Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 99 of 182
Found at i:29879176 original size:19 final size:20
Alignment explanation
Indices: 29879140--29879177 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29879130 TCATTCCTTC
*
29879140 AAAAAAACAAAATTCTCTCT
1 AAAAAAACAAAATGCTCTCT
29879160 AAAAAAACAAAA-GCTCTC
1 AAAAAAACAAAATGCTCTC
29879178 AACCTTCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.58, C:0.21, G:0.03, T:0.18
Consensus pattern (20 bp):
AAAAAAACAAAATGCTCTCT
Found at i:29881508 original size:30 final size:30
Alignment explanation
Indices: 29881467--29881528 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
29881457 ATGTCATGTT
*
29881467 AATAAATAATTAAAATTTAAAAATTAAAAA
1 AATAAAAAATTAAAATTTAAAAATTAAAAA
* * **
29881497 AATAAAAAATTATAATTTCAATTTTAAAAA
1 AATAAAAAATTAAAATTTAAAAATTAAAAA
29881527 AA
1 AA
29881529 AAACCTTCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (30 bp):
AATAAAAAATTAAAATTTAAAAATTAAAAA
Found at i:29881808 original size:14 final size:14
Alignment explanation
Indices: 29881771--29881810 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 14
29881761 TGTTGTATGC
29881771 ATTTTATTAATAA-
1 ATTTTATTAATAAT
29881784 A-TTTA--AATAAT
1 ATTTTATTAATAAT
29881795 ATTTTATTAATAAT
1 ATTTTATTAATAAT
29881809 AT
1 AT
29881811 GGTTACGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
10 5 0.22
11 1 0.04
12 8 0.35
13 1 0.04
14 8 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTTTATTAATAAT
Found at i:29882996 original size:30 final size:30
Alignment explanation
Indices: 29882961--29883018 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
29882951 CTGAGCATTT
*
29882961 CCACACGGGCTTGGCACACGCCTGTGTGAG
1 CCACACGGGCTTGACACACGCCTGTGTGAG
29882991 CCACACGGGCTTGACACACGCCTGTGTG
1 CCACACGGGCTTGACACACGCCTGTGTG
29883019 CCAGCCGGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.17, C:0.34, G:0.31, T:0.17
Consensus pattern (30 bp):
CCACACGGGCTTGACACACGCCTGTGTGAG
Found at i:29885332 original size:97 final size:98
Alignment explanation
Indices: 29885207--29885402 Score: 315
Period size: 97 Copynumber: 2.0 Consensus size: 98
29885197 CTAAAAATAA
* *
29885207 TAAAGGAAATATTCCGAGTTTGAGATTTTAGAGGAATCGTGACCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCAAGTTTGAGATTTTAGAGGAATCGTGACCTAACATATTGGGTGTGATTTC
* *
29885272 TTAAATCTTGGGTAAGTGAAT-TTTTTTTAAAG
66 TTAAATCTTGGATAAGTGAATGTTCTTTTAAAG
*
29885304 TAAAGGAAATATTCCAAGTTT-AGGATTTTAGAGGAATCGTGCCCTAACATATTGGGTGTGATTT
1 TAAAGGAAATATTCCAAGTTTGA-GATTTTAGAGGAATCGTGACCTAACATATTGGGTGTGATTT
*
29885368 CTTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
65 CTTAAATCTTGGATAAGTGAATGTTCTTTTAAAG
29885402 T
1 T
29885403 TTTATTGCAC
Statistics
Matches: 91, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
96 1 0.01
97 79 0.87
98 11 0.12
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.38
Consensus pattern (98 bp):
TAAAGGAAATATTCCAAGTTTGAGATTTTAGAGGAATCGTGACCTAACATATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGAATGTTCTTTTAAAG
Found at i:29890299 original size:40 final size:40
Alignment explanation
Indices: 29890248--29890364 Score: 207
Period size: 40 Copynumber: 2.9 Consensus size: 40
29890238 CGTTTGGAGC
* **
29890248 AAAAGCGCCGCTAAAGAGTGAGCATTAGCGGCGTTTAATT
1 AAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTAAGG
29890288 AAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTAAGG
1 AAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTAAGG
29890328 AAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTA
1 AAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTA
29890365 TAGATAACGC
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 74 1.00
ACGTcount: A:0.32, C:0.16, G:0.30, T:0.21
Consensus pattern (40 bp):
AAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTAAGG
Found at i:29890506 original size:111 final size:111
Alignment explanation
Indices: 29890312--29890671 Score: 684
Period size: 111 Copynumber: 3.2 Consensus size: 111
29890302 AGAGTGAGCA
** * *
29890312 TTAGTGGCGTTTAAGGAAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCG
1 TTAGTGGCGTTTATTGTAAAGCACCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCG
29890377 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGAC
66 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGAC
29890423 TTAGTGGCGTTTATTGTAAAGCACCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCG
1 TTAGTGGCGTTTATTGTAAAGCACCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCG
29890488 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGAC
66 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGAC
29890534 TTAGTGGCGTTTATTGTAAAGCACCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCG
1 TTAGTGGCGTTTATTGTAAAGCACCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCG
29890599 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGAC
66 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGAC
29890645 TTAGTGGCGTTTATTGTAAAGCACCGC
1 TTAGTGGCGTTTATTGTAAAGCACCGC
29890672 AGGACTTAGT
Statistics
Matches: 245, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 245 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (111 bp):
TTAGTGGCGTTTATTGTAAAGCACCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCG
CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGAC
Found at i:29890677 original size:32 final size:32
Alignment explanation
Indices: 29890641--29890703 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
29890631 GCCTTTGGGG
*
29890641 GGACTTAGTGGCGTTTATTGTAAAGCACCGCA
1 GGACTTAGTGGCGTTTATTGCAAAGCACCGCA
*
29890673 GGACTTAGTGGCGTTTATTGCAAAGCGCCGC
1 GGACTTAGTGGCGTTTATTGCAAAGCACCGC
29890704 TAAAGAGTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.27
Consensus pattern (32 bp):
GGACTTAGTGGCGTTTATTGCAAAGCACCGCA
Found at i:29890734 original size:254 final size:255
Alignment explanation
Indices: 29890419--29890926 Score: 982
Period size: 254 Copynumber: 2.0 Consensus size: 255
29890409 GCCTTTGGGG
*
29890419 GGACTTAGTGGCGTTTATTGTAAAGCACCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAAC
1 GGACTTAGTGGCGTTTATTGCAAAGCACCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAAC
29890484 GCCGCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGACTTAGTGGCGTTTATT
66 GCCGCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGACTTAGTGGCGTTTATT
*
29890549 GTAAAGCACCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCGCAAATAATACACCCA
131 GTAAAGCACCGCTAAAGAGTGAGCATTAGTGGCGTTTATAAATAACGCCGCAAATAATACACCCA
29890614 GACGGTGCCGTTTTGTGGCCTTT-GGGGGGACTTAGTGGCGTTTATTGTAAAGCACCGCA
196 GACGGTGCCGTTTTGTGGCCTTTGGGGGGGACTTAGTGGCGTTTATTGTAAAGCACCGCA
*
29890673 GGACTTAGTGGCGTTTATTGCAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAAC
1 GGACTTAGTGGCGTTTATTGCAAAGCACCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAAC
29890738 GCCGCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGACTTAGTGGCGTTTATT
66 GCCGCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGACTTAGTGGCGTTTATT
29890803 GTAAAGCACCGCTAAAGAGTGAGCATTAGTGGCGTTTATAAATAACGCCGCAAATAATACACCCA
131 GTAAAGCACCGCTAAAGAGTGAGCATTAGTGGCGTTTATAAATAACGCCGCAAATAATACACCCA
29890868 GACGGTGCCGTTTTGTGGCCTTTGGGGGGGACTTAGTGGCGTTTATTGTAAAGCACCGC
196 GACGGTGCCGTTTTGTGGCCTTTGGGGGGGACTTAGTGGCGTTTATTGTAAAGCACCGC
29890927 TAAAGAGTGA
Statistics
Matches: 250, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
254 215 0.86
255 35 0.14
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (255 bp):
GGACTTAGTGGCGTTTATTGCAAAGCACCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAAC
GCCGCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGACTTAGTGGCGTTTATT
GTAAAGCACCGCTAAAGAGTGAGCATTAGTGGCGTTTATAAATAACGCCGCAAATAATACACCCA
GACGGTGCCGTTTTGTGGCCTTTGGGGGGGACTTAGTGGCGTTTATTGTAAAGCACCGCA
Found at i:29890788 original size:143 final size:143
Alignment explanation
Indices: 29890530--29890814 Score: 552
Period size: 143 Copynumber: 2.0 Consensus size: 143
29890520 GCCTTTGGGG
*
29890530 GGACTTAGTGGCGTTTATTGTAAAGCACCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAAC
1 GGACTTAGTGGCGTTTATTGCAAAGCACCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAAC
29890595 GCCGCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGACTTAGTGGCGTTTATT
66 GCCGCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGACTTAGTGGCGTTTATT
29890660 GTAAAGCACCGCA
131 GTAAAGCACCGCA
*
29890673 GGACTTAGTGGCGTTTATTGCAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAAC
1 GGACTTAGTGGCGTTTATTGCAAAGCACCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAAC
29890738 GCCGCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGACTTAGTGGCGTTTATT
66 GCCGCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGACTTAGTGGCGTTTATT
29890803 GTAAAGCACCGC
131 GTAAAGCACCGC
29890815 TAAAGAGTGA
Statistics
Matches: 140, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
143 140 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (143 bp):
GGACTTAGTGGCGTTTATTGCAAAGCACCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAAC
GCCGCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGACTTAGTGGCGTTTATT
GTAAAGCACCGCA
Found at i:29890953 original size:112 final size:112
Alignment explanation
Indices: 29890673--29891265 Score: 1003
Period size: 111 Copynumber: 5.3 Consensus size: 112
29890663 AAGCACCGCA
*
29890673 GGACTTAGTGGCGTTTATTGCAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAAC
1 GGACTTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAAC
29890738 GCCGCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTT-GGGG
66 GCCGCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGG
* *
29890784 GGACTTAGTGGCGTTTATTGTAAAGCACCGCTAAAGAGTGAGCATTAGTGGCGTTTATAAATAAC
1 GGACTTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAAC
29890849 GCCGCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGG
66 GCCGCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGG
*
29890896 GGACTTAGTGGCGTTTATTGTAAAGCACCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAAC
1 GGACTTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAAC
29890961 GCCGCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTT-GGGG
66 GCCGCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGG
29891007 GGACTTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAAC
1 GGACTTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAAC
*
29891072 GCCGCAAATAATACACCCAGACGGTGCTGTTTTGTGGCCTTTGGGGG
66 GCCGCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGG
* ** * * *
29891119 GGACTTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGCTTATAAAAAAA
1 GGACTTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTAT-AGATAA
* * *
29891184 TGCCGCAAATAATACTCCCAGACGGTGCCGTTTTGTGTCCTTTGGGGG
65 CGCCGCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGG
* *
29891232 GG-CATTAGTGGCATTTTTTGTAAAGCGCCGCTAA
1 GGAC-TTAGTGGCGTTTATTGTAAAGCGCCGCTAA
29891266 TCTAGGTGTT
Statistics
Matches: 460, Mismatches: 18, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
111 213 0.46
112 169 0.37
113 78 0.17
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (112 bp):
GGACTTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAAC
GCCGCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGG
Found at i:29891061 original size:223 final size:223
Alignment explanation
Indices: 29890673--29891265 Score: 1015
Period size: 223 Copynumber: 2.7 Consensus size: 223
29890663 AAGCACCGCA
*
29890673 GGACTTAGTGGCGTTTATTGCAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAAC
1 GGACTTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAAC
29890738 GCCGCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGACTTAGTGGCGTTTATT
66 GCCGCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGACTTAGTGGCGTTTATT
*
29890803 GTAAAGCACCGCTAAAGAGTGAGCATTAGTGGCGTTTATAAATAACGCCGCAAATAATACACCCA
131 GTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAAATAACGCCGCAAATAATACACCCA
29890868 GACGGTGCCGTTTTGTGGCCTTTGGGGG
196 GACGGTGCCGTTTTGTGGCCTTTGGGGG
*
29890896 GGACTTAGTGGCGTTTATTGTAAAGCACCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAAC
1 GGACTTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAAC
