Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008940.1 Hibiscus syriacus cultivar Beakdansim tig00112259_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: 476028
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:46 original size:29 final size:31
Alignment explanation
Indices: 1--60 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
1 TTTACCTATGTTCTTC-GGA-CATATGGACTG
1 TTTACCTATGTTCTTCGGGATC-TATGGACTG
31 TTTACCTA-GTTCTTCGGGATCTATGGACTG
1 TTTACCTATGTTCTTCGGGATCTATGGACTG
61 GTCCTTCGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 7 0.25
30 20 0.71
31 1 0.04
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.40
Consensus pattern (31 bp):
TTTACCTATGTTCTTCGGGATCTATGGACTG
Found at i:1831 original size:14 final size:14
Alignment explanation
Indices: 1771--1832 Score: 51
Period size: 14 Copynumber: 4.5 Consensus size: 14
1761 TATATATAAT
*
1771 AAAAATCAA-AGAG
1 AAAAATAAATAGAG
1784 AAAATATAAA-AGA-
1 AAAA-ATAAATAGAG
1797 AAATAATAAATAGAG
1 AAA-AATAAATAGAG
*
1812 ATAAATAAATA-AG
1 AAAAATAAATAGAG
1825 TAAAAATA
1 -AAAAATA
1833 TGTATATACT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
13 14 0.34
14 25 0.61
15 2 0.05
ACGTcount: A:0.71, C:0.02, G:0.10, T:0.18
Consensus pattern (14 bp):
AAAAATAAATAGAG
Found at i:1976 original size:2 final size:2
Alignment explanation
Indices: 1969--2007 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1959 AAATAATAGA
1969 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
2008 AATGAAGAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2170 original size:21 final size:20
Alignment explanation
Indices: 2136--2174 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2126 AATAAATATA
2136 TAATATAAAAATATATATTT
1 TAATATAAAAATATATATTT
*
2156 TAATAATAAATATATATAT
1 TAAT-ATAAAAATATATAT
2175 ACTAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TAATATAAAAATATATATTT
Found at i:2185 original size:21 final size:20
Alignment explanation
Indices: 2137--2188 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
2127 ATAAATATAT
* * *
2137 AATATAAAAATATATATTTT
1 AATATAAATATATATATCTA
2157 AATAATAAATATATATATACTA
1 AAT-ATAAATATATATAT-CTA
2179 AATATAAATA
1 AATATAAATA
2189 GAAGTAGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.11
21 20 0.74
22 4 0.15
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
AATATAAATATATATATCTA
Found at i:2700 original size:263 final size:254
Alignment explanation
Indices: 2233--2747 Score: 888
Period size: 263 Copynumber: 2.0 Consensus size: 254
2223 TGTGTGTGCT
*
2233 TGTGTGTATATATAATTAATGTTAATAACATAATATGTATATAAATAAAAACTAAATAAGATGGC
1 TGTGTATATATATAATTAATGTTAATAACATAATATGTATATAAATAAAAACTAAATAAGATGGC
2298 TAAGACCTAAAAAAATAATTGTTTTCATGGAGAAATCTTAAGAAATGTTAGATTTTTTTAAAAAA
66 TAAGACCTAAAAAAATAATTGTTTTCATGGAGAAATCTTAAGAAATGTTAGATTTTTTTAAAAAA
*
2363 AATGTATTCGAGATCATTTTCCTTGTAAGTTTCTTTTCTCCAATAAATTTTTCAAAAGAACAAAA
131 AATGTATTCGAGATCATTTTCCTTGTAAGTTTCTTTTCTACAATAAATTTTTCAAAAGAACAAAA
*
2428 CTATAACGTATGAAATAATCACAAA-AAAAGTCAAGAATAAAAAGAGAATTACCTTGTG
196 CTATAACGTATGAAATAATCACAAATAAAAGTCAAGAATAAAAAGAGAAATACCTTGTG
2486 TGTGTATATATATAATTAATGTTAATAACATAAATATGTATATAAATAAAAAACTAAAATAAGAT
1 TGTGTATATATATAATTAATGTTAATAACAT-AATATGTATATAAAT-AAAAACT-AAATAAGAT
2551 GGCTAAGACCTAAAAAAATAATTGTTTTTCATGGAGAAATCTTAAGAAATGTTAGATTTTTTTAA
63 GGCTAAGACCTAAAAAAATAATTG-TTTTCATGGAGAAATCTTAAGAAATGTTAGATTTTTTT--
* *
2616 AAAAAAAATGTATTCGAGATCATTTTCCTTGTTCTTCAGTTTCTTTTCTACAATAAATTTTTTAA
125 AAAAAAAATGTATTCGAGATCATTTTCCTTG----TAAGTTTCTTTTCTACAATAAATTTTTCAA
2681 AAGAACAAAACTATAACGTATGAAATAATCACAAATAAAAGTCAAGAATAAAAAGAGAAATACCT
186 AAGAACAAAACTATAACGTATGAAATAATCACAAATAAAAGTCAAGAATAAAAAGAGAAATACCT
2746 TG
251 TG
2748 AAACAAAAAG
Statistics
Matches: 246, Mismatches: 5, Indels: 11
0.94 0.02 0.04
Matches are distributed among these distances:
253 30 0.12
254 15 0.06
255 7 0.03
256 33 0.13
257 38 0.15
259 31 0.13
263 62 0.25
264 30 0.12
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.34
Consensus pattern (254 bp):
TGTGTATATATATAATTAATGTTAATAACATAATATGTATATAAATAAAAACTAAATAAGATGGC
TAAGACCTAAAAAAATAATTGTTTTCATGGAGAAATCTTAAGAAATGTTAGATTTTTTTAAAAAA
AATGTATTCGAGATCATTTTCCTTGTAAGTTTCTTTTCTACAATAAATTTTTCAAAAGAACAAAA
CTATAACGTATGAAATAATCACAAATAAAAGTCAAGAATAAAAAGAGAAATACCTTGTG
Found at i:2989 original size:18 final size:20
Alignment explanation
Indices: 2951--2988 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2941 GATACATAAT
2951 TAAAAGAAAAAATCTTAAAA
1 TAAAAGAAAAAATCTTAAAA
*
2971 TAAAA-AAAAATTCTTAAA
1 TAAAAGAAAAAATCTTAAA
2989 TTATCCTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (20 bp):
TAAAAGAAAAAATCTTAAAA
Found at i:3815 original size:14 final size:15
Alignment explanation
Indices: 3779--3815 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
3769 CGCGGATAAT
*
3779 GCCCGCCCCGCATCC
1 GCCCGCCCCACATCC
3794 GCCCGCCCCACATCC
1 GCCCGCCCCACATCC
3809 G-CCGCCC
1 GCCCGCCC
3816 AGCTAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.08, C:0.68, G:0.19, T:0.05
Consensus pattern (15 bp):
GCCCGCCCCACATCC
Found at i:6492 original size:16 final size:17
Alignment explanation
Indices: 6464--6495 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6454 AACTTTGACC
6464 AAAAAGTCAAAATTTTT
1 AAAAAGTCAAAATTTTT
6481 AAAAAGTC-AAATTTT
1 AAAAAGTCAAAATTTT
6496 ATGTTTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.34
Consensus pattern (17 bp):
AAAAAGTCAAAATTTTT
Found at i:6614 original size:18 final size:20
Alignment explanation
Indices: 6570--6614 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 20
6560 GTTTTTCAGT
6570 GTTTTG-TTTTCGAATTTAA
1 GTTTTGTTTTTCGAATTTAA
*
6589 -TTTGGTTTTTCG-A-TTAA
1 GTTTTGTTTTTCGAATTTAA
6606 GTTTTGTTT
1 GTTTTGTTT
6615 CTGATGTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
17 4 0.18
18 12 0.55
19 6 0.27
ACGTcount: A:0.16, C:0.04, G:0.18, T:0.62
Consensus pattern (20 bp):
GTTTTGTTTTTCGAATTTAA
Found at i:8310 original size:2 final size:2
Alignment explanation
Indices: 8303--8364 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
8293 ATACTATTTG
8303 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8345 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
8365 CTGATTACTT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11995 original size:26 final size:26
Alignment explanation
Indices: 11966--12018 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
11956 TCCAATGTTC
* *
11966 AAATGACCAAAATACCTTGAACCCTA
1 AAATAACCAAAATACCTTAAACCCTA
* *
11992 AAATAACTAAAATACCTTAAACTCTA
1 AAATAACCAAAATACCTTAAACCCTA
12018 A
1 A
12019 GATGGTCGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.51, C:0.23, G:0.04, T:0.23
Consensus pattern (26 bp):
AAATAACCAAAATACCTTAAACCCTA
Found at i:12840 original size:2 final size:2
Alignment explanation
Indices: 12833--12864 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
12823 CGACTATTTG
12833 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12865 GGTTACTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16102 original size:22 final size:21
Alignment explanation
Indices: 16037--16115 Score: 65
Period size: 22 Copynumber: 3.6 Consensus size: 21
16027 AAATAGTAAG
16037 TAAA-AAAACAAATAATAAAATA
1 TAAATAAAACAAATAA-AAAA-A
* *
16059 TATATAAAA-AAGAAAAAGAAAA
1 TAAATAAAACAA-ATAAA-AAAA
16081 TAAATAAAACAAATAAACAAAA
1 TAAATAAAACAAATAAA-AAAA
16103 T-AATAATAACAAA
1 TAAATAA-AACAAA
16116 GTACGAATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
21 5 0.11
22 30 0.64
23 12 0.26
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.16
Consensus pattern (21 bp):
TAAATAAAACAAATAAAAAAA
Found at i:16526 original size:34 final size:32
Alignment explanation
Indices: 16449--16527 Score: 81
Period size: 34 Copynumber: 2.4 Consensus size: 32
16439 ATATAACAAC
*
16449 AATAAT-ATCAATAAAAAAGAAAATAAATATAA
1 AATAATGAT-AATAAAAAAGAAAATAAATAAAA
* *
16481 TATAATGATAATAAAATATAGAAAATTAATAAAA
1 AATAATGATAATAAAA-A-AGAAAATAAATAAAA
16515 AAT-ATGTATAATA
1 AATAATG-ATAATA
16528 TTATAAATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
32 12 0.31
33 6 0.15
34 21 0.54
ACGTcount: A:0.66, C:0.01, G:0.05, T:0.28
Consensus pattern (32 bp):
AATAATGATAATAAAAAAGAAAATAAATAAAA
Found at i:16662 original size:12 final size:11
Alignment explanation
Indices: 16634--16674 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
16624 TAACAAAATA
* *
16634 AATAATATAAA
1 AATAATACAAG
16645 AATAATACAAG
1 AATAATACAAG
16656 TAATAATACAAG
1 -AATAATACAAG
16668 AATAATA
1 AATAATA
16675 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (11 bp):
AATAATACAAG
Found at i:17408 original size:37 final size:37
Alignment explanation
Indices: 17367--17471 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
17357 GTGCTTGTGG
* *
17367 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
* * * *
17404 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
* *
17441 ATCCTATTTTTATGAGTTTTAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAG
17472 GACGAAAAGG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
Found at i:18507 original size:106 final size:106
Alignment explanation
Indices: 18188--19668 Score: 2099
Period size: 106 Copynumber: 14.0 Consensus size: 106
18178 GCATTGTTCC
* * ** * *
18188 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTATTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * * *
18252 ACCAGTC-GTCCCTTTCATTGTGAAGTTGAACTTGTGTTGTCTT
65 ACCAG-CGGTCCC-TTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
18295 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCT-AAA---AGAA-AT-TTTGTTAACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
18354 TCAGTC-G-CCCTTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTG
66 CCAG-CGGTCCC-TTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * * * *
18396 G-GTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTTTAAAATTGGGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
18460 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
18501 GAGTCCAATATCCTAT-GTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
1 GAGTCCAATATCCT-TCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
*
18565 ACCAGCGGTCCCTTCGTCGTGAATTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
18607 GAGTCCAATATCC-TCGTTGTGAAGTTGAAAGTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
18671 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
18712 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTCGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
18777 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
18818 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
18883 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
18924 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTTTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
18989 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
19030 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
19095 CCAGTGGTCCCTTAGTTGTTAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
19136 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
19201 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
19242 GAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
19307 CCAGCGGTCCCTTCATTGTGAAGTTGAACTTGCGTTGTTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
19348 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
19413 CCAGCGGTCCCTTCGCCATGAAGTTGAACTTGTGTTATCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
19454 GAGTCCAATATCCCTCGCTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
19519 CCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
19560 GAGTCCAATATCCTTCCCTGTGAAGTTGAAATTGGCTCCGAAATTGGAAATTTG-TTGTTGTCAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
19624 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
19665 GAGT
1 GAGT
19669 GGCACGATAT
Statistics
Matches: 1244, Mismatches: 116, Indels: 30
0.89 0.08 0.02
Matches are distributed among these distances:
100 62 0.05
101 21 0.02
102 1 0.00
103 3 0.00
104 4 0.00
105 150 0.12
106 963 0.77
107 39 0.03
108 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.35
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:21160 original size:26 final size:27
Alignment explanation
Indices: 21130--21189 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
21120 GTTTTTATCC
21130 CTTTTTCTTTT-TGATTTTTGTTC-TTT
1 CTTTTT-TTTTCTGATTTTTGTTCTTTT
** *
21156 CTTTTTTTTTCTTCTTTTTTTTCTTTT
1 CTTTTTTTTTCTGATTTTTGTTCTTTT
21183 CTTTTTT
1 CTTTTTT
21190 CCCTTTTTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 4 0.14
26 15 0.52
27 10 0.34
ACGTcount: A:0.02, C:0.13, G:0.03, T:0.82
Consensus pattern (27 bp):
CTTTTTTTTTCTGATTTTTGTTCTTTT
Found at i:21161 original size:14 final size:13
Alignment explanation
Indices: 21144--21189 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
21134 TTCTTTTTGA
*
21144 TTTTTGTTCTTTC
1 TTTTTTTTCTTTC
21157 TTTTTTTT-TCTTC
1 TTTTTTTTCT-TTC
21170 TTTTTTTTCTTTTC
1 TTTTTTTTC-TTTC
21184 TTTTTT
1 TTTTTT
21190 CCCTTTTTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 1 0.03
13 18 0.62
14 9 0.31
15 1 0.03
ACGTcount: A:0.00, C:0.13, G:0.02, T:0.85
Consensus pattern (13 bp):
TTTTTTTTCTTTC
Found at i:21170 original size:17 final size:17
Alignment explanation
Indices: 21144--21190 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
21134 TTCTTTTTGA
*
21144 TTTTTGTTCTTTCTTTT
1 TTTTTCTTCTTTCTTTT
21161 TTTTTCTTCTTT-TTTT
1 TTTTTCTTCTTTCTTTT
*
21177 TCTTTTCTTTTTTC
1 T-TTTTCTTCTTTC
21191 CCTTTTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 5 0.19
17 21 0.81
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (17 bp):
TTTTTCTTCTTTCTTTT
Found at i:21187 original size:12 final size:12
Alignment explanation
Indices: 21144--21190 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
21134 TTCTTTTTGA
*
21144 TTTTTGTTCTTTC
1 TTTTTTTTC-TTC
21157 TTTTTTTTTCTTC
1 -TTTTTTTTCTTC
21170 TTTTTTTTCTT-
1 TTTTTTTTCTTC
21181 TTCTTTTTTC
1 TT-TTTTTTC
21191 CCTTTTTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
11 2 0.06
12 18 0.58
13 3 0.10
14 8 0.26
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (12 bp):
TTTTTTTTCTTC
Found at i:21195 original size:23 final size:23
Alignment explanation
Indices: 21153--21202 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
21143 ATTTTTGTTC
*
21153 TTTC-TTTTTTTTTCTTCTTTTT
1 TTTCTTTTTTTTTTCTCCTTTTT
21175 TTTCTTTTCTTTTTTC-CCTTTTT
1 TTTCTTTT-TTTTTTCTCCTTTTT
*
21198 GTTCT
1 TTTCT
21203 GATTGAATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 4 0.17
23 13 0.54
24 7 0.29
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (23 bp):
TTTCTTTTTTTTTTCTCCTTTTT
Found at i:25653 original size:20 final size:19
Alignment explanation
Indices: 25595--25653 Score: 50
Period size: 20 Copynumber: 3.1 Consensus size: 19
25585 AAAAGAAAAC
**
25595 AAAT-TAAGTAAAATGATA
1 AAATGTAAGTAAAAAAATA
*
25613 AAATG-AAGAAAACAAAGATA
1 AAATGTAAGTAAA-AAA-ATA
25633 AAATAGTAAGTAAAAAAATA
1 AAAT-GTAAGTAAAAAAATA
25653 A
1 A
25654 TAAAATATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 10 0.31
19 1 0.03
20 11 0.34
21 4 0.12
22 6 0.19
ACGTcount: A:0.68, C:0.02, G:0.12, T:0.19
Consensus pattern (19 bp):
AAATGTAAGTAAAAAAATA
Found at i:25984 original size:2 final size:2
Alignment explanation
Indices: 25941--25965 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25931 CTTGTGTAGA
25941 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
25966 ATAGTAAAAT
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:26218 original size:12 final size:11
Alignment explanation
Indices: 26190--26230 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
26180 TAACAAAATA
* *
26190 AATAATATAAA
1 AATAATACAAT
26201 AATAATACAAGT
1 AATAATACAA-T
26213 AATAATACAAT
1 AATAATACAAT
26224 AATAATA
1 AATAATA
26231 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (11 bp):
AATAATACAAT
Found at i:26337 original size:12 final size:12
Alignment explanation
Indices: 26315--26359 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
26305 GAATAAAAGG
26315 AAAATATAATAGT
1 AAAA-ATAATAGT
*
26328 AAAAATAATAAT
1 AAAAATAATAGT
*
26340 AAATATAATAGT
1 AAAAATAATAGT
*
26352 AATAATAA
1 AAAAATAA
26360 AAATGCAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 23 0.85
13 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (12 bp):
AAAAATAATAGT
Found at i:26966 original size:37 final size:37
Alignment explanation
Indices: 26925--27029 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
26915 GTGCTTGTGG
* * * *
26925 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTAT
* * *
26962 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTAT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTAT
*
26999 ATCCTATTTTTATGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
27030 GACGAAAAGG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTAT
Found at i:30180 original size:49 final size:49
Alignment explanation
Indices: 30123--30223 Score: 202
Period size: 49 Copynumber: 2.1 Consensus size: 49
30113 TTAGTTAATT
30123 AGTTATCGATTGTTAAATCGGTCGGATTATAAAATTATTATTAAAGCTG
1 AGTTATCGATTGTTAAATCGGTCGGATTATAAAATTATTATTAAAGCTG
30172 AGTTATCGATTGTTAAATCGGTCGGATTATAAAATTATTATTAAAGCTG
1 AGTTATCGATTGTTAAATCGGTCGGATTATAAAATTATTATTAAAGCTG
30221 AGT
1 AGT
30224 CTTTGGATAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.39
Consensus pattern (49 bp):
AGTTATCGATTGTTAAATCGGTCGGATTATAAAATTATTATTAAAGCTG
Found at i:36258 original size:12 final size:12
Alignment explanation
Indices: 36233--36290 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
36223 ACGAAGATAT
* *
36233 CAGAAATCAAAA
1 CAGAATTCAGAA
36245 CAGAATTCAGAA
1 CAGAATTCAGAA
* *
36257 CAGAATCCAGAT
1 CAGAATTCAGAA
*
36269 CAGAAATCAGAA
1 CAGAATTCAGAA
36281 CAGAATTCAG
1 CAGAATTCAG
36291 GTCATTTATC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.52, C:0.19, G:0.16, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:36301 original size:24 final size:24
Alignment explanation
Indices: 36245--36327 Score: 87
Period size: 24 Copynumber: 3.5 Consensus size: 24
36235 GAAATCAAAA
* *
36245 CAGAATTCAGAACAGAATCCAGAT
1 CAGAAATCAGAACAGAATTCAGAT
*
36269 CAGAAATCAGAACAGAATTCAGGT
1 CAGAAATCAGAACAGAATTCAGAT
***
36293 CATTTATCAGAACAGAATTCA-AGT
1 CAGAAATCAGAACAGAATTCAGA-T
*
36317 CGGAAATCAGA
1 CAGAAATCAGA
36328 TAAAATATTT
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.19
Consensus pattern (24 bp):
CAGAAATCAGAACAGAATTCAGAT
Found at i:38091 original size:30 final size:30
Alignment explanation
Indices: 38056--38117 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
38046 CCGGAGTATT
38056 ATCATAATTTCCCATCCAAGTACCTTTAAC
1 ATCATAATTTCCCATCCAAGTACCTTTAAC
38086 ATCATAATTTCCCATCCAAGTACCTTTAAC
1 ATCATAATTTCCCATCCAAGTACCTTTAAC
38116 AT
1 AT
38118 TTAACCTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (30 bp):
ATCATAATTTCCCATCCAAGTACCTTTAAC
Found at i:38863 original size:18 final size:18
Alignment explanation
Indices: 38840--38910 Score: 58
Period size: 18 Copynumber: 3.9 Consensus size: 18
38830 GTCGGTCAAC
38840 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
* *
38858 GGTCAACAGGTTGGGTAAACG
1 GGTCAACGGGTCGGGT---CG
*
38879 GG-C--CGGGTCGTGTCG
1 GGTCAACGGGTCGGGTCG
*
38894 GGTCAATGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
38911 AATGGGTCGG
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
15 4 0.10
16 1 0.03
18 30 0.75
20 1 0.03
21 4 0.10
ACGTcount: A:0.14, C:0.20, G:0.46, T:0.20
