Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004615.1 Hibiscus syriacus cultivar Beakdansim tig00010322_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: 136040
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:16605 original size:16 final size:15
Alignment explanation
Indices: 16580--16609 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
16570 TGTTGTGGCC
16580 GGTCATCCCGGGATG
1 GGTCATCCCGGGATG
16595 GGTCAATCCCGGGAT
1 GGTC-ATCCCGGGAT
16610 TTTCGGTCGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.17, C:0.27, G:0.37, T:0.20
Consensus pattern (15 bp):
GGTCATCCCGGGATG
Found at i:16852 original size:14 final size:14
Alignment explanation
Indices: 16830--16863 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
16820 AATGAAAGTA
*
16830 AAATTAATAAAAAT
1 AAATAAATAAAAAT
16844 AAATAAATAAAAAT
1 AAATAAATAAAAAT
16858 AAATAA
1 AAATAA
16864 CAACGATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AAATAAATAAAAAT
Found at i:16950 original size:36 final size:36
Alignment explanation
Indices: 16903--16978 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 36
16893 TTCTACAAAC
*
16903 TATATAATATATATTTTC-AAAA-GTATTTTAAAATTA
1 TATATAATATAT-TTTTCTAAAACGT-TTTCAAAATTA
*
16939 TATATTATATATTTTTCTAAAACGTTTTCAAAATTA
1 TATATAATATATTTTTCTAAAACGTTTTCAAAATTA
16975 TATA
1 TATA
16979 GTTTTCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
35 5 0.14
36 29 0.81
37 2 0.06
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (36 bp):
TATATAATATATTTTTCTAAAACGTTTTCAAAATTA
Found at i:16975 original size:29 final size:30
Alignment explanation
Indices: 16942--17010 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
16932 AAAATTATAT
*
16942 ATTATATATTTTTCTAAAACG-TTTTCAAA
1 ATTATATATTTTTCAAAAACGTTTTTCAAA
* * *
16971 ATTATATAGTTTTCAAAAATGTTTTTTAAA
1 ATTATATATTTTTCAAAAACGTTTTTCAAA
*
17001 ACTATATATT
1 ATTATATATT
17011 ATAAGTTTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 18 0.55
30 15 0.45
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.49
Consensus pattern (30 bp):
ATTATATATTTTTCAAAAACGTTTTTCAAA
Found at i:17019 original size:36 final size:34
Alignment explanation
Indices: 16885--17219 Score: 193
Period size: 34 Copynumber: 9.8 Consensus size: 34
16875 ATAATAATAT
* *
16885 AAAATATTTTCTACAAACTATATAATATATATTTTC-
1 AAAATGTTTT-TA-AAACTATATATTATA-ATTTTCA
* *
16921 AAAA-GTATTTTAAAATTATATATTATATATTTTTCT
1 AAAATGT-TTTTAAAACTATATATTATA-A-TTTTCA
* * *
16957 AAAACG-TTTTCAAA--AT-TA-TATAGTTTTCA
1 AAAATGTTTTTAAAACTATATATTATAATTTTCA
16986 AAAATGTTTTTTAAAACTATATATTATAAGTTTTC-
1 AAAATG-TTTTTAAAACTATATATTATAA-TTTTCA
* *
17021 AAAATGATTTAAAAACTATATAATATATATATGTTTTC-
1 AAAATGTTTTTAAAACTATAT-AT-TATA-A--TTTTCA
*
17059 AAAATGTTTCTTTTTAAAAAT-TATATT-T-ATTTT-A
1 AAAATG----TTTTTAAAACTATATATTATAATTTTCA
* *
17093 AAAATGTTTTTAAAACCATATAATATATATTTTCA
1 AAAATGTTTTTAAAACTATATATTATA-ATTTTCA
* *
17128 AAAACG-TTTTAAAAAT-TATATT-T-ATTTTC-
1 AAAATGTTTTTAAAACTATATATTATAATTTTCA
* * *
17157 AAAGTGTTTTAAAAACTATATAATATAAATGTTTCA
1 AAAATGTTTTTAAAACTATATATTAT-AAT-TTTCA
* *
17193 AATATGTTTTCAAAACTATATATTATA
1 AAAATGTTTTTAAAACTATATATTATA
17220 TACATATATA
Statistics
Matches: 237, Mismatches: 30, Indels: 65
0.71 0.09 0.20
Matches are distributed among these distances:
29 14 0.06
30 23 0.10
31 21 0.09
32 5 0.02
33 9 0.04
34 55 0.23
35 38 0.16
36 43 0.18
37 2 0.01
38 13 0.05
39 1 0.00
40 2 0.01
41 3 0.01
42 8 0.03
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (34 bp):
AAAATGTTTTTAAAACTATATATTATAATTTTCA
