Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008272.1 Hibiscus syriacus cultivar Beakdansim tig00110929_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 465257
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:4707 original size:36 final size:35
Alignment explanation
Indices: 4650--4755 Score: 203
Period size: 35 Copynumber: 3.0 Consensus size: 35
4640 ATGACACTAT
4650 ATACTTAAGCAAATGTCACATCACATATCTTTAAC
1 ATACTTAAGCAAATGTCACATCACATATCTTTAAC
4685 ATACTTAAGCAAAATGTCACATCACATATCTTTAAC
1 ATACTTAAGC-AAATGTCACATCACATATCTTTAAC
4721 ATACTTAAGCAAATGTCACATCACATATCTTTAAC
1 ATACTTAAGCAAATGTCACATCACATATCTTTAAC
4756 GAATAAATAA
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
35 35 0.50
36 35 0.50
ACGTcount: A:0.41, C:0.23, G:0.06, T:0.31
Consensus pattern (35 bp):
ATACTTAAGCAAATGTCACATCACATATCTTTAAC
Found at i:8271 original size:20 final size:20
Alignment explanation
Indices: 8246--8303 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
8236 ATCCTATTCT
**
8246 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
8266 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
*
8286 CTGATAATCTTACATTCC
1 CTGGTAATCTTACATTCC
8304 GTGAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.24, C:0.28, G:0.09, T:0.40
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:15545 original size:35 final size:35
Alignment explanation
Indices: 15488--15555 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
15478 AACAGTCCTT
* * * *
15488 AATTTCATTCTAAACTCTAAATTCCAAAATAATTC
1 AATTACATTATAAACCCCAAATTCCAAAATAATTC
15523 AATTACATTATAAACCCCAAATTCCAAAATAAT
1 AATTACATTATAAACCCCAAATTCCAAAATAAT
15556 CAAAATAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (35 bp):
AATTACATTATAAACCCCAAATTCCAAAATAATTC
Found at i:16652 original size:22 final size:21
Alignment explanation
Indices: 16627--16669 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
16617 TTTATTATAT
**
16627 ATATTTATGAATATATATAAAA
1 ATATTTAACAATATA-ATAAAA
16649 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
16670 GAAAAATACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATTTAACAATATAATAAAA
Found at i:17629 original size:28 final size:28
Alignment explanation
Indices: 17572--17629 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
17562 GCTGTTGTTT
*
17572 TCTCTGTTTTTTTTTTCGGTTCTATTTC
1 TCTCTGTTTTTTTTTTCGGTTCTATGTC
* *
17600 TCTCT-TTTTTTTTTTCTGTTTCTGTGTC
1 TCTCTGTTTTTTTTTTC-GGTTCTATGTC
17628 TC
1 TC
17630 GTTCTGTCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 11 0.42
28 15 0.58
ACGTcount: A:0.02, C:0.19, G:0.10, T:0.69
Consensus pattern (28 bp):
TCTCTGTTTTTTTTTTCGGTTCTATGTC
Found at i:18024 original size:3 final size:3
Alignment explanation
Indices: 18016--18140 Score: 178
Period size: 3 Copynumber: 41.0 Consensus size: 3
18006 TTATTTATTA
* *
18016 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAAT ACT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
**
18063 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GCT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
18111 AAT ACT AAT AAT AAT AAT ATT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
18141 GATATGGATA
Statistics
Matches: 108, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
3 102 0.94
4 6 0.06
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:18506 original size:118 final size:118
Alignment explanation
Indices: 18280--18787 Score: 809
Period size: 118 Copynumber: 4.4 Consensus size: 118
18270 ATTGAATAAA
* ** *
18280 TTCTTCTT-TTTCTTCAGAT---GAGTTCTTCTCATTATGAA--CTTTCTGCTGGGGATGATGTT
1 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTTCT-CTGGAAATGATGAT
** *
18339 CCATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
65 CCATCAAGCGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
18393 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTTCTCTGGAAATGATGATC
1 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTTCTCTGGAAATGATGATC
**
18458 CATCTGGCGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
66 CATCAAGCGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
*
18511 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTTCTCTGGAAATGTTGATC
1 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTTCTCTGGAAATGATGATC
*
18576 CATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
66 CATCAAGCGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
18629 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTCTTTCTCTGGAAATGATGATC
1 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTTCTCTGGAAATGATGATC
**
18691 CATCTGGCGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
66 CATCAAGCGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
* *
18744 TTCTTCTTCCTTTTTTAGATGACGAGTTCTTCTCATTATGAACT
1 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACT
18788 TCTTCTTCCT
Statistics
Matches: 367, Mismatches: 19, Indels: 13
0.92 0.05 0.03
Matches are distributed among these distances:
113 8 0.02
114 10 0.03
115 109 0.30
117 19 0.05
118 215 0.59
119 6 0.02
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (118 bp):
TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTTCTCTGGAAATGATGATC
CATCAAGCGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
Found at i:18811 original size:40 final size:41
Alignment explanation
Indices: 18725--18828 Score: 165
Period size: 43 Copynumber: 2.5 Consensus size: 41
18715 AGGTTGAACA
* *
18725 AGTTCTTCTCATTATGAACTTCTTCTTCCTTTTTTAGATGACG
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-A-G
18768 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-G
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAG
18808 AGTTCTTCTCATTATGAACTT
1 AGTTCTTCTCATTATGAACTT
18829 TCTCTGGAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
40 22 0.37
43 37 0.63
ACGTcount: A:0.19, C:0.22, G:0.11, T:0.48
Consensus pattern (41 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAG
Found at i:18901 original size:156 final size:154
Alignment explanation
Indices: 18610--18941 Score: 513
Period size: 156 Copynumber: 2.1 Consensus size: 154
18600 AGGTTGAACA
18610 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-CTTTC
* * *** *
18675 TCTGGAAATGATGATCCATCTGGCGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTAT
65 TCTGGAAAAGATGATCCACCAAACGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTAT
* *
18740 GAACTTCTTCTTCCTTTTTTAGATGACG
130 GAACTTCTTCTTCCTTCTTCAGAT---G
18768 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA-CTTTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTTCT
* * * *
18832 CTGGAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATG
66 CTGGAAAAGATGATCCACCAAACGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATG
18897 AACTTCTTCTTCCTTCTTCAGATG
131 AACTTCTTCTTCCTTCTTCAGATG
18921 AGTTCTTCTCATTATGAACTT
1 AGTTCTTCTCATTATGAACTT
18942 TCTCTGGAAA
Statistics
Matches: 162, Mismatches: 12, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
153 22 0.14
156 82 0.51
158 58 0.36
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (154 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTTCT
CTGGAAAAGATGATCCACCAAACGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATG
AACTTCTTCTTCCTTCTTCAGATG
Found at i:19031 original size:114 final size:114
Alignment explanation
Indices: 18770--19319 Score: 960
Period size: 114 Copynumber: 4.8 Consensus size: 114
18760 AGATGACGAG
18770 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
18835 GAAAAG-ATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAAGAATGATCCACCAAATGATGGATTCAGGCAAAAGGTTGAACAAA
18883 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * *
18948 GAAAAGAATGATCCATCAAGTGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAAGAATGATCCACCAAATGATGGATTCAGGCAAAAGGTTGAACAAA
18997 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
19062 GAAAAG-ATGATCCACCAAATGATGGATTCAGGCAAAAGGTTGAACAAG
66 GAAAAGAATGATCCACCAAATGATGGATTCAGGCAAAAGGTTGAACAAA
*
19110 TTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * * *
19175 GAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAAGTTGAACAAG
66 GAAAAGAATGATCCACCAAATGATGGATTCAGGCAAAAGGTTGAACAAA
19224 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
19289 GAAAAAAATGATCCACCAAACGATGGATTCA
66 GAAAAGAATGATCCACCAAATGATGGATTCA
19320 TCTTTGCTAA
Statistics
Matches: 417, Mismatches: 18, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
113 179 0.43
114 238 0.57
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (114 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAGAATGATCCACCAAATGATGGATTCAGGCAAAAGGTTGAACAAA
Found at i:19165 original size:227 final size:227
Alignment explanation
Indices: 18770--19319 Score: 1001
Period size: 227 Copynumber: 2.4 Consensus size: 227
18760 AGATGACGAG
18770 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
18835 GAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAAC
66 GAAAAGATGATCCACCAAATGATGGATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
18900 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGAATGATCCATC
131 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGAATGATCCATC
* * * *
18965 AAGTGATGGATTCAGGTAAAAGGTTGAACAAA
196 AAGTGATGAATTCAAGCAAAAAGTTGAACAAA
18997 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
19062 GAAAAGATGATCCACCAAATGATGGATTCAGGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
66 GAAAAGATGATCCACCAAATGATGGATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
*
19127 TTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGAATGATCCATC
131 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGAATGATCCATC
*
19192 AAGTGATGAATTCAAGCAAAAAGTTGAACAAG
196 AAGTGATGAATTCAAGCAAAAAGTTGAACAAA
19224 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
19289 GAAAAAAATGATCCACCAAACGATGGATTCA
66 G-AAAAGATGATCCACCAAATGATGGATTCA
19320 TCTTTGCTAA
Statistics
Matches: 312, Mismatches: 10, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
227 285 0.91
228 27 0.09
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (227 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAGATGATCCACCAAATGATGGATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGAATGATCCATC
AAGTGATGAATTCAAGCAAAAAGTTGAACAAA
Found at i:20031 original size:50 final size:50
Alignment explanation