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:38888 original size:36 final size:36
Alignment explanation
Indices: 38846--38927 Score: 101
Period size: 36 Copynumber: 2.3 Consensus size: 36
38836 CAACGGTCAA
*
38846 CGGGTCGGGTCGGGTCAACAGGTTGGGTAAACGGGC
1 CGGGTCGGGTCGGGTCAACAGGTCGGGTAAACGGGC
* ** * * *
38882 CGGGTCGTGTCGGGTCAATGGGTCGGGTCAATGGGT
1 CGGGTCGGGTCGGGTCAACAGGTCGGGTAAACGGGC
38918 CGGGTCGGGT
1 CGGGTCGGGT
38928 TGTGACCGGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.12, C:0.18, G:0.49, T:0.21
Consensus pattern (36 bp):
CGGGTCGGGTCGGGTCAACAGGTCGGGTAAACGGGC
Found at i:38908 original size:13 final size:13
Alignment explanation
Indices: 38890--38923 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
38880 GCCGGGTCGT
38890 GTCGGGTCAATGG
1 GTCGGGTCAATGG
38903 GTCGGGTCAATGG
1 GTCGGGTCAATGG
38916 GTCGGGTC
1 GTCGGGTC
38924 GGGTTGTGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.12, C:0.18, G:0.47, T:0.24
Consensus pattern (13 bp):
GTCGGGTCAATGG
Found at i:41022 original size:12 final size:12
Alignment explanation
Indices: 40997--41054 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
40987 ACGAAGATAT
* *
40997 CAGAAATCAAAA
1 CAGAATTCAGAA
41009 CAGAATTCAGAA
1 CAGAATTCAGAA
* *
41021 CAGAATCCAGAT
1 CAGAATTCAGAA
*
41033 CAGAAATCAGAA
1 CAGAATTCAGAA
41045 CAGAATTCAG
1 CAGAATTCAG
41055 GTCATTTATC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.52, C:0.19, G:0.16, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:41050 original size:24 final size:24
Alignment explanation
Indices: 41009--41091 Score: 87
Period size: 24 Copynumber: 3.5 Consensus size: 24
40999 GAAATCAAAA
* *
41009 CAGAATTCAGAACAGAATCCAGAT
1 CAGAAATCAGAACAGAATTCAGAT
*
41033 CAGAAATCAGAACAGAATTCAGGT
1 CAGAAATCAGAACAGAATTCAGAT
***
41057 CATTTATCAGAACAGAATTCA-AGT
1 CAGAAATCAGAACAGAATTCAGA-T
*
41081 CGGAAATCAGA
1 CAGAAATCAGA
41092 TAAATATTTA
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.19
Consensus pattern (24 bp):
CAGAAATCAGAACAGAATTCAGAT
Found at i:43586 original size:13 final size:13
Alignment explanation
Indices: 43568--43633 Score: 66
Period size: 13 Copynumber: 5.3 Consensus size: 13
43558 GTCGGTCAAC
43568 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
43581 GGTCAACGGGTTG
1 GGTCAACGGGTCG
* *
43594 GGTAAACGGGCCG
1 GGTCAACGGGTCG
43607 GGT---CGGGTCG
1 GGTCAACGGGTCG
* *
43617 GTTCAATGGGTCG
1 GGTCAACGGGTCG
43630 GGTC
1 GGTC
43634 GGGTTGTGAC
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
10 8 0.19
13 34 0.81
ACGTcount: A:0.14, C:0.20, G:0.47, T:0.20
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:53841 original size:2 final size:2
Alignment explanation
Indices: 53834--53873 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
53824 GAATTTGTCA
53834 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53874 GATAAATTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55478 original size:2 final size:2
Alignment explanation
Indices: 55473--55796 Score: 95
Period size: 2 Copynumber: 168.5 Consensus size: 2
55463 AAAAATTAAA
* *
55473 AT AT AT AT AT AT AT AT A- AT AT A- AGT TT AT AT AT AA ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT
* * * *
55515 AT AT -T TT AT AT AT A- AA AT AT AT AT AA ACT AT AT TT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* * * *
55555 AT AA ACT AT AT A- AT -T AT -T AT A- AG CT AT AT AT AT AA AT -T
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
55593 AT GT TT AT AT -T A- ACT AT AT AT AT AA AT -T AT GT AT AT AA ACT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT A-T
* * * * * *
55634 AT AT AT GT AT AA ACT AT AA AA AGT AT AT A- AT TT AT AA ACT AT
1 AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT A-T AT
* *
55676 A- AT TT AT AT -T A- AT A- AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
55714 AGT TT AT A- AT TT AT AT -T A- AT AT AGT AT AT AT AT GT AT GT AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* * *
55755 A- ACT A- AT AT AA AT A- AT CT AT AG AT -T AT AT AT AT AT AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55794 AT A
1 AT A
55797 GTTTATAGAA
Statistics
Matches: 231, Mismatches: 54, Indels: 74
0.64 0.15 0.21
Matches are distributed among these distances:
1 25 0.11
2 194 0.84
3 12 0.05
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:55513 original size:11 final size:11
Alignment explanation
Indices: 55499--55566 Score: 63
Period size: 11 Copynumber: 6.5 Consensus size: 11
55489 AATATAAGTT
55499 TATATATAAAC
1 TATATATAAAC
***
55510 TATATATATTT
1 TATATATAAAC
*
55521 TATATATAAAA
1 TATATATAAAC
55532 TATATATAAAC
1 TATATATAAAC
*
55543 TATAT-T-TA-
1 TATATATAAAC
55551 TAT-TATAAAC
1 TATATATAAAC
55561 TATATA
1 TATATA
55567 ATTATTATAA
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
7 1 0.02
8 4 0.09
9 2 0.05
10 4 0.09
11 33 0.75
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (11 bp):
TATATATAAAC
Found at i:55515 original size:13 final size:13
Alignment explanation
Indices: 55469--55651 Score: 88
Period size: 13 Copynumber: 14.7 Consensus size: 13
55459 ATTAAAAAAT
*
55469 TAAAATATATATA
1 TAAACTATATATA
*
55482 TATA-TATA-ATA
1 TAAACTATATATA
* *
55493 T-AAGTTTATATA
1 TAAACTATATATA
55505 TAAACTATATATA
1 TAAACTATATATA
*
55518 T----TTTATATA
1 TAAACTATATATA
55527 TAAA--ATATATA
1 TAAACTATATATA
55538 TAAACTATAT-T-
1 TAAACTATATATA
* * *
55549 TATATTATAAACTA
1 TAAACTATATA-TA
55563 TATAA-T-TAT-TA
1 TA-AACTATATATA
*
55574 TAAGCTATATATA
1 TAAACTATATATA
* *
55587 TAAATTATGTTTATA
1 TAAACTA--TATATA
*
55602 TTAACTATATATA
1 TAAACTATATATA
* *
55615 TAAATTATGTATA
1 TAAACTATATATA
55628 TAAACTATATATGTA
1 TAAACTATATA--TA
55643 TAAACTATA
1 TAAACTATA
55652 AAAAGTATAT
Statistics
Matches: 127, Mismatches: 24, Indels: 36
0.68 0.13 0.19
Matches are distributed among these distances:
9 8 0.06
10 2 0.02
11 29 0.23
12 12 0.09
13 51 0.40
14 3 0.02
15 22 0.17
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.45
Consensus pattern (13 bp):
TAAACTATATATA
Found at i:55534 original size:9 final size:10
Alignment explanation
Indices: 55475--55714 Score: 50
Period size: 11 Copynumber: 22.9 Consensus size: 10
55465 AAATTAAAAT
*
55475 ATATATATAT
1 ATATATATAA
55485 ATATAATATAA
1 ATAT-ATATAA
*
55496 GTTTATATATAA
1 --ATATATATAA
*
55508 ACTATATATATT
1 A-TATATATA-A
*
55520 TTATATATAAA
1 ATATATAT-AA
55531 ATATATATAA
1 ATATATATAA
*
55541 ACTATAT-T-T
1 A-TATATATAA
55550 ATAT-TATAA
1 ATATATATAA
*
55559 A-CTATATAA
1 ATATATATAA
*
55568 TTAT-TATAA
1 ATATATATAA
55577 GCTATATATATAA
1 ---ATATATATAA
*
55590 AT-TATGT--
1 ATATATATAA
*
55597 TTATAT-TAA
1 ATATATATAA
55606 CTATATATATAA
1 --ATATATATAA
55618 ATTATGTATATAA
1 A-TA--TATATAA
**
55631 ACTATATATGT
1 A-TATATATAA
*
55642 ATAAACTATAA
1 ATATA-TATAA
*
55653 AAAGTATATAA
1 ATA-TATATAA
* *
55664 TTTATAAACTATA
1 -ATATATA-TA-A
* *
55677 ATTTATATTA
1 ATATATATAA
*
55687 ATA-ATATAT
1 ATATATATAA
*
55696 ATATATATAC
1 ATATATATAA
55706 ATATATATA
1 ATATATATA
55715 GTTTATAATT
Statistics
Matches: 165, Mismatches: 35, Indels: 60
0.63 0.13 0.23
Matches are distributed among these distances:
7 3 0.02
8 8 0.05
9 23 0.14
10 32 0.19
11 59 0.36
12 21 0.13
13 19 0.12
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.45
Consensus pattern (10 bp):
ATATATATAA
Found at i:55876 original size:14 final size:14
Alignment explanation
Indices: 55853--55919 Score: 73
Period size: 14 Copynumber: 4.8 Consensus size: 14
55843 TAGTTTATAA
55853 AAACCCTAAATCAT
1 AAACCCTAAATCAT
* * *
55867 AAACCATAAAACCT
1 AAACCCTAAATCAT
*
55881 AAACCCTAGATCAT
1 AAACCCTAAATCAT
*
55895 GAACCCTAAAATC-T
1 AAACCCT-AAATCAT
55909 AAACCCTAAAT
1 AAACCCTAAAT
55920 TTTATAAACT
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
13 4 0.10
14 34 0.81
15 4 0.10
ACGTcount: A:0.49, C:0.28, G:0.03, T:0.19
Consensus pattern (14 bp):
AAACCCTAAATCAT
Found at i:55885 original size:28 final size:28
Alignment explanation
Indices: 55853--55919 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
55843 TAGTTTATAA
55853 AAACCCTAAATCATAAACCATAAAACCT
1 AAACCCTAAATCATAAACCATAAAACCT
* * * *
55881 AAACCCTAGATCATGAACCCTAAAATCT
1 AAACCCTAAATCATAAACCATAAAACCT
55909 AAACCCTAAAT
1 AAACCCTAAAT
55920 TTTATAAACT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.49, C:0.28, G:0.03, T:0.19
Consensus pattern (28 bp):
AAACCCTAAATCATAAACCATAAAACCT
Found at i:56116 original size:20 final size:20
Alignment explanation
Indices: 56099--56176 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
56089 ACATGTATGA
*
56099 ATAAACTATGTATAGTATAT
1 ATAAACTATATATAGTATAT
*
56119 ATAAACTATATATA-TATAAC
1 ATAAACTATATATAGTAT-AT
*
56139 ATAATACATAAATATA-TATAT
1 ATAA-AC-TATATATAGTATAT
* *
56160 AGAAACTATATAAAGTA
1 ATAAACTATATATAGTA
56177 AATTACTTAT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
19 9 0.19
20 22 0.47
21 6 0.13
22 10 0.21
ACGTcount: A:0.54, C:0.06, G:0.05, T:0.35
Consensus pattern (20 bp):
ATAAACTATATATAGTATAT
Found at i:56521 original size:16 final size:17
Alignment explanation
Indices: 56500--56532 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
56490 CCTTGATATT
56500 ATTTAAA-AAATTAAAA
1 ATTTAAATAAATTAAAA
*
56516 ATTTAAATAGATTAAAA
1 ATTTAAATAAATTAAAA
56533 TTAATAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
ATTTAAATAAATTAAAA
Found at i:57256 original size:13 final size:12
Alignment explanation
Indices: 57188--57257 Score: 61
Period size: 13 Copynumber: 5.4 Consensus size: 12
57178 GTTCAGTGCC
57188 AATAATTTTATT
1 AATAATTTTATT
*
57200 AATAATGTT-TT
1 AATAATTTTATT
*
57211 ATATAATTTACATTT
1 A-ATAATTT-TA-TT
57226 AAATAATTTTATT
1 -AATAATTTTATT
57239 AAATAATTTTATAT
1 -AATAATTTTAT-T
57253 AATAA
1 AATAA
57258 GTATATTTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
11 3 0.06
12 14 0.29
13 19 0.40
