Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A10
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: 110302803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1825971 characters in sequence are not A, C, G, or T
File 180 of 343
Found at i:59748713 original size:18 final size:18
Alignment explanation
Indices: 59748690--59748735 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
59748680 GAGTTAAACG
*
59748690 AATCGAATTATTCGAGTT
1 AATCGAATTATTCGAGTC
*
59748708 AATCGAGTTATTCGAGTC
1 AATCGAATTATTCGAGTC
59748726 AACTCGAATT
1 AA-TCGAATT
59748736 TTTTTTTTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (18 bp):
AATCGAATTATTCGAGTC
Found at i:59749062 original size:30 final size:29
Alignment explanation
Indices: 59749013--59749069 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
59749003 AACTTTTTAT
* *
59749013 TTTCTCCCTAAAATTTTACTCCCTTCCAC
1 TTTCCCCCCAAAATTTTACTCCCTTCCAC
*
59749042 TTTCCCCCCAAAACTTTTACTTCCTTCC
1 TTTCCCCCCAAAA-TTTTACTCCCTTCC
59749070 CATCCCACGC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.19, C:0.40, G:0.00, T:0.40
Consensus pattern (29 bp):
TTTCCCCCCAAAATTTTACTCCCTTCCAC
Found at i:59749720 original size:5 final size:5
Alignment explanation
Indices: 59749710--59749735 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
59749700 GAACAAATAT
59749710 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
59749736 ATTCCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:59756910 original size:51 final size:51
Alignment explanation
Indices: 59756834--59756935 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
59756824 TAATGAGTAG
*
59756834 GACCATGGATGAAAGGCTCTATGGCATCATATGATAGTATGTCATGATGGC
1 GACCATGGATGAAAGGCTCTATGGCATCATATGATAGTACGTCATGATGGC
59756885 GACCATGGATGAAAGGCTCTATGGCATCATATGATAGTACGTCATGATGGC
1 GACCATGGATGAAAGGCTCTATGGCATCATATGATAGTACGTCATGATGGC
59756936 AAATCAGTGT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.26
Consensus pattern (51 bp):
GACCATGGATGAAAGGCTCTATGGCATCATATGATAGTACGTCATGATGGC
Found at i:59757035 original size:33 final size:33
Alignment explanation
Indices: 59756979--59757073 Score: 95
Period size: 33 Copynumber: 2.9 Consensus size: 33
59756969 TGGCATCCAC
* *
59756979 AAAGATAGTCCGCTAGGGCAGTAAACATA-GAAA
1 AAAGATAGTCCACTAGGGCAGTAAACACATG-AA
* *
59757012 AAAGATAGTCCACT-GGGATAGTAAACACATGAC
1 AAAGATAGTCCACTAGGG-CAGTAAACACATGAA
* * *
59757045 AAAGATAGTCCACTAAGACAATAAACACA
1 AAAGATAGTCCACTAGGGCAGTAAACACA
59757074 AAACAGTCAG
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
32 3 0.06
33 46 0.90
34 2 0.04
ACGTcount: A:0.47, C:0.18, G:0.19, T:0.16
Consensus pattern (33 bp):
AAAGATAGTCCACTAGGGCAGTAAACACATGAA
Found at i:59757295 original size:22 final size:22
Alignment explanation
Indices: 59757269--59757312 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
59757259 ATACTGCCAG
59757269 GGCGACAAGTATGAGAACCACA
1 GGCGACAAGTATGAGAACCACA
59757291 GGCGACAAGTATGAGAACCACA
1 GGCGACAAGTATGAGAACCACA
59757313 CATGTAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.23, G:0.27, T:0.09
Consensus pattern (22 bp):
GGCGACAAGTATGAGAACCACA
Found at i:59759503 original size:40 final size:40
Alignment explanation
Indices: 59759445--59759662 Score: 298
Period size: 40 Copynumber: 5.5 Consensus size: 40
59759435 AGGATGATAA
* *
59759445 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
59759485 CCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
59759525 CCGGGCTAAGTCTCGAAGGCATTTGTGCTAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
59759565 CCGGGCTAGGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
59759605 CCGGGCTAAGTCCCGAAGACATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
59759645 CC-AGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
59759663 TACTTGGTTT
Statistics
Matches: 159, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
39 15 0.09
40 143 0.90
41 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:59762870 original size:20 final size:21
Alignment explanation
Indices: 59762839--59762900 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
59762829 TGAATGCACA
*
59762839 CACGTGCCCCTGTTTGTACTT
1 CACGTACCCCTGTTTGTACTT
* *
59762860 CA-GTACCCCTGATTGTACAT
1 CACGTACCCCTGTTTGTACTT
* *
59762880 -ACGTGCCCCTGTTTATACTT
1 CACGTACCCCTGTTTGTACTT
59762900 C
1 C
59762901 GGTAATTTCA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
19 1 0.03
20 29 0.91
21 2 0.06
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.35
Consensus pattern (21 bp):
CACGTACCCCTGTTTGTACTT
Found at i:59765754 original size:21 final size:21
Alignment explanation
Indices: 59765730--59765773 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
59765720 GAAAAATTAT
*
59765730 TAAAATATTTCTATT-TAAAAA
1 TAAAATATAT-TATTATAAAAA
*
59765751 TAAATTATATTATTATAAAAA
1 TAAAATATATTATTATAAAAA
59765772 TA
1 TA
59765774 TGTTTTTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAAATATATTATTATAAAAA
Found at i:59774804 original size:6 final size:6
Alignment explanation
Indices: 59774795--59774834 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
59774785 ATGGAGATGG
59774795 AGGTCA AGGTCA AGGTCA AGGTCA AGGTCA AGGTCA AGGT
1 AGGTCA AGGTCA AGGTCA AGGTCA AGGTCA AGGTCA AGGT
59774835 GGGACATAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.33, C:0.15, G:0.35, T:0.17
Consensus pattern (6 bp):
AGGTCA
Found at i:59777626 original size:15 final size:15
Alignment explanation
Indices: 59777606--59777673 Score: 82
Period size: 16 Copynumber: 4.4 Consensus size: 15
59777596 TAAATAATTA
59777606 ATTTAACATTAAAAT
1 ATTTAACATTAAAAT
* *
59777621 ATTTAATATCAACAAT
1 ATTTAACATTAA-AAT
59777637 ATTTAACATTAAAAT
1 ATTTAACATTAAAAT
* *
59777652 ATTTAATATAAAAAAT
1 ATTTAACAT-TAAAAT
59777668 ATTTAA
1 ATTTAA
59777674 TAACATAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
15 21 0.47
16 24 0.53
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTTAACATTAAAAT
Found at i:59777639 original size:16 final size:16
Alignment explanation
Indices: 59777616--59777689 Score: 87
Period size: 16 Copynumber: 4.6 Consensus size: 16
59777606 ATTTAACATT
59777616 AAAATATTTAATATCA
1 AAAATATTTAATATCA
* * *
59777632 ACAATATTTAACAT-T
1 AAAATATTTAATATCA
*
59777647 AAAATATTTAATATAA
1 AAAATATTTAATATCA
*
59777663 AAAATATTTAATAACA
1 AAAATATTTAATATCA
59777679 TAAAATATTTA
1 -AAAATATTTA
59777690 TAAAATTATA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
15 12 0.25
16 26 0.54
17 10 0.21
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAATATTTAATATCA
Found at i:59777641 original size:31 final size:31
Alignment explanation
Indices: 59777606--59777673 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
59777596 TAAATAATTA
* *
59777606 ATTTAACATTAAAATATTTAATATCAACAAT
1 ATTTAACATTAAAATATTTAATATAAAAAAT
59777637 ATTTAACATTAAAATATTTAATATAAAAAAT
1 ATTTAACATTAAAATATTTAATATAAAAAAT
59777668 ATTTAA
1 ATTTAA
59777674 TAACATAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (31 bp):
ATTTAACATTAAAATATTTAATATAAAAAAT
Found at i:59777692 original size:16 final size:18
Alignment explanation
Indices: 59777609--59777706 Score: 81
Period size: 16 Copynumber: 5.9 Consensus size: 18
59777599 ATAATTAATT
59777609 TAACATTAAAATATTTAA
1 TAACATTAAAATATTTAA
* *
59777627 TATCA--ACAATA-TT--
1 TAACATTAAAATATTTAA
59777640 TAACATTAAAATATTTAA
1 TAACATTAAAATATTTAA
59777658 TATA-A--AAAATATTTAA
1 TA-ACATTAAAATATTTAA
59777674 TAACA-TAAAATATTT-A
1 TAACATTAAAATATTTAA
*
59777690 TAAAATTATAAATATTT
1 TAACATTA-AAATATTT
59777707 TTATAGAATT
Statistics
Matches: 65, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
13 4 0.06
15 8 0.12
16 26 0.40
17 11 0.17
18 15 0.23
19 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (18 bp):
TAACATTAAAATATTTAA
Found at i:59777839 original size:45 final size:43
Alignment explanation
Indices: 59777695--59777842 Score: 112
Period size: 45 Copynumber: 3.4 Consensus size: 43
59777685 ATTTATAAAA
* *
59777695 TTATAAA-TATTTTTATAGA--ATTTTATGTATTTTTA-AGATAT-
1 TTATAAATTATTTTTATA-ATTTTTTTAT-TAATTTTATAGAT-TC
59777736 TTATAAATTATTTTTTATAATTTTTTTATTAAATTTTATAGATTC
1 TTATAAATTA-TTTTTATAATTTTTTTATT-AATTTTATAGATTC
**
59777781 TTATGTATGTATTTTTATAACTTTTTTTATT-ATTTTATCATGTATT-
1 TTATAAAT-TATTTTTATAA-TTTTTTTATTAATTTTAT-A-G-ATTC
*
59777827 TTTTAAATTATTTTTA
1 TTATAAATTATTTTTA
59777843 AAAATTTTAA
Statistics
Matches: 88, Mismatches: 7, Indels: 20
0.77 0.06 0.17
Matches are distributed among these distances:
41 7 0.08
42 3 0.03
43 9 0.10
44 20 0.23
45 28 0.32
46 18 0.20
47 3 0.03
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (43 bp):
TTATAAATTATTTTTATAATTTTTTTATTAATTTTATAGATTC
Found at i:59778254 original size:19 final size:19
Alignment explanation
Indices: 59778217--59778254 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
59778207 CTGCTTTTCT
59778217 TTTCTTTTTTCTTTCACCAG
1 TTTCTTTTTTC-TTCACCAG
59778237 TTTCTTCTTTTC-TCACCA
1 TTTCTT-TTTTCTTCACCA
59778255 ACAAGACTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 6 0.35
21 5 0.29
ACGTcount: A:0.11, C:0.29, G:0.03, T:0.58
Consensus pattern (19 bp):
TTTCTTTTTTCTTCACCAG
Found at i:59782881 original size:26 final size:24
Alignment explanation
Indices: 59782835--59782882 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
59782825 ATGATTAAAT
*
59782835 TCACTCATTTAATCATTACATTAA
1 TCACTCATTTAATCATCACATTAA
*
59782859 TCACTACATTTTATACATCACATT
1 TCACT-CATTTAAT-CATCACATT
59782883 TTTGCAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 7 0.35
26 8 0.40
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (24 bp):
TCACTCATTTAATCATCACATTAA
Found at i:59785177 original size:27 final size:26
Alignment explanation
Indices: 59785091--59785234 Score: 171
Period size: 27 Copynumber: 5.4 Consensus size: 26
59785081 GAAAACTAAT
