCGTGTTATTGG
261 AGCTGTCCCATAGTCGCCAACATATGAATAACCATTCATAAACTTTTGGAAGTGCGTGTTATTGG
* *
2732780 GTTCGTCTGTTAAACTGTTTTAATAAACAAACATATGAATTCATAATCTCAAAATACAAAGGAGA
326 GTTCGTCTATTAAACTGCTTTAATAAACAAACATATGAATTCATAATCTCAAAATACAAAGGAGA
* * * *
2732845 ATGAACATTTCTGCTTTCTACCCTTTCACATCCATTTTTTTGACTTAAGTAAAAAGCCCTCTAAC
391 ATGAACATCTCTGCTTTCTACCTTTTCACATCCATTTTTTTGGCTTAAGTAAAAAGCCCTCCAAC
2732910 TTTTAAAAAGAAACAATTAAGCCACTGCTTTGATACAAGCATGCAGGCACAAGCATGCAGGCACA
456 TTTTAAAAAGAAACAATTAAGCCACTGCTTTGATACAAGCATGCAGG-AC-AG-ATGCAGG--CA
2732975 AGCATGCAGGCGTCGGAAGCTATCAGCTTTGATAAACTTAAATCCCACCAGCTGTCCCATAACCG
516 AGCAT-CA---GT-----GCTA-CAGCTTTGATAAACTTAAATCCCACCAGCTGTCCCATAACCG
2733040 CCAACATATGAATAACCAT
571 CCAACATATGAATAACCAT
2733059 TCATAAACTTTTGGAAGTGCGTGTTATTGGGTTCGTCTGTTAAACTGCTTTAATAAACAAACATA
1 TCATAAACTTTTGGAAGTGCGTGTTATTGGGTTCGTCTGTTAAACTGCTTTAATAAACAAACATA
* *
2733124 TGAATTCATAATCTCAAAATACAAAGGAGAATGAATATCTCTGCTTTCTACCTTTTCACATCCAT
66 TGAATTCATAATCTCAAAATACAAAGGAGAATGAACATCTCTGCTTTCTACCTTTTCACATCTAT
2733189 TTTTTTGGCTTAAGTAAAAAGCTCTCAAACTTTAAAAAAGAAACAATTAAGCCACTGCTTTGATA
131 TTTTTTGGCTTAAGTAAAAAGCTCTCAAACTTTAAAAAAGAAACAATTAAGCCACTGCTTTGATA
*
2733254 CAAGCATGTAGGCACAAGCATGCAGGCGTCGGAAGCTATCAGCTTTGATAAACTTAAATCCCACC
196 CAAGCATGCAGGCACAAGCATGCAGGCGTCGGAAGCTATCAGCTTTGATAAACTTAAATCCCACC
*
2733319 AACTGTCCCATAGTCGCCAACATATGAATAACCATTCATAAACTTTTGGAAGTGCGTGTTATTGG
261 AGCTGTCCCATAGTCGCCAACATATGAATAACCATTCATAAACTTTTGGAAGTGCGTGTTATTGG
* *
2733384 GTTCGTCTATTAAACTGCTTTAATAAACAAACATATGAATTCATAATATCAAAATACAAAGAAGA
326 GTTCGTCTATTAAACTGCTTTAATAAACAAACATATGAATTCATAATCTCAAAATACAAAGGAGA
2733449 ATGAACATCTCTGCTTTCTACCTTTTCACATCCATTTTTTTGGCTTAAGTAAAAAGCCCTCCAAC
391 ATGAACATCTCTGCTTTCTACCTTTTCACATCCATTTTTTTGGCTTAAGTAAAAAGCCCTCCAAC
2733514 TTTTAAAAAGAAACAATTAAGCCACTGCTTTGATACAAGCATGCAGG-C-G-T-C-GG-AAGC-T
456 TTTTAAAAAGAAACAATTAAGCCACTGCTTTGATACAAGCATGCAGGACAGATGCAGGCAAGCAT
*
2733572 -A-T-C-A-A-CTTTGATAAACTTAAATCCCACCAGCTGTCCCATAGCCGCCAACATATGAATAA
521 CAGTGCTACAGCTTTGATAAACTTAAATCCCACCAGCTGTCCCATAACCGCCAACATATGAATAA
2733631 CCAT
586 CCAT
2733635 TCATAAACTTTTGGAAGTGCGTGTTATTGGGTTCGTCTGTTAAACTGCTTTAATAAACAAACATA
1 TCATAAACTTTTGGAAGTGCGTGTTATTGGGTTCGTCTGTTAAACTGCTTTAATAAACAAACATA
*
2733700 TGAATTCATAATCTCAAAATACAAAGGAGAATGAACATCTCTGCTTGCTACCTTTTCACATCTAT
66 TGAATTCATAATCTCAAAATACAAAGGAGAATGAACATCTCTGCTTTCTACCTTTTCACATCTAT
2733765 TTTTTTGGCTTAAGTAAAAAGCTCTCAAACTTTAAAAAAGAAACAATTAAGCCACTGCTTTGATA
131 TTTTTTGGCTTAAGTAAAAAGCTCTCAAACTTTAAAAAAGAAACAATTAAGCCACTGCTTTGATA
*
2733830 CAAGCATGCAGGCATAAGCATGCAGGCGTCGGAAGCTATCAGCTTTGATAAACTTAAATCCCACC
196 CAAGCATGCAGGCACAAGCATGCAGGCGTCGGAAGCTATCAGCTTTGATAAACTTAAATCCCACC
*
2733895 AGCTGTCCCATAGCCGCCAACATATGAATAACCATTCATAAACTTTTGGAAGTGCGTGTTATTGG
