Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold9
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: 3883850
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 144036 characters in sequence are not A, C, G, or T
File 16 of 24
Found at i:2391330 original size:19 final size:19
Alignment explanation
Indices: 2391306--2391376 Score: 99
Period size: 19 Copynumber: 3.7 Consensus size: 19
2391296 ATTTGCCTAC
2391306 ATGTATCGATACATTGA-T
1 ATGTATCGATACATTGAGT
2391324 AATGTATCGATACATTGAGT
1 -ATGTATCGATACATTGAGT
* *
2391344 GATGTATCGACACACTGAGT
1 -ATGTATCGATACATTGAGT
2391364 ATGTATCGATACA
1 ATGTATCGATACA
2391377 AAACTTATGT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
19 29 0.62
20 18 0.38
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (19 bp):
ATGTATCGATACATTGAGT
Found at i:2391401 original size:13 final size:13
Alignment explanation
Indices: 2391383--2391409 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2391373 TACAAAACTT
2391383 ATGTATCGATACA
1 ATGTATCGATACA
2391396 ATGTATCGATACA
1 ATGTATCGATACA
2391409 A
1 A
2391410 ATTGTAAAAA
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2391899 original size:84 final size:83
Alignment explanation
Indices: 2391742--2392304 Score: 315
Period size: 84 Copynumber: 6.7 Consensus size: 83
2391732 CTTGTCGGTG
* * * * * ** ** * *
2391742 TTGACCCTGGAGACTTCCTTACCCTTAAGTCTGCCTATCGGCTTTGACCTTGGAGACTTTCTTAC
1 TTGACCTTGGAGACTTTCTTA-CCTTAAGTTTGCCTGTCGGTTTTGACC-TAAAGACTACCTCAT
* * *
2391807 CTTC-AGTCTGCCTGTTGGCT
64 C-TCAAGTCTGCCTATCGACT
* * * * * * *
2391827 TTGACCTTGGAGACTATCTCATCTAAAGTTTGCGTGCCGGTTTTGACACTAAAGACTGCCTCATC
1 TTGACCTTGGAGACTTTCTTACCTTAAGTTTGCCTGTCGGTTTTGAC-CTAAAGACTACCTCATC
* *
2391892 TCAAGTCTACTTATCGACT
65 TCAAGTCTGCCTATCGACT
* * ** * *
2391911 TTGACCCTAGAGACTTTCTTACCTTTTGTTTGCCTATCGGTTTTGACCTTGAAGACTACCTCATC
1 TTGACCTTGGAGACTTTCTTACCTTAAGTTTGCCTGTCGGTTTTGACC-TAAAGACTACCTCATC
*
2391976 TCAAGTGTGCCTATCGACT
65 TCAAGTCTGCCTATCGACT
* * * * * * * *
2391995 TTGACCTTGGAGACTTTCTTACCTTCAGTTTGCTTGTTGATTTTGACCCTAGAGACTTCCTTACC
1 TTGACCTTGGAGACTTTCTTACCTTAAGTTTGCCTGTCGGTTTTGA-CCTAAAGACTACCTCA-T
2392060 CTCAAGTCTGCCTATC-AGCT
64 CTCAAGTCTGCCTATCGA-CT
* * * * * ** * * *
2392080 TTGACCTTGGATACTTTCTTACCTTCAGTCTGTCTATTAGCTTTGACCTTAACGACTGCCTCATC
1 TTGACCTTGGAGACTTTCTTACCTTAAGTTTGCCTGTCGGTTTTGACC-TAAAGACTACCTCATC
* *
2392145 GT-AATTCTGCC-AGTCAACT
65 -TCAAGTCTGCCTA-TCGACT
** * * * ** *** ** ** *
2392164 TTGACCTTGGAGGTTTTTTTACCTTCAGTCTGTTTGTCAACTTTGACCTTGGAGGTTGCCTCATC
1 TTGACCTTGGAGACTTTCTTACCTTAAGTTTGCCTGTCGGTTTTGACC-TAAAGACTACCTCATC
*
2392229 TCAAGTCTGCCTATCGGCT
65 TCAAGTCTGCCTATCGACT
* ** * * * * *
2392248 TTGACCTTAGAGACTGCCTTATCTTAAGTTTGCTTGTCAGCTTTGACCCTGAAGACT
1 TTGACCTTGGAGACTTTCTTACCTTAAGTTTGCCTGTCGGTTTTGA-CCTAAAGACT
2392305 TCCTTATCCT
Statistics
Matches: 369, Mismatches: 96, Indels: 27
0.75 0.20 0.05
Matches are distributed among these distances:
83 5 0.01
84 274 0.74
85 90 0.24
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.37
Consensus pattern (83 bp):
TTGACCTTGGAGACTTTCTTACCTTAAGTTTGCCTGTCGGTTTTGACCTAAAGACTACCTCATCT
CAAGTCTGCCTATCGACT
Found at i:2392266 original size:42 final size:42
Alignment explanation
Indices: 2391742--2392354 Score: 265
Period size: 42 Copynumber: 14.5 Consensus size: 42
2391732 CTTGTCGGTG
* *
2391742 TTGACCCTGGAGACTTCCTTACCCTTAAGTCTGCCTATCGGCT
1 TTGACCTTGGAGACTTCCTTA-CCTCAAGTCTGCCTATCGGCT
* * *
2391785 TTGACCTTGGAGACTTTCTTACCTTC-AGTCTGCCTGTTGGCT
1 TTGACCTTGGAGACTTCCTTACC-TCAAGTCTGCCTATCGGCT
* * * * * ** *
2391827 TTGACCTTGGAGACTAT-CTCATCTAAAGTTTGCGTGCCGGTT
1 TTGACCTTGGAGACT-TCCTTACCTCAAGTCTGCCTATCGGCT
** * * * * * *
2391869 TTGACAC-TAAAGACTGCCTCATCTCAAGTCTACTTATCGACT
1 TTGAC-CTTGGAGACTTCCTTACCTCAAGTCTGCCTATCGGCT
* * * *** * *
2391911 TTGACCCTAGAGACTTTCTTACCTTTTGTTTGCCTATCGGTT
1 TTGACCTTGGAGACTTCCTTACCTCAAGTCTGCCTATCGGCT
* * * * * *
2391953 TTGACCTTGAAGACTACCTCATCTCAAGTGTGCCTATCGACT
1 TTGACCTTGGAGACTTCCTTACCTCAAGTCTGCCTATCGGCT
* * * * * **
2391995 TTGACCTTGGAGACTTTCTTACCTTC-AGTTTGCTTGTTGATT
1 TTGACCTTGGAGACTTCCTTACC-TCAAGTCTGCCTATCGGCT
* * *
2392037 TTGACCCTAGAGACTTCCTTACCCTCAAGTCTGCCTATCAGCT
1 TTGACCTTGGAGACTTCCTTA-CCTCAAGTCTGCCTATCGGCT
* * * **
2392080 TTGACCTTGGATACTTTCTTACCTTC-AGTCTGTCTATTAGCT
1 TTGACCTTGGAGACTTCCTTACC-TCAAGTCTGCCTATCGGCT
* * * * * **
2392122 TTGACCTT-AACGACTGCCTCATCGT-AATTCTGCC-AGTCAACT
1 TTGACCTTGGA-GACTTCCTTA-CCTCAAGTCTGCCTA-TCGGCT
** ** ** * **
2392164 TTGACCTTGGAGGTTTTTTTACCTTC-AGTCTGTTTGTCAACT
1 TTGACCTTGGAGACTTCCTTACC-TCAAGTCTGCCTATCGGCT
* * *
2392206 TTGACCTTGGAG-GTTGCCTCATCTCAAGTCTGCCTATCGGCT
1 TTGACCTTGGAGACTT-CCTTACCTCAAGTCTGCCTATCGGCT
* * * * * * * *
2392248 TTGACCTTAGAGACTGCCTTATCTTAAGTTTGCTTGTCAGCT
1 TTGACCTTGGAGACTTCCTTACCTCAAGTCTGCCTATCGGCT
* * * * * **
2392290 TTGACCCTGAAGACTTCCTTATCCTTAAGTTTGCTTATTAGCT
1 TTGACCTTGGAGACTTCCTTA-CCTCAAGTCTGCCTATCGGCT
**
2392333 TCAACCTTGGAGACTTCCTTAC
1 TTGACCTTGGAGACTTCCTTAC
2392355 TTTTAGTTTG
Statistics
Matches: 420, Mismatches: 128, Indels: 45
0.71 0.22 0.08
Matches are distributed among these distances:
41 9 0.02
42 319 0.76
43 92 0.22
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.38
Consensus pattern (42 bp):
TTGACCTTGGAGACTTCCTTACCTCAAGTCTGCCTATCGGCT
Found at i:2392333 original size:43 final size:43
Alignment explanation
Indices: 2392245--2392390 Score: 147
Period size: 42 Copynumber: 3.4 Consensus size: 43
2392235 CTGCCTATCG
* * *
2392245 GCTTTGA-CCTTAGAGACTGCCTTAT-CTTAAGTTTGCTTGTCA
1 GCTTTGACCCTGA-AGACTTCCTTATCCTTAAGTTTGCTTGTTA
*
2392287 GCTTTGACCCTGAAGACTTCCTTATCCTTAAGTTTGCTTATTA
1 GCTTTGACCCTGAAGACTTCCTTATCCTTAAGTTTGCTTGTTA
** * * * * *
2392330 GCTTCAACCTTGGAGACTTCCTTA-CTTTTAGTTTGCTTGTTG
1 GCTTTGACCCTGAAGACTTCCTTATCCTTAAGTTTGCTTGTTA
2392372 GCTTTGACTCC-GAAGACTT
1 GCTTTGAC-CCTGAAGACTT
2392391 TTTTCCTTTT
Statistics
Matches: 85, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
42 45 0.53
43 40 0.47
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.41
Consensus pattern (43 bp):
GCTTTGACCCTGAAGACTTCCTTATCCTTAAGTTTGCTTGTTA
Found at i:2392518 original size:84 final size:84
Alignment explanation
Indices: 2392425--2392585 Score: 250
Period size: 84 Copynumber: 1.9 Consensus size: 84
2392415 TTTGACCCGA
* * **
2392425 GAGATTTTTTTTCCTCTAATTTGCCCGTCGATTTTAACTTGGGAGACTTTTTTTCCTTTTGTTTG
1 GAGACTTTTTTTCCTCTAATTTGCCCATCGATTTTAACGCGGGAGACTTTTTTTCCTTTTGTTTG
2392490 CTCATCGGTTTTAACTTTG
66 CTCATCGGTTTTAACTTTG
* ** *
2392509 GAGACTTTTTTTCCTTTTGTTTGCCCATCGGTTTTAACGCGGGAGACTTTTTTTCCTTTTGTTTG
1 GAGACTTTTTTTCCTCTAATTTGCCCATCGATTTTAACGCGGGAGACTTTTTTTCCTTTTGTTTG
2392574 CTCATCGGTTTT
66 CTCATCGGTTTT
2392586 GACCCGGGGG
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
84 69 1.00
ACGTcount: A:0.12, C:0.19, G:0.18, T:0.51
Consensus pattern (84 bp):
GAGACTTTTTTTCCTCTAATTTGCCCATCGATTTTAACGCGGGAGACTTTTTTTCCTTTTGTTTG
CTCATCGGTTTTAACTTTG
Found at i:2392580 original size:42 final size:42
Alignment explanation
Indices: 2392385--2392585 Score: 224
Period size: 42 Copynumber: 4.8 Consensus size: 42
2392375 TTGACTCCGA
* * ** * * *
2392385 AGAC-TTTTTTCCTTTTCTTTGCCCGTCAATTTTGACCCGAG
1 AGACTTTTTTTCCTTTTGTTTGCCCATCGGTTTTAACTCGGG
* * ** * * *
2392426 AGATTTTTTTTCCTCTAATTTGCCCGTCGATTTTAACTTGGG
1 AGACTTTTTTTCCTTTTGTTTGCCCATCGGTTTTAACTCGGG
* **
2392468 AGACTTTTTTTCCTTTTGTTTGCTCATCGGTTTTAACTTTGG
1 AGACTTTTTTTCCTTTTGTTTGCCCATCGGTTTTAACTCGGG
*
2392510 AGACTTTTTTTCCTTTTGTTTGCCCATCGGTTTTAACGCGGG
1 AGACTTTTTTTCCTTTTGTTTGCCCATCGGTTTTAACTCGGG
*
2392552 AGACTTTTTTTCCTTTTGTTTGCTCATCGGTTTT
1 AGACTTTTTTTCCTTTTGTTTGCCCATCGGTTTT
2392586 GACCCGGGGG
Statistics
Matches: 137, Mismatches: 22, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
41 3 0.02
42 134 0.98
ACGTcount: A:0.13, C:0.20, G:0.17, T:0.50
Consensus pattern (42 bp):
AGACTTTTTTTCCTTTTGTTTGCCCATCGGTTTTAACTCGGG
Found at i:2392610 original size:42 final size:41
Alignment explanation
Indices: 2392476--2392611 Score: 112
Period size: 42 Copynumber: 3.3 Consensus size: 41
2392466 GGAGACTTTT
* *** **
2392476 TTTC-CTTTTGTTTGCTCATCGGTTTTAACTTTGGAGACTT
1 TTTCTCTTTTGTTTGCCCATCGGTTTTAACCCGGGAGACCC
* * **
2392516 TTTTTCCTTTTGTTTGCCCATCGGTTTTAACGCGGGAGACTT
1 TTTCT-CTTTTGTTTGCCCATCGGTTTTAACCCGGGAGACCC
* * * *
2392558 TTTTTCCTTTTGTTTGCTCATCGGTTTTGACCCGGGGGACACC
1 TTTCT-CTTTTGTTTGCCCATCGGTTTTAACCCGGGAGAC-CC
2392601 TTTCTCTTTTG
1 TTTCTCTTTTG
2392612 CTTACCTGTT
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
40 3 0.04
42 74 0.91
43 4 0.05
ACGTcount: A:0.10, C:0.21, G:0.20, T:0.49
Consensus pattern (41 bp):
TTTCTCTTTTGTTTGCCCATCGGTTTTAACCCGGGAGACCC
Found at i:2392610 original size:84 final size:84
Alignment explanation
Indices: 2392444--2392611 Score: 212
Period size: 84 Copynumber: 2.0 Consensus size: 84
2392434 TTTCCTCTAA
* ** ***
2392444 TTTGCCCGTCGATTTTAACTTGGGAGACTTTTTTTCCTTTTGTTTGCTCATCGGTTTTAACTTTG
1 TTTGCCCATCGATTTTAACGCGGGAGACTTTTTTTCCTTTTGTTTGCTCATCGGTTTTAACCCGG
** *
2392509 GAGACTTTTTTTCCTTTTG
66 GAGACCCTTTCTCCTTTTG
* *
2392528 TTTGCCCATCGGTTTTAACGCGGGAGACTTTTTTTCCTTTTGTTTGCTCATCGGTTTTGACCCGG
1 TTTGCCCATCGATTTTAACGCGGGAGACTTTTTTTCCTTTTGTTTGCTCATCGGTTTTAACCCGG
