Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 118 of 313
Found at i:38158418 original size:32 final size:31
Alignment explanation
Indices: 38158377--38158444 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
38158367 TATTATGCCT
38158377 AAAAAAACAAAAAAAAAACAAACAAA-AAAAAC
1 AAAAAAAC-AAAAAAAAACAAA-AAAGAAAAAC
*
38158409 AAAAAAACAAAAAAAAACAAAAAAGAAAAAG
1 AAAAAAACAAAAAAAAACAAAAAAGAAAAAC
38158440 AAAAA
1 AAAAA
38158445 TCAAGATGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 3 0.09
31 23 0.68
32 8 0.24
ACGTcount: A:0.88, C:0.09, G:0.03, T:0.00
Consensus pattern (31 bp):
AAAAAAACAAAAAAAAACAAAAAAGAAAAAC
Found at i:38159381 original size:19 final size:19
Alignment explanation
Indices: 38159357--38159395 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
38159347 TTTTTAATTT
38159357 CGGTTTTTTTTTAAATCAA
1 CGGTTTTTTTTTAAATCAA
38159376 CGGTTTTTTTTTAAATCAA
1 CGGTTTTTTTTTAAATCAA
38159395 C
1 C
38159396 TCATAATACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.10, T:0.51
Consensus pattern (19 bp):
CGGTTTTTTTTTAAATCAA
Found at i:38159458 original size:92 final size:94
Alignment explanation
Indices: 38159297--38159469 Score: 296
Period size: 92 Copynumber: 1.9 Consensus size: 94
38159287 TTTTCCAAAT
*
38159297 ATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTCGGT-
1 ATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTAGGTC
**
38159361 TTTTTTTTAAATCAACGGTTTTTTTTTAA
66 TTTTTTAAAAATCAACGGTTTTTTTTTAA
*
38159390 ATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTATGTC
1 ATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTAGGTC
38159454 TTTTTTAAAAATCAAC
66 TTTTTTAAAAATCAAC
38159470 TCATAATACA
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
92 46 0.61
93 29 0.39
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (94 bp):
ATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTAGGTC
TTTTTTAAAAATCAACGGTTTTTTTTTAA
Found at i:38159491 original size:74 final size:74
Alignment explanation
Indices: 38159378--38160716 Score: 1303
Period size: 75 Copynumber: 17.7 Consensus size: 74
38159368 TAAATCAACG
**
38159378 GTTTTTTTTTAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
1 GTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
38159442 TTAATTTAT
66 TTAATTTAT
* *
38159451 GTCTTTTTTAAAAATCAACTCATAATAC-AGAGGTGGGTTGAGCCTCGGGTCACGCTGAGGTTTT
1 GT-TTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
*
38159515 TTTAATTTCT
65 TTTAATTTAT
38159525 GTCTTTTTT-AAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
1 GT-TTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
*
38159589 TTTAATTTCGTT
65 TTTAATTT--AT
* * *
38159601 TTTTTTTTTAAAATCAACTCATAATA-TAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
1 GTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
38159665 TTAATTTAT
66 TTAATTTAT
** * *
38159674 GTCTTTTTTAAAAAATCAACTCATAATAC-AGATATGAGTTGAGCCTAGGGTCACGCTGAGGCAT
1 GT-TTTTTT-AAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTAT
38159738 TTTTAATTTAT
64 TTTTAATTTAT
* *
38159749 GTCTTTTTAAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGATAT
1 GT-TTTTT-TAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTAT
38159813 TTTTAATTTAT
64 TTTTAATTTAT
*
38159824 GTCTTTTTAAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTAT
1 GT-TTTTT-TAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTAT
38159888 TTTTAATTTAT
64 TTTTAATTTAT
**
38159899 GTCTTTTTTTTAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
1 GT-TTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
38159963 TTTAATTTAT
65 TTTAATTTAT
* *
38159973 GTCTTTTTT-TAAATCAACTCATAATATGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
1 GT-TTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
*
38160037 TTTAATTTCT
65 TTTAATTTAT
* *
38160047 GTTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
1 GTTTTTTT-AAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA--
38160112 TTTTTTAATTT-T
63 -TTTTTAATTTAT
* * * ** * *
38160124 -TTTTTTCATAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGACCATGCCGAGG
1 GTTTTTT--T---AAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGG
*
38160188 TATTTCTTTTAAATTTCT
61 TA--T-TTTT-AATTTAT
* * * * * * ** *
38160206 G-TTTCTCAAAAATCAACTCATATTGCGAGAGGTGGGTTGAGCCTC-GGACAATACCGAGGTATT
1 GTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTC-ACGCTGAGGTA--
*
38160269 TCTTTTAAATTTCT
63 T-TTTT-AATTTAT
** * * ** * *
38160283 GTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTATTT
1 GTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA--T
*
38160348 CTTTTAAATTTCT
64 -TTTT-AATTTAT
* * * ** * *
38160361 G-TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTATTT
1 GTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA--T
*
38160425 CTTTTAAATTTCT
64 -TTTT-AATTTAT
* * * * * * * ** * *
38160438 G-TTTTTCAAAAATCAACTTATATTGCTAGAGATGAGTTGAGCCTTGGACCATGCCGAGGTATTT
1 GTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA--T
*
38160502 CTTTTAAATTTCT
64 -TTTT-AATTTAT
* * * * * *
38160515 G-TTTTTCAAAAATCAACTCATACTGCGAGGGGTAAGTTGAGCCTCGGGTCACGCCGAGGTATTT
1 GTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
*
38160579 TTCAATTCAT
66 TT-AATTTAT
* * * * * * *
38160589 G-TTTTTCAAAAATCAACTCATACTGCGAGGGGTAAGTTGAGCCTCGGGTCGCATGCCGAGGTAT
1 GTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGT--CACGCTGAGGTA-
38160653 TCTTTTCAAATTT-T
63 T-TTTT--AATTTAT
* * * * *
38160667 G-TTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTGGGTC
1 GTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTC
38160717 GCACGCCGAG
Statistics
Matches: 1155, Mismatches: 80, Indels: 59
0.89 0.06 0.05
Matches are distributed among these distances:
73 45 0.04
74 300 0.26
75 309 0.27
76 39 0.03
77 263 0.23
78 127 0.11
79 9 0.01
80 53 0.05
81 5 0.00
82 5 0.00
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (74 bp):
GTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
TTAATTTAT
Found at i:38160324 original size:155 final size:153
Alignment explanation
Indices: 38159388--38160710 Score: 1127
Period size: 155 Copynumber: 8.7 Consensus size: 153
38159378 GTTTTTTTTT
* * ** * *
38159388 AAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA--T-TTTT-AATT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTATTTCTTTTAAATT
* * * * * * *
38159448 TATGTCTTTTTTAAAAATCAACTCATAATAC-AGAGGTGGGTTGAGCCTCGGGTCACGCTGAGG-
66 TCTG--TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCCGAGGT
**
38159511 -TTTTTTT-AATTTCTGTCTTTTTTA
129 ATTTTTTTAAATTTCTGT-TTTTCAA
* * ** * *
38159535 AAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA--T-TTTT-AATT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTATTTCTTTTAAATT
* ** * ** * *
38159596 TCGTTTTTTTTTTTAAAATCAACTCATAAT-ATAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGG
66 TC---TGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCCGAGG
* * *
38159660 TATTTTTAATT-TATGTCT-TTTTTAAA
128 TATTTTT--TTAAATTTCTGTTTTTCAA
* * ** * ** * * *
38159686 AAATCAACTCATAATAC-AGATATGAGTTGAGCCTAGGGTCACGCTGAGGCA--T-TTTT-AATT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTATTTCTTTTAAATT
* * * * * *
38159746 TATGTCTTTTTAAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGA-G
66 TCTG--TTTTT-CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCCGAGG
* * *
38159809 -ATATTTTT-AATTTATGTCTTTTTAAAA
128 TATTTTTTTAAATTTCTG--TTTTT-CAA
* * ** * *
38159836 AAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA--T-TTTT-AATT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTATTTCTTTTAAATT
* *** * * * *
38159896 TATGTCTTTTTTTTAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGT
66 TCTG--TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCCGAGGT
* ***
38159960 A--TTTTT-AATTTATGTCTTTTTTT
129 ATTTTTTTAAATTTCTGT-TTTTCAA
* ** ** * *
38159983 AAATCAACTCATAATATGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA--T-TTTT-AATT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTATTTCTTTTAAATT
* *
38160044 TCTGTTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGT
66 TCTG--TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCCGAGGT
* *
38160109 ATTTTTTTTAATTT-TTTTTTTCATAAAAA
129 ATTTTTTTAAATTTCTGTTTTTC-----AA
*
38160138 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGACCATGCCGAGGTATTTCTTTTAAATT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTATTTCTTTTAAATT
* * **
38160203 TCTGTTTCTCAAAAATCAACTCATATTGCGAGAGGTGGGTTGAGCCTC-GGACAATACCGAGGTA
66 TCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGAC-ACGCCGAGGTA
38160267 TTTCTTTTAAATTTCTGTTTTTCAAA
130 TTT-TTTTAAATTTCTGTTTTTC-AA
38160293 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTATTTCTTTTAAATT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTATTTCTTTTAAATT
*
38160358 TCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACCATGCCGAGGTA
66 TCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGA-CACGCCGAGGTA
38160422 TTTCTTTTAAATTTCTGTTTTTCAA
130 TTT-TTTTAAATTTCTGTTTTTCAA
* * * *
38160447 AAATCAACTTATATTGCTAGAGATGAGTTGAGCCTTGGACCATGCCGAGGTATTTCTTTTAAATT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTATTTCTTTTAAATT
* * * *
38160512 TCTGTTTTTCAAAAATCAACTCATACTGCGAGGGGTAAGTTGAGCCTCGGGTCACGCCGAGGTA-
66 TCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCCGAGGTAT
*
38160576 -TTTTTCAA-TTCATGTTTTTCAA
131 TTTTTTAAATTTC-TGTTTTTCAA
* * * *
38160598 AAATCAACTCATACTGCGAGGGGTAAGTTGAGCCTCGGGTCGCATGCCGAGGTA-TTCTTTTCAA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGAC-CATGCCGAGGTATTTCTTTT-AA
*
38160662 ATTT-TGTTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCT
63 ATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
38160711 TGGGTCGCAC
Statistics
Matches: 1047, Mismatches: 86, Indels: 81
0.86 0.07 0.07
Matches are distributed among these distances:
146 6 0.01
147 35 0.03
148 120 0.11
149 158 0.15
150 164 0.16
151 81 0.08
152 58 0.06
153 25 0.02
154 119 0.11
155 195 0.19
156 4 0.00
157 54 0.05
158 13 0.01
159 15 0.01
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (153 bp):
AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTATTTCTTTTAAATT
TCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCCGAGGTAT
TTTTTTAAATTTCTGTTTTTCAA
Found at i:38161010 original size:29 final size:29
Alignment explanation
Indices: 38160920--38161044 Score: 130
Period size: 29 Copynumber: 4.2 Consensus size: 29
38160910 TTTATTTTTG
*
38160920 CATTTTGACCCCTAAACTTTTCCAAAATTG
1 CATTTTGACCCCTAAACTTTT-CAAAATTA
*
38160950 CATTTTGACCCCTAAACTTTTCAAAATCA
1 CATTTTGACCCCTAAACTTTTCAAAATTA
**
38160979 CATTTCT-ACCCCTAAACTTTTCTGAATTA
1 CATTT-TGACCCCTAAACTTTTCAAAATTA
* *
38161008 CA-TTTGAGCCCTTAAA-ATTTCTATAAATTA
1 CATTTTGA-CCCCTAAACTTTTC-A-AAATTA
38161038 CATTTTG
1 CATTTTG
38161045 GCACCATATT
Statistics
Matches: 80, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
27 1 0.01
28 7 0.09
29 39 0.49
30 29 0.36
31 4 0.05
ACGTcount: A:0.31, C:0.24, G:0.06, T:0.39
Consensus pattern (29 bp):
CATTTTGACCCCTAAACTTTTCAAAATTA
Found at i:38161283 original size:12 final size:12
Alignment explanation
Indices: 38161266--38161299 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
38161256 CCAAGCAAGA
*
38161266 AGCAAAAAAAAG
1 AGCAAAAAAAAC
*
38161278 AGCAAAAACAAC
1 AGCAAAAAAAAC
38161290 AGCAAAAAAA
1 AGCAAAAAAA
38161300 GGCATACCGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.74, C:0.15, G:0.12, T:0.00
Consensus pattern (12 bp):
AGCAAAAAAAAC
Found at i:38161435 original size:16 final size:16
Alignment explanation
Indices: 38161416--38161446 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38161406 ACAACAAGCA
38161416 AAAGAGAAAAAAAGAG
1 AAAGAGAAAAAAAGAG
*
38161432 AAAGAGAAAAGAAGA
1 AAAGAGAAAAAAAGA
38161447 AAGATGGGGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (16 bp):
AAAGAGAAAAAAAGAG
Found at i:38161558 original size:4 final size:4
Alignment explanation
Indices: 38161549--38161621 Score: 60
Period size: 4 Copynumber: 17.8 Consensus size: 4
38161539 GGCTGATCGG
* *
38161549 GAAA GAAA GAAA AAAGA GAAA GAAAA GAGAA GAAA GAAA GAGAA -AGA
1 GAAA GAAA GAAA GAA-A GAAA G-AAA GA-AA GAAA GAAA GA-AA GAAA
* *
38161596 GAAA AAAA GAAA GAAA -ACA GAAA GAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAA
38161622 GAAGGAAGAA
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
3 3 0.05
4 39 0.71
5 13 0.24
ACGTcount: A:0.74, C:0.01, G:0.25, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:38161570 original size:13 final size:13
Alignment explanation
Indices: 38161552--38161612 Score: 74
Period size: 13 Copynumber: 4.8 Consensus size: 13
38161542 TGATCGGGAA
38161552 AGAAAGAAAAAAG
1 AGAAAGAAAAAAG
38161565 AGAAAG--AAAAG
1 AGAAAGAAAAAAG
38161576 AG-AAGAAAGAAAG
1 AGAAAGAAA-AAAG
*
38161589 AGAAAGAGAAAAAA
1 AGAAAGA-AAAAAG
38161603 AGAAAGAAAA
1 AGAAAGAAAA
38161613 CAGAAAGAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
10 3 0.07
11 7 0.17
12 1 0.02
13 15 0.36
14 14 0.33
15 2 0.05
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (13 bp):
AGAAAGAAAAAAG
Found at i:38161584 original size:31 final size:30
Alignment explanation
Indices: 38161549--38161637 Score: 96
Period size: 29 Copynumber: 3.0 Consensus size: 30
38161539 GGCTGATCGG
38161549 GAAAGAAAGAAAAAAGAGAAAGAAAAGAGAA
1 GAAAGAAAGAAAAAAGAGAAAGAAAAGA-AA
*
38161580 GAAAGAAAG-AGAAAGAGAAA-AAAAGAAA
1 GAAAGAAAGAAAAAAGAGAAAGAAAAGAAA
* * *
38161608 GAAA-ACAGAAAGAAGAAGGAAGAAAA-AAA
1 GAAAGAAAGAAAAAAG-AGAAAGAAAAGAAA
38161637 G
1 G
38161638 TGAGATAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
27 3 0.06
28 10 0.20
29 14 0.28
30 14 0.28
31 9 0.18
ACGTcount: A:0.73, C:0.01, G:0.26, T:0.00
Consensus pattern (30 bp):
GAAAGAAAGAAAAAAGAGAAAGAAAAGAAA
Found at i:38161588 original size:24 final size:24
Alignment explanation
Indices: 38161550--38161637 Score: 94
Period size: 24 Copynumber: 3.7 Consensus size: 24
38161540 GCTGATCGGG
38161550 AAAGA-AAGAAA-AAAGAGAAAGA
1 AAAGAGAAGAAAGAAAGAGAAAGA
38161572 AAAGAGAAGAAAGAAAGAGAAAGA
1 AAAGAGAAGAAAGAAAGAGAAAGA
* *
38161596 GAAA-AAAAGAAAGAAAACAGAAAGA
1 -AAAGAGAAGAAAG-AAAGAGAAAGA
*
38161621 AGAAG-GAAGAAAAAAAG
1 A-AAGAGAAGAAAGAAAG
38161638 TGAGATAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
22 5 0.09
23 6 0.11
24 23 0.42
25 21 0.38
ACGTcount: A:0.74, C:0.01, G:0.25, T:0.00
Consensus pattern (24 bp):
AAAGAGAAGAAAGAAAGAGAAAGA
Found at i:38161594 original size:6 final size:6
Alignment explanation
Indices: 38161561--38161599 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
38161551 AAGAAAGAAA
*
38161561 AAAGAG AAAGA- AAAGAG AAGAAAG AAAGAG AAAGAG AAA
1 AAAGAG AAAGAG AAAGAG AA-AGAG AAAGAG AAAGAG AAA
38161600 AAAAGAAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 5 0.17
6 19 0.66
7 5 0.17
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (6 bp):
AAAGAG
Found at i:38161624 original size:38 final size:37
Alignment explanation
Indices: 38161552--38161636 Score: 106
Period size: 38 Copynumber: 2.4 Consensus size: 37
38161542 TGATCGGGAA
* *
38161552 AGAAAGAAAAAAGAGAAAGAAAAGAGAAGAAAGAAAG
1 AGAAAGAAAAAAAAGAAAGAAAACAGAAGAAAGAAAG
38161589 AGAAAGAGAAAAAAAGAAAGAAAACAGAA-AGAAG-AAG
1 AGAAAGA-AAAAAAAGAAAGAAAACAGAAGA-AAGAAAG
38161626 -G-AAGAAAAAAA
1 AGAAAGAAAAAAA
38161637 GTGAGATAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
34 6 0.14
35 4 0.09
36 1 0.02
37 11 0.25
38 22 0.50
ACGTcount: A:0.74, C:0.01, G:0.25, T:0.00
Consensus pattern (37 bp):
AGAAAGAAAAAAAAGAAAGAAAACAGAAGAAAGAAAG
Found at i:38162388 original size:17 final size:17
Alignment explanation
Indices: 38162368--38162568 Score: 109
Period size: 17 Copynumber: 10.8 Consensus size: 17
38162358 CTTAAAAAAA
38162368 TCGTGTTTCAAAAATTT
1 TCGTGTTTCAAAAATTT
38162385 TCGTGTTTTCAAAAAAATTT
1 TCGTG-TTTC--AAAAATTT
* *
38162405 CCCGTGTTTTC-AAAATTC
1 -TCGTG-TTTCAAAAATTT
*
38162423 TCGTATTTC-AAAATTT
1 TCGTGTTTCAAAAATTT
*
38162439 TCTTGTTTTCAAAAAAAATGATT
1 TCGTG-TTTC---AAAAAT--TT
*
38162462 TCCGTGTTTCATAAATTT
1 T-CGTGTTTCAAAAATTT
* * *
38162480 TTGTGTTTAAAAAAAAATTC
1 TCGTGTTT---CAAAAATTT
*
38162500 TCGTCTTTCAAAAATTT
1 TCGTGTTTCAAAAATTT
*
38162517 TCGTGTTTTCAAAAAAATTGA
1 TCGTG-TTTC--AAAAATT-T
* *
38162538 CCGTGTTTCATAAATTT
1 TCGTGTTTCAAAAATTT
38162555 TCGTGTTTCAAAAA
1 TCGTGTTTCAAAAA
38162569 AAATTCTCGT
Statistics
Matches: 141, Mismatches: 24, Indels: 38
0.69 0.12 0.19
Matches are distributed among these distances:
16 13 0.09
17 41 0.29
18 23 0.16
20 36 0.26
21 18 0.13
23 7 0.05
24 3 0.02
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.44
Consensus pattern (17 bp):
TCGTGTTTCAAAAATTT
Found at i:38162410 original size:21 final size:20
Alignment explanation
Indices: 38162377--38162419 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
38162367 ATCGTGTTTC
*
38162377 AAAAATTTTCGTGTTTTCAA
1 AAAAATTTCCGTGTTTTCAA
38162397 AAAAATTTCCCGTGTTTTCAA
1 AAAAATTT-CCGTGTTTTCAA
38162418 AA
1 AA
38162420 TTCTCGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (20 bp):
AAAAATTTCCGTGTTTTCAA
Found at i:38162552 original size:75 final size:75
Alignment explanation
Indices: 38162416--38162578 Score: 247
Period size: 75 Copynumber: 2.1 Consensus size: 75
38162406 CCGTGTTTTC
*
38162416 AAAATTCTCGTATTTCAAAATTTTCTTGTTTTCAAAAAAAATGATTTCCGTGTTTCATAAATTTT
1 AAAATTCTCGTATTTCAAAATTTTCGTGTTTTCAAAAAAAATGA--TCCGTGTTTCATAAATTTT
*
38162481 TGTGTTTAAAAA
64 CGTGTTTAAAAA
* *
38162493 AAAATTCTCGTCTTTCAAAAATTTTCGTGTTTTCAAAAAAATTGA-CCGTGTTTCATAAATTTTC
1 AAAATTCTCGTATTTC-AAAATTTTCGTGTTTTCAAAAAAAATGATCCGTGTTTCATAAATTTTC
*
38162557 GTGTTTCAAAA
65 GTGTTTAAAAA
38162568 AAAATTCTCGT
1 AAAATTCTCGT
38162579 GCTTCGTTTT
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
75 39 0.49
77 15 0.19
78 26 0.32
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (75 bp):
AAAATTCTCGTATTTCAAAATTTTCGTGTTTTCAAAAAAAATGATCCGTGTTTCATAAATTTTCG
TGTTTAAAAA
Found at i:38162637 original size:16 final size:17
Alignment explanation
Indices: 38162616--38162651 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
38162606 TTTCAAAAAC
*
38162616 AAATTTT-GTGTTTTAA
1 AAATTTTCGTGTTTCAA
38162632 AAATTTTCGTGTTTCAA
1 AAATTTTCGTGTTTCAA
38162649 AAA
1 AAA
38162652 GAAAATTCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.47
Consensus pattern (17 bp):
AAATTTTCGTGTTTCAA
Found at i:38162647 original size:37 final size:38
Alignment explanation
Indices: 38162416--38162672 Score: 188
Period size: 37 Copynumber: 6.6 Consensus size: 38
38162406 CCGTGTTTTC
* *
38162416 AAAATTCTCGTATTTC-AAAATTTTCTTGTTTTCAAAA
1 AAAATTCTCGTGTTTCAAAAATTTTCGTGTTTTCAAAA
* * * *
38162453 AAAATGATTTCCGTGTTTCATAAATTTTTGTG-TTTAAAAA
1 AAAAT--TCT-CGTGTTTCAAAAATTTTCGTGTTTTCAAAA
*
38162493 AAAATTCTCGTCTTTCAAAAATTTTCGTGTTTTC-AAA
1 AAAATTCTCGTGTTTCAAAAATTTTCGTGTTTTCAAAA
*
38162530 AAAATTGAC-CGTGTTTCATAAATTTTCGTG-TTTCAAAA
1 AAAATT--CTCGTGTTTCAAAAATTTTCGTGTTTTCAAAA
* **
38162568 AAAATTCTCGTGCTTCGTTTTTATCAAAATTTTTATGTTTTCAAAA
1 AAAATTCTC--G--T-G-TTTCA--AAAATTTTCGTGTTTTCAAAA
* *
38162614 ACAAATT-TTGTGTTTTAAAAATTTTCGTG-TTTCAAAA
1 A-AAATTCTCGTGTTTCAAAAATTTTCGTGTTTTCAAAA
*
38162651 AGAAAAT-TCGTGTTTTCAAAAA
1 A-AAATTCTCGTG-TTTCAAAAA
38162673 AAAACCTCGT
Statistics
Matches: 176, Mismatches: 24, Indels: 39
0.74 0.10 0.16
Matches are distributed among these distances:
36 1 0.01
37 54 0.31
38 51 0.29
39 4 0.02
40 24 0.14
41 11 0.06
42 2 0.01
43 4 0.02
44 1 0.01
45 9 0.05
46 10 0.06
47 5 0.03
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.44
Consensus pattern (38 bp):
AAAATTCTCGTGTTTCAAAAATTTTCGTGTTTTCAAAA
Found at i:38162698 original size:37 final size:36
Alignment explanation
Indices: 38162657--38162763 Score: 112
Period size: 37 Copynumber: 2.9 Consensus size: 36
38162647 AAAAAGAAAA
*
38162657 TTCGTGTTTTCAAAAAAAAACCTCGTGTTTCAAAATT-
1 TTCGTGTTTT-AAAAAAAAA-ATCGTGTTTCAAAATTC
**
38162694 TTCGTGTTTTTAAAAAAAATTTCGTGTTTCTAAAATTC
1 TTCGTG-TTTTAAAAAAAAAATCGTGTTTC-AAAATTC
*
38162732 TT-GT-ATTTAAAAAAAAAATCGTGTTTTCAAAA
1 TTCGTGTTTTAAAAAAAAAATCGTG-TTTCAAAA
38162764 AAAAAAGTTG
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
35 20 0.33
36 13 0.21
37 22 0.36
38 6 0.10
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.41
Consensus pattern (36 bp):
TTCGTGTTTTAAAAAAAAAATCGTGTTTCAAAATTC
Found at i:38162719 original size:36 final size:34
Alignment explanation
Indices: 38162653--38162763 Score: 123
Period size: 35 Copynumber: 3.1 Consensus size: 34
38162643 TTTCAAAAAG
* *