14 2 0.04
15 9 0.19
16 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (12 bp):
AATAATTTTATT
Found at i:57600 original size:11 final size:11
Alignment explanation
Indices: 57586--57617 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
57576 TCTGTTCAAT
57586 TCGGGTTCAGG
1 TCGGGTTCAGG
*
57597 TCGGGTGCAGG
1 TCGGGTTCAGG
57608 TCGGGTTCAG
1 TCGGGTTCAG
57618 ATCTACAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.09, C:0.19, G:0.47, T:0.25
Consensus pattern (11 bp):
TCGGGTTCAGG
Found at i:62796 original size:36 final size:36
Alignment explanation
Indices: 62744--62882 Score: 251
Period size: 36 Copynumber: 3.9 Consensus size: 36
62734 AGTTGAGTAT
*
62744 TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
62780 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
62816 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
* *
62852 TATCAACTTTGGTACATTCATGTATCAATGT
1 TATCAGCTTTGGTACATTCGTGTATCAATGT
62883 CCAGCACCGT
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 100 1.00
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.42
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:67797 original size:35 final size:35
Alignment explanation
Indices: 67724--67798 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
67714 CGTCACTAAC
**
67724 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
67759 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
67794 AGTAA
1 AGTAA
67799 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:67903 original size:24 final size:24
Alignment explanation
Indices: 67876--67966 Score: 103
Period size: 24 Copynumber: 3.8 Consensus size: 24
67866 CATAATTCAA
* *
67876 GTCAAGCATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
67900 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
*
67924 GTCAA-TATCAGATCATAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* * *
67947 GTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAAT
67967 TCAAGTCGGA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
23 20 0.36
24 35 0.64
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:67936 original size:23 final size:24
Alignment explanation
Indices: 67883--67950 Score: 93
Period size: 23 Copynumber: 2.9 Consensus size: 24
67873 CAAGTCAAGC
* *
67883 ATCATATCAGAATCCAGGTCATGT
1 ATCAGATCAGAATCCAGGTCATAT
*
67907 ATCAGATCAGAATCCATGTCA-AT
1 ATCAGATCAGAATCCAGGTCATAT
*
67930 ATCAGATCATAATCCAGGTCA
1 ATCAGATCAGAATCCAGGTCA
67951 GGTATCATAA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
23 20 0.51
24 19 0.49
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAGATCAGAATCCAGGTCATAT
Found at i:70485 original size:7 final size:7
Alignment explanation
Indices: 70473--70504 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
70463 TGGTCAACTC
70473 CGGTCAA
1 CGGTCAA
70480 CGGTCAA
1 CGGTCAA
70487 CGGGTCAA
1 C-GGTCAA
70495 CGGTCAA
1 CGGTCAA
70502 CGG
1 CGG
70505 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:70494 original size:8 final size:8
Alignment explanation
Indices: 70474--70520 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
70464 GGTCAACTCC
70474 GGTCAAC-
1 GGTCAACG
70481 GGTCAACG
1 GGTCAACG
70489 GGTCAAC-
1 GGTCAACG
70496 GGTCAACG
1 GGTCAACG
70504 GGT---CG
1 GGTCAACG
70509 GGTCAACG
1 GGTCAACG
70517 GGTC
1 GGTC
70521 GGGTCGGGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.14
7 14 0.40
8 16 0.46
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:70494 original size:15 final size:15
Alignment explanation
Indices: 70474--70520 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
70464 GGTCAACTCC
70474 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
70489 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
70504 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
70517 GGTC
1 GGTC
70521 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:70514 original size:13 final size:13
Alignment explanation
Indices: 70481--70569 Score: 70
Period size: 13 Copynumber: 6.3 Consensus size: 13
70471 TCCGGTCAAC
*
70481 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
70496 GGTCAACGGGTCG
1 GGTCAACGGGTCG
70509 GGTCAACGGGTCGGGTCG
1 GGTCAA-----CGGGTCG
*
70527 GGTCAACTGGTCG
1 GGTCAACGGGTCG
*
70540 GGTAAACGGGTCG
1 GGTCAACGGGTCG
* *
70553 GGTAAACGGGTCA
1 GGTCAACGGGTCG
70566 GGTC
1 GGTC
70570 GGGTCGGGTT
Statistics
Matches: 63, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
13 38 0.60
15 12 0.19
18 13 0.21
ACGTcount: A:0.19, C:0.21, G:0.43, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:70525 original size:18 final size:18
Alignment explanation
Indices: 70502--70542 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
70492 CAACGGTCAA
70502 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
*
70520 CGGGTCGGGTCAACTGGT
1 CGGGTCGGGTCAACGGGT
70538 CGGGT
1 CGGGT
70543 AAACGGGTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.10, C:0.22, G:0.49, T:0.20
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:70539 original size:31 final size:31
Alignment explanation
Indices: 70496--70555 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
70486 ACGGGTCAAC
*
70496 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
*
70527 GGTCAACTGGTCGGGTAAACGGGTCGGGT
1 GGTCAACGGGTCGGGTAAACGGGTCGGGT
70556 AAACGGGTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.15, C:0.20, G:0.47, T:0.18
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
Found at i:72679 original size:35 final size:35
Alignment explanation
Indices: 72606--72680 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
72596 CGTCACTAAC
**
72606 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
72641 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
72676 AGTAA
1 AGTAA
72681 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:72785 original size:24 final size:24
Alignment explanation
Indices: 72758--72848 Score: 103
Period size: 24 Copynumber: 3.8 Consensus size: 24
72748 CATAATTCAA
* *
72758 GTCAAGCATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
72782 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
*
72806 GTCAA-TATCAGATCATAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* * *
72829 GTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAAT
72849 TCAAGTCGGA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
23 20 0.36
24 35 0.64
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:72818 original size:23 final size:24
Alignment explanation
Indices: 72765--72832 Score: 93
Period size: 23 Copynumber: 2.9 Consensus size: 24
72755 CAAGTCAAGC
* *
72765 ATCATATCAGAATCCAGGTCATGT
1 ATCAGATCAGAATCCAGGTCATAT
*
72789 ATCAGATCAGAATCCATGTCA-AT
1 ATCAGATCAGAATCCAGGTCATAT
*
72812 ATCAGATCATAATCCAGGTCA
1 ATCAGATCAGAATCCAGGTCA
72833 GGTATCATAA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
23 20 0.51
24 19 0.49
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAGATCAGAATCCAGGTCATAT
Found at i:75372 original size:7 final size:7
Alignment explanation
Indices: 75360--75399 Score: 62
Period size: 7 Copynumber: 5.4 Consensus size: 7
75350 TGGTCAACTC
75360 CGGTCAA
1 CGGTCAA
75367 CGGTCAA
1 CGGTCAA
75374 CGGGTCAA
1 C-GGTCAA
75382 CGGTCAA
1 CGGTCAA
75389 CGGGTCAA
1 C-GGTCAA
75397 CGG
1 CGG
75400 GTCGGGTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 17 0.55
8 14 0.45
ACGTcount: A:0.25, C:0.28, G:0.35, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:75381 original size:8 final size:8
Alignment explanation
Indices: 75361--75415 Score: 75
Period size: 8 Copynumber: 7.5 Consensus size: 8
75351 GGTCAACTCC
75361 GGTCAAC-
1 GGTCAACG
75368 GGTCAACG
1 GGTCAACG
75376 GGTCAAC-
1 GGTCAACG
75383 GGTCAACG
1 GGTCAACG
75391 GGTCAACG
1 GGTCAACG
75399 GGT---CG
1 GGTCAACG
75404 GGTCAACG
1 GGTCAACG
75412 GGTC
1 GGTC
75416 GGGTCCGGTC
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.12
7 14 0.33
8 24 0.56
ACGTcount: A:0.22, C:0.25, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:75381 original size:15 final size:15
Alignment explanation
Indices: 75361--75399 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
75351 GGTCAACTCC
75361 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
75376 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
75391 GGTCAACGG
1 GGTCAACGG
75400 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.26, C:0.26, G:0.36, T:0.13
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:75407 original size:13 final size:13
Alignment explanation
Indices: 75389--75464 Score: 71
Period size: 13 Copynumber: 5.5 Consensus size: 13
75379 CAACGGTCAA
75389 CGGGTCAACGGGT
1 CGGGTCAACGGGT
75402 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
75415 CGGGTCCGGTCAACTGGT
1 C--G---GGTCAACGGGT
* *
75433 CGGGTAAATGGGT
1 CGGGTCAACGGGT
*
75446 CGGGTAAACGGGT
1 CGGGTCAACGGGT
75459 CGGGTC
1 CGGGTC
75465 GGGTCGGGTT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
13 39 0.75
15 1 0.02
16 1 0.02
18 11 0.21
ACGTcount: A:0.16, C:0.21, G:0.45, T:0.18
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:75420 original size:18 final size:18
Alignment explanation
Indices: 75382--75437 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 18
75372 AACGGGTCAA
75382 CGGTCAACGGGTCAACGGGTC
1 CGGTCAACGGGT---CGGGTC
*
75403 GGGTCAACGGGTCGGGTC
1 CGGTCAACGGGTCGGGTC
*
75421 CGGTCAACTGGTCGGGT
1 CGGTCAACGGGTCGGGT
75438 AAATGGGTCG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 21 0.66
21 11 0.34
ACGTcount: A:0.14, C:0.25, G:0.43, T:0.18
Consensus pattern (18 bp):
CGGTCAACGGGTCGGGTC
Found at i:75434 original size:31 final size:31
Alignment explanation
Indices: 75391--75450 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
75381 ACGGTCAACG
*
75391 GGTCAACGGGTCGGGTCAACGGGTCGGGTCC