59785091 AACTGCCTTTGTGGTGTACTCTGAAAG
1 AACTGCCTTTGT-GTGTACTCTGAAAG
*
59785118 AATTGCCTTTGTGTGTACTCTGAAAG
1 AACTGCCTTTGTGTGTACTCTGAAAG
* * * * *
59785144 AATTGCCTTGGTGACGTTCTCTGAAGG
1 AACTGCCTTTGTG-TGTACTCTGAAAG
* *
59785171 AACTGCCTTTGTGGTGTACTTTGAAAT
1 AACTGCCTTTGT-GTGTACTCTGAAAG
*
59785198 AATTGCCTTTGTGGTGTACTCTGAAAG
1 AACTGCCTTTGT-GTGTACTCTGAAAG
59785225 AACTGCCTTT
1 AACTGCCTTT
59785235 ATGGCAAAAT
Statistics
Matches: 99, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
26 26 0.26
27 72 0.73
28 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (26 bp):
AACTGCCTTTGTGTGTACTCTGAAAG
Found at i:59785261 original size:80 final size:80
Alignment explanation
Indices: 59785091--59785294 Score: 236
Period size: 80 Copynumber: 2.5 Consensus size: 80
59785081 GAAAACTAAT
* *
59785091 AACTGCCTTTGTGGTGTACTCTGAAAGAATTGCCTTTGTGTGTACTCTGAAAGAATTGCCTTGGT
1 AACTGCCTTTGTGGTGTACTCTGAAAGAATTGCCTTTGTGTGTACTCTGAAAGAACTGCCTTGAT
*** *
59785156 GACGTTCTCTGAAGG
66 GAAAATCTCTAAAGG
* * *
59785171 AACTGCCTTTGTGGTGTACTTTGAAATAATTGCCTTTGTGGTGTACTCTGAAAGAACTGCCTTTA
1 AACTGCCTTTGTGGTGTACTCTGAAAGAATTGCCTTTGT-GTGTACTCTGAAAGAACTGCCTTGA
59785236 TGGCAAAATCT-TAAAGG
65 T-G-AAAATCTCTAAAGG
* **
59785253 AA-TG-CTTTGTGGTGTGA-TCTAAAAGAGGTGCCTTTGTGTGTA
1 AACTGCCTTTGTGGTGT-ACTCTGAAAGAATTGCCTTTGTGTGTA
59785295 TTTTGGGGGA
Statistics
Matches: 106, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
79 5 0.05
80 63 0.59
81 26 0.25
82 8 0.08
83 4 0.04
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.36
Consensus pattern (80 bp):
AACTGCCTTTGTGGTGTACTCTGAAAGAATTGCCTTTGTGTGTACTCTGAAAGAACTGCCTTGAT
GAAAATCTCTAAAGG
Found at i:59794219 original size:40 final size:40
Alignment explanation
Indices: 59794182--59794313 Score: 151
Period size: 40 Copynumber: 3.3 Consensus size: 40
59794172 GCTACTCGTT
*
59794182 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATT-TAGTAACTCGCA
* * *
59794222 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * * * *
59794262 CAAATGCCTTCGGG-CTTAGCTCAGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
59794301 CAAATGCCTTCGG
1 CAAATGCCTTCGG
59794314 ATCTTAGTCC
Statistics
Matches: 80, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
39 32 0.40
40 46 0.57
41 2 0.03
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:59794299 original size:79 final size:80
Alignment explanation
Indices: 59794210--59794361 Score: 193
Period size: 79 Copynumber: 1.9 Consensus size: 80
59794200 AGCCCGGTTA
* *
59794210 TAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCCGGATTTAGTAACTCA-CACAAATGCCTTC
1 TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGGATATAGTAACTCAGCACAAA-GCCTTC
59794273 GGG-CTTAGCTCAGAAT
64 GGGACTTAGCTCAGAAT
* ** * * *
59794289 TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAAGCCTTCGG
1 TAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGATATAGTAACTCAGCACAAAGCCTTCGG
59794354 GACTTAGC
66 GACTTAGC
59794362 CCGGACATCA
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
78 3 0.05
79 47 0.76
80 12 0.19
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.27
Consensus pattern (80 bp):
TAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGATATAGTAACTCAGCACAAAGCCTTCGG
GACTTAGCTCAGAAT
Found at i:59801519 original size:80 final size:81
Alignment explanation
Indices: 59801415--59801600 Score: 218
Period size: 80 Copynumber: 2.3 Consensus size: 81
59801405 GCTACTCGTT
* * *
59801415 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
*
59801478 GGATTTAGTAACTAAAAA
64 GGATATAGTAACTAAAAA
* **
59801496 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
* * * **
59801560 ATATGGTCACTTAGCA
66 ATATAGTAACTAAAAA
59801576 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
59801601 CATCATTCAA
Statistics
Matches: 90, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
79 12 0.13
80 63 0.70
81 15 0.17
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTAAAAA
Found at i:59801600 original size:40 final size:41
Alignment explanation
Indices: 59801415--59801600 Score: 186
Period size: 40 Copynumber: 4.6 Consensus size: 41
59801405 GCTACTCGTT
* * *
59801415 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAAC-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTAGCA
* * * * **
59801455 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTAAAAA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTAGCA
* *
59801496 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATC-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTTAGCA
* * *
59801535 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAACTTAGCA
59801576 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
59801601 CATCATTCAA
Statistics
Matches: 116, Mismatches: 23, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
38 2 0.02
39 12 0.10
40 76 0.66
41 26 0.22
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (41 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTAGCA
Found at i:59804332 original size:47 final size:47
Alignment explanation
Indices: 59804278--59804682 Score: 684
Period size: 47 Copynumber: 8.6 Consensus size: 47
59804268 TATTTGAATA
59804278 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
59804325 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
59804372 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
59804421 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGTCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
59804468 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
59804515 AATGTGAAAGTGTATATATGTGATAAGGTCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
59804562 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * *
59804609 AATGTGAAAGTGTATATATGTGATAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
59804656 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
59804683 TCCCGAAGGG
Statistics
Matches: 340, Mismatches: 16, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
47 294 0.86
49 46 0.14
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:59809415 original size:26 final size:26
Alignment explanation
Indices: 59809383--59809434 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
59809373 CCTATTTGGC
59809383 CATAACA-AATATAAATTCTAACATTT
1 CATAACAGAATATAAATT-TAACATTT
**
59809409 CATAACAGCGTATAAATTTAACATTT
1 CATAACAGAATATAAATTTAACATTT
59809435 AATTACCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.35
Consensus pattern (26 bp):
CATAACAGAATATAAATTTAACATTT
Found at i:59810634 original size:28 final size:27
Alignment explanation
Indices: 59810591--59810697 Score: 74
Period size: 28 Copynumber: 3.7 Consensus size: 27
59810581 GAATTTAGTG
59810591 TTAAT-TGGGCCTTAGCCCATATCAGTA
1 TTAATCTGGGCC-TAGCCCATATCAGTA
*
59810618 TTAATCTGGGCCATAGCCC-TATTACAATA
1 TTAATCTGGGCC-TAGCCCATA-T-CAGTA
*
59810647 TCAGAGCATACTGGGCCTAGCCCATATCAGTA
1 T--TA--AT-CTGGGCCTAGCCCATATCAGTA
* *
59810679 TCAGTCTGGGCCGTAGCCC
1 TTAATCTGGGCC-TAGCCC
59810698 TATTACAAGT
Statistics
Matches: 64, Mismatches: 6, Indels: 19
0.72 0.07 0.21
Matches are distributed among these distances:
27 14 0.22
28 20 0.31
29 5 0.08
30 1 0.02
31 1 0.02
32 5 0.08
33 9 0.14
34 9 0.14
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (27 bp):
TTAATCTGGGCCTAGCCCATATCAGTA
Found at i:59810769 original size:19 final size:20
Alignment explanation
Indices: 59810726--59810781 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
59810716 ATTGGGTCTT
59810726 GCCCATATTAACACAGTTGG
1 GCCCATATTAACACAGTTGG
* *
59810746 GCCCATTTTAATACAGTT-G
1 GCCCATATTAACACAGTTGG
* *
59810765 GCCCATAATAAAACAGT
1 GCCCATATTAACACAGT
59810782 CTCATATGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (20 bp):
GCCCATATTAACACAGTTGG
Found at i:59812896 original size:9 final size:9
Alignment explanation
Indices: 59812884--59812908 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
59812874 TAAAATAATA
59812884 ATAATAACC
1 ATAATAACC
59812893 ATAATAACC
1 ATAATAACC
59812902 ATAATAA
1 ATAATAA
59812909 TGAAAATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (9 bp):
ATAATAACC
Found at i:59823672 original size:40 final size:40
Alignment explanation
Indices: 59823574--59823791 Score: 266
Period size: 40 Copynumber: 5.5 Consensus size: 40
59823564 AAGCCAAGTA
* * *
59823574 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTC-AATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
59823612 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
59823652 CCTTCGGGACTTAGCTCGGATATAGTAACTCGCAAAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
59823692 CCTTCGGGACTTAGCCCGGATGTAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
59823732 CCTTCGGGACTTAGCCCAGA-ACTAGTCACTGGCGCA-AAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACT--CGCACAAATG
59823773 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
59823792 TTATCATCCA
Statistics
Matches: 157, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
38 12 0.08
39 17 0.11
40 101 0.64
41 23 0.15
42 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:59831769 original size:40 final size:40
Alignment explanation
Indices: 59831676--59831893 Score: 293
Period size: 40 Copynumber: 5.5 Consensus size: 40
59831666 AAGCCAAGTA
* * *
59831676 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTC-AATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
59831714 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
59831754 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
59831794 CCTTCGGGACTTAGCCCGGATGTAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
59831834 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCA-AAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACT--CGCACAAATG
59831875 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