38162653 AAAATTCGTGTTTTCAAAAAAAAACCTCGTGTTTC
1 AAAATTCGTGTTTTTAAAAAAAAA-ATCGTGTTTC
**
38162688 AAAATTTTCGTGTTTTTAAAAAAAATTTCGTGTTTC
1 AAAA--TTCGTGTTTTTAAAAAAAAAATCGTGTTTC
* *
38162724 TAAAATTCTTGTATTTAAAAAAAAAATCGTGTTTTC
1 -AAAATTCGTGTTTTTAAAAAAAAAATCGTG-TTTC
38162760 AAAA
1 AAAA
38162764 AAAAAAGTTG
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
35 30 0.46
36 13 0.20
37 22 0.34
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.40
Consensus pattern (34 bp):
AAAATTCGTGTTTTTAAAAAAAAAATCGTGTTTC
Found at i:38162719 original size:57 final size:58
Alignment explanation
Indices: 38162603--38162722 Score: 154
Period size: 57 Copynumber: 2.1 Consensus size: 58
38162593 AAAATTTTTA
* ** *
38162603 TGTTTTCAAAAACAAATTTTGTGTTTTAAAAATTTTCGTGTTTCAAAAAGAAAATTCG
1 TGTTTTCAAAAAAAAACCTCGTGTTTTAAAAATTTTCGTGTTTCAAAAAGAAAATTCG
* * *
38162661 TGTTTTCAAAAAAAAACCTCGTG-TTTCAAAATTTTCGTGTTTTTAAAAA-AAATTTCG
1 TGTTTTCAAAAAAAAACCTCGTGTTTTAAAAATTTTCGTG-TTTCAAAAAGAAAATTCG
38162718 TGTTT
1 TGTTT
38162723 CTAAAATTCT
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
57 27 0.50
58 27 0.50
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (58 bp):
TGTTTTCAAAAAAAAACCTCGTGTTTTAAAAATTTTCGTGTTTCAAAAAGAAAATTCG
Found at i:38162727 original size:20 final size:19
Alignment explanation
Indices: 38162606--38162728 Score: 85
Period size: 20 Copynumber: 6.4 Consensus size: 19
38162596 ATTTTTATGT
*
38162606 TTTCAAAAACAAATTTTGTG
1 TTTCAAAAA-AAATTTCGTG
* *
38162626 TTT--TAAAAATTTTCGTG
1 TTTCAAAAAAAATTTCGTG
*
38162643 TTTCAAAAAGAAAATTCGTG
1 TTTCAAAAA-AAATTTCGTG
**
38162663 TTTTCAAAAAAAAACCTCGTG
1 -TTTC-AAAAAAAATTTCGTG
*
38162684 TTTC---AAAATTTTCGTG
1 TTTCAAAAAAAATTTCGTG
*
38162700 TTTTTAAAAAAAATTTCGTG
1 -TTTCAAAAAAAATTTCGTG
38162720 TTTCTAAAA
1 TTTC-AAAA
38162729 TTCTTGTATT
Statistics
Matches: 79, Mismatches: 14, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
16 9 0.11
17 14 0.18
18 3 0.04
19 6 0.08
20 30 0.38
21 12 0.15
22 5 0.06
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (19 bp):
TTTCAAAAAAAATTTCGTG
Found at i:38163927 original size:131 final size:132
Alignment explanation
Indices: 38163694--38163951 Score: 482
Period size: 131 Copynumber: 2.0 Consensus size: 132
38163684 ATATAAAAAC
* *
38163694 ATAATTAAATATTTAAATTAACTTTTAATCCAGTGCGATTTTTAGTTGATAAAAACATTAACCCA
1 ATAATTAAATATTTAAATTAAATTTTAATCCAGTGCAATTTTTAGTTGATAAAAACATTAACCCA
38163759 CGTTAGACTATATGATTATATAAGTATATATATGGTAACACTTCTTAATTAC-ATTTTTTTTGAA
66 CGTTAGACTATATGATTATATAAGTATATATATGGTAACACTTCTTAATTACAATTTTTTTTGAA
38163823 TT
131 TT
38163825 ATAATTAAATATTTAAATTAAATTTTAATCCAGTGCAATTTTTAGTTGATAAAAACATTAACCCA
1 ATAATTAAATATTTAAATTAAATTTTAATCCAGTGCAATTTTTAGTTGATAAAAACATTAACCCA
*
38163890 CGTTAGACTATATGGTTATATAAGTATATATATGGTAACACTTCTTAATTACAATTTTTTTT
66 CGTTAGACTATATGATTATATAAGTATATATATGGTAACACTTCTTAATTACAATTTTTTTT
38163952 TTTGAATTAT
Statistics
Matches: 123, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
131 114 0.93
132 9 0.07
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.43
Consensus pattern (132 bp):
ATAATTAAATATTTAAATTAAATTTTAATCCAGTGCAATTTTTAGTTGATAAAAACATTAACCCA
CGTTAGACTATATGATTATATAAGTATATATATGGTAACACTTCTTAATTACAATTTTTTTTGAA
TT
Found at i:38170769 original size:35 final size:35
Alignment explanation
Indices: 38170680--38170750 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
38170670 GTTTACAATT
*
38170680 ATATTGATACACTATTAATATTTATCAATTTTTAC
1 ATATGGATACACTATTAATATTTATCAATTTTTAC
38170715 ATATGGATACACTATTAATATTTATCAATTTTTAC
1 ATATGGATACACTATTAATATTTATCAATTTTTAC
38170750 A
1 A
38170751 AGGTTAATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.46
Consensus pattern (35 bp):
ATATGGATACACTATTAATATTTATCAATTTTTAC
Found at i:38173924 original size:18 final size:20
Alignment explanation
Indices: 38173894--38173930 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
38173884 TAAAGTATTT
38173894 AATTTATAGCATAA-ATAAC
1 AATTTATAGCATAATATAAC
38173913 AATTTA-AGCATAATATAA
1 AATTTATAGCATAATATAA
38173931 GGAACAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.32
Consensus pattern (20 bp):
AATTTATAGCATAATATAAC
Found at i:38189351 original size:45 final size:45
Alignment explanation
Indices: 38189271--38189390 Score: 120
Period size: 45 Copynumber: 2.7 Consensus size: 45
38189261 GCAGATTTTT
* * * * *
38189271 ATATG-CGAACTCATATATGCT-AACTCGTAGAAGAAAATTCATAG
1 ATATGACGAACTCATACATG-TGAATTCATAGTAGAAAATTCATAA
*
38189315 ATGTGGA-GAACTCATACATGTGAATTCATAGTAGAAAATTCATAA
1 ATAT-GACGAACTCATACATGTGAATTCATAGTAGAAAATTCATAA
* **
38189360 ATATGACGGACTCATACATGTGGGTTCATAG
1 ATATGACGAACTCATACATGTGAATTCATAG
38189391 ACATAGTGAA
Statistics
Matches: 62, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
44 6 0.10
45 56 0.90
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (45 bp):
ATATGACGAACTCATACATGTGAATTCATAGTAGAAAATTCATAA
Found at i:38189503 original size:31 final size:31
Alignment explanation
Indices: 38189352--38189509 Score: 140
Period size: 31 Copynumber: 5.1 Consensus size: 31
38189342 ATAGTAGAAA
* *
38189352 ATTCATAAATAT-GACGGACTCATACATGTGG
1 ATTCATAGATATGGA-GAACTCATACATGTGG
* * * * * ****
38189383 GTTCATAGACATAGTGAACTTATACATACAA
1 ATTCATAGATATGGAGAACTCATACATGTGG
* * *
38189414 ATTCATAGATATGGCGAACTCATACAAGCGG
1 ATTCATAGATATGGAGAACTCATACATGTGG
* *
38189445 ATTCATAGATATAGCA-AACTCATACATGTTG
1 ATTCATAGATAT-GGAGAACTCATACATGTGG
38189476 ATTCATAGATATGGAGAACTCATACATGTGG
1 ATTCATAGATATGGAGAACTCATACATGTGG
38189507 ATT
1 ATT
38189510 GTGTCACGGA
Statistics
Matches: 98, Mismatches: 26, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
30 2 0.02
31 94 0.96
32 2 0.02
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (31 bp):
ATTCATAGATATGGAGAACTCATACATGTGG
Found at i:38189509 original size:62 final size:62
Alignment explanation
Indices: 38189350--38189509 Score: 178
Period size: 62 Copynumber: 2.6 Consensus size: 62
38189340 TCATAGTAGA
* * * ** *
38189350 AAATTCATAAATAT-GACGGACTCATACATGTGGGTTCATAGACATAGTGAACTTATACATAC
1 AAATTCATAGATATGGA-GAACTCATACATGTGGATTCATAGACATAGCAAACTCATACATAC
* * * * **
38189412 AAATTCATAGATATGGCGAACTCATACAAGCGGATTCATAGATATAGCAAACTCATACATGT
1 AAATTCATAGATATGGAGAACTCATACATGTGGATTCATAGACATAGCAAACTCATACATAC
**
38189474 TGATTCATAGATATGGAGAACTCATACATGTGGATT
1 AAATTCATAGATATGGAGAACTCATACATGTGGATT
38189510 GTGTCACGGA
Statistics
Matches: 80, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
62 79 0.99
63 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (62 bp):
AAATTCATAGATATGGAGAACTCATACATGTGGATTCATAGACATAGCAAACTCATACATAC
Found at i:38195625 original size:29 final size:30
Alignment explanation
Indices: 38195579--38195666 Score: 88
Period size: 31 Copynumber: 2.9 Consensus size: 30
38195569 TGATTTAATA
*
38195579 TGCAATTATATGCATG-AACTTTAATTTGG
1 TGCAATTATATACATGAAACTTTAATTTGG
* * *
38195608 TGCAATTATACACGTGAAACTCTAATTGTGG
1 TGCAATTATATACATGAAACTTTAATT-TGG
* * * *
38195639 TTCAAATGTATACTTGAAACTTTAATTT
1 TGCAATTATATACATGAAACTTTAATTT
38195667 TGATTTAATC
Statistics
Matches: 47, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
29 13 0.28
30 10 0.21
31 24 0.51
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (30 bp):
TGCAATTATATACATGAAACTTTAATTTGG
Found at i:38196116 original size:17 final size:17
Alignment explanation
Indices: 38196090--38196123 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
38196080 AGACATAACT
*
38196090 AAAGTTTTAAAATTAAA
1 AAAGTATTAAAATTAAA
38196107 AAAGTATTAAAATTAAA
1 AAAGTATTAAAATTAAA
38196124 TGATCAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (17 bp):
AAAGTATTAAAATTAAA
Found at i:38201623 original size:7 final size:7
Alignment explanation
Indices: 38201613--38201638 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
38201603 TTGGGGTAGA
38201613 TGGGAGG
1 TGGGAGG
38201620 TGGGAGG
1 TGGGAGG
38201627 TGGGAGG
1 TGGGAGG
38201634 TGGGA
1 TGGGA
38201639 TGGGAAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.69, T:0.15
Consensus pattern (7 bp):
TGGGAGG
Found at i:38201674 original size:31 final size:30
Alignment explanation
Indices: 38201639--38201698 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
38201629 GGAGGTGGGA
* *
38201639 TGGGAAGAGAATGAAAGTTTTAGGGGAAAAG
1 TGGG-AGAGAATAAAAATTTTAGGGGAAAAG
* *
38201670 TGGGAGGGAGTAAAAATTTTAGGGGAAAA
1 TGGGAGAGAATAAAAATTTTAGGGGAAAA
38201699 TAAAATGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (30 bp):
TGGGAGAGAATAAAAATTTTAGGGGAAAAG
Found at i:38201925 original size:9 final size:9
Alignment explanation
Indices: 38201911--38201947 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
38201901 TATAGTTTGA
38201911 TATTCGAAT
1 TATTCGAAT
38201920 TATTCGAAT
1 TATTCGAAT
*
38201929 TATTCGAGT
1 TATTCGAAT
38201938 TATTCGAAT
1 TATTCGAAT
38201947 T
1 T
38201948 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:38209223 original size:21 final size:20
Alignment explanation
Indices: 38209199--38209240 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
38209189 AATGTTATTA
38209199 ATATAAAAGTA-AATACAAATT
1 ATATAAAA-TATAATA-AAATT
*
38209220 ATATCAAATATAATAAAATT
1 ATATAAAATATAATAAAATT
38209240 A
1 A
38209241 AACTTTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (20 bp):
ATATAAAATATAATAAAATT
Found at i:38211015 original size:13 final size:13
Alignment explanation
Indices: 38210999--38211037 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
38210989 TAGGGTCAAA
*
38210999 GTGTAGGTTGAGT
1 GTGTAGGTTGAGC
38211012 GTGTAGGTTGAGC
1 GTGTAGGTTGAGC
38211025 GTGTAGGTTGAGC
1 GTGTAGGTTGAGC
38211038 AATTGTGTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.15, C:0.05, G:0.46, T:0.33
Consensus pattern (13 bp):
GTGTAGGTTGAGC
Found at i:38211295 original size:25 final size:25
Alignment explanation
Indices: 38211257--38211313 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
38211247 TTTTCTCATG
* *
38211257 TTCTCTTCTCCCTCTTTCATTTT-TT
1 TTCTCTTATCCCTCTCTC-TTTTCTT
*
38211282 TTCTCTTATTCCTCTCTCTTTTCTT
1 TTCTCTTATCCCTCTCTCTTTTCTT
*
38211307 TTTTCTT
1 TTCTCTT
38211314 TATCAGTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 4 0.15
25 23 0.85
ACGTcount: A:0.04, C:0.30, G:0.00, T:0.67
Consensus pattern (25 bp):