1 GGTCAACGGGTCGGGTAAACGGGTCGGGTCC
* *
75422 GGTCAACTGGTCGGGTAAATGGGTCGGGT
1 GGTCAACGGGTCGGGTAAACGGGTCGGGT
75451 AAACGGGTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.15, C:0.20, G:0.45, T:0.20
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTAAACGGGTCGGGTCC
Found at i:85918 original size:19 final size:19
Alignment explanation
Indices: 85894--85935 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
85884 TAAATTATCA
85894 TTGATGAAATTGTGAAATT
1 TTGATGAAATTGTGAAATT
** *
85913 TTGATGACGTTGTGAGATT
1 TTGATGAAATTGTGAAATT
85932 TTGA
1 TTGA
85936 GTTTATAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.29, C:0.02, G:0.26, T:0.43
Consensus pattern (19 bp):
TTGATGAAATTGTGAAATT
Found at i:86662 original size:23 final size:23
Alignment explanation
Indices: 86632--86679 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
86622 TAACAAGCAG
86632 CAACAAACAACATTGCATCAATT
1 CAACAAACAACATTGCATCAATT
**
86655 CAACAAACATTATTGCATCAATT
1 CAACAAACAACATTGCATCAATT
86678 CA
1 CA
86680 GCATTCAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.46, C:0.25, G:0.04, T:0.25
Consensus pattern (23 bp):
CAACAAACAACATTGCATCAATT
Found at i:86691 original size:7 final size:7
Alignment explanation
Indices: 86675--86712 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
86665 TATTGCATCA
*
86675 ATTCAGC
1 ATTCAAC
86682 ATTCAAC
1 ATTCAAC
86689 ATTCAAC
1 ATTCAAC
86696 ATTCAAC
1 ATTCAAC
*
86703 ATTCATC
1 ATTCAAC
86710 ATT
1 ATT
86713 TCTGCATTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (7 bp):
ATTCAAC
Found at i:88329 original size:22 final size:22
Alignment explanation
Indices: 88291--88339 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
88281 AAGTCGGAGC
88291 CTTCTTCGCTCTTATCGTCTT-T
1 CTTCTTCGCTCTTATCG-CTTCT
*
88313 CTTCTTC-TTCTTCATCGCTTCT
1 CTTCTTCGCTCTT-ATCGCTTCT
88335 CTTCT
1 CTTCT
88340 GCCTGTAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.04, C:0.35, G:0.06, T:0.55
Consensus pattern (22 bp):
CTTCTTCGCTCTTATCGCTTCT
Found at i:92674 original size:17 final size:17
Alignment explanation
Indices: 92648--92680 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
92638 AGAACTTTGA
92648 AAAATATGTAAACAAAT
1 AAAATATGTAAACAAAT
*
92665 AAAATCTGTAAACAAA
1 AAAATATGTAAACAAA
92681 AATGAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.09, G:0.06, T:0.21
Consensus pattern (17 bp):
AAAATATGTAAACAAAT
Found at i:96266 original size:29 final size:29
Alignment explanation
Indices: 96229--96394 Score: 138
Period size: 29 Copynumber: 5.7 Consensus size: 29
96219 AAGTTTTTTC
*
96229 TTTGATTGTAATTTATAAAAACAATTGGAA
1 TTTG-TTGTAATTTATAAAAACATTTGGAA
*
96259 TTTGTTGTAATTTATAAAAACAATTGGAA
1 TTTGTTGTAATTTATAAAAACATTTGGAA
* **** *
96288 TTTTGTTGTAATTT-TTAATTTTTTTGGCA
1 -TTTGTTGTAATTTATAAAAACATTTGGAA
* ** *
96317 TTTGTTGCAATTTATAAAAAGTTTTGGTAT
1 TTTGTTGTAATTTATAAAAACATTTGG-AA
* * *
96347 TTTTTTGTAATTTATAAAAA-GTTTGGCA
1 TTTGTTGTAATTTATAAAAACATTTGGAA
*
96375 TTTGTTTGTAGTTTATAAAA
1 TTTG-TTGTAATTTATAAAA
96395 GTGTTGGTCT
Statistics
Matches: 111, Mismatches: 21, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
28 15 0.14
29 61 0.55
30 35 0.32
ACGTcount: A:0.33, C:0.03, G:0.14, T:0.50
Consensus pattern (29 bp):
TTTGTTGTAATTTATAAAAACATTTGGAA
Found at i:96395 original size:58 final size:58
Alignment explanation
Indices: 96233--96423 Score: 179
Period size: 58 Copynumber: 3.3 Consensus size: 58
96223 TTTTTCTTTG
* * ** *
96233 ATTGTAATTTATAAAAACAATTGGAATTTGTTGTAATTTATAAAAACAATTGGAATTTT
1 ATTGTAATTTATAAAAA-ATTTGGCATTTGTTGTAATTTATAAAAAGTATTGGTATTTT
* * **** * *
96292 GTTGTAATTTTTAATTTTTTTGGCATTTGTTGCAATTTATAAAAAGTTTTGGTATTTT
1 ATTGTAATTTATAAAAAATTTGGCATTTGTTGTAATTTATAAAAAGTATTGGTATTTT
* * * * *
96350 TTTGTAATTTATAAAAAGTTTGGCATTTGTTTGTAGTTTAT-AAAAGTGTTGGT-CTTT
1 ATTGTAATTTATAAAAAATTTGGCATTTG-TTGTAATTTATAAAAAGTATTGGTATTTT
*
96407 ATTGTAATTTATCAAAA
1 ATTGTAATTTATAAAAA
96424 TGTTATTTTT
Statistics
Matches: 106, Mismatches: 25, Indels: 4
0.79 0.19 0.03
Matches are distributed among these distances:
57 18 0.17
58 67 0.63
59 21 0.20
ACGTcount: A:0.32, C:0.04, G:0.15, T:0.49
Consensus pattern (58 bp):
ATTGTAATTTATAAAAAATTTGGCATTTGTTGTAATTTATAAAAAGTATTGGTATTTT
Found at i:96401 original size:29 final size:29
Alignment explanation
Indices: 96229--96423 Score: 132
Period size: 29 Copynumber: 6.7 Consensus size: 29
96219 AAGTTTTTTC
* ** *
96229 TTTGATTGTAATTTATAAAAACAATTGGAA
1 TTTGTTTGTAATTTATAAAAA-GTTTGGCA
** *
96259 TTTG-TTGTAATTTATAAAAACAATTGGAA
1 TTTGTTTGTAATTTATAAAAA-GTTTGGCA
* ****
96288 TTT-TGTTGTAATTTTTAATTTTTTTGGCA
1 TTTGT-TTGTAATTTATAAAAAGTTTGGCA
* *
96317 TTTG-TTGCAATTTATAAAAAGTTTTGGTA
1 TTTGTTTGTAATTTATAAAAAG-TTTGGCA
*
96346 TTTTTTTGTAATTTATAAAAAGTTTGGCA
1 TTTGTTTGTAATTTATAAAAAGTTTGGCA
*
96375 TTTGTTTGTAGTTTAT-AAAAGTGTTGGTC-
1 TTTGTTTGTAATTTATAAAAAGT-TTGG-CA
* *
96404 TTT-ATTGTAATTTATCAAAA
1 TTTGTTTGTAATTTATAAAAA
96424 TGTTATTTTT
Statistics
Matches: 136, Mismatches: 21, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
28 27 0.20
29 76 0.56
30 33 0.24
ACGTcount: A:0.32, C:0.04, G:0.15, T:0.50
Consensus pattern (29 bp):
TTTGTTTGTAATTTATAAAAAGTTTGGCA
Found at i:96496 original size:13 final size:13
Alignment explanation
Indices: 96480--96509 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
96470 ATTTTAAATT
96480 TTTATTTTTTAAA
1 TTTATTTTTTAAA
96493 TTTATTTTTTAAA
1 TTTATTTTTTAAA
96506 TTTA
1 TTTA
96510 AACAAAGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTATTTTTTAAA
Found at i:100750 original size:342 final size:342
Alignment explanation
Indices: 100118--100806 Score: 1193
Period size: 342 Copynumber: 2.0 Consensus size: 342
100108 TCCCTATCTT
*
100118 AAAATCTTAAATTATAAAGCTTAAGTTAGGGTTTAAAAAATTTAAAGTTTAGGGTTTAAGGTTTT
1 AAAATCCTAAATTATAAAGCTTAAGTTAGGGTTTAAAAAATTTAAAGTTTAGGGTTTAAGGTTTT
*
100183 AAATTTAAGATTTTAAGTTAGGAGTAGGGTATAGAATAATGCAATTGAGCAACTTCGAGGGCTAA
66 AAATTTAAGATTTTAAGTTAGGAGTAGGGTATAAAATAATGCAATTGAGCAACTTCGAGGGCTAA
* * *
100248 ATTGATGCGAAAATACAATAGGAGAAAAAACGATAAATTTAATCTATTACGGGAGAAAAAATTAC
131 ATTGATGCGAAAATACAATAGGAGAAAAAACAATAAATTTAATCTATTACGGAAGAAAAAAATAC
*
100313 CCTTTCCTGATTTTAATAAATACAACTTATAGTGAGTATAATATATTTCGAGCACTAATCACGTA
196 CCTTTCCTGATTTTAATAAATACAACTTATAGTGAGTATAATATATTTCAAGCACTAATCACGTA
* * *
100378 AATTTTGTTATTAAAAAATTATTATTTTTAAAGTTTTGAATTCATATATTATATATTTAAATATT
261 AATTTTGTTATTAAAAAATTATTATTTTTAAAGTTCTGAATTCACATATTATATATTTAAATAGT
100443 TGATATTAAATAACTAA
326 TGATATTAAATAACTAA
*
100460 AAAATCCTAAATTATAAAGCTTAAGTTAGGG-TTAAAAATGATTTAAAGTTTAGGGTTTAGGGTT
1 AAAATCCTAAATTATAAAGCTTAAGTTAGGGTTTAAAAA--ATTTAAAGTTTAGGGTTTAAGGTT
* *
100524 TTAAATTTAAGATTTTAAGTTAGGGGTATGGTATAAAATAATGCAATTGAGCAACTTCGAGGGCT
64 TTAAATTTAAGATTTTAAGTTAGGAGTAGGGTATAAAATAATGCAATTGAGCAACTTCGAGGGCT
* * *
100589 AACTTGATGCGAAAATACGATAGGAGCAAAAACAATAAATTTAATCTATTAC-GAAGAAAAAAAT
129 AAATTGATGCGAAAATACAATAGGAGAAAAAACAATAAATTTAATCTATTACGGAAGAAAAAAAT
**
100653 ACCCTTTTGTGATTTTAATAAATACAACTTATAGTGAGTATAATATATTTCAAGCACTAATCACG
194 ACCCTTTCCTGATTTTAATAAATACAACTTATAGTGAGTATAATATATTTCAAGCACTAATCACG
100718 TAAATTTTGTTATTAAAAAATTATTATTTTTAAAGTTCTGAATTCACATATTATATATTTAAATA
259 TAAATTTTGTTATTAAAAAATTATTATTTTTAAAGTTCTGAATTCACATATTATATATTTAAATA
100783 GTTGATATTAAATAACTAA
324 GTTGATATTAAATAACTAA
100802 AAAAT
1 AAAAT
100807 TATAAATATA
Statistics
Matches: 328, Mismatches: 17, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
341 7 0.02
342 188 0.57
343 133 0.41
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (342 bp):
AAAATCCTAAATTATAAAGCTTAAGTTAGGGTTTAAAAAATTTAAAGTTTAGGGTTTAAGGTTTT
AAATTTAAGATTTTAAGTTAGGAGTAGGGTATAAAATAATGCAATTGAGCAACTTCGAGGGCTAA
ATTGATGCGAAAATACAATAGGAGAAAAAACAATAAATTTAATCTATTACGGAAGAAAAAAATAC
CCTTTCCTGATTTTAATAAATACAACTTATAGTGAGTATAATATATTTCAAGCACTAATCACGTA
AATTTTGTTATTAAAAAATTATTATTTTTAAAGTTCTGAATTCACATATTATATATTTAAATAGT
TGATATTAAATAACTAA
Found at i:113330 original size:21 final size:21
Alignment explanation
Indices: 113288--113326 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
113278 TATTAAGGTC
*
113288 TTTGTGGAGGCCATGAAATCT
1 TTTGTCGAGGCCATGAAATCT
113309 TTTGTCGAGGCCAT-AAAT
1 TTTGTCGAGGCCATGAAAT
113327 TCTTGCAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (21 bp):
TTTGTCGAGGCCATGAAATCT
Found at i:118771 original size:20 final size:20
Alignment explanation
Indices: 118746--118790 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
118736 TTCCACCATG
*
118746 TGAGTCTTTCCTTTACTCTT
1 TGAGTCTGTCCTTTACTCTT
118766 TGAGTCTGTCCTTTACTCTT
1 TGAGTCTGTCCTTTACTCTT
118786 TGAGT
1 TGAGT
118791 AATACTGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.11, C:0.22, G:0.16, T:0.51
Consensus pattern (20 bp):
TGAGTCTGTCCTTTACTCTT
Found at i:129963 original size:209 final size:212
Alignment explanation
Indices: 129280--129967 Score: 1056
Period size: 209 Copynumber: 3.3 Consensus size: 212
129270 ATTTAATAAT
* *
129280 TAAATTGAACAAATATGAAATTACAAATTAAAATTTAAATAAATTAAACAACACGCATTGACGAG
1 TAAATTGAACAAATATGAAATTACAAATTAAAATTTAAATAAATTAAACAACACACATTGATGAG
* * * *
129345 GGATCAAATCAAAATAATTTTAAATTGTGAGGTTAAAATTAATATAAAAAAGTATTAAATTTTAC
66 GGATCAAATCAAAATAATTTTAAATTGTGAGGTTTAAATTAATACAAAAAAGTAATAAATTATAC
*
129410 CCATTTAAAAAGTTACGGGCCAATTAAAAATATAAATAAGTAATAAGTATGGGTCAATTTCATAT
131 CCATTTAAAAAGTTATGGGCCAATTAAAAA-AT-AATAAG-AATAAGTATGGGTCAATTTCATAT
*
129475 GCAAATATAATTTTGAGGAC
193 GCAAATATAATTTTAAGGAC
* * *
129495 TAAATTGAACAAATATGAAATTACAAATAGAAAATTTAAAAAAATT-----A-A-ATATTGATGA
1 TAAATTGAACAAATATGAAATTACAAAT-TAAAATTTAAATAAATTAAACAACACACATTGATGA
129553 GGGATCAAATCAAAATAATTTTAAATTGTGAGGTTTAAATTAATACAAAAAAGTAAT-AATTATA
65 GGGATCAAATCAAAATAATTTTAAATTGTGAGGTTTAAATTAATACAAAAAAGTAATAAATTATA
*
129617 CTCATTTAAAAAGTTATGGGCCAATTAAAAAATACAAATAAGTAATAAGTATGGGTCAATTTCAT