Found at i:17041 original size:64 final size:63
Alignment explanation
Indices: 16910--17042 Score: 162
Period size: 64 Copynumber: 2.1 Consensus size: 63
16900 AACTATATAA
* * * * *
16910 TATATATTTTCAAAAGTATTTTAAAATTATATATTATATATTTTTCTAAAACGTTTTCAAAAT
1 TATATATTTTCAAAAGTATTTTAAAACTATATATTATATAGTTTTCTAAAACGATTTAAAAAC
* *
16973 TATATAGTTTTCAAAAATGTTTTTTAAAACTATATATTATA-AGTTTTC-AAAATGATTTAAAAA
1 TATATA-TTTTC-AAAA-GTATTTTAAAACTATATATTATATAGTTTTCTAAAACGATTTAAAAA
17036 C
63 C
17037 TATATA
1 TATATA
17043 ATATATATAT
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
63 6 0.10
64 23 0.38
65 10 0.17
66 21 0.35
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.47
Consensus pattern (63 bp):
TATATATTTTCAAAAGTATTTTAAAACTATATATTATATAGTTTTCTAAAACGATTTAAAAAC
Found at i:17148 original size:64 final size:65
Alignment explanation
Indices: 17070--17218 Score: 201
Period size: 64 Copynumber: 2.3 Consensus size: 65
17060 AAATGTTTCT
* *
17070 TTTTAAAAATTATATTTATTTTAAAAATGTTTTTAAAACCATATAATATATAT-TTTCAAAAACG
1 TTTTAAAAATTATATTTATTTTAAAAATGTTTTAAAAACCATATAATATAAATGTTTCAAAAACG
* * * * *
17134 TTTTAAAAATTATATTTATTTTCAAAGTGTTTTAAAAACTATATAATATAAATGTTTCAAATATG
1 TTTTAAAAATTATATTTATTTTAAAAATGTTTTAAAAACCATATAATATAAATGTTTCAAAAACG
* *
17199 TTTTCAAAACTATATATTAT
1 TTTTAAAAATTATAT-TTAT
17219 ATACATATAT
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
64 48 0.65
65 22 0.30
66 4 0.05
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (65 bp):
TTTTAAAAATTATATTTATTTTAAAAATGTTTTAAAAACCATATAATATAAATGTTTCAAAAACG
Found at i:17214 original size:172 final size:172
Alignment explanation
Indices: 16909--17221 Score: 420
Period size: 172 Copynumber: 1.8 Consensus size: 172
16899 AAACTATATA
* ** * * *
16909 ATATATATTTTCAAAAGTATTTTAAAATTATATATTATATATTTTTCTAAAACGTTTTCAAAATT
1 ATATATATTTTAAAAAGTATTTTAAAACCATATAATATATATTTTTCAAAAACGTTTTAAAAATT
* * *
16974 ATATAGTTTTCAAAAATGTTTTTTAAAACTATATATTATAAGTTTTCAAAATGATTTAAAAACTA
66 ATATAGTTTTCAAAAATGTTTTTAAAAACTATATAATATAAATTTTCAAAATGATTTAAAAACTA
17039 TATAATATATATATGTTTTCAAAATGTTTCTTTTTAAAAATT
131 TATAATATATATATGTTTTCAAAATGTTTCTTTTTAAAAATT
*
17081 ATATTTATTTTAAAAATGT-TTTTAAAACCATATAATATATA-TTTTCAAAAACGTTTTAAAAAT
1 ATATATATTTTAAAAA-GTATTTTAAAACCATATAATATATATTTTTCAAAAACGTTTTAAAAAT
* * *
17144 TATATTTA-TTTTC-AAAGTG-TTTTAAAAACTATATAATATAAATGTTTCAAATATGTTTTCAA
65 TATA--TAGTTTTCAAAAATGTTTTTAAAAACTATATAATATAAAT-TTTCAAA-ATGATTTAAA
*
17206 AACTATATATTATATA
126 AACTATATAATATATA
17222 CATATATATG
Statistics
Matches: 122, Mismatches: 14, Indels: 10
0.84 0.10 0.07
Matches are distributed among these distances:
170 21 0.17
171 36 0.30
172 61 0.50
173 4 0.03
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (172 bp):
ATATATATTTTAAAAAGTATTTTAAAACCATATAATATATATTTTTCAAAAACGTTTTAAAAATT
ATATAGTTTTCAAAAATGTTTTTAAAAACTATATAATATAAATTTTCAAAATGATTTAAAAACTA
TATAATATATATATGTTTTCAAAATGTTTCTTTTTAAAAATT
Found at i:17308 original size:13 final size:13
Alignment explanation
Indices: 17290--17315 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17280 TTTGTCCTTT
17290 TTCGTGGAACGAA
1 TTCGTGGAACGAA
17303 TTCGTGGAACGAA
1 TTCGTGGAACGAA
17316 AAATAGGACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (13 bp):
TTCGTGGAACGAA
Found at i:17983 original size:84 final size:84
Alignment explanation
Indices: 17876--18578 Score: 747
Period size: 84 Copynumber: 8.5 Consensus size: 84
17866 TCGGGGGTCT
* * *
17876 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGATCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAGCTGATCGTAGT
17941 CGAACTCAAAGGTCTTTTG
66 CGAACTCAAAGGTCTTTTG
* * * * * *
17960 TTGGCAGACAACCCTTGTAGACTTAAGTTGTGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTT-GAGCTGATCGTAG
* *
18024 TCGAACTCGAAGGTCTTTGG
65 TCGAACTCAAAGGTCTTTTG
*
18044 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGT-GTA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTG-AGCTGA-TCGTA
* ***
18108 ATCGAACTCGGGGGTC---T-
64 GTCGAACTCAAAGGTCTTTTG
* * * *
18125 TTGGCATATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGATCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAGCTGATCGTAGT
18190 CGAACTCAAAGGTCTTTTG
66 CGAACTCAAAGGTCTTTTG
* * * * * *
18209 TTGGCAGACAACCCTTGTAGACTTAAGTTGTGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTT-GAGCTGATCGTAG
* *
18273 TCGAACTCGAAGGTCTTTGG
65 TCGAACTCAAAGGTCTTTTG
*
18293 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGT-GTA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTG-AGCTGA-TCGTA
* ***
18357 ATCGAACTCGGGGGTC---T-
64 GTCGAACTCAAAGGTCTTTTG
* * *
18374 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGATCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAGCTGATCGTAGT
18439 CGAACTCAAAGGTCTTTTG
66 CGAACTCAAAGGTCTTTTG
* ** * * * * * * *
18458 GTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATAATGTACCCTCGAAGCTGAGT-GTA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTG-AGCTGA-TCGTA
* **
18522 ATCGAACTCAGGGGTC---T-
64 GTCGAACTCAAAGGTCTTTTG
* * *
18539 TTGGCAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAAT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAAT
18579 AGTTTGTTTA
Statistics
Matches: 513, Mismatches: 86, Indels: 43
0.80 0.13 0.07
Matches are distributed among these distances:
79 2 0.00
80 42 0.08
81 127 0.25
82 1 0.00
83 8 0.02
84 260 0.51
85 72 0.14
86 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (84 bp):
TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAGCTGATCGTAGT
CGAACTCAAAGGTCTTTTG
Found at i:18119 original size:249 final size:249
Alignment explanation
Indices: 17831--18578 Score: 1227
Period size: 249 Copynumber: 3.0 Consensus size: 249
17821 GCTATGTTGT
* * *
17831 AAATGATATGACCTCGAAGTTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
17896 ACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGATCGTAGTCGAACTCAAAGGTCTTTTGT
66 ACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGATCGTAGTCGAACTCAAAGGTCTTTTGT
17961 TGGCAGACAACCCTTGTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTC
131 TGGCAGACAACCCTTGTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTC
18026 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
196 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
*
18080 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCATATAGCCCTTCTCG
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
18145 ACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGATCGTAGTCGAACTCAAAGGTCTTTTGT
66 ACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGATCGTAGTCGAACTCAAAGGTCTTTTGT
18210 TGGCAGACAACCCTTGTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTC
131 TGGCAGACAACCCTTGTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTC
18275 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
196 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
18329 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
*
18394 ACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGATCGTAGTCGAACTCAAAGGTCTTTTGG
66 ACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGATCGTAGTCGAACTCAAAGGTCTTTTGT