59831894 TTATCATCCA
Statistics
Matches: 163, Mismatches: 11, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
38 12 0.07
39 17 0.10
40 106 0.65
41 24 0.15
42 4 0.02
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.22
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:59838685 original size:43 final size:43
Alignment explanation
Indices: 59838582--59838689 Score: 155
Period size: 43 Copynumber: 2.5 Consensus size: 43
59838572 TAGCTCAACT
* *
59838582 ATGGTCTTATACGA-AATCAAATAACGATGCCAATGTCCCAAAC
1 ATGGTCTTACAC-ATAATCACATAACGATGCCAATGTCCCAAAC
* * *
59838625 ATGGTCTTACACGTAATCACATAATGATGCCAATGTCCCAGAC
1 ATGGTCTTACACATAATCACATAACGATGCCAATGTCCCAAAC
59838668 ATGGTCTTACACATAATCACAT
1 ATGGTCTTACACATAATCACAT
59838690 CTCGTTAATC
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
43 58 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (43 bp):
ATGGTCTTACACATAATCACATAACGATGCCAATGTCCCAAAC
Found at i:59844196 original size:21 final size:20
Alignment explanation
Indices: 59844172--59844210 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
59844162 GAGTATTTTG
59844172 ATGTTTGATGATAGATTATGA
1 ATGTTTGATGATAG-TTATGA
59844193 ATGTTTGATGATAGTTAT
1 ATGTTTGATGATAGTTAT
59844211 ACAAGTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (20 bp):
ATGTTTGATGATAGTTATGA
Found at i:59844220 original size:21 final size:21
Alignment explanation
Indices: 59844172--59844218 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
59844162 GAGTATTTTG
*
59844172 ATGTTTGATGATAGATTATGA
1 ATGTTTGATGATAGATTATCA
59844193 ATGTTTGATGATAG-TTATACA
1 ATGTTTGATGATAGATTAT-CA
59844214 A-GTTT
1 ATGTTT
59844219 TGTTAAGTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.45
Consensus pattern (21 bp):
ATGTTTGATGATAGATTATCA
Found at i:59845363 original size:20 final size:20
Alignment explanation
Indices: 59845338--59845380 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
59845328 GAGGCAATGC
59845338 ACACGCCTGTGTGCATGGGG
1 ACACGCCTGTGTGCATGGGG
59845358 ACACGCCTGTGTGCATGGGG
1 ACACGCCTGTGTGCATGGGG
59845378 ACA
1 ACA
59845381 TGCCCATGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.19, C:0.26, G:0.37, T:0.19
Consensus pattern (20 bp):
ACACGCCTGTGTGCATGGGG
Found at i:59848870 original size:29 final size:27
Alignment explanation
Indices: 59848852--59848921 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
59848842 ATATTAAGTC
59848852 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
59848879 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
59848907 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
59848922 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:59848915 original size:28 final size:28
Alignment explanation
Indices: 59848852--59848949 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
59848842 ATATTAAGTC
*
59848852 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
59848879 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
59848907 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
59848936 CGCACACTTAGTGC
1 CGCACACTTAGTGC
59848950 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:59857175 original size:29 final size:27
Alignment explanation
Indices: 59857157--59857226 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
59857147 ATATTAAGTC
59857157 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
59857184 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
59857212 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
59857227 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:59857220 original size:28 final size:28
Alignment explanation
Indices: 59857157--59857254 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
59857147 ATATTAAGTC
*
59857157 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
59857184 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
59857212 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
59857241 CGCACACTTAGTGC
1 CGCACACTTAGTGC
59857255 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:59859086 original size:56 final size:57
Alignment explanation
Indices: 59859023--59859130 Score: 191
Period size: 56 Copynumber: 1.9 Consensus size: 57
59859013 AAGTACTATC
*
59859023 ACACATATAAGATATGCAAATAAAATTTT-CTAAATTTTATGACTCGGTTTCCCGAA
1 ACACATATAAGATATGCAAATAAAATTTTACTAAATTTTATGACTCAGTTTCCCGAA
59859079 ACACATATAAGATATGCAAATAAAATTTTAACTAAATTTTATGACTCAGTTT
1 ACACATATAAGATATGCAAATAAAATTTT-ACTAAATTTTATGACTCAGTTT
59859131 TGTGGTCCCG
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
56 29 0.59
58 20 0.41
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (57 bp):
ACACATATAAGATATGCAAATAAAATTTTACTAAATTTTATGACTCAGTTTCCCGAA
Found at i:59861308 original size:23 final size:23
Alignment explanation
Indices: 59861278--59861327 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
59861268 AACATTAATC
59861278 AAATGTATGAATTGCAGCCCTTT
1 AAATGTATGAATTGCAGCCCTTT
59861301 AAATGTATGAATTGCAGCCCTTT
1 AAATGTATGAATTGCAGCCCTTT
59861324 AAAT
1 AAAT
59861328 AAACTTGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (23 bp):
AAATGTATGAATTGCAGCCCTTT
Found at i:59861883 original size:241 final size:241
Alignment explanation
Indices: 59861460--59862180 Score: 1309
Period size: 241 Copynumber: 3.0 Consensus size: 241
59861450 ATGAATTAAT
*
59861460 TTTATTACCATGTATCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
1 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
59861525 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
66 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
*
59861590 CTGTAAGATATAATAGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC
131 CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC
59861655 AAAAAGACTTGGAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
196 AAAAAGACTTGGAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
*
59861701 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTAACCTTCTCTCCAACCTT
1 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
59861766 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
66 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
*
59861831 CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACTCCACGTATGATGAATCTTAAAAAATTC
131 CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC
* * * *
59861896 AAAATGACTTGAAAAAAGTTCTATCGGGCTCATTTACCATTGAATA
196 AAAAAGACTTGGAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
* *
59861942 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAACTGATCTTCTCTCCAACCTT
1 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
* * *
59862007 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGAAAACTTGACGGGTTACCTTATATCGAG
66 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
59862072 CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATC-TAAAAAATTC
131 CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC
*
59862136 AAAAAGACTTGGAAAAAGTTCTATCGATCTCATTTACTATTGAAT
196 AAAAAGACTTGGAAAAAGTTCTATCGAGCTCATTTACTATTGAAT
59862181 TTTGATATAA
Statistics
Matches: 460, Mismatches: 20, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
240 50 0.11
241 410 0.89
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (241 bp):
TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC
AAAAAGACTTGGAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
Found at i:59862389 original size:9 final size:9
Alignment explanation
Indices: 59862366--59862537 Score: 129
Period size: 9 Copynumber: 18.6 Consensus size: 9
59862356 ATTGATCATT
*
59862366 ACTTAAATA
1 ACTTACATA
*
59862375 AATTACATA
1 ACTTACATA
59862384 ACTTACATA
1 ACTTACATA
* *
59862393 ACTCATATA
1 ACTTACATA
59862402 ACTTACATA
1 ACTTACATA
*
59862411 ATTTACATAACA
1 ACTTACAT---A
59862423 ACTTACATA
1 ACTTACATA
59862432 A-TTCACATA
1 ACTT-ACATA
59862441 ACTTACATA
1 ACTTACATA
*
59862450 ATTTACATAACA
1 ACTTACAT---A
59862462 ACTTACATA
1 ACTTACATA
59862471 A--T--ATA
1 ACTTACATA
*
59862476 ACTCACATA
1 ACTTACATA
59862485 ACTTACATA
1 ACTTACATA
*
59862494 ATTTACATA
1 ACTTACATA
*
59862503 ACTCACATA
1 ACTTACATA
*
59862512 ACGTACATAACA
1 ACTTACAT---A
59862524 ACTTACATA
1 ACTTACATA
59862533 ACTTA
1 ACTTA
59862538 ACTAATACAT
Statistics
Matches: 129, Mismatches: 19, Indels: 30
0.72 0.11 0.17
Matches are distributed among these distances:
5 4 0.03
7 1 0.01
8 2 0.02
9 96 0.74
10 2 0.02
12 24 0.19
ACGTcount: A:0.47, C:0.20, G:0.01, T:0.32
Consensus pattern (9 bp):
ACTTACATA
Found at i:59862442 original size:39 final size:39
Alignment explanation
Indices: 59862383--59862504 Score: 181
Period size: 39 Copynumber: 3.0 Consensus size: 39
59862373 TAAATTACAT
* *
59862383 AACTTACATAACTCATATAACTTACATAATTTACATAAC
1 AACTTACATAATTCACATAACTTACATAATTTACATAAC
59862422 AACTTACATAATTCACATAACTTACATAATTTACATAAC
1 AACTTACATAATTCACATAACTTACATAATTTACATAAC
59862461 AACTTACATAATATAACTCACATAACTTACATAATTTACATAAC
1 AACTTACAT-A-AT---TCACATAACTTACATAATTTACATAAC
59862505 TCACATAACG
Statistics
Matches: 76, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
39 46 0.61
40 1 0.01
41 2 0.03
44 27 0.36
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (39 bp):
AACTTACATAATTCACATAACTTACATAATTTACATAAC
Found at i:59864395 original size:64 final size:64
Alignment explanation
Indices: 59864323--59864507 Score: 264
Period size: 67 Copynumber: 2.8 Consensus size: 64
59864313 ATATAGTTCG
*
59864323 GCTCTCTTGTAC-ACATGGTGAACACTTGGAACCACGCATGCGACCTAGCTACATATATCCCGTA
1 GCTCTCTTGT-CTACATGGTGTACACTTGGAACCACGCATGCGACCTAGCTACATATATCCCGTA
*
59864387 GCTCTCTTGTCTACATGGTGTCCTTCACTTGGAACCACGCATGCGACCTAGCTACATATATCCCG
1 GCTCTCTTGTCTACATGGTG---TACACTTGGAACCACGCATGCGACCTAGCTACATATATCCCG
59864452 TA
63 TA
* * * * *
59864454 GCTCTCTTGTCTACATGGTGTACACATAGTATCACCCATGCGACCTAGCTACAT
1 GCTCTCTTGTCTACATGGTGTACACTTGGAACCACGCATGCGACCTAGCTACAT