29890961 GCCGCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGACTTAGTGGCGTTTATT
66 GCCGCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGACTTAGTGGCGTTTATT
*
29891026 GTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCGCAAATAATACACCCA
131 GTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAAATAACGCCGCAAATAATACACCCA
*
29891091 GACGGTGCTGTTTTGTGGCCTTTGGGGG
196 GACGGTGCCGTTTTGTGGCCTTTGGGGG
* ** * * *
29891119 GGACTTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGCTTATAAAAAAA
1 GGACTTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTAT-AGATAA
* * * * * *
29891184 TGCCGCAAATAATACTCCCAGACGGTGCCGTTTTGTGTCCTTTGGGGGGGCATTAGTGGCATTTT
65 CGCCGCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGAC-TTAGTGGCGTTTA
29891249 TTGTAAAGCGCCGCTAA
129 TTGTAAAGCGCCGCTAA
29891266 TCTAGGTGTT
Statistics
Matches: 350, Mismatches: 18, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
223 271 0.77
224 51 0.15
225 28 0.08
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (223 bp):
GGACTTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAAC
GCCGCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGACTTAGTGGCGTTTATT
GTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAAATAACGCCGCAAATAATACACCCA
GACGGTGCCGTTTTGTGGCCTTTGGGGG
Found at i:29893031 original size:84 final size:84
Alignment explanation
Indices: 29892940--29893308 Score: 666
Period size: 84 Copynumber: 4.4 Consensus size: 84
29892930 TAGTTAAACT
*** * *
29892940 TTTAGTGGCGTTTTTAGGAAAATGCCACAAATAATGCAATTCCAGACCACGAAAACGGTGTCGTT
1 TTTAGTGGCGTTTTTCTAAAAACGCCACAAAAAATGCAATTCCAGACCACGAAAACGGTGTCGTT
29893005 TCTGTTCACAGCTGTAATA
66 TCTGTTCACAGCTGTAATA
29893024 TTTAGTGGCGTTTTTCTAAAAACGCCACAAAAAATGCAATTCCAGACCACGAAAACGGTGTCGTT
1 TTTAGTGGCGTTTTTCTAAAAACGCCACAAAAAATGCAATTCCAGACCACGAAAACGGTGTCGTT
29893089 TCTGTTCACAGCTGTAATA
66 TCTGTTCACAGCTGTAATA
29893108 TTTAGTGGCGTTTTTCTAAAAACGCCACAAAAAATGCAATTCCAGACCACGAAAACGGTGTCGTT
1 TTTAGTGGCGTTTTTCTAAAAACGCCACAAAAAATGCAATTCCAGACCACGAAAACGGTGTCGTT
29893173 TCTGTTCACAGCTGTAATA
66 TCTGTTCACAGCTGTAATA
29893192 TTTAGTGGCGTTTTTCTAAAAACGCCACAAAAAATGCAATTCCAGACCACGAAAACGGTGTCGTT
1 TTTAGTGGCGTTTTTCTAAAAACGCCACAAAAAATGCAATTCCAGACCACGAAAACGGTGTCGTT
29893257 TCTGTTCACAGCTGTAATA
66 TCTGTTCACAGCTGTAATA
* *
29893276 TTTAGTGGCGTTTTTACCAAAAATGCCACAAAA
1 TTTAGTGGCGTTTTT-CTAAAAACGCCACAAAA
29893309 CGGTGTTAAT
Statistics
Matches: 277, Mismatches: 7, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
84 262 0.95
85 15 0.05
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (84 bp):
TTTAGTGGCGTTTTTCTAAAAACGCCACAAAAAATGCAATTCCAGACCACGAAAACGGTGTCGTT
TCTGTTCACAGCTGTAATA
Found at i:29894530 original size:11 final size:11
Alignment explanation
Indices: 29894510--29894538 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
29894500 GAATATCTCA
29894510 AACT-ATGGGT
1 AACTAATGGGT
29894520 AACTAATGGGT
1 AACTAATGGGT
29894531 AACTAATG
1 AACTAATG
29894539 TATTATCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.28
Consensus pattern (11 bp):
AACTAATGGGT
Found at i:29896037 original size:40 final size:40
Alignment explanation
Indices: 29895896--29896171 Score: 227
Period size: 40 Copynumber: 6.7 Consensus size: 40
29895886 AATACATTAC
*
29895896 TTACTAAAATAAATTACTTACTAAAA----TTTAAATTTA
1 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
29895932 TTACTAAAATACATTACTTAC-ATAAATTTGTTTAAATTTA
1 TTACTAAAATACATTACTTACTA-AAATTTGTTTAAATTTA
*
29895972 TTTCTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
1 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
29896012 TTACTAAAATACATTACTTACTAAAA------TAAA-TTA
1 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
* *
29896045 CTTACTAAAATTTAAATTTA-TTACTAAAATACATTACTTACATAAATTTGTTTAAA
1 -TTACTAAAA--TACA-TTACTTACTAAAAT---TT-GTT---TAAA----TTT--A
29896101 TTTATTTCTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
1 -TTA---CTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
29896145 TTACTAAAATACATTACTTACTAAAAT
1 TTACTAAAATACATTACTTACTAAAAT
29896172 AAATTACTTA
Statistics
Matches: 199, Mismatches: 7, Indels: 64
0.74 0.03 0.24
Matches are distributed among these distances:
33 3 0.02
34 13 0.07
35 1 0.01
36 35 0.18
37 3 0.02
40 96 0.48
41 1 0.01
43 3 0.02
44 1 0.01
46 3 0.02
49 4 0.02
50 4 0.02
53 2 0.01
54 4 0.02
56 7 0.04
57 13 0.07
59 6 0.03
ACGTcount: A:0.45, C:0.11, G:0.01, T:0.43
Consensus pattern (40 bp):
TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
Found at i:29896069 original size:133 final size:133
Alignment explanation
Indices: 29895870--29896292 Score: 830
Period size: 133 Copynumber: 3.2 Consensus size: 133
29895860 CGATTGAATG
29895870 TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTAAAATTTAAATTTATTA
1 TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTAAAATTTAAATTTATTA
29895935 CTAAAATACATTACTTACATAAATTTGTTTAAATTTATTTCTAAAATACATTACTTACTAAAATT
66 CTAAAATACATTACTTACATAAATTTGTTTAAATTTATTTCTAAAATACATTACTTACTAAAATT
29896000 TGT
131 TGT
29896003 TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTAAAATTTAAATTTATTA
1 TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTAAAATTTAAATTTATTA
29896068 CTAAAATACATTACTTACATAAATTTGTTTAAATTTATTTCTAAAATACATTACTTACTAAAATT
66 CTAAAATACATTACTTACATAAATTTGTTTAAATTTATTTCTAAAATACATTACTTACTAAAATT
29896133 TGT
131 TGT
29896136 TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTAAAATTTAAATTTATTA
1 TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTAAAATTTAAATTTATTA
29896201 CTAAAATACATTACTTACATAAATTTGTTTAAATTTATTTCTAAAATACATTACTTACTAAAATT
66 CTAAAATACATTACTTACATAAATTTGTTTAAATTTATTTCTAAAATACATTACTTACTAAAATT
29896266 TGT
131 TGT
*
29896269 TTAAATTTATTACTTAAATA-ATTA
1 TTAAATTTATTACTAAAATACATTA
29896293 TAAATAAGAT
Statistics
Matches: 289, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
132 4 0.01
133 285 0.99
ACGTcount: A:0.44, C:0.10, G:0.01, T:0.44
Consensus pattern (133 bp):
TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTAAAATTTAAATTTATTA
CTAAAATACATTACTTACATAAATTTGTTTAAATTTATTTCTAAAATACATTACTTACTAAAATT
TGT
Found at i:29896092 original size:93 final size:89
Alignment explanation
Indices: 29895870--29896223 Score: 346
Period size: 93 Copynumber: 3.8 Consensus size: 89
29895860 CGATTGAATG
* *
29895870 TTAAATTTATTACTAAAATACATTACTTACTAAA--ATAAA-TTACTTACTAAAATTTAAATTTA
1 TTAAATTTATTACTAAAATACATTACTTACTAAAGTTTAAATTTA-TTACTAAAA--TACA-TTA
* *
29895932 -TTACTAAAATACATTACTTACATAAATTTGT
62 CTTACTAAAATAAATTACTTAC-TAAA---AT
*
29895963 TTAAATTTATTTCTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTA
1 TTAAATTTATTACTAAAATACATTACTTACT-AAA---GTTTAAATTTATTACTAAAATACATTA
29896028 CTTACTAAAATAAATTACTTACTAAAAT
62 CTTACTAAAATAAATTACTTACTAAAAT
*
29896056 TTAAATTTATTACTAAAATACATTACTTACATAAATTTGTTTAAATTTATTTCTAAAATACATTA
1 TTAAATTTATTACTAAAATACATTACTTAC-TAAA---GTTTAAATTTATTACTAAAATACATTA
29896121 CTTACTAAAATTTGTTTAAATTTA-TTACTAAAA-
62 CTTACTAAAA------TAAA-TTACTTACTAAAAT
* * *
29896154 -TACA-TTACTTACTAAAATAAATTACTTACTAAAATTTAAATTTATTACTAAAATACATTACTT
1 TTAAATTTA-TTACTAAAATACATTACTTACTAAAGTTTAAATTTATTACTAAAATACATTACTT
29896217 ACATAAA
65 AC-TAAA
29896224 TTTGTTTAAA
Statistics
Matches: 232, Mismatches: 11, Indels: 35
0.83 0.04 0.13
Matches are distributed among these distances:
93 132 0.57
94 8 0.03
96 14 0.06
97 46 0.20
99 26 0.11
100 6 0.03
ACGTcount: A:0.45, C:0.11, G:0.01, T:0.43
Consensus pattern (89 bp):
TTAAATTTATTACTAAAATACATTACTTACTAAAGTTTAAATTTATTACTAAAATACATTACTTA
CTAAAATAAATTACTTACTAAAAT
Found at i:29896224 original size:17 final size:17
Alignment explanation
Indices: 29895879--29896223 Score: 191
Period size: 17 Copynumber: 18.5 Consensus size: 17
29895869 GTTAAATTTA
*
29895879 TTACTAAAATACATTAC
1 TTACTAAAATAAATTAC
29895896 TTACTAAAATAAATTAC
1 TTACTAAAATAAATTAC
29895913 TTACTAAAATTTAAATTTA-
1 TTACTAAAA--TAAA-TTAC
*
29895932 TTACTAAAATACATTAC
1 TTACTAAAATAAATTAC
*
29895949 TTACATAAATTTGTTTAAATTTA-
1 TTAC-TAAA-----ATAAA-TTAC
* *
29895972 TTTCTAAAATACATTAC
1 TTACTAAAATAAATTAC
29895989 TTACTAAAATTTGTTTAAATTTA-
1 TTACTAAAA------TAAA-TTAC
*
29896012 TTACTAAAATACATTAC
1 TTACTAAAATAAATTAC
29896029 TTACTAAAATAAATTAC
1 TTACTAAAATAAATTAC
29896046 TTACTAAAATTTAAATTTA-
1 TTACTAAAA--TAAA-TTAC
*
29896065 TTACTAAAATACATTAC
1 TTACTAAAATAAATTAC
*
29896082 TTACATAAATTTGTTTAAATTTA-
1 TTAC-TAAA-----ATAAA-TTAC
* *
29896105 TTTCTAAAATACATTAC
1 TTACTAAAATAAATTAC
29896122 TTACTAAAATTTGTTTAAATTTA-
1 TTACTAAAA------TAAA-TTAC
*
29896145 TTACTAAAATACATTAC
1 TTACTAAAATAAATTAC
29896162 TTACTAAAATAAATTAC
1 TTACTAAAATAAATTAC
29896179 TTACTAAAATTTAAATTTA-
1 TTACTAAAA--TAAA-TTAC
*
29896198 TTACTAAAATACATTAC
1 TTACTAAAATAAATTAC
29896215 TTACATAAA
1 TTAC-TAAA
29896224 TTTGTTTAAA
Statistics
Matches: 261, Mismatches: 22, Indels: 89
0.70 0.06 0.24
Matches are distributed among these distances:
16 21 0.08
17 124 0.48
18 12 0.05
19 39 0.15
20 9 0.03
22 8 0.03
23 36 0.14
24 12 0.05
ACGTcount: A:0.46, C:0.11, G:0.01, T:0.42
Consensus pattern (17 bp):
TTACTAAAATAAATTAC
Found at i:29896225 original size:93 final size:92
Alignment explanation
Indices: 29895975--29896264 Score: 351
Period size: 93 Copynumber: 3.1 Consensus size: 92
29895965 AAATTTATTT
29895975 CTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAA---
1 CTAAAATACATTACTTACTAAAA----TTTAAATTTATTACTAAAATACATTACTTACTAAATTT
* *
29896037 --ATAAA-TTACTTACTAAAATTTAAATTTA-TTA
62 GTTTAAATTTA-TTACTAAAA--TACA-TTACTTA
* *
29896068 CTAAAATACATTACTTACATAAATTTGTTTAAATTTATTTCTAAAATACATTACTTACTAAAATT
1 CTAAAATACATTACTTAC-TAAA---ATTTAAATTTATTACTAAAATACATTACTTACT-AAATT
29896133 TGTTTAAATTTATTACTAAAATACATTACTTA
61 TGTTTAAATTTATTACTAAAATACATTACTTA
*
29896165 CTAAAATAAATTACTTACTAAAATTTAAATTTATTACTAAAATACATTACTTACATAAATTTGTT
1 CTAAAATACATTACTTACTAAAATTTAAATTTATTACTAAAATACATTACTTAC-TAAATTTGTT
*
29896230 TAAATTTATTTCTAAAATACATTACTTA
65 TAAATTTATTACTAAAATACATTACTTA
29896258 CTAAAAT
1 CTAAAAT
29896265 TTGTTTAAAT
Statistics
Matches: 176, Mismatches: 8, Indels: 26
0.84 0.04 0.12
Matches are distributed among these distances:
93 122 0.69
94 8 0.05
96 7 0.04
97 23 0.13
99 13 0.07
100 3 0.02
ACGTcount: A:0.45, C:0.11, G:0.01, T:0.43
Consensus pattern (92 bp):
CTAAAATACATTACTTACTAAAATTTAAATTTATTACTAAAATACATTACTTACTAAATTTGTTT
AAATTTATTACTAAAATACATTACTTA
Found at i:29896267 original size:40 final size:40
Alignment explanation
Indices: 29896162--29896292 Score: 184
Period size: 40 Copynumber: 3.4 Consensus size: 40
29896152 AATACATTAC
*
29896162 TTACTAAAATAAATTACTTACTAAAA----TTTAAATTTA
1 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
29896198 TTACTAAAATACATTACTTAC-ATAAATTTGTTTAAATTTA
1 TTACTAAAATACATTACTTACTA-AAATTTGTTTAAATTTA
*
29896238 TTTCTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
1 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
*
29896278 TTACTTAAATA-ATTA
1 TTACTAAAATACATTA
29896293 TAAATAAGAT
Statistics
Matches: 85, Mismatches: 4, Indels: 9
0.87 0.04 0.09
Matches are distributed among these distances:
35 1 0.01
36 23 0.27
39 4 0.05
40 56 0.66
41 1 0.01
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.45
Consensus pattern (40 bp):
TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
Found at i:29896574 original size:19 final size:19
Alignment explanation
Indices: 29896550--29896630 Score: 84
Period size: 19 Copynumber: 4.5 Consensus size: 19
29896540 TATTAAATAA
29896550 TACATAATAACTTACAACT
1 TACATAATAACTTACAACT
*
29896569 TACATAAT-ACATT-TAACT
1 TACATAATAAC-TTACAACT
*
29896587 TACAT--T-ACTTACATA-A
1 TACATAATAACTTACA-ACT
29896603 TACATAATAACTTACAACT
1 TACATAATAACTTACAACT
29896622 TACATAATA
1 TACATAATA
29896631 CATTTAACTT
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
15 2 0.04
16 9 0.18
17 1 0.02
18 13 0.25
19 26 0.51
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.35
Consensus pattern (19 bp):
TACATAATAACTTACAACT
Found at i:29896588 original size:18 final size:18
Alignment explanation
Indices: 29896565--29896733 Score: 94
Period size: 18 Copynumber: 9.6 Consensus size: 18
29896555 AATAACTTAC
29896565 AACTTACATAATACATTT
1 AACTTACATAATACATTT
*