*
2392593 GGGACACCTTTCT-CTTTTG
66 GAGAC-CCTTTCTCCTTTTG
2392612 CTTACCTGTT
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
84 67 0.94
85 4 0.06
ACGTcount: A:0.11, C:0.21, G:0.20, T:0.48
Consensus pattern (84 bp):
TTTGCCCATCGATTTTAACGCGGGAGACTTTTTTTCCTTTTGTTTGCTCATCGGTTTTAACCCGG
GAGACCCTTTCTCCTTTTG
Found at i:2393135 original size:7 final size:7
Alignment explanation
Indices: 2393123--2393173 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
2393113 AAAAAAGAAT
2393123 AATAAAA
1 AATAAAA
2393130 AATAAAA
1 AATAAAA
2393137 ATATAAAA
1 A-ATAAAA
2393145 AAT-AAA
1 AATAAAA
*
2393151 AATAAAT
1 AATAAAA
*
2393158 AAT--TA
1 AATAAAA
2393163 AATAAAA
1 AATAAAA
2393170 AATA
1 AATA
2393174 TACATAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
5 3 0.08
6 6 0.17
7 20 0.56
8 7 0.19
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (7 bp):
AATAAAA
Found at i:2393142 original size:15 final size:15
Alignment explanation
Indices: 2393124--2393154 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2393114 AAAAAGAATA
2393124 ATAAAAAATAAAAAT
1 ATAAAAAATAAAAAT
2393139 ATAAAAAATAAAAAT
1 ATAAAAAATAAAAAT
2393154 A
1 A
2393155 AATAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (15 bp):
ATAAAAAATAAAAAT
Found at i:2393157 original size:25 final size:25
Alignment explanation
Indices: 2393111--2393188 Score: 74
Period size: 25 Copynumber: 3.1 Consensus size: 25
2393101 GAGTTATTTT
*
2393111 TAAAA-AAAGAATAATAAAAAATAA
1 TAAAATAAAAAATAATAAAAAATAA
2393135 -AAATATAAAAAATAA-AAATAAATAA
1 TAAA-ATAAAAAATAATAAA-AAATAA
*
2393160 TTAAATAAAAAAT-ATACATAAAATAA
1 TAAAATAAAAAATAATA-A-AAAATAA
2393186 TAA
1 TAA
2393189 TAAATTAATC
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
23 3 0.07
24 5 0.11
25 24 0.55
26 11 0.25
27 1 0.02
ACGTcount: A:0.76, C:0.01, G:0.01, T:0.22
Consensus pattern (25 bp):
TAAAATAAAAAATAATAAAAAATAA
Found at i:2393172 original size:15 final size:14
Alignment explanation
Indices: 2393113--2393193 Score: 73
Period size: 13 Copynumber: 6.0 Consensus size: 14
2393103 GTTATTTTTA
*
2393113 AAAAAAGAAT-AAT
1 AAAAAATAATAAAT
2393126 AAAAAATAA-AAAT
1 AAAAAATAATAAAT
*
2393139 ATAAAA-AATAAA-
1 AAAAAATAATAAAT
*
2393151 AATAAATAATTAAAT
1 AAAAAATAA-TAAAT
*
2393166 AAAAAAT-ATACAT
1 AAAAAATAATAAAT
2393179 AAAATAATAATAAAT
1 AAAA-AATAATAAAT
2393194 TAATCAAAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
12 6 0.11
13 29 0.54
14 8 0.15
15 11 0.20
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.22
Consensus pattern (14 bp):
AAAAAATAATAAAT
Found at i:2393187 original size:21 final size:19
Alignment explanation
Indices: 2393120--2393193 Score: 53
Period size: 21 Copynumber: 3.7 Consensus size: 19
2393110 TTAAAAAAAG
2393120 AATAATAAAAAATAAAAATATA
1 AATAATAAAAAAT--AAATA-A
*
2393142 AAAAAT-AAAAATAAAT-A
1 AATAATAAAAAATAAATAA
*
2393159 ATTAAATAAAAAATATACATAA
1 AAT-AATAAAAAATA-A-ATAA
*
2393181 AATAATAATAAAT
1 AATAATAAAAAAT
2393194 TAATCAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
17 2 0.05
18 3 0.07
19 11 0.26
20 1 0.02
21 17 0.40
22 8 0.19
ACGTcount: A:0.74, C:0.01, G:0.00, T:0.24
Consensus pattern (19 bp):
AATAATAAAAAATAAATAA
Found at i:2393188 original size:33 final size:34
Alignment explanation
Indices: 2393112--2393204 Score: 83
Period size: 33 Copynumber: 2.9 Consensus size: 34
2393102 AGTTATTTTT
*
2393112 AAAAA-AAGAATAATAAA--AAAT-AAAAATATA
1 AAAAATAAAAATAATAAATTAAATAAAAAATATA
2393142 AAAAATAAAAATAA-ATAATTAAATAAAAAATATA
1 AAAAATAAAAATAATA-AATTAAATAAAAAATATA
* * *
2393176 CATAA-AATAATAATAAATT-AATCAAAAAA
1 AAAAATAAAAATAATAAATTAAAT-AAAAAA
2393205 AGGGAGATCG
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
30 6 0.12
31 9 0.17
32 3 0.06
33 21 0.40
34 13 0.25
ACGTcount: A:0.75, C:0.02, G:0.01, T:0.22
Consensus pattern (34 bp):
AAAAATAAAAATAATAAATTAAATAAAAAATATA
Found at i:2393382 original size:58 final size:59
Alignment explanation
Indices: 2393317--2393430 Score: 185
Period size: 58 Copynumber: 1.9 Consensus size: 59
2393307 ATGCCATAAA
* * *
2393317 TTCATTTCATGCATTACATTTCATGCATACTTTCTTTCATGTTTCAC-TCATGCATATG
1 TTCATTTCATGCACTACATTTCATGCATACTTTCCTTCATGTTTCACGCCATGCATATG
*
2393375 TTCATTTCATGCACTGCATTTCATGCATACTTTCCTTCATGTTTCACGCCATGCAT
1 TTCATTTCATGCACTACATTTCATGCATACTTTCCTTCATGTTTCACGCCATGCAT
2393431 TGCATTGCAT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
58 44 0.86
59 7 0.14
ACGTcount: A:0.21, C:0.25, G:0.10, T:0.44
Consensus pattern (59 bp):
TTCATTTCATGCACTACATTTCATGCATACTTTCCTTCATGTTTCACGCCATGCATATG
Found at i:2393534 original size:11 final size:11
Alignment explanation
Indices: 2393518--2393544 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2393508 GCAAACGACA
2393518 GCAATGAAAAT
1 GCAATGAAAAT
2393529 GCAATGAAAAT
1 GCAATGAAAAT
2393540 GCAAT
1 GCAAT
2393545 TCAATTGCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.11, G:0.19, T:0.19
Consensus pattern (11 bp):
GCAATGAAAAT
Found at i:2393970 original size:21 final size:21
Alignment explanation
Indices: 2393927--2393984 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
2393917 TGAAGAGAAG
2393927 AAGAAACAAAAGAATAA-ATAAAA
1 AAGAAA-AAAA-AA-AACATAAAA
*
2393950 AAGAAGAAAAAAAACATAAAA
1 AAGAAAAAAAAAAACATAAAA
2393971 AAGAAAAAAAAAAA
1 AAGAAAAAAAAAAA
2393985 AACCAAGATG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 2 0.06
21 21 0.66
22 4 0.12
23 5 0.16
ACGTcount: A:0.83, C:0.03, G:0.09, T:0.05
Consensus pattern (21 bp):
AAGAAAAAAAAAAACATAAAA
Found at i:2393977 original size:26 final size:26
Alignment explanation
Indices: 2393919--2393986 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
2393909 ACAGCAAGTG
* *
2393919 AAGAGAAGAAGAAACAAAAGAATAAAT
1 AAGAAAAGAAGAAA-AAAAGAATAAAA
2393946 AA-AAAAGAAGAAAAAAA-ACATAAAA
1 AAGAAAAGAAGAAAAAAAGA-ATAAAA
2393971 AAGAAAA-AA-AAAAAAA
1 AAGAAAAGAAGAAAAAAA
2393987 CCAAGATGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
24 8 0.22
25 13 0.35
26 14 0.38
27 2 0.05
ACGTcount: A:0.81, C:0.03, G:0.12, T:0.04
Consensus pattern (26 bp):
AAGAAAAGAAGAAAAAAAGAATAAAA
Found at i:2393982 original size:23 final size:23
Alignment explanation
Indices: 2393927--2393987 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
2393917 TGAAGAGAAG
* *
2393927 AAGAAACAAAAGAATAA-ATAAAA
1 AAGAAA-AAAAAAAAAACATAAAA
*
2393950 AAG--AAGAAAAAAAACATAAAA
1 AAGAAAAAAAAAAAAACATAAAA
2393971 AAGAAAAAAAAAAAAAC
1 AAGAAAAAAAAAAAAAC
2393988 CAAGATGAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
20 7 0.23
21 10 0.32
23 14 0.45
ACGTcount: A:0.82, C:0.05, G:0.08, T:0.05
Consensus pattern (23 bp):
AAGAAAAAAAAAAAAACATAAAA
Found at i:2396527 original size:15 final size:14
Alignment explanation
Indices: 2396507--2396625 Score: 69
Period size: 14 Copynumber: 8.3 Consensus size: 14
2396497 CCAAAGATAC
2396507 TTTGGCACAAGTAGT
1 TTTGGCACAAGTA-T
* *
2396522 TTTGGCA-TAGATAC
1 TTTGGCACAAG-TAT
*
2396536 TTTGACACAAGTACT
1 TTTGGCACAAGTA-T
* * *
2396551 TTTAGCATAAGTAC
1 TTTGGCACAAGTAT
*
2396565 TTTGGCAAAAGTAT
1 TTTGGCACAAGTAT
* *
2396579 TTTGGTACAAATACT
1 TTTGGCACAAGTA-T
* * *
2396594 TTTGGTATAAATAT
1 TTTGGCACAAGTAT
* *
2396608 TTCGGCACAGGTAT
1 TTTGGCACAAGTAT
2396622 TTTG
1 TTTG
2396626 ATATAAGTAC
Statistics
Matches: 78, Mismatches: 22, Indels: 9
0.72 0.20 0.08
Matches are distributed among these distances:
14 44 0.56
15 34 0.44
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (14 bp):
TTTGGCACAAGTAT
Found at i:2396533 original size:29 final size:28
Alignment explanation
Indices: 2396501--2396583 Score: 105
Period size: 29 Copynumber: 2.9 Consensus size: 28
2396491 ATTATACCAA
2396501 AGATACTTTGGCACAAGTAGTTTTGGCAT
1 AGATACTTTGGCACAAGTA-TTTTGGCAT
* *
2396530 AGATACTTTGACACAAGTACTTTTAGCAT
1 AGATACTTTGGCACAAGTA-TTTTGGCAT
*
2396559 A-AGTACTTTGGCAAAAGTATTTTGG
1 AGA-TACTTTGGCACAAGTATTTTGG
2396584 TACAAATACT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
28 6 0.13
29 41 0.87
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.35
Consensus pattern (28 bp):
AGATACTTTGGCACAAGTATTTTGGCAT
Found at i:2396685 original size:44 final size:43
Alignment explanation
Indices: 2396616--2396698 Score: 130
Period size: 44 Copynumber: 1.9 Consensus size: 43
2396606 ATTTCGGCAC
*
2396616 AGGTATTTTGATATAAGTACTTTTGGTAAATGTACTTTAGCAT
1 AGGTATTTGGATATAAGTACTTTTGGTAAATGTACTTTAGCAT
* *
2396659 AGGTACTTTGGATATAAGTATTTTTGGTACATGTACTTTA
1 AGGTA-TTTGGATATAAGTACTTTTGGTAAATGTACTTTA
2396699 ATGCAAGTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
43 5 0.14
44 31 0.86
ACGTcount: A:0.29, C:0.07, G:0.19, T:0.45
Consensus pattern (43 bp):
AGGTATTTGGATATAAGTACTTTTGGTAAATGTACTTTAGCAT
Found at i:2397263 original size:25 final size:26
Alignment explanation
Indices: 2397229--2397280 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
2397219 TATTCGTAAA
*
2397229 ACCTATAACCAC-TGTAACTTTCATC
1 ACCTATAACCACTTGTAACCTTCATC
* *
2397254 ACCTTTAACCACTTGTAGCCTTCATC
1 ACCTATAACCACTTGTAACCTTCATC
2397280 A
1 A
2397281 TAATTGTCTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.29, C:0.33, G:0.06, T:0.33
Consensus pattern (26 bp):
ACCTATAACCACTTGTAACCTTCATC
Found at i:2400515 original size:17 final size:17