TTCTCTTATCCCTCTCTCTTTTCTT
Found at i:38213213 original size:16 final size:15
Alignment explanation
Indices: 38213181--38213216 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
38213171 TTTAATTTTC
38213181 AAAATTTCAAAAAAA
1 AAAATTTCAAAAAAA
* *
38213196 AAAATTTTAAAAATA
1 AAAATTTCAAAAAAA
38213211 AAAATT
1 AAAATT
38213217 GCATTTTGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (15 bp):
AAAATTTCAAAAAAA
Found at i:38213246 original size:30 final size:31
Alignment explanation
Indices: 38213212--38213313 Score: 122
Period size: 30 Copynumber: 3.4 Consensus size: 31
38213202 TTAAAAATAA
*
38213212 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
38213242 AAATTTCATTTTGACCCTTAAAC-TTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
38213272 AAATTTCACTTAGACCCCTAAAC-TTTCAT-T
1 AAATTTCATTTTGACCCCTAAACTTTTC-TCT
38213302 AAATTTCATTTT
1 AAATTTCATTTT
38213314 AATCCTAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
29 4 0.06
30 57 0.92
31 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.04, T:0.44
Consensus pattern (31 bp):
AAATTTCATTTTGACCCCTAAACTTTTCTCT
Found at i:38213564 original size:20 final size:21
Alignment explanation
Indices: 38213539--38213587 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
38213529 GAATCTCCAA
* *
38213539 AAAAAAAGTTTCAAAAA-GAG
1 AAAAAAAGCTTCAAAAATAAG
38213559 AAAAAAAGCTTCAAAAATAAG
1 AAAAAAAGCTTCAAAAATAAG
38213580 AAAAAAAG
1 AAAAAAAG
38213588 GGAGAGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.69, C:0.06, G:0.12, T:0.12
Consensus pattern (21 bp):
AAAAAAAGCTTCAAAAATAAG
Found at i:38213692 original size:3 final size:3
Alignment explanation
Indices: 38213684--38213742 Score: 64
Period size: 3 Copynumber: 18.0 Consensus size: 3
38213674 GCTCGGTTTT
*
38213684 GAA GAA GAA GAA GAA GGAA GAA GAA GAA GAA GAAA GAAA GAGA GAA GAC
1 GAA GAA GAA GAA GAA -GAA GAA GAA GAA GAA G-AA G-AA GA-A GAA GAA
38213733 GAAA GAA GAA
1 G-AA GAA GAA
38213743 AAAAAAAGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
3 35 0.70
4 15 0.30
ACGTcount: A:0.64, C:0.02, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:38213720 original size:13 final size:13
Alignment explanation
Indices: 38213684--38213752 Score: 70
Period size: 13 Copynumber: 5.2 Consensus size: 13
38213674 GCTCGGTTTT
38213684 GAAGAAGAAG-AA
1 GAAGAAGAAGAAA
38213696 GAAGGAAGAAG-AA
1 GAA-GAAGAAGAAA
38213709 GAAGAAGAAAGAAA
1 GAAGAAG-AAGAAA
*
38213723 GAGAGAAGACGAAA
1 GA-AGAAGAAGAAA
* *
38213737 GAAGAAAAAAAAA
1 GAAGAAGAAGAAA
38213750 GAA
1 GAA
38213753 AAAAAANNNN
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
12 7 0.14
13 26 0.53
14 11 0.22
15 5 0.10
ACGTcount: A:0.68, C:0.01, G:0.30, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAGAAA
Found at i:38221571 original size:30 final size:31
Alignment explanation
Indices: 38221537--38221638 Score: 122
Period size: 30 Copynumber: 3.4 Consensus size: 31
38221527 AAAAAAATAA
*
38221537 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
38221567 AAATTTCATTTTGACCCTTAAAC-TTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
38221597 AAATTTCACTTAGACCCCTAAAC-TTTCAT-T
1 AAATTTCATTTTGACCCCTAAACTTTTC-TCT
38221627 AAATTTCATTTT
1 AAATTTCATTTT
38221639 AATCCTAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
29 4 0.06
30 57 0.92
31 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.04, T:0.44
Consensus pattern (31 bp):
AAATTTCATTTTGACCCCTAAACTTTTCTCT
Found at i:38221921 original size:10 final size:10
Alignment explanation
Indices: 38221902--38221951 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
38221892 TTTTTCGAAG
*
38221902 GAAAAAAGAA
1 GAAAAGAGAA
38221912 GAAAAGAGAA
1 GAAAAGAGAA
38221922 GAAAAGAGAA
1 GAAAAGAGAA
* *
38221932 -AGAGGAGAA
1 GAAAAGAGAA
38221941 GAAAAGA-AA
1 GAAAAGAGAA
38221950 GA
1 GA
38221952 GTACCGGCGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 23 0.68
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
GAAAAGAGAA
Found at i:38221952 original size:17 final size:19
Alignment explanation
Indices: 38221905--38221947 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
38221895 TTCGAAGGAA
38221905 AAAAGAAGAAA-A-GAGAAG
1 AAAAG-AGAAAGAGGAGAAG
38221923 AAAAGAGAAAGAGGAGAAG
1 AAAAGAGAAAGAGGAGAAG
38221942 AAAAGA
1 AAAAGA
38221948 AAGAGTACCG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.22
18 6 0.26
19 12 0.52
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (19 bp):
AAAAGAGAAAGAGGAGAAG
Found at i:38222013 original size:3 final size:3
Alignment explanation
Indices: 38222007--38222052 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
38221997 GCTAGACTTT
*
38222007 GAA GAA GAA GAA GGAA GAA GAA GGAA GAA GAA -AA GAG GAA GAA GAA
1 GAA GAA GAA GAA -GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA GAA
38222053 AGAAAGANGG
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 30 0.79
4 6 0.16
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:38222025 original size:10 final size:10
Alignment explanation
Indices: 38222010--38222038 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
38222000 AGACTTTGAA
38222010 GAAGAAGAAG
1 GAAGAAGAAG
38222020 GAAGAAGAAG
1 GAAGAAGAAG
38222030 GAAGAAGAA
1 GAAGAAGAA
38222039 AAGAGGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (10 bp):
GAAGAAGAAG
Found at i:38222025 original size:13 final size:13
Alignment explanation
Indices: 38222007--38222052 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
38221997 GCTAGACTTT
38222007 GAAGAAGAAGAAG
1 GAAGAAGAAGAAG
38222020 GAAGAAGAAGGAA-
1 GAAGAAGAA-GAAG
38222033 GAAGAA-AAG-AG
1 GAAGAAGAAGAAG
38222044 GAAGAAGAA
1 GAAGAAGAA
38222053 AGAAAGANGG
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.03
11 7 0.23
12 4 0.13
13 15 0.50
14 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAGAAG
Found at i:38222412 original size:19 final size:19
Alignment explanation
Indices: 38222353--38222412 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
38222343 TATTTACAAA
* *
38222353 AAAATTTTTCT-ATTTTTC
1 AAAATTTTTCTCGTGTTTC
*
38222371 AAAA-TTTT-TCGTGCCTTC
1 AAAATTTTTCTCGTG-TTTC
38222389 AAAAATTTTTCTCGTGTTTC
1 -AAAATTTTTCTCGTGTTTC
38222409 AAAA
1 AAAA
38222413 AAAATATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
16 1 0.03
17 5 0.15
18 7 0.21
19 8 0.24
20 7 0.21
21 5 0.15
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.48
Consensus pattern (19 bp):
AAAATTTTTCTCGTGTTTC
Found at i:38222665 original size:18 final size:17
Alignment explanation
Indices: 38222591--38222753 Score: 159
Period size: 17 Copynumber: 9.4 Consensus size: 17
38222581 ATCCATTTTC
* *
38222591 CAAAATTTTTAGTGTCTT
1 CAAAAATTTTCGTGT-TT
*
38222609 CTAAAAATTTTTGTGTTT
1 C-AAAAATTTTCGTGTTT
38222627 CAAAAATTTTCGT-TTT
1 CAAAAATTTTCGTGTTT
*
38222643 CAAAAATTTCCGTGTTT
1 CAAAAATTTTCGTGTTT
38222660 CAAAAATTTTCGTGTTTT
1 CAAAAATTTTCGTG-TTT
* *
38222678 CAAAATTTTTCGTATTT
1 CAAAAATTTTCGTGTTT
** *
38222695 CAAAAATCCTCTTGTTTT
1 CAAAAATTTTCGTG-TTT
38222713 CAAAAA-TTTCGGTGTTT
1 CAAAAATTTTC-GTGTTT
**
38222730 TGAAAATTTTCGTGTTTT
1 CAAAAATTTTCGTG-TTT
38222748 CAAAAA
1 CAAAAA
38222754 AAAATATCGT
Statistics
Matches: 119, Mismatches: 19, Indels: 14
0.78 0.12 0.09
Matches are distributed among these distances:
16 15 0.13
17 51 0.43
18 41 0.34
19 12 0.10
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.47
Consensus pattern (17 bp):
CAAAAATTTTCGTGTTT
Found at i:38222753 original size:35 final size:34
Alignment explanation
Indices: 38222591--38222753 Score: 168
Period size: 35 Copynumber: 4.7 Consensus size: 34
38222581 ATCCATTTTC
* * * *
38222591 CAAAATTTTTAGTGTCTTCTAAAAATTTTTGTGTTT
1 CAAAAATTTTCGTGTTTTC-AAAAA-TTTCGTGTTT
38222627 CAAAAATTTTC--GTTTTCAAAAATTTCCGTGTTT
1 CAAAAATTTTCGTGTTTTCAAAAATTT-CGTGTTT
* *
38222660 CAAAAATTTTCGTGTTTTCAAAATTTTTCGTATTT
1 CAAAAATTTTCGTGTTTTCAAAA-ATTTCGTGTTT
** *
38222695 CAAAAATCCTCTTGTTTTCAAAAATTTCGGTGTTT
1 CAAAAATTTTCGTGTTTTCAAAAATTTC-GTGTTT
**
38222730 TGAAAATTTTCGTGTTTTCAAAAA
1 CAAAAATTTTCGTGTTTTCAAAAA
38222754 AAAATATCGT
Statistics
Matches: 106, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
32 3 0.03
33 22 0.21
34 9 0.08
35 60 0.57
36 12 0.11
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.47
Consensus pattern (34 bp):
CAAAAATTTTCGTGTTTTCAAAAATTTCGTGTTT
Found at i:38222766 original size:38 final size:37
Alignment explanation
Indices: 38222714--38222842 Score: 120
Period size: 35 Copynumber: 3.4 Consensus size: 37
38222704 TCTTGTTTTC
*
38222714 AAAAATTTCGGTGTTTTGAAAATTTTCGTGTTTTCAAAA
1 AAAAATATC-GTGTTTT-AAAATTTTCGTGTTTTCAAAA
*
38222753 AAAAATATCGTGTTTCATAAATTTT-G-GTTTT-AAAA
1 AAAAATATCGTGTTTTA-AAATTTTCGTGTTTTCAAAA
** * *
38222788 AAAAATATTATGTCTTAAAATTCTCGTGTTTTCAAAA
1 AAAAATATCGTGTTTTAAAATTTTCGTGTTTTCAAAA
*
38222825 CAAGAAATTCTCGTGTTT
1 -AA-AAA-TATCGTGTTT
38222843 CAATCGGATC
Statistics
Matches: 72, Mismatches: 11, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
34 6 0.08
35 18 0.25
36 10 0.14
37 6 0.08
38 15 0.21
39 11 0.15
40 6 0.08
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.42
Consensus pattern (37 bp):
AAAAATATCGTGTTTTAAAATTTTCGTGTTTTCAAAA
Found at i:38224687 original size:38 final size:38
Alignment explanation
Indices: 38224640--38224734 Score: 127
Period size: 38 Copynumber: 2.5 Consensus size: 38
38224630 ATACAAAAAT
* * *
38224640 AGTAAACATGCTTAACATGTATTCAATTCAATAGTAGC
1 AGTAGACATGCTTAACATGTATTCAATTCAACAATAGC
* * *
38224678 AGTAGACATGTTTAACATGTATTCGATTTAACAATAGC
1 AGTAGACATGCTTAACATGTATTCAATTCAACAATAGC
*
38224716 AGTAGGCATGCTTAACATG
1 AGTAGACATGCTTAACATG
38224735 CAATCAGTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.32
Consensus pattern (38 bp):
AGTAGACATGCTTAACATGTATTCAATTCAACAATAGC
Found at i:38232085 original size:31 final size:31
Alignment explanation
Indices: 38232050--38232113 Score: 78
Period size: 31 Copynumber: 2.0 Consensus size: 31
38232040 ATATTAATAT
38232050 AATATTTA-AATTTATTATTATATTT-TTTGAA
1 AATATTTAGAATTT-TTA-TATATTTCTTTGAA
*
38232081 AATATTTATGTATTTTTATATATTTCTTTGAA
1 AATATTTA-GAATTTTTATATATTTCTTTGAA
38232113 A
1 A
38232114 TCTTTTAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
31 15 0.52
32 10 0.34
33 4 0.14