29896583 AACTTACATTACTTACA--T
1 AACTTACA-TA-ATACATTT
*
29896601 AA--TACATAATA-ACTTAC
1 AACTTACATAATACA-TT-T
29896618 AACTTACATAATACATTT
1 AACTTACATAATACATTT
* *
29896636 AACTTACA-ACTTACA--C
1 AACTTACATA-ATACATTT
* *
29896652 AA--TACAT-TTA-ACTTAC
1 AACTTACATAATACA-TT-T
*
29896668 AACTTACATAATACATAAT
1 AACTTACATAATACAT-TT
*
29896687 AACTTACA-ACTTACATTT
1 AACTTACATA-ATACATTT
29896705 AACTTACATAATACATTT
1 AACTTACATAATACATTT
29896723 AACTTACATAA
1 AACTTACATAA
29896734 CTTACATAAC
Statistics
Matches: 117, Mismatches: 12, Indels: 44
0.68 0.07 0.25
Matches are distributed among these distances:
12 1 0.01
13 4 0.03
14 6 0.05
15 2 0.02
16 9 0.08
17 3 0.03
18 56 0.48
19 30 0.26
20 6 0.05
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.35
Consensus pattern (18 bp):
AACTTACATAATACATTT
Found at i:29896590 original size:25 final size:26
Alignment explanation
Indices: 29896546--29896702 Score: 239
Period size: 25 Copynumber: 6.1 Consensus size: 26
29896536 ATTTTATTAA
29896546 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
29896572 ATAATACAT-TTAACTTACATTACTTAC
1 ATAATACATAATAACTTACA--ACTTAC
29896599 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
29896625 ATAATACAT-TTAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
* *
29896650 ACAATACAT-TTAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
29896675 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
29896701 AT
1 AT
29896703 TTAACTTACA
Statistics
Matches: 121, Mismatches: 6, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
25 56 0.46
26 41 0.34
27 15 0.12
28 9 0.07
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (26 bp):
ATAATACATAATAACTTACAACTTAC
Found at i:29896604 original size:53 final size:51
Alignment explanation
Indices: 29896546--29896702 Score: 253
Period size: 53 Copynumber: 3.0 Consensus size: 51
29896536 ATTTTATTAA
29896546 ATAATACATAATAACTTACAACTTACATAATACATTTAACTTACATTACTTAC
1 ATAATACATAATAACTTACAACTTACATAATACATTTAACTTACA--ACTTAC
29896599 ATAATACATAATAACTTACAACTTACATAATACATTTAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTACATAATACATTTAACTTACAACTTAC
* * *
29896650 ACAATACAT-TTAACTTACAACTTACATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTACATAATACAT-TTAACTTACAACTTAC
29896701 AT
1 AT
29896703 TTAACTTACA
Statistics
Matches: 99, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
50 24 0.24
51 30 0.30
53 45 0.45
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (51 bp):
ATAATACATAATAACTTACAACTTACATAATACATTTAACTTACAACTTAC
Found at i:29896710 original size:11 final size:10
Alignment explanation
Indices: 29896694--29896747 Score: 55
Period size: 9 Copynumber: 5.7 Consensus size: 10
29896684 AATAACTTAC
29896694 AACTTACATTT
1 AACTTACA-TT
29896705 AACTTACA-T
1 AACTTACATT
29896714 AA--TACATTT
1 AACTTACA-TT
29896723 AACTTACA-T
1 AACTTACATT
29896732 AACTTACA-T
1 AACTTACATT
29896741 AACTTAC
1 AACTTAC
29896748 CATTGCAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
7 4 0.10
9 23 0.59
11 12 0.31
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (10 bp):
AACTTACATT
Found at i:29896743 original size:18 final size:18
Alignment explanation
Indices: 29896556--29896747 Score: 82
Period size: 18 Copynumber: 11.0 Consensus size: 18
29896546 ATAATACATA
29896556 ATAACTTAC--AACTTAC
1 ATAACTTACATAACTTAC
29896572 ATAA--TACATTTAACTTAC
1 ATAACTTACA--TAACTTAC
* *
29896590 ATTACTTACATAATACATA-
1 ATAACTTACAT-A-ACTTAC
29896609 ATAACTTAC--AACTTAC
1 ATAACTTACATAACTTAC
29896625 ATAA--TACATTTAACTTAC
1 ATAACTTACA--TAACTTAC
*
29896643 --AACTTACACAA--TAC
1 ATAACTTACATAACTTAC
29896657 ATTTAACTTAC--AACTTAC
1 A--TAACTTACATAACTTAC
*
29896675 ATAATACATA-ATAACTTAC
1 AT-A-ACTTACATAACTTAC
29896694 --AACTTACATTTAACTTAC
1 ATAACTTACA--TAACTTAC
29896712 ATAA--TACATTTAACTTAC
1 ATAACTTACA--TAACTTAC
29896730 ATAACTTACATAACTTAC
1 ATAACTTACATAACTTAC
29896748 CATTGCAATT
Statistics
Matches: 137, Mismatches: 7, Indels: 62
0.67 0.03 0.30
Matches are distributed among these distances:
14 9 0.07
15 8 0.06
16 18 0.13
17 1 0.01
18 71 0.52
19 16 0.12
20 14 0.10
ACGTcount: A:0.45, C:0.20, G:0.00, T:0.35
Consensus pattern (18 bp):
ATAACTTACATAACTTAC
Found at i:29902208 original size:21 final size:21
Alignment explanation
Indices: 29902182--29902252 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 21
29902172 CTACAACTTA
* *
29902182 AAGCAGAGGCGGAAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
*
29902203 AAGCAGCGGCTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* *
29902224 AAGCGGAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGGG
29902245 AAGCAGAG
1 AAGCAGAG
29902253 CAGAGCAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.31, C:0.18, G:0.48, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:29902626 original size:41 final size:41
Alignment explanation
Indices: 29902566--29902735 Score: 187
Period size: 42 Copynumber: 4.1 Consensus size: 41
29902556 TAGTGGCGTT
* *
29902566 TTTGTATAAAAGCGCCACTAAAGAACATGTTCTTTCGCGGCG
1 TTTGTA-AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCG
* *
29902608 TTTGTAAAAAATGCCACTAAAGAACATGTTATTTAGCGGCG
1 TTTGTAAAAAACGCCACTAAAGAACATGTTCTTTAGCGGCG
* * * *
29902649 CTTAGAAAAAAACGCCGCTAAAGAACATGATCTTTAGCGGCG
1 -TTTGTAAAAAACGCCACTAAAGAACATGTTCTTTAGCGGCG
* *** * *
29902691 TTTTTCCTTAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCG
1 TTTGT-AAAAAACGCCACTAAAGAACATGTTCTTTAGCGGCG
29902733 TTT
1 TTT
29902736 TTATTTGTAA
Statistics
Matches: 108, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
41 33 0.31
42 75 0.69
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.29
Consensus pattern (41 bp):
TTTGTAAAAAACGCCACTAAAGAACATGTTCTTTAGCGGCG
Found at i:29904756 original size:46 final size:46
Alignment explanation
Indices: 29904705--29904799 Score: 163
Period size: 46 Copynumber: 2.1 Consensus size: 46
29904695 ACAAAGATAG
*
29904705 AAACCAAAAAATTATCTCCTAAATTTTAACATCTAATCTCCTAATT
1 AAACCAAAAAATTATCTCCTAAACTTTAACATCTAATCTCCTAATT
* *
29904751 AAACCAAAACATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
1 AAACCAAAAAATTATCTCCTAAACTTTAACATCTAATCTCCTAATT
29904797 AAA
1 AAA
29904800 AGAAAAGAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.43, C:0.23, G:0.01, T:0.33
Consensus pattern (46 bp):
AAACCAAAAAATTATCTCCTAAACTTTAACATCTAATCTCCTAATT
Found at i:29915122 original size:68 final size:71
Alignment explanation
Indices: 29915049--29915186 Score: 203
Period size: 68 Copynumber: 2.0 Consensus size: 71
29915039 TTTAATAGAT
*
29915049 TTAATATTAAATTTAATTTAATACTTATCTTAATAG-T-AT-TT-TATTAATTTAATATTAAAGT
1 TTAATATTAAATTAAATTTAATACTTATCTT-ATAGATAATATTCTATTAATTTAATATTAAAGT
29915110 GATTATC
65 GATTATC
* *
29915117 TTAATATTAAATTAAATTTAATATTTATCTTATAGATAAATATTCTATTAATTTACTATTAAAGT
1 TTAATATTAAATTAAATTTAATACTTATCTTATAGAT-AATATTCTATTAATTTAATATTAAAGT
29915182 GATTA
65 GATTA
29915187 AATTTAATCA
Statistics
Matches: 62, Mismatches: 3, Indels: 6
0.87 0.04 0.08
Matches are distributed among these distances:
67 4 0.06
68 30 0.48
70 2 0.03
71 2 0.03
72 24 0.39
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.50
Consensus pattern (71 bp):
TTAATATTAAATTAAATTTAATACTTATCTTATAGATAATATTCTATTAATTTAATATTAAAGTG
ATTATC
Found at i:29918359 original size:14 final size:13
Alignment explanation
Indices: 29918337--29918370 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
29918327 TTATTTCAAT
29918337 AAAAAAAACACAA
1 AAAAAAAACACAA
*
29918350 AAAGAAAAACAGAA
1 AAA-AAAAACACAA
29918364 AAAAAAA
1 AAAAAAA
29918371 CTCCAAGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.85, C:0.09, G:0.06, T:0.00
Consensus pattern (13 bp):
AAAAAAAACACAA
Found at i:29919850 original size:297 final size:296
Alignment explanation
Indices: 29919316--29920492 Score: 1803
Period size: 297 Copynumber: 4.0 Consensus size: 296
29919306 CTCACGACGT
* *
29919316 TTCTGAAAACATCGTTGTTAGCACCATTGGCATAGGTACCATGACGCTTTGGAAAAAGCATTAGC
1 TTCTGAAAACATCGTTGTTAGCACCATTGGCATAGGTACCATGACGCTTTGGAAAAAGCGTCAGC
* * *
29919381 ATAATTCAACCTAAGTCAACCTTTATTCAAGGGTTGGTAAAAACCTAGTCAAGGTCGACGTTTAA
66 ATAATTCAACCTAGGTCAACCTTTATTCAAGGGTTGGTAAAGACCTAGTCAAGGTCAACGTTTAA
* *
29919446 AAAAGGTTGGGATAGGAGGAATT-AGACGATCGAAAAAAGTCGAAATAAAGCATTCATATGCCAA
131 AAAAGGTTGGGATAGGAGGAATTAAG-CGACCGAAAAAAGTCG-AATAAAGCATTCATATGCCGA
29919510 CTTATAAAGAGTTGGTTCATGCCCCCGTCAAAGGCT-ACATAAAAATAGTCGAGTTAGGTCGCAC
194 CTTATAAAGAGTTGGTTCATGCCCCCGTCAAAGG-TGACATAAAAATAGTCGAGTTAGGTCGCAC
29919574 TTAGT-CAGACTTTTAAAGAGTTGGCACATGTGTCGACAC
258 TTAGTCCA-ACTTTTAAAGAGTTGGCACATGTGTCGACAC
* *
29919613 TTCTGAAAACATCGTTGTTAGCACCATTGGCATAGGTGCCATGACGCTTTGGAAAAAGCGTCGGC
1 TTCTGAAAACATCGTTGTTAGCACCATTGGCATAGGTACCATGACGCTTTGGAAAAAGCGTCAGC
29919678 ATAATTCAACCTAGGTCAACCTTTATTCAAGGGTTGGTAAAGACCTAGTCAAGGTCAACGTTTAA
66 ATAATTCAACCTAGGTCAACCTTTATTCAAGGGTTGGTAAAGACCTAGTCAAGGTCAACGTTTAA
*
29919743 AAAAGGTTGGGATAGGAGGAATTAAGCGACCCAAAAAAGTCAGAATAAAGCATTCATATGCCGAC
131 AAAAGGTTGGGATAGGAGGAATTAAGCGACCGAAAAAAGTC-GAATAAAGCATTCATATGCCGAC
* * *
29919808 TTATAAAGAATTGGTTCATGCCCCCTTCAAAGGTGACATAAAAATAGTTGAGTTAGGTCGCACTT
195 TTATAAAGAGTTGGTTCATGCCCCCGTCAAAGGTGACATAAAAATAGTCGAGTTAGGTCGCACTT
* * *
29919873 AGTCCATCTTTTAAAGAGTTGGCACATGCGTCGACGC
260 AGTCCAACTTTTAAAGAGTTGGCACATGTGTCGACAC
*
29919910 TTCTGAAAACATCATTGTTAGCACCATTGGCATAGGTACCATGACGCTTTGGAAAAAGCGTCAGC
1 TTCTGAAAACATCGTTGTTAGCACCATTGGCATAGGTACCATGACGCTTTGGAAAAAGCGTCAGC
* *
29919975 ATAATTCAACCTAGGTCAACCTTTATTCAAGGGTTGGTAAAGACCTAGTCAAGGTCGACATTTAA
66 ATAATTCAACCTAGGTCAACCTTTATTCAAGGGTTGGTAAAGACCTAGTCAAGGTCAACGTTTAA
* * * * * * *
29920040 AACAGGTTGAGATAGGAGGAATTAGGCGATCGAAAAAATTCG--GAAA-CATTCATATACCGACT
131 AAAAGGTTGGGATAGGAGGAATTAAGCGACCGAAAAAAGTCGAATAAAGCATTCATATGCCGACT
* *
29920102 TATAAAGAGTTGGTTCATTCCCCAGTCAAAGG-GACA-AAAAATAGTCGAGTTAGGTCGCACTTA
196 TATAAAGAGTTGGTTCATGCCCCCGTCAAAGGTGACATAAAAATAGTCGAGTTAGGTCGCACTTA
* * *
29920165 GTCCAACTTTTAAAGAATTGGCACATGTGTCAACTC
261 GTCCAACTTTTAAAGAGTTGGCACATGTGTCGACAC
* * * *
29920201 TTCTGAAAACATCGTTGTTAGCACCATTAGCATAGGTACCATAACACTTTGGAAAAAGCGTCGGC
1 TTCTGAAAACATCGTTGTTAGCACCATTGGCATAGGTACCATGACGCTTTGGAAAAAGCGTCAGC
* *
29920266 ATAATTCAACCAAGGTCAACCTTTATTTAAGGGTTGGTAAAGACCTAGTCAAGGTCAACGTTTAA
66 ATAATTCAACCTAGGTCAACCTTTATTCAAGGGTTGGTAAAGACCTAGTCAAGGTCAACGTTTAA
* * * ** * *
29920331 AAAAGGTTGGCATAGGAGGAATTAGGAGACAAAAAAAAGTCAGAATAAAGAATTCATATGTCGAC
131 AAAAGGTTGGGATAGGAGGAATTAAGCGACCGAAAAAAGTC-GAATAAAGCATTCATATGCCGAC
* * *
29920396 TTATAAAGAGTTGGTTCATGCCCTCGTCAAAGGAGACATAAAAATAGTCGAGTTAGGTCACACTT
195 TTATAAAGAGTTGGTTCATGCCCCCGTCAAAGGTGACATAAAAATAGTCGAGTTAGGTCGCACTT
**
29920461 AGTCTGACTTTTAAAGAGTTGGCACATGTGTC
260 AGTCCAACTTTTAAAGAGTTGGCACATGTGTC
29920493 AACCAAAGCC
Statistics
Matches: 803, Mismatches: 67, Indels: 20
0.90 0.08 0.02
Matches are distributed among these distances:
291 211 0.26
292 5 0.01
293 43 0.05
294 6 0.01
295 42 0.05
296 6 0.01
297 485 0.60
298 5 0.01
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (296 bp):
TTCTGAAAACATCGTTGTTAGCACCATTGGCATAGGTACCATGACGCTTTGGAAAAAGCGTCAGC
ATAATTCAACCTAGGTCAACCTTTATTCAAGGGTTGGTAAAGACCTAGTCAAGGTCAACGTTTAA
AAAAGGTTGGGATAGGAGGAATTAAGCGACCGAAAAAAGTCGAATAAAGCATTCATATGCCGACT
TATAAAGAGTTGGTTCATGCCCCCGTCAAAGGTGACATAAAAATAGTCGAGTTAGGTCGCACTTA
GTCCAACTTTTAAAGAGTTGGCACATGTGTCGACAC
Found at i:29920438 original size:588 final size:592
Alignment explanation
Indices: 29919310--29920488 Score: 1920
Period size: 588 Copynumber: 2.0 Consensus size: 592
29919300 ACGATTCTCA
* *
29919310 CGACGTTTCTGAAAACATCGTTGTTAGCACCATTGGCATAGGTACCATGACGCTTTGGAAAAAGC
1 CGACGCTTCTGAAAACATCATTGTTAGCACCATTGGCATAGGTACCATGACGCTTTGGAAAAAGC
*
29919375 ATTAGCATAATTCAACCTAAGTCAACCTTTATTCAAGGGTTGGTAAAAACCTAGTCAAGGTCGAC
66 ATCAGCATAATTCAACCTAAGTCAACCTTTATTCAAGGGTTGGTAAAAACCTAGTCAAGGTCGAC
* * *
29919440 GTTTAAAAAAGGTTGGGATAGGAGGAATTAGACGATCGAAAAAAGTCGAAATAAAGCATTCATAT
131 ATTTAAAAAAGGTTGAGATAGGAGGAATTAGACGATCGAAAAAAGTCG--AGAAAGCATTCATAT
* * *
29919505 GCCAACTTATAAAGAGTTGGTTCATGCCCCCGTCAAAGGCTACATAAAAATAGTCGAGTTAGGTC
194 ACCAACTTATAAAGAGTTGGTTCATGCCCCAGTCAAAGGCGACATAAAAATAGTCGAGTTAGGTC
* *
29919570 GCACTTAGTCAGACTTTTAAAGAGTTGGCACATGTGTCGACACTTCTGAAAACATCGTTGTTAGC