Indices: 19956--20646 Score: 1274
Period size: 50 Copynumber: 13.8 Consensus size: 50
19946 CTTACGAAAC
*
19956 CAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
*
20006 CAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATTCTGTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
*
20056 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTTTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
* *
20106 TAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATTCTGTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
* *
20156 TAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATTCTGTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
20206 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
*
20256 CAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATTCTGTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
20306 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
*
20356 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTTTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
* *
20406 TAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATTCTGTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
20456 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
*
20506 CAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATTCTGTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
20556 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
20606 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
20647 GAGCACATAT
Statistics
Matches: 622, Mismatches: 19, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 622 1.00
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.27
Consensus pattern (50 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
Found at i:21572 original size:1 final size:1
Alignment explanation
Indices: 21566--21624 Score: 73
Period size: 1 Copynumber: 59.0 Consensus size: 1
21556 ACCTTGACCC
* * * * *
21566 TTTTTTTTTTTTTTTCTTTCTTTTTTTTTTCTTTTTCTTTTTTTTTTCTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
21625 CAAGCATAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (1 bp):
T
Found at i:21589 original size:17 final size:16
Alignment explanation
Indices: 21565--21624 Score: 95
Period size: 17 Copynumber: 3.8 Consensus size: 16
21555 CACCTTGACC
21565 CTTTTTTTTTTTTTTT
1 CTTTTTTTTTTTTTTT
*
21581 C-TTTCTTTTTTTTTT
1 CTTTTTTTTTTTTTTT
21596 CTTTTTCTTTTTTTTTT
1 CTTTTT-TTTTTTTTTT
21613 CTTTTTTTTTTT
1 CTTTTTTTTTTT
21625 CAAGCATAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
15 14 0.35
16 10 0.25
17 16 0.40
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (16 bp):
CTTTTTTTTTTTTTTT
Found at i:21623 original size:11 final size:11
Alignment explanation
Indices: 21566--21623 Score: 84
Period size: 11 Copynumber: 5.5 Consensus size: 11
21556 ACCTTGACCC
21566 TTTTT-TTTTT
1 TTTTTCTTTTT
*
21576 TTTTTCTTTCT
1 TTTTTCTTTTT
*
21587 TTTTT-TTTTC
1 TTTTTCTTTTT
21597 TTTTTCTTTTT
1 TTTTTCTTTTT
21608 TTTTTCTTTTT
1 TTTTTCTTTTT
21619 TTTTT
1 TTTTT
21624 TCAAGCATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
10 13 0.31
11 29 0.69
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:33893 original size:27 final size:27
Alignment explanation
Indices: 33841--33893 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
33831 GTAGCTGTTG
* *
33841 TTTCTCTGTTTTTTTTTTTTGGTTCTA
1 TTTCTCTCTTTTTTTTTTCTGGTTCTA
*
33868 TTTCTCTCTTTTTTTTTTCTGTTTCT
1 TTTCTCTCTTTTTTTTTTCTGGTTCT
33894 GTGTCTCGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.02, C:0.15, G:0.08, T:0.75
Consensus pattern (27 bp):
TTTCTCTCTTTTTTTTTTCTGGTTCTA
Found at i:33900 original size:27 final size:27
Alignment explanation
Indices: 33843--33900 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
33833 AGCTGTTGTT
* * *
33843 TCTCTGTTTTTTTTTTTTGGTTCTATT
1 TCTCTCTTTTTTTTTTCTGGTTCTATG
* *
33870 TCTCTCTTTTTTTTTTCTGTTTCTGTG
1 TCTCTCTTTTTTTTTTCTGGTTCTATG
33897 TCTC
1 TCTC
33901 GTTCTGTCTC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.02, C:0.17, G:0.10, T:0.71
Consensus pattern (27 bp):
TCTCTCTTTTTTTTTTCTGGTTCTATG
Found at i:34292 original size:3 final size:3
Alignment explanation
Indices: 34280--34335 Score: 80
Period size: 3 Copynumber: 19.3 Consensus size: 3
34270 AATTATTTAT
* *
34280 TAA T-A TAA TAA TAA T-A TAA TAA TAA TAA TAC TAA TAA TAA TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
34326 TAA TAA TAA T
1 TAA TAA TAA T
34336 GATATGGATA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
2 4 0.09
3 43 0.91
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:34346 original size:15 final size:15
Alignment explanation
Indices: 34284--34346 Score: 76
Period size: 15 Copynumber: 4.3 Consensus size: 15
34274 ATTTATTAAT
34284 ATAATAATAATAT-A
1 ATAATAATAATATGA
34298 ATAATAATAATACT-A
1 ATAATAATAATA-TGA
*
34313 ATAATAATAATATTA
1 ATAATAATAATATGA
* *
34328 ATAATAATGATATGG
1 ATAATAATAATATGA
34343 ATAA
1 ATAA
34347 AAAATTAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
14 13 0.30
15 31 0.70
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.35
Consensus pattern (15 bp):
ATAATAATAATATGA
Found at i:50412 original size:134 final size:130
Alignment explanation
Indices: 50158--50424 Score: 482
Period size: 134 Copynumber: 2.0 Consensus size: 130
50148 TCTTTTTTTC
50158 AATGGTGTCGCCTTGCTTGTGTCTATCATTGTCTAGCGTGCAATCAATTTATTATGTTTTGCAGA
1 AATGGTGTCGCCTTGCTTGTGTCTATCATTGTCTAGCGTGCAATCAATTTATTATGTTTTGCAGA
50223 TACCAGGAGTATCCTGACCGAGAACAACAGAGTTCAGATTAGGTGAAAGCTTGAATTTTGGGGTT
66 TACCAGGAGTATCCTGACCGAGAACAACAGAGTTCAGATTAGGTGAAAGCTTGAATTTTGGGGTT
50288 AATGGTGTCGCCTTGCTTGTTGTCTATCATTGTCTAGCGTGCAATCAATTTATTATAATGTTTTG
1 AATGGTGTCGCCTTGCTTG-TGTCTATCATTGTCTAGCGTGCAATCAATTTA-T-T-ATGTTTTG
50353 CAGATACCAGGAGTATCCATGACCGAGAACAACAGAGTTCAGATTAGGTG-AAGCTTGAATTTTG
62 CAGATACCAGGAGTATCC-TGACCGAGAACAACAGAGTTCAGATTAGGTGAAAGCTTGAATTTTG
50417 GGGTT
126 GGGTT
50422 AAT
1 AAT
50425 ATTCCGGCAA
Statistics
Matches: 132, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
130 19 0.14
131 32 0.24
132 1 0.01
133 1 0.01
134 48 0.36
135 31 0.23
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (130 bp):
AATGGTGTCGCCTTGCTTGTGTCTATCATTGTCTAGCGTGCAATCAATTTATTATGTTTTGCAGA
TACCAGGAGTATCCTGACCGAGAACAACAGAGTTCAGATTAGGTGAAAGCTTGAATTTTGGGGTT
Found at i:50651 original size:2 final size:2
Alignment explanation
Indices: 50644--50668 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
50634 AACTTATTCA
50644 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
50669 ATTACTCACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52291 original size:83 final size:83
Alignment explanation
Indices: 52152--52311 Score: 320
Period size: 83 Copynumber: 1.9 Consensus size: 83
52142 ATAAACAATG
52152 TTTTATAATTCATTTTATATGAATTATTAATTTTTAGGTTTAATATAAAAATAAATATTCAAACT
1 TTTTATAATTCATTTTATATGAATTATTAATTTTTAGGTTTAATATAAAAATAAATATTCAAACT
52217 TTACTCTAAATTTAAAAA
66 TTACTCTAAATTTAAAAA
52235 TTTTATAATTCATTTTATATGAATTATTAATTTTTAGGTTTAATATAAAAATAAATATTCAAACT
1 TTTTATAATTCATTTTATATGAATTATTAATTTTTAGGTTTAATATAAAAATAAATATTCAAACT
52300 TTACTCTAAATT
66 TTACTCTAAATT
52312 AATTTTAAAT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 77 1.00
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (83 bp):
TTTTATAATTCATTTTATATGAATTATTAATTTTTAGGTTTAATATAAAAATAAATATTCAAACT
TTACTCTAAATTTAAAAA
Found at i:62093 original size:16 final size:16
Alignment explanation
Indices: 62072--62104 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
62062 TAATAAATAG
62072 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
62088 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
62104 A
1 A
62105 AAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:62185 original size:10 final size:10
Alignment explanation
Indices: 62170--62244 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
62160 CATTTAATAA
62170 ATAAACGAAC
1 ATAAACGAAC
62180 ATAAACGAAC
1 ATAAACGAAC
62190 ----ACGAAC
1 ATAAACGAAC
62196 ATAAACGAAC
1 ATAAACGAAC
** *
62206 ACGAAC-ATAA
1 ATAAACGA-AC
62216 ATGAACACGAAC
1 AT-AA-ACGAAC
62228 ATAAACGAAC
1 ATAAACGAAC
62238 ATAAACG
1 ATAAACG
62245 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 35 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:62195 original size:16 final size:16
Alignment explanation
Indices: 62174--62238 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
62164 TAATAAATAA
62174 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
62190 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
62206 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
62222 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
62238 A
1 A
62239 TAAACGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:63008 original size:14 final size:14
Alignment explanation
Indices: 62991--63046 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
62981 AATGAACATA
*
62991 AACGAACATAATCG
1 AACGAACATAACCG
63005 AACGAACAT-A---
1 AACGAACATAACCG
63015 AACGAACATAACCG
1 AACGAACATAACCG
63029 AACGAACATAACCG
1 AACGAACATAACCG
63043 AACG
1 AACG
63047 TTCACGAACG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.52, C:0.25, G:0.14, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:63011 original size:24 final size:24
Alignment explanation
Indices: 62971--63045 Score: 107
Period size: 24 Copynumber: 3.1 Consensus size: 24
62961 GATTGGGTTA
*
62971 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
62995 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
* *
63019 AACATAACCGAACGAACATAACCG
1 AACATAATCGAACGAACATAAACG
63043 AAC
1 AAC
63046 GTTCACGAAC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 3 0.06
24 44 0.94
ACGTcount: A:0.55, C:0.21, G:0.12, T:0.12
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:63045 original size:10 final size:10
Alignment explanation
Indices: 62984--63031 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
62974 ATAAATGAAT
62984 GAACATAAAC
1 GAACATAAAC
62994 GAACATAATCGAAC
1 GAACAT-A---AAC
63008 GAACATAAAC
1 GAACATAAAC
*
63018 GAACATAACC
1 GAACATAAAC
63028 GAAC
1 GAAC
63032 GAACATAACC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Found at i:64345 original size:12 final size:12
Alignment explanation
Indices: 64330--64358 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