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.58
Consensus pattern (31 bp):
AATATTTAGAATTTTTATATATTTCTTTGAA
Found at i:38238452 original size:28 final size:28
Alignment explanation
Indices: 38238420--38238473 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
38238410 ATGTTAAAAG
*
38238420 AAATTTTCATTTTTTTTAAAAATTATAC
1 AAATTTTAATTTTTTTTAAAAATTATAC
*
38238448 AAATTTTAATTTTTTTTAAATATTAT
1 AAATTTTAATTTTTTTTAAAAATTAT
38238474 TAAAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (28 bp):
AAATTTTAATTTTTTTTAAAAATTATAC
Found at i:38238848 original size:16 final size:16
Alignment explanation
Indices: 38238827--38238857 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38238817 TTAAAAAATA
38238827 TATAAAAATAATAATC
1 TATAAAAATAATAATC
*
38238843 TATAAAAATATTAAT
1 TATAAAAATAATAAT
38238858 AATATTATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
TATAAAAATAATAATC
Found at i:38242280 original size:27 final size:27
Alignment explanation
Indices: 38242221--38242281 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
38242211 TAATACAAAG
* *
38242221 TAGTGGCGCCTATCTCAGAGGCGCCAA
1 TAGTGGTGCCTATCTCACAGGCGCCAA
* * *
38242248 TGGTGGTGCCTATCTGACAGGCGCCAT
1 TAGTGGTGCCTATCTCACAGGCGCCAA
38242275 TAGTGGT
1 TAGTGGT
38242282 ACCATGTTGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.18, C:0.25, G:0.33, T:0.25
Consensus pattern (27 bp):
TAGTGGTGCCTATCTCACAGGCGCCAA
Found at i:38245383 original size:21 final size:21
Alignment explanation
Indices: 38245352--38245572 Score: 113
Period size: 21 Copynumber: 10.4 Consensus size: 21
38245342 AATTAATTAT
38245352 AAAATAATTACAATATTCATAC
1 AAAA-AATTACAATATTCATAC
38245374 AAAAAATTACAATATTCAT--
1 AAAAAATTACAATATTCATAC
* * * *
38245393 ATAAAATTACAAAATTAATTAT
1 AAAAAATTACAATATTCA-TAC
38245415 AAAATAATTACAA-A--C--AC
1 AAAA-AATTACAATATTCATAC
* * * *
38245432 AAAAATTTATAACATAATCCTA-
1 AAAAAATTA-CA-ATATTCATAC
** * * * *
38245454 AATTACTAACAA-ATTAATTAT
1 AAAAAATTACAATATTCA-TAC
38245475 AAAATAATTACAATATTCATAC
1 AAAA-AATTACAATATTCATAC
38245497 --AAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
38245516 AAAATTAAAAAATTACAATATTCATAC
1 ------AAAAAATTACAATATTCATAC
38245543 AAAAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
*
38245564 AAAATATTA
1 AAAAAATTA
38245573 ATCTAAAATT
Statistics
Matches: 153, Mismatches: 23, Indels: 47
0.69 0.10 0.21
Matches are distributed among these distances:
16 4 0.03
17 6 0.04
18 1 0.01
19 35 0.23
20 6 0.04
21 48 0.31
22 21 0.14
23 13 0.08
27 19 0.12
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAAAATTACAATATTCATAC
Found at i:38245400 original size:19 final size:19
Alignment explanation
Indices: 38245357--38245419 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
38245347 ATTATAAAAT
*
38245357 AATTACAATATTCATACAAAA
1 AATTACAATATTCAT--ATAA
38245378 AATTACAATATTCATATAA
1 AATTACAATATTCATATAA
* *
38245397 AATTACAAAATTAATTATAA
1 AATTACAATATTCA-TATAA
38245417 AAT
1 AAT
38245420 AATTACAAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
19 15 0.39
20 8 0.21
21 15 0.39
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (19 bp):
AATTACAATATTCATATAA
Found at i:38245565 original size:48 final size:47
Alignment explanation
Indices: 38245474--38245568 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 47
38245464 AAATTAATTA
38245474 TAAAATAATTACAATATTCATACAAAATTACAATATTCATACAAAAT
1 TAAAATAATTACAATATTCATACAAAATTACAATATTCATACAAAAT
38245521 TAAAA-AATTACAATATTCATACAAAAAATTACAATATTCATACAAAAT
1 TAAAATAATTACAATATTCATAC--AAAATTACAATATTCATACAAAAT
38245569 ATTAATCTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
46 17 0.37
47 5 0.11
48 24 0.52
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.31
Consensus pattern (47 bp):
TAAAATAATTACAATATTCATACAAAATTACAATATTCATACAAAAT
Found at i:38245647 original size:61 final size:62
Alignment explanation
Indices: 38245341--38245648 Score: 230
Period size: 61 Copynumber: 4.9 Consensus size: 62
38245331 ATTTGTCTAC
* * *
38245341 AAATTAATTATAAAATAATTACAATATTCATACAAAA-A--ATTACAATATTCATATAAAATTAC
1 AAATTAATTATAAAATAATTACAATATTCATACAAAATACTAATCCAA-A-AC-TAT-AAATTAC
38245403 A
62 A
* * *
38245404 AAATTAATTATAAAATAATTACAA-A--CACA-AAAATTTA-TAA--CATAA-TCCTAAATTACT
1 AAATTAATTATAAAATAATTACAATATTCATACAAAA--TACTAATCCAAAACT-ATAAATTAC-
38245461 AA
62 -A
* * *
38245463 CAAATTAATTATAAAATAATTACAATATTCATACAAAATTACAATATTCATACAAAATTAAAAAA
1 -AAATTAATTATAAAATAATTACAATATTCATACAAAA-TAC--TA---ATCCAAAACT-ATAAA
38245528 TTACA
58 TTACA
* * * * * *
38245533 ATATTCA-TACAAAA-AATTACAATATTCATACAAAATATTAATCTAAAATTATAAA-TACA
1 AAATTAATTATAAAATAATTACAATATTCATACAAAATACTAATCCAAAACTATAAATTACA
38245592 AAATTAATTATAAAATAATTACAATATTCATACAAAATACTAATCCAAAACTATAAA
1 AAATTAATTATAAAATAATTACAATATTCATACAAAATACTAATCCAAAACTATAAA
38245649 CACTAAACAT
Statistics
Matches: 199, Mismatches: 23, Indels: 48
0.74 0.09 0.18
Matches are distributed among these distances:
57 8 0.04
58 1 0.01
59 14 0.07
60 38 0.19
61 49 0.25
62 2 0.01
63 31 0.16
64 6 0.03
66 4 0.02
67 21 0.11
68 6 0.03
69 6 0.03
70 1 0.01
71 4 0.02
72 8 0.04
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.31
Consensus pattern (62 bp):
AAATTAATTATAAAATAATTACAATATTCATACAAAATACTAATCCAAAACTATAAATTACA
Found at i:38245670 original size:7 final size:7
Alignment explanation
Indices: 38245660--38245685 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
38245650 ACTAAACATA
38245660 AATAATT
1 AATAATT
38245667 AATAATT
1 AATAATT
38245674 AATAATT
1 AATAATT
38245681 AATAA
1 AATAA
38245686 CAAAAAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
AATAATT
Found at i:38247131 original size:3 final size:3
Alignment explanation
Indices: 38247101--38247160 Score: 66
Period size: 3 Copynumber: 19.7 Consensus size: 3
38247091 AAAATAAAAC
* * *
38247101 TAA TAA TATT TAA TAG TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
38247147 TAA TTA TCA TAA TA
1 TAA TAA TAA TAA TA
38247161 CAAAAATAAC
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
3 45 0.96
4 2 0.04
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:38248575 original size:27 final size:27
Alignment explanation
Indices: 38248522--38248576 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
38248512 CATTGGCGCT
* **
38248522 TCCCTATGAGGCACTGTTAATGACACC
1 TCCCTATGAGACACAATTAATGACACC
* *
38248549 TCCCTATGAGACACAATTAGTGGCACC
1 TCCCTATGAGACACAATTAATGACACC
38248576 T
1 T
38248577 ACCTGACAGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.25
Consensus pattern (27 bp):
TCCCTATGAGACACAATTAATGACACC
Found at i:38257499 original size:26 final size:29
Alignment explanation
Indices: 38257463--38257515 Score: 76
Period size: 26 Copynumber: 1.9 Consensus size: 29
38257453 AGAGGAACTG
38257463 TATTCTATTTT-A-TTTTAT-ATATAATT
1 TATTCTATTTTAATTTTTATAATATAATT
*
38257489 TATTTTATTTTAATTTTTATAATATAA
1 TATTCTATTTTAATTTTTATAATATAA
38257516 AAATTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 10 0.43
27 1 0.04
28 6 0.26
29 6 0.26
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (29 bp):
TATTCTATTTTAATTTTTATAATATAATT
Found at i:38262488 original size:11 final size:11
Alignment explanation
Indices: 38262447--38262492 Score: 56
Period size: 12 Copynumber: 4.0 Consensus size: 11
38262437 TTCACGAACA
38262447 AACTCGTTTAT
1 AACTCGTTTAT
*
38262458 AAGCTTGTTTATT
1 AA-CTCGTTTA-T
38262471 AACTCGTTTAT
1 AACTCGTTTAT
*
38262482 GACTCGTTTAT
1 AACTCGTTTAT
38262493 TTATTAATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 13 0.43
12 14 0.47
13 3 0.10
ACGTcount: A:0.24, C:0.15, G:0.13, T:0.48
Consensus pattern (11 bp):
AACTCGTTTAT
Found at i:38263913 original size:21 final size:22
Alignment explanation
Indices: 38263889--38263983 Score: 77
Period size: 23 Copynumber: 4.2 Consensus size: 22
38263879 GAGTGCCTGG
* *
38263889 GTGGC-ATTTTGATTGGCCTTT
1 GTGGCAATTCTGATTAGCCTTT
*
38263910 GTGGCGAATTCTGGTTAGCCTTT
1 GTGGC-AATTCTGATTAGCCTTT
* * *
38263933 GTGGCGAATTATG-TTTGACATTT
1 GTGGC-AATTCTGATTAG-CCTTT
*
38263956 GTGGCTAATTCTAATTAGCCTTT
1 GTGGC-AATTCTGATTAGCCTTT
38263979 GTGGC
1 GTGGC
38263984 GTATTCAGTA
Statistics
Matches: 59, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
21 5 0.08
22 3 0.05
23 48 0.81
24 3 0.05
ACGTcount: A:0.16, C:0.15, G:0.27, T:0.42
Consensus pattern (22 bp):
GTGGCAATTCTGATTAGCCTTT
Found at i:38263931 original size:23 final size:22
Alignment explanation
Indices: 38263904--38263989 Score: 91
Period size: 23 Copynumber: 3.8 Consensus size: 22
38263894 ATTTTGATTG
38263904 GCCTTTGTGGCGAATTCTGGTTA
1 GCCTTTGTGGCGAATTCT-GTTA
* *
38263927 GCCTTTGTGGCGAATTATGTTT
1 GCCTTTGTGGCGAATTCTGTTA
* * *
38263949 GACATTTGTGGCTAATTCTAATTA
1 G-CCTTTGTGGCGAATTCT-GTTA
*
38263973 GCCTTTGTGGCGTATTC
1 GCCTTTGTGGCGAATTC
38263990 AGTATGCTAC
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
22 4 0.08
23 44 0.86
24 3 0.06
ACGTcount: A:0.16, C:0.16, G:0.26, T:0.42
Consensus pattern (22 bp):
GCCTTTGTGGCGAATTCTGTTA
Found at i:38268892 original size:37 final size:38
Alignment explanation
Indices: 38268838--38268912 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 38
38268828 CTGCATCAGG
* *
38268838 AGAAAATTGAGGAAAATTATACAA-CGAAGCACAAAAT
1 AGAAAATAGAGGAAAATTAGACAATCGAAGCACAAAAT
* *
38268875 AGAAAATAGAGGGAAATTAGACAATGGAAGCACAAAAT
1 AGAAAATAGAGGAAAATTAGACAATCGAAGCACAAAAT
38268913 CAAGCAGCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
37 21 0.64
38 12 0.36
ACGTcount: A:0.56, C:0.09, G:0.20, T:0.15
Consensus pattern (38 bp):
AGAAAATAGAGGAAAATTAGACAATCGAAGCACAAAAT
Found at i:38272648 original size:21 final size:21
Alignment explanation
Indices: 38272624--38272668 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
38272614 TTTTTTATAC
*
38272624 TTATTATGTAAATTAATATTT
1 TTATTATGTAAATAAATATTT
* *
38272645 TTATTTTTTAAATAAATATTT
1 TTATTATGTAAATAAATATTT
38272666 TTA
1 TTA
38272669 AGTAATTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TTATTATGTAAATAAATATTT
Found at i:38273595 original size:63 final size:63
Alignment explanation
Indices: 38273528--38273665 Score: 258
Period size: 63 Copynumber: 2.2 Consensus size: 63
38273518 GAGGTGAAGT
*
38273528 TGGTGGTGGTGGAGATTGAACTGGTGGAGGTGGGAAGGAGACGGGTGGTGGAGGGGATAGAAC