Alignment explanation
Indices: 2400493--2400526 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2400483 GTTTTGGGTA
2400493 ATTGGATT-TGGGCTTTG
1 ATTGGATTATGGG-TTTG
2400510 ATTGGATTATGGGTTTG
1 ATTGGATTATGGGTTTG
2400527 GGTTAGAGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.15, C:0.03, G:0.35, T:0.47
Consensus pattern (17 bp):
ATTGGATTATGGGTTTG
Found at i:2400953 original size:11 final size:11
Alignment explanation
Indices: 2400937--2400977 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
2400927 TTTTTAAAAT
2400937 TTTATATTTGA
1 TTTATATTTGA
2400948 TTTATATTT-A
1 TTTATATTTGA
2400958 TTTA-ATTTGA
1 TTTATATTTGA
2400968 TTATATATTT
1 TT-TATATTT
2400978 TATGTTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 4 0.15
10 8 0.30
11 11 0.41
12 4 0.15
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (11 bp):
TTTATATTTGA
Found at i:2400961 original size:21 final size:21
Alignment explanation
Indices: 2400937--2400977 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2400927 TTTTTAAAAT
2400937 TTTATATTTGATT-TATATTTA
1 TTTA-ATTTGATTATATATTTA
2400958 TTTAATTTGATTATATATTT
1 TTTAATTTGATTATATATTT
2400978 TATGTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (21 bp):
TTTAATTTGATTATATATTTA
Found at i:2401077 original size:27 final size:28
Alignment explanation
Indices: 2401021--2401083 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 28
2401011 TTTTGAGTAA
* * *
2401021 ATTAAAAATATTTAATTATTTACTCGAT
1 ATTAAAAATATTTAACTATTTAATAGAT
* *
2401049 A-TAAAAATTTTTAACTATTTAATATAT
1 ATTAAAAATATTTAACTATTTAATAGAT
2401076 ATTAAAAA
1 ATTAAAAA
2401084 ATTAATATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 22 0.76
28 7 0.24
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (28 bp):
ATTAAAAATATTTAACTATTTAATAGAT
Found at i:2401269 original size:2 final size:2
Alignment explanation
Indices: 2401262--2401298 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
2401252 AAATCTTCTA
2401262 AT AT AT AT AT AT AT AT AT AT AT AT CA- AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT
2401299 TTTTTTGGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 2 0.06
2 29 0.91
3 1 0.03
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2412903 original size:13 final size:13
Alignment explanation
Indices: 2412885--2412909 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2412875 CATTATGCTT
2412885 TGTATCGATACAA
1 TGTATCGATACAA
2412898 TGTATCGATACA
1 TGTATCGATACA
2412910 TAATCATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2412925 original size:32 final size:33
Alignment explanation
Indices: 2412864--2412928 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
2412854 ACGCACCCAG
* *
2412864 ATGTATCGATACATTATGCTTTGTATCGATACA
1 ATGTATCGATACATAATGCATTGTATCGATACA
2412897 ATGTATCGATACATAAT-CATTGTATCGATACA
1 ATGTATCGATACATAATGCATTGTATCGATACA
2412929 TGAACAATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.47
33 16 0.53
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (33 bp):
ATGTATCGATACATAATGCATTGTATCGATACA
Found at i:2412940 original size:20 final size:20
Alignment explanation
Indices: 2412894--2412952 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
2412884 TTGTATCGAT
2412894 ACAA-TGTATCGATACAT-A
1 ACAATTGTATCGATACATGA
2412912 ATC-ATTGTATCGATACATGA
1 A-CAATTGTATCGATACATGA
2412932 ACAATTGTATCGATACATGA
1 ACAATTGTATCGATACATGA
2412952 A
1 A
2412953 ACTGATAGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.05
19 15 0.41
20 20 0.54
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.31
Consensus pattern (20 bp):
ACAATTGTATCGATACATGA
Found at i:2413014 original size:13 final size:13
Alignment explanation
Indices: 2412996--2413025 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2412986 GATACATAGG
2412996 ACATTGTATCGAT
1 ACATTGTATCGAT
2413009 ACATTGTATCGAT
1 ACATTGTATCGAT
2413022 ACAT
1 ACAT
2413026 GATGAATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:2413021 original size:33 final size:33
Alignment explanation
Indices: 2412979--2413047 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
2412969 CTACCACTAT
2412979 TTGTATCGATACAT-AGGACATTGTATCGATACA
1 TTGTATCGATACATGAGGA-ATTGTATCGATACA
* *
2413012 TTGTATCGATACATGATGAATTGTATTGATACA
1 TTGTATCGATACATGAGGAATTGTATCGATACA
2413045 TTG
1 TTG
2413048 CTTGTAACAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 30 0.91
34 3 0.09
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.38
Consensus pattern (33 bp):
TTGTATCGATACATGAGGAATTGTATCGATACA
Found at i:2415885 original size:21 final size:19
Alignment explanation
Indices: 2415859--2415932 Score: 85
Period size: 19 Copynumber: 3.7 Consensus size: 19
2415849 CTGGCAGTTT
**
2415859 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAA--TGAA
2415880 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
* *
2415899 CATGTATCGATACAAAGCAG
1 CATGTATCGATACAATG-AA
2415919 CATGTATCGATACA
1 CATGTATCGATACA
2415933 TCTGGGTGTG
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
19 18 0.38
20 15 0.31
21 15 0.31
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.28
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:2418382 original size:13 final size:13
Alignment explanation
Indices: 2418361--2418402 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
2418351 AAATAGTACC
*
2418361 CAATGTATCAATA
1 CAATGTATCGATA
*
2418374 CATTGTATCGATA
1 CAATGTATCGATA
2418387 CAATGTATCGATA
1 CAATGTATCGATA
2418400 CAA
1 CAA
2418403 GGAATGTTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:2424581 original size:20 final size:20
Alignment explanation
Indices: 2424556--2424621 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
2424546 ATTACAAGCT
2424556 ATGTATCGATACATTTCTTC
1 ATGTATCGATACATTTCTTC
2424576 ATGTATCGATACA-------
1 ATGTATCGATACATTTCTTC
2424589 ATGTATCGATACATTTCTTC
1 ATGTATCGATACATTTCTTC
2424609 ATGTATCGATACA
1 ATGTATCGATACA
2424622 ATGTATCAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 13 0.33
20 26 0.67
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTTCTTC
Found at i:2424594 original size:13 final size:13
Alignment explanation
Indices: 2424576--2424639 Score: 59
Period size: 13 Copynumber: 5.4 Consensus size: 13
2424566 ACATTTCTTC
2424576 ATGTATCGATACA
1 ATGTATCGATACA
2424589 ATGTATCGATAC-
1 ATGTATCGATACA
*
2424601 AT-T-TC--TTC-
1 ATGTATCGATACA
2424609 ATGTATCGATACA
1 ATGTATCGATACA
*
2424622 ATGTATCAATACA
1 ATGTATCGATACA
*
2424635 TTGTA
1 ATGTA
2424640 CCATGTATCG
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
8 4 0.10
9 1 0.02
10 4 0.10
11 1 0.02
12 4 0.10
13 28 0.67
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2424594 original size:33 final size:33
Alignment explanation
Indices: 2424556--2424655 Score: 159
Period size: 33 Copynumber: 3.0 Consensus size: 33
2424546 ATTACAAGCT
2424556 ATGTATCGATACATTTCTTCATGTATCGATACA
1 ATGTATCGATACATTTCTTCATGTATCGATACA
2424589 ATGTATCGATACATTTCTTCATGTATCGATACA
1 ATGTATCGATACATTTCTTCATGTATCGATACA
*
2424622 ATGTATCAATACATTGTAC--CATGTATCGATACA
1 ATGTATCGATACATT-T-CTTCATGTATCGATACA
2424655 A
1 A
2424656 ATAGTGATAT
Statistics
Matches: 64, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
33 62 0.97
34 1 0.02
35 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (33 bp):
ATGTATCGATACATTTCTTCATGTATCGATACA
Found at i:2424743 original size:13 final size:13
Alignment explanation
Indices: 2424725--2424751 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2424715 TACGATGAAC
2424725 ATGTATCGATACA
1 ATGTATCGATACA
2424738 ATGTATCGATACA
1 ATGTATCGATACA
2424751 A
1 A
2424752 AGCAACATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2424764 original size:33 final size:32
Alignment explanation
Indices: 2424706--2424770 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 32
2424696 CAATTTTTCC
* *
2424706 ATGTATCGATACGATGAACATGTATCGATACA
1 ATGTATCGATACAAAGAACATGTATCGATACA
2424738 ATGTATCGATACAAAGCAACATGTATCGATACA
1 ATGTATCGATACAAAG-AACATGTATCGATACA
2424771 TCTGGGTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.47
33 16 0.53
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (32 bp):
ATGTATCGATACAAAGAACATGTATCGATACA
Found at i:2431258 original size:13 final size:13
Alignment explanation
Indices: 2431240--2431265 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2431230 CAATTTTTTG
2431240 TGTATCGATACAT
1 TGTATCGATACAT
2431253 TGTATCGATACAT
1 TGTATCGATACAT
2431266 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2431350 original size:20 final size:20
Alignment explanation
Indices: 2431325--2431397 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2431315 CATCCTTTTT
2431325 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
2431345 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACA-TTGCAAC
2431366 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
2431386 ATGTATCGATAC
1 ATGTATCGATAC
2431398 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:2431370 original size:21 final size:21
Alignment explanation
Indices: 2431304--2431380 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
2431294 CTGCCAAGAA
*
2431304 ATGTATCGATACATCCTTTTT-