59864508 CATAATGTCT
Statistics
Matches: 109, Mismatches: 8, Indels: 8
0.87 0.06 0.06
Matches are distributed among these distances:
63 1 0.01
64 46 0.42
67 62 0.57
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (64 bp):
GCTCTCTTGTCTACATGGTGTACACTTGGAACCACGCATGCGACCTAGCTACATATATCCCGTA
Found at i:59871636 original size:19 final size:19
Alignment explanation
Indices: 59871612--59871650 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
59871602 ACTTAGAGCG
*
59871612 GAGGCACAGCGCGGGAGGC
1 GAGGCACAGCGAGGGAGGC
59871631 GAGGCACAGCGAGGGAGGC
1 GAGGCACAGCGAGGGAGGC
59871650 G
1 G
59871651 GAGCAGAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.23, G:0.54, T:0.00
Consensus pattern (19 bp):
GAGGCACAGCGAGGGAGGC
Found at i:59874965 original size:28 final size:28
Alignment explanation
Indices: 59874904--59874999 Score: 106
Period size: 28 Copynumber: 3.4 Consensus size: 28
59874894 ATATTAAGTC
* *
59874904 CGCACACTCAGTGATA-ATTAATC-AACT
1 CGCACACTTAGTGCTATA-TAATCAAACT
59874931 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
59874959 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
59874988 CGCACACTTAGT
1 CGCACACTTAGT
59875000 TGCCAATCTC
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
27 19 0.32
28 24 0.40
29 17 0.28
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:59883339 original size:29 final size:27
Alignment explanation
Indices: 59883321--59883390 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
59883311 ATATTAAGTC
59883321 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
59883348 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
59883376 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
59883391 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:59883384 original size:28 final size:28
Alignment explanation
Indices: 59883321--59883418 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
59883311 ATATTAAGTC
*
59883321 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
59883348 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
59883376 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
59883405 CGCACACTTAGTGC
1 CGCACACTTAGTGC
59883419 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:59887778 original size:27 final size:27
Alignment explanation
Indices: 59887724--59887788 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
59887714 ATTACCAAAG
* * *
59887724 TACCCTCGATTTATATAATCACTATTT
1 TACCCTCGATTTACAAAATCACCATTT
* *
59887751 TACCCTCGATTTACAAAATTACCGTTT
1 TACCCTCGATTTACAAAATCACCATTT
*
59887778 TATCCTCGATT
1 TACCCTCGATT
59887789 GTGAAATTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.28, C:0.25, G:0.06, T:0.42
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATCACCATTT
Found at i:59887853 original size:27 final size:26
Alignment explanation
Indices: 59887823--59887943 Score: 100
Period size: 27 Copynumber: 4.5 Consensus size: 26
59887813 AGGGTAGAAT
59887823 TACCAAAATACCCCTAGTTTGTAAACA
1 TACCAAAATACCCCTAGTTTGTAAA-A
* * *
59887850 TACCAAAATACCACTGGTTTGTGAAAT
1 TACCAAAATACCCCTAGTTTGT-AAAA
* * *
59887877 TATCGAAATA-CCCTCAATTTGTAAAA
1 TACCAAAATACCCCT-AGTTTGTAAAA
* **
59887903 TTACCAAAATACCCCTAATTTACAAAA
1 -TACCAAAATACCCCTAGTTTGTAAAA
*
59887930 TTACAAAAATACCC
1 -TACCAAAATACCC
59887944 TTGACTTTCT
Statistics
Matches: 76, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
26 6 0.08
27 63 0.83
28 7 0.09
ACGTcount: A:0.43, C:0.23, G:0.07, T:0.27
Consensus pattern (26 bp):
TACCAAAATACCCCTAGTTTGTAAAA
Found at i:59887994 original size:27 final size:27
Alignment explanation
Indices: 59887955--59888006 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
59887945 TGACTTTCTA
59887955 AAAATTATAGAAATACCATTGGTTTAC
1 AAAATTATAGAAATACCATTGGTTTAC
*
59887982 AAAATTACT-GAAATACCCTTGGTTT
1 AAAATTA-TAGAAATACCATTGGTTT
59888007 GTAGATTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (27 bp):
AAAATTATAGAAATACCATTGGTTTAC
Found at i:59888124 original size:27 final size:27
Alignment explanation
Indices: 59888047--59888124 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
59888037 AAATGACTAA
* *
59888047 AATACCCCT-AATAGGTAAAAAGACCGT
1 AATACCCCTGTAT-GGTAAAATGACCGT
* * *
59888074 AA-AGCCCCTGTAGGGGAAAGTGACCGT
1 AATA-CCCCTGTATGGTAAAATGACCGT
59888101 AATACCCCTGTATGGTAAAATGAC
1 AATACCCCTGTATGGTAAAATGAC
59888125 GAATATGCCC
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
26 1 0.03
27 37 0.93
28 2 0.05
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (27 bp):
AATACCCCTGTATGGTAAAATGACCGT
Found at i:59888972 original size:25 final size:25
Alignment explanation
Indices: 59888934--59889003 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
59888924 AGGAAGTGCT
* * *
59888934 AAAAGGGCTATGCCTCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCA
*
59888959 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
59888984 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
59889004 ATTAAAAGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:59889016 original size:24 final size:24
Alignment explanation
Indices: 59888959--59889030 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 24
59888949 CAGTTTACCG
59888959 AAAAG-GGCTTTGCCCCAGTTTATC
1 AAAAGAGGCTTTGCCCCAG-TTATC
*
59888983 AAAA-AGGGCTTTGCCCCAGTTATT
1 AAAAGA-GGCTTTGCCCCAGTTATC
**
59889007 AAAAGAGGCTAGGCCTCCAGTTAT
1 AAAAGAGGCTTTGCC-CCAGTTAT
59889031 ATGATAAAGC
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
24 19 0.46
25 22 0.54
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (24 bp):
AAAAGAGGCTTTGCCCCAGTTATC
Found at i:59889272 original size:31 final size:31
Alignment explanation
Indices: 59889223--59889305 Score: 152
Period size: 31 Copynumber: 2.7 Consensus size: 31
59889213 CGCTTACAAT
59889223 AAAGGCTTCGG-CCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
59889253 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
59889284 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
59889306 TCAAGATTGA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
30 16 0.31
31 36 0.69
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:59892420 original size:28 final size:28
Alignment explanation
Indices: 59892388--59892441 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
59892378 AAATATTAAA
59892388 AATATTAATATAAA-ATAT-TATATTTTTT
1 AATATT-AT-TAAACATATATATATTTTTT
59892416 AATATTATTAAACATATATATATTTT
1 AATATTATTAAACATATATATATTTT
59892442 ATTATTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 4 0.17
27 6 0.25
28 14 0.58
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (28 bp):
AATATTATTAAACATATATATATTTTTT
Found at i:59892435 original size:26 final size:28
Alignment explanation
Indices: 59892388--59892452 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 28
59892378 AAATATTAAA
*
59892388 AATATTAATATAAAATATTATATTTTTT
1 AATATTAATATAAAATATTATATATTTT
59892416 AATATT-AT-TAAACATA-TATATATTTT
1 AATATTAATATAAA-ATATTATATATTTT
* *
59892442 ATTATTTATAT
1 AATATTAATAT
59892453 TTAGTCATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 18 0.56
27 7 0.22
28 7 0.22
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (28 bp):
AATATTAATATAAAATATTATATATTTT
Found at i:59892549 original size:15 final size:16
Alignment explanation
Indices: 59892522--59892552 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
59892512 ATTTTACTTT
59892522 AATAATAAATTTTAAA
1 AATAATAAATTTTAAA
59892538 AATAAT-AATTTTAAA
1 AATAATAAATTTTAAA
59892553 TAGTATTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAATAAATTTTAAA
Found at i:59892610 original size:15 final size:15
Alignment explanation
Indices: 59892590--59892646 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
59892580 ATTCAATATT
59892590 AATATTTTAATAATA
1 AATATTTTAATAATA
*
59892605 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
59892624 AATATATTAATAATA
1 AATATTTTAATAATA
*
59892639 AATGTTTT
1 AATATTTT
59892647 GTATTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:59892969 original size:25 final size:25
Alignment explanation
Indices: 59892941--59893018 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 25
59892931 TAAAGATAAA
*
59892941 ATAAATTCGATTAAACAATGAAAAT
1 ATAAATTCAATTAAACAATGAAAAT
** ** * *
59892966 AT-AATAAAATTTTATAAAGATAAA-
1 ATAAATTCAATTAAACAATGA-AAAT
59892990 ATAAATTCAATTAAACAATGAAAAT
1 ATAAATTCAATTAAACAATGAAAAT
59893015 ATAA
1 ATAA
59893019 GAAAATCTCA
Statistics
Matches: 37, Mismatches: 13, Indels: 6
0.66 0.23 0.11
Matches are distributed among these distances:
24 16 0.43
25 21 0.57
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.29
Consensus pattern (25 bp):
ATAAATTCAATTAAACAATGAAAAT
Found at i:59892984 original size:49 final size:49
Alignment explanation
Indices: 59892908--59893024 Score: 179
Period size: 49 Copynumber: 2.5 Consensus size: 49
59892898 ATATATGCAA
* *
59892908 AAACAATGTAAA-AT-AT-AAA-TTTATAAAGATAAAATAAATTCGATT
1 AAACAATGAAAATATAATAAAATTTTATAAAGATAAAATAAATTCAATT
59892953 AAACAATGAAAATATAATAAAATTTTATAAAGATAAAATAAATTCAATT
1 AAACAATGAAAATATAATAAAATTTTATAAAGATAAAATAAATTCAATT
*
59893002 AAACAATGAAAATATAAGAAAAT
1 AAACAATGAAAATATAATAAAAT
59893025 CTCAAATGTA
Statistics
Matches: 65, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
45 11 0.17
46 2 0.03
47 2 0.03
48 3 0.05
49 47 0.72
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (49 bp):
AAACAATGAAAATATAATAAAATTTTATAAAGATAAAATAAATTCAATT
Found at i:59893172 original size:14 final size:14
Alignment explanation
Indices: 59893153--59893182 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
59893143 TCAGGAAAGT
59893153 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
59893167 AAATCATTTTTCAG
1 AAATCATTTTCCAG
59893181 AA
1 AA
59893183 GCCATTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.37