1 TGGTGGTGGTGGAGATTGAACTGGTGGAGGTGGGAAGGAGACGGGTGGTGGAGGGGACAGAAC
38273591 TGGTGGTGGTGGAGATTGAACTGGTGGAGGTGGGAAGGAGACGGGTGGTGGAGGGGACAGAAC
1 TGGTGGTGGTGGAGATTGAACTGGTGGAGGTGGGAAGGAGACGGGTGGTGGAGGGGACAGAAC
*
38273654 TGGTGGAGGTGG
1 TGGTGGTGGTGG
38273666 GAAGGAGACG
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 73 1.00
ACGTcount: A:0.21, C:0.05, G:0.55, T:0.19
Consensus pattern (63 bp):
TGGTGGTGGTGGAGATTGAACTGGTGGAGGTGGGAAGGAGACGGGTGGTGGAGGGGACAGAAC
Found at i:38273617 original size:42 final size:41
Alignment explanation
Indices: 38273528--38273779 Score: 129
Period size: 42 Copynumber: 6.0 Consensus size: 41
38273518 GAGGTGAAGT
* * *
38273528 TGGTGGTGGTGGAGATTGAACTGGTGGAGGTGG-GAAG-GAGAC
1 TGGTGGTGG-GGGGATAGAACTGGTGGTGGTGGAG-AGTGA-AC
* *
38273570 GGGTGGTGGAGGGGATAGAACTGGTGGTGGTGGAGATTGAAC
1 TGGTGGTGG-GGGGATAGAACTGGTGGTGGTGGAGAGTGAAC
* * * * * **
38273612 TGGTGGAGGTGGGA-AGGAGACGGGTGGTGGAGGGGACAGAAC
1 TGGTGGTGGGGGGATA-GA-ACTGGTGGTGGTGGAGAGTGAAC
* * * * *
38273654 TGGTGGAGGTGGGA-AGGAGACGGGTGGTGGAGGGGA-TAGAAC
1 TGGTGGTGGGGGGATA-GA-ACTGGTGGTGGTGGAGAGT-GAAC
* * *
38273696 TGGTGGTGGTGGAGATTGAACTGGTGGAGGTGGAGAGT-AGAC
1 TGGTGGTGG-GGGGATAGAACTGGTGGTGGTGGAGAGTGA-AC
* * * * *
38273738 AGGTGGTGGAGGGGAGAGAACTTGTTGTGGTGGTGAGTGAAC
1 TGGTGGTGG-GGGGATAGAACTGGTGGTGGTGGAGAGTGAAC
38273780 GGGAGGTTTT
Statistics
Matches: 168, Mismatches: 32, Indels: 20
0.76 0.15 0.09
Matches are distributed among these distances:
40 1 0.01
41 7 0.04
42 150 0.89
43 10 0.06
ACGTcount: A:0.22, C:0.05, G:0.53, T:0.19
Consensus pattern (41 bp):
TGGTGGTGGGGGGATAGAACTGGTGGTGGTGGAGAGTGAAC
Found at i:38273680 original size:63 final size:63
Alignment explanation
Indices: 38273528--38273731 Score: 225
Period size: 63 Copynumber: 3.2 Consensus size: 63
38273518 GAGGTGAAGT
* ** *
38273528 TGGTGGTGGTGGAGATTGAACTGGTGGAGGTGGGAAGGAGACGGGTGGTGGAGGGGATAGAAC
1 TGGTGGAGGTGGAGAAGGAACGGGTGGAGGTGGGAAGGAGACGGGTGGTGGAGGGGATAGAAC
* ** * *
38273591 TGGTGGTGGTGGAGATTGAACTGGTGGAGGTGGGAAGGAGACGGGTGGTGGAGGGGACAGAAC
1 TGGTGGAGGTGGAGAAGGAACGGGTGGAGGTGGGAAGGAGACGGGTGGTGGAGGGGATAGAAC
* * * * * *
38273654 TGGTGGAGGTGG-GAAGGAGACGGGTGGTGGAGGGGATA-GA-ACTGGTGGTGGTGGAGATTGAA
1 TGGTGGAGGTGGAGAAGGA-ACGGGTGGAGG-TGGGA-AGGAGACGGGTGGTGGAGGGGATAGAA
38273716 C
63 C
38273717 TGGTGGAGGTGGAGA
1 TGGTGGAGGTGGAGA
38273732 GTAGACAGGT
Statistics
Matches: 125, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
62 4 0.03
63 112 0.90
64 8 0.06
65 1 0.01
ACGTcount: A:0.22, C:0.05, G:0.54, T:0.19
Consensus pattern (63 bp):
TGGTGGAGGTGGAGAAGGAACGGGTGGAGGTGGGAAGGAGACGGGTGGTGGAGGGGATAGAAC
Found at i:38273743 original size:63 final size:63
Alignment explanation
Indices: 38273650--38273779 Score: 181
Period size: 63 Copynumber: 2.1 Consensus size: 63
38273640 GGAGGGGACA
* * *
38273650 GAACTGGTGGAGGTGGGAAGGAGACGGGTGGTGGAGGGGATAGAACTGGTGGTGGTGGAGATT
1 GAACTGGTGGAGGTGGGAAGGAGACAGGTGGTGGAGGGGAGAGAACTGGTGGTGGTGGAGAGT
* * * *
38273713 GAACTGGTGGAGGT-GGAGAGTAGACAGGTGGTGGAGGGGAGAGAACTTGTTGTGGTGGTGAGT
1 GAACTGGTGGAGGTGGGA-AGGAGACAGGTGGTGGAGGGGAGAGAACTGGTGGTGGTGGAGAGT
38273776 GAAC
1 GAAC
38273780 GGGAGGTTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
62 3 0.05
63 56 0.95
ACGTcount: A:0.23, C:0.05, G:0.52, T:0.20
Consensus pattern (63 bp):
GAACTGGTGGAGGTGGGAAGGAGACAGGTGGTGGAGGGGAGAGAACTGGTGGTGGTGGAGAGT
Found at i:38273782 original size:105 final size:105
Alignment explanation
Indices: 38273545--38273759 Score: 387
Period size: 105 Copynumber: 2.0 Consensus size: 105
38273535 GGTGGAGATT
38273545 GAACTGGTGGAGGTGGGAAGGAGACGGGTGGTGGAGGGGATAGAACTGGTGGTGGTGGAGATTGA
1 GAACTGGTGGAGGTGGGAAGGAGACGGGTGGTGGAGGGGATAGAACTGGTGGTGGTGGAGATTGA
*
38273610 ACTGGTGGAGGTGGGAAGGAGACGGGTGGTGGAGGGGACA
66 ACTGGTGGAGGTGGGAAGGAGACAGGTGGTGGAGGGGACA
38273650 GAACTGGTGGAGGTGGGAAGGAGACGGGTGGTGGAGGGGATAGAACTGGTGGTGGTGGAGATTGA
1 GAACTGGTGGAGGTGGGAAGGAGACGGGTGGTGGAGGGGATAGAACTGGTGGTGGTGGAGATTGA
* *
38273715 ACTGGTGGAGGT-GGAGAGTAGACAGGTGGTGGAGGGGAGA
66 ACTGGTGGAGGTGGGA-AGGAGACAGGTGGTGGAGGGGACA
38273755 GAACT
1 GAACT
38273760 TGTTGTGGTG
Statistics
Matches: 106, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
104 3 0.03
105 103 0.97
ACGTcount: A:0.24, C:0.06, G:0.54, T:0.17
Consensus pattern (105 bp):
GAACTGGTGGAGGTGGGAAGGAGACGGGTGGTGGAGGGGATAGAACTGGTGGTGGTGGAGATTGA
ACTGGTGGAGGTGGGAAGGAGACAGGTGGTGGAGGGGACA
Found at i:38280181 original size:22 final size:22
Alignment explanation
Indices: 38280154--38280202 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
38280144 TGTGATGTCA
*
38280154 CGACGTCACACACATGTCATTG
1 CGACGTCACACACATGTCAATG
*
38280176 CGACGTCACACATATGTCAATG
1 CGACGTCACACACATGTCAATG
38280198 CGACG
1 CGACG
38280203 AGTTCCGAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (22 bp):
CGACGTCACACACATGTCAATG
Found at i:38285293 original size:42 final size:42
Alignment explanation
Indices: 38285246--38285444 Score: 213
Period size: 42 Copynumber: 4.7 Consensus size: 42
38285236 GCCCAAAGGC
** * *
38285246 TGAACAGAATTTCGTAAGAGCTAAATGAAAACCCATAAGAGT
1 TGAACAGAAGCTCGTAAGAGCTAAATGGAAACTCATAAGAGT
* * *
38285288 TGAACAGAAGCTTGTAAGAGCTGAATGGAAACTCATATGAGT
1 TGAACAGAAGCTCGTAAGAGCTAAATGGAAACTCATAAGAGT
* * * *
38285330 TAAACGGAAGCTCATAAGAGCTGAACAT--AAACTCATAAGAGC
1 TGAACAGAAGCTCGTAAGAGCT-AA-ATGGAAACTCATAAGAGT
** * *
38285372 TGAACAGAAGCTCAAAAGAGCTAAACGGAAACTCATATGAGT
1 TGAACAGAAGCTCGTAAGAGCTAAATGGAAACTCATAAGAGT
* *
38285414 TAAACAGAAGCTCGTAAGAGCTAAACGGAAA
1 TGAACAGAAGCTCGTAAGAGCTAAATGGAAA
38285445 GTAAAACATG
Statistics
Matches: 130, Mismatches: 23, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
40 1 0.01
41 2 0.02
42 124 0.95
43 1 0.01
44 2 0.02
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.19
Consensus pattern (42 bp):
TGAACAGAAGCTCGTAAGAGCTAAATGGAAACTCATAAGAGT
Found at i:38285343 original size:21 final size:21
Alignment explanation
Indices: 38285260--38285444 Score: 136
Period size: 21 Copynumber: 8.8 Consensus size: 21
38285250 CAGAATTTCG
* * *
38285260 TAAGAGCTAAATGAAAACCCA
1 TAAGAGCTAAACGGAAACTCA
* * * * **
38285281 TAAGAGTTGAACAGAAGCTTG
1 TAAGAGCTAAACGGAAACTCA
* *
38285302 TAAGAGCTGAATGGAAACTCA
1 TAAGAGCTAAACGGAAACTCA
* * *
38285323 TATGAGTTAAACGGAAGCTCA
1 TAAGAGCTAAACGGAAACTCA
* **
38285344 TAAGAGCTGAACATAAACTCA
1 TAAGAGCTAAACGGAAACTCA
* * *
38285365 TAAGAGCTGAACAGAAGCTCA
1 TAAGAGCTAAACGGAAACTCA
*
38285386 AAAGAGCTAAACGGAAACTCA
1 TAAGAGCTAAACGGAAACTCA
* * * * *
38285407 TATGAGTTAAACAGAAGCTCG
1 TAAGAGCTAAACGGAAACTCA
38285428 TAAGAGCTAAACGGAAA
1 TAAGAGCTAAACGGAAA
38285445 GTAAAACATG
Statistics
Matches: 122, Mismatches: 42, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 122 1.00
ACGTcount: A:0.45, C:0.16, G:0.22, T:0.18
Consensus pattern (21 bp):
TAAGAGCTAAACGGAAACTCA
Found at i:38285402 original size:84 final size:84
Alignment explanation
Indices: 38285274--38285435 Score: 243
Period size: 84 Copynumber: 1.9 Consensus size: 84
38285264 AGCTAAATGA
* *** * * *
38285274 AAACCCATAAGAGTTGAACAGAAGCTTGTAAGAGCTGAATGGAAACTCATATGAGTTAAACGGAA
1 AAACCCATAAGAGCTGAACAGAAGCTCAAAAGAGCTAAACGGAAACTCATATGAGTTAAACAGAA
38285339 GCTCATAAGAGCTGAACAT
66 GCTCATAAGAGCTGAACAT
*
38285358 AAACTCATAAGAGCTGAACAGAAGCTCAAAAGAGCTAAACGGAAACTCATATGAGTTAAACAGAA
1 AAACCCATAAGAGCTGAACAGAAGCTCAAAAGAGCTAAACGGAAACTCATATGAGTTAAACAGAA
*
38285423 GCTCGTAAGAGCT
66 GCTCATAAGAGCT
38285436 AAACGGAAAG
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
84 69 1.00
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.19
Consensus pattern (84 bp):
AAACCCATAAGAGCTGAACAGAAGCTCAAAAGAGCTAAACGGAAACTCATATGAGTTAAACAGAA
GCTCATAAGAGCTGAACAT
Found at i:38299833 original size:15 final size:15
Alignment explanation
Indices: 38299767--38299836 Score: 52
Period size: 15 Copynumber: 4.6 Consensus size: 15
38299757 ATAGCAAGAA
* *
38299767 TTATATAAAATATTA
1 TTATATAATATATTT
*
38299782 CTACTATAA-ATATTT
1 TTA-TATAATATATTT
* * * *
38299797 ATATTTTATATTTTT
1 TTATATAATATATTT
38299812 GTTATATAATATATTT
1 -TTATATAATATATTT
38299828 TTATATAAT
1 TTATATAAT
38299837 TTGGTATTTA
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
14 3 0.07
15 23 0.55
16 16 0.38
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (15 bp):
TTATATAATATATTT
Found at i:38301026 original size:9 final size:9
Alignment explanation
Indices: 38301004--38301066 Score: 81
Period size: 9 Copynumber: 6.9 Consensus size: 9
38300994 ATTATGTAGT
*
38301004 GGTTCAATTT
1 GGTT-AATTC
38301014 GGTTAATTC
1 GGTTAATTC
38301023 GGTTAATTC
1 GGTTAATTC
* *
38301032 GGGTAATCC
1 GGTTAATTC
*
38301041 GATTAATTC
1 GGTTAATTC
38301050 GGTTAATTC
1 GGTTAATTC
38301059 GGTTAATT
1 GGTTAATT
38301067 TTTAACCAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
9 42 0.91
10 4 0.09
ACGTcount: A:0.24, C:0.11, G:0.22, T:0.43
Consensus pattern (9 bp):
GGTTAATTC
Found at i:38308327 original size:17 final size:16
Alignment explanation
Indices: 38308305--38308339 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
38308295 AATAGTAGGG
38308305 AAGGAAAAAGAAGAAAA
1 AAGGAAAAA-AAGAAAA
*
38308322 AAGGAAAAAAGGAAAA
1 AAGGAAAAAAAGAAAA
38308338 AA
1 AA
38308340 AAAACCTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
AAGGAAAAAAAGAAAA
Found at i:38308328 original size:8 final size:8
Alignment explanation
Indices: 38308305--38308339 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
38308295 AATAGTAGGG
38308305 AAGGAAAA
1 AAGGAAAA
*
38308313 AGAAGAAAA
1 A-AGGAAAA
38308322 AAGGAAAA
1 AAGGAAAA
38308330 AAGGAAAA
1 AAGGAAAA
38308338 AA
1 AA
38308340 AAAACCTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (8 bp):
AAGGAAAA
Found at i:38309217 original size:24 final size:24
Alignment explanation
Indices: 38309190--38309235 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
38309180 TAAAATTTTT
38309190 TGTGATT-AAATTATTGCTATTAAA
1 TGTGATTGAAATTATTG-TATTAAA
*
38309214 TGTGCTTGAAATTATTGTATTA
1 TGTGATTGAAATTATTGTATTA
38309236 TATATTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.33, C:0.04, G:0.15, T:0.48
Consensus pattern (24 bp):
TGTGATTGAAATTATTGTATTAAA
Found at i:38310383 original size:24 final size:23
Alignment explanation