64320 CGGTGGTTTT
64330 TTCTCTTCTTTC
1 TTCTCTTCTTTC
64342 TTCTCTTCTTTC
1 TTCTCTTCTTTC
64354 TTCTC
1 TTCTC
64359 CTCGGGTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (12 bp):
TTCTCTTCTTTC
Found at i:65199 original size:4 final size:4
Alignment explanation
Indices: 65192--65236 Score: 63
Period size: 4 Copynumber: 11.2 Consensus size: 4
65182 AGAGAGAGGG
* * *
65192 GTAT GTAT GTAT GTAT GTAT GTAT GTAG GTAT GTAG GTAC GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
65237 ATGGTCATTG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.24, C:0.02, G:0.31, T:0.42
Consensus pattern (4 bp):
GTAT
Found at i:70308 original size:236 final size:236
Alignment explanation
Indices: 69895--70347 Score: 870
Period size: 236 Copynumber: 1.9 Consensus size: 236
69885 CGCGTCGCAC
69895 ACTTAATTTTGGTGATGAGTCCCCTAGCATGGATTTTTTGCATACACAAAAACTTAAATTTGAGA
1 ACTTAATTTTGGTGATGAGTCCCCTAGCATGGATTTTTTGCATACACAAAAACTTAAATTTGAGA
*
69960 TATTGCTTAAGCGGAATCAAACTGCTTACTACTTAAACCAACCCCTATTGGTACTCCCACTTGAT
66 TATTGCTTAAGCGGAATCAAACTGCTTACTACTTAAACCAACCCCTATTGATACTCCCACTTGAT
70025 ATTTATTTCATCATATAAGCTTCAATTTTATTAATTGCATATCTAACTATTTTTGGCAATTGTAA
131 ATTTATTTCATCATATAAGCTTCAATTTTATTAATTGCATATCTAACTATTTTTGGCAATTGTAA
70090 CTATCACACATTCAATGTTTCCTTTTTCGTTCCAACCCCCA
196 CTATCACACATTCAATGTTTCCTTTTTCGTTCCAACCCCCA
* *
70131 ACTTAATTTTGGTGATGAGTCCCCTAGTATGGATTTTTTGCATACACAATAACTTAAATTTGAGA
1 ACTTAATTTTGGTGATGAGTCCCCTAGCATGGATTTTTTGCATACACAAAAACTTAAATTTGAGA
70196 TATTGCTTAAGCGGAATCAAACTGCTTACTACTTAAACCAACCCCTATTGATACTCCCACTTGAT
66 TATTGCTTAAGCGGAATCAAACTGCTTACTACTTAAACCAACCCCTATTGATACTCCCACTTGAT
70261 ATTTATTTCATCATATAAGCTTCAATTTTATTAATTGCATATCTAACTATTTTTGGCAATTGTAA
131 ATTTATTTCATCATATAAGCTTCAATTTTATTAATTGCATATCTAACTATTTTTGGCAATTGTAA
*
70326 CTATCGCACATTCAATGTTTCC
196 CTATCACACATTCAATGTTTCC
70348 ATTCAATGTT
Statistics
Matches: 213, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
236 213 1.00
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (236 bp):
ACTTAATTTTGGTGATGAGTCCCCTAGCATGGATTTTTTGCATACACAAAAACTTAAATTTGAGA
TATTGCTTAAGCGGAATCAAACTGCTTACTACTTAAACCAACCCCTATTGATACTCCCACTTGAT
ATTTATTTCATCATATAAGCTTCAATTTTATTAATTGCATATCTAACTATTTTTGGCAATTGTAA
CTATCACACATTCAATGTTTCCTTTTTCGTTCCAACCCCCA
Found at i:70352 original size:13 final size:13
Alignment explanation
Indices: 70334--70360 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
70324 AACTATCGCA
70334 CATTCAATGTTTC
1 CATTCAATGTTTC
70347 CATTCAATGTTTC
1 CATTCAATGTTTC
70360 C
1 C
70361 TTTTTCGTTC
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:0.22, C:0.26, G:0.07, T:0.44
Consensus pattern (13 bp):
CATTCAATGTTTC
Found at i:70659 original size:13 final size:13
Alignment explanation
Indices: 70641--70667 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
70631 AACTATCGCA
70641 CATTCAATGTTTC
1 CATTCAATGTTTC
70654 CATTCAATGTTTC
1 CATTCAATGTTTC
70667 C
1 C
70668 TTTTTCGTTC
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:0.22, C:0.26, G:0.07, T:0.44
Consensus pattern (13 bp):
CATTCAATGTTTC
Found at i:70947 original size:308 final size:308
Alignment explanation
Indices: 70204--71128 Score: 1816
Period size: 308 Copynumber: 3.0 Consensus size: 308
70194 GATATTGCTT
*
70204 AAGCGGAATCAAACTGCTTACTACTTAAACCAACCCCTATTGATACTCCCACTTGATATTTATTT
1 AAGCGGAATCAAACTGCTTACTACTTAAACCAACCCCTATTGGTACTCCCACTTGATATTTATTT
70269 CATCATATAAGCTTCAATTTTATTAATTGCATATCTAACTATTTTTGGCAATTGTAACTATCGCA
66 CATCATATAAGCTTCAATTTTATTAATTGCATATCTAACTATTTTTGGCAATTGTAACTATCGCA
70334 CATTCAATGTTTCCATTCAATGTTTCCTTTTTCGTTCCAACCCCCAACTTAATTCAGAGAATTAT
131 CATTCAATGTTTCCATTCAATGTTTCCTTTTTCGTTCCAACCCCCAACTTAATTCAGAGAATTAT
70399 GATATTCACGTAGGGTTTCGATATCATTTTATTTTTCAAAACA-TTACTAAATTCCATTTTGGCG
196 GATATTCACGTAGGGTTTCGATATCATTTTATTTTTCAAAACATTTACTAAATTCCATTTTGGCG
70463 GCTTATTTTATCAATTAAAATATATAAATTAGCTCCCAACGTTTATTG
261 GCTTATTTTATCAATTAAAATATATAAATTAGCTCCCAACGTTTATTG
*
70511 AAGCGGAATCAAATTGCTTACTACTTAAACCAACCCCTATTGGTACTCCCACTTGATATTTATTT
1 AAGCGGAATCAAACTGCTTACTACTTAAACCAACCCCTATTGGTACTCCCACTTGATATTTATTT
70576 CATCATATAAGCTTCAATTTTATTAATTGCATATCTAACTATTTTTGGCAATTGTAACTATCGCA
66 CATCATATAAGCTTCAATTTTATTAATTGCATATCTAACTATTTTTGGCAATTGTAACTATCGCA
70641 CATTCAATGTTTCCATTCAATGTTTCCTTTTTCGTTCCAACCCCCAACTTAATTCAGAGAATTAT
131 CATTCAATGTTTCCATTCAATGTTTCCTTTTTCGTTCCAACCCCCAACTTAATTCAGAGAATTAT
70706 GATATTCACGTAGGGTTTCGATATCATTTTATTTTTCAAAACATTTACTAAATTCCATTTTGGCG
196 GATATTCACGTAGGGTTTCGATATCATTTTATTTTTCAAAACATTTACTAAATTCCATTTTGGCG
70771 GCTTATTTTATCAATTAAAATATATAAATTAGCTCCCAACGTTTATTG
261 GCTTATTTTATCAATTAAAATATATAAATTAGCTCCCAACGTTTATTG
70819 AAGCGGAATCAAACTGCTTACTACTTAAACCAACCCCTATTGGTACTCCCACTTGATATTTATTT
1 AAGCGGAATCAAACTGCTTACTACTTAAACCAACCCCTATTGGTACTCCCACTTGATATTTATTT
70884 CATCATATAAGCTTCAATTTTATTAATTGCATATCTAACTATTTTTGGCAATTGTAACTATCGCA
66 CATCATATAAGCTTCAATTTTATTAATTGCATATCTAACTATTTTTGGCAATTGTAACTATCGCA
*
70949 CATTCAATGTTTCCATTCAATGTTTCCTTTTTCGTTCCAACCCCCAACTTAATTCATAGAATTAT
131 CATTCAATGTTTCCATTCAATGTTTCCTTTTTCGTTCCAACCCCCAACTTAATTCAGAGAATTAT
71014 GATATTCACGTAGGGTTTCGATATCATTTTATTTTTCAAAACATTTACTAAATTCCATTTTGGCG
196 GATATTCACGTAGGGTTTCGATATCATTTTATTTTTCAAAACATTTACTAAATTCCATTTTGGCG
71079 GCTTATTTTATCAATTAAAATATATAAATTAGCTCCCAACGTTTATTG
261 GCTTATTTTATCAATTAAAATATATAAATTAGCTCCCAACGTTTATTG
71127 AA
1 AA
71129 ATGATCATTT
Statistics
Matches: 613, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
307 236 0.38
308 377 0.62
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (308 bp):
AAGCGGAATCAAACTGCTTACTACTTAAACCAACCCCTATTGGTACTCCCACTTGATATTTATTT
CATCATATAAGCTTCAATTTTATTAATTGCATATCTAACTATTTTTGGCAATTGTAACTATCGCA
CATTCAATGTTTCCATTCAATGTTTCCTTTTTCGTTCCAACCCCCAACTTAATTCAGAGAATTAT
GATATTCACGTAGGGTTTCGATATCATTTTATTTTTCAAAACATTTACTAAATTCCATTTTGGCG
GCTTATTTTATCAATTAAAATATATAAATTAGCTCCCAACGTTTATTG
Found at i:70967 original size:13 final size:13
Alignment explanation
Indices: 70949--70975 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
70939 AACTATCGCA
70949 CATTCAATGTTTC
1 CATTCAATGTTTC
70962 CATTCAATGTTTC
1 CATTCAATGTTTC
70975 C
1 C
70976 TTTTTCGTTC
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:0.22, C:0.26, G:0.07, T:0.44
Consensus pattern (13 bp):
CATTCAATGTTTC
Found at i:72646 original size:2 final size:2
Alignment explanation
Indices: 72639--72665 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
72629 GGATTTAGTA
72639 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
72666 CCATAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:74402 original size:32 final size:31
Alignment explanation
Indices: 74324--74406 Score: 98
Period size: 35 Copynumber: 2.6 Consensus size: 31
74314 TTAAAAATTT
*
74324 TAAAATAATCATTTTAT--TATTTAATAAAA
1 TAAAATAATCATTTTATAATATTCAATAAAA
74353 TAAAATAATCATTATTTTATAATAATTCAATAAAA
1 TAAAATAATC---ATTTTATAAT-ATTCAATAAAA
*
74388 TAAAATGATCATTTTATAA
1 TAAAATAATCATTTTATAA
74407 ATTTTAAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
29 10 0.22
32 16 0.35
34 1 0.02
35 19 0.41
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (31 bp):
TAAAATAATCATTTTATAATATTCAATAAAA
Found at i:80041 original size:2 final size:2
Alignment explanation
Indices: 80034--80067 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
80024 ATCCTAACCC
*
80034 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
80068 TTATCATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:86722 original size:51 final size:50
Alignment explanation
Indices: 86659--86779 Score: 131
Period size: 51 Copynumber: 2.4 Consensus size: 50
86649 AGTAAAGCGT
* * *
86659 ACCCCTGCACCGCGTTATACGA-TTATTTGGCGCCACATAGGGTATAGCGCG
1 ACCCCTGAACCGCGTTATACGAGTGAGTTGGCGCCACAT--GGTATAGCGCG
* * *
86710 -CCCCTTGAACCGCGCTATAC-AGTGAGTTGGCGTCACGTGGTATAGCGCG
1 ACCCC-TGAACCGCGTTATACGAGTGAGTTGGCGCCACATGGTATAGCGCG
*
86759 ACCCCTGAAGCGCGTTATACG
1 ACCCCTGAACCGCGTTATACG
86780 CCACATAAGG
Statistics
Matches: 58, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
49 24 0.41
50 9 0.16
51 25 0.43
ACGTcount: A:0.21, C:0.30, G:0.27, T:0.22
Consensus pattern (50 bp):
ACCCCTGAACCGCGTTATACGAGTGAGTTGGCGCCACATGGTATAGCGCG
Found at i:86891 original size:50 final size:51
Alignment explanation
Indices: 86816--86914 Score: 146
Period size: 50 Copynumber: 2.0 Consensus size: 51
86806 GTATTGCGCT
* * *
86816 ATACCTTTACTCCCGACATAATTTTATATAGTGCGGAACATGTACCGCGAC
1 ATACATTTACTCCCGACATAATTTTATATAGCGCGGAACAGGTACCGCGAC
* *
86867 ATACATTTACT-CTGACATAATTTTATATAGCGCGGATCAGGTACCGCG
1 ATACATTTACTCCCGACATAATTTTATATAGCGCGGAACAGGTACCGCG
86915 TTTTATATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
50 33 0.77
51 10 0.23
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.30
Consensus pattern (51 bp):
ATACATTTACTCCCGACATAATTTTATATAGCGCGGAACAGGTACCGCGAC
Found at i:91040 original size:17 final size:18
Alignment explanation
Indices: 91009--91047 Score: 71
Period size: 17 Copynumber: 2.2 Consensus size: 18
90999 AAAGGCGATG
91009 GCGGCATCATATATGGTT
1 GCGGCATCATATATGGTT
91027 GCGGCATC-TATATGGTT
1 GCGGCATCATATATGGTT
91044 GCGG
1 GCGG
91048 TGGCTGCTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.18, C:0.18, G:0.33, T:0.31
Consensus pattern (18 bp):
GCGGCATCATATATGGTT
Found at i:92809 original size:19 final size:21
Alignment explanation
Indices: 92772--92811 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
92762 ATACTTAAAA
92772 AGAGAGATTTGAGAGAAATTT
1 AGAGAGATTTGAGAGAAATTT
92793 AGAGA-ATTTGAGA-AAATTT
1 AGAGAGATTTGAGAGAAATTT
92812 GGTGTGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 8 0.42
21 5 0.26
ACGTcount: A:0.45, C:0.00, G:0.25, T:0.30
Consensus pattern (21 bp):
AGAGAGATTTGAGAGAAATTT
Found at i:93029 original size:51 final size:50
Alignment explanation
Indices: 92924--93046 Score: 156
Period size: 51 Copynumber: 2.4 Consensus size: 50
92914 AGATATACAG
* * * **
92924 GTATAGCGCGCTGCAGGGGTCGTGCTATACCCACGTGGCGCCAGCTCACC
1 GTATAGCGCGGTGCAGGGGGCGTGCTATACCCACGTGACGCCAAATCACC
* *
92974 GTATAGCGCGGTGCAGGGGGCGTGTTATACCCCACGTGACGCCAAATCATC
1 GTATAGCGCGGTGCAGGGGGCGTGCTATA-CCCACGTGACGCCAAATCACC
* *
93025 GTATAGCGCAGTGCAGGAGGCG
1 GTATAGCGCGGTGCAGGGGGCG
93047 CACTTTACTG
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
50 26 0.41
51 37 0.59