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:59898597 original size:27 final size:27
Alignment explanation
Indices: 59898566--59898962 Score: 486
Period size: 27 Copynumber: 14.7 Consensus size: 27
59898556 CCCCAAAATA
* *
59898566 GGTAAAATGATCGTAATAACCCTGTAG
1 GGTAAAATGACCGTAATGACCCTGTAG
59898593 GGTAAAATGACCGTAATGACCCTGTAG
1 GGTAAAATGACCGTAATGACCCTGTAG
*
59898620 GGTAAAATGACCGTAAT-ACCCCTATAG
1 GGTAAAATGACCGTAATGA-CCCTGTAG
59898647 GGTAAAATGACCGTAAT-ACCCATGTAG
1 GGTAAAATGACCGTAATGACCC-TGTAG
* * *
59898674 TGTAAAATGACCGTAATG-CTCCTATTG
1 GGTAAAATGACCGTAATGAC-CCTGTAG
**
59898701 GGTAAAATGATTGTAATG-CCCTTGTAG
1 GGTAAAATGACCGTAATGACCC-TGTAG
*
59898728 GGTAAAATGATCGTAATG-CCCTTGTAG
1 GGTAAAATGACCGTAATGACCC-TGTAG
*
59898755 GGTAAAATGATCGTAAT-ACCCCTGTAG
1 GGTAAAATGACCGTAATGA-CCCTGTAG
*
59898782 GGTAAAATGACCGTAATGACCCTATAG
1 GGTAAAATGACCGTAATGACCCTGTAG
* *
59898809 GGTAAAATGACCGAAATGACCCTATAG
1 GGTAAAATGACCGTAATGACCCTGTAG
*
59898836 GGTAAAATGACCGTAATGCCCCTGTAG
1 GGTAAAATGACCGTAATGACCCTGTAG
* * *
59898863 GGTAAAAT-ACCATAATGCCCCTATAG
1 GGTAAAATGACCGTAATGACCCTGTAG
59898889 GGTAAAATGACCGTAATG-CCCTTGTAG
1 GGTAAAATGACCGTAATGACCC-TGTAG
*
59898916 GGTAAAATGACCGTAATGGCCCTGTAG
1 GGTAAAATGACCGTAATGACCCTGTAG
* **
59898943 GATAAAATGACTATAATGAC
1 GGTAAAATGACCGTAATGAC
59898963 TGTAATGCCC
Statistics
Matches: 332, Mismatches: 27, Indels: 22
0.87 0.07 0.06
Matches are distributed among these distances:
26 33 0.10
27 290 0.87
28 9 0.03
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.25
Consensus pattern (27 bp):
GGTAAAATGACCGTAATGACCCTGTAG
Found at i:59898968 original size:36 final size:36
Alignment explanation
Indices: 59898921--59898989 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
59898911 TGTAGGGTAA
*
59898921 AATGACCGTAATGGCCCTGTAGGATAAAATGACTAT
1 AATGACCGTAATGCCCCTGTAGGATAAAATGACTAT
* *
59898957 AATGACTGTAATGCCCCTGTAGGGTAAAATGAC
1 AATGACCGTAATGCCCCTGTAGGATAAAATGAC
59898990 GATTATGTCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (36 bp):
AATGACCGTAATGCCCCTGTAGGATAAAATGACTAT
Found at i:59906414 original size:14 final size:15
Alignment explanation
Indices: 59906388--59906416 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
59906378 ATAATTTAGC
59906388 AAATAATAACAAAAT
1 AAATAATAACAAAAT
59906403 AAATAA-AACAAAAT
1 AAATAATAACAAAAT
59906417 TAAGCTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (15 bp):
AAATAATAACAAAAT
Found at i:59907381 original size:25 final size:25
Alignment explanation
Indices: 59907343--59907420 Score: 84
Period size: 25 Copynumber: 3.1 Consensus size: 25
59907333 TTCCAACCCA
* *
59907343 CAGCTTGTGTGAGCATACTGATTTG
1 CAGCTCGTGTGAGCATACCGATTTG
* * * * *
59907368 TAGCTCGTGAGAGCCTACCGATCTA
1 CAGCTCGTGTGAGCATACCGATTTG
*
59907393 CAGCTCGAGTGAGCATACCGATTTG
1 CAGCTCGTGTGAGCATACCGATTTG
59907418 CAG
1 CAG
59907421 GTTGTATTAG
Statistics
Matches: 40, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (25 bp):
CAGCTCGTGTGAGCATACCGATTTG
Found at i:59911130 original size:9 final size:9
Alignment explanation
Indices: 59911116--59911146 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
59911106 ATTGGCCCAC
*
59911116 CATTTGGAA
1 CATTTGAAA
59911125 CATTTGAAA
1 CATTTGAAA
59911134 CATTTGAAA
1 CATTTGAAA
59911143 CATT
1 CATT
59911147 ACTGGTTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (9 bp):
CATTTGAAA
Found at i:59911377 original size:11 final size:11
Alignment explanation
Indices: 59911329--59911384 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
59911319 AAGGTCCATC
59911329 TTGAATTGTCT
1 TTGAATTGTCT
* *
59911340 TTGAGTTGTTCG
1 TTGAATTG-TCT
*
59911352 TTCACATCT-TCT
1 TTGA-AT-TGTCT
59911364 TTGAATTGTCT
1 TTGAATTGTCT
59911375 TTGAATTGTC
1 TTGAATTGTC
59911385 ATAAACACTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
10 1 0.03
11 22 0.63
12 10 0.29
13 1 0.03
14 1 0.03
ACGTcount: A:0.16, C:0.14, G:0.18, T:0.52
Consensus pattern (11 bp):
TTGAATTGTCT
Found at i:59915668 original size:31 final size:31
Alignment explanation
Indices: 59915628--59915713 Score: 113
Period size: 31 Copynumber: 2.8 Consensus size: 31
59915618 TCAATCTCAG
*
59915628 CATAT-ACTGGGCCAAAGCCTTTACATTATT
1 CATATCACTGGGCCGAAGCCTTTACATTATT
*
59915658 CATATCACTGGGCCGAAGCCTCTT-TATTATT
1 CATATCACTGGGCCGAAGCCT-TTACATTATT
* *
59915689 CATATCACTAGGCTGAAGCCTTTAC
1 CATATCACTGGGCCGAAGCCTTTAC
59915714 TGTAAACGGT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
30 7 0.15
31 39 0.81
32 2 0.04
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.33
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTACATTATT
Found at i:59915965 original size:25 final size:25
Alignment explanation
Indices: 59915932--59916000 Score: 111
Period size: 25 Copynumber: 2.8 Consensus size: 25
59915922 CTCTTTTAAT
*
59915932 AACTAGGGCAAAGCCCTTTTCGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
59915957 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
59915982 AACTGGGGCATAGCCCTTT
1 AACTGGGGCAAAGCCCTTT
59916001 AGCACTTCCT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:59916073 original size:21 final size:20
Alignment explanation
Indices: 59916049--59916093 Score: 72
Period size: 21 Copynumber: 2.2 Consensus size: 20
59916039 ATATATATAT
59916049 ATATCATGGCATATCATGTGC
1 ATATCATGGCATATCATG-GC
*
59916070 ATATCATGGCATATTATGGC
1 ATATCATGGCATATCATGGC
59916090 ATAT
1 ATAT
59916094 TATGTACAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.36
Consensus pattern (20 bp):
ATATCATGGCATATCATGGC
Found at i:59916097 original size:10 final size:10
Alignment explanation
Indices: 59916049--59916093 Score: 72
Period size: 10 Copynumber: 4.4 Consensus size: 10
59916039 ATATATATAT
59916049 ATATCATGGC
1 ATATCATGGC
59916059 ATATCATGTGC
1 ATATCATG-GC
59916070 ATATCATGGC
1 ATATCATGGC
*
59916080 ATATTATGGC
1 ATATCATGGC
59916090 ATAT
1 ATAT
59916094 TATGTACAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
10 23 0.70
11 10 0.30
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.36
Consensus pattern (10 bp):
ATATCATGGC
Found at i:59920268 original size:40 final size:40
Alignment explanation
Indices: 59920222--59920446 Score: 281
Period size: 40 Copynumber: 5.6 Consensus size: 40
59920212 CTTGCACAAG
* * *
59920222 GCCTTCGGGTCTTAGCCCGGATGTGGTCACTAGCATAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* *
59920262 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* * *
59920302 GCCTTCGGGTTTTAGCCCGGATATAATCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* * *
59920342 GCCTTAGGGTCTTAGCCCGGATATAG-CAACTCGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAAT
* * * *
59920382 GCCTTCGGATCTTAGTCCGGTTATAGTCACCTAGCACAAAA
1 GCCTTCGGGTCTTAGCCCGGATATAGTCA-CTAGCACAAAT
*
59920423 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
59920447 CATTCGAATA
Statistics
Matches: 157, Mismatches: 25, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
39 1 0.01
40 127 0.81
41 29 0.18
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
Found at i:59920317 original size:80 final size:80
Alignment explanation
Indices: 59920186--59920446 Score: 294
Period size: 80 Copynumber: 3.3 Consensus size: 80
59920176 CTCAAGTAAT
* * * * * * * *
59920186 CTTCGGGATTTAG-CTGGATATAACTACTTGCAC-AAGGCCTTCGGGTCTTAGCCCGGATGTGGT
1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGT
*
59920249 CACTAGCATAAATGC
66 CACTAGCACAAATGC
* * *
59920264 CTTCGGGACTTAGCCCGGATATAGTC-GCTAGCACAAATGCCTTCGGGTTTTAGCCCGGATATAA
1 CTTCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATAG
*
59920328 TCGCTAGCACAAATGC
65 TCACTAGCACAAATGC
* * * * * * *
59920344 CTTAGGGTCTTAGCCCGGATATAGCAACTCGCACGAATGCCTTCGGATCTTAGTCCGGTTATAGT
1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGT
*
59920409 CACCTAGCACAAAAGC
66 CA-CTAGCACAAATGC
59920425 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
59920447 CATTCGAATA
Statistics
Matches: 152, Mismatches: 26, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
78 12 0.08
79 15 0.10
80 93 0.61
81 32 0.21
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGT
CACTAGCACAAATGC
Found at i:59932523 original size:14 final size:14
Alignment explanation
Indices: 59932504--59932532 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
59932494 ATAAGAAGAA
59932504 TGAAGAACATGGCT
1 TGAAGAACATGGCT
59932518 TGAAGAACATGGCT
1 TGAAGAACATGGCT
59932532 T
1 T
59932533 TAATTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.14, G:0.28, T:0.24
Consensus pattern (14 bp):
TGAAGAACATGGCT
Found at i:59933572 original size:19 final size:20
Alignment explanation
Indices: 59933550--59933598 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 20
59933540 ATTATTTTCG
* *
59933550 AAAAATAATGAATTTTTA-T
1 AAAAATAATGAAATTGTACT
*
59933569 -AAAATAATTAAATTGTACT
1 AAAAATAATGAAATTGTACT
59933588 AAAAAT-ATGAA
1 AAAAATAATGAA
59933599 CATGATGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
18 14 0.58
19 5 0.21
20 5 0.21
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.35
Consensus pattern (20 bp):
AAAAATAATGAAATTGTACT
Found at i:59936976 original size:17 final size:19
Alignment explanation
Indices: 59936934--59936977 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
59936924 ATGAAATTTT
*
59936934 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
59936953 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
59936971 AA-TATTA
1 AATTATTA
59936978 CTGTAAGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:59938066 original size:20 final size:19
Alignment explanation
Indices: 59938041--59938082 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
59938031 ATTTTCTTTC
59938041 CTTCTCTTATCTATTCCCCT
1 CTTCTCTTATCT-TTCCCCT
* *
59938061 CTTCTCTTTTCTTTCTCCT
1 CTTCTCTTATCTTTCCCCT
59938080 CTT
1 CTT