** * * * * * * * * * * * * *
18459 TCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATAATGTACCCTCGAAGCTGAGTGTAAT
131 TGGCAGACAACCCTTGTAGACTTAAGTTGTGCTGCAAATGATAT-GCCTTGGAGCTGAGCGTAGT
* * * *
18524 CGAACTC-AGGGGTC--T--TTGGCAGATAGCCCTTCTAGACTTAAGCTATGCTGC
195 CGAACTCGA-AGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
18575 AAAT
1 AAAT
18579 AGTTTGTTTA
Statistics
Matches: 472, Mismatches: 25, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
246 37 0.08
248 1 0.00
249 408 0.86
250 26 0.06
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (249 bp):
AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
ACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGATCGTAGTCGAACTCAAAGGTCTTTTGT
TGGCAGACAACCCTTGTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTC
GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
Found at i:18204 original size:165 final size:164
Alignment explanation
Indices: 17876--18578 Score: 716
Period size: 165 Copynumber: 4.2 Consensus size: 164
17866 TCGGGGGTCT
* *
17876 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGA-TCGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTTGAGCTGAGT-GTAG
* * * * * *
17940 TCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTGTAGACTTAAGTTGTGCTGCAAATGATAT
65 TCGAACTCGAAGGTC--TTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
*
18005 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
128 GCCTT-GAGCTGATCGTAGTCGAACTCGAAGGTCTTT-G
* * *
18044 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTTG-AGCTGAGTGTAG
** * * *
18109 TCGAACTCGGGGGTC-T-TTGGCATATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGC
65 TCGAACTCGAAGGTCTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGC
*
18172 CGTTGAGCTGATCGTAGTCGAACTCAAAGGTCTTTTG
130 C-TTGAGCTGATCGTAGTCGAACTCGAAGGTC-TTTG
* * * * * * *
18209 TTGGCAGACAACCCTTGTAGACTTAAGTTGTGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTT-GAGCTGAGTGTAG
18273 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
65 TCGAACTCGAAGGTC-TT-GTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* * **
18338 GCCCTCGAAGCTGAGT-GTAATCGAACTCGGGGGTC--T-
128 G-CCTTG-AGCTGA-TCGTAGTCGAACTCGAAGGTCTTTG
* *
18374 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGA-TCGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTTGAGCTGAGT-GTAG
* * * * * *
18438 TCGAACTCAAAGGTCTT-TTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATAATG
65 TCGAACTCGAAGGTCTTGTTGG---CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
* * * *
18502 TACCCTCGAAGCTGAGT-GTAATCGAACTC-AGGGGTC--T-
127 T-GCCTTG-AGCTGA-TCGTAGTCGAACTCGA-AGGTCTTTG
* *
18539 TTGGCAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAAT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAAT
18579 AGTTTGTTTA
Statistics
Matches: 462, Mismatches: 54, Indels: 41
0.83 0.10 0.07
Matches are distributed among these distances:
162 4 0.01
164 28 0.06
165 280 0.61
166 11 0.02
168 93 0.20
169 44 0.10
170 2 0.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (164 bp):
TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTTGAGCTGAGTGTAGT
CGAACTCGAAGGTCTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC
TTGAGCTGATCGTAGTCGAACTCGAAGGTCTTTG
Found at i:21990 original size:19 final size:18
Alignment explanation
Indices: 21966--22010 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 18
21956 AGTTAATGTG
21966 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAA-AA
21985 AATGCAAAGAAAATAAAA
1 AATGCAAAGAAAATAAAA
*