ACGTcount: A:0.20, C:0.28, G:0.34, T:0.18
Consensus pattern (50 bp):
GTATAGCGCGGTGCAGGGGGCGTGCTATACCCACGTGACGCCAAATCACC
Found at i:97054 original size:13 final size:13
Alignment explanation
Indices: 97012--97054 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
97002 TTTATATATG
*
97012 TAAAAAAATTAAA
1 TAAAATAATTAAA
97025 TAAAAT-ATTAAA
1 TAAAATAATTAAA
97037 TTAAAATAATTAAA
1 -TAAAATAATTAAA
97051 TAAA
1 TAAA
97055 TTACTAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 6 0.22
13 15 0.56
14 6 0.22
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
TAAAATAATTAAA
Found at i:97062 original size:26 final size:26
Alignment explanation
Indices: 97012--97062 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
97002 TTTATATATG
*
97012 TAAAAAAATTAAATAAAATATTAAAT
1 TAAAAAAATTAAATAAAATACTAAAT
* *
97038 TAAAATAATTAAATAAATTACTAAA
1 TAAAAAAATTAAATAAAATACTAAA
97063 AAATACTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (26 bp):
TAAAAAAATTAAATAAAATACTAAAT
Found at i:103532 original size:6 final size:6
Alignment explanation
Indices: 103523--104238 Score: 1273
Period size: 6 Copynumber: 121.5 Consensus size: 6
103513 TAATATATAG
*
103523 TACAAA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
103571 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
103619 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
103667 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
103715 TAC--A TACATA TAC--A TACATA TACATA TACATA TAC--A TAC-TA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
103756 TACATA TACATA TACATA T--ATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
103802 TACATA TACATA TACATA TACATACA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACAT--A TACATA TACATA TACATA TACATA
103852 TACATA TAC--A TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
103898 TACATA TACATA TACATA T--ATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
* *
103944 TACATA TACATA TACATA TACATA TACATA TACATA TACATA CATATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
103992 TACATA TACATA TACATA TACATA TACATA TACATA TAC--A TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
104038 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
*
104086 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TATATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
104134 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
104182 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
104230 TACATA TAC
1 TACATA TAC
104239 GAGTGTTGCT
Statistics
Matches: 687, Mismatches: 7, Indels: 32
0.95 0.01 0.04
Matches are distributed among these distances:
4 28 0.04
5 4 0.01
6 649 0.94
8 6 0.01
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
TACATA
Found at i:105442 original size:19 final size:19
Alignment explanation
Indices: 105403--105442 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
105393 GAATGATAAA
* *
105403 ATTTATTTGGCCTCTTCTT
1 ATTTATTTGGCCACTTATT
105422 ATTTATTTGGCCACTTATT
1 ATTTATTTGGCCACTTATT
105441 AT
1 AT
105443 CAATATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.17, C:0.17, G:0.10, T:0.55
Consensus pattern (19 bp):
ATTTATTTGGCCACTTATT
Found at i:107127 original size:19 final size:20
Alignment explanation
Indices: 107093--107131 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
107083 TTATCTAAAG
*
107093 TTTATGGATTAAATTAGTAT
1 TTTATGGATCAAATTAGTAT
107113 TTTATGG-TCAAATTAGTAT
1 TTTATGGATCAAATTAGTAT
107132 GTGTCTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.33, C:0.03, G:0.15, T:0.49
Consensus pattern (20 bp):
TTTATGGATCAAATTAGTAT
Found at i:116421 original size:25 final size:24
Alignment explanation
Indices: 116393--116443 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
116383 TTATAAGTGA
116393 TAAATAATTTAATTTAATTTTAAAT
1 TAAATAATTTAATTT-ATTTTAAAT
* *
116418 TAAATTATTTAATTTATTTTGAAT
1 TAAATAATTTAATTTATTTTAAAT
116442 TA
1 TA
116444 TAACAAGTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (24 bp):
TAAATAATTTAATTTATTTTAAAT
Found at i:121165 original size:38 final size:38
Alignment explanation
Indices: 121114--121198 Score: 125
Period size: 38 Copynumber: 2.2 Consensus size: 38
121104 CACTATATTC
*
121114 CTTAAATAAGGTCAAGAGTTCGAATCTTGAAATTGTAA
1 CTTAAATAAGGTCAAGAGTTCGAATCATGAAATTGTAA
* *
121152 CTTAAATAAGGTCAGGAGTTTGAATCATGAAATTGTAA
1 CTTAAATAAGGTCAAGAGTTCGAATCATGAAATTGTAA
* *
121190 ATGAAATAA
1 CTTAAATAA
121199 ACTAAATTGA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.42, C:0.08, G:0.19, T:0.31
Consensus pattern (38 bp):
CTTAAATAAGGTCAAGAGTTCGAATCATGAAATTGTAA
Found at i:125717 original size:23 final size:23
Alignment explanation
Indices: 125685--125728 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
125675 TAATTTTTTA
125685 AATTTAGTTTTTATATTAATTAT
1 AATTTAGTTTTTATATTAATTAT
*
125708 AATTTGGTTTTTATATTAATT
1 AATTTAGTTTTTATATTAATT
125729 CCAATTCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (23 bp):
AATTTAGTTTTTATATTAATTAT
Found at i:125734 original size:23 final size:23
Alignment explanation
Indices: 125685--125734 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
125675 TAATTTTTTA
*
125685 AATTTAGTTTTTATATTAATTAT
1 AATTTAGTTTTTATATTAATTAC
* *
125708 AATTTGGTTTTTATATTAATTCC
1 AATTTAGTTTTTATATTAATTAC
125731 AATT
1 AATT
125735 CTTTATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.58
Consensus pattern (23 bp):
AATTTAGTTTTTATATTAATTAC
Found at i:126287 original size:20 final size:20
Alignment explanation
Indices: 126264--126321 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
126254 CTATAGTATG
126264 TAGTATATAAATATAAAATA
1 TAGTATATAAATATAAAATA
* * **
126284 TAGTTTATATATATAGTATA
1 TAGTATATAAATATAAAATA
126304 TAGTATATAATATATAAA
1 TAGTATATAA-ATATAAA
126322 TAGTTTATAT
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 24 0.83
21 5 0.17
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (20 bp):
TAGTATATAAATATAAAATA
Found at i:126310 original size:40 final size:38
Alignment explanation
Indices: 126255--126332 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 38
126245 TATTTTCAAC
*
126255 TATAGTATGTAGTATATAAATATAAAATATAGTTTATATA
1 TATAGTATATAGTATAT-AATATAAAA-ATAGTTTATATA
*
126295 TATAGTATATAGTATATAATATATAAATAGTTTATATA
1 TATAGTATATAGTATATAATATAAAAATAGTTTATATA
126333 GTTCACTAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 12 0.33
39 8 0.22
40 16 0.44
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (38 bp):
TATAGTATATAGTATATAATATAAAAATAGTTTATATA
Found at i:126330 original size:20 final size:20
Alignment explanation
Indices: 126267--126332 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 20
126257 TAGTATGTAG
*
126267 TATATAAATATAAAATATAGTT
1 TATAT-AATATATAA-ATAGTT
*
126289 TATAT-ATATAGTATATAG--
1 TATATAATATA-TAAATAGTT
126307 TATATAATATATAAATAGTT
1 TATATAATATATAAATAGTT
126327 TATATA
1 TATATA
126333 GTTCACTAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
18 11 0.30
19 5 0.14
20 15 0.41
21 1 0.03
22 5 0.14
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (20 bp):
TATATAATATATAAATAGTT
Found at i:126438 original size:7 final size:7
Alignment explanation
Indices: 126426--126617 Score: 53
Period size: 7 Copynumber: 27.0 Consensus size: 7
126416 ATATGTAAAC
126426 TATATAA
1 TATATAA
126433 TATATATA
1 TATATA-A
126441 GTATATAA
1 -TATATAA
126449 -ATATCAA
1 TATAT-AA
* *
126456 -CTATAG
1 TATATAA
* *
126462 TATGTAG
1 TATATAA
126469 TATATAA
1 TATATAA
126476 -ATATAA
1 TATATAA
126482 -ATTATAGTA
1 TA-TATA--A
*
126491 TATATAG
1 TATATAA
* *
126498 TATGTAG
1 TATATAA
126505 TATATAA
1 TATATAA
126512 -ATATCAA
1 TATAT-AA
126519 CTATATATA
1 -TATATA-A
126528 TATATATA
1 TATATA-A
*
126536 GTATGTAA
1 -TATATAA
126544 -ATATCAA
1 TATAT-AA
* *
126551 -CTATAG
1 TATATAA
* *
126557 TATGTAG
1 TATATAA
126564 TATATAA
1 TATATAA
126571 -ATATAA
1 TATATAA
*
126577 -ACTATAG
1 TA-TATAA
*
126584 TTTAT-A
1 TATATAA
126590 TATATAA
1 TATATAA
*
126597 TATATAG
1 TATATAA
*
126604 TATATAC
1 TATATAA
126611 TATATAA
1 TATATAA
126618 ATAGTTTATA
Statistics
Matches: 142, Mismatches: 25, Indels: 36
0.70 0.12 0.18
Matches are distributed among these distances:
6 31 0.22
7 77 0.54
8 12 0.08
9 21 0.15
10 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (7 bp):
TATATAA
Found at i:126473 original size:36 final size:35
Alignment explanation
Indices: 126432--126569 Score: 138
Period size: 32 Copynumber: 4.2 Consensus size: 35
126422 AAACTATATA
126432 ATATATATAGTATATAAATATCAACTATAGTATGT
1 ATATATATAGTATATAAATATCAACTATAGTATGT
*
126467 AGTATATA-A--ATAT-AA-AT----TATAGTATAT
1 A-TATATATAGTATATAAATATCAACTATAGTATGT
*
126494 ATAGTATGTAGTATATAAATATCAACTATA-TA--T
1 ATA-TATATAGTATATAAATATCAACTATAGTATGT
*
126527 ATATATATAGTATGTAAATATCAACTATAGTATGT
1 ATATATATAGTATATAAATATCAACTATAGTATGT
126562 AGTATATA
1 A-TATATA
126570 AATATAAACT
Statistics
Matches: 84, Mismatches: 4, Indels: 29
0.72 0.03 0.25
Matches are distributed among these distances:
26 2 0.02
27 13 0.15
28 1 0.01
30 4 0.05
31 4 0.05
32 28 0.33
33 10 0.12
35 6 0.07
36 16 0.19
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.40
Consensus pattern (35 bp):
ATATATATAGTATATAAATATCAACTATAGTATGT
Found at i:126525 original size:15 final size:15
Alignment explanation
Indices: 126505--126555 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
126495 TAGTATGTAG
126505 TATATAAATATCAAC
1 TATATAAATATCAAC
*
126520 TATATATATATAT-ATAG
1 TATATA-A-ATATCA-AC
*
126537 TATGTAAATATCAAC
1 TATATAAATATCAAC
126552 TATA
1 TATA
126556 GTATGTAGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
15 14 0.50
16 4 0.14
17 10 0.36
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (15 bp):
TATATAAATATCAAC
Found at i:126584 original size:20 final size:19
Alignment explanation
Indices: 126466--126620 Score: 81
Period size: 20 Copynumber: 8.0 Consensus size: 19
126456 CTATAGTATG
126466 TAGTATATAAATATAAATTA
1 TAGTATATAAATATAAA-TA
*
126486 TAGTATAT--ATAGT--ATG
1 TAGTATATAAATA-TAAATA
*
126502 TAGTATATAAATATCAACTA
1 TAGTATATAAATAT-AAATA
* *
126522 TA-TATATATATAT-AGTA
1 TAGTATATAAATATAAATA
* * *
126539 T-GTAAATATCAACTATAGTATG
1 TAGT--ATAT-AAATATA-AATA
126561 TAGTATATAAATATAAACTA
1 TAGTATATAAATATAAA-TA
* *
126581 TAGTTTATATATATAATATA
1 TAGTATATAAATATAA-ATA
*
126601 TAGTATATACTATATAAATA
1 TAGTATATA-AATATAAATA