59938083 GCCGATTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.05, C:0.38, G:0.00, T:0.57
Consensus pattern (19 bp):
CTTCTCTTATCTTTCCCCT
Found at i:59939496 original size:20 final size:20
Alignment explanation
Indices: 59939473--59939531 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
59939463 TAAACATGGT
59939473 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
* * * *
59939493 ATGTATGATAAT-AAAATTAT
1 ATGTATGAT-ATGCACATGAC
59939513 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
59939532 TGTATTCATA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
19 2 0.07
20 26 0.87
21 2 0.07
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.34
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:59939640 original size:23 final size:24
Alignment explanation
Indices: 59939582--59939746 Score: 223
Period size: 23 Copynumber: 7.0 Consensus size: 24
59939572 GAAGAAGTGC
59939582 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
59939606 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
59939630 -AAAGGGTTTATGCCCC-GTTTATT
1 AAAAGGGCTTATGCCCCAG-TTATT
**
59939653 AAAAGGGCTTACACCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
59939677 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
59939700 AAAAGGGCTT-CGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
59939723 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
59939747 ATGATAAAGC
Statistics
Matches: 126, Mismatches: 8, Indels: 13
0.86 0.05 0.09
Matches are distributed among these distances:
22 1 0.01
23 59 0.47
24 57 0.45
25 9 0.07
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.28
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:59939652 original size:47 final size:47
Alignment explanation
Indices: 59939583--59939725 Score: 236
Period size: 47 Copynumber: 3.1 Consensus size: 47
59939573 AAGAAGTGCA
*
59939583 AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTACGCCCCAGTTATT
* *
59939630 AAAGGGTTTATGCCCC-GTTTATTAAAAGGGCTTACACCCCAGTTATT
1 AAAGGGCTTATGCCCCAG-TTATTAAAAGGGCTTACGCCCCAGTTATT
59939677 AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTT-CGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTACGCCCCAGTTATT
59939723 AAA
1 AAA
59939726 AGAGGCTAGG
Statistics
Matches: 89, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
46 16 0.18
47 72 0.81
48 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (47 bp):
AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTACGCCCCAGTTATT
Found at i:59939975 original size:31 final size:31
Alignment explanation
Indices: 59939940--59940002 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
59939930 CGTTTACAGT
59939940 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
59939971 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
59940002 A
1 A
59940003 TTATGAAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:59947510 original size:44 final size:44
Alignment explanation
Indices: 59947445--59947528 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
59947435 TTGATATCTC
* *
59947445 AAAGTCCATGGTTGTACCATGGCAATTAAGGAAGAATTGAAGGA
1 AAAGTCCATGGTTATAACATGGCAATTAAGGAAGAATTGAAGGA
* *
59947489 AAAGTCCAT-GTTCATAACATGGCATTTAAGGAGGAATTGA
1 AAAGTCCATGGTT-ATAACATGGCAATTAAGGAAGAATTGA
59947529 CGGTTAAGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 3 0.09
44 32 0.91
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (44 bp):
AAAGTCCATGGTTATAACATGGCAATTAAGGAAGAATTGAAGGA
Found at i:59947726 original size:47 final size:47
Alignment explanation
Indices: 59947668--59947789 Score: 208
Period size: 47 Copynumber: 2.6 Consensus size: 47
59947658 GCATTGGCAC
* *
59947668 TAAGACAAGGATACCATGTAACACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGACATTTGG
59947715 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGACATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGACATTTGG
* *
59947762 TAAGATAAGGATATCATGTAAGACCATG
1 TAAGACAAGGATACCATGTAAGACCATG
59947790 CCAAGGCATG
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 71 1.00
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (47 bp):
TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGACATTTGG
Found at i:59947732 original size:95 final size:92
Alignment explanation
Indices: 59947534--59947803 Score: 213
Period size: 95 Copynumber: 2.9 Consensus size: 92
59947524 ATTGACGGTT
* * * * *
59947534 AAGGATACCATGTAAGACCATATCAAAATATGGCATTGGTAAGGCAAGGATCCCGTGTAAGACCA
1 AAGGATACCATGTAAGACCACATCAAAATATGGCATTGGTAAGACAAGGATACCATGTAACACCA
* *
59947599 TGTCAAGACATGGCATCGGCATTGATT
66 TGTCAAGACATGGCATCGGCATAGATC
* *
59947626 AAGGACT-CCATGTAAGACCACATCAAGATGTGGCATTGGCACTAAGACAAGGATACCATGTAAC
1 AAGGA-TACCATGTAAGACCACATCAAAATATGGCATTGG---TAAGACAAGGATACCATGTAAC
*** * *
59947690 ACCATGTTTGGAACATGGCATTTGGTA-AGA-C
62 ACCATGTCAAG-ACATGGCA-TCGGCATAGATC
** *** * * * * *
59947721 AAGGATACCATGTAAGACCATGTTTGGAACATGACATTTGGTAAGATAAGGATATCATGTAAGAC
1 AAGGATACCATGTAAGACCA-CATCAAAATATGGCA-TTGGTAAGACAAGGATACCATGTAACAC
* *
59947786 CATGCCAAGGCATGGCAT
64 CATGTCAAGACATGGCAT
59947804 TGATAAGTTC
Statistics
Matches: 138, Mismatches: 31, Indels: 18
0.74 0.17 0.10
Matches are distributed among these distances:
92 35 0.25
93 8 0.06
94 27 0.20
95 44 0.32
96 16 0.12
97 8 0.06
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (92 bp):
AAGGATACCATGTAAGACCACATCAAAATATGGCATTGGTAAGACAAGGATACCATGTAACACCA
TGTCAAGACATGGCATCGGCATAGATC
Found at i:59947902 original size:108 final size:107
Alignment explanation
Indices: 59947776--59947972 Score: 295
Period size: 107 Copynumber: 1.8 Consensus size: 107
59947766 ATAAGGATAT
* * * *
59947776 CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGTAAGGAAATCATGTAATACC
1 CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTC-ATAAGGCAAGGAAACCACGTAAGACC
* *
59947841 ATGTCGAGACATGGCATTGATGAGTACTATAAGGCAAAGGTCC
65 ATGTCAAGACATGGCAATGATGAGTACTATAAGGCAAAGGTCC
* * *
59947884 CATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGCAAGGATACCACGTAAGACCA
1 CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCATAAGGCAAGGAAACCACGTAAGACCA
*
59947949 TGTCAAGACATGGCAATGGTGAGT
66 TGTCAAGACATGGCAATGATGAGT
59947973 TCAAAAAGGA
Statistics
Matches: 79, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
107 43 0.54
108 36 0.46
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.22
Consensus pattern (107 bp):
CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCATAAGGCAAGGAAACCACGTAAGACCA
TGTCAAGACATGGCAATGATGAGTACTATAAGGCAAAGGTCC
Found at i:59947975 original size:53 final size:54
Alignment explanation
Indices: 59947768--59947974 Score: 238
Period size: 54 Copynumber: 3.9 Consensus size: 54
59947758 TTGGTAAGAT
* * * *
59947768 AAGGATATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
* * * * * *
59947822 AAGGAAATCATGTAATACCATGTCGAGACATGGCATTGATGAGTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
* * *
59947876 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
* * * *
59947929 AAGGATACCACGTAAGACCATGTCAAGACATGGCAATGGTGAGTTC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTC
59947975 AAAAAGGAAA
Statistics
Matches: 129, Mismatches: 22, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
52 4 0.03
53 43 0.33
54 78 0.60
55 4 0.03
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
Found at i:59948099 original size:16 final size:17
Alignment explanation
Indices: 59948078--59948111 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
59948068 TTATTTAATA
*
59948078 TTGAGATTGT-AAGTAT
1 TTGAGATTATCAAGTAT
59948094 TTGAGATTATCAAGTAT
1 TTGAGATTATCAAGTAT
59948111 T
1 T
59948112 AAGTAAGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.32, C:0.03, G:0.21, T:0.44
Consensus pattern (17 bp):
TTGAGATTATCAAGTAT
Found at i:59948666 original size:55 final size:55
Alignment explanation
Indices: 59948600--59948711 Score: 197
Period size: 55 Copynumber: 2.0 Consensus size: 55
59948590 TGGTATGTAA
59948600 ATATTTGATAATGATTAGCTACTGAAATGGATAATGAAGAACATGTTTTGGTGTT
1 ATATTTGATAATGATTAGCTACTGAAATGGATAATGAAGAACATGTTTTGGTGTT
* * *
59948655 ATATTTGATAATGGTTAGCTATTGAAATGGCTAATGAAGAACATGTTTTGGTGTT
1 ATATTTGATAATGATTAGCTACTGAAATGGATAATGAAGAACATGTTTTGGTGTT
59948710 AT
1 AT
59948712 GTATGCCTAA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.33, C:0.05, G:0.22, T:0.39
Consensus pattern (55 bp):
ATATTTGATAATGATTAGCTACTGAAATGGATAATGAAGAACATGTTTTGGTGTT
Found at i:59956693 original size:28 final size:28
Alignment explanation
Indices: 59956661--59956718 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
59956651 CCATTTGTGG
59956661 TTTTAAGTTTTATTTGGGCTTTGATTTC
1 TTTTAAGTTTTATTTGGGCTTTGATTTC
59956689 TTTTAAGTTTTATTTGGGCTTTGATTTC
1 TTTTAAGTTTTATTTGGGCTTTGATTTC
59956717 TT
1 TT
59956719 ACCTTAAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.14, C:0.07, G:0.17, T:0.62
Consensus pattern (28 bp):
TTTTAAGTTTTATTTGGGCTTTGATTTC
Found at i:59964203 original size:125 final size:125
Alignment explanation
Indices: 59964063--59964288 Score: 314
Period size: 127 Copynumber: 1.8 Consensus size: 125
59964053 ATGTTTTTAA
* *
59964063 TTTAAAAATAAAAGATGATAAT-TATTAATATATAATTATATCTATTATAA-TATCTATTGATTA
1 TTTAAAAATAAAAGATGATAATCT-TTAATATATAATTATATCTATTATAATTATATATTAATTA
* * *
59964126 TTATCAACTTTA-TATAGAGTTAGGATTTGTGTTAATTTCATCATATTTTATTTGATAAGTT
65 TTATCAA-TTTAGCATAGAATTAGGATTAGTGTTAATTTCATCATATTTTATTTGATAAGTT
* *
59964187 TTTAATAATAATAAGATGATAATCTTTAATATATAATTATATCTATTTTAATTTATATATTAATT
1 TTTAAAAATAA-AAGATGATAATCTTTAATATATAATTATATCTATTATAA-TTATATATTAATT
* *
59964252 TTTATCAATTTAGCATAGAATTAGGATTAGTTTTAAT
64 ATTATCAATTTAGCATAGAATTAGGATTAGTGTTAAT
59964289 CATATCTCAT
Statistics
Matches: 88, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
124 10 0.11
125 36 0.41
126 5 0.06
127 37 0.42