1 ATGTATCGATACAT-TTTTTTC
****
2431325 ATGTATCGATACA-TTGCAAC
1 ATGTATCGATACATTTTTTTC
2431345 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACATTTTTTTC
2431366 ATGTATCGATACATT
1 ATGTATCGATACATT
2431381 GCAACATGTA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 13 0.29
21 31 0.69
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.43
Consensus pattern (21 bp):
ATGTATCGATACATTTTTTTC
Found at i:2431370 original size:41 final size:41
Alignment explanation
Indices: 2431304--2431397 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
2431294 CTGCCAAGAA
2431304 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
*
2431345 ATGTATCGATACAT-TTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTT-ATGTATCGATACATTGCAAC
2431386 ATGTATCGATAC
1 ATGTATCGATAC
2431398 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
Found at i:2432009 original size:48 final size:48
Alignment explanation
Indices: 2431954--2432049 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
2431944 AAATTTTACG
2431954 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
1 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
2432002 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
1 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
2432050 TTATCTCCCC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.25, C:0.29, G:0.08, T:0.38
Consensus pattern (48 bp):
AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
Found at i:2433912 original size:13 final size:13
Alignment explanation
Indices: 2433890--2433928 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
2433880 ATAATCACCC
* *
2433890 TGTATGGATACAG
1 TGTATCGATACAA
2433903 TGTATCGATACAA
1 TGTATCGATACAA
2433916 TGTATCGATACAA
1 TGTATCGATACAA
2433929 GGAAAAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2436027 original size:15 final size:15
Alignment explanation
Indices: 2436007--2436037 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2435997 ATTTCGTTTG
*
2436007 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
2436022 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
2436037 G
1 G
2436038 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:2440117 original size:13 final size:13
Alignment explanation
Indices: 2440099--2440124 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2440089 CAATTTTTTG
2440099 TGTATCGATACAT
1 TGTATCGATACAT
2440112 TGTATCGATACAT
1 TGTATCGATACAT
2440125 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2440209 original size:20 final size:20
Alignment explanation
Indices: 2440184--2440256 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2440174 CATCCTTTTT
2440184 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
2440204 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACA-TTGCAAC
2440225 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
2440245 ATGTATCGATAC
1 ATGTATCGATAC
2440257 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:2440229 original size:21 final size:21
Alignment explanation
Indices: 2440163--2440239 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
2440153 CTGCCAAGAA
*
2440163 ATGTATCGATACATCCTTTTT-
1 ATGTATCGATACAT-TTTTTTC
****
2440184 ATGTATCGATACA-TTGCAAC
1 ATGTATCGATACATTTTTTTC
2440204 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACATTTTTTTC
2440225 ATGTATCGATACATT
1 ATGTATCGATACATT
2440240 GCAACATGTA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 13 0.29
21 31 0.69
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.43
Consensus pattern (21 bp):
ATGTATCGATACATTTTTTTC
Found at i:2440229 original size:41 final size:41
Alignment explanation
Indices: 2440163--2440256 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
2440153 CTGCCAAGAA
2440163 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
*
2440204 ATGTATCGATACAT-TTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTT-ATGTATCGATACATTGCAAC
2440245 ATGTATCGATAC
1 ATGTATCGATAC
2440257 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
Found at i:2441277 original size:41 final size:40
Alignment explanation
Indices: 2441232--2441308 Score: 136
Period size: 41 Copynumber: 1.9 Consensus size: 40
2441222 TTTGATTAAT
*
2441232 GGGGAGAAATATTGTTTTAAATCTAGGGGGAGTAAATCTAG
1 GGGGAGAAATATTATTTTAAATCTAGGGGGAG-AAATCTAG
2441273 GGGGAGAAATATTATTTTAAATCTAGGGGGAGAAAT
1 GGGGAGAAATATTATTTTAAATCTAGGGGGAGAAAT
2441309 ATTATTTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 4 0.11
41 31 0.89
ACGTcount: A:0.36, C:0.04, G:0.31, T:0.29
Consensus pattern (40 bp):
GGGGAGAAATATTATTTTAAATCTAGGGGGAGAAATCTAG
Found at i:2441282 original size:14 final size:15
Alignment explanation
Indices: 2441249--2441282 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2441239 AATATTGTTT
2441249 TAAATCTAGGGGGAG
1 TAAATCTAGGGGGAG
2441264 TAAATCTAGGGGGAG
1 TAAATCTAGGGGGAG
2441279 -AAAT
1 TAAAT
2441283 ATTATTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.38, C:0.06, G:0.35, T:0.21
Consensus pattern (15 bp):
TAAATCTAGGGGGAG
Found at i:2441293 original size:26 final size:26
Alignment explanation
Indices: 2441264--2441335 Score: 135
Period size: 26 Copynumber: 2.7 Consensus size: 26
2441254 CTAGGGGGAG
2441264 TAAATCTAGGGGGAGAAATATTATTT
1 TAAATCTAGGGGGAGAAATATTATTT
2441290 TAAATCTAGGGGGAGAAATATTATTT
1 TAAATCTAGGGGGAGAAATATTATTT
2441316 TAAATCTAGGGGGAGTAAAT
1 TAAATCTAGGGGGAG-AAAT
2441336 CTCTTTAACC
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
26 41 0.91
27 4 0.09
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.32
Consensus pattern (26 bp):
TAAATCTAGGGGGAGAAATATTATTT
Found at i:2441954 original size:13 final size:13
Alignment explanation
Indices: 2441936--2441962 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2441926 ACATTATGCT
2441936 TTGTATCGATACA
1 TTGTATCGATACA
2441949 TTGTATCGATACA
1 TTGTATCGATACA
2441962 T
1 T
2441963 GGACAATTGT
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2442037 original size:20 final size:20
Alignment explanation
Indices: 2442012--2442065 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
2442002 CTACCACTGT
2442012 TTGTATCGATACAT-AGGACA
1 TTGTATCGATACATGAGGA-A
* *
2442032 TTGTATTGATACATGATGAA
1 TTGTATCGATACATGAGGAA
2442052 TTGTATCGATACAT
1 TTGTATCGATACAT
2442066 TACTTGTCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 27 0.90
21 3 0.10
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGAGGAA
Found at i:2443919 original size:22 final size:22
Alignment explanation
Indices: 2443888--2443930 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2443878 TTGAACAAAA
*
2443888 TTTTTTTAATTTT-ACAATTTAG
1 TTTTTATAATTTTCAC-ATTTAG
2443910 TTTTTATAATTTTCACATTTA
1 TTTTTATAATTTTCACATTTA
2443931 CTAAATAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (22 bp):
TTTTTATAATTTTCACATTTAG
Found at i:2449483 original size:51 final size:51
Alignment explanation
Indices: 2449416--2449538 Score: 147
Period size: 51 Copynumber: 2.4 Consensus size: 51
2449406 TTGAAAATAA
* * * *
2449416 CAGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAAC
1 CAGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTAGAAATAAAAC
* * * * *
2449467 CAGGGTTGGAGTATCCCGGATTATGAGAAATCAATATTTTGGGAATAAAGC
1 CAGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTAGAAATAAAAC
* *
2449518 CGGGGTTGGAGTATCTCCGAT
1 CAGGGTTGGAGTATCCCCGAT
2449539 GAAATAACGA
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.28
Consensus pattern (51 bp):
CAGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTAGAAATAAAAC
Found at i:2449544 original size:130 final size:131
Alignment explanation
Indices: 2449359--2449623 Score: 344
Period size: 130 Copynumber: 2.0 Consensus size: 131
2449349 ATATTTTTTG
* *
2449359 ATGAGAAATTTAATATTTTGGGATAATAACGAGGTTGGAGTATCCCCTTGAAAATAAC-AGGGTT
1 ATGAGAAATTCAATATTTTGGGATAATAACGAGGTTGGAGTATCCCCATGAAAATAACGA-GGTT
* *
2449423 GGAGTATCCCCGATTGTGAAAAATTAGTG-TTTTAGAAATAAAACCAGG-GTTGGAGTATCCCGG
65 GGAGTATCACCGATTGTGAAAAATTAGTGTTTTTAGAAATAAAACC-GGAGTTGGAGTATCCCCG
2449486 ATT
129 ATT
* * *
2449489 ATGAGAAA-TCAATATTTTGGGAATAA-AGCCGGGGTTGGAGTATCTCCGATG-AAATAACGAGG
1 ATGAGAAATTCAATATTTTGGG-ATAATA-ACGAGGTTGGAGTATC-CCCATGAAAATAACGAGG
* * * *
2449551 TTGGAGTATCATCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCC
63 TTGGAGTATCACCGATTGTGAAAAATTAGTGTTTTTAGAAATAAAACCGGAGTTGGAGTATCCCC
2449616 GATT
128 GATT
2449620 ATGA
1 ATGA
2449624 ACAATTGAGA
Statistics
Matches: 118, Mismatches: 11, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
129 13 0.11
130 65 0.55
131 40 0.34
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (131 bp):
ATGAGAAATTCAATATTTTGGGATAATAACGAGGTTGGAGTATCCCCATGAAAATAACGAGGTTG
GAGTATCACCGATTGTGAAAAATTAGTGTTTTTAGAAATAAAACCGGAGTTGGAGTATCCCCGAT
T
Found at i:2451984 original size:13 final size:13
Alignment explanation
Indices: 2451966--2451992 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2451956 CAAAGATCGA
2451966 TGTATCGATACAT
1 TGTATCGATACAT
2451979 TGTATCGATACAT
1 TGTATCGATACAT
2451992 T
1 T
2451993 TCCTTAATGT
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2452003 original size:21 final size:21
Alignment explanation