130 CCCATTTAAAAAGTTATGGGCCAATTAAAAAAT---AATAAG-AATAAGTATGGGTCAATTTCAT
*
129682 ATGCAAATATAGTTTTAAGGAC
191 ATGCAAATATAATTTTAAGGAC
* *
129704 TAAATTGAACAAATATGAAATTACACATTAAATTTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATTAAAATTTAAATAAATTAAACAACACACATTGATGAG
* * *
129769 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTTAAATTAATACAAAAAAGTACTAAATAATAC
66 GGATCAAATCAAAATAATTTTAAATTGTGAGGTTTAAATTAATACAAAAAAGTAATAAATTATAC
129834 CCATTTAAAAAGTTATGGGCCAATTAAAAAAT-A-AA-AATAAGTATGGGTCAATTTCATATGCA
131 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAATAAGAATAAGTATGGGTCAATTTCATATGCA
129896 AATATAATTTTAAGGAC
196 AATATAATTTTAAGGAC
*
129913 TAAATTGAACAAATATGAAATTACAAATTAAATTTTAAATAAATTAAACAACACA
1 TAAATTGAACAAATATGAAATTACAAATTAAAATTTAAATAAATTAAACAACACA
129968 AAGGGGTCAA
Statistics
Matches: 438, Mismatches: 24, Indels: 28
0.89 0.05 0.06
Matches are distributed among these distances:
207 2 0.00
208 49 0.11
209 235 0.54
210 1 0.00
211 3 0.01
212 1 0.00
213 1 0.00
214 1 0.00
215 92 0.21
216 53 0.12
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.31
Consensus pattern (212 bp):
TAAATTGAACAAATATGAAATTACAAATTAAAATTTAAATAAATTAAACAACACACATTGATGAG
GGATCAAATCAAAATAATTTTAAATTGTGAGGTTTAAATTAATACAAAAAAGTAATAAATTATAC
CCATTTAAAAAGTTATGGGCCAATTAAAAAATAATAAGAATAAGTATGGGTCAATTTCATATGCA
AATATAATTTTAAGGAC
Found at i:130077 original size:2 final size:2
Alignment explanation
Indices: 130066--130224 Score: 102
Period size: 2 Copynumber: 80.0 Consensus size: 2
130056 TTGAAACAAC
130066 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
130104 CTA TA TA GTT TA TA TA TA AA GTA TA TG TA -A TA TA TA TA AA CTA
1 -TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA
* * *
130147 TA TA GTT TA TA TT TA TA T- TA T- TA TA TA CTA TA TA TA AA CTA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA
* *
130188 TA TA T- TA TA TA TA TA TA T- TA TG TA TA AA CTA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
130225 CCATGTATAA
Statistics
Matches: 122, Mismatches: 18, Indels: 34
0.70 0.10 0.20
Matches are distributed among these distances:
1 9 0.07
2 104 0.85
3 9 0.07
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:130128 original size:11 final size:10
Alignment explanation
Indices: 130066--130224 Score: 60
Period size: 11 Copynumber: 15.4 Consensus size: 10
130056 TTGAAACAAC
130066 TATAATATATA
1 TATAA-ATATA
*
130077 TATATATATA
1 TATAAATATA
*
130087 TATATATATAA
1 TATAAATAT-A
*
130098 TATTAACTATA
1 TA-TAAATATA
*
130109 TAGT--TTATA
1 TA-TAAATATA
130118 TATAAAGTATA
1 TATAAA-TATA
*
130129 TGT-AATATA
1 TATAAATATA
130138 TATAAACTATA
1 TATAAA-TATA
** *
130149 TAGTTTATATT
1 TA-TAAATATA
*
130160 TAT-ATTAT-
1 TATAAATATA
*
130168 TATATACTATA
1 TATA-AATATA
130179 TATAAACTATA
1 TATAAA-TATA
*
130190 TAT-TATATA
1 TATAAATATA
* *
130199 TATATATTATG
1 TATA-AATATA
130210 TATAAACTATA
1 TATAAA-TATA
130221 TATA
1 TATA
130225 CCATGTATAA
Statistics
Matches: 112, Mismatches: 21, Indels: 30
0.69 0.13 0.18
Matches are distributed among these distances:
8 4 0.04
9 22 0.20
10 26 0.23
11 53 0.47
12 7 0.06
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (10 bp):
TATAAATATA
Found at i:130230 original size:20 final size:20
Alignment explanation
Indices: 130197--130244 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
130187 ATATATTATA
**
130197 TATATATATTATGTATAAAC
1 TATATATACCATGTATAAAC
130217 TATATATACCATGTATAAAC
1 TATATATACCATGTATAAAC
130237 TATA-ATAC
1 TATATATAC
130245 TATATAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (20 bp):
TATATATACCATGTATAAAC
Found at i:130313 original size:22 final size:20
Alignment explanation
Indices: 130273--130439 Score: 98
Period size: 22 Copynumber: 8.4 Consensus size: 20
130263 ACTATTGAAC
* * *
130273 TATATAGAAACTACATAGTT
1 TATATATAAATTATATAGTT
130293 TATTAATATAAATTATATAGTT
1 TA-T-ATATAAATTATATAGTT
*
130315 TATATATAAATTATATATGAAT
1 TATATATAAATTATATA-G-TT
* * *
130337 TATATAT-AACTATACAATT
1 TATATATAAATTATATAGTT
* *
130356 TATATTATATATTATGTA--T
1 TATA-TATAAATTATATAGTT
* *
130375 AAT-TATAAA-TA-ATA-TA
1 TATATATAAATTATATAGTT
*
130391 T-TGTATAAATTATATAGTT
1 TATATATAAATTATATAGTT
*
130410 TATTAATATAAACTATATAGTT
1 TA-T-ATATAAATTATATAGTT
130432 TATATATA
1 TATATATA
130440 TATATAATAT
Statistics
Matches: 113, Mismatches: 20, Indels: 28
0.70 0.12 0.17
Matches are distributed among these distances:
15 3 0.03
16 8 0.07
17 7 0.06
18 3 0.03
19 10 0.09
20 24 0.21
21 17 0.15
22 41 0.36
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (20 bp):
TATATATAAATTATATAGTT
Found at i:130331 original size:13 final size:11
Alignment explanation
Indices: 130294--130345 Score: 58
Period size: 11 Copynumber: 5.0 Consensus size: 11
130284 TACATAGTTT
130294 ATTA-ATATAA
1 ATTATATATAA
130304 ATTATATAGT--
1 ATTATATA-TAA
130314 -TTATATATAA
1 ATTATATATAA
*
130324 ATTATATATGA
1 ATTATATATAA
130335 ATTATATATAA
1 ATTATATATAA
130346 CTATACAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
8 1 0.03
9 7 0.20
10 4 0.11
11 22 0.63
12 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (11 bp):
ATTATATATAA
Found at i:130365 original size:33 final size:32
Alignment explanation
Indices: 130328--130406 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 32
130318 ATATAAATTA
*
130328 TATATGAATTATATATAACTATACAAT-TTATAT
1 TATAT-AATTATATATAACTATA-AATAATATAT
* *
130361 TATAT-ATTATGTATAATTATAAATAATATAT
1 TATATAATTATATATAACTATAAATAATATAT
*
130392 TGTATAAATTATATA
1 TATAT-AATTATATA
130407 GTTTATTAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
30 3 0.08
31 23 0.61
33 12 0.32
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (32 bp):
TATATAATTATATATAACTATAAATAATATAT
Found at i:130440 original size:22 final size:22
Alignment explanation
Indices: 130394--130452 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
130384 TAATATATTG
*
130394 TATAAATTATATAGTTTATTAA
1 TATAAACTATATAGTTTATTAA
130416 TATAAACTATATAGTTTATATATA
1 TATAAACTATATAGTTTAT-TA-A
130440 TATATAA-TATATA
1 TATA-AACTATATA
130453 TGGTTTAGGG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
22 18 0.55
23 2 0.06
24 11 0.33
25 2 0.06
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (22 bp):
TATAAACTATATAGTTTATTAA
Found at i:130793 original size:13 final size:13
Alignment explanation
Indices: 130775--130815 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
130765 TTTACATATG
130775 AACTATATGTATA
1 AACTATATGTATA
130788 AAC--TA--TATA
1 AACTATATGTATA
130797 AACTATATGTATA
1 AACTATATGTATA
130810 AACTAT
1 AACTAT
130816 GTAAACTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
9 7 0.29
11 4 0.17
13 13 0.54
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.37
Consensus pattern (13 bp):
AACTATATGTATA
Found at i:130800 original size:22 final size:22
Alignment explanation
Indices: 130770--130826 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
130760 TATAGTTTAC
*
130770 ATATGAACTATATGTATAAACT
1 ATATAAACTATATGTATAAACT
130792 ATATAAACTATATGTATAAACT
1 ATATAAACTATATGTATAAACT
*
130814 ATGTAAACTATAT
1 ATATAAACTATAT
130827 AGTTTACATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.37
Consensus pattern (22 bp):
ATATAAACTATATGTATAAACT
Found at i:130873 original size:2 final size:2
Alignment explanation
Indices: 130866--130973 Score: 67
Period size: 2 Copynumber: 51.0 Consensus size: 2
130856 ATTAGTGAAC
* * *
130866 TA TA TA TA CTA TT TG TA TA GTA TA TA CTA TA TA TA TA -A AA TA
1 TA TA TA TA -TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA
* * *
130908 TA GTT TA TA TT TA TA TT TA TA TA CTA TA TA T- TA TA TA TA TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
*
130951 AA CTA TA TA TA CTA TA TA GTA TA
1 TA -TA TA TA TA -TA TA TA -TA TA
130974 ATTTACACAT
Statistics
Matches: 84, Mismatches: 12, Indels: 20
0.72 0.10 0.17
Matches are distributed among these distances:
1 2 0.02
2 68 0.81
3 14 0.17
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:130896 original size:7 final size:6
Alignment explanation
Indices: 130866--130973 Score: 67
Period size: 7 Copynumber: 17.0 Consensus size: 6
130856 ATTAGTGAAC
* * * *
130866 TATATA TACTATT TGTATA GTATATA CTATATA TATA-A AATATA GTTTATA
1 TATATA TA-TATA TATATA -TATATA -TATATA TATATA TATATA -TATATA
* * *
130917 TTTATA TTTATA TACTATA TAT-TA TATATA TATAAA CTATATA TACTATA
1 TATATA TATATA TA-TATA TATATA TATATA TATATA -TATATA TA-TATA
130967 TAGTATA
1 TA-TATA
130974 ATTTACACAT
Statistics
Matches: 82, Mismatches: 12, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
5 9 0.11
6 33 0.40
7 40 0.49
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.48
Consensus pattern (6 bp):
TATATA
Found at i:130900 original size:9 final size:8
Alignment explanation
Indices: 130866--130973 Score: 67
Period size: 9 Copynumber: 12.8 Consensus size: 8
130856 ATTAGTGAAC
130866 TATATATA
1 TATATATA
* *
130874 CTATTTGTA
1 -TATATATA
130883 TAGTATATA
1 TA-TATATA
130892 CTATATATA
1 -TATATATA
*
130901 TA-AAATA
1 TATATATA
*
130908 TAGTTTATA
1 TA-TATATA
* *
130917 TTTATATT
1 TATATATA
130925 TATATACTA
1 TATATA-TA
130934 TATAT-TA
1 TATATATA
130941 TATATATA
1 TATATATA
*
130949 TAAACTATA
1 TATA-TATA
130958 TATACTATA
1 TATA-TATA
130967 TAGTATA
1 TA-TATA
130974 ATTTACACAT
Statistics
Matches: 77, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
7 13 0.17
8 18 0.23
9 42 0.55
10 4 0.05
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.48
Consensus pattern (8 bp):
TATATATA
Found at i:130902 original size:18 final size:17
Alignment explanation
Indices: 130866--130973 Score: 76
Period size: 18 Copynumber: 6.1 Consensus size: 17
130856 ATTAGTGAAC
* *
130866 TATATATACTATTTGTA
1 TATATATACTATATATA
130883 TAGTATATACTATATATA