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.48
Consensus pattern (125 bp):
TTTAAAAATAAAAGATGATAATCTTTAATATATAATTATATCTATTATAATTATATATTAATTAT
TATCAATTTAGCATAGAATTAGGATTAGTGTTAATTTCATCATATTTTATTTGATAAGTT
Found at i:59964334 original size:17 final size:18
Alignment explanation
Indices: 59964308--59964341 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
59964298 TTTTTGTTTA
59964308 AATAAATTAATA-GCATT
1 AATAAATTAATATGCATT
*
59964325 AATAATTTAATATGCAT
1 AATAAATTAATATGCAT
59964342 ATATTTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (18 bp):
AATAAATTAATATGCATT
Found at i:59965908 original size:13 final size:13
Alignment explanation
Indices: 59965890--59965914 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59965880 CCAAGCACAC
59965890 GCCCGTGTCCTTG
1 GCCCGTGTCCTTG
59965903 GCCCGTGTCCTT
1 GCCCGTGTCCTT
59965915 TACACGGCCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.40, G:0.28, T:0.32
Consensus pattern (13 bp):
GCCCGTGTCCTTG
Found at i:59969631 original size:22 final size:22
Alignment explanation
Indices: 59969606--59969650 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
59969596 CTGGATATTC
59969606 ACATACTATTGGTATGGACTCA
1 ACATACTATTGGTATGGACTCA
59969628 ACATACTATTGGTATGGACTCA
1 ACATACTATTGGTATGGACTCA
59969650 A
1 A
59969651 TCTTCAACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (22 bp):
ACATACTATTGGTATGGACTCA
Found at i:59972794 original size:47 final size:47
Alignment explanation
Indices: 59972725--59972977 Score: 389
Period size: 47 Copynumber: 5.4 Consensus size: 47
59972715 CCCTTCGGGA
* ** * *
59972725 CTTATCACATTTATTCACTTTCACATCCATCACATTGGCCATTAGGT
1 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTAGGC
* * *
59972772 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTAGGC
* *
59972819 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTAGGC
*
59972866 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTAGGC
* *
59972913 CTTAGCACATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTAGGC
59972960 CTTATCACATATACACAC
1 CTTATCACATATACACAC
59972978 CTTGTACATC
Statistics
Matches: 190, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 190 1.00
ACGTcount: A:0.28, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTAGGC
Found at i:59989364 original size:40 final size:40
Alignment explanation
Indices: 59989257--59989408 Score: 200
Period size: 40 Copynumber: 3.8 Consensus size: 40
59989247 AGTGATTAAT
*
59989257 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
59989296 TTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
* * * *
59989337 TCCGGGCCAAGTCCCGAAGGCATTTGTGCTAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
** * *
59989377 TCCGGGCTAACACCCGATGGC-CTTGTGCGAGT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
59989409 GGTTATATTC
Statistics
Matches: 100, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
39 9 0.09
40 90 0.90
41 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
Found at i:59999675 original size:48 final size:49
Alignment explanation
Indices: 59999604--59999830 Score: 239
Period size: 48 Copynumber: 4.7 Consensus size: 49
59999594 TATGTGTGCT
* *
59999604 AGTGTAAGAACATGTCTGGGACATAGCATCGGCCA-CATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACCATTATGAGAGCC
* * * * *
59999652 AGTGTAGGACCATGTCTGGGACATGGCATCAGCC-TCAATATGCGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACCATTATGAGAGCC
* * * *** * *
59999700 AGTGTAAGACCATGTTTGGAACATGGCATC-ACCATTGTTAT-ATGTGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACCATTATGA-GAGCC
59999748 AGTGTAAGACCATGTCTGGGACATGGCATCGG-CACCGATGTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACC-AT-TATGAGAGCC
* *
59999798 AGTGTAAGACCATGTCTGAGACATGACATCGGC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC
59999831 ATTTTACCCT
Statistics
Matches: 145, Mismatches: 26, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
47 2 0.01
48 105 0.72
49 1 0.01
50 36 0.25
51 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (49 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACCATTATGAGAGCC
Found at i:60011336 original size:29 final size:29
Alignment explanation
Indices: 60011304--60011380 Score: 118
Period size: 29 Copynumber: 2.7 Consensus size: 29
60011294 AATCATACTC
*
60011304 ATATTGCCCATTAGGCCCAAATCACCTGT
1 ATATGGCCCATTAGGCCCAAATCACCTGT
*
60011333 ATATGGCCCATTAGGCCCAAATCACCTTT
1 ATATGGCCCATTAGGCCCAAATCACCTGT
* *
60011362 ATATGGCTCGTTAGGCCCA
1 ATATGGCCCATTAGGCCCA
60011381 GTCACATTCA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (29 bp):
ATATGGCCCATTAGGCCCAAATCACCTGT
Found at i:60011630 original size:24 final size:24
Alignment explanation
Indices: 60011603--60011653 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
60011593 GTAGCCAAAC
*
60011603 TTTCGACTTTTC-AGCATTTCTGCT
1 TTTCGACTTTTCGA-CATTTCGGCT
60011627 TTTCGACTTTTCGACATTTCGGCT
1 TTTCGACTTTTCGACATTTCGGCT
60011651 TTT
1 TTT
60011654 GCCGATACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.12, C:0.24, G:0.14, T:0.51
Consensus pattern (24 bp):
TTTCGACTTTTCGACATTTCGGCT
Found at i:60016505 original size:43 final size:43
Alignment explanation
Indices: 60016423--60016515 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 43
60016413 ACATGTAATC
* * *
60016423 ACATATCAATGCCACTGTCCCATACAGGGTTTTACACGAGAAA
1 ACATATCAATGCCACTGTCCCAAACAGGGTCTTAAACGAGAAA
* *
60016466 ACATGTCAATGCCAAC-GTCCCAAAC-GTGGTCTTAAACGAGAAC
1 ACATATCAATGCC-ACTGTCCCAAACAG-GGTCTTAAACGAGAAA
60016509 ACATATC
1 ACATATC
60016516 GAAAATCCTA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
42 1 0.02
43 39 0.93
44 2 0.05
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (43 bp):
ACATATCAATGCCACTGTCCCAAACAGGGTCTTAAACGAGAAA
Found at i:60022636 original size:46 final size:46
Alignment explanation
Indices: 60022564--60022715 Score: 175
Period size: 46 Copynumber: 3.4 Consensus size: 46
60022554 GCTAATTATG
*
60022564 TGCACTTAGTGTGCGAAATCGAGATAGCTTCGGCTATATATATTTT
1 TGCACTTAGTGTGCGAGATCGAGATAGCTTCGGCTATATATATTTT
* * * *
60022610 TGCATTTAGTGTGCGAGATCAAGATAGCTTCAGCTATATATATATT
1 TGCACTTAGTGTGCGAGATCGAGATAGCTTCGGCTATATATATTTT
* * * * *
60022656 GGCACTTAGTGTGCAAGATTGATACAGCTTCGGCTAT-T-TA-TTT
1 TGCACTTAGTGTGCGAGATCGAGATAGCTTCGGCTATATATATTTT
* *
60022699 TGTACTAAGTGTGCGAG
1 TGCACTTAGTGTGCGAG
60022716 TTTCTCGAGT
Statistics
Matches: 88, Mismatches: 18, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
43 15 0.17
44 2 0.02
45 1 0.01
46 70 0.80
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.36
Consensus pattern (46 bp):
TGCACTTAGTGTGCGAGATCGAGATAGCTTCGGCTATATATATTTT
Found at i:60023616 original size:33 final size:33
Alignment explanation
Indices: 60023579--60023642 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
60023569 ATGCAGTAAT
* * *
60023579 AGTCTGGGCCTGAGCCCTATTCAGTATCAGTAC
1 AGTCTGGGCCTAAGCCCTATACAGTAGCAGTAC
60023612 AGTCTGGGCCTAAGCCCTATACAGTAGCAGT
1 AGTCTGGGCCTAAGCCCTATACAGTAGCAGT
60023643 GTGGGCCTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (33 bp):
AGTCTGGGCCTAAGCCCTATACAGTAGCAGTAC
Found at i:60023647 original size:28 final size:27
Alignment explanation
Indices: 60023606--60023665 Score: 84
Period size: 28 Copynumber: 2.2 Consensus size: 27
60023596 TATTCAGTAT
*
60023606 CAGTACAGTCTGGGCCTAAGCCCTATA
1 CAGTACAGTCTGGGCCTAAGCCCAATA
* *
60023633 CAGTAGCAGTGTGGGCCTAAGCCCAATG
1 CAGTA-CAGTCTGGGCCTAAGCCCAATA
60023661 CAGTA
1 CAGTA
60023666 ACAATACAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 5 0.17
28 24 0.83
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (27 bp):
CAGTACAGTCTGGGCCTAAGCCCAATA
Found at i:60023817 original size:26 final size:26
Alignment explanation
Indices: 60023788--60023858 Score: 124
Period size: 26 Copynumber: 2.7 Consensus size: 26
60023778 CACCAATATC
* *
60023788 GCAGCAAAGCTACCAGAAATAATGAT
1 GCAGCATAGCTGCCAGAAATAATGAT
60023814 GCAGCATAGCTGCCAGAAATAATGAT
1 GCAGCATAGCTGCCAGAAATAATGAT
60023840 GCAGCATAGCTGCCAGAAA
1 GCAGCATAGCTGCCAGAAA
60023859 CAATAAATGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.41, C:0.21, G:0.23, T:0.15
Consensus pattern (26 bp):
GCAGCATAGCTGCCAGAAATAATGAT
Found at i:60023904 original size:27 final size:27
Alignment explanation
Indices: 60023874--60023938 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
60023864 AATGTGGTAA
* *
60023874 AGCCACCAGTATCAGT-AATTATGGCAT
1 AGCCACCAGTAACAGTGAA-TATGACAT
*
60023901 AGCCACCAGTAACAGTGAATGTGACAT
1 AGCCACCAGTAACAGTGAATATGACAT
*
60023928 AGTCACCAGTA
1 AGCCACCAGTA
60023939 CAGAACTTCC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 31 0.94
28 2 0.06
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (27 bp):
AGCCACCAGTAACAGTGAATATGACAT
Found at i:60024109 original size:27 final size:27
Alignment explanation
Indices: 60024079--60024183 Score: 90
Period size: 27 Copynumber: 3.9 Consensus size: 27
60024069 ATGCACAATC
*
60024079 GTCATTTTACCATA-TAGGGGTATCACG
1 GTCATTTTACC-TACTAGGGGTATTACG
* * *
60024106 GTCACTTTACCCTACAAGGGCT-TTACG
1 GTCATTTTA-CCTACTAGGGGTATTACG
* *
60024133 GTCATTGTATCCTAC-AGGGGCATTACG
1 GTCATTTTA-CCTACTAGGGGTATTACG
* *
60024160 GTCTTTTTACCTATTAGGGGTATT
1 GTCATTTTACCTACTAGGGGTATT
60024184 TTAGTCATTT
Statistics
Matches: 61, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
26 8 0.13
27 46 0.75
28 7 0.11
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCTACTAGGGGTATTACG
Found at i:60024364 original size:54 final size:54
Alignment explanation
Indices: 60024221--60024401 Score: 179
Period size: 54 Copynumber: 3.3 Consensus size: 54
60024211 TTGGTAAATC
* *** * *
60024221 TACAAACTAAGGGTATTTCAATAATTTTGCAAACCAATGGTATTTC-AGTAATTTT
1 TACAAATTAAGGGTATTTTGGTAATTTTGCAAATCAAGGGTATTTCTA-TAA-TTT
* *
60024276 TA-AAAGTTAAGGGTATTTTTGTAATTTTGTAAATCAAGGGTATTTCTATAATTT