Indices: 2451979--2452018 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
2451969 ATCGATACAT
2451979 TGTATCGATACATTTCCTTAA
1 TGTATCGATACATTTCCTTAA
2452000 TGTATCGATACATTTCCTT
1 TGTATCGATACATTTCCTT
2452019 GGCAGTAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.45
Consensus pattern (21 bp):
TGTATCGATACATTTCCTTAA
Found at i:2452067 original size:19 final size:18
Alignment explanation
Indices: 2452043--2452105 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
2452033 AGCGATACAT
2452043 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
2452062 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
*
2452075 TGTATTGATACAACACTTA
1 TGTATCGATACAA-ACTTA
2452094 TGTATCGATACA
1 TGTATCGATACA
2452106 TTTACGGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 10 0.28
14 1 0.03
16 2 0.06
18 1 0.03
19 22 0.61
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:2452076 original size:32 final size:32
Alignment explanation
Indices: 2452027--2452107 Score: 128
Period size: 32 Copynumber: 2.6 Consensus size: 32
2452017 TTGGCAGTAG
*
2452027 CTTA-GTAGCGATACATTGTATCGATACAAAA
1 CTTATGTATCGATACATTGTATCGATACAAAA
* *
2452058 CTTATGTATCGATACATTGTATTGATACAACA
1 CTTATGTATCGATACATTGTATCGATACAAAA
2452090 CTTATGTATCGATACATT
1 CTTATGTATCGATACATT
2452108 TACGGTTTGT
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
31 4 0.09
32 42 0.91
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.36
Consensus pattern (32 bp):
CTTATGTATCGATACATTGTATCGATACAAAA
Found at i:2452103 original size:64 final size:65
Alignment explanation
Indices: 2451965--2452107 Score: 152
Period size: 64 Copynumber: 2.2 Consensus size: 65
2451955 ACAAAGATCG
*** * * **
2451965 ATGTATCGATACATTGTATCGATACATTTCCTTAATGTATCGATACATTTCCTTGGCAGTAGCTT
1 ATGTATCGATACATTGTATCGATACATAAACTTAATGTATCGATACATTTCATTGACAACAGCTT
*
2452030 A-GTAGCGATACATTGTATCGATACA-AAACTT-ATGTATCGATACATTGT-ATTGATACAACA-
1 ATGTATCGATACATTGTATCGATACATAAACTTAATGTATCGATACATT-TCATTG--ACAACAG
2452090 CTT
63 CTT
2452093 ATGTATCGATACATT
1 ATGTATCGATACATT
2452108 TACGGTTTGT
Statistics
Matches: 65, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
62 18 0.28
63 8 0.12
64 38 0.58
65 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (65 bp):
ATGTATCGATACATTGTATCGATACATAAACTTAATGTATCGATACATTTCATTGACAACAGCTT
Found at i:2452647 original size:51 final size:51
Alignment explanation
Indices: 2452592--2452735 Score: 159
Period size: 51 Copynumber: 2.8 Consensus size: 51
2452582 CCTGATTAAA
*
2452592 GGAAAATTGGTGTTTT-GAAAATAAAACC-GAGGTTGGAGTATCCTCGATTGT
1 GGAAAATTAGTGTTTTAG-AAATAAAACCAG-GGTTGGAGTATCCTCGATTGT
*
2452643 GGAAAATTAGTGTTTTAGAAATAAAACCAGGGTTGGAGTATCCTCGATTAT
1 GGAAAATTAGTGTTTTAGAAATAAAACCAGGGTTGGAGTATCCTCGATTGT
* * * * * * *
2452694 -GAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTATC
1 GGA-AAATTAGTGTTTTAGAAATAAAACCAGGGTTGGAGTATC
2452736 TCCTCGGAGG
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
50 2 0.02
51 77 0.95
52 2 0.02
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.30
Consensus pattern (51 bp):
GGAAAATTAGTGTTTTAGAAATAAAACCAGGGTTGGAGTATCCTCGATTGT
Found at i:2455391 original size:3 final size:3
Alignment explanation
Indices: 2455385--2455419 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2455375 TTTTTTTAAT
2455385 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2455420 CCTTTTTGCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2458180 original size:20 final size:19
Alignment explanation
Indices: 2458154--2458205 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
2458144 CTGCCAGTTT
*
2458154 CATGTATTGATACTTTTCAA
1 CATGTATTGATAC-TATCAA
* * *
2458174 GATGTATCGATACTATGAA
1 CATGTATTGATACTATCAA
2458193 CATGTATTGATAC
1 CATGTATTGATAC
2458206 AATGTATCGA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (19 bp):
CATGTATTGATACTATCAA
Found at i:2458238 original size:33 final size:32
Alignment explanation
Indices: 2458175--2458239 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
2458165 ACTTTTCAAG
* * *
2458175 ATGTATCGATACTATGAACATGTATTGATACA
1 ATGTATCGATAATAAGAACATGTATCGATACA
*
2458207 ATGTATCGATAATAAGCAATATGTATCGATACA
1 ATGTATCGATAATAAG-AACATGTATCGATACA
2458240 TCTGGGTGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.32
Consensus pattern (32 bp):
ATGTATCGATAATAAGAACATGTATCGATACA
Found at i:2461041 original size:13 final size:13
Alignment explanation
Indices: 2461018--2461059 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
2461008 CAAATAGTAC
2461018 CTATGTATCGATA
1 CTATGTATCGATA
2461031 CTA-GATATCGATA
1 CTATG-TATCGATA
*
2461044 CAATGTATCGATA
1 CTATGTATCGATA
2461057 CTA
1 CTA
2461060 AAAACTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 1 0.04
13 23 0.92
14 1 0.04
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (13 bp):
CTATGTATCGATA
Found at i:2461740 original size:20 final size:20
Alignment explanation
Indices: 2461715--2461772 Score: 84
Period size: 19 Copynumber: 3.0 Consensus size: 20
2461705 TTGCCAGTTT
*
2461715 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGTA
*
2461735 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGTA
2461754 CATGTATCGATAC-ATTGTA
1 CATGTATCGATACAATTGTA
2461773 TCAATACAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 1 0.03
19 18 0.53
20 15 0.44
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGTA
Found at i:2462283 original size:62 final size:62
Alignment explanation
Indices: 2462089--2463158 Score: 1205
Period size: 62 Copynumber: 17.4 Consensus size: 62
2462079 GATCCTAACA
* * ** *
2462089 GCCACGAACTTGTGTGGGCTTTAAAAAGAAAAAGATGTCCTACTCTTTGAGGACTG-AAGGT
1 GCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGT
** * * * * * * *
2462150 GCTGCTAACTTGTGTGGGCTTT-AAAAGGAGAAGGCATCATCCTCTTTAAGGACTAAAAGGT
1 GCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGT
* *
2462211 -CTCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGTGTCCTGCTCTTTGAAGACTGAAAGGT
1 GC-CACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGT
** * * * * *
2462273 GCCATTAACTTGTATGGGCTTTAAAAA-GAGAAGGCATCCTACTCTTTGAGGACTGAAAGAT
1 GCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGT
* * * * *
2462334 GCCACCAACTTATGTGCGCTTT-AAAAGGAGAAGGCATCCTGCTCTTTGAGGACAGAAAGGT
1 GCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGT
* * * * * *
2462395 GCCACCAACTTGTGTGGGCCTTAAAAAAGAAAAGACG-CCTTACTCTTTGAGGACTAAAATGT
1 GCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCC-TGCTCTTTGAGGACTGAAAGGT
* * * * *
2462457 GCCACCAACTTGTGTGGGCTTTACAAAGGAAAAGACGTCCTGTTCTTTAAGGACTAAAAGGT
1 GCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGT
* * * *
2462519 AG-CACCAACATGTGTGGGC-TTAAAAA-GAAAAGGCGTCCTACTCTTTGAGGATTGAAAAGT
1 -GCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGT
* * *
2462579 GCCACCAACTTGTGTGGG-TTTTAAAAGGAGAAGGCGTCCTACTCTTTGAGGACTGAAAGGT
1 GCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGT
* * * * * *
2462640 GCCACCAACTTGTGTGGGCTTT-AAAAGGAGAAGGTGTCTTGCTTTTTGAGGACTAAAATGT
1 GCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGT
* * ** * * *
2462701 GCCACCAACTTGTGTGAGCTTTAAAAAGAAAAAGGTATCTTTCTCTTTGAAGACTGAAAGGT
1 GCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGT
* * * * *
2462763 GCCACCAACTTGTGTGGGCTTTAAAAAGAAAAATGCATCTTGCTCTTTGAGGACTAAAAGGT
1 GCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGT
* * * * *
2462825 GCCACCAATTTGTGTGGTCTTTAAAAAGGAAAATGCGTCATGCTCTTTGAGGAATGAAAGGT
1 GCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGT
* * * * *
2462887 GCCACCAACTTGTGTGGGCTTTGAAAAGGAAATGGCGTCTTGCTCTTTGAGGAATGAAAGAT
1 GCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGT
* * * * *
2462949 GCCACCAACTAGTGTGGGCTTT-AAAA-GAAGAAGGCGCCCTGCTCTTTGAGGATTAAAAAGT
1 GCCACCAACTTGTGTGGGCTTTAAAAAGGAA-AAGGCGTCCTGCTCTTTGAGGACTGAAAGGT
* * * * * *
2463010 GCCACCAACTTATGTGGGCTTTAAAAAGGAAAAGGCATCCTACTCTCTGAGGATTGAAAGTT
1 GCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGT
* * * *
2463072 GGCACCAACTTGTGTGGGCTTT-AAAAGGAGAAGGCATCTTGCTCTTTGAGGACTGAAAGGT
1 GCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGT
2463133 GCCACCAACTTGTGTGGGCTTTAAAA
1 GCCACCAACTTGTGTGGGCTTTAAAA
2463159 GAGGTTGCCA
Statistics
Matches: 858, Mismatches: 133, Indels: 35
0.84 0.13 0.03
Matches are distributed among these distances:
59 1 0.00
60 80 0.09
61 349 0.41
62 421 0.49
63 7 0.01
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (62 bp):
GCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGT
Found at i:2462318 original size:123 final size:123
Alignment explanation
Indices: 2462089--2463158 Score: 1208
Period size: 123 Copynumber: 8.7 Consensus size: 123
2462079 GATCCTAACA
* * ** * *
2462089 GCCACGAACTTGTGTGGGCTTTAAAAAGAAAAAGATGTCCTACTCTTTGAGGACTG-AAGGTGCT
1 GCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCC
* * * * * * *
2462153 GCTAACTTGTGTGGGCTTTAAAAGGAGAAGGCATCATCCTCTTTAAGGACTAAAAGGT
66 ACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCATCCTACTCTTTGAGGACTAAAAGGT
* *
2462211 -CTCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGTGTCCTGCTCTTTGAAGACTGAAAGGTGC
1 GC-CACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGC
** * * * *
2462275 CATTAACTTGTATGGGCTTTAAAAAGAGAAGGCATCCTACTCTTTGAGGACTGAAAGAT
65 CACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCATCCTACTCTTTGAGGACTAAAAGGT
* * * * *
2462334 GCCACCAACTTATGTGCGCTTT-AAAAGGAGAAGGCATCCTGCTCTTTGAGGACAGAAAGGTGCC
1 GCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCC
* * * *
2462398 ACCAACTTGTGTGGGCCTTAAAAAAGAAAAGAC-GCCTTACTCTTTGAGGACTAAAATGT
66 ACCAACTTGTGTGGG-CTTTAAAAAGAAAAGGCATCC-TACTCTTTGAGGACTAAAAGGT
* * * * *
2462457 GCCACCAACTTGTGTGGGCTTTACAAAGGAAAAGACGTCCTGTTCTTTAAGGACTAAAAGGTAG-
1 GCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGT-GC
* * *
2462521 CACCAACATGTGTGGGC-TTAAAAAGAAAAGGCGTCCTACTCTTTGAGGATTGAAAA-GT
65 CACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCATCCTACTCTTTGAGGACT-AAAAGGT
* * *
2462579 GCCACCAACTTGTGTGGG-TTTTAAAAGGAGAAGGCGTCCTACTCTTTGAGGACTGAAAGGTGCC
1 GCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCC
* * ** * * * *
2462643 ACCAACTTGTGTGGGCTTTAAAAGGAGAAGGTGTCTTGCTTTTTGAGGACTAAAATGT
66 ACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCATCCTACTCTTTGAGGACTAAAAGGT
* * ** * * *
2462701 GCCACCAACTTGTGTGAGCTTTAAAAAGAAAAAGGTATCTTTCTCTTTGAAGACTGAAAGGTGCC
1 GCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCC
* * *
2462766 ACCAACTTGTGTGGGCTTTAAAAAGAAAAATGCATCTTGCTCTTTGAGGACTAAAAGGT
66 ACCAACTTGTGTGGGCTTTAAAAAG-AAAAGGCATCCTACTCTTTGAGGACTAAAAGGT
* * * * *
2462825 GCCACCAATTTGTGTGGTCTTTAAAAAGGAAAATGCGTCATGCTCTTTGAGGAATGAAAGGTGCC
1 GCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCC
* * * * * * * *
2462890 ACCAACTTGTGTGGGCTTTGAAAAGGAAATGGCGTCTTGCTCTTTGAGGAATGAAAGAT
66 ACCAACTTGTGTGGGCTTT-AAAAAGAAAAGGCATCCTACTCTTTGAGGACTAAAAGGT
* * * * *
2462949 GCCACCAACTAGTGTGGGCTTT-AAAA-GAAGAAGGCGCCCTGCTCTTTGAGGATTAAAAAGTGC
1 GCCACCAACTTGTGTGGGCTTTAAAAAGGAA-AAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGC
* * * * *
2463012 CACCAACTTATGTGGGCTTTAAAAAGGAAAAGGCATCCTACTCTCTGAGGATTGAAAGTT
65 CACCAACTTGTGTGGGCTTTAAAAA-GAAAAGGCATCCTACTCTTTGAGGACTAAAAGGT
* * * *
2463072 GGCACCAACTTGTGTGGGCTTT-AAAAGGAGAAGGCATCTTGCTCTTTGAGGACTGAAAGGTGCC
1 GCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCC
2463136 ACCAACTTGTGTGGGCTTTAAAA
66 ACCAACTTGTGTGGGCTTTAAAA
2463159 GAGGTTGCCA
Statistics
Matches: 805, Mismatches: 125, Indels: 35
0.83 0.13 0.04
Matches are distributed among these distances:
120 1 0.00
121 56 0.07
122 200 0.25
123 347 0.43
124 195 0.24
125 6 0.01
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (123 bp):
GCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCC
ACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCATCCTACTCTTTGAGGACTAAAAGGT
Found at i:2463168 original size:32 final size:32
Alignment explanation
Indices: 2463132--2463255 Score: 171
Period size: 32 Copynumber: 3.9 Consensus size: 32
2463122 GACTGAAAGG
2463132 TGCCACCAACTTGTGTGGGCTTTAAAAGAGGT
1 TGCCACCAACTTGTGTGGGCTTTAAAAGAGGT
* *
2463164 TGCCACCAACTTGTGTGGGCTTTAGATG-GAGT
1 TGCCACCAACTTGTGTGGGCTTTAAAAGAG-GT
2463196 TGCCACCAACTTGTGTGGGCTTTAAGAA-AGGT
1 TGCCACCAACTTGTGTGGGCTTTAA-AAGAGGT
* **
2463228 TACCACCAGTTTGTGTGGGCTTTAAAAG
1 TGCCACCAACTTGTGTGGGCTTTAAAAG
2463256 CAAACCACTG
Statistics
Matches: 81, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
31 3 0.04
32 76 0.94
33 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (32 bp):
TGCCACCAACTTGTGTGGGCTTTAAAAGAGGT
Found at i:2463234 original size:64 final size:64
Alignment explanation
Indices: 2463132--2463251 Score: 197
Period size: 64 Copynumber: 1.9 Consensus size: 64
2463122 GACTGAAAGG
*
2463132 TGCCACCAACTTGTGTGGGCTTTAAAAGAGGTTGCCACCAACTTGTGTGGGCTTTAGATGGAGT
1 TGCCACCAACTTGTGTGGGCTTTAAAAGAGGTTACCACCAACTTGTGTGGGCTTTAGATGGAGT
**
2463196 TGCCACCAACTTGTGTGGGCTTTAAGAA-AGGTTACCACCAGTTTGTGTGGGCTTTA
1 TGCCACCAACTTGTGTGGGCTTTAA-AAGAGGTTACCACCAACTTGTGTGGGCTTTA
2463252 AAAGCAAACC
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
64 50 0.96
65 2 0.04
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (64 bp):
TGCCACCAACTTGTGTGGGCTTTAAAAGAGGTTACCACCAACTTGTGTGGGCTTTAGATGGAGT
Found at i:2463291 original size:28 final size:28
Alignment explanation
Indices: 2463260--2463365 Score: 106
Period size: 28 Copynumber: 3.8 Consensus size: 28
2463250 TAAAAGCAAA
*
2463260 CCACTGACTTGTGGGCTTTGAAATGATG
1 CCACTGACTCGTGGGCTTTGAAATGATG
* * * *
2463288 CCACTAATTCATGGGCTTT-AAATGGGTG
1 CCACTGACTCGTGGGCTTTGAAAT-GATG
* * * *
2463316 CTACTGACTCGAGGTCTTTGAAAGGATG
1 CCACTGACTCGTGGGCTTTGAAATGATG
*
2463344 CTACTGACTCGTGGGCTTTGAA
1 CCACTGACTCGTGGGCTTTGAA
2463366 GAGGTTACAT
Statistics
Matches: 61, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
27 4 0.07
28 54 0.89
29 3 0.05
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (28 bp):
CCACTGACTCGTGGGCTTTGAAATGATG
Found at i:2470199 original size:12 final size:11
Alignment explanation
Indices: 2470177--2470219 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
2470167 TTTTCTTCGG
2470177 TTTTC-TTTTT
1 TTTTCTTTTTT
*
2470187 TTCTCTTTTTT
1 TTTTCTTTTTT
2470198 TTTTCTTTTTT
1 TTTTCTTTTTT
2470209 TCTTTCTTTTT
1 T-TTTCTTTTT
2470220 CCTTCCTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 4 0.14
11 16 0.55
12 9 0.31
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:2470200 original size:13 final size:12
Alignment explanation
Indices: 2470177--2470219 Score: 59
Period size: 12 Copynumber: 3.4 Consensus size: 12
2470167 TTTTCTTCGG
2470177 TTTTCTTTTTTTC
1 TTTT-TTTTTTTC
2470190 TCTTTTTTTTTTC
1 T-TTTTTTTTTTC
*
2470203 TTTTTTTCTTTC
1 TTTTTTTTTTTC
2470215 TTTTT
1 TTTTT
2470220 CCTTCCTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 15 0.54
13 10 0.36
14 3 0.11
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTTTTTTTC
Found at i:2470203 original size:21 final size:20
Alignment explanation
Indices: 2470177--2470219 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
2470167 TTTTCTTCGG
*
2470177 TTTTCTTTTTTTCTCTTTTTT
1 TTTTCTTTTTTTCT-TTCTTT
2470198 TTTTCTTTTTTTCTTTCTTT
1 TTTTCTTTTTTTCTTTCTTT
2470218 TT
1 TT
2470220 CCTTCCTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (20 bp):
TTTTCTTTTTTTCTTTCTTT
Found at i:2470818 original size:98 final size:97
Alignment explanation
Indices: 2470710--2470906 Score: 304
Period size: 98 Copynumber: 2.0 Consensus size: 97
2470700 TTTTTTGCTA
*
2470710 TTGCAGCTACCCATGCTCTTCTTCATCATTTCCTCCACGTTGCTTTAGCTATGGTTGCTTCACGT
1 TTGCAGCTACCCATGCTCTTCTTCATCATTTCCTCCACGTTGCTTTAGCTATGGCTGCTTCAC-T
* * ** * * *
2470775 TGTCCCTATTCTTCTTTGTTGTGATGCTGTCTG
65 TGCCCCCATTCTAATTTGCTATGATGCTGTATG
*
2470808 TTGCAGCTACCCATGCTCTTCTTCATCATTTGCTCCACGTTGCTTTAGCTATGGCTGCTTCACTT
1 TTGCAGCTACCCATGCTCTTCTTCATCATTTCCTCCACGTTGCTTTAGCTATGGCTGCTTCACTT
2470873 GCCCCCATTCTAATTTGCTATGATGCTGTATG
66 GCCCCCATTCTAATTTGCTATGATGCTGTATG
2470905 TT
1 TT
2470907 TATCTCCTCA
Statistics
Matches: 90, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
97 29 0.32
98 61 0.68
ACGTcount: A:0.13, C:0.28, G:0.17, T:0.42
Consensus pattern (97 bp):
TTGCAGCTACCCATGCTCTTCTTCATCATTTCCTCCACGTTGCTTTAGCTATGGCTGCTTCACTT
GCCCCCATTCTAATTTGCTATGATGCTGTATG
Found at i:2471112 original size:26 final size:26
Alignment explanation
Indices: 2471094--2471168 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 26
2471084 TTTTTATATA
2471094 TTTTT-TTATTT-TTGATTTTTGATT
1 TTTTTATTATTTCTTGATTTTTGATT
*
2471118 TTTTTATTATTTCTTGAATATTTGATT
1 TTTTTATTATTTCTTG-ATTTTTGATT
* *
2471145 TTTTATATTTTTTATTTGATTTTT
1 TTTT-TATTATTT-CTTGATTTTT
2471169 TATTAATTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
24 5 0.12
25 6 0.14
26 3 0.07
27 13 0.31
28 12 0.29
29 3 0.07
ACGTcount: A:0.17, C:0.01, G:0.07, T:0.75
Consensus pattern (26 bp):
TTTTTATTATTTCTTGATTTTTGATT
Found at i:2471119 original size:21 final size:21
Alignment explanation
Indices: 2471095--2471172 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
2471085 TTTTATATAT
2471095 TTTTTTATTTTTGATTTTTGA
1 TTTTTTATTTTTGATTTTTGA
*
2471116 TTTTTTTATTATTTCTTGAATATTTGA
1 ---TTTT-TTATTT-TTG-ATTTTTGA
2471143 TTTTTTATATTTT--TTATTTGA
1 TTTTTTAT-TTTTGATT-TTTGA
2471164 TTTTTTATT
1 TTTTTTATT
2471173 AATTTAATTT
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
20 2 0.04
21 13 0.28
23 6 0.13
24 10 0.21
25 6 0.13
26 3 0.06
27 7 0.15
ACGTcount: A:0.18, C:0.01, G:0.06, T:0.74
Consensus pattern (21 bp):
TTTTTTATTTTTGATTTTTGA
Found at i:2471168 original size:12 final size:12
Alignment explanation
Indices: 2471136--2471172 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
2471126 ATTTCTTGAA
2471136 TATTTGATTTTT
1 TATTTGATTTTT
2471148 TA--T-ATTTTT
1 TATTTGATTTTT
2471157 TATTTGATTTTT
1 TATTTGATTTTT
2471169 TATT
1 TATT
2471173 AATTTAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
9 8 0.36
10 1 0.05
11 1 0.05
12 12 0.55
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.76
Consensus pattern (12 bp):
TATTTGATTTTT
Found at i:2471182 original size:21 final size:21
Alignment explanation
Indices: 2471137--2471182 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2471127 TTTCTTGAAT
* *
2471137 ATTTGATTTTTTATATTTTTT
1 ATTTGATTTTTTATATATTTA
2471158 ATTTGATTTTTTAT-TAATTTA
1 ATTTGATTTTTTATAT-ATTTA
2471179 ATTT
1 ATTT