259 GCACTTAGTCAGACTTTTAAAGAATTGGCACATGTGTCAACACTTCTGAAAACATCGTTGTTAGC
* * * * *
29919635 ACCATTGGCATAGGTGCCATGACGCTTTGGAAAAAGCGTCGGCATAATTCAACCTAGGTCAACCT
324 ACCATTAGCATAGGTACCATAACACTTTGGAAAAAGCGTCGGCATAATTCAACCAAGGTCAACCT
*
29919700 TTATTCAAGGGTTGGTAAAGACCTAGTCAAGGTCAACGTTTAAAAAAGGTTGGGATAGGAGGAAT
389 TTATTCAAGGGTTGGTAAAGACCTAGTCAAGGTCAACGTTTAAAAAAGGTTGGCATAGGAGGAAT
* ** *
29919765 TAAGCGACCCAAAAAAGTCAGAATAAAGCATTCATATGCCGACTTATAAAGAATTGGTTCATGCC
454 TAAGAGACAAAAAAAAGTCAGAATAAAGAATTCATATGCCGACTTATAAAGAATTGGTTCATGCC
* * * *
29919830 CCCTTCAAAGGTGACATAAAAATAGTTGAGTTAGGTCGCACTTAGTC-CATCTTTTAAAGAGTTG
519 CCCGTCAAAGGAGACATAAAAATAGTCGAGTTAGGTCACACTTAGTCTCA-CTTTTAAAGAGTTG
29919894 GCACATGCGT
583 GCACATGCGT
29919904 CGACGCTTCTGAAAACATCATTGTTAGCACCATTGGCATAGGTACCATGACGCTTTGGAAAAAGC
1 CGACGCTTCTGAAAACATCATTGTTAGCACCATTGGCATAGGTACCATGACGCTTTGGAAAAAGC
* * *
29919969 GTCAGCATAATTCAACCTAGGTCAACCTTTATTCAAGGGTTGGTAAAGACCTAGTCAAGGTCGAC
66 ATCAGCATAATTCAACCTAAGTCAACCTTTATTCAAGGGTTGGTAAAAACCTAGTCAAGGTCGAC
* * *
29920034 ATTTAAAACAGGTTGAGATAGGAGGAATTAGGCGATCGAAAAAATTCG-GAAA-CATTCATATAC
131 ATTTAAAAAAGGTTGAGATAGGAGGAATTAGACGATCGAAAAAAGTCGAGAAAGCATTCATATAC
* *
29920097 CGACTTATAAAGAGTTGGTTCATTCCCCAGTCAAAGG-GACA-AAAAATAGTCGAGTTAGGTCGC
196 CAACTTATAAAGAGTTGGTTCATGCCCCAGTCAAAGGCGACATAAAAATAGTCGAGTTAGGTCGC
*
29920160 ACTTAGTCCA-ACTTTTAAAGAATTGGCACATGTGTCAACTCTTCTGAAAACATCGTTGTTAGCA
261 ACTTAGT-CAGACTTTTAAAGAATTGGCACATGTGTCAACACTTCTGAAAACATCGTTGTTAGCA
29920224 CCATTAGCATAGGTACCATAACACTTTGGAAAAAGCGTCGGCATAATTCAACCAAGGTCAACCTT
325 CCATTAGCATAGGTACCATAACACTTTGGAAAAAGCGTCGGCATAATTCAACCAAGGTCAACCTT
*
29920289 TATTTAAGGGTTGGTAAAGACCTAGTCAAGGTCAACGTTTAAAAAAGGTTGGCATAGGAGGAATT
390 TATTCAAGGGTTGGTAAAGACCTAGTCAAGGTCAACGTTTAAAAAAGGTTGGCATAGGAGGAATT
* * *
29920354 AGGAGACAAAAAAAAGTCAGAATAAAGAATTCATATGTCGACTTATAAAGAGTTGGTTCATGCCC
455 AAGAGACAAAAAAAAGTCAGAATAAAGAATTCATATGCCGACTTATAAAGAATTGGTTCATGCCC
* *
29920419 TCGTCAAAGGAGACATAAAAATAGTCGAGTTAGGTCACACTTAGTCTGACTTTTAAAGAGTTGGC
520 CCGTCAAAGGAGACATAAAAATAGTCGAGTTAGGTCACACTTAGTCTCACTTTTAAAGAGTTGGC
29920484 ACATG
585 ACATG
29920489 TGTCAACCAA
Statistics
Matches: 543, Mismatches: 40, Indels: 10
0.92 0.07 0.02
Matches are distributed among these distances:
588 323 0.59
589 6 0.01
590 44 0.08
591 3 0.01
594 167 0.31
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (592 bp):
CGACGCTTCTGAAAACATCATTGTTAGCACCATTGGCATAGGTACCATGACGCTTTGGAAAAAGC
ATCAGCATAATTCAACCTAAGTCAACCTTTATTCAAGGGTTGGTAAAAACCTAGTCAAGGTCGAC
ATTTAAAAAAGGTTGAGATAGGAGGAATTAGACGATCGAAAAAAGTCGAGAAAGCATTCATATAC
CAACTTATAAAGAGTTGGTTCATGCCCCAGTCAAAGGCGACATAAAAATAGTCGAGTTAGGTCGC
ACTTAGTCAGACTTTTAAAGAATTGGCACATGTGTCAACACTTCTGAAAACATCGTTGTTAGCAC
CATTAGCATAGGTACCATAACACTTTGGAAAAAGCGTCGGCATAATTCAACCAAGGTCAACCTTT
ATTCAAGGGTTGGTAAAGACCTAGTCAAGGTCAACGTTTAAAAAAGGTTGGCATAGGAGGAATTA
AGAGACAAAAAAAAGTCAGAATAAAGAATTCATATGCCGACTTATAAAGAATTGGTTCATGCCCC
CGTCAAAGGAGACATAAAAATAGTCGAGTTAGGTCACACTTAGTCTCACTTTTAAAGAGTTGGCA
CATGCGT
Found at i:29925496 original size:29 final size:29
Alignment explanation
Indices: 29925428--29925575 Score: 127
Period size: 30 Copynumber: 5.0 Consensus size: 29
29925418 AATACTAAAA
29925428 TTTAAAATTTACATTTTAACCCCCCAACTT
1 TTTAAAATTTACATTTTAA-CCCCCAACTT
* *
29925458 TTTAAAATTTATATTTTAACCTCCAACTT
1 TTTAAAATTTACATTTTAACCCCCAACTT
*** **
29925487 TTTGTTATTTACATTTTGGCCCCCAACTT
1 TTTAAAATTTACATTTTAACCCCCAACTT
** *
29925516 TTCCTAAAA-TTACATTTTGTCCTCCTAACTT
1 TT--TAAAATTTACATTTTAACC-CCCAACTT
** *
29925547 TTTACTATTTACATTTTGATCCCCCAACT
1 TTTAAAATTTACATTTT-AACCCCCAACT
29925576 GCTATATGAA
Statistics
Matches: 95, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
29 36 0.38
30 45 0.47
31 14 0.15
ACGTcount: A:0.27, C:0.24, G:0.03, T:0.45
Consensus pattern (29 bp):
TTTAAAATTTACATTTTAACCCCCAACTT
Found at i:29925556 original size:60 final size:58
Alignment explanation
Indices: 29925434--29925575 Score: 160
Period size: 60 Copynumber: 2.4 Consensus size: 58
29925424 AAAATTTAAA
* * **
29925434 ATTTACATTTTAACCCCCCAACTTTTTAAAATTTATATTTTAACCTCCAACTTTTTGTT
1 ATTTACATTTT-GCCCCCCAACTTTTTAAAATTTACATTTTAACCTCCAACTTTTTACT
* **
29925493 ATTTACATTTTGGCCCCCAACTTTTCCTAAAA-TTACATTTTGTCCTCCTAACTTTTTACT
1 ATTTACATTTTGCCCCCCAACTTTT--TAAAATTTACATTTTAACCTCC-AACTTTTTACT
*
29925553 ATTTACATTTTGATCCCCCAACT
1 ATTTACATTTTG-CCCCCCAACT
29925576 GCTATATGAA
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
58 12 0.17
59 24 0.34
60 26 0.37
61 9 0.13
ACGTcount: A:0.26, C:0.25, G:0.04, T:0.45
Consensus pattern (58 bp):
ATTTACATTTTGCCCCCCAACTTTTTAAAATTTACATTTTAACCTCCAACTTTTTACT
Found at i:29925995 original size:15 final size:15
Alignment explanation
Indices: 29925977--29926022 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
29925967 TTAAAAGTAG
*
29925977 AGAAAATAAATAAAA
1 AGAAAAAAAATAAAA
*
29925992 AGAAAAGAAA-AAAA
1 AGAAAAAAAATAAAA
29926006 AGAAAAAATAATAAAA
1 AGAAAAAA-AATAAAA
29926022 A
1 A
29926023 TATAAAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 11 0.41
15 11 0.41
16 5 0.19
ACGTcount: A:0.83, C:0.00, G:0.09, T:0.09
Consensus pattern (15 bp):
AGAAAAAAAATAAAA
Found at i:29930243 original size:4 final size:4
Alignment explanation
Indices: 29930226--29930264 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
29930216 GCATGACTAA
* *
29930226 CATT CATT -AGT CATT CATT CACT CATT CATT CATT CATT
1 CATT CATT CATT CATT CATT CATT CATT CATT CATT CATT
29930265 GTATGTACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
3 2 0.07
4 28 0.93
ACGTcount: A:0.26, C:0.26, G:0.03, T:0.46
Consensus pattern (4 bp):
CATT
Found at i:29938760 original size:77 final size:76
Alignment explanation
Indices: 29938581--29939253 Score: 698
Period size: 77 Copynumber: 8.9 Consensus size: 76
29938571 TCCTATTTCA
* * * * * * ** *
29938581 TTTTTCAAAAATCAACTCAAAATCCGAAAGGTGAGTTAAGCATCGGGTCACACGCTAAGGT-GTT
1 TTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAGGTATTT
*
29938645 TTCAATTTATAT
66 TTCAATTT-TTT
** * * *
29938657 TTTTT-AAA-ATCAACTCATAATCCGAGAACTGAGTTGAGCCTCGGGTTGCATGCCGAGATATTT
1 TTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAGGTATTT
*
29938720 TTCTATTTCTATT
66 TTCAATTT-T-TT
* * * * * *
29938733 TTTTTGAAA-ATTAACTCATAATTCGAGAGGTGAGTTGAGCCTCGGGTCGCATGCTGAGATATTT
1 TTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAGGTATTT
*
29938797 TTCAATTTTTG
66 TTCAATTTTTT
* * *
29938808 TTTTTCAAAGATCAACTCATAGTCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGT-GTT
1 TTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAGGTATTT
29938872 TTCAATTTTTGT
66 TTCAATTTTT-T
* * * ** * *
29938884 TTTTTCAAAAATCAACTCATAATCTGAGAGGTGAGTTGAACCTCAAGTCACACGCTGAGGTATAT
1 TTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAGGTAT-T
***
29938949 TTTCAATTTCAG
65 TTTCAATTTTTT
* * *
29938961 TTTTTCGAAA-ATCAACTCATAATCTGAGAGGTGAGTTGAGCCTGGGGTCGCATGCCGAGGTATT
1 TTTTTC-AAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAGGTA-T
* *
29939025 TTTTCTATTTTTA
64 TTTTCAATTTTTT
* * * *
29939038 TTTTTCAAAGATCGACTCATAATCCGAGAGGTGAGTTGAGCCTTGGGTCGCACGTCGAGCTATTT
1 TTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAGGTATTT
*
29939103 TT-AATTTTTC
66 TTCAATTTTTT
* * * ** *
29939113 TTTTTCAAATATCAACTCATAGTCCGAGAGGTGAGTTGAGCCTCAGGTCGCACGTGGAGCTA-TT
1 TTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAGGTATTT
*
29939177 TT-ATATTTTTG
66 TTCA-ATTTTTT
* * * *
29939188 TTTTTCAAAGATCAACCCATAATCCGAGAGATGAGTTGAGCCTCGGGTTGCACGCCGAGGAATTT
1 TTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAGGTATTT
29939253 T
66 T
29939254 AAATTTCAGT
Statistics
Matches: 506, Mismatches: 79, Indels: 24
0.83 0.13 0.04
Matches are distributed among these distances:
74 44 0.09
75 154 0.30
76 123 0.24
77 171 0.34
78 14 0.03
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (76 bp):
TTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAGGTATTT
TTCAATTTTTT
Found at i:29938999 original size:229 final size:229
Alignment explanation
Indices: 29938580--29939246 Score: 780
Period size: 229 Copynumber: 2.9 Consensus size: 229
29938570 TTCCTATTTC
* * * * * * *
29938580 ATTTTTCAAAAATCAACTCAAAATCCGAAAGGTGAGTTAAGCATCGGGTCACACGCTAAGGTGTT
1 ATTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTGTT
* ** * * *
29938645 TTCAATTTATATTTTTT--AAAATCAACTCATAATCCGAGAACTGAGTTGAGCCTCGGGTTGCAT
66 TTCAATTT-TTTTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCAGGTCGCAC
* * * * * *
29938708 GCCGAGATAT-TTTTCTATTTCTATTTTTTTGAAAATTAACTCATAAT-TCGAGAGGTGAGTTGA
130 GCTGAGGTATATTTTCAATTTC-AGTTTTTCGAAAATCAACTCATAATCT-GAGAGGTGAGTTGA
*
29938771 GCCTCGGGTCGCATGCTGAGATA-TTTTTCAATTTTT
193 GCCTCGGGTCGCATGCCGAGATATTTTTTCAATTTTT
* *
29938807 GTTTTTCAAAGATCAACTCATAGTCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTGTT
1 ATTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTGTT
* * * *
29938872 TTCAATTTTTGTTTTTTCAAAAATCAACTCATAATCTGAGAGGTGAGTTGAACCTCAAGTCACAC
66 TTCAATTTTT-TTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCAGGTCGCAC
29938937 GCTGAGGTATATTTTCAATTTCAGTTTTTCGAAAATCAACTCATAATCTGAGAGGTGAGTTGAGC
130 GCTGAGGTATATTTTCAATTTCAGTTTTTCGAAAATCAACTCATAATCTGAGAGGTGAGTTGAGC
* * *
29939002 CTGGGGTCGCATGCCGAGGTATTTTTTCTATTTTT
195 CTCGGGTCGCATGCCGAGATATTTTTTCAATTTTT
* * * *
29939037 ATTTTTCAAAGATCGACTCATAATCCGAGAGGTGAGTTGAGCCTTGGGTCGCACG-TCGAGCTAT
1 ATTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCT-GAGGTGT
* * * *
29939101 TTTTAATTTTTCTTTTTCAAATATCAACTCATAGTCCGAGAGGTGAGTTGAGCCTCAGGTCGCAC
65 TTTCAATTTTTTTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCAGGTCGCAC
* ** * * *
29939166 G-TG-GAG-CTATTTT-ATATTTTTGTTTTTC-AAAGATCAACCCATAATCCGAGAGATGAGTTG
130 GCTGAG-GTATATTTTCA-ATTTCAGTTTTTCGAAA-ATCAACTCATAATCTGAGAGGTGAGTTG
* *
29939226 AGCCTCGGGTTGCACGCCGAG
192 AGCCTCGGGTCGCATGCCGAG
29939247 GAATTTTAAA
Statistics
Matches: 378, Mismatches: 52, Indels: 20
0.84 0.12 0.04
Matches are distributed among these distances:
226 5 0.01
227 131 0.35
228 3 0.01
229 150 0.40
230 89 0.24
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (229 bp):
ATTTTTCAAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTGTT
TTCAATTTTTTTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCAGGTCGCACG
CTGAGGTATATTTTCAATTTCAGTTTTTCGAAAATCAACTCATAATCTGAGAGGTGAGTTGAGCC
TCGGGTCGCATGCCGAGATATTTTTTCAATTTTT
Found at i:29939805 original size:29 final size:29
Alignment explanation
Indices: 29939752--29939882 Score: 120
Period size: 29 Copynumber: 4.5 Consensus size: 29
29939742 ACAAAAACTA
* *
29939752 AAAATATACATTTTTACCCCTTAACTTTTT
1 AAAATTTACATTTTAACCCC-TAACTTTTT
29939782 AAAATTTACATTTTAACCCCTAACTTTTT
1 AAAATTTACATTTTAACCCCTAACTTTTT
** ** * *
29939811 ACTATTTACATTTTGTCCCTTAACTTTCCT
1 AAAATTTACATTTTAACCCCTAACTTT-TT
* * *
29939841 AAAA-TTAAATTTTAACCCCCAATTTTTT
1 AAAATTTACATTTTAACCCCTAACTTTTT
**
29939869 ACTATTTACATTTT
1 AAAATTTACATTTT
29939883 GATCCCCCAA
Statistics
Matches: 79, Mismatches: 20, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
28 3 0.04
29 55 0.70
30 21 0.27
ACGTcount: A:0.31, C:0.21, G:0.01, T:0.47
Consensus pattern (29 bp):
AAAATTTACATTTTAACCCCTAACTTTTT
Found at i:29939834 original size:58 final size:59
Alignment explanation
Indices: 29939758--29939888 Score: 185
Period size: 58 Copynumber: 2.2 Consensus size: 59
29939748 ACTAAAAATA
* * * * *
29939758 TACATTTTTACCCCTTAACTTT-TTAAAATTTACATTTTAACCCCTAACTTTTTACTATT
1 TACATTTTGATCCCTTAACTTTCCTAAAA-TTAAATTTTAACCCCCAACTTTTTACTATT
*
29939817 TACATTTTG-TCCCTTAACTTTCCTAAAATTAAATTTTAACCCCCAATTTTTTACTATT
1 TACATTTTGATCCCTTAACTTTCCTAAAATTAAATTTTAACCCCCAACTTTTTACTATT
29939875 TACATTTTGATCCC
1 TACATTTTGATCCC
29939889 CCAACTGCTA
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
58 47 0.73
59 17 0.27
ACGTcount: A:0.28, C:0.23, G:0.02, T:0.47
Consensus pattern (59 bp):
TACATTTTGATCCCTTAACTTTCCTAAAATTAAATTTTAACCCCCAACTTTTTACTATT
Found at i:29940305 original size:5 final size:5
Alignment explanation
Indices: 29940295--29940348 Score: 51
Period size: 5 Copynumber: 11.2 Consensus size: 5
29940285 TTAAAAGTAG
* *
29940295 AGAAA AGAAA AGAAAA AGAAA GGAAA AG-AA A-AAA AG-AA AGGAA AGAAA