126621 GTTTATATAA
Statistics
Matches: 103, Mismatches: 16, Indels: 32
0.68 0.11 0.21
Matches are distributed among these distances:
16 9 0.09
17 7 0.07
18 6 0.06
19 16 0.16
20 49 0.48
21 12 0.12
22 2 0.02
23 2 0.02
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.41
Consensus pattern (19 bp):
TAGTATATAAATATAAATA
Found at i:126695 original size:24 final size:24
Alignment explanation
Indices: 126668--126719 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
126658 ATATGTAAAC
*
126668 TATATAGTTTACATAGTTTATATA
1 TATATAGTTTACATAGTTTATACA
*
126692 TATATAGTTTATATAGTTTATACA
1 TATATAGTTTACATAGTTTATACA
126716 TATA
1 TATA
126720 GTTCATATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
TATATAGTTTACATAGTTTATACA
Found at i:126704 original size:9 final size:9
Alignment explanation
Indices: 126668--126713 Score: 62
Period size: 9 Copynumber: 5.4 Consensus size: 9
126658 ATATGTAAAC
126668 TATATAGTT
1 TATATAGTT
*
126677 TACATAGTT
1 TATATAGTT
126686 TATATA---
1 TATATAGTT
126692 TATATAGTT
1 TATATAGTT
126701 TATATAGTT
1 TATATAGTT
126710 TATA
1 TATA
126714 CATATAGTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 6 0.19
9 26 0.81
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.52
Consensus pattern (9 bp):
TATATAGTT
Found at i:126900 original size:22 final size:22
Alignment explanation
Indices: 126882--126923 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
126872 ACCATATATA
126882 CTATA-TATATAAACTATATAGT
1 CTATATTA-ATAAACTATATAGT
*
126904 TTATATTAATAAACTATATA
1 CTATATTAATAAACTATATA
126924 ATTTATACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (22 bp):
CTATATTAATAAACTATATAGT
Found at i:127045 original size:19 final size:20
Alignment explanation
Indices: 127021--127072 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
127011 ATAAACTATG
* *
127021 TAGTTTCTATATAGTAT-TA
1 TAGTTTATACATAGTATATA
*
127040 TAGTTTATACATGGTATATA
1 TAGTTTATACATAGTATATA
127060 TAGTTTATACATA
1 TAGTTTATACATA
127073 TAAATTGTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.48
Consensus pattern (20 bp):
TAGTTTATACATAGTATATA
Found at i:127063 original size:20 final size:19
Alignment explanation
Indices: 127034--127071 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
127024 TTTCTATATA
127034 GTATTATAGTTTATACATG
1 GTATTATAGTTTATACATG
127053 GTATATATAGTTTATACAT
1 GTAT-TATAGTTTATACAT
127072 ATAAATTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.47
Consensus pattern (19 bp):
GTATTATAGTTTATACATG
Found at i:127068 original size:11 final size:11
Alignment explanation
Indices: 127021--127126 Score: 55
Period size: 11 Copynumber: 10.2 Consensus size: 11
127011 ATAAACTATG
*
127021 TAGTTTCTATA
1 TAGTTTATATA
127032 TAG--TAT-TA
1 TAGTTTATATA
*
127040 TAGTTTATACA
1 TAGTTTATATA
*
127051 T-G-GTATATA
1 TAGTTTATATA
*
127060 TAGTTTATACA
1 TAGTTTATATA
** *
127071 TA-TAAATTGTA
1 TAGTTTA-TATA
*
127082 GAGTTTATATA
1 TAGTTTATATA
* *
127093 TAATTCATATA
1 TAGTTTATATA
127104 TAGTTTATATA
1 TAGTTTATATA
*
127115 TA-TATATATA
1 TAGTTTATATA
127125 TA
1 TA
127127 TTAGTTGTTT
Statistics
Matches: 68, Mismatches: 20, Indels: 15
0.66 0.19 0.15
Matches are distributed among these distances:
8 5 0.07
9 8 0.12
10 16 0.24
11 37 0.54
12 2 0.03
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (11 bp):
TAGTTTATATA
Found at i:127108 original size:22 final size:21
Alignment explanation
Indices: 127021--127126 Score: 78
Period size: 22 Copynumber: 5.1 Consensus size: 21
127011 ATAAACTATG
*
127021 TAGTTTCTATAT-AGTAT-TA
1 TAGTTTATATATAAGTATATA
* *
127040 TAGTTTATACAT-GGTATATA
1 TAGTTTATATATAAGTATATA
* *
127060 TAGTTTATACATATAAAT-TGTA
1 TAGTTTAT--ATATAAGTATATA
* *
127082 GAGTTTATATATAATTCATATA
1 TAGTTTATATATAAGT-ATATA
127104 TAGTTTATATATATA-TATATA
1 TAGTTTATATATA-AGTATATA
127125 TA
1 TA
127127 TTAGTTGTTT
Statistics
Matches: 69, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
19 14 0.20
20 17 0.25
21 7 0.10
22 29 0.42
23 2 0.03
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (21 bp):
TAGTTTATATATAAGTATATA
Found at i:127444 original size:139 final size:141
Alignment explanation
Indices: 127213--127486 Score: 471
Period size: 140 Copynumber: 2.0 Consensus size: 141
127203 ATCCTTTGTG
127213 TTGTTTAATTTATTTAAATTTTTATTTATAATTTCATATTTTTTCAATTTAGTCCTCCAAATTTT
1 TTGTTTAATTTATTTAAATTTTTATTTATAATTTCATATTTTTTCAATTTAGTCCTCCAAATTTT
*
127278 ATTTACATCTAAAATTGACCCATACTTATTACTTATTTCT-TTTTTTAATTGGCCCATAACTTTT
66 ATTTACATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGACCCATAACTTTT
127342 TAAATGAGTAT
131 TAAATGAGTAT
* *
127353 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTTATA-TTTTTCAATTTAGTCCTCCAAATTTT
1 TTGTTTAATTTATTTAAATTTTTATTTATAATTTCATATTTTTTCAATTTAGTCCTCCAAATTTT
** * *
127417 ATTTGTATCTGAAATTGACTCATACTTATTACTTATTTCTATTTTTTAATTGACCCATAACTTTT
66 ATTTACATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGACCCATAACTTTT
127482 TAAAT
131 TAAAT
127487 AGATATAATT
Statistics
Matches: 126, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
139 62 0.49
140 64 0.51
ACGTcount: A:0.29, C:0.12, G:0.05, T:0.54
Consensus pattern (141 bp):
TTGTTTAATTTATTTAAATTTTTATTTATAATTTCATATTTTTTCAATTTAGTCCTCCAAATTTT
ATTTACATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGACCCATAACTTTT
TAAATGAGTAT
Found at i:127668 original size:217 final size:216
Alignment explanation
Indices: 127357--127837 Score: 777
Period size: 217 Copynumber: 2.2 Consensus size: 216
127347 GAGTATTTGT
* * *
127357 TTAATTTATTTAAATTTTTATTTGTAATTTTATATTT-TTCAATTTAGTCCTCCAAATTTTATTT
1 TTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAATCCTCCAAAGTTTATTT
* * * *
127421 GTATCTGAAATTGACTCATACTTATTACTTATTTCTATTTTTTAATTGACCCATAACTTTTTAAA
66 GCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGACCCATAACTTTCTAAA
* * **
127486 TAGATATAATTTAGTACTTTTTTTTATTAATTTCAACCTGTCAATTTAAAATTATTTCGATTTGA
131 TAGATATAATTTAGTACTTGTTTATATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGA
127551 TCCCTCATCAATGTGTGTTGC
196 TCCCTCATCAATGTGTGTTGC
*
127572 TTAATTTATTTAAATTTTTATTT-TAAATTTCATATTTGTTCAATTTAATCCTCCAAAGTTTGTT
1 TTAATTTATTTAAATTTTTATTTGT-AATTTCATATTTGTTCAATTTAATCCTCCAAAGTTTATT
*
127636 TGCATCTAAAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGACTCATAACTTTCTA
65 TGCATCT-AAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGACCCATAACTTTCTA
*
127701 AATAGGTATAATTTAGTACTTGTTTATATTAATTTCAACCTCACAATTTAAAATTATTTCGATTT
129 AATAGATATAATTTAGTACTTGTTTATATTAATTTCAACCTCACAATTTAAAATTATTTCGATTT
* *
127766 GATCCCTCTTCAATGTGTGTTGT
194 GATCCCTCATCAATGTGTGTTGC
*
127789 TTAATTTATTTAAATTTTTATTTGTAATTCCATATTTGTTCAATTTAAT
1 TTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAAT
127838 TCTTAAATTT
Statistics
Matches: 245, Mismatches: 17, Indels: 6
0.91 0.06 0.02
Matches are distributed among these distances:
214 1 0.00
215 34 0.14
216 29 0.12
217 180 0.73
218 1 0.00
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.51
Consensus pattern (216 bp):
TTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAATCCTCCAAAGTTTATTT
GCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGACCCATAACTTTCTAAA
TAGATATAATTTAGTACTTGTTTATATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGA
TCCCTCATCAATGTGTGTTGC
Found at i:128847 original size:24 final size:24
Alignment explanation
Indices: 128834--128952 Score: 177
Period size: 24 Copynumber: 5.0 Consensus size: 24
128824 AAACATAATT
* *
128834 CATGTCAAGTATCATATCAAAATC
1 CATGTCAAGTATCAGATCAGAATC
* *
128858 CAAGTCAAGTATCAGATCAGAATT
1 CATGTCAAGTATCAGATCAGAATC
*
128882 CAAGTCAAGTATCAGATCAGAATC
1 CATGTCAAGTATCAGATCAGAATC
128906 CATGTC-AGATATCAGATCAGAATC
1 CATGTCAAG-TATCAGATCAGAATC
128930 CATGTCAAGTATCAGATCAGAAT
1 CATGTCAAGTATCAGATCAGAAT
128953 TCAAATCGAA
Statistics
Matches: 87, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
23 2 0.02
24 83 0.95
25 2 0.02
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.25
Consensus pattern (24 bp):
CATGTCAAGTATCAGATCAGAATC
Found at i:128968 original size:48 final size:47
Alignment explanation
Indices: 128834--128970 Score: 175
Period size: 48 Copynumber: 2.9 Consensus size: 47
128824 AAACATAATT
* * *
128834 CATGTCAAGTATCATATCAAAATCCAAGTCAAGTATCAGATCAGAATT
1 CATGTCAAGTATCAGATCAGAATCCAAGTCAA-TATCAGATCAGAATC
* *
128882 CAAGTCAAGTATCAGATCAGAATCCATGTCAGATATCAGATCAGAATC
1 CATGTCAAGTATCAGATCAGAATCCAAGTCA-ATATCAGATCAGAATC
* * *
128930 CATGTCAAGTATCAGATCAGAATTCAAATCGAAAATCAGAT
1 CATGTCAAGTATCAGATCAGAATCCAAGTC-AATATCAGAT
128971 AAAATATTCA
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
48 75 0.97
49 2 0.03
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.25
Consensus pattern (47 bp):
CATGTCAAGTATCAGATCAGAATCCAAGTCAATATCAGATCAGAATC
Found at i:128968 original size:72 final size:72
Alignment explanation
Indices: 128834--128970 Score: 197
Period size: 72 Copynumber: 1.9 Consensus size: 72
128824 AAACATAATT
* * *
128834 CATGTCAAGTATCATATCAAAATCCAAGTCAAGTATCAGATCAGAATTCAAGTCAAGTATCAGAT
1 CATGTCAAGTATCAGATCAAAATCCAAGTCAAGTATCAGATCAGAATTCAAATCAAGAATCAGAT
128899 CAGAATC
66 CAGAATC
* *
128906 CATGTC-AGATATCAGATCAGAATCCATGTCAAGTATCAGATCAGAATTCAAATCGAA-AATCAG
1 CATGTCAAG-TATCAGATCAAAATCCAAGTCAAGTATCAGATCAGAATTCAAATC-AAGAATCAG
128969 AT
64 AT
128971 AAAATATTCA
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
71 2 0.03
72 54 0.93
73 2 0.03
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.25
Consensus pattern (72 bp):
CATGTCAAGTATCAGATCAAAATCCAAGTCAAGTATCAGATCAGAATTCAAATCAAGAATCAGAT
CAGAATC
Found at i:131358 original size:13 final size:13
Alignment explanation
Indices: 131316--131345 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
131306 GGTCAACGCA
*
131316 GGTCAACGGGTCG
1 GGTCAACGGATCG
131329 GGTCAACGGATCG
1 GGTCAACGGATCG
131342 GGTC
1 GGTC
131346 GGGTCAACGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (13 bp):
GGTCAACGGATCG
Found at i:144765 original size:37 final size:36
Alignment explanation
Indices: 144702--144821 Score: 163
Period size: 35 Copynumber: 3.3 Consensus size: 36
144692 ATCCCATTAT
* *
144702 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
* * *
144738 TATTTTTCAAAGAAATATTTACCAAACTTTGAAATC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
144774 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