1 TACAAA-TTAAGGGTATTTTGGTAATTTTGCAAATCAAGGGTATTTCTATAATTT
* * * * * *
60024330 TCCAAATCAAAGGTATTTTGGTAATTTTCCAAATCAGGGGTATTT-TGGTAATTT
1 TACAAATTAAGGGTATTTTGGTAATTTTGCAAATCAAGGGTATTTCT-ATAATTT
60024384 TACAAATTAAGGGTATTT
1 TACAAATTAAGGGTATTT
60024402 CGATAATGTT
Statistics
Matches: 104, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
53 1 0.01
54 61 0.59
55 41 0.39
56 1 0.01
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (54 bp):
TACAAATTAAGGGTATTTTGGTAATTTTGCAAATCAAGGGTATTTCTATAATTT
Found at i:60024408 original size:81 final size:81
Alignment explanation
Indices: 60024204--60024462 Score: 259
Period size: 81 Copynumber: 3.2 Consensus size: 81
60024194 CACCCTACAA
* * * * * * * *
60024204 GGGTGTTTTGGTAAATCTACAAACTAAGGGTATTTCAATAATTTTGCAAACCAATGGTATTTCAG
1 GGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCAATAATTTTACAAATCAAAGGTATTTCGG
* *
60024269 TAATTTTTA-AAAGTTAA
66 TAA-TTTTACAAA-TCAG
* ** * * * *
60024286 GGGTATTTTTGTAATTTTGTAAATCAAGGGTATTTCTATAATTTTCCAAATCAAAGGTATTTTGG
1 GGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCAATAATTTTACAAATCAAAGGTATTTCGG
*
60024351 TAATTTTCCAAATCAG
66 TAATTTTACAAATCAG
* * ** *
60024367 GGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGATAATGTTACAGGTCGAAGGTATTTCGG
1 GGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCAATAATTTTACAAATCAAAGGTATTTCGG
* *
60024432 TAACTTTACAAACCAG
66 TAATTTTACAAATCAG
*
60024448 GGGTATTTTAGTAAT
1 GGGTATTTTGGTAAT
60024463 ACTAGCCTAC
Statistics
Matches: 144, Mismatches: 32, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
81 87 0.60
82 57 0.40
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (81 bp):
GGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCAATAATTTTACAAATCAAAGGTATTTCGG
TAATTTTACAAATCAG
Found at i:60024413 original size:27 final size:27
Alignment explanation
Indices: 60024221--60024455 Score: 156
Period size: 27 Copynumber: 8.7 Consensus size: 27
60024211 TTGGTAAATC
*
60024221 TACAAA-CTAAGGGTATTTCAATAATTT
1 TACAAATC-AAGGGTATTTCGATAATTT
* * *
60024248 TGCAAACCAATGGTATTTC-AGTAATTTT
1 TACAAATCAAGGGTATTTCGA-TAA-TTT
* *
60024276 TA-AAAGTTAAGGGTATTTTTG-TAATTT
1 TACAAA-TCAAGGGTA-TTTCGATAATTT
** *
60024303 TGTAAATCAAGGGTATTTCTATAATTT
1 TACAAATCAAGGGTATTTCGATAATTT
* * * *
60024330 TCCAAATCAAAGGTATTTTGGTAATTT
1 TACAAATCAAGGGTATTTCGATAATTT
* * * *
60024357 TCCAAATCAGGGGTATTTTGGTAATTT
1 TACAAATCAAGGGTATTTCGATAATTT
* *
60024384 TACAAATTAAGGGTATTTCGATAATGT
1 TACAAATCAAGGGTATTTCGATAATTT
** * *
60024411 TACAGGTCGAA-GGTATTTCGGTAACTT
1 TACAAATC-AAGGGTATTTCGATAATTT
* *
60024438 TACAAACCAGGGGTATTT
1 TACAAATCAAGGGTATTT
60024456 TAGTAATACT
Statistics
Matches: 163, Mismatches: 35, Indels: 20
0.75 0.16 0.09
Matches are distributed among these distances:
26 5 0.03
27 136 0.83
28 19 0.12
29 3 0.02
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (27 bp):
TACAAATCAAGGGTATTTCGATAATTT
Found at i:60027215 original size:33 final size:33
Alignment explanation
Indices: 60027177--60027239 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
60027167 GAGGTGTACA
60027177 TTCC-TTTCTAAATGGTACACACAAAGTATACCT
1 TTCCTTTTC-AAATGGTACACACAAAGTATACCT
* *
60027210 TTCCTTTTCATATGGTATACACAAAGTATA
1 TTCCTTTTCAAATGGTACACACAAAGTATA
60027240 TCTAACCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 23 0.85
34 4 0.15
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.37
Consensus pattern (33 bp):
TTCCTTTTCAAATGGTACACACAAAGTATACCT
Found at i:60044950 original size:16 final size:16
Alignment explanation
Indices: 60044910--60044952 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
60044900 CTTACCATTC
*
60044910 ATGTTCATCAAGTAAT
1 ATGTTCATTAAGTAAT
*
60044926 -TCGTACATTAAGTAAT
1 AT-GTTCATTAAGTAAT
60044942 ATGTTCATTAA
1 ATGTTCATTAA
60044953 CTTAGTCAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
15 1 0.05
16 20 0.91
17 1 0.05
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.40
Consensus pattern (16 bp):
ATGTTCATTAAGTAAT
Found at i:60045250 original size:32 final size:33
Alignment explanation
Indices: 60045191--60045255 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 33
60045181 CATATAGTAT
*
60045191 ACACAAAGTAGACCTAACATTTCCAAG-TGTAC
1 ACACAAAGTAGACATAACATTTCCAAGTTGTAC
* *
60045223 ACACAAAG-AGTACATAACCTTTTCAAGTTGTAC
1 ACACAAAGTAG-ACATAACATTTCCAAGTTGTAC
60045256 CATTTGGGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 2 0.07
32 21 0.75
33 5 0.18
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.25
Consensus pattern (33 bp):
ACACAAAGTAGACATAACATTTCCAAGTTGTAC
Found at i:60048021 original size:96 final size:96
Alignment explanation
Indices: 60047837--60048022 Score: 241
Period size: 96 Copynumber: 1.9 Consensus size: 96
60047827 TTTACTTTCT
* * *
60047837 TCTCTTGTTGGATATTTAATTGGACATCGAAAACCCTTATATCCTTTTCAACTACACCAATAACA
1 TCTCTAGTTGGATATTTAATTGGACATCGAAAACCCTCATATCCTTTGCAACTACACCAATAACA
* * * *
60047902 TTGCATAAAAGGTGATAGCTCAATCTTGTTC
66 TTGCACAAAAGGTAAAAGATCAATCTTGTTC
* * *
60047933 TCTCTAGTTGGATATTTTATTGGACATCGGAAACCCTCATGAT-CTTTGGAACTACACCAATAAC
1 TCTCTAGTTGGATATTTAATTGGACATCGAAAACCCTCAT-ATCCTTTGCAACTACACCAATAAC
*
60047997 AGTT-CACAATAGGTAAAAGATCAATC
65 A-TTGCACAAAAGGTAAAAGATCAATC
60048023 ATACTCCTAT
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
96 73 0.95
97 4 0.05
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (96 bp):
TCTCTAGTTGGATATTTAATTGGACATCGAAAACCCTCATATCCTTTGCAACTACACCAATAACA
TTGCACAAAAGGTAAAAGATCAATCTTGTTC
Found at i:60055383 original size:56 final size:56
Alignment explanation
Indices: 60055297--60055528 Score: 455
Period size: 56 Copynumber: 4.1 Consensus size: 56
60055287 ACAAGGGATG
*
60055297 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
60055353 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
60055409 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
60055465 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
60055521 ATGGGCAA
1 ATGGGCAA
60055529 TAAACTAATA
Statistics
Matches: 175, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 175 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
Found at i:60055635 original size:10 final size:10
Alignment explanation
Indices: 60055601--60055634 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
60055591 CATGACCAAA
*
60055601 AAAAAAAGAA
1 AAAAAAAGAG
60055611 AAAAAAAGAG
1 AAAAAAAGAG
*
60055621 AAAAGAAGAG
1 AAAAAAAGAG
60055631 AAAA
1 AAAA
60055635 GCTCTCATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAG
Found at i:60056110 original size:39 final size:40
Alignment explanation
Indices: 60056012--60056193 Score: 192
Period size: 40 Copynumber: 4.6 Consensus size: 40
60056002 AATGATGTCT
* * * *
60056012 GGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCC
* * *
60056052 GGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATTCC
1 GGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATCC
* *
60056092 GGGCTAAG-CCCGAAGGCATTTGTACGAGTTACTAAATCT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCC
*
60056131 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCC
* **
60056171 GGGCTATGTTTCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTG
60056194 AACGAGTAGC
Statistics
Matches: 118, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
39 33 0.28
40 75 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCC
Found at i:60056215 original size:79 final size:79
Alignment explanation
Indices: 60056062--60056226 Score: 192
Period size: 79 Copynumber: 2.1 Consensus size: 79
60056052 GGACTAAGAT
* *
60056062 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTACGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
* *
60056127 ATCTGGGTTAAGTC
66 ATCTCGGTTAAATC
* * **
60056141 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTTTCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
60056204 TATATC-CGGTTAAATT
63 TAAATCTCGGTTAAATC
60056220 CCGAAGG
1 CCGAAGG
60056227 TACGTGATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.66
80 23 0.32
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCTCGGTTAAATC
Found at i:60062728 original size:56 final size:56
Alignment explanation
Indices: 60062642--60062817 Score: 343
Period size: 56 Copynumber: 3.1 Consensus size: 56
60062632 ACAAGGGATG
*
60062642 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
60062698 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
60062754 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
60062810 ATGGGCAA
1 ATGGGCAA
60062818 TAAACTAATA
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 119 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
Found at i:60062921 original size:10 final size:10
Alignment explanation
Indices: 60062887--60062920 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
60062877 GCATGACCAA
*
60062887 AAAAAAAGAA
1 AAAAAAAGAG
60062897 AAAAAAAGAG
1 AAAAAAAGAG
*
60062907 AAAAGAAGAG
1 AAAAAAAGAG
60062917 AAAA
1 AAAA
60062921 GCTCTCATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAG
Found at i:60063431 original size:79 final size:81
Alignment explanation
Indices: 60063295--60063479 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
60063285 TCGAATGATG
*
60063295 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAATGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAATGACCAAATCCGGACTAAGATCCGAAGGCATT
60063359 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * * **
60063374 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAATGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
60063436 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
60063454 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
60063480 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAATGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Done.