1 AGAAA AGAAA AG-AAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA
*
29940343 GGAAA A
1 AGAAA A
29940349 AAATAATAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
4 10 0.25
5 25 0.62
6 5 0.12
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:29940334 original size:22 final size:21
Alignment explanation
Indices: 29940295--29940351 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
29940285 TTAAAAGTAG
*
29940295 AGAAAAGAAAAGAAAAA-GAA
1 AGAAAAGAAAAAAAAAAGGAA
29940315 AGGAAAAGAAAAAAAGAAAGGAA
1 A-GAAAAGAAAAAAA-AAAGGAA
*
29940338 AGAAAGGAAAAAAA
1 AGAAAAGAAAAAAA
29940352 TAATAATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 1 0.03
21 12 0.38
22 15 0.47
23 4 0.12
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (21 bp):
AGAAAAGAAAAAAAAAAGGAA
Found at i:29940339 original size:17 final size:18
Alignment explanation
Indices: 29940295--29940342 Score: 66
Period size: 16 Copynumber: 2.8 Consensus size: 18
29940285 TTAAAAGTAG
*
29940295 AGAAAAGAAAAG--AAAA
1 AGAAAGGAAAAGAAAAAA
29940311 AGAAAGGAAAAGAAAAAA
1 AGAAAGGAAAAGAAAAAA
29940329 AGAAAGG-AAAGAAA
1 AGAAAGGAAAAGAAA
29940343 GGAAAAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 11 0.38
17 7 0.24
18 11 0.38
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (18 bp):
AGAAAGGAAAAGAAAAAA
Found at i:29945956 original size:43 final size:43
Alignment explanation
Indices: 29945864--29945958 Score: 138
Period size: 43 Copynumber: 2.2 Consensus size: 43
29945854 GTTTATGTGG
*
29945864 AAAAACGCCGCTATAGAACATGGCCTTTAGCAGCGCTTTTTCC
1 AAAAACGCCGCTATAGAACATGACCTTTAGCAGCGCTTTTTCC
* * *
29945907 ACAAACGCCGCTATAGGACATGACCTTTAGCGGCGC-TTTTCC
1 AAAAACGCCGCTATAGAACATGACCTTTAGCAGCGCTTTTTCC
29945949 TAAAAACGCC
1 -AAAAACGCC
29945959 ACTAAAGGTC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 6 0.13
43 40 0.87
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.23
Consensus pattern (43 bp):
AAAAACGCCGCTATAGAACATGACCTTTAGCAGCGCTTTTTCC
Found at i:29945979 original size:43 final size:43
Alignment explanation
Indices: 29945864--29945971 Score: 119
Period size: 43 Copynumber: 2.5 Consensus size: 43
29945854 GTTTATGTGG
* * * *
29945864 AAAAACGCCGCTATAGAACATGGCCTTTAGCAGCGCTTTTTCC
1 AAAAACGCCACTAAAGGACATGACCTTTAGCAGCGCTTTTTCC
* * * *
29945907 ACAAACGCCGCTATAGGACATGACCTTTAGCGGCGC-TTTTCC
1 AAAAACGCCACTAAAGGACATGACCTTTAGCAGCGCTTTTTCC
*
29945949 TAAAAACGCCACTAAAGGTCATG
1 -AAAAACGCCACTAAAGGACATG
29945972 TTCTTTAGTG
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 6 0.11
43 50 0.89
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (43 bp):
AAAAACGCCACTAAAGGACATGACCTTTAGCAGCGCTTTTTCC
Found at i:29946426 original size:66 final size:65
Alignment explanation
Indices: 29946327--29946457 Score: 158
Period size: 66 Copynumber: 2.0 Consensus size: 65
29946317 CTGAAGTTAC
* * *
29946327 AGCTGGAGTTCGTCATATTTTCTGCTTGTCTCTACTTCCCT-TACTGCTGTCTCCACTTTAAGTT
1 AGCTGGAGTTCGTCATATTTTCT-CTTGCCTCTACTTCCCTCGA-TGCTGCCTCCACTTTAAGTT
29946391 GT
64 GT
* * *
29946393 AGCTGGAGTTCTTCATATTTTCT-TTGAGCCTCTACTTCTCTCGATGTTGCCTCCACTTTAAGTT
1 AGCTGGAGTTCGTCATATTTTCTCTT--GCCTCTACTTCCCTCGATGCTGCCTCCACTTTAAGTT
29946457 G
64 G
29946458 AGCAATTTGC
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
64 2 0.04
66 53 0.95
67 1 0.02
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.44
Consensus pattern (65 bp):
AGCTGGAGTTCGTCATATTTTCTCTTGCCTCTACTTCCCTCGATGCTGCCTCCACTTTAAGTTGT
Found at i:29946535 original size:13 final size:13
Alignment explanation
Indices: 29946517--29946541 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29946507 AACCTCTAAA
29946517 CTTCAGCTTGAGC
1 CTTCAGCTTGAGC
29946530 CTTCAGCTTGAG
1 CTTCAGCTTGAG
29946542 TCTGATTCCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.28, G:0.24, T:0.32
Consensus pattern (13 bp):
CTTCAGCTTGAGC
Found at i:29951830 original size:7 final size:7
Alignment explanation
Indices: 29951820--29951844 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29951810 AGATAATACA
29951820 TATCAAG
1 TATCAAG
29951827 TATCAAG
1 TATCAAG
29951834 TATCAAG
1 TATCAAG
29951841 TATC
1 TATC
29951845 TAATGGGTGT
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:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (7 bp):
TATCAAG
Found at i:29951907 original size:9 final size:9
Alignment explanation
Indices: 29951893--29952032 Score: 132
Period size: 9 Copynumber: 16.0 Consensus size: 9
29951883 CAAGTATAGT
29951893 TAAGTTATG
1 TAAGTTATG
29951902 TAAGTTATG
1 TAAGTTATG
* * *
29951911 ATATGATATA
1 -TAAGTTATG
*
29951921 T-ATTTATG
1 TAAGTTATG
29951929 TAAGTTATG
1 TAAGTTATG
29951938 TAAGTTATG
1 TAAGTTATG
*
29951947 -ATA-TGATG
1 TA-AGTTATG
*
29951955 TATATTTATG
1 TA-AGTTATG
29951965 T-A-TTATG
1 TAAGTTATG
29951972 TAAGTTATG
1 TAAGTTATG
29951981 TAAGTTATG
1 TAAGTTATG
*
29951990 TAGGTTATG
1 TAAGTTATG
29951999 TAAGTTATG
1 TAAGTTATG
29952008 T-A-TTATG
1 TAAGTTATG
29952015 TAAGTTATG
1 TAAGTTATG
*
29952024 TATGTTATG
1 TAAGTTATG
29952033 ATCCAAAGTT
Statistics
Matches: 109, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
7 12 0.11
8 13 0.12
9 73 0.67
10 11 0.10
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (9 bp):
TAAGTTATG
Found at i:29951935 original size:36 final size:36
Alignment explanation
Indices: 29951893--29952009 Score: 159
Period size: 36 Copynumber: 3.3 Consensus size: 36
29951883 CAAGTATAGT
29951893 TAAGTTATGTAAGTTATGATATGATATATATTTATG
1 TAAGTTATGTAAGTTATGATATGATATATATTTATG
*
29951929 TAAGTTATGTAAGTTATGATATGATGTATATTTATG
1 TAAGTTATGTAAGTTATGATATGATATATATTTATG
* * * *
29951965 T-A-TTATGTAAGTTATG-TAAGTTATGTAGGTTATG
1 TAAGTTATGTAAGTTATGATATGATATATA-TTTATG
29951999 TAAGTTATGTA
1 TAAGTTATGTA
29952010 TTATGTAAGT
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
33 7 0.10
34 20 0.28
35 2 0.03
36 43 0.60
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (36 bp):
TAAGTTATGTAAGTTATGATATGATATATATTTATG
Found at i:29951976 original size:43 final size:43
Alignment explanation
Indices: 29951924--29952034 Score: 163
Period size: 43 Copynumber: 2.6 Consensus size: 43
29951914 TGATATATAT
*
29951924 TTATGTAAGTTATGTAAGTTATGATA-TGATGTATATTTATGTA
1 TTATGTAAGTTATGTAAGTTATGATAGTGATGTA-AGTTATGTA
*
29951967 TTATGTAAGTTATGTAAGTTATG-TAGGTTATGTAAGTTATGTA
1 TTATGTAAGTTATGTAAGTTATGATA-GTGATGTAAGTTATGTA
*
29952010 TTATGTAAGTTATGTATGTTATGAT
1 TTATGTAAGTTATGTAAGTTATGAT
29952035 CCAAAGTTTT
Statistics
Matches: 62, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
42 2 0.03
43 53 0.85
44 7 0.11
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.49
Consensus pattern (43 bp):
TTATGTAAGTTATGTAAGTTATGATAGTGATGTAAGTTATGTA
Found at i:29951998 original size:34 final size:34
Alignment explanation
Indices: 29951960--29952032 Score: 105
Period size: 34 Copynumber: 2.1 Consensus size: 34
29951950 TGATGTATAT
29951960 TTATGT-A-TTATGTAAGTTATGTAAGTTATGTAGG
1 TTATGTAAGTTATGT-A-TTATGTAAGTTATGTAGG
*
29951994 TTATGTAAGTTATGTATTATGTAAGTTATGTATG
1 TTATGTAAGTTATGTATTATGTAAGTTATGTAGG
29952028 TTATG
1 TTATG
29952033 ATCCAAAGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
34 28 0.78
35 2 0.06
36 6 0.17
ACGTcount: A:0.29, C:0.00, G:0.22, T:0.49
Consensus pattern (34 bp):
TTATGTAAGTTATGTATTATGTAAGTTATGTAGG
Found at i:29952091 original size:35 final size:35
Alignment explanation
Indices: 29952052--29952118 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
29952042 TTTTTTTATT
*
29952052 CTTTAAATGTTTATGTAAGTTATGATAATCATAAA
1 CTTTAAATGTTTATGTAAGATATGATAATCATAAA
*
29952087 CTTTAAATGTTTATGTAAGATATGATTATCAT
1 CTTTAAATGTTTATGTAAGATATGATAATCAT
29952119 CTTTAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.45
Consensus pattern (35 bp):
CTTTAAATGTTTATGTAAGATATGATAATCATAAA
Found at i:29952137 original size:13 final size:13
Alignment explanation
Indices: 29952119--29952145 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29952109 TGATTATCAT
29952119 CTTTAAATTTTAA
1 CTTTAAATTTTAA
29952132 CTTTAAATTTTAA
1 CTTTAAATTTTAA
29952145 C
1 C
29952146 CCTTTAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (13 bp):
CTTTAAATTTTAA
Found at i:29953257 original size:21 final size:22
Alignment explanation
Indices: 29953232--29953277 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
29953222 TTTGCAAATA
*
29953232 AAATAT-GAGAATGAAGCCTTT
1 AAATATAGACAATGAAGCCTTT
*
29953253 AAATATAGGACAATGAAGGCTTT
1 AAATATA-GACAATGAAGCCTTT
29953276 AA
1 AA
29953278 CAGTTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
23 15 0.71
ACGTcount: A:0.46, C:0.09, G:0.20, T:0.26
Consensus pattern (22 bp):
AAATATAGACAATGAAGCCTTT
Found at i:29953335 original size:12 final size:12
Alignment explanation
Indices: 29953318--29953348 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
29953308 CAATAGCATG
29953318 CTCCATTCTCAA
1 CTCCATTCTCAA
*
29953330 CTCCATTCTCAC
1 CTCCATTCTCAA
29953342 CTCCATT
1 CTCCATT
29953349 TATAACTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.45, G:0.00, T:0.35
Consensus pattern (12 bp):
CTCCATTCTCAA
Found at i:29961893 original size:41 final size:41
Alignment explanation
Indices: 29961833--29961952 Score: 141
Period size: 41 Copynumber: 2.9 Consensus size: 41
29961823 TTTAAGGCGT
* * *
29961833 TAAACGCCACTACTGCTTGACCTTTTACGGCGTTTTTCTCA
1 TAAACACCGCTACTGCTTGACCTTTTGCGGCGTTTTTCTCA
** * * *
29961874 TAAACATTGCTACTACTTGATCTTTTGTGGCGTTTTTCTCA
1 TAAACACCGCTACTGCTTGACCTTTTGCGGCGTTTTTCTCA
** *
29961915 TAAATGCCGCTACTGCTTGACCTATTGCGGCGTTTTTC
1 TAAACACCGCTACTGCTTGACCTTTTGCGGCGTTTTTC
29961953 CGTTAGCGCC
Statistics
Matches: 63, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.40
Consensus pattern (41 bp):
TAAACACCGCTACTGCTTGACCTTTTGCGGCGTTTTTCTCA
Found at i:29962134 original size:30 final size:31
Alignment explanation
Indices: 29962100--29962162 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
29962090 TTGTTGGAAA
* *
29962100 CATTTTCAGGTG-AAATCAGAAAAACGCTTC
1 CATTTTCAAGTGAAAATCAGAAAAACACTTC
29962130 CATTTTCAAGTGAAAATCAGAAAAACACTTC
1 CATTTTCAAGTGAAAATCAGAAAAACACTTC
29962161 CA
1 CA
29962163 CCTTGTAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 11 0.37
31 19 0.63
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.25
Consensus pattern (31 bp):
CATTTTCAAGTGAAAATCAGAAAAACACTTC
Found at i:29965220 original size:17 final size:18
Alignment explanation
Indices: 29965186--29965221 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
29965176 TTATTTTTCA
*
29965186 TTATTAAATTATAAAAAT
1 TTATTAAAATATAAAAAT
29965204 TTATTAAAATA-AAAAAT
1 TTATTAAAATATAAAAAT
29965221 T
1 T
29965222 GATGTTTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TTATTAAAATATAAAAAT
Found at i:29968045 original size:19 final size:19
Alignment explanation
Indices: 29968017--29968056 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
29968007 TAGCTACAGA
*
29968017 ATTAAAACAATTAAAATTC
1 ATTAAAACAATAAAAATTC
*
29968036 ATTAATACAATAAAAATTC
1 ATTAAAACAATAAAAATTC
29968055 AT
1 AT
29968057 ATTGAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAACAATAAAAATTC
Found at i:29969175 original size:29 final size:29
Alignment explanation
Indices: 29969138--29969193 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
29969128 TAATAATATA
29969138 ATATATTTTAAATATAAAA-TGATATTTTC
1 ATATATTTTAAAT-TAAAATTGATATTTTC
* **
29969167 ATATTTTTTTCATTAAAATTGATATTT
1 ATATATTTTAAATTAAAATTGATATTT
29969194 GATTGACTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.54
Consensus pattern (29 bp):
ATATATTTTAAATTAAAATTGATATTTTC
Found at i:29969692 original size:21 final size:19
Alignment explanation
Indices: 29969627--29969720 Score: 152
Period size: 19 Copynumber: 4.8 Consensus size: 19
29969617 AATTTTTGAG
29969627 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
29969646 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
29969665 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
29969684 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
29969705 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
29969721 AGATATGATT
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
19 51 0.73
21 19 0.27
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:29969702 original size:40 final size:38