144809 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
144822 TTGGTTACCA
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
35 33 0.45
36 12 0.16
37 28 0.38
ACGTcount: A:0.42, C:0.19, G:0.05, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:148906 original size:16 final size:16
Alignment explanation
Indices: 148882--148915 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
148872 TATCGCCGAC
*
148882 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
148898 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
148914 CG
1 CG
148916 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:149369 original size:37 final size:36
Alignment explanation
Indices: 149310--149428 Score: 170
Period size: 35 Copynumber: 3.3 Consensus size: 36
149300 ATCCCATTAT
* *
149310 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAAAAACATTTACCAAACTTTG-AAAAC
*
149346 TATTTTTCAAAAAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAAAAACATTTACCAAACTTTGAAAAC
*
149382 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAAAAACATTTACCAAACTTTGAAAAC
149417 CATTTTTTCAAA
1 CA-TTTTTCAAA
149429 GTTGGTTACC
Statistics
Matches: 75, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 34 0.45
36 13 0.17
37 28 0.37
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAAAAACATTTACCAAACTTTGAAAAC
Found at i:149385 original size:21 final size:21
Alignment explanation
Indices: 149356--149421 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 21
149346 TATTTTTCAA
*
149356 AAAAACATTTACCAAACTTTG
1 AAAACCATTTACCAAACTTTG
*
149377 AAAACCATTT-TCAAA----G
1 AAAACCATTTACCAAACTTTG
149393 -AAA-CATTTACCAAACTTTG
1 AAAACCATTTACCAAACTTTG
149412 AAAACCATTT
1 AAAACCATTT
149422 TTTCAAAGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 14
0.67 0.06 0.27
Matches are distributed among these distances:
14 5 0.14
15 7 0.20
16 1 0.03
19 1 0.03
20 7 0.20
21 14 0.40
ACGTcount: A:0.47, C:0.20, G:0.05, T:0.29
Consensus pattern (21 bp):
AAAACCATTTACCAAACTTTG
Found at i:149438 original size:35 final size:36
Alignment explanation
Indices: 149312--149456 Score: 133
Period size: 35 Copynumber: 4.1 Consensus size: 36
149302 CCCATTATCA
*
149312 TTTTTCAACA-AACA-TCTACCAAACTTTGAAAAAC-T
1 TTTTTCAA-AGAACAGT-TACCAAACTTTGAAAACCAT
* *
149347 ATTTTTCAAAAAAACATTTACCAAACTTTGAAAACCA-
1 -TTTTTC-AAAGAACAGTTACCAAACTTTGAAAACCAT
*
149384 -TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
1 TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
***
149420 TTTTTCAAAG-TTGGTTACCAAAC-TTGAAAACCAT
1 TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
149454 TTT
1 TTT
149457 AATAATTTCA
Statistics
Matches: 96, Mismatches: 6, Indels: 16
0.81 0.05 0.14
Matches are distributed among these distances:
34 17 0.18
35 39 0.41
36 7 0.07
37 32 0.33
38 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (36 bp):
TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
Found at i:153186 original size:25 final size:24
Alignment explanation
Indices: 153152--153198 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
153142 TTTCAAAAAA
*
153152 AATTATATTTAAAACTTTTTTTTG
1 AATTATATTTAAAACTTATTTTTG
153176 AATTGATATTTAAAACTTATTTT
1 AATT-ATATTTAAAACTTATTTT
153199 GATTTCTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.55
Consensus pattern (24 bp):
AATTATATTTAAAACTTATTTTTG
Found at i:153198 original size:24 final size:24
Alignment explanation
Indices: 153152--153200 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
153142 TTTCAAAAAA
*
153152 AATTATATTTAAAACTTTTTTTTG
1 AATTATATTTAAAACTTTATTTTG
153176 AATTGATATTTAAAAC-TTATTTTG
1 AATT-ATATTTAAAACTTTATTTTG
153200 A
1 A
153201 TTTCTCTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.53
Consensus pattern (24 bp):
AATTATATTTAAAACTTTATTTTG
Found at i:153375 original size:29 final size:29
Alignment explanation
Indices: 153333--153391 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
153323 CTAAAATCTT
153333 AGCACAAAATATTAGATGAATGCGGTAAC
1 AGCACAAAATATTAGATGAATGCGGTAAC
153362 AGCACAAAATATTAGATGAATGCGGTAAC
1 AGCACAAAATATTAGATGAATGCGGTAAC
153391 A
1 A
153392 ACGCAAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.46, C:0.14, G:0.20, T:0.20
Consensus pattern (29 bp):
AGCACAAAATATTAGATGAATGCGGTAAC
Found at i:153398 original size:29 final size:29
Alignment explanation
Indices: 153335--153399 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
153325 AAAATCTTAG
*
153335 CACAAAATATTAGATGAATGCGGTAACAG
1 CACAAAATATTAGATGAATGCGGTAACAA
153364 CACAAAATATTAGATGAATGCGGTAACAA
1 CACAAAATATTAGATGAATGCGGTAACAA
*
153393 CGCAAAA
1 CACAAAA
153400 GAAAGGGAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.48, C:0.15, G:0.18, T:0.18
Consensus pattern (29 bp):
CACAAAATATTAGATGAATGCGGTAACAA
Found at i:158435 original size:31 final size:31
Alignment explanation
Indices: 158399--158463 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
158389 TTATCTTCTT
*
158399 AAAATTTTATAAGTTCATATCGTCTAGAATA
1 AAAATTTTATAAGTTCATATCGCCTAGAATA
* * *
158430 AAAATTTTATAAGTTTATCTCGCCTAGGATA
1 AAAATTTTATAAGTTCATATCGCCTAGAATA
158461 AAA
1 AAA
158464 TTATGCATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (31 bp):
AAAATTTTATAAGTTCATATCGCCTAGAATA
Found at i:158657 original size:59 final size:60
Alignment explanation
Indices: 158594--158706 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
158584 TAAACAAATT
* * * * *
158594 ATCCCCT-ATTATGGGGCGTTGTTTTATTGAGTCTCTCGACTAAT-AAAAGTTACGAAACA
1 ATCCCCTGATTATGAGACATTGCTTTATTGAGTC-CCCGACTAATAAAAAGTTACGAAACA
* *
158653 ATCCCCTGATTATGAGACATTGCTTTGTTGAGTCCCCGACTATTAAAAAGTTAC
1 ATCCCCTGATTATGAGACATTGCTTTATTGAGTCCCCGACTAATAAAAAGTTAC
158707 AAATGGCTAC
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
59 15 0.33
60 30 0.67
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (60 bp):
ATCCCCTGATTATGAGACATTGCTTTATTGAGTCCCCGACTAATAAAAAGTTACGAAACA
Found at i:159002 original size:31 final size:31
Alignment explanation
Indices: 158955--159032 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
158945 TTTAACAGTG
* *
158955 GAGAGTCTTAACAAAGCAATGTCCTATAGTC
1 GAGAGACTCAACAAAGCAATGTCCTATAGTC
*
158986 GAGGGACTCAACAAAGCAATGTCCTATAGTC
1 GAGAGACTCAACAAAGCAATGTCCTATAGTC
159017 GAGAGACTCAACAAAG
1 GAGAGACTCAACAAAG
159033 TAAAATCCTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.19
Consensus pattern (31 bp):
GAGAGACTCAACAAAGCAATGTCCTATAGTC
Found at i:159042 original size:31 final size:31
Alignment explanation
Indices: 158955--159044 Score: 108
Period size: 31 Copynumber: 2.9 Consensus size: 31
158945 TTTAACAGTG
* * **
158955 GAGAGTCTTAACAAAGCAATGTCCTATAGTC
1 GAGAGACTCAACAAAGCAAAATCCTATAGTC
* **
158986 GAGGGACTCAACAAAGCAATGTCCTATAGTC
1 GAGAGACTCAACAAAGCAAAATCCTATAGTC
*
159017 GAGAGACTCAACAAAGTAAAATCCTATA
1 GAGAGACTCAACAAAGCAAAATCCTATA
159045 ATCAATGATC
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (31 bp):
GAGAGACTCAACAAAGCAAAATCCTATAGTC
Found at i:167754 original size:60 final size:60
Alignment explanation
Indices: 167651--167793 Score: 162
Period size: 60 Copynumber: 2.4 Consensus size: 60
167641 ATATGTATAG
** * * * * *
167651 TTTA-GGATGAAATTGGAATGTTCAAAAAGTTTGGGGACCAATTTATAATGAAAGTCATAG
1 TTTAGGGATGAAATTAAAATATTC-AAATGTTTGAGGACCAATTTAAAATGAAAGTCATAA
* * * * *
167711 TTTGGGGTTGAAATTAAAATATTCAAATGTTTGAGGACTAATTTAAAATGATATTCATAA
1 TTTAGGGATGAAATTAAAATATTCAAATGTTTGAGGACCAATTTAAAATGAAAGTCATAA
167771 TTTAGGGATGAAATTAAAATATT
1 TTTAGGGATGAAATTAAAATATT
167794 TTTATGAATC
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
60 53 0.78
61 15 0.22
ACGTcount: A:0.40, C:0.05, G:0.20, T:0.36
Consensus pattern (60 bp):
TTTAGGGATGAAATTAAAATATTCAAATGTTTGAGGACCAATTTAAAATGAAAGTCATAA
Found at i:172562 original size:65 final size:63
Alignment explanation
Indices: 172493--172675 Score: 208
Period size: 65 Copynumber: 2.8 Consensus size: 63
172483 AATTAAATTG
* *
172493 AACATCGAATACATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACAT-CCATGCACCGATGCACTGAGGATATTT-T-A
172557 A
63 A
* * * ** *
172558 AACATCGAATGCATTTGATGCATCGATGCACCAGCCATCCATCGATGCACTCTGGCTATTTTAA
1 AACATCGAATGCATTTGATGCATCGATGCA-CATCCATGCACCGATGCACTGAGGATATTTTAA
* *
172622 AACATCGAATGCACTTGATGCATCGATGCAC-TCTTAGTGCACCGATGCACTGAG
1 AACATCGAATGCATTTGATGCATCGATGCACATC-CA-TGCACCGATGCACTGAG
172676 AGTCCAACGG
Statistics
Matches: 99, Mismatches: 15, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 44 0.44
65 47 0.47
66 5 0.05
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACATCCATGCACCGATGCACTGAGGATATTTTAA
Found at i:172652 original size:17 final size:19
Alignment explanation
Indices: 172624--172672 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
172614 TATTTTAAAA
172624 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
172642 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
172661 CACCGATGCACT
1 CATCGATGCACT
172673 GAGAGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:174206 original size:6 final size:6
Alignment explanation
Indices: 174191--174223 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
174181 GAGTGATTTG
*
174191 GATGAA GATGAC GATGAC GATGAC GATGA- GATG
1 GATGAC GATGAC GATGAC GATGAC GATGAC GATG
174224 GCATTGTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.36, C:0.09, G:0.36, T:0.18
Consensus pattern (6 bp):
GATGAC
Found at i:176489 original size:15 final size:15
Alignment explanation
Indices: 176465--176499 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
176455 ATCAAAGGAA
*
176465 GAAACGAAAAATGAG
1 GAAACAAAAAATGAG
176480 GAAACAAAAAATGAG
1 GAAACAAAAAATGAG
176495 GAAAC
1 GAAAC
176500 TCATTATCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.63, C:0.09, G:0.23, T:0.06
Consensus pattern (15 bp):
GAAACAAAAAATGAG
Found at i:176553 original size:152 final size:152
Alignment explanation
Indices: 176272--176575 Score: 560
Period size: 152 Copynumber: 2.0 Consensus size: 152
176262 ATAAATACAA
176272 ATAAGTTAGACATGACGTTGGAGAACCCATCATCAAAGGAAGAAGAACGAAAAATGAGGAAACAA
1 ATAAGTTAGACATGACGTTGGAGAACCCATCATCAAAGGAAGAAGAACGAAAAATGAGGAAACAA
176337 AAAATGAGGAACTCATTATCCTCTCGAGAATCCAACCATTGAGAAAGGGAAGTCTCTTACCCAAG
66 AAAATGAGGAACTCATTATCCTCTCGAGAATCCAACCATTGAGAAAGGGAAGTCTCTTACCCAAG
176402 GGAATGCAACTATGTCAAGGAT
131 GGAATGCAACTATGTCAAGGAT