1 TA-TATATACTATATATA
* * * *
130901 TAAAATATAGTTTATATT
1 T-ATATATACTATATATA
*
130919 TATATTTA-TATACTATA
1 TATATATACTATA-TATA
*
130936 TATTATATA-TATATAAA
1 TA-TATATACTATATATA
130953 CTATATATACTATATAGTA
1 -TATATATACTATATA-TA
130972 TA
1 TA
130974 ATTTACACAT
Statistics
Matches: 71, Mismatches: 13, Indels: 13
0.73 0.13 0.13
Matches are distributed among these distances:
16 3 0.04
17 21 0.30
18 45 0.63
19 2 0.03
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.48
Consensus pattern (17 bp):
TATATATACTATATATA
Found at i:131063 original size:20 final size:18
Alignment explanation
Indices: 131042--131112 Score: 90
Period size: 18 Copynumber: 3.8 Consensus size: 18
131032 TATACTATAT
*
131042 ATATGAACTATAGTTTAC
1 ATATAAACTATAGTTTAC
*
131060 ATATAAACTATATAGTTTAT
1 ATATAAAC--TATAGTTTAC
131080 ATACT-AACTATAGTTTAC
1 ATA-TAAACTATAGTTTAC
131098 ATATAAACTATAGTT
1 ATATAAACTATAGTT
131113 GATATTTACA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
17 1 0.02
18 29 0.63
20 15 0.33
21 1 0.02
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (18 bp):
ATATAAACTATAGTTTAC
Found at i:131081 original size:38 final size:38
Alignment explanation
Indices: 131030--131109 Score: 126
Period size: 38 Copynumber: 2.1 Consensus size: 38
131020 AGTTTATATT
131030 TATATACTATATATA-TGAACTATAGTTTACATATAAAC
1 TATATACTATATATACT-AACTATAGTTTACATATAAAC
* *
131068 TATATAGTTTATATACTAACTATAGTTTACATATAAAC
1 TATATACTATATATACTAACTATAGTTTACATATAAAC
131106 TATA
1 TATA
131110 GTTGATATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
38 38 0.97
39 1 0.03
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (38 bp):
TATATACTATATATACTAACTATAGTTTACATATAAAC
Found at i:131199 original size:23 final size:21
Alignment explanation
Indices: 131141--131186 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
131131 ATATATAAAC
*
131141 TATATAGTTACATA-TGAACTA
1 TATATAGTTA-TTAGTGAACTA
131162 TATATAGTTATTAGTGAACTA
1 TATATAGTTATTAGTGAACTA
131183 TATA
1 TATA
131187 CTATTTGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (21 bp):
TATATAGTTATTAGTGAACTA
Found at i:131204 original size:2 final size:2
Alignment explanation
Indices: 131194--131282 Score: 56
Period size: 2 Copynumber: 42.0 Consensus size: 2
131184 ATACTATTTG
* * * *
131194 TA TA GTA TA TA CTA TA TA TA -A AA TA TA GTT TA TA TT TA TA TT
1 TA TA -TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
*
131236 TA TA TA CTA TA TA T- TA TA TA TA TA AA CTA TA TA TA CTA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA
131278 GTA TA
1 -TA TA
131283 ATTTACACGT
Statistics
Matches: 69, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
1 2 0.03
2 55 0.80
3 12 0.17
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:131252 original size:20 final size:20
Alignment explanation
Indices: 131224--131283 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
131214 AAATATAGTT
* *
131224 TATAT-TTATATTTATATAC
1 TATATATTATATATATAAAC
131243 TATATATTATATATATAAAC
1 TATATATTATATATATAAAC
131263 TATATATACTATATAGTATAA
1 TATATAT--TATATA-TATAA
131284 TTTACACGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.14
20 19 0.54
22 6 0.17
23 5 0.14
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (20 bp):
TATATATTATATATATAAAC
Found at i:131391 original size:309 final size:313
Alignment explanation
Indices: 130817--131391 Score: 895
Period size: 309 Copynumber: 1.8 Consensus size: 313
130807 ATAAACTATG
130817 TAAACTATATAGTTTACATATAACCTATATATATAGTTTATTAGTGAACTATATATACTATTTGT
1 TAAACTATATAGTTTACATATAACC-ATATATATAGTTTATTAGTGAAC-ATATATACTATTTGT
130882 ATAGTATATACTATATATATAAAATATAGTTTATATTTATATTTATATACTATATATTATATATA
64 ATAGTATATAC-ATATATATAAAATATAGTTTATATTTATATTTATATACTATATATTATATATA
130947 TATAAACTATATATACTATATAGTATAATTTACACATGAACTATATATAAAAACCCTAAACTATA
128 TATAAACTATATATACTATATAGTATAATTTACACATGAACTATATATAAAAACCCTAAACTATA
* * * *
131012 CAGTATATAGTTTATATTTATATACTATATATATGAACTATAGTTTACATATAAACTATATAGTT
193 CAGTATATAGTTTATATATATATACTATATATATAAACTATAGTGTA-ATATAAAC-ATACAG-T
131077 TATATACTAACTATAGTTTACATATAAACTATAGTTGATATTTACATATGAACTATATA
255 TATATACTAACTATAGTTTACATATAAACTATAGTTGATATTTACATATGAACTATATA
131136 TAAACTATATAG-TTACATATGAA-C-TATATATAG-TTATTAGTGAAC-TATATACTATTTGTA
1 TAAACTATATAGTTTACATAT-AACCATATATATAGTTTATTAGTGAACATATATACTATTTGTA
131196 TAGTATATAC-TATATATAAAATATAGTTTATATTTATATTTATATACTATATA-T-TATATATA
65 TAGTATATACATATATATAAAATATAGTTTATATTTATATTTATATACTATATATTATATATATA
*
131258 TAAACTATATATACTATATAGTATAATTTACACGTGAACTATATATAAAAACCCTAAACTATACA
130 TAAACTATATATACTATATAGTATAATTTACACATGAACTATATATAAAAACCCTAAACTATACA
131323 GTATATAGTTTATTAGTATATATAACTATATAATATATAAACTATA-TGGT-ATATAAA-ATACA
195 GTATATAGTTTA-TA-TATATAT-AC--TAT-ATATATAAACTATAGT-GTAATATAAACATACA
131385 -TTATATA
253 GTTATATA
131392 TATTTCATTA
Statistics
Matches: 243, Mismatches: 5, Indels: 26
0.89 0.02 0.09
Matches are distributed among these distances:
309 91 0.37
310 3 0.01
311 53 0.22
312 2 0.01
313 32 0.13
314 4 0.02
315 26 0.11
316 9 0.04
318 9 0.04
319 14 0.06
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (313 bp):
TAAACTATATAGTTTACATATAACCATATATATAGTTTATTAGTGAACATATATACTATTTGTAT
AGTATATACATATATATAAAATATAGTTTATATTTATATTTATATACTATATATTATATATATAT
AAACTATATATACTATATAGTATAATTTACACATGAACTATATATAAAAACCCTAAACTATACAG
TATATAGTTTATATATATATACTATATATATAAACTATAGTGTAATATAAACATACAGTTATATA
CTAACTATAGTTTACATATAAACTATAGTTGATATTTACATATGAACTATATA
Found at i:131406 original size:31 final size:33
Alignment explanation
Indices: 131313--131455 Score: 125
Period size: 33 Copynumber: 4.4 Consensus size: 33
131303 TAAAAACCCT
* * *
131313 AAACTATACAGTATATAGTTTATTAGTATAT-A
1 AAACTATATATTATATAGTTCATTAGTATATAA
* * ** *
131345 TAACTATATAATATATA-AACTATATGGTATATAA
1 AAACTATATATTATATAGTTC-AT-TAGTATATAA
* *
131379 AATAC-AT-TA-TATATATTTCATTAGTATATAT
1 AA-ACTATATATTATATAGTTCATTAGTATATAA
*
131410 AAACTATATATTATATAGTTCATTAGTATATAT
1 AAACTATATATTATATAGTTCATTAGTATATAA
131443 AAACTATATATTA
1 AAACTATATATTA
131456 ATTTATTAAT
Statistics
Matches: 90, Mismatches: 13, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
30 2 0.02
31 12 0.13
32 26 0.29
33 44 0.49
34 4 0.04
35 2 0.02
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (33 bp):
AAACTATATATTATATAGTTCATTAGTATATAA
Found at i:131418 original size:26 final size:27
Alignment explanation
Indices: 131388--131480 Score: 84
Period size: 33 Copynumber: 3.3 Consensus size: 27
131378 AAATACATTA
131388 TATATATTTCATTAGTATATATAAACTAT
1 TATATATTTCATTAGTATATATAAAC--T
131417 ATATTATATAGTTCATTAGTATATATAAAC-
1 -TA-TATAT--TTCATTAGTATATATAAACT
* *
131447 TATATA-TTAATTTATTA-ATATAAACT
1 TATATATTTCA-TTAGTATATATAAACT
131473 TATATATT
1 TATATATT
131481 AATTGAAAGA
Statistics
Matches: 55, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
25 11 0.20
26 11 0.20
27 1 0.02
28 4 0.07
29 2 0.04
30 2 0.04
31 5 0.09
33 19 0.35
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.48
Consensus pattern (27 bp):
TATATATTTCATTAGTATATATAAACT
Found at i:131426 original size:16 final size:16
Alignment explanation
Indices: 131339--131426 Score: 56
Period size: 16 Copynumber: 5.4 Consensus size: 16
131329 AGTTTATTAG
*
131339 TATATATAACTATATAA
1 TATATA-AACTATATAT
**
131356 TATATAAACTATATGG
1 TATATAAACTATATAT
*
131372 TATATAAA--ATACAT
1 TATATAAACTATATAT
* *
131386 TATATATA-TTTCATTAGT
1 TATATAAACTAT-A-TA-T
131404 ATATATAAACTATATAT
1 -TATATAAACTATATAT
131421 TATATA
1 TATATA
131427 GTTCATTAGT
Statistics
Matches: 55, Mismatches: 10, Indels: 13
0.71 0.13 0.17
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 23 0.42
17 8 0.15
18 3 0.05
19 8 0.15
20 2 0.04
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (16 bp):
TATATAAACTATATAT
Found at i:131593 original size:61 final size:61
Alignment explanation
Indices: 131528--131645 Score: 155
Period size: 61 Copynumber: 1.9 Consensus size: 61
131518 AAAAAAATTT
* * ** * *
131528 AAATATGAAGCTTAAGTTAATAAATTGTAACATTAAATTTGGATTAAATTAAATAAAGTTG
1 AAATATGAAACTTAAATTAATAAATTACAACATTAAATTTGAACTAAATTAAATAAAGTTG
* * *
131589 AAATATGAAACTTAAATTAATATATTACATCATTAAATTTGAACTAAATTGAATAAA
1 AAATATGAAACTTAAATTAATAAATTACAACATTAAATTTGAACTAAATTAAATAAA
131646 TTTAAAATTA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (61 bp):
AAATATGAAACTTAAATTAATAAATTACAACATTAAATTTGAACTAAATTAAATAAAGTTG
Found at i:134074 original size:18 final size:17
Alignment explanation
Indices: 133998--134071 Score: 58
Period size: 18 Copynumber: 4.0 Consensus size: 17
133988 TAATATAAGA
133998 AATATAAAGAATTGAAATT
1 AATATAAA-AATT-AAATT
* **
134017 AACATAAAAACCAAATTTAT
1 AATATAAAAATTAAA--T-T
*
134037 AATATACAAATTATAATT
1 AATATAAAAATTA-AATT
134055 AATATAAAAATTAAATT
1 AATATAAAAATTAAATT
134072 TAAAAAAATA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
17 7 0.16
18 15 0.35
19 9 0.21
20 10 0.23
21 2 0.05
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (17 bp):
AATATAAAAATTAAATT
Found at i:136169 original size:42 final size:42
Alignment explanation
Indices: 136110--136189 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
136100 TAATTATTTT
136110 CTATCGAGAATAATCGACCTCTTATACCTTAAAACAATTGTC
1 CTATCGAGAATAATCGACCTCTTATACCTTAAAACAATTGTC
* *
136152 CTATCGAGAATAATCGACCTCTTATACTTTAAGACAAT
1 CTATCGAGAATAATCGACCTCTTATACCTTAAAACAAT
136190 CGATTCTTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (42 bp):
CTATCGAGAATAATCGACCTCTTATACCTTAAAACAATTGTC
Found at i:136518 original size:131 final size:131
Alignment explanation
Indices: 136284--136643 Score: 429
Period size: 131 Copynumber: 2.7 Consensus size: 131
136274 ATTTTAAGAA
* * * *
136284 AGAAAATGATAATATCAAATTATTTCCAATCGAGAATAAATAATCTCTCATGCCTTAAAGCAGTC
1 AGAAAA-GATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGTCTTAAAGCAGTC
* * * *
136349 ATTTATTACTTCGACTGACATGAAGAGATATTACTATTTCGTCTTA-AAATTCAATATTGATTC-
65 ATTTATTAC-TCCAATGAAATGAAGAGATATCACTATTTCGTCTTATAAA-TCAATATTGATTCG
136412 A-AG
128 AGAG
* * *
136415 AGAAAACGATAATATCTAATGATTTCCAATCGAGAATAAATGACCTCTCATGTTTTAAAACAGTC
1 AGAAAA-GATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGTCTTAAAGCAGTC
* *
136480 ATTTATTACTCCAATAGAAATGAAGAGATATCCCTATTTTGTCTTATAAATCAATATTGATTCGA
65 ATTTATTACTCCAAT-GAAATGAAGAGATATCACTATTTCGTCTTATAAATCAATATTGATTCGA
136545 GAG
129 GAG
* * * * * *
136548 GGAAAATAGTAATATCTAATTATTTCTAATCGAGAATAAATGACATCTCATGTCTTGAAGCAATC
1 AGAAAAGA-TAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGTCTTAAAGCAGTC
* * * *
136613 ATTTATTATTCTAACCGAAATGAAAAGATAT
65 ATTTATTACTCCAA-TGAAATGAAGAGATAT
136644 TATGATTTTC
Statistics
Matches: 196, Mismatches: 27, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
130 4 0.02
131 105 0.54
132 5 0.03
133 82 0.42
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (131 bp):
AGAAAAGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGTCTTAAAGCAGTCA
TTTATTACTCCAATGAAATGAAGAGATATCACTATTTCGTCTTATAAATCAATATTGATTCGAGA
G
Found at i:139979 original size:19 final size:18
Alignment explanation
Indices: 139923--139985 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 18
139913 TTGAAACGTC
139923 TTAATTAAAATAAATAAT
1 TTAATTAAAATAAATAAT
**
139941 TTAAAGGAAAA-AGAATAAT
1 TT-AATTAAAATA-AATAAT
139960 TTAATTAAAATAAATAAAT
1 TTAATTAAAATAAAT-AAT
139979 TT-ATTAA
1 TTAATTAA
139986 GGAATCAAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 17 0.46
19 20 0.54
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (18 bp):
TTAATTAAAATAAATAAT
Found at i:140675 original size:15 final size:15
Alignment explanation
Indices: 140652--140681 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
140642 TACTAGTATT
140652 AAAACATCAAAATGA
1 AAAACATCAAAATGA
*
140667 AAAATATCAAAATGA
1 AAAACATCAAAATGA
140682 GGACATTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.10, G:0.07, T:0.17
Consensus pattern (15 bp):
AAAACATCAAAATGA
Found at i:142524 original size:3 final size:3
Alignment explanation
Indices: 142516--142559 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
142506 ATGAAAATCG
* * * *
142516 AGA AGA AGA AGA AGA AGA AGA AGA GGA GGA GGA GGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
142560 TATGAAGACT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:144726 original size:125 final size:127
Alignment explanation
Indices: 144549--144800 Score: 490
Period size: 125 Copynumber: 2.0 Consensus size: 127
144539 TGAGGGATTT
144549 ATATATATCCCATTATAAAGTTTTAACAATCCTAGCCCATTTTTTCTTCCCTCGTCGTTTCTTAC
1 ATATATATCCCATTATAAAGTTTTAACAATCCTAGCCCATTTTTTCTTCCCTCGTCGTTTCTTAC
144614 TCTCCAGCCA-CTCCT-AATAGCTCTGATGAAGGGTTGATGGCCCCTTTTTTACTTTCTTAA
66 TCTCCAGCCACCTCCTAAATAGCTCTGATGAAGGGTTGATGGCCCCTTTTTTACTTTCTTAA
144674 ATATATATCCCATTATAAAGTTTTAACAATCCTAGCCCATTTTTTCTTCCCTCGTCGTTTCTTAC
1 ATATATATCCCATTATAAAGTTTTAACAATCCTAGCCCATTTTTTCTTCCCTCGTCGTTTCTTAC
144739 TCTCCAGCCACCTCCTAAATAGCTCTGATGAAGGGTTGATGGCCCCTTTTTTACTTTCTTAA
66 TCTCCAGCCACCTCCTAAATAGCTCTGATGAAGGGTTGATGGCCCCTTTTTTACTTTCTTAA
144801 CCCCATTTCT
Statistics
Matches: 125, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
125 75 0.60
126 5 0.04
127 45 0.36
ACGTcount: A:0.23, C:0.27, G:0.11, T:0.40
Consensus pattern (127 bp):
ATATATATCCCATTATAAAGTTTTAACAATCCTAGCCCATTTTTTCTTCCCTCGTCGTTTCTTAC
TCTCCAGCCACCTCCTAAATAGCTCTGATGAAGGGTTGATGGCCCCTTTTTTACTTTCTTAA
Found at i:145497 original size:17 final size:17
Alignment explanation
Indices: 145475--145509 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
145465 TATTTGGAAT
145475 GCCATCCTTGTAATATG
1 GCCATCCTTGTAATATG
145492 GCCATCCTTGTAATATG
1 GCCATCCTTGTAATATG
145509 G
1 G
145510 ATATCTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (17 bp):
GCCATCCTTGTAATATG
Found at i:145519 original size:17 final size:17
Alignment explanation
Indices: 145477--145521 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
145467 TTTGGAATGC
*
145477 CATCCTTGTAATATGGC
1 CATCCTTGTAATATGGA
145494 CATCCTTGTAATATGGA
1 CATCCTTGTAATATGGA
* *
145511 TATCTTTGTAA
1 CATCCTTGTAA
145522 CCTATAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.40
Consensus pattern (17 bp):
CATCCTTGTAATATGGA
Found at i:146225 original size:4 final size:4
Alignment explanation
Indices: 146213--146263 Score: 59
Period size: 4 Copynumber: 12.5 Consensus size: 4
146203 ATATATATGT
* *
146213 ATAA A-AA ATAA ATAA ATAA ATAA ATAA ATAAA AGTAA ATAT ATAT ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT-AA A-TAA ATAA ATAA ATAA
146262 AT
1 AT
146264 TAATGAAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
3 3 0.07
4 32 0.76
5 6 0.14
6 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:148432 original size:30 final size:30
Alignment explanation
Indices: 148398--148462 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
148388 TTGGTTTTAA
148398 GGAAAATAGATTAAAAGA-TTTTGCTTCAAG
1 GGAAAAT-GATTAAAAGATTTTTGCTTCAAG
* * *
148428 GGAAACTGATTCAAAGATTTTTGTTTCAAG
1 GGAAAATGATTAAAAGATTTTTGCTTCAAG
148458 GGAAA
1 GGAAA
148463 CTGTCTCCAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 9 0.29
30 22 0.71
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.31
Consensus pattern (30 bp):
GGAAAATGATTAAAAGATTTTTGCTTCAAG
Found at i:148438 original size:29 final size:30
Alignment explanation
Indices: 148406--148465 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
148396 AAGGAAAATA
148406 GATTAAAAGA-TTTTGCTTCAAGGGAAACT
1 GATTAAAAGATTTTTGCTTCAAGGGAAACT
* *
148435 GATTCAAAGATTTTTGTTTCAAGGGAAACT
1 GATTAAAAGATTTTTGCTTCAAGGGAAACT
148465 G
1 G
148466 TCTCCAGAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 9 0.32
30 19 0.68
ACGTcount: A:0.35, C:0.10, G:0.22, T:0.33
Consensus pattern (30 bp):
GATTAAAAGATTTTTGCTTCAAGGGAAACT
Found at i:148507 original size:32 final size:32
Alignment explanation
Indices: 148455--148517 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
148445 TTTTTGTTTC
* * *
148455 AAGGGAAACTGTCTCCAGAGAGACAAAATTTT
1 AAGGGAAAATGACTCAAGAGAGACAAAATTTT
148487 AAGGGAAAATGACTCAAGAGAGACAAAATTT
1 AAGGGAAAATGACTCAAGAGAGACAAAATTT
148518 GTTTTAAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.46, C:0.13, G:0.22, T:0.19
Consensus pattern (32 bp):
AAGGGAAAATGACTCAAGAGAGACAAAATTTT
Found at i:148539 original size:36 final size:35
Alignment explanation
Indices: 148459--148553 Score: 90
Period size: 36 Copynumber: 2.8 Consensus size: 35
148449 TGTTTCAAGG
* **
148459 GAAACTGTCTCCAGAGAGACAAAA---TTTTAAGG
1 GAAACTGTCTCAAGAGAGACAAAATTTTTTTAAAA
* *
148491 GAAAATGACTCAAGAGAGACAAAATTTGTTTTAAAA
1 GAAACTGTCTCAAGAGAGACAAAATTT-TTTTAAAA
*
148527 GAAACTGTCTCAAG-GAAGACGAAATTT
1 GAAACTGTCTCAAGAG-AGACAAAATTT
148554 ATTTCAAGGA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
32 21 0.42
35 1 0.02
36 28 0.56
ACGTcount: A:0.44, C:0.13, G:0.20, T:0.23
Consensus pattern (35 bp):
GAAACTGTCTCAAGAGAGACAAAATTTTTTTAAAA
Found at i:148608 original size:101 final size:101
Alignment explanation
Indices: 148487--148812 Score: 485
Period size: 101 Copynumber: 3.2 Consensus size: 101
148477 ACAAAATTTT
* *
148487 AAGGGAAAATGACTCAAGAGAGACAAAATTTGTTTTAAAAGAAACTGTCTCAAGGAAGACGAAAT
1 AAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACTGTCTCAAGGAAGACGAAAT
* * *
148552 TTATTTCAAGGAAAACAGATTTAAAGATTTCGTTTC
66 TTGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTC
** * * *
148588 AAGGGAAACAT-TCTCAAGAGAGACAAAATTTGTTTTAAAATTAACTGTCTCAAGGGACATGAAA
1 AAGGGAAAC-TGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACTGTCTCAAGGAAGACGAAA
*
148652 TTTGTTTTAAGGAAAACAGATTCAAAGATTTTGTTTC
65 TTTGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTC
* *
148689 ACGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAA-GAGAGACGAAA
1 AAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACTGTCTCAAGGA-AGACGAAA
* *
148753 TTTGTTTCAAGGAAAGCAGATTCAAAGATTTTATTTC
65 TTTGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTC
148790 AAGGGAAACTGTCTCAAGAGAGA
1 AAGGGAAACTGTCTCAAGAGAGA
148813 AAATTTATTT
Statistics
Matches: 200, Mismatches: 22, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
100 2 0.01
101 197 0.99
102 1 0.00
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.28
Consensus pattern (101 bp):
AAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACTGTCTCAAGGAAGACGAAAT
TTGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTC
Found at i:148733 original size:36 final size:35
Alignment explanation
Indices: 148681--148929 Score: 131
Period size: 36 Copynumber: 7.3 Consensus size: 35
148671 ATTCAAAGAT
*
148681 TTTGTTTCACGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCA-AGGAAACTGTCTCAAGAGAGACAAAA
* *
148717 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACGAAA
1 TTTGTTTCAAG-GAAACTGTCTCAAGAGAGACAAAA
* *
148753 TTTGTTTCAAGGAAAGCAGAT-TC-A-A-AG----AT
1 TTTGTTTCAAGGAAA-CTG-TCTCAAGAGAGACAAAA
*
148782 TTTATTTCAAGGGAAACTGTCTCAAGAGAG--AAAA
1 TTTGTTTCAA-GGAAACTGTCTCAAGAGAGACAAAA
* * * *
148816 TTTATTTCAAGGGAAA-TGGTTTC-A-A-TG-----T
1 TTTGTTTCAA-GGAAACT-GTCTCAAGAGAGACAAAA
* *
148844 TTATGTTTCAAGAGAAACTGTCTCAAGGGAGATAAAA
1 TT-TGTTTCAAG-GAAACTGTCTCAAGAGAGACAAAA
*
148881 TTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA
1 -TTTGTTTCAA-GGAAACTGTCTCAAGAGAGACAAAA
**
148918 TTCATTTCAAGG
1 TTTGTTTCAAGG
148930 GAAATGTTTT
Statistics
Matches: 167, Mismatches: 22, Indels: 49
0.70 0.09 0.21
Matches are distributed among these distances:
28 4 0.02
29 29 0.17
30 8 0.05
31 2 0.01
32 4 0.02
33 4 0.02
34 22 0.13
35 8 0.05
36 53 0.32
37 30 0.18
38 3 0.02
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (35 bp):
TTTGTTTCAAGGAAACTGTCTCAAGAGAGACAAAA
Done.