261 AGCTGTCCCATAGTCGCCAACATATGAATAACCATTCATAAACTTTTGGAAGTGCGTGTTATTGG
2733960 GTTCGTCTATTAAACTGCTTTAATAAACAAACATATGAATTCATAATCTCAAAATACAAAGGAGA
326 GTTCGTCTATTAAACTGCTTTAATAAACAAACATATGAATTCATAATCTCAAAATACAAAGGAGA
* *
2734025 ATGAACATCTCTGCTTTCTACCTTTTCACATCTA-TTTTTTGGCTTAAGTAAAAAGCTCTCCAAC
391 ATGAACATCTCTGCTTTCTACCTTTTCACATCCATTTTTTTGGCTTAAGTAAAAAGCCCTCCAAC
*
2734089 TTTTAAAAATAAACAATTAAGCC
456 TTTTAAAAAGAAACAATTAAGCC
2734112 GCTACAATTA
Statistics
Matches: 1027, Mismatches: 26, Indels: 29
0.95 0.02 0.03
Matches are distributed among these distances:
575 51 0.05
576 471 0.46
577 1 0.00
579 1 0.00
580 1 0.00
586 1 0.00
590 1 0.00
592 1 0.00
593 4 0.00
596 2 0.00
597 1 0.00
598 1 0.00
600 1 0.00
602 1 0.00
604 489 0.48
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.30
Consensus pattern (589 bp):
TCATAAACTTTTGGAAGTGCGTGTTATTGGGTTCGTCTGTTAAACTGCTTTAATAAACAAACATA
TGAATTCATAATCTCAAAATACAAAGGAGAATGAACATCTCTGCTTTCTACCTTTTCACATCTAT
TTTTTTGGCTTAAGTAAAAAGCTCTCAAACTTTAAAAAAGAAACAATTAAGCCACTGCTTTGATA
CAAGCATGCAGGCACAAGCATGCAGGCGTCGGAAGCTATCAGCTTTGATAAACTTAAATCCCACC
AGCTGTCCCATAGTCGCCAACATATGAATAACCATTCATAAACTTTTGGAAGTGCGTGTTATTGG
GTTCGTCTATTAAACTGCTTTAATAAACAAACATATGAATTCATAATCTCAAAATACAAAGGAGA
ATGAACATCTCTGCTTTCTACCTTTTCACATCCATTTTTTTGGCTTAAGTAAAAAGCCCTCCAAC
TTTTAAAAAGAAACAATTAAGCCACTGCTTTGATACAAGCATGCAGGACAGATGCAGGCAAGCAT
CAGTGCTACAGCTTTGATAAACTTAAATCCCACCAGCTGTCCCATAACCGCCAACATATGAATAA
CCAT
Found at i:2734118 original size:14 final size:14
Alignment explanation
Indices: 2734101--2734129 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2734091 TTAAAAATAA
2734101 ACAATTAAGCCGCT
1 ACAATTAAGCCGCT
2734115 ACAATTAAGCCGCT
1 ACAATTAAGCCGCT
2734129 A
1 A
2734130 TGTATAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.28, G:0.14, T:0.21
Consensus pattern (14 bp):
ACAATTAAGCCGCT
Found at i:2741997 original size:15 final size:15
Alignment explanation
Indices: 2741963--2742021 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
2741953 TAAATTTGAT
* *
2741963 ACTTAAATTTTCAAT
1 ACTTAATTTTTCAAC
2741978 ACTTAATTTTTCAAC
1 ACTTAATTTTTCAAC
* * ***
2741993 CCTTATTTTTTTTTC
1 ACTTAATTTTTCAAC
2742008 ACTTAATTTTTCAA
1 ACTTAATTTTTCAA
2742022 TTTATCAAAA
Statistics
Matches: 32, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (15 bp):
ACTTAATTTTTCAAC
Found at i:2745954 original size:116 final size:112
Alignment explanation
Indices: 2745802--2746065 Score: 384
Period size: 116 Copynumber: 2.3 Consensus size: 112
2745792 AACGTGCTAG
* * * *
2745802 AATTTGAAGAAATGATTGTCTAAAATGGCTGTTGTTTTCATAATTTATTATGTCAGAAATTTGAA
1 AATTTGAACAAATGGTTGTCTAAAATGGCTGCTGTTTTCACAATTTATTATGTCAGAAATTTGAA
*
2745867 GAAATGATTGTCTAAAATGGCTGCTGTTTTCACAATTTATTATGTCTGA