176424 ATAACGTTAGACATGACGTTGGAGAA-CCATCATCAAAGGAAG-A-AACGAAAAATGAGGAAACA
1 ATAA-GTTAGACATGACGTTGGAGAACCCATCATCAAAGGAAGAAGAACGAAAAATGAGGAAACA
176486 AAAAATGAGGAAACTCATTATCCTCTCGAGAATCCAACCATTGAAGAAAGGGAAGTCTCTTACCC
65 AAAAATGAGG-AACTCATTATCCTCTCGAGAATCCAACCATTG-AGAAAGGGAAGTCTCTTACCC
176551 AAGGGAATGCAACTATGTCAAGGAT
128 AAGGGAATGCAACTATGTCAAGGAT
176576 TGTGAGATTA
Statistics
Matches: 149, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
150 29 0.19
151 33 0.22
152 66 0.44
153 21 0.14
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.18
Consensus pattern (152 bp):
ATAAGTTAGACATGACGTTGGAGAACCCATCATCAAAGGAAGAAGAACGAAAAATGAGGAAACAA
AAAATGAGGAACTCATTATCCTCTCGAGAATCCAACCATTGAGAAAGGGAAGTCTCTTACCCAAG
GGAATGCAACTATGTCAAGGAT
Found at i:177448 original size:15 final size:13
Alignment explanation
Indices: 177412--177438 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
177402 TTAGATGAAG
177412 GAGGTAAATGTGT
1 GAGGTAAATGTGT
177425 GAGGTAAATGTGT
1 GAGGTAAATGTGT
177438 G
1 G
177439 GATGTTAAAT
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:0.00, G:0.41, T:0.30
Consensus pattern (13 bp):
GAGGTAAATGTGT
Found at i:180033 original size:21 final size:21
Alignment explanation
Indices: 179995--180034 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
179985 CGGGAGCTAG
*
179995 CTCTTCACGAGCTTCTCCTAA
1 CTCTTCACGAGCTCCTCCTAA
* *
180016 CTCTTCTCGTGCTCCTCCT
1 CTCTTCACGAGCTCCTCCT
180035 CCTCTACGAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.10, C:0.42, G:0.10, T:0.38
Consensus pattern (21 bp):
CTCTTCACGAGCTCCTCCTAA
Found at i:181108 original size:65 final size:63
Alignment explanation
Indices: 180989--181198 Score: 205
Period size: 65 Copynumber: 3.3 Consensus size: 63
180979 TTTTTCAGAG
* * *
180989 TGATGCACCGATGCACCAATCCATGCATCGACGCAC-CATGA-ATTAAATTG-AACATCGAATGC
1 TGATGCATCGATGCA-CAA-CCATGCATCGATGCACTCAGGATATT---TTGAAACATCGAATGC
181051 ATT
61 ATT
* * *
181054 TCATGCATCGATGCACATACCATGCA-CTGATGCACTGAGGAT-TTTATGAAAACATCGATTGCA
1 TGATGCATCGATGCACA-ACCATGCATC-GATGCACTCAGGATATTT-TG-AAACATCGAATGCA
181117 TT
62 TT
* * * *
181119 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCA-CAACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
181183 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
181199 TCTTAGTGAA
Statistics
Matches: 122, Mismatches: 13, Indels: 22
0.78 0.08 0.14
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 44 0.36
65 67 0.55
66 6 0.05
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (63 bp):
TGATGCATCGATGCACAACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:182104 original size:21 final size:21
Alignment explanation
Indices: 182067--182112 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
182057 CAACACAAAT
182067 TTTTCAAATTCGTAATTCAG-
1 TTTTCAAATTCGTAATTCAGA
182087 TTTTCAAATT-GTCGAATTCAGA
1 TTTTCAAATTCGT--AATTCAGA
182109 TTTT
1 TTTT
182113 TTACCAGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.09
20 10 0.43
21 7 0.30
22 4 0.17
ACGTcount: A:0.28, C:0.13, G:0.11, T:0.48
Consensus pattern (21 bp):
TTTTCAAATTCGTAATTCAGA
Found at i:183337 original size:51 final size:51
Alignment explanation
Indices: 183281--183385 Score: 210
Period size: 51 Copynumber: 2.1 Consensus size: 51
183271 TAATATTTTT
183281 ATTTATGATTTATATAGAGTCTCATATCTCCTTAATGGTTACAATCTCACG
1 ATTTATGATTTATATAGAGTCTCATATCTCCTTAATGGTTACAATCTCACG
183332 ATTTATGATTTATATAGAGTCTCATATCTCCTTAATGGTTACAATCTCACG
1 ATTTATGATTTATATAGAGTCTCATATCTCCTTAATGGTTACAATCTCACG
183383 ATT
1 ATT
183386 AGATCTCTAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.42
Consensus pattern (51 bp):
ATTTATGATTTATATAGAGTCTCATATCTCCTTAATGGTTACAATCTCACG
Found at i:186815 original size:144 final size:146
Alignment explanation
Indices: 186600--186950 Score: 379
Period size: 144 Copynumber: 2.4 Consensus size: 146
186590 TGAGTTTGGA
* ** * * * * * **
186600 AATTTCAATAGCTTGAGTTGTCAATCACCGTT-AGGAACCAAT-GTCATTTTGAATCGTCGAATC
1 AATTCCAATAGCTTGAGCAGTCGATCACC-TTCAGGAACCACTAGT-ATTCTGAATTGTGGAAAG
** * *
186663 TTGAATTGTTACTAGGACGTGATTATAAATCTTATGAAC-TTTAATGCCTTTT-TATTTTGAATA
64 TTGAATTGTTACTAGGACGTGAAGATAAATCATATGAACATTTAAGGCCTTTTGTATTTTGAATA
186726 TGTCACTCTGACTATGCT
129 TGTCACTCTGACTATGCT
* * * * *
186744 AATTCCAATAGCTCT-AGTAGTCGATCACCTTTAGGAATCAGTAGTATTCTTAATTGTGGAAAGT
1 AATTCCAATAGCT-TGAGCAGTCGATCACCTTCAGGAACCACTAGTATTCTGAATTGTGGAAAGT
* * * * *
186808 TGAATTGTTGCTAGGATGTGAAGATAAATCATATGAACATTTAAGGGCTTTTGTCTTTTGGATAT
65 TGAATTGTTACTAGGACGTGAAGATAAATCATATGAACATTTAAGGCCTTTTGTATTTTGAATAT
* *
186873 GTCACTTTGAGTATGCT
130 GTCACTCTGACTATGCT
* * *
186890 AATTCGAATGGCTTGAGCAGTCGATCACCTTCAGGAACCACTGGTATTCTGAATTGTGGAA
1 AATTCCAATAGCTTGAGCAGTCGATCACCTTCAGGAACCACTAGTATTCTGAATTGTGGAA
186951 TGTGTGCTAG
Statistics
Matches: 171, Mismatches: 30, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
143 2 0.01
144 78 0.46
145 15 0.09
146 76 0.44
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (146 bp):
AATTCCAATAGCTTGAGCAGTCGATCACCTTCAGGAACCACTAGTATTCTGAATTGTGGAAAGTT
GAATTGTTACTAGGACGTGAAGATAAATCATATGAACATTTAAGGCCTTTTGTATTTTGAATATG
TCACTCTGACTATGCT
Found at i:186918 original size:146 final size:144
Alignment explanation
Indices: 186663--186950 Score: 371
Period size: 146 Copynumber: 2.0 Consensus size: 144
186653 TCGTCGAATC
** * *
186663 TTGAATTGTTACTAGGACGTGATTATAAATCTTATGAACTTTAATGCCTTTTTATTTTGAATATG
1 TTGAATTGTTACTAGGACGTGAAGATAAATCATATGAACTTTAAGGCCTTTTTATTTTGAATATG
* * * *
186728 TCACTCTGACTATGCTAATTCCAATAGCTCTAGTAGTCGATCACCTTTAGGAATCAGTAGTATTC
66 TCACTCTGACTATGCTAATTCCAATAGCTCTAGCAGTCGATCACCTTCAGGAACCACTAGTATTC
*
186793 TTAATTGTGGAAAG
131 TGAATTGTGGAAAG
* * * * *
186807 TTGAATTGTTGCTAGGATGTGAAGATAAATCATATGAACATTTAAGGGCTTTTGTCTTTTGGATA
1 TTGAATTGTTACTAGGACGTGAAGATAAATCATATGAAC-TTTAAGGCCTTTT-TATTTTGAATA
* * * * *
186872 TGTCACTTTGAGTATGCTAATTCGAATGGCT-TGAGCAGTCGATCACCTTCAGGAACCACTGGTA
64 TGTCACTCTGACTATGCTAATTCCAATAGCTCT-AGCAGTCGATCACCTTCAGGAACCACTAGTA
186936 TTCTGAATTGTGGAA
128 TTCTGAATTGTGGAA
186951 TGTGTGCTAG
Statistics
Matches: 122, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
144 34 0.28
145 12 0.10
146 76 0.62
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (144 bp):
TTGAATTGTTACTAGGACGTGAAGATAAATCATATGAACTTTAAGGCCTTTTTATTTTGAATATG
TCACTCTGACTATGCTAATTCCAATAGCTCTAGCAGTCGATCACCTTCAGGAACCACTAGTATTC
TGAATTGTGGAAAG
Found at i:191067 original size:17 final size:18
Alignment explanation
Indices: 191038--191072 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
191028 TAAATCATAA
191038 AAAAACAGAAAAATTACT
1 AAAAACAGAAAAATTACT
191056 AAAAACAG-AAAATTACT
1 AAAAACAGAAAAATTACT
191073 CATTAAAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.66, C:0.11, G:0.06, T:0.17
Consensus pattern (18 bp):
AAAAACAGAAAAATTACT
Found at i:193448 original size:15 final size:15
Alignment explanation
Indices: 193408--193450 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
193398 TTTTTTAAAA
193408 ATAATAATATAAATT
1 ATAATAATATAAATT
193423 ATATATAA-ATAAAATTT
1 ATA-ATAATAT-AAA-TT
193440 ATAATAATATA
1 ATAATAATATA
193451 TTCACATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
15 5 0.21
16 12 0.50
17 7 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAATAATATAAATT
Found at i:193449 original size:23 final size:23
Alignment explanation
Indices: 193406--193451 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
193396 ATTTTTTTAA
*
193406 AAATAATAATATAAATTATATAT
1 AAATAATAATATAAATAATATAT
*
193429 AAATAA-AATTTATAATAATATAT
1 AAATAATAATATA-AATAATATAT
193452 TCACATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
AAATAATAATATAAATAATATAT
Found at i:206941 original size:15 final size:15
Alignment explanation
Indices: 206921--206953 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
206911 GGAAAAGAGG
206921 AGAGAGTTTGCTAGA
1 AGAGAGTTTGCTAGA
206936 AGAGAGTTTGCTAGA
1 AGAGAGTTTGCTAGA
206951 AGA
1 AGA
206954 AATAATCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.36, C:0.06, G:0.33, T:0.24
Consensus pattern (15 bp):
AGAGAGTTTGCTAGA
Found at i:208302 original size:24 final size:25
Alignment explanation
Indices: 208257--208303 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
208247 ATTCATGATT
*
208257 TAATTTCGCACCCCCTGGAATTTTG
1 TAATTTCGCACCCCCTGAAATTTTG
*
208282 TAATTTTGCACCCCCT-AAATTT
1 TAATTTCGCACCCCCTGAAATTT
208304 CTAATATAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.23, C:0.28, G:0.11, T:0.38
Consensus pattern (25 bp):
TAATTTCGCACCCCCTGAAATTTTG
Found at i:214037 original size:18 final size:19
Alignment explanation
Indices: 214014--214053 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
214004 TTACTAAGGG
*
214014 TTAGGGGTGAA-CTTGACA
1 TTAGGGATGAATCTTGACA
*
214032 TTAGGGATGAATTTTGACA
1 TTAGGGATGAATCTTGACA
214051 TTA
1 TTA
214054 TGCCTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.30, C:0.07, G:0.28, T:0.35
Consensus pattern (19 bp):
TTAGGGATGAATCTTGACA
Found at i:240467 original size:22 final size:22
Alignment explanation
Indices: 240438--240511 Score: 93
Period size: 22 Copynumber: 3.5 Consensus size: 22
240428 GGGTATATAA
240438 ATCCTTCGGGACGTATCCAGTG
1 ATCCTTCGGGACGTATCCAGTG
*
240460 ATCTTTCGGGACGTATCCAGTG
1 ATCCTTCGGGACGTATCCAGTG
*
240482 GTCCTTCGGGA--TAT--AGTG
1 ATCCTTCGGGACGTATCCAGTG
*
240500 GTCCTTCGGGAC
1 ATCCTTCGGGAC
240512 AAATACTGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.31
20 3 0.06
22 30 0.62
ACGTcount: A:0.16, C:0.24, G:0.30, T:0.30
Consensus pattern (22 bp):
ATCCTTCGGGACGTATCCAGTG
Found at i:243908 original size:29 final size:29
Alignment explanation
Indices: 243864--243919 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
243854 AAAGGATTTC
*
243864 AGAAAATAATAGTAGCAACTGTAAAGAGT
1 AGAAAATAATAGTAGCAAATGTAAAGAGT
*
243893 AGAAAATAATATTAGCAAATGTAAAGA
1 AGAAAATAATAGTAGCAAATGTAAAGA
243920 ATAGCGACAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.55, C:0.05, G:0.18, T:0.21
Consensus pattern (29 bp):
AGAAAATAATAGTAGCAAATGTAAAGAGT
Found at i:249855 original size:30 final size:30
Alignment explanation
Indices: 249821--249891 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
249811 TCATCCATCC
*
249821 ATATAATATTTTCATCATCTTCTACATTTA
1 ATATAATATTTTCATCATCTTCCACATTTA
*
249851 ATATAATATTTTCATCATTTTCCACATTTA
1 ATATAATATTTTCATCATCTTCCACATTTA