Indices: 38310356--38310400 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
38310346 TATAAGAAAG
38310356 TTAAAATTTTAAAATTAAAAAAAT
1 TTAAAATTTTAAAA-TAAAAAAAT
*
38310380 TTAAATTTTTAAAATAAAAAA
1 TTAAAATTTTAAAATAAAAAA
38310401 TATATTAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
TTAAAATTTTAAAATAAAAAAAT
Found at i:38322097 original size:3 final size:3
Alignment explanation
Indices: 38322091--38322121 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
38322081 AAAGATGATG
38322091 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
38322122 CAAAGCTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:38324875 original size:13 final size:13
Alignment explanation
Indices: 38324857--38324884 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
38324847 CACACCTCAC
38324857 AATTTTTTGAGCT
1 AATTTTTTGAGCT
38324870 AATTTTTTGAGCT
1 AATTTTTTGAGCT
38324883 AA
1 AA
38324885 GAGAAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (13 bp):
AATTTTTTGAGCT
Found at i:38336646 original size:50 final size:50
Alignment explanation
Indices: 38336588--38336693 Score: 212
Period size: 50 Copynumber: 2.1 Consensus size: 50
38336578 TTCCATGAAT
38336588 TTTACATCTTTTTAATTTTGTCCCTAAATCATAATTTCATCAAAATTCTC
1 TTTACATCTTTTTAATTTTGTCCCTAAATCATAATTTCATCAAAATTCTC
38336638 TTTACATCTTTTTAATTTTGTCCCTAAATCATAATTTCATCAAAATTCTC
1 TTTACATCTTTTTAATTTTGTCCCTAAATCATAATTTCATCAAAATTCTC
38336688 TTTACA
1 TTTACA
38336694 AAAGTTGTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 56 1.00
ACGTcount: A:0.30, C:0.20, G:0.02, T:0.48
Consensus pattern (50 bp):
TTTACATCTTTTTAATTTTGTCCCTAAATCATAATTTCATCAAAATTCTC
Found at i:38342551 original size:24 final size:24
Alignment explanation
Indices: 38342519--38342565 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
38342509 CTAAATTTAT
*
38342519 AACACTTTCCTTTC-CTTTCTCTTC
1 AACACTTTCC-ATCACTTTCTCTTC
*
38342543 AACATTTTCCATCACTTTCTCTT
1 AACACTTTCCATCACTTTCTCTT
38342566 ATTTCCCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.17, C:0.34, G:0.00, T:0.49
Consensus pattern (24 bp):
AACACTTTCCATCACTTTCTCTTC
Found at i:38346627 original size:10 final size:10
Alignment explanation
Indices: 38346566--38346619 Score: 51
Period size: 10 Copynumber: 5.7 Consensus size: 10
38346556 AAATTAGAAA
*
38346566 AAAAAATTAT
1 AAAATATTAT
*
38346576 -AAAT-TTGT
1 AAAATATTAT
*
38346584 AAAATTTTAT
1 AAAATATTAT
*
38346594 AAAA-ATCAT
1 AAAATATTAT
38346603 AAAATATTAT
1 AAAATATTAT
38346613 AAAATAT
1 AAAATAT
38346620 ATAGAAATGT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
8 3 0.09
9 14 0.40
10 18 0.51
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (10 bp):
AAAATATTAT
Found at i:38347182 original size:16 final size:16
Alignment explanation
Indices: 38347161--38347192 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
38347151 TTTTATAATA
38347161 TTTTTTACAATTTTAT
1 TTTTTTACAATTTTAT
*
38347177 TTTTTTACTATTTTAT
1 TTTTTTACAATTTTAT
38347193 AAAAAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTTACAATTTTAT
Found at i:38347285 original size:22 final size:20
Alignment explanation
Indices: 38347260--38347414 Score: 111
Period size: 20 Copynumber: 7.6 Consensus size: 20
38347250 AAAAAATTCA
38347260 ATTTTTTTATAAATTATTTAT
1 ATTTTTTTATAAATT-TTTAT
*
38347281 GATTTTTTTAT-AATTTTTGT
1 -ATTTTTTTATAAATTTTTAT
*
38347301 GA--TTTTTATAAATTTTTTT
1 -ATTTTTTTATAAATTTTTAT
* * *
38347320 ATTTTATAATAAATTTTAAAT
1 ATTTTTTTATAAATTTT-TAT
*
38347341 ATTTTTTCTACAAATTTTT-T
1 ATTTTTT-TATAAATTTTTAT
* * **
38347361 ATATTTTTAATATATTTCCAT
1 AT-TTTTTTATAAATTTTTAT
*
38347382 AATTTTTTATAAATTTTTAAT
1 ATTTTTTTATAAATTTTT-AT
*
38347403 AATTTTTTATAA
1 ATTTTTTTATAA
38347415 CTTTATTGAT
Statistics
Matches: 105, Mismatches: 20, Indels: 17
0.74 0.14 0.12
Matches are distributed among these distances:
18 8 0.08
19 8 0.08
20 39 0.37
21 32 0.30
22 18 0.17
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.63
Consensus pattern (20 bp):
ATTTTTTTATAAATTTTTAT
Found at i:38347306 original size:18 final size:17
Alignment explanation
Indices: 38347285--38347329 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
38347275 ATTTATGATT
38347285 TTTTTATAATTTTTGTGA
1 TTTTTATAATTTTT-TGA
*
38347303 TTTTTATAAATTTTTTTA
1 TTTTTAT-AATTTTTTGA
38347321 -TTTTATAAT
1 TTTTTATAAT
38347330 AAATTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 3 0.12
17 6 0.24
18 9 0.36
19 7 0.28
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (17 bp):
TTTTTATAATTTTTTGA
Found at i:38347317 original size:11 final size:10
Alignment explanation
Indices: 38347262--38347414 Score: 66
Period size: 11 Copynumber: 15.0 Consensus size: 10
38347252 AAAATTCAAT
38347262 TTTTTTATAAA
1 TTTTTTAT-AA
* *
38347273 TTATTTATGAT
1 TTTTTTAT-AA
38347284 TTTTTTATAA
1 TTTTTTATAA
* *
38347294 -TTTTTGTGA
1 TTTTTTATAA
38347303 -TTTTTATAAA
1 TTTTTTAT-AA
38347313 TTTTTT-T-A
1 TTTTTTATAA
*
38347321 TTTTATAATAAA
1 TTTT-TTAT-AA
** *
38347333 TTTTAAATAT
1 TTTTTTATAA
*
38347343 TTTTTCTACAAA
1 TTTTT-TA-TAA
38347355 TTTTTTAT-A
1 TTTTTTATAA
*
38347364 TTTTTAAT-A
1 TTTTTTATAA
**
38347373 TATTTCCATAA
1 T-TTTTTATAA
38347384 TTTTTTATAAA
1 TTTTTTAT-AA
*
38347395 TTTTTAATAA
1 TTTTTTATAA
38347405 TTTTTTATAA
1 TTTTTTATAA
38347415 CTTTATTGAT
Statistics
Matches: 107, Mismatches: 24, Indels: 23
0.69 0.16 0.15
Matches are distributed among these distances:
8 5 0.05
9 24 0.22
10 30 0.28
11 37 0.35
12 11 0.10
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.63
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:38347373 original size:31 final size:31
Alignment explanation
Indices: 38347331--38347410 Score: 85
Period size: 31 Copynumber: 2.5 Consensus size: 31
38347321 TTTTATAATA
*
38347331 AATTTTAAATATTTTTTCTACA-AATTTTTTAT
1 AATTTTTAATATTTTTTC--CATAATTTTTTAT
*
38347363 -ATTTTTAATA-TATTTCCATAATTTTTTAT
1 AATTTTTAATATTTTTTCCATAATTTTTTAT
38347392 AAATTTTTAATAATTTTTT
1 -AATTTTTAAT-ATTTTTT
38347411 ATAACTTTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
28 2 0.05
29 10 0.25
30 5 0.12
31 18 0.45
32 1 0.03
33 4 0.10
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (31 bp):
AATTTTTAATATTTTTTCCATAATTTTTTAT
Found at i:38347410 original size:42 final size:41
Alignment explanation
Indices: 38347224--38347411 Score: 113
Period size: 42 Copynumber: 4.6 Consensus size: 41
38347214 ATACTATATA
* ** *
38347224 TTTTAT-AATTTTTATGATTTTTATAAAAAAAATTCAAT--TT
1 TTTTATAAATTTTTAT-ATTTTT-TAATAAATTTTAAATAATT
* ** *
38347264 TTTTATAAATTATTTATGATTTTTTTAT-AATTTT-TGTGA-T
1 TTTTATAAATT-TTTAT-ATTTTTTAATAAATTTTAAATAATT
* * *
38347304 TTTTATAAATTTTTTTATTTTATAATAAATTTTAAATATTT
1 TTTTATAAATTTTTATATTTTTTAATAAATTTTAAATAATT
* * **
38347345 TTTCTACAAATTTTT-TATATTTTTAATATA-TTTCCATAATT
1 TTT-TATAAATTTTTATAT-TTTTTAATAAATTTTAAATAATT
38347386 TTTTATAAATTTTTAATAATTTTTTA
1 TTTTATAAATTTTT-AT-ATTTTTTA
38347412 TAACTTTATT
Statistics
Matches: 116, Mismatches: 20, Indels: 22
0.73 0.13 0.14
Matches are distributed among these distances:
38 8 0.07
39 11 0.09
40 33 0.28
41 24 0.21
42 38 0.33
43 2 0.02
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (41 bp):
TTTTATAAATTTTTATATTTTTTAATAAATTTTAAATAATT
Found at i:38354843 original size:36 final size:36
Alignment explanation
Indices: 38354778--38354880 Score: 98
Period size: 36 Copynumber: 2.9 Consensus size: 36
38354768 GATTCTGGGT
* *
38354778 ATAGTCAGGATTTGCCCCTTGCCCAAAATTCTGCCC
1 ATAGCCAGGATTTGCCCCCTGCCCAAAATTCTGCCC
* * * *
38354814 ATAGCCAGGATTTGCCCCCTGTCCGAAATTTTGTCC
1 ATAGCCAGGATTTGCCCCCTGCCCAAAATTCTGCCC
* * * ** *
38354850 ATAACCAGAACTTGGTCCCTGCCCATAATTC
1 ATAGCCAGGATTTGCCCCCTGCCCAAAATTC
38354881 CCACCTTGTG
Statistics
Matches: 52, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.28
Consensus pattern (36 bp):
ATAGCCAGGATTTGCCCCCTGCCCAAAATTCTGCCC
Found at i:38356723 original size:9 final size:9
Alignment explanation
Indices: 38356676--38356875 Score: 57
Period size: 9 Copynumber: 20.2 Consensus size: 9
38356666 AAATAATAAA
*
38356676 ATAAAAATCA
1 ATAAAAAT-T
38356686 ATAAAAATT
1 ATAAAAATT
* *
38356695 ATTAAATTT
1 ATAAAAATT
38356704 CAATAAAAAATT
1 --AT-AAAAATT
38356716 ATAAAAATCGT
1 ATAAAAAT--T
*
38356727 AAAAAAATTAT
1 ATAAAAA-T-T
38356738 AATAAAAATT
1 -ATAAAAATT
*
38356748 ATAAAATTTT
1 ATAAAA-ATT
*
38356758 ATAAAAATC
1 ATAAAAATT
38356767 ATAAAAA-T
1 ATAAAAATT
*
38356775 ATAGAAA-T
1 ATAAAAATT
38356783 ATAGGGAAAATT
1 ATA---AAAATT
38356795 AT-AAAATT
1 ATAAAAATT
* * *
38356803 TTATAGAGTT
1 ATA-AAAATT
*
38356813 GTAAGAAAATT
1 AT-A-AAAATT
*
38356824 ATAAAGAAAT
1 ATAAA-AATT
*
38356834 ATAAAGAAAT
1 ATAAA-AATT
38356844 AT-AAAATT
1 ATAAAAATT
38356852 CATAAAAAAAATT
1 -AT---AAAAATT
38356865 ATAAAAATT
1 ATAAAAATT
38356874 AT
1 AT
38356876 TTTAACAAAA
Statistics
Matches: 145, Mismatches: 24, Indels: 43
0.68 0.11 0.20
Matches are distributed among these distances:
8 20 0.14
9 42 0.29
10 40 0.28
11 20 0.14
12 17 0.12
13 6 0.04
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.30
Consensus pattern (9 bp):
ATAAAAATT
Found at i:38356753 original size:20 final size:20
Alignment explanation
Indices: 38356730--38356777 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
38356720 AAATCGTAAA
*
38356730 AAAATTATAATAAAAATTAT
1 AAAATTATAATAAAAATCAT
*
38356750 AAAATT-TTATAAAAATCAT
1 AAAATTATAATAAAAATCAT
*
38356769 AAAAATATA
1 AAAATTATA
38356778 GAAATATAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAATTATAATAAAAATCAT
Found at i:38356838 original size:10 final size:10
Alignment explanation
Indices: 38356823--38356848 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
38356813 GTAAGAAAAT
38356823 TATAAAGAAA
1 TATAAAGAAA
38356833 TATAAAGAAA
1 TATAAAGAAA
38356843 TATAAA
1 TATAAA
38356849 ATTCATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (10 bp):
TATAAAGAAA
Found at i:38357069 original size:9 final size:9
Alignment explanation
Indices: 38357043--38357136 Score: 57
Period size: 9 Copynumber: 10.2 Consensus size: 9
38357033 TGATTAAATG
38357043 ATATTTTTT
1 ATATTTTTT
***
38357052 ATGCATTTT
1 ATATTTTTT
38357061 ATATTTTTT
1 ATATTTTTT
38357070 ATATTTTTT
1 ATATTTTTT
*
38357079 -TACTATTTT
1 ATA-TTTTTT
38357088 ATAATTTTTT
1 AT-ATTTTTT
* *
38357098 CTAATTTTTA
1 AT-ATTTTTT
**
38357108 ATAAATTTT