Alignment explanation
Indices: 29969627--29969727 Score: 152
Period size: 40 Copynumber: 2.7 Consensus size: 38
29969617 AATTTTTGAG
29969627 GATATGCAATCTTAGATATGATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATATGATATGCAATCCTAGATAT
*
29969665 GATATGCAATCTTAGATATGATATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATATG--ATATGCAATCCTAGATAT
*
29969705 GATATGTAATCTTAGA-A-GATATG
1 GATATGCAATCTTAGATATGATATG
29969728 ATTTTGTAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
36 5 0.08
38 21 0.36
39 1 0.02
40 32 0.54
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (38 bp):
GATATGCAATCTTAGATATGATATGCAATCCTAGATAT
Found at i:29969739 original size:23 final size:22
Alignment explanation
Indices: 29969659--29969743 Score: 81
Period size: 21 Copynumber: 4.0 Consensus size: 22
29969649 ATGCAATCCT
*
29969659 AGATATGATATGCAATCTTAG-
1 AGATATGATATGTAATCTTAGA
* *
29969680 ATATGAT-ATATGCAATCTT---
1 AGAT-ATGATATGTAATCTTAGA
29969699 AGATATGATATGTAATCTTAGA
1 AGATATGATATGTAATCTTAGA
*
29969721 AGATATGATTTTGTAATCTTAGA
1 AGATATGA-TATGTAATCTTAGA
29969744 GATTTAATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
18 2 0.04
19 14 0.26
21 15 0.28
22 10 0.19
23 13 0.24
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.39
Consensus pattern (22 bp):
AGATATGATATGTAATCTTAGA
Found at i:29969753 original size:22 final size:23
Alignment explanation
Indices: 29969709--29969753 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
29969699 AGATATGATA
*
29969709 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
29969732 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
29969754 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:29970317 original size:25 final size:25
Alignment explanation
Indices: 29970266--29970317 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
29970256 AATTTTTTTA
**
29970266 ATGTAATTATTATTATTATTTTCAT
1 ATGTAATTATTATTATTATTAGCAT
29970291 ATGTAATTATTATTATT-TTAGCTAT
1 ATGTAATTATTATTATTATTAGC-AT
29970316 AT
1 AT
29970318 ATATATGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 3 0.12
25 21 0.88
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.58
Consensus pattern (25 bp):
ATGTAATTATTATTATTATTAGCAT
Found at i:29970420 original size:33 final size:30
Alignment explanation
Indices: 29970383--29970443 Score: 77
Period size: 33 Copynumber: 1.9 Consensus size: 30
29970373 TTTTCGCATA
*
29970383 TTTATTTTCTTAATATGAGGTAATTATTTTTAT
1 TTTATTTTATTAATAT-A--TAATTATTTTTAT
*
29970416 TTTATTTTATTTATATATAATTATTTTT
1 TTTATTTTATTAATATATAATTATTTTT
29970444 TTATAATCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 11 0.42
32 1 0.04
33 14 0.54
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.66
Consensus pattern (30 bp):
TTTATTTTATTAATATATAATTATTTTTAT
Found at i:29970924 original size:19 final size:20
Alignment explanation
Indices: 29970883--29970924 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
29970873 ATTTCTAGGC
* *
29970883 CATTGTAATATTTATTATTG
1 CATTGTAATATTTAATATAG
29970903 CATTGT-ATATTTAATATAG
1 CATTGTAATATTTAATATAG
29970922 CAT
1 CAT
29970925 CACATCATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Found at i:29971279 original size:98 final size:98
Alignment explanation
Indices: 29971163--29972045 Score: 1721
Period size: 98 Copynumber: 9.0 Consensus size: 98
29971153 TTAAAAATAA
* * ** *
29971163 TAAAGGAAATATTTCGAGTTTGGGATTTTAAAGGAATTATGTCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
29971228 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
29971261 TAAAGGAAATATTCCGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
29971326 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
29971359 TAAAGGAAATATTCCGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
29971424 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
29971457 TAAAGGAAATATTCCGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
29971522 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
29971555 TAAAGGAAATATTCCGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
29971620 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
29971653 TAAAGGAAATATTCCGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
29971718 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
29971751 TAAAGGAAATATTCCGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
29971816 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
29971849 TAAAGGAAATATTCCGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
29971914 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
29971947 TAAAGGAAATATTCCGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
29972012 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
29972045 T
1 T
29972046 TTTATTGCAC
Statistics
Matches: 780, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
98 780 1.00
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.37
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:29977670 original size:22 final size:22
Alignment explanation
Indices: 29977642--29977696 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
29977632 AATAGATTAT
*
29977642 TATTATTAAATTTTAAT-GTGAC
1 TATTATTAAATTATAATAG-GAC
* *
29977664 TATTATTTAATTATAATAGGAT
1 TATTATTAAATTATAATAGGAC
29977686 TATTATTAAAT
1 TATTATTAAAT
29977697 ATTTTATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 27 0.96
23 1 0.04
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (22 bp):
TATTATTAAATTATAATAGGAC
Found at i:29977721 original size:23 final size:25
Alignment explanation
Indices: 29977674--29977751 Score: 81
Period size: 23 Copynumber: 3.2 Consensus size: 25
29977664 TATTATTTAA
*
29977674 TTATAATAGGATTATTATT-AAATATT
1 TTATAATA-AATTA-TATTAAAATATT
* * *
29977700 TTATATTAATTTA-ATT-TAATATT
1 TTATAATAAATTATATTAAAATATT
29977723 TTATAATAAATTATATTAAAATATT
1 TTATAATAAATTATATTAAAATATT
29977748 TTAT
1 TTAT
29977752 TTTTTTATTT
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
23 20 0.47
24 3 0.07
25 13 0.30
26 7 0.16
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (25 bp):
TTATAATAAATTATATTAAAATATT
Found at i:29985352 original size:40 final size:40
Alignment explanation
Indices: 29985237--29985361 Score: 116
Period size: 40 Copynumber: 3.1 Consensus size: 40
29985227 AAGTTATACT
*
29985237 TTCTGTTTGGCGTGA-TTCGAA-TGGATCAA-CTCTTATGAGC
1 TTCTGTTTGGCAT-ATTTC-AAGTGGA-CAAGCTCTTATGAGC
* * *
29985277 TTATG-TTGGCATGTTTCAAGTGGACCAGCTCTTATGAGC
1 TTCTGTTTGGCATATTTCAAGTGGACAAGCTCTTATGAGC
* * *
29985316 TTCTGTTTGGCATATTT-ACGTTGGATAAGCTTTTATGAGC
1 TTCTGTTTGGCATATTTCAAG-TGGACAAGCTCTTATGAGC
29985356 TTCTGT
1 TTCTGT
29985362 CTGGTGTGTT
Statistics
Matches: 70, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
38 4 0.06
39 30 0.43
40 36 0.51
ACGTcount: A:0.19, C:0.16, G:0.24, T:0.41
Consensus pattern (40 bp):
TTCTGTTTGGCATATTTCAAGTGGACAAGCTCTTATGAGC
Found at i:29988178 original size:15 final size:14
Alignment explanation
Indices: 29988142--29988181 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
29988132 AATGTAAGTG
29988142 ATTAAAATATAAAA
1 ATTAAAATATAAAA
* *
29988156 TTTTAAATATAAATA
1 ATTAAAATATAAA-A
29988171 ATTAAAATATA
1 ATTAAAATATA
29988182 GTATGAGACA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
ATTAAAATATAAAA
Found at i:29991942 original size:22 final size:21
Alignment explanation
Indices: 29991912--29991956 Score: 81
Period size: 22 Copynumber: 2.1 Consensus size: 21
29991902 AGATTGGCAA
29991912 AATGAAAGCCCATGTGGAGGG
1 AATGAAAGCCCATGTGGAGGG
29991933 AANTGAAAGCCCATGTGGAGGG
1 AA-TGAAAGCCCATGTGGAGGG
29991955 AA
1 AA
29991957 AGAGGACCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.36, C:0.13, G:0.36, T:0.13
Consensus pattern (21 bp):
AATGAAAGCCCATGTGGAGGG
Found at i:29992319 original size:19 final size:19
Alignment explanation
Indices: 29992272--29992309 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
29992262 AAATTTCTCA
29992272 ATTACTTTTGTTTAAGATT
1 ATTACTTTTGTTTAAGATT
29992291 ATTACTTTTGTTTAAGATT
1 ATTACTTTTGTTTAAGATT
29992310 TTTTGTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.05, G:0.11, T:0.58
Consensus pattern (19 bp):
ATTACTTTTGTTTAAGATT
Found at i:29996020 original size:13 final size:13
Alignment explanation
Indices: 29996002--29996045 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 13
29995992 ATTAATAAAC
29996002 ATTCTGTAGGAAT
1 ATTCTGTAGGAAT
29996015 ATTCTGTA--AAT
1 ATTCTGTAGGAAT
29996026 ATT-T-TAGGAAT
1 ATTCTGTAGGAAT
*
29996037 ATTTTGTAG
1 ATTCTGTAG
29996046 ATATTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
9 2 0.07
10 1 0.04
11 12 0.44
12 1 0.04
13 11 0.41
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (13 bp):
ATTCTGTAGGAAT
Found at i:29996033 original size:22 final size:22
Alignment explanation
Indices: 29996008--29996052 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
29995998 AAACATTCTG
29996008 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
29996030 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
29996052 T
1 T
29996053 TTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:30000637 original size:22 final size:22
Alignment explanation
Indices: 30000609--30000653 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
30000599 AGGGGGAGTG
30000609 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
30000631 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
30000653 T
1 T
30000654 TTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:30001561 original size:3 final size:3
Alignment explanation
Indices: 30001553--30001585 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
30001543 ATTTTCTTAC
30001553 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
30001586 TGCATGTAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:30008101 original size:24 final size:24
Alignment explanation
Indices: 30008074--30008122 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
30008064 AAAGAAGTAA
30008074 GATTATAAGATAAGAACATAAGGC
1 GATTATAAGATAAGAACATAAGGC
*
30008098 GATTATAAGATAGGAACATAAGGC
1 GATTATAAGATAAGAACATAAGGC
30008122 G
1 G
30008123 TGTGAGTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.47, C:0.08, G:0.24, T:0.20
Consensus pattern (24 bp):
GATTATAAGATAAGAACATAAGGC
Found at i:30017357 original size:20 final size:20
Alignment explanation
Indices: 30017319--30017358 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
30017309 CTTGTTTTCA
*
30017319 AGTAGTTTTAGTGTCTTTTT
1 AGTAGTTTTAGTGTATTTTT
*
30017339 AGTAGTTTTA-TGTAATTTT
1 AGTAGTTTTAGTGTATTTTT
30017358 A
1 A
30017359 ATTTGTACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.23, C:0.03, G:0.17, T:0.57
Consensus pattern (20 bp):
AGTAGTTTTAGTGTATTTTT
Found at i:30020818 original size:30 final size:31
Alignment explanation
Indices: 30020772--30020829 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
30020762 GAAATGATAG
* *
30020772 CAAAATAGTGAAAAAAATAAGAAAATAGCAA
1 CAAAACAGTGAAAAAAACAAGAAAATAGCAA
30020803 CAAAACAGT-AAAAAAACAAGAAAATAG
1 CAAAACAGTGAAAAAAACAAGAAAATAG
30020830 TACAAAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.69, C:0.09, G:0.12, T:0.10
Consensus pattern (31 bp):
CAAAACAGTGAAAAAAACAAGAAAATAGCAA
Found at i:30020826 original size:19 final size:20
Alignment explanation
Indices: 30020804--30020841 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
30020794 AAATAGCAAC
30020804 AAAACAGTA-AAAAAACAAG
1 AAAACAGTACAAAAAACAAG
*
30020823 AAAATAGTACAAAAAACAA
1 AAAACAGTACAAAAAACAA
30020842 TAGTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.74, C:0.11, G:0.08, T:0.08
Consensus pattern (20 bp):
AAAACAGTACAAAAAACAAG
Found at i:30023178 original size:22 final size:22
Alignment explanation
Indices: 30023147--30023191 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
30023137 AAAAATCAAA
*
30023147 ATTTAGTTCTATGTTTGTAGGG
1 ATTTAATTCTATGTTTGTAGGG
30023169 ATTTAATTCTATGTTTGTAGGG
1 ATTTAATTCTATGTTTGTAGGG
30023191 A
1 A
30023192 AAGGAGTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.22, C:0.04, G:0.24, T:0.49
Consensus pattern (22 bp):
ATTTAATTCTATGTTTGTAGGG