249881 ATATAAT-TTTT
1 ATATAATATTTT
249892 AATTAATAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 4 0.10
30 35 0.90
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (30 bp):
ATATAATATTTTCATCATCTTCCACATTTA
Found at i:260740 original size:17 final size:16
Alignment explanation
Indices: 260714--260747 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
260704 TTTCACTAAT
*
260714 AGAGGAAATATTACAA
1 AGAGGAAATAATACAA
260730 AGAGAGAAATAATACAA
1 AGAG-GAAATAATACAA
260747 A
1 A
260748 TAGCCTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.62, C:0.06, G:0.18, T:0.15
Consensus pattern (16 bp):
AGAGGAAATAATACAA
Found at i:265338 original size:17 final size:16
Alignment explanation
Indices: 265312--265345 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
265302 TTTCACTAAT
*
265312 AGAGGAAATATTACAA
1 AGAGGAAATAATACAA
265328 AGAGAGAAATAATACAA
1 AGAG-GAAATAATACAA
265345 A
1 A
265346 TAGCCTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.62, C:0.06, G:0.18, T:0.15
Consensus pattern (16 bp):
AGAGGAAATAATACAA
Found at i:269472 original size:38 final size:36
Alignment explanation
Indices: 269429--269504 Score: 89
Period size: 38 Copynumber: 2.1 Consensus size: 36
269419 TTACGAGAAT
* *
269429 ATGTGGAACATGTTAAATACGTTATCAATAAATTATTA
1 ATGTGGAACACGTTAAATACATTATCAAT--ATTATTA
** *
269467 ATGTGGAGGACGTTAACTACATTATCAATATTATTA
1 ATGTGGAACACGTTAAATACATTATCAATATTATTA
269503 AT
1 AT
269505 AAAGTATTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
36 9 0.27
38 24 0.73
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.37
Consensus pattern (36 bp):
ATGTGGAACACGTTAAATACATTATCAATATTATTA
Found at i:270687 original size:18 final size:19
Alignment explanation
Indices: 270652--270688 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
270642 CACAGAATGT
270652 AAGATTACCAGTGAGAATAA
1 AAGATTACCAG-GAGAATAA
270672 AAGATTACCA-GAGAATA
1 AAGATTACCAGGAGAATA
270689 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.51, C:0.11, G:0.19, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGAGAATAA
Found at i:273810 original size:18 final size:19
Alignment explanation
Indices: 273783--273840 Score: 82
Period size: 18 Copynumber: 3.1 Consensus size: 19
273773 CTAGACAACC
273783 AGGAAAAAATCAAAAGCAA
1 AGGAAAAAATCAAAAGCAA
*
273802 AGG-AAAAATTAAAAGCAA
1 AGGAAAAAATCAAAAGCAA
*
273820 AGGAAAAGAATCAAAATCAA
1 AGGAAAA-AATCAAAAGCAA
273840 A
1 A
273841 ATCAAAAGCA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 17 0.50
19 6 0.18
20 11 0.32
ACGTcount: A:0.67, C:0.09, G:0.16, T:0.09
Consensus pattern (19 bp):
AGGAAAAAATCAAAAGCAA
Found at i:274574 original size:33 final size:35
Alignment explanation
Indices: 274536--274601 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
274526 CATTAAACCT
*
274536 TTTTAT-AATTTCAATTTTGTAAA-AAAATATAAA
1 TTTTATGAATTTAAATTTTGTAAAGAAAATATAAA
*
274569 TTTTATGAATTTAAATTTTTTAAAGAAAATATA
1 TTTTATGAATTTAAATTTTGTAAAGAAAATATA
274602 TAAATATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 6 0.21
34 15 0.52
35 8 0.28
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (35 bp):
TTTTATGAATTTAAATTTTGTAAAGAAAATATAAA
Found at i:276008 original size:52 final size:52
Alignment explanation
Indices: 275950--276048 Score: 189
Period size: 52 Copynumber: 1.9 Consensus size: 52
275940 GTAGGGAGTG
*
275950 GGGGTATGACTTACTGTCCCCTGTTCGAGCATTTCAACGTCTATAGGGGAGA
1 GGGGTATGACTTACTGTCCCCTGTTCGAGCATTTCAACATCTATAGGGGAGA
276002 GGGGTATGACTTACTGTCCCCTGTTCGAGCATTTCAACATCTATAGG
1 GGGGTATGACTTACTGTCCCCTGTTCGAGCATTTCAACATCTATAGG
276049 TAGCATTTCT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.30
Consensus pattern (52 bp):
GGGGTATGACTTACTGTCCCCTGTTCGAGCATTTCAACATCTATAGGGGAGA
Found at i:276608 original size:28 final size:27
Alignment explanation
Indices: 276512--276608 Score: 83
Period size: 28 Copynumber: 3.6 Consensus size: 27
276502 TGTTGAGTAA
* *
276512 AAGCACTGAGGTGCTTGATTTTAGATTG
1 AAGCACAGAGGTGC-TGAATTTAGATTG
* * * *
276540 TAGCACAGAGGTGCTCAA--T-CATTCC
1 AAGCACAGAGGTGCTGAATTTAGATT-G
276565 AATGCACAGAGGTGCTAGAATTTAGATTG
1 AA-GCACAGAGGTGCT-GAATTTAGATTG
276594 AAGCACAGAGGTGCT
1 AAGCACAGAGGTGCT
276609 CAGTCATAGT
Statistics
Matches: 53, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
24 3 0.06
25 2 0.04
26 13 0.25
27 4 0.08
28 25 0.47
29 3 0.06
30 3 0.06
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (27 bp):
AAGCACAGAGGTGCTGAATTTAGATTG
Found at i:276654 original size:27 final size:28
Alignment explanation
Indices: 276589--276832 Score: 120
Period size: 27 Copynumber: 8.8 Consensus size: 28
276579 CTAGAATTTA
* *
276589 GATTGAAGCACAGAGGTGCTCAGTCATA
1 GATTGAAGCACAGAGGTGCTCAGTCCTC
**
276617 G-TTGGCTGCACAGAGGTG-TCAGTCCTC
1 GATT-GAAGCACAGAGGTGCTCAGTCCTC
* *
276644 GATTGAAGCACAGAGGTGCTCAATCATC
1 GATTGAAGCACAGAGGTGCTCAGTCCTC
276672 --TT--AGCTACATAGAGGTG-TCAGCTCC-C
1 GATTGAAGC-AC--AGAGGTGCTCAG-TCCTC
** * * *
276698 GGCTAAAGCACAGAGGTGCTCAGTCATTT
1 GATTGAAGCACAGAGGTGCTCAGTC-CTC
** * *
276727 TTTTTAACTGCACAGAGGTG-TCAGTTCTC
1 GATTGAA--GCACAGAGGTGCTCAGTCCTC
*
276756 GATTGAAGCACAGAGGTGCTCAATCACT-
1 GATTGAAGCACAGAGGTGCTCAGTC-CTC
* *
276784 -TTTGGCTA-CACAGAGGTG-TCAG-CTCTC
1 GATT-G-AAGCACAGAGGTGCTCAGTC-CTC
276811 GATTGAAGCACAGAGGTGCTCA
1 GATTGAAGCACAGAGGTGCTCA
276833 ATCGTTAATT
Statistics
Matches: 161, Mismatches: 31, Indels: 48
0.67 0.13 0.20
Matches are distributed among these distances:
24 3 0.02
25 2 0.01
26 10 0.06
27 67 0.42
28 47 0.29
29 13 0.08
30 8 0.05
31 11 0.07
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (28 bp):
GATTGAAGCACAGAGGTGCTCAGTCCTC
Found at i:276659 original size:55 final size:55
Alignment explanation
Indices: 276589--276835 Score: 284
Period size: 55 Copynumber: 4.5 Consensus size: 55
276579 CTAGAATTTA
* ** * *
276589 GATTGAAGCACAGAGGTGCTCAGTCATAGTTGGCTGCACAGAGGTGTCAGTCCTC
1 GATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAGTCCTC
* *
276644 GATTGAAGCACAGAGGTGCTCAATCA-TCTTAGCTACATAGAGGTGTCAGCTCC-C
1 GATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAG-TCCTC
** * * * * *
276698 GGCTAAAGCACAGAGGTGCTCAGTCATTTTTTTTAACTGCACAGAGGTGTCAGTTCTC
1 GATTGAAGCACAGAGGTGCTCAATCA---TTTTTAGCTACACAGAGGTGTCAGTCCTC
* *
276756 GATTGAAGCACAGAGGTGCTCAATCACTTTTGGCTACACAGAGGTGTCAG-CTCTC
1 GATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAGTC-CTC
276811 GATTGAAGCACAGAGGTGCTCAATC
1 GATTGAAGCACAGAGGTGCTCAATC
276836 GTTAATTCTA
Statistics
Matches: 161, Mismatches: 24, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
54 41 0.25
55 76 0.47
57 2 0.01
58 42 0.26
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (55 bp):
GATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAGTCCTC
Found at i:276660 original size:109 final size:109
Alignment explanation
Indices: 276535--276832 Score: 273
Period size: 112 Copynumber: 2.7 Consensus size: 109
276525 CTTGATTTTA
* ** * *
276535 GATTGTAGCACAGAGGTGCTCAATCATTCCAATGC-AC-AGAGGTG-CTAGAATTTAGATTGAAG
1 GATTGAAGCACAGAGGTGCTCAATCA-TCCAA-GCTACAAGAGGTGTC-AG-ATCCAGACTAAAG
**
276597 CACAGAGGTGCTCAGTCA-TAGTTGGCTGCACAGAGGTGTCAGTCCTC
62 CACAGAGGTGCTCAGTCATTAGTTAACTGCACAGAGGTGTCAGTCCTC
** * * *
276644 GATTGAAGCACAGAGGTGCTCAATCATCTTAGCTACATAGAGGTGTCAGCTCCCGGCTAAAGCAC
1 GATTGAAGCACAGAGGTGCTCAATCATCCAAGCTACA-AGAGGTGTCAGATCCAGACTAAAGCAC
** *
276709 AGAGGTGCTCAGTCATTTTTTTTAACTGCACAGAGGTGTCAGTTCTC
65 AGAGGTGCTCAGTCA--TTAGTTAACTGCACAGAGGTGTCAGTCCTC
**** * * *
276756 GATTGAAGCACAGAGGTGCTCAATCACTTTTGGCTACACAGAGGTGTCAGCTCTC-GATTGAAGC
1 GATTGAAGCACAGAGGTGCTCAATCA-TCCAAGCTACA-AGAGGTGTCAGATC-CAGACTAAAGC
276820 ACAGAGGTGCTCA
63 ACAGAGGTGCTCA
276833 ATCGTTAATT
Statistics
Matches: 159, Mismatches: 21, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
107 2 0.01
108 5 0.03
109 49 0.31
110 9 0.06
111 1 0.01
112 50 0.31
113 42 0.26
114 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (109 bp):
GATTGAAGCACAGAGGTGCTCAATCATCCAAGCTACAAGAGGTGTCAGATCCAGACTAAAGCACA
GAGGTGCTCAGTCATTAGTTAACTGCACAGAGGTGTCAGTCCTC
Found at i:276777 original size:112 final size:113
Alignment explanation
Indices: 276622--276832 Score: 343
Period size: 112 Copynumber: 1.9 Consensus size: 113
276612 TCATAGTTGG
*
276622 CTGCACAGAGGTGTCAGTCCTCGATTGAAGCACAGAGGTGCTCAATCA-TCTTAGCTACATAGAG
1 CTGCACAGAGGTGTCAGTCCTCGATTGAAGCACAGAGGTGCTCAATCACTCTTAGCTACACAGAG
*
276686 GTGTCAGCTCCCGGCTAAAGCACAGAGGTGCTCAGTCATTTTTTTTAA
66 GTGTCAGCTCCCGACTAAAGCACAGAGGTGCTCAGTCATTTTTTTTAA
* * *
276734 CTGCACAGAGGTGTCAGTTCTCGATTGAAGCACAGAGGTGCTCAATCACTTTTGGCTACACAGAG
1 CTGCACAGAGGTGTCAGTCCTCGATTGAAGCACAGAGGTGCTCAATCACTCTTAGCTACACAGAG
* * *
276799 GTGTCAGCTCTCGATTGAAGCACAGAGGTGCTCA
66 GTGTCAGCTCCCGACTAAAGCACAGAGGTGCTCA
276833 ATCGTTAATT
Statistics
Matches: 90, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
112 47 0.52
113 43 0.48
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (113 bp):
CTGCACAGAGGTGTCAGTCCTCGATTGAAGCACAGAGGTGCTCAATCACTCTTAGCTACACAGAG
GTGTCAGCTCCCGACTAAAGCACAGAGGTGCTCAGTCATTTTTTTTAA
Found at i:276851 original size:55 final size:55
Alignment explanation
Indices: 276535--276856 Score: 256
Period size: 55 Copynumber: 5.8 Consensus size: 55
276525 CTTGATTTTA
* * * *
276535 GATTGTAGCACAGAGGTGCTCAATCATTCCAA---T-GCACAGAGGTG-CTAGAATTTA
1 GATTGAAGCACAGAGGTGCTCAATCATT--AATTCTAGCACAGAGGTGTC-AG-CTCTC
* *
276589 GATTGAAGCACAGAGGTGCTCAGTCA-TAGTTGGCT-GCACAGAGGTGTCAG-TCCTC
1 GATTGAAGCACAGAGGTGCTCAATCATTAATT--CTAGCACAGAGGTGTCAGCT-CTC
* * * *
276644 GATTGAAGCACAGAGGTGCTCAATCATCTTA-GCTA-CATAGAGGTGTCAGCTCCC
1 GATTGAAGCACAGAGGTGCTCAATCAT-TAATTCTAGCACAGAGGTGTCAGCTCTC
** * * ** * *
276698 GGCTAAAGCACAGAGGTGCTCAGTCATTTTTTTTAACTGCACAGAGGTGTCAGTTCTC
1 GATTGAAGCACAGAGGTGCTCAATCATTAATTCT-A--GCACAGAGGTGTCAGCTCTC
276756 GATTGAAGCACAGAGGTGCTCAATCACTT--TTGGCTA-CACAGAGGTGTCAGCTCTC
1 GATTGAAGCACAGAGGTGCTCAATCA-TTAATT--CTAGCACAGAGGTGTCAGCTCTC
*
276811 GATTGAAGCACAGAGGTGCTCAATCGTTAATTCTAGCACAGAGGTG
1 GATTGAAGCACAGAGGTGCTCAATCATTAATTCTAGCACAGAGGTG
276857 CTATGGATTC
Statistics
Matches: 218, Mismatches: 28, Indels: 43
0.75 0.10 0.15
Matches are distributed among these distances:
51 1 0.00
53 3 0.01
54 71 0.33
55 81 0.37
56 16 0.07
57 4 0.02
58 39 0.18
59 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (55 bp):
GATTGAAGCACAGAGGTGCTCAATCATTAATTCTAGCACAGAGGTGTCAGCTCTC
Done.