2471183 TTTTTCAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (21 bp):
ATTTGATTTTTTATATATTTA
Found at i:2471217 original size:16 final size:16
Alignment explanation
Indices: 2471145--2471244 Score: 61
Period size: 16 Copynumber: 6.4 Consensus size: 16
2471135 ATATTTGATT
2471145 TTTTA-TATTTTTT-A
1 TTTTATTATTTTTTAA
*
2471159 TTTGATT-TTTTATTAA
1 TTTTATTATTTT-TTAA
*
2471175 TTTAATT-TTTTTTCAAA
1 TTTTATTATTTTTT--AA
* *
2471192 ATTTA-AATTTTTTAA
1 TTTTATTATTTTTTAA
*
2471207 TTTT-TTGATTTTTT-G
1 TTTTATT-ATTTTTTAA
2471222 TTTTATTATTATTTTAA
1 TTTTATTATT-TTTTAA
2471239 TTTTAT
1 TTTTAT
2471245 ATATATAAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 19
0.70 0.10 0.20
Matches are distributed among these distances:
14 8 0.12
15 17 0.26
16 24 0.36
17 17 0.26
ACGTcount: A:0.25, C:0.01, G:0.03, T:0.71
Consensus pattern (16 bp):
TTTTATTATTTTTTAA
Found at i:2472470 original size:18 final size:17
Alignment explanation
Indices: 2472443--2472477 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2472433 ATGACGTTAC
*
2472443 TTTATTTTTAATAAAAA
1 TTTATTTTTAAGAAAAA
2472460 TTTATTTTTTAAGAAAAA
1 TTTA-TTTTTAAGAAAAA
2472478 AAGATATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (17 bp):
TTTATTTTTAAGAAAAA
Found at i:2473096 original size:39 final size:39
Alignment explanation
Indices: 2473050--2473147 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
2473040 GTTTTAAGTA
* * * *
2473050 TAAAGTTATAGAGCTTTTGATTAGAAGAATGCTTAATTT
1 TAAAGTTATAGAGCCTCTAATTAGAAGAACGCTTAATTT
* * * *
2473089 TAAAGTTAT-GAAGCCTCTAATTAGAGGAGCGGTTGATTT
1 TAAAGTTATAG-AGCCTCTAATTAGAAGAACGCTTAATTT
2473128 TAAAGTTATAGAGCCTCTAA
1 TAAAGTTATAGAGCCTCTAA
2473148 GTAAAGGAAC
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
38 1 0.02
39 47 0.96
40 1 0.02
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.36
Consensus pattern (39 bp):
TAAAGTTATAGAGCCTCTAATTAGAAGAACGCTTAATTT
Found at i:2477887 original size:20 final size:20
Alignment explanation
Indices: 2477862--2477919 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
2477852 TATACAATAG
2477862 GTGAATGTATCGATACATAA
1 GTGAATGTATCGATACATAA
* **
2477882 GTGAATGTATAGATACATGT
1 GTGAATGTATCGATACATAA
*
2477902 CTGAAATGTATCGATACA
1 GTG-AATGTATCGATACA
2477920 GGACCATGTC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 19 0.59
21 13 0.41
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (20 bp):
GTGAATGTATCGATACATAA
Found at i:2480305 original size:27 final size:27
Alignment explanation
Indices: 2480275--2480333 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
2480265 TCCTTCAAAA
*
2480275 CATTAAAAAGGGATACTCCAACCTTAC
1 CATTAAAAAGGGATACTCCAACCCTAC
*** *
2480302 CATTTCTGAGGGGATACTCCAACCCTAC
1 CA-TTAAAAAGGGATACTCCAACCCTAC
2480330 CATT
1 CATT
2480334 TCTGAGGGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 4 0.15
28 22 0.85
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.25
Consensus pattern (27 bp):
CATTAAAAAGGGATACTCCAACCCTAC
Found at i:2480319 original size:28 final size:28
Alignment explanation
Indices: 2480284--2480354 Score: 133
Period size: 28 Copynumber: 2.5 Consensus size: 28
2480274 ACATTAAAAA
*
2480284 GGGATACTCCAACCTTACCATTTCTGAG
1 GGGATACTCCAACCCTACCATTTCTGAG
2480312 GGGATACTCCAACCCTACCATTTCTGAG
1 GGGATACTCCAACCCTACCATTTCTGAG
2480340 GGGATACTCCAACCC
1 GGGATACTCCAACCC
2480355 CATTTTTACT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.24
Consensus pattern (28 bp):
GGGATACTCCAACCCTACCATTTCTGAG
Found at i:2480545 original size:79 final size:81
Alignment explanation
Indices: 2480313--2480618 Score: 354
Period size: 79 Copynumber: 3.8 Consensus size: 81
2480303 ATTTCTGAGG
* * *
2480313 GGATACTCCAACCCTACCATTTCTGAGGGGATACTCCAACCCCATTTTTACTTCTAAAAATATCA
1 GGATACTCCAACCCCACCATTTCTGAAGGGATACTCCAACCCCATTTTTACTCCTAAAAATATCA
* *
2480378 AATTTTCCAT-TTACGA
66 AATTTTTCATCTT-TGA
* **
2480394 GGATACTCCAACCCTACCATTTCTG-AGGGAATACTTTAACCCCATTTTTACTCCT-AAAATATC
1 GGATACTCCAACCCCACCATTTCTGAAGGG-ATACTCCAACCCCATTTTTACTCCTAAAAATATC
* *
2480457 AAAATTTTCATCTTTGG
65 AAATTTTTCATCTTTGA
* * *
2480474 GGATACTCCAACCCCACTATTTTTGAAGGGATACTCCAACCCC-GTTTTACTCCTAAAAA-ATCA
1 GGATACTCCAACCCCACCATTTCTGAAGGGATACTCCAACCCCATTTTTACTCCTAAAAATATCA
* *
2480537 ATTTTTTCATCTTTAA
66 AATTTTTCATCTTTGA
* * * * * **
2480553 GGATACTCTAACCTCGCCATTTTTGAGGGGATACTTTAACCCCA-TTTTACTCCTAAAAATATCA
1 GGATACTCCAACCCCACCATTTCTGAAGGGATACTCCAACCCCATTTTTACTCCTAAAAATATCA
2480617 AA
66 AA
2480619 CTCCAACCCC
Statistics
Matches: 193, Mismatches: 26, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
79 77 0.40
80 63 0.33
81 53 0.27
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (81 bp):
GGATACTCCAACCCCACCATTTCTGAAGGGATACTCCAACCCCATTTTTACTCCTAAAAATATCA
AATTTTTCATCTTTGA
Found at i:2480717 original size:81 final size:81
Alignment explanation
Indices: 2480618--2480863 Score: 257
Period size: 81 Copynumber: 3.0 Consensus size: 81
2480608 AAAATATCAA
* *
2480618 ACTCCAACCCCACGATTTTTGAAAGGATACTCCAACCCCATTTTTACTTCTAAAAATATCAAATT
1 ACTCCAACCCCACCATTTTCGAAAGGATACTCCAACCCCATTTTTACTTCTAAAAATATCAAATT
2480683 TTCCATCTACGGGGAT
66 TTCCATCTACGGGGAT
* * * ** *
2480699 ACTCCAACCCCACCATTTTCG-AGGAGATATTCCAACCCCGTTTTTA-TAGTAGTAAATATCAAA
1 ACTCCAACCCCACCATTTTCGAAAG-GATACTCCAACCCCATTTTTACTTCTA-AAAATATC-AA
* ***
2480762 ATTTT-CATTTACAAAGAT
63 ATTTTCCATCTACGGGGAT
* * * * *
2480780 ACTCCAATCCTACTATTTTCGAGAA-GATACTGCAACCCTATTTTTACTTCTAAAAATATCAAAT
1 ACTCCAACCCCACCATTTTCGA-AAGGATACTCCAACCCCATTTTTACTTCTAAAAATATCAAAT
**
2480844 TTTCCATCTTTGGGGAT
65 TTTCCATCTACGGGGAT
2480861 ACT
1 ACT
2480864 TTAACCCACC
Statistics
Matches: 129, Mismatches: 29, Indels: 14
0.75 0.17 0.08
Matches are distributed among these distances:
80 12 0.09
81 106 0.82
82 10 0.08
83 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.33
Consensus pattern (81 bp):
ACTCCAACCCCACCATTTTCGAAAGGATACTCCAACCCCATTTTTACTTCTAAAAATATCAAATT
TTCCATCTACGGGGAT
Found at i:2486794 original size:52 final size:52
Alignment explanation
Indices: 2486713--2486833 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
2486703 GAAAATATAT
*
2486713 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
* *
2486765 TTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
2486817 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
2486834 AAGATCGGTG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:2486846 original size:52 final size:52
Alignment explanation
Indices: 2486713--2486853 Score: 187
Period size: 52 Copynumber: 2.7 Consensus size: 52
2486703 GAAAATATAT
*
2486713 CTGCATGTATCGATACATTTA-ATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TAAGATAGTGTATCGATACATCTGGGCAAATTTGC
* *** *
2486765 TTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGC
*
2486817 CTGCATGTATCGATACA-AAGATCGGTGTATCGATACA
1 CTGCATGTATCGATACATAAGAT-AGTGTATCGATACA
2486854 ATGTATCGAT
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
51 4 0.05
52 74 0.95
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (52 bp):
CTGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:2486860 original size:13 final size:13
Alignment explanation
Indices: 2486842--2486866 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2486832 CAAAGATCGG
2486842 TGTATCGATACAA
1 TGTATCGATACAA
2486855 TGTATCGATACA
1 TGTATCGATACA
2486867 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2486948 original size:13 final size:13
Alignment explanation
Indices: 2486930--2486954 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2486920 CAAAAAAATA
2486930 TGTATCGATACAT
1 TGTATCGATACAT
2486943 TGTATCGATACA
1 TGTATCGATACA
2486955 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2486950 original size:33 final size:33
Alignment explanation
Indices: 2486908--2486974 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2486898 AGTAGCTTAA
2486908 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
2486941 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
2486974 A
1 A
2486975 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:2487295 original size:17 final size:18
Alignment explanation
Indices: 2487273--2487309 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
2487263 TGGTGTATCG
2487273 ATACTTTG-TATCGATAC
1 ATACTTTGCTATCGATAC
2487290 ATACTTTGTCTATCGATAC
1 ATACTTTG-CTATCGATAC
2487309 A
1 A
2487310 AGTTTGGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
19 10 0.56
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.41
Consensus pattern (18 bp):
ATACTTTGCTATCGATAC
Found at i:2487400 original size:13 final size:13
Alignment explanation
Indices: 2487382--2487406 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2487372 ACAATGCAAC
2487382 ATGTATCGATACA
1 ATGTATCGATACA
2487395 ATGTATCGATAC
1 ATGTATCGATAC
2487407 TGTGCAACAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2487401 original size:33 final size:33
Alignment explanation
Indices: 2487364--2487429 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
2487354 TTTTTTTCAA
2487364 GTATCGATACAATGCAACATGTATCGATACAAT
1 GTATCGATACAATGCAACATGTATCGATACAAT
**
2487397 GTATCGATACTGTGCAACATGTATCGATACAAT
1 GTATCGATACAATGCAACATGTATCGATACAAT