Found at i:30026266 original size:19 final size:19
Alignment explanation
Indices: 30026242--30026281 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
30026232 AAAATATCAT
30026242 ATTAATTTTAATTGATTTG
1 ATTAATTTTAATTGATTTG
* *
30026261 ATTAATTTTATTTTATTTG
1 ATTAATTTTAATTGATTTG
30026280 AT
1 AT
30026282 CAAAATTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.62
Consensus pattern (19 bp):
ATTAATTTTAATTGATTTG
Found at i:30027459 original size:15 final size:14
Alignment explanation
Indices: 30027437--30027472 Score: 63
Period size: 15 Copynumber: 2.5 Consensus size: 14
30027427 GCTATGCATG
30027437 CAAAATATAAAAGA
1 CAAAATATAAAAGA
30027451 CATAAATATAAAAGA
1 CA-AAATATAAAAGA
30027466 CAAAATA
1 CAAAATA
30027473 GTGAAATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.69, C:0.08, G:0.06, T:0.17
Consensus pattern (14 bp):
CAAAATATAAAAGA
Found at i:30036122 original size:6 final size:6
Alignment explanation
Indices: 30036111--30036140 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
30036101 TAATATAAGG
30036111 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
30036141 TGAAGGGTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:30045387 original size:20 final size:20
Alignment explanation
Indices: 30045364--30045410 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
30045354 GTAGACGAGA
30045364 TGCCAGTAATGCAGATAAAC
1 TGCCAGTAATGCAGATAAAC
*
30045384 TGCCAGTATTGCAGATAAAC
1 TGCCAGTAATGCAGATAAAC
30045404 TGCCAGT
1 TGCCAGT
30045411 TGCAAACAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.23
Consensus pattern (20 bp):
TGCCAGTAATGCAGATAAAC
Found at i:30050762 original size:18 final size:18
Alignment explanation
Indices: 30050741--30050782 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
30050731 GAAACATTTA
*
30050741 TTTTAATG-ATTTTAGTAT
1 TTTTAATGTATTATA-TAT
*
30050759 TTTTGATGTATTATATAT
1 TTTTAATGTATTATATAT
30050777 TTTTAA
1 TTTTAA
30050783 AAATTATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.62
Consensus pattern (18 bp):
TTTTAATGTATTATATAT
Found at i:30051145 original size:40 final size:40
Alignment explanation
Indices: 30051055--30051166 Score: 129
Period size: 40 Copynumber: 2.8 Consensus size: 40
30051045 ACACACCAGT
*
30051055 TTGTGGACAAGCCACCAGTAATGCAGAAAAACTGCTAGAA
1 TTGTGGACAAGCCACCAGTAATGCAGAAAAACTACTAGAA
* * * *
30051095 TTGTGTACAAGCCACTAGTATTGCA-AAAGAGCTACTAGTAA
1 TTGTGGACAAGCCACCAGTAATGCAGAAA-AACTACTAG-AA
* *
30051136 -TGTGGACAAGCCACCAATAATGCAGATAAAC
1 TTGTGGACAAGCCACCAGTAATGCAGAAAAAC
30051167 AGCCAATATT
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
39 3 0.05
40 51 0.88
41 4 0.07
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.21
Consensus pattern (40 bp):
TTGTGGACAAGCCACCAGTAATGCAGAAAAACTACTAGAA
Found at i:30052791 original size:9 final size:9
Alignment explanation
Indices: 30052777--30052825 Score: 71
Period size: 9 Copynumber: 5.4 Consensus size: 9
30052767 GTAGTGATTC
30052777 AATTCGGTT
1 AATTCGGTT
*
30052786 AATTCGGGT
1 AATTCGGTT
*
30052795 AATTCGGGT
1 AATTCGGTT
*
30052804 AATTTGGTT
1 AATTCGGTT
30052813 AATTCGGTT
1 AATTCGGTT
30052822 AATT
1 AATT
30052826 TTTAACCAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.43
Consensus pattern (9 bp):
AATTCGGTT
Found at i:30057683 original size:6 final size:6
Alignment explanation
Indices: 30057672--30057699 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
30057662 TTTTTATTGC
30057672 TTTTTA TTTTTA TTTTTA TTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTT
30057700 GGATTTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:30057706 original size:18 final size:18
Alignment explanation
Indices: 30057672--30057707 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
30057662 TTTTTATTGC
*
30057672 TTTTTATTTTTATTTTTA
1 TTTTTATTTTGATTTTTA
30057690 TTTTTATTTTGGATTTTT
1 TTTTTATTTT-GATTTTT
30057708 TATACAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.81
Consensus pattern (18 bp):
TTTTTATTTTGATTTTTA
Found at i:30058081 original size:2 final size:2
Alignment explanation
Indices: 30058074--30058116 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
30058064 CCCTCCCACT
30058074 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
30058116 T
1 T
30058117 ACACCCTTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:30062201 original size:29 final size:29
Alignment explanation
Indices: 30062167--30062363 Score: 214
Period size: 29 Copynumber: 6.8 Consensus size: 29
30062157 TGGTCAAAAT
*
30062167 CATCCCTTTTCATATTCGATGGTTGCCAC
1 CATCCCTTTTCATATTCGATGGTTGTCAC
* *
30062196 CGTCCCTTTTCTTATTCGATGGTTGTCAC
1 CATCCCTTTTCATATTCGATGGTTGTCAC
* * * * *
30062225 CGTCCCTTTTCAGATTCGATGGTCGTTAG
1 CATCCCTTTTCATATTCGATGGTTGTCAC
*
30062254 CATCCCTTTTCATATTCGATGATTGTCAC
1 CATCCCTTTTCATATTCGATGGTTGTCAC
* * *****
30062283 CATTCCTTTTCAAATTCGATGGCCCAAAC
1 CATCCCTTTTCATATTCGATGGTTGTCAC
* * * *
30062312 TAACCCTTTTCATATTTGATGGTTGTCAG
1 CATCCCTTTTCATATTCGATGGTTGTCAC
30062341 CATCCCTTTTCATATTCGATGGT
1 CATCCCTTTTCATATTCGATGGT
30062364 GATAGAGGGT
Statistics
Matches: 132, Mismatches: 36, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 132 1.00
ACGTcount: A:0.18, C:0.26, G:0.15, T:0.40
Consensus pattern (29 bp):
CATCCCTTTTCATATTCGATGGTTGTCAC
Found at i:30066282 original size:107 final size:107
Alignment explanation
Indices: 30066095--30066734 Score: 1154
Period size: 107 Copynumber: 6.0 Consensus size: 107
30066085 AAAAGAAGGT
** *
30066095 TTTTCTAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTGGGTT
1 TTTTCTAAATAAGAAAATATTTCGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTAGGTT
*
30066160 TCGATTTCTCATTCGACCAAATAGCCAAGTATCCTTTTAAGA
66 TCGATTTCTCGTTCGACCAAATAGCCAAGTATCCTTTTAAGA
30066202 TTTTCTAAATAAGAAAATATTTCGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTAGGTT
1 TTTTCTAAATAAGAAAATATTTCGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTAGGTT
30066267 TCGATTTCTCGTTCGACCAAATAGCCAAGTATCCTTTTAAGA
66 TCGATTTCTCGTTCGACCAAATAGCCAAGTATCCTTTTAAGA
30066309 TTTTCTAAATAAGAAAATATTTCGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTAGGTT
1 TTTTCTAAATAAGAAAATATTTCGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTAGGTT
30066374 TCGATTTCTCGTTCGACCAAATAGCCAAGTATCCTTTTAAGA
66 TCGATTTCTCGTTCGACCAAATAGCCAAGTATCCTTTTAAGA
30066416 TTTTCTAAATAAGAAAATATTTCGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTAGGTT
1 TTTTCTAAATAAGAAAATATTTCGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTAGGTT
30066481 TCGATTTCTCGTTCGACCAAATAGCCAAGTATCCTTTTAAGA
66 TCGATTTCTCGTTCGACCAAATAGCCAAGTATCCTTTTAAGA
30066523 TTTTCTAAATAAGAAAATATTTCGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTAGGTT
1 TTTTCTAAATAAGAAAATATTTCGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTAGGTT
30066588 TCGATTTCTCGTTCGACCAAATAGCCAAGTATCCTTTTAAGA
66 TCGATTTCTCGTTCGACCAAATAGCCAAGTATCCTTTTAAGA
** * * * *
30066630 TTTTCTAAATAAGGCAATATTTTGCGTTTGGAAAATCGAGAAAACATGCCCTAACGTGCTGGGTT
1 TTTTCTAAATAAGAAAATATTTCGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTAGGTT
* * * *
30066695 TCGATTTCTCGTTTGACTAAATAGCCAAATATCCTCTTAA
66 TCGATTTCTCGTTCGACCAAATAGCCAAGTATCCTTTTAA
30066735 AACTTCAAAG
Statistics
Matches: 519, Mismatches: 14, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
107 519 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (107 bp):
TTTTCTAAATAAGAAAATATTTCGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTAGGTT
TCGATTTCTCGTTCGACCAAATAGCCAAGTATCCTTTTAAGA
Found at i:30078251 original size:44 final size:43
Alignment explanation
Indices: 30078177--30078314 Score: 116
Period size: 44 Copynumber: 3.1 Consensus size: 43
30078167 GCCATTAAAG
* * * * *
30078177 CAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAA
1 CAGATCCTGTCTTCCTATATTGGTAGGAAGTAGATCAAAGAT-A
* * *
30078221 CAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCAAAGATG
1 CAGATCCTGTCTTCCTATATTGGTAGGAAGTAGATCAAAGATA
* * * * *
30078264 CAGATCTTGTCTTACC-ATACTGGTGGCGAAGTAGATCGAAGAAA
1 CAGATCCTGTCTT-CCTATATTGGTAG-GAAGTAGATCAAAGATA
30078308 GCAGATC
1 -CAGATC
30078315 TTCGATCTTG
Statistics
Matches: 75, Mismatches: 16, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
43 19 0.25
44 50 0.67
45 6 0.08
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (43 bp):
CAGATCCTGTCTTCCTATATTGGTAGGAAGTAGATCAAAGATA
Found at i:30078344 original size:52 final size:52
Alignment explanation
Indices: 30078266--30078524 Score: 518
Period size: 52 Copynumber: 5.0 Consensus size: 52
30078256 CAAAGATGCA
30078266 GATCTTGTCTTACCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTC
1 GATCTTGTCTTACCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTC
30078318 GATCTTGTCTTACCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTC
1 GATCTTGTCTTACCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTC
30078370 GATCTTGTCTTACCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTC
1 GATCTTGTCTTACCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTC
30078422 GATCTTGTCTTACCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTC
1 GATCTTGTCTTACCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTC
30078474 GATCTTGTCTTACCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTT
1 GATCTTGTCTTACCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTT
30078525 GTCTTCATGT
Statistics
Matches: 207, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 207 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (52 bp):
GATCTTGTCTTACCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTC
Found at i:30078679 original size:88 final size:87
Alignment explanation
Indices: 30078587--30078749 Score: 188
Period size: 88 Copynumber: 1.9 Consensus size: 87
30078577 ATATTAGTAG
* *
30078587 GAAGTGGATCGACGAT-GCAGA-TCTTGTCTTCCCATACTGGT-GGCAAAGTAGATCGAAGAAAG
1 GAAGTGGATCAAAGATAGCAGATTC-TGTCTTCCCATACTGGTAGG--AAGTAGATCGAAGAAA-
*
30078649 CCGATCTTGTCTTCATTTATTGGCGT
62 CAGATCTTGTCTTCATTTATTGGCGT
* * * * * *
30078675 GAAGTTGATCAAAGATAGCAGGTTCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATACAGA
1 GAAGTGGATCAAAGATAGCAGATTCTGTCTTCCCATACTGGTAGGAAGTAGATCGAAGAAACAGA
30078740 TCTTGTCTTC
66 TCTTGTCTTC
30078750 CCATACTGGT
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
87 13 0.21
88 27 0.43
89 19 0.30
90 4 0.06
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (87 bp):
GAAGTGGATCAAAGATAGCAGATTCTGTCTTCCCATACTGGTAGGAAGTAGATCGAAGAAACAGA
TCTTGTCTTCATTTATTGGCGT
Found at i:30078723 original size:44 final size:45
Alignment explanation
Indices: 30078175--30078777 Score: 274
Period size: 52 Copynumber: 13.0 Consensus size: 45
30078165 AAGCCATTAA
* * * * *
30078175 AGCA-GATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGAT
1 AGCAGGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGAT
* * * *
30078219 AACAGG-TCCTGTCTTCCTATATTGGTAGGAAGTGGATCAAAGAT
1 AGCAGGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGAT
* * *
30078263 -GCA-GATCTTGTCTTACC-ATACTGGTGGCGAAGTAGATCGAAGAA
1 AGCAGGATCTTGTCTT-CCTATATTGGTAG-GAAGTAGATCGAAGAT
* * *
30078307 AGCAGATCTTCGATCTTGTCTTACC-ATACTGGTGGCGAAGTAGATCGAAGAA
1 AGCAG------GATCTTGTCTT-CCTATATTGGTAG-GAAGTAGATCGAAGAT
* * *
30078359 AGCAGATCTTCGATCTTGTCTTACC-ATACTGGTGGCGAAGTAGATCGAAGAA
1 AGCAG------GATCTTGTCTT-CCTATATTGGTAG-GAAGTAGATCGAAGAT
* * *
30078411 AGCAGATCTTCGATCTTGTCTTACC-ATACTGGTGGCGAAGTAGATCGAAGAA
1 AGCAG------GATCTTGTCTT-CCTATATTGGTAG-GAAGTAGATCGAAGAT
* * *
30078463 AGCAGATCTTCGATCTTGTCTTACC-ATACTGGTGGCGAAGTAGATCGAAGAA
1 AGCAG------GATCTTGTCTT-CCTATATTGGTAG-GAAGTAGATCGAAGAT
* * * *
30078515 AGCA-GATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCCAAGAT
1 AGCAGGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAGAT
* * * * * *
30078559 AGTAGG-TCCTGTATTCCTATATTAGTAGGAAGTGGATCGACGAT
1 AGCAGGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGAT
* * *
30078603 -GCA-GATCTTGTCTTCCCATACTGGT-GGCAAAGTAGATCGAAGAA
1 AGCAGGATCTTGTCTTCCTATATTGGTAGG--AAGTAGATCGAAGAT
* * * * * *
30078647 AGC-CGATCTTGTCTTCATTTATTGG-CGTGAAGTTGATCAAAGAT
1 AGCAGGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAGAT
* *
30078691 AGCAGGTTC-TGTCTTCCTATATTGGTAGGAAGTGGATCGAAGAT