1 ATATTTTTT
*
38357117 AAATATTTTT
1 ATAT-TTTTT
38357127 -TATTTTTT
1 ATATTTTTT
38357135 AT
1 AT
38357137 TAAAATTTAA
Statistics
Matches: 62, Mismatches: 18, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
8 7 0.11
9 35 0.56
10 19 0.31
11 1 0.02
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (9 bp):
ATATTTTTT
Found at i:38357086 original size:27 final size:28
Alignment explanation
Indices: 38357043--38357136 Score: 97
Period size: 27 Copynumber: 3.4 Consensus size: 28
38357033 TGATTAAATG
*
38357043 ATATTTTTTATGCATTTTAT-ATTTTTT
1 ATATTTTTTATACATTTTATAATTTTTT
38357070 ATATTTTTT-TACTATTTTATAATTTTTT
1 ATATTTTTTATAC-ATTTTATAATTTTTT
* * *
38357098 CTAATTTTTAATAAATTTTA-AATATTTTT
1 AT-ATTTTTTATACATTTTATAAT-TTTTT
38357127 -TATTTTTTAT
1 ATATTTTTTAT
38357137 TAAAATTTAA
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
26 2 0.04
27 24 0.42
28 12 0.21
29 17 0.30
30 2 0.04
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (28 bp):
ATATTTTTTATACATTTTATAATTTTTT
Found at i:38357111 original size:20 final size:18
Alignment explanation
Indices: 38357065--38357107 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
38357055 CATTTTATAT
*
38357065 TTTTTAT-ATTTTTTTAC
1 TTTTTATAATTTTTTTAA
38357082 TATTTTATAATTTTTTCTAA
1 T-TTTTATAATTTTTT-TAA
38357102 TTTTTA
1 TTTTTA
38357108 ATAAATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 6 0.27
19 12 0.55
20 3 0.14
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTATAATTTTTTTAA
Found at i:38362233 original size:43 final size:43
Alignment explanation
Indices: 38362183--38362268 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 43
38362173 TCATATTTCA
38362183 TTTCTCATCTCATAATCATTTCTCATATTTGT-CATTTCAATAT
1 TTTCTCATCTCATAATCATTTCTCATATTT-TCCATTTCAATAT
* *
38362226 TTTCTCATCTCATATTCATTTCTCATCTTTTCCATTTCAATAT
1 TTTCTCATCTCATAATCATTTCTCATATTTTCCATTTCAATAT
38362269 CAATCACATA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
42 1 0.03
43 39 0.98
ACGTcount: A:0.23, C:0.23, G:0.01, T:0.52
Consensus pattern (43 bp):
TTTCTCATCTCATAATCATTTCTCATATTTTCCATTTCAATAT
Found at i:38372199 original size:20 final size:21
Alignment explanation
Indices: 38372149--38372210 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
38372139 TATAAAAAAA
* * *
38372149 TTGTTATTTTTTATTGCTTTC
1 TTGTTATTTTTTACTGTTTTG
*
38372170 TTGTTGTTTTTTACTGTTTTG
1 TTGTTATTTTTTACTGTTTTG
* *
38372191 TTGTT-TTTTTCACTATTTTG
1 TTGTTATTTTTTACTGTTTTG
38372211 CTACCTTTTC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
20 13 0.37
21 22 0.63
ACGTcount: A:0.08, C:0.08, G:0.13, T:0.71
Consensus pattern (21 bp):
TTGTTATTTTTTACTGTTTTG
Found at i:38373588 original size:31 final size:31
Alignment explanation
Indices: 38373553--38373618 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
38373543 TATTCGAAGG
38373553 CAATTTAATCTTTTTATTTTTCTAAAAAAAC
1 CAATTTAATCTTTTTATTTTTCTAAAAAAAC
38373584 CAATTTAATCTTTTTATTTTTCTAAAAAAAC
1 CAATTTAATCTTTTTATTTTTCTAAAAAAAC
38373615 CAAT
1 CAAT
38373619 AAAAATTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47
Consensus pattern (31 bp):
CAATTTAATCTTTTTATTTTTCTAAAAAAAC
Found at i:38377645 original size:11 final size:11
Alignment explanation
Indices: 38377629--38377654 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
38377619 ATTTTTTTAA
38377629 TTTTAAAATAC
1 TTTTAAAATAC
38377640 TTTTAAAATAC
1 TTTTAAAATAC
38377651 TTTT
1 TTTT
38377655 TTTAATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:38377704 original size:8 final size:9
Alignment explanation
Indices: 38377651--38377711 Score: 61
Period size: 9 Copynumber: 6.4 Consensus size: 9
38377641 TTTAAAATAC
38377651 TTTTTTTAA
1 TTTTTTTAA
38377660 TTTTTTTAA
1 TTTTTTTAA
**
38377669 -TTTTAAAA
1 TTTTTTTAA
38377677 TTTTTTTAAA
1 TTTTTTT-AA
38377687 TGCTTTTTTTAA
1 ---TTTTTTTAA
38377699 TTTTTTTAA
1 TTTTTTTAA
38377708 TTTT
1 TTTT
38377712 AAAATACTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
8 6 0.14
9 26 0.60
10 2 0.05
12 2 0.05
13 7 0.16
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:38377723 original size:40 final size:40
Alignment explanation
Indices: 38377605--38377723 Score: 181
Period size: 39 Copynumber: 3.0 Consensus size: 40
38377595 GCCCGAATAA
38377605 TAAATA-TATTTTTT-ATTTTTTTAATTTTAAAATACTTTT
1 TAAATACT-TTTTTTAATTTTTTTAATTTTAAAATACTTTT
* *
38377644 AAAATACTTTTTTTAATTTTTTTAATTTTAAAAT-TTTTT
1 TAAATACTTTTTTTAATTTTTTTAATTTTAAAATACTTTT
*
38377683 TAAATGCTTTTTTTAATTTTTTTAATTTTAAAATACTTTT
1 TAAATACTTTTTTTAATTTTTTTAATTTTAAAATACTTTT
38377723 T
1 T
38377724 TTAATTTTTA
Statistics
Matches: 72, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
39 47 0.65
40 25 0.35
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (40 bp):
TAAATACTTTTTTTAATTTTTTTAATTTTAAAATACTTTT
Found at i:38377759 original size:26 final size:27
Alignment explanation
Indices: 38377703--38377762 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 27
38377693 TTTTAATTTT
* * *
38377703 TTTAATTTTAAAATACTTTTTTTAATT
1 TTTATTTTTAAAATACATTTTTTAATA
**
38377730 TTTATTTTTAAAATA-ATTTTTTGGTA
1 TTTATTTTTAAAATACATTTTTTAATA
38377756 TTTATTT
1 TTTATTT
38377763 AAAAAACGGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 14 0.50
27 14 0.50
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (27 bp):
TTTATTTTTAAAATACATTTTTTAATA
Found at i:38377954 original size:29 final size:30
Alignment explanation
Indices: 38377915--38377971 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
38377905 GGTGGGAGAG
* *
38377915 GAGGAGAGTAAAAGTTTTGGGGGAAAGTGA
1 GAGGAGAGTAAAAGTATTAGGGGAAAGTGA
38377945 GAGG-GAGTAAAAGTATTAGGGGAAAGT
1 GAGGAGAGTAAAAGTATTAGGGGAAAGT
38377972 AAAAAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.42, T:0.19
Consensus pattern (30 bp):
GAGGAGAGTAAAAGTATTAGGGGAAAGTGA
Found at i:38380972 original size:17 final size:16
Alignment explanation
Indices: 38380940--38380981 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
38380930 AAAAATGATA
38380940 ATTTAATTTTTAATTT
1 ATTTAATTTTTAATTT
*
38380956 ATTTAACTTTTTTATTT
1 ATTTAA-TTTTTAATTT
*
38380973 AATTAATTT
1 ATTTAATTT
38380982 AATAAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTTAATTTTTAATTT
Found at i:38384702 original size:15 final size:15
Alignment explanation
Indices: 38384682--38384725 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
38384672 AGAAGATGGG
38384682 GATGCA-AAGGAAGAA
1 GATGCAGAA-GAAGAA
38384697 GATGCAGAAGAAGAA
1 GATGCAGAAGAAGAA
38384712 G-T--AGAAGAAGAA
1 GATGCAGAAGAAGAA
38384724 GA
1 GA
38384726 CGAAGAAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 11 0.41
14 1 0.04
15 13 0.48
16 2 0.07
ACGTcount: A:0.55, C:0.05, G:0.34, T:0.07
Consensus pattern (15 bp):
GATGCAGAAGAAGAA
Found at i:38384708 original size:3 final size:3
Alignment explanation
Indices: 38384691--38384734 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
38384681 GGATGCAAAG
* * * *
38384691 GAA GAA GAT GCA GAA GAA GAA GTA GAA GAA GAA GAC GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
38384735 TGAGTACGAG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.57, C:0.05, G:0.34, T:0.05
Consensus pattern (3 bp):
GAA
Found at i:38387038 original size:14 final size:13
Alignment explanation
Indices: 38387012--38387050 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
38387002 ATAATATATG
38387012 AAAAATATTATTT
1 AAAAATATTATTT
38387025 AAAAATATTAATTT
1 AAAAATATT-ATTT
38387039 ATAAAAT-TTATT
1 A-AAAATATTATT
38387051 ATTAAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.50
14 7 0.29
15 5 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAAAATATTATTT
Found at i:38387197 original size:15 final size:15
Alignment explanation
Indices: 38387151--38387199 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
38387141 TGTATGTTTA
38387151 ATAATATTGAAAATT
1 ATAATATTGAAAATT
* *
38387166 AT--T-TTTAAAA-A
1 ATAATATTGAAAATT
38387177 ATAATATTGAAAATT
1 ATAATATTGAAAATT
38387192 ATAATATT
1 ATAATATT
38387200 TTATTAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
11 2 0.08
12 6 0.23
13 2 0.08
14 6 0.23
15 10 0.38
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (15 bp):
ATAATATTGAAAATT
Found at i:38401950 original size:32 final size:32
Alignment explanation
Indices: 38401914--38401975 Score: 108
Period size: 32 Copynumber: 1.9 Consensus size: 32
38401904 TCAACACAAA
38401914 AATT-AATGATGTTAATGTTGTTAATAAAAAGG
1 AATTAAATGATG-TAATGTTGTTAATAAAAAGG
38401946 AATTAAATGATGTAATGTTGTTAATAAAAA
1 AATTAAATGATGTAATGTTGTTAATAAAAA
38401976 AGAGTATGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 22 0.76
33 7 0.24
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.37
Consensus pattern (32 bp):
AATTAAATGATGTAATGTTGTTAATAAAAAGG
Found at i:38403523 original size:32 final size:32
Alignment explanation
Indices: 38403480--38403551 Score: 128
Period size: 32 Copynumber: 2.3 Consensus size: 32
38403470 AGTTGTACTG
*
38403480 TGATAG-CAAAACTGCTATTAACATTTGAGTT
1 TGATAGACAAAACTGCCATTAACATTTGAGTT
38403511 TGATAGACAAAACTGCCATTAACATTTGAGTT
1 TGATAGACAAAACTGCCATTAACATTTGAGTT
38403543 TGATAGACA
1 TGATAGACA
38403552 CTTTATCAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
31 6 0.15
32 33 0.85
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (32 bp):
TGATAGACAAAACTGCCATTAACATTTGAGTT
Found at i:38407125 original size:14 final size:13
Alignment explanation
Indices: 38407106--38407139 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
38407096 TTTTTAAAAA
38407106 TTAAAACAAAAATT
1 TTAAAA-AAAAATT
*
38407120 TTAAAAAAATATT
1 TTAAAAAAAAATT
38407133 TTAAAAA
1 TTAAAAA
38407140 TATTTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (13 bp):
TTAAAAAAAAATT
Found at i:38407133 original size:13 final size:13
Alignment explanation
Indices: 38407106--38407149 Score: 56
Period size: 11 Copynumber: 3.5 Consensus size: 13
38407096 TTTTTAAAAA
*
38407106 TTAAAACAAAAATT
1 TTAAAA-AAATATT
38407120 TTAAAAAAATATT
1 TTAAAAAAATATT
38407133 TT--AAAAATATT
1 TTAAAAAAATATT
38407144 TTAAAA
1 TTAAAA
38407150 TTAAAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 11 0.41
13 10 0.37
14 6 0.22
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (13 bp):
TTAAAAAAATATT
Done.