66 GAAATGATTGTCTAAAATGGCTGCTGTTTCCACAATTTATTATG--TGA
*
2745916 AATTTGAATTCAAATGGTTGTCTAAAATGGCTGCTGTTTTCACAATTTATTATGTCTGAAATTTG
1 AATTTGAA--CAAATGGTTGTCTAAAATGGCTGCTGTTTTCACAATTTATTATGTCAGAAATTTG
* * *
2745981 AAGAAATGGTTGTCTAAAATGGCTGCTGTTTCCAGAATTTATTCTGTGA
64 AAGAAATGATTGTCTAAAATGGCTGCTGTTTCCACAATTTATTATGTGA
* * *
2746030 CATTTGAAGAAATGGTTGTCTAAAACGGCTGCTGTT
1 AATTTGAACAAATGGTTGTCTAAAATGGCTGCTGTT
2746066 CTGTTATGGT
Statistics
Matches: 136, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
112 26 0.19
114 18 0.13
116 92 0.68
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (112 bp):
AATTTGAACAAATGGTTGTCTAAAATGGCTGCTGTTTTCACAATTTATTATGTCAGAAATTTGAA
GAAATGATTGTCTAAAATGGCTGCTGTTTCCACAATTTATTATGTGA
Found at i:2745955 original size:59 final size:57
Alignment explanation
Indices: 2745802--2746065 Score: 397
Period size: 57 Copynumber: 4.6 Consensus size: 57
2745792 AACGTGCTAG
* * * *
2745802 AATTTGAAGAAATGATTGTCTAAAATGGCTGTTGTTTTCATAATTTATTATGTCAGA
1 AATTTGAAGAAATGGTTGTCTAAAATGGCTGCTGTTTTCACAATTTATTATGTCTGA
*
2745859 AATTTGAAGAAATGATTGTCTAAAATGGCTGCTGTTTTCACAATTTATTATGTCTGA
1 AATTTGAAGAAATGGTTGTCTAAAATGGCTGCTGTTTTCACAATTTATTATGTCTGA
*
2745916 AATTTGAATTCAAATGGTTGTCTAAAATGGCTGCTGTTTTCACAATTTATTATGTCTGA
1 AATTTGAA--GAAATGGTTGTCTAAAATGGCTGCTGTTTTCACAATTTATTATGTCTGA
* * *
2745975 AATTTGAAGAAATGGTTGTCTAAAATGGCTGCTGTTTCCAGAATTTATTCTG--TGA
1 AATTTGAAGAAATGGTTGTCTAAAATGGCTGCTGTTTTCACAATTTATTATGTCTGA
* *
2746030 CATTTGAAGAAATGGTTGTCTAAAACGGCTGCTGTT
1 AATTTGAAGAAATGGTTGTCTAAAATGGCTGCTGTT
2746066 CTGTTATGGT
Statistics
Matches: 194, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
55 37 0.19
57 102 0.53
59 55 0.28
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (57 bp):
AATTTGAAGAAATGGTTGTCTAAAATGGCTGCTGTTTTCACAATTTATTATGTCTGA
Found at i:2747553 original size:17 final size:18
Alignment explanation
Indices: 2747518--2747558 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
2747508 ATTTTTTAGG
*
2747518 TTTAAATTTATTATTAAA
1 TTTAAATTCATTATTAAA
2747536 TTTAAATTCATT-TTAAA
1 TTTAAATTCATTATTAAA
2747553 TTTAAA
1 TTTAAA
2747559 ATATTTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTAAATTCATTATTAAA
Found at i:2747643 original size:13 final size:13
Alignment explanation
Indices: 2747627--2747692 Score: 64
Period size: 13 Copynumber: 4.9 Consensus size: 13
2747617 GTCCACTTAC
*
2747627 AAAGGTCCAAATT
1 AAAGGCCCAAATT
2747640 AAAGGCCC-AATT
1 AAAGGCCCAAATT
2747652 ACAAAGGCCCAAATT
1 --AAAGGCCCAAATT
*
2747667 GAAGGCCC-AATT
1 AAAGGCCCAAATT
2747679 ACAATGGCCCAAAT
1 A-AA-GGCCCAAAT
2747693 AGGCCCAATG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
12 8 0.18
13 16 0.36
14 13 0.30
15 7 0.16
ACGTcount: A:0.42, C:0.24, G:0.17, T:0.17
Consensus pattern (13 bp):
AAAGGCCCAAATT
Done.