1 AGCAGGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGAT
* * * *
30078735 A-CA-GATCTTGTCTTCCCATACTGGTGGCGAAGTAGATTGAAGA
1 AGCAGGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAGA
30078778 CCACAGATCT
Statistics
Matches: 473, Mismatches: 60, Indels: 52
0.81 0.10 0.09
Matches are distributed among these distances:
42 7 0.01
43 53 0.11
44 165 0.35
45 46 0.10
46 1 0.00
52 201 0.42
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.29
Consensus pattern (45 bp):
AGCAGGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGAT
Found at i:30078788 original size:132 final size:132
Alignment explanation
Indices: 30078474--30078777 Score: 491
Period size: 132 Copynumber: 2.3 Consensus size: 132
30078464 GCAGATCTTC
*
30078474 GATCTTGTCTTACCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTG
1 GATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTG
* * * *
30078539 GCGTGAAGTAGATCCAAGATAGTAGGTCCTGTATTCCTATATTAGTAGGAAGTGGATCGACGATG
66 GCGTGAAGTAGATCAAAGATAGCAGGTCCTGTATTCCTATATTAGTAGGAAGTGGATCGAAGATA
30078604 CA
131 CA
* * *
30078606 GATCTTGTCTTCCCATACTGGTGGCAAAGTAGATCGAAGAAAGCCGATCTTGTCTTCATTTATTG
1 GATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTG
* * * *
30078671 GCGTGAAGTTGATCAAAGATAGCAGGTTCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATA
66 GCGTGAAGTAGATCAAAGATAGCAGGTCCTGTATTCCTATATTAGTAGGAAGTGGATCGAAGATA
30078736 CA
131 CA
*
30078738 GATCTTGTCTTCCCATACTGGTGGCGAAGTAGATTGAAGA
1 GATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGA
30078778 CCACAGATCT
Statistics
Matches: 158, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
132 158 1.00
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (132 bp):
GATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTG
GCGTGAAGTAGATCAAAGATAGCAGGTCCTGTATTCCTATATTAGTAGGAAGTGGATCGAAGATA
CA
Found at i:30080636 original size:106 final size:106
Alignment explanation
Indices: 30080511--30080713 Score: 372
Period size: 106 Copynumber: 1.9 Consensus size: 106
30080501 TTTTACAATC
*
30080511 AATATATACATACTTATATTTTATATGCTATAATCTATATGTTTT-TTTTCTCTTTCTCCTATAT
1 AATATATACATACTTATATTTTATATGCTATAATCTATAT-TTTTATTTTCTCTTTCTCATATAT
30080575 ACATGTATATACACACTTTTTATAATACACATATGGTCTGGT
65 ACATGTATATACACACTTTTTATAATACACATATGGTCTGGT
*
30080617 AATATATACATACTTATATTTTATATGCTATAATCTATCTTTTTATTTTCTCTTTCTCATATATA
1 AATATATACATACTTATATTTTATATGCTATAATCTATATTTTTATTTTCTCTTTCTCATATATA
30080682 CATGTATATACACACTTTTTATAATACACATA
66 CATGTATATACACACTTTTTATAATACACATA
30080714 CACACATATT
Statistics
Matches: 94, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
105 4 0.04
106 90 0.96
ACGTcount: A:0.32, C:0.15, G:0.04, T:0.48
Consensus pattern (106 bp):
AATATATACATACTTATATTTTATATGCTATAATCTATATTTTTATTTTCTCTTTCTCATATATA
CATGTATATACACACTTTTTATAATACACATATGGTCTGGT
Found at i:30085340 original size:19 final size:19
Alignment explanation
Indices: 30085316--30085408 Score: 77
Period size: 19 Copynumber: 5.1 Consensus size: 19
30085306 AATAAATTAC
*
30085316 TCATCTTAGTTAATTGAGT
1 TCATCTTAGTTAATTAAGT
30085335 TCATCTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
** * * *
30085354 TGC-T-GGAATAAATT-A-C
1 T-CATCTTAGTTAATTAAGT
*
30085370 TCATCTTAGTTAATTGAGT
1 TCATCTTAGTTAATTAAGT
*
30085389 TCATTTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
30085408 T
1 T
30085409 GCTGAAATAA
Statistics
Matches: 56, Mismatches: 13, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
15 1 0.02
16 2 0.04
17 7 0.12
18 7 0.12
19 38 0.68
20 1 0.02
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.46
Consensus pattern (19 bp):
TCATCTTAGTTAATTAAGT
Found at i:30085466 original size:54 final size:54
Alignment explanation
Indices: 30085297--30085443 Score: 267
Period size: 54 Copynumber: 2.7 Consensus size: 54
30085287 ATAAGTATTT
30085297 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTGAGTTCATCTTAGTTAATTA
1 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTGAGTTCATCTTAGTTAATTA
*
30085351 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTGAGTTCATTTTAGTTAATTA
1 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTGAGTTCATCTTAGTTAATTA
* *
30085405 AGTTGCTGAAATAAATTACTCATCTTAGTTAATTAAGTT
1 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTGAGTT
30085444 AAACTTAGCT
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 90 1.00
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (54 bp):
AGTTGCTGGAATAAATTACTCATCTTAGTTAATTGAGTTCATCTTAGTTAATTA
Found at i:30088301 original size:21 final size:23
Alignment explanation
Indices: 30088275--30088324 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
30088265 ATGTGTGTTA
30088275 TGTTTAATAAG-T-A-TTTATATG
1 TGTTTAATAAGCTCATTTTA-ATG
30088296 TGTTTAATAAGCTCATTTTAATG
1 TGTTTAATAAGCTCATTTTAATG
30088319 TGTTTA
1 TGTTTA
30088325 TTGCAGATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 11 0.42
22 1 0.04
23 10 0.38
24 4 0.15
ACGTcount: A:0.30, C:0.04, G:0.14, T:0.52
Consensus pattern (23 bp):
TGTTTAATAAGCTCATTTTAATG
Found at i:30088319 original size:23 final size:21
Alignment explanation
Indices: 30088275--30088324 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 21
30088265 ATGTGTGTTA
30088275 TGTTTAATAAGTATTTATATG
1 TGTTTAATAAGTATTTATATG
30088296 TGTTTAATAAGCTCATTT-TAATG
1 TGTTTAATAAG-T-ATTTAT-ATG
30088319 TGTTTA
1 TGTTTA
30088325 TTGCAGATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 11 0.42
22 2 0.08
23 13 0.50
ACGTcount: A:0.30, C:0.04, G:0.14, T:0.52
Consensus pattern (21 bp):
TGTTTAATAAGTATTTATATG
Found at i:30088998 original size:46 final size:46
Alignment explanation
Indices: 30088947--30089039 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
30088937 TAGTGTGGCC
*
30088947 TTCATCATACACCAAGGTTCCTATCATCCTTGATAGTGGGTCGAGG
1 TTCATCATACACCAACGTTCCTATCATCCTTGATAGTGGGTCGAGG
* *
30088993 TTCATCATATACCAACGTTCCTATCATTCTTGATAGTGGGTCGAGG
1 TTCATCATACACCAACGTTCCTATCATCCTTGATAGTGGGTCGAGG
30089039 T
1 T
30089040 CTTTTAAACC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (46 bp):
TTCATCATACACCAACGTTCCTATCATCCTTGATAGTGGGTCGAGG
Found at i:30089609 original size:33 final size:33
Alignment explanation
Indices: 30089572--30089639 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
30089562 TGGGAGTTAC
* *
30089572 ATAATGCATGATA-TAATTAAGATATGTAGATTA
1 ATAATGCAGGATATTAATTAA-AGATGTAGATTA
*
30089605 ATAATGCAGGATATTAATTAAAGATGTATATTA
1 ATAATGCAGGATATTAATTAAAGATGTAGATTA
30089638 AT
1 AT
30089640 GATGTTCAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.46, C:0.03, G:0.15, T:0.37
Consensus pattern (33 bp):
ATAATGCAGGATATTAATTAAAGATGTAGATTA
Found at i:30093743 original size:10 final size:10
Alignment explanation
Indices: 30093704--30093744 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
30093694 CATATTTTCA
30093704 CTTTTTCCTTT
1 CTTTTT-CTTT
*
30093715 CTTTTTCTCT
1 CTTTTTCTTT
*
30093725 ATTTTTCTTT
1 CTTTTTCTTT
30093735 CTTTTTCTTT
1 CTTTTTCTTT
30093745 TTCAATTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
10 20 0.77
11 6 0.23
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (10 bp):
CTTTTTCTTT
Found at i:30093743 original size:26 final size:28
Alignment explanation
Indices: 30093712--30093772 Score: 81
Period size: 26 Copynumber: 2.2 Consensus size: 28
30093702 CACTTTTTCC
**
30093712 TTTCTTTTTCTCTATTTTTC-T-TTCTT
1 TTTCTTTTTCAATATTTTTCTTGTTCTT
*
30093738 TTTCTTTTTCAATTTTTTTCTTGTTCTT
1 TTTCTTTTTCAATATTTTTCTTGTTCTT
30093766 TTTCTTT
1 TTTCTTT
30093773 CATCTTTTCC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 17 0.57
27 1 0.03
28 12 0.40
ACGTcount: A:0.05, C:0.16, G:0.02, T:0.77
Consensus pattern (28 bp):
TTTCTTTTTCAATATTTTTCTTGTTCTT
Found at i:30093745 original size:16 final size:15
Alignment explanation
Indices: 30093712--30093773 Score: 52
Period size: 16 Copynumber: 3.9 Consensus size: 15
30093702 CACTTTTTCC
* *
30093712 TTTCTTTTTCTCTATT
1 TTTCTTTTT-TTTCTT
30093728 TTTCTTTCTTTTTCTT
1 TTTCTTT-TTTTTCTT
*
30093744 TTTCAATTTTTTTCTT
1 TTTC-TTTTTTTTCTT
*
30093760 GTTCTTTTTCTTTC
1 TTTCTTTTT-TTTC
30093774 ATCTTTTCCA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
15 4 0.11
16 30 0.79
17 4 0.11
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.76
Consensus pattern (15 bp):
TTTCTTTTTTTTCTT
Found at i:30093764 original size:22 final size:23
Alignment explanation
Indices: 30093727--30093769 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
30093717 TTTTCTCTAT
*
30093727 TTTTCTTTCTTTTTCTTTTTCAA
1 TTTTCTTTCTTGTTCTTTTTCAA
30093750 TTTT-TTTCTTGTTCTTTTTC
1 TTTTCTTTCTTGTTCTTTTTC
30093770 TTTCATCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.05, C:0.16, G:0.02, T:0.77
Consensus pattern (23 bp):
TTTTCTTTCTTGTTCTTTTTCAA
Found at i:30093780 original size:26 final size:25
Alignment explanation
Indices: 30093712--30093780 Score: 63
Period size: 26 Copynumber: 2.6 Consensus size: 25
30093702 CACTTTTTCC
30093712 TTTCTTTTTC-TCTATTTTTCTTTCTT
1 TTTC-TTTTCATCT-TTTTTCTTTCTT
30093738 TTTCTTTTTCAAT-TTTTTTCTTGTTCTT
1 TTTC-TTTTC-ATCTTTTTTC-T-TTCTT
30093766 TTTC-TTTCATCTTTT
1 TTTCTTTTCATCTTTT
30093781 CCAAAGACTC
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
25 2 0.05
26 24 0.63
27 2 0.05
28 10 0.26
ACGTcount: A:0.06, C:0.17, G:0.01, T:0.75
Consensus pattern (25 bp):
TTTCTTTTCATCTTTTTTCTTTCTT
Found at i:30098954 original size:14 final size:15
Alignment explanation
Indices: 30098924--30098954 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
30098914 CGATTTTTTT
30098924 TCACTTTTTTTTGAA
1 TCACTTTTTTTTGAA
30098939 TCACTTTTTTTT-AA
1 TCACTTTTTTTTGAA
30098953 TC
1 TC
30098955 CAATACAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.19, C:0.16, G:0.03, T:0.61
Consensus pattern (15 bp):
TCACTTTTTTTTGAA
Found at i:30102235 original size:46 final size:46
Alignment explanation
Indices: 30102166--30102263 Score: 119
Period size: 46 Copynumber: 2.1 Consensus size: 46
30102156 AGTTGTCTTG
30102166 GCTTAAGACACTTTAAATGGCTGTAG-AACAAAGACAAATTAAATTA
1 GCTTAAGACACTTTAAATGGCTGTAGTAACAAAGACAAATT-AATTA
* ***
30102212 GCTTAAGACAAC-TTAAATTGCTGTAGTAATTTAGACAAATTAATTA
1 GCTTAAGAC-ACTTTAAATGGCTGTAGTAACAAAGACAAATTAATTA
*
30102258 ACTTAA
1 GCTTAA
30102264 CTTATTAATG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
46 32 0.71
47 13 0.29
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (46 bp):
GCTTAAGACACTTTAAATGGCTGTAGTAACAAAGACAAATTAATTA
Found at i:30103652 original size:6 final size:6
Alignment explanation
Indices: 30103643--30103672 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
30103633 CTCATTTTCA
30103643 TCATTT TCATTT TCATTT TCATTT TCATTT
1 TCATTT TCATTT TCATTT TCATTT TCATTT
30103673 ATTTCAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.67
Consensus pattern (6 bp):
TCATTT
Found at i:30103677 original size:27 final size:27
Alignment explanation
Indices: 30103634--30103690 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
30103624 TTTTGAAATC
*
30103634 TCATTTTCATCATTTTCATTTTCATTT
1 TCATTTTCATCATTTTCAATTTCATTT
* *
30103661 TCATTTTCAT-TTATTTCAATTTCTTTT
1 TCATTTTCATCAT-TTTCAATTTCATTT
30103688 TCA
1 TCA
30103691 ATGTTCTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.19, C:0.18, G:0.00, T:0.63
Consensus pattern (27 bp):
TCATTTTCATCATTTTCAATTTCATTT
Found at i:30105857 original size:12 final size:12
Alignment explanation
Indices: 30105835--30105871 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
30105825 TATTGTGCAC
30105835 GAATATTTTTTTA
1 GAAT-TTTTTTTA
*
30105848 GAATTTTTTTTT
1 GAATTTTTTTTA
30105860 GAATTTTTTTTA
1 GAATTTTTTTTA
30105872 CAAACCTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 18 0.82
13 4 0.18
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (12 bp):
GAATTTTTTTTA
Found at i:30112989 original size:23 final size:24
Alignment explanation
Indices: 30112954--30112998 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
30112944 TTTCTTTTGT
30112954 TTCTTTTTCTAAC-TCATTTTCTC
1 TTCTTTTTCTAACGTCATTTTCTC
*
30112977 TTCTTTCTT-TAACGTCTTTTTC
1 TTCTTT-TTCTAACGTCATTTTC
30112999 AATTTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.11, C:0.24, G:0.02, T:0.62
Consensus pattern (24 bp):
TTCTTTTTCTAACGTCATTTTCTC
Done.