2487430 TAAATGTGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (33 bp):
GTATCGATACAATGCAACATGTATCGATACAAT
Found at i:2490074 original size:8 final size:8
Alignment explanation
Indices: 2490063--2490090 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
2490053 TCACTCATTC
2490063 ATCACAAA
1 ATCACAAA
2490071 ATCACAAA
1 ATCACAAA
2490079 ATCACAAA
1 ATCACAAA
2490087 ATCA
1 ATCA
2490091 TACAATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.61, C:0.25, G:0.00, T:0.14
Consensus pattern (8 bp):
ATCACAAA
Found at i:2495908 original size:14 final size:14
Alignment explanation
Indices: 2495889--2495925 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2495879 TTGTAGCCGT
*
2495889 TGGAGTTTGATTGG
1 TGGAGTTTAATTGG
2495903 TGGAGTTTAATTGG
1 TGGAGTTTAATTGG
2495917 TGGAGTTTA
1 TGGAGTTTA
2495926 TAGCCGTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.38, T:0.43
Consensus pattern (14 bp):
TGGAGTTTAATTGG
Found at i:2496086 original size:13 final size:13
Alignment explanation
Indices: 2496068--2496093 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2496058 CATTTTATGG
2496068 TGTATCGATACAT
1 TGTATCGATACAT
2496081 TGTATCGATACAT
1 TGTATCGATACAT
2496094 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2496090 original size:33 final size:32
Alignment explanation
Indices: 2496048--2496111 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
2496038 TACAAGCCAA
*
2496048 TGTATCGATACAT-TTTATGGTGTATCGATACAT
1 TGTATCGATACATACTT-T-GTGTATCGATACAT
2496081 TGTATCGATACATACTTTGTGTATCGATACA
1 TGTATCGATACATACTTTGTGTATCGATACA
2496112 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.45
33 14 0.48
34 2 0.07
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATACTTTGTGTATCGATACAT
Found at i:2496953 original size:28 final size:29
Alignment explanation
Indices: 2496922--2496976 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
2496912 TTTATAGGAT
2496922 AACTGTTAAAG-CTAATTTTTATCTTTAA
1 AACTGTTAAAGACTAATTTTTATCTTTAA
* *
2496950 AACTTTTAAAGACTATTTTTTATCTTT
1 AACTGTTAAAGACTAATTTTTATCTTT
2496977 TAGAAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.33, C:0.11, G:0.05, T:0.51
Consensus pattern (29 bp):
AACTGTTAAAGACTAATTTTTATCTTTAA
Found at i:2497086 original size:3 final size:3
Alignment explanation
Indices: 2497080--2497141 Score: 52
Period size: 3 Copynumber: 20.7 Consensus size: 3
2497070 TTTCTTAGTA
* * * * * * * *
2497080 ATT ATT ATT ATT ACT ATT TTT ATT GTT GTT GTT ATT GTT ATT GTT GTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2497128 ATT ATT ATT ATT AT
1 ATT ATT ATT ATT AT
2497142 ATATAAGTTA
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.23, C:0.02, G:0.10, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2497115 original size:18 final size:18
Alignment explanation
Indices: 2497080--2497139 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
2497070 TTTCTTAGTA
* * *
2497080 ATTATTATTATTACTATT
1 ATTATTGTTGTTATTATT
* *
2497098 TTTATTGTTGTTGTTATT
1 ATTATTGTTGTTATTATT
*
2497116 GTTATTGTTGTTATTATT
1 ATTATTGTTGTTATTATT
2497134 ATTATT
1 ATTATT
2497140 ATATATAAGT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.22, C:0.02, G:0.10, T:0.67
Consensus pattern (18 bp):
ATTATTGTTGTTATTATT
Found at i:2497125 original size:15 final size:15
Alignment explanation
Indices: 2497099--2497136 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
2497089 ATTACTATTT
*
2497099 TTATTGTTGTTGTTA
1 TTATTATTGTTGTTA
*
2497114 TTGTTATTGTTGTTA
1 TTATTATTGTTGTTA
2497129 TTATTATT
1 TTATTATT
2497137 ATTATATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (15 bp):
TTATTATTGTTGTTA
Found at i:2497553 original size:21 final size:20
Alignment explanation
Indices: 2497529--2497567 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2497519 ATATTTTTTT
2497529 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TA-AAAATATA
2497550 TAAATATTAATAAAAATA
1 TAAATATTAATAAAAATA
2497568 ATTTTTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 7 0.41
22 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAATATTAATAAAAATATA
Found at i:2497627 original size:18 final size:18
Alignment explanation
Indices: 2497581--2497621 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2497571 TTTAATAATA
2497581 TAAATAA-TAATTTAAATT
1 TAAATAATTAA-TTAAATT
2497599 TAAATAATTAATTAAATT
1 TAAATAATTAATTAAATT
2497617 TAAAT
1 TAAAT
2497622 TTTTAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAATAATTAATTAAATT
Found at i:2499212 original size:27 final size:26
Alignment explanation
Indices: 2499142--2499213 Score: 63
Period size: 27 Copynumber: 2.7 Consensus size: 26
2499132 GAATATCATC
* * *
2499142 TTTTTAATATATTTTTAATGGTTAAAA
1 TTTTTAATTTA-TTTAAATAGTTAAAA
* ** *
2499169 TTTTTATTTTAAATAAATAGTTAATTA
1 TTTTTAATTTATTTAAATAGTTAA-AA
2499196 TTTTTAATTTATTTAAAT
1 TTTTTAATTTATTTAAAT
2499214 TTTTATGTGT
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
26 9 0.26
27 25 0.74
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (26 bp):
TTTTTAATTTATTTAAATAGTTAAAA
Found at i:2500640 original size:17 final size:17
Alignment explanation
Indices: 2500618--2500651 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2500608 AAAATTATTC
2500618 CACTCGTTTTATGTGGG
1 CACTCGTTTTATGTGGG
2500635 CACTCGTTTTATGTGGG
1 CACTCGTTTTATGTGGG
2500652 TGTTTGTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.18, G:0.29, T:0.41
Consensus pattern (17 bp):
CACTCGTTTTATGTGGG
Found at i:2501379 original size:17 final size:16
Alignment explanation
Indices: 2501343--2501376 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
2501333 AAGTGATTAT
2501343 AGATTTTAAAATTTAA
1 AGATTTTAAAATTTAA
2501359 AGATTATTAAACATTTAA
1 AGATT-TTAAA-ATTTAA
2501377 GATATAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 5 0.31
18 6 0.38
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (16 bp):
AGATTTTAAAATTTAA
Found at i:2505710 original size:21 final size:22
Alignment explanation
Indices: 2505669--2505711 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2505659 AATATTATTA
* *
2505669 TTATTTTTAAAATAATTAATAT
1 TTATTATTAAAATAATAAATAT
2505691 TTATTATTAAAAT-ATAAATAT
1 TTATTATTAAAATAATAAATAT
2505712 GCATATTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTATTATTAAAATAATAAATAT
Found at i:2505757 original size:15 final size:15
Alignment explanation
Indices: 2505723--2505765 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
2505713 CATATTCAAT
*
2505723 AATATTCAAAA-TAA
1 AATATTAAAAATTAA
*
2505737 AATATTAAAAATTAC
1 AATATTAAAAATTAA
2505752 AATATTAAATAATT
1 AATATTAAA-AATT
2505766 TTATATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 10 0.40
15 11 0.44
16 4 0.16
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (15 bp):
AATATTAAAAATTAA
Found at i:2506344 original size:30 final size:30
Alignment explanation
Indices: 2506277--2506344 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 30
2506267 GATATAGGTG
*
2506277 TATATATATATATAATAAAAATATATTTAAT
1 TATATTTATATATAATAAAAATATATTT-AT
2506308 T-T-TTTATATATTAA-AAAAATTATATTT-T
1 TATATTTATATA-TAATAAAAA-TATATTTAT
2506336 TATATTTAT
1 TATATTTAT
2506345 GTTTAAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
28 2 0.06
29 13 0.41
30 16 0.50
31 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (30 bp):
TATATTTATATATAATAAAAATATATTTAT
Found at i:2506815 original size:22 final size:20
Alignment explanation
Indices: 2506786--2506841 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 20
2506776 CATAAGTAAA
2506786 TGTATCGATACATGCTT-TCAT
1 TGTATCGATACAT--TTCTCAT
2506807 TGGTATCGATACATTTCTCAT
1 T-GTATCGATACATTTCTCAT
*
2506828 TGTGTCGATACATT
1 TGTATCGATACATT
2506842 CTTGGTTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 14 0.44
21 6 0.19
22 12 0.38
ACGTcount: A:0.23, C:0.18, G:0.16, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATTTCTCAT
Found at i:2509583 original size:13 final size:13
Alignment explanation
Indices: 2509564--2509602 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2509554 ACTATTTATG
2509564 ATGTATCGATACA
1 ATGTATCGATACA
*
2509577 CTGTATCGATACA
1 ATGTATCGATACA
2509590 ATGTATCGATACA
1 ATGTATCGATACA
2509603 TGAATAGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2509669 original size:22 final size:22
Alignment explanation
Indices: 2509612--2509669 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 22
2509602 ATGAATAGTG
*
2509612 ATGAACAGTGATTTTTAACGATAC
1 ATGAACAGTGA--TGTAACGATAC
*
2509636 ATGAA-AGTGATGTATCGATAC
1 ATGAACAGTGATGTAACGATAC
2509657 ATGAACAGTGATG
1 ATGAACAGTGATG
2509670 AATAGTGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 14 0.45
22 7 0.23
23 5 0.16
24 5 0.16
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.29
Consensus pattern (22 bp):
ATGAACAGTGATGTAACGATAC
Found at i:2509676 original size:10 final size:10
Alignment explanation
Indices: 2509657--2509687 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2509647 GTATCGATAC
2509657 ATGAACAGTG
1 ATGAACAGTG
*
2509667 ATGAATAGTG
1 ATGAACAGTG
2509677 ATGAACAGTG
1 ATGAACAGTG
2509687 A
1 A
2509688 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Done.