22003 AATACAAA
1 AATGCAAA
22011 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.71, C:0.09, G:0.09, T:0.11
Consensus pattern (18 bp):
AATGCAAAGAAAATAAAA
Found at i:24517 original size:16 final size:15
Alignment explanation
Indices: 24491--24520 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
24481 TGTTGTGGCC
24491 GGTCATCCCGGGATG
1 GGTCATCCCGGGATG
24506 GGTCAGTCCCGGGAT
1 GGTCA-TCCCGGGAT
24521 TTTCGGCCGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.13, C:0.27, G:0.40, T:0.20
Consensus pattern (15 bp):
GGTCATCCCGGGATG
Found at i:24763 original size:14 final size:14
Alignment explanation
Indices: 24741--24774 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
24731 AATGAAAGTA
*
24741 AAATTAATAAAAAT
1 AAATAAATAAAAAT
24755 AAATAAATAAAAAT
1 AAATAAATAAAAAT
24769 AAATAA
1 AAATAA
24775 CAACGATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AAATAAATAAAAAT
Found at i:24859 original size:34 final size:36
Alignment explanation
Indices: 24814--24889 Score: 104
Period size: 36 Copynumber: 2.2 Consensus size: 36
24804 TTCTACAAAC
*
24814 TATATAATATATA-TTTTC-AAAA-GTATTTTAAAAT
1 TATATAATATATATTTTTCTAAAACGT-TTTCAAAAT
*
24848 TATATATTATATATTTTTCTAAAACGTTTTCAAAAT
1 TATATAATATATATTTTTCTAAAACGTTTTCAAAAT
24884 TATATA
1 TATATA
24890 GTTTTCAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
34 12 0.32
35 5 0.14
36 18 0.49
37 2 0.05
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (36 bp):
TATATAATATATATTTTTCTAAAACGTTTTCAAAAT
Found at i:24886 original size:29 final size:30
Alignment explanation
Indices: 24853--24921 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
24843 AAAATTATAT
*
24853 ATTATATATTTTTCTAAAACG-TTTTCAAA
1 ATTATATATTTTTCAAAAACGTTTTTCAAA
* * *
24882 ATTATATAGTTTTCAAAAATGTTTTTTAAA
1 ATTATATATTTTTCAAAAACGTTTTTCAAA
*
24912 ACTATATATT
1 ATTATATATT
24922 ATAAGTTTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 18 0.55
30 15 0.45
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.49
Consensus pattern (30 bp):
ATTATATATTTTTCAAAAACGTTTTTCAAA
Found at i:24895 original size:64 final size:63
Alignment explanation
Indices: 24821--24953 Score: 171
Period size: 64 Copynumber: 2.1 Consensus size: 63
24811 AACTATATAA
* * * *
24821 TATATATTTTC-AAAA-GTATTTTAAAATTATATATTATATATTTTTCTAAAACGTTTTCAAAAT
1 TATATATTTTCAAAAATGTATTTTAAAACTATATATTATA-AGTTTTC-AAAACGATTTCAAAAC
* *
24884 TATATAGTTTTCAAAAATGTTTTTTAAAACTATATATTATAAGTTTTCAAAATGATTTCAAAAC
1 TATATA-TTTTCAAAAATGTATTTTAAAACTATATATTATAAGTTTTCAAAACGATTTCAAAAC
24948 TATATA
1 TATATA
24954 ATATATATAT
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
63 6 0.10
64 24 0.39
65 10 0.16
66 21 0.34
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.47
Consensus pattern (63 bp):
TATATATTTTCAAAAATGTATTTTAAAACTATATATTATAAGTTTTCAAAACGATTTCAAAAC
Found at i:24952 original size:34 final size:37
Alignment explanation
Indices: 24882--24960 Score: 110
Period size: 34 Copynumber: 2.2 Consensus size: 37
24872 CGTTTTCAAA
* *
24882 ATTATATAGTTTTCAAAAATGTTTTTTAAAACTATAT
1 ATTATATAGTTTTCAAAAATGTATTTCAAAACTATAT
24919 ATTATA-AGTTTTC-AAAATG-ATTTCAAAACTATAT
1 ATTATATAGTTTTCAAAAATGTATTTCAAAACTATAT
*
24953 AATATATA
1 ATTATATA
24961 TATATATATG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
34 18 0.47
35 7 0.18
36 7 0.18
37 6 0.16
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.44
Consensus pattern (37 bp):
ATTATATAGTTTTCAAAAATGTATTTCAAAACTATAT
Found at i:25031 original size:78 final size:79
Alignment explanation
Indices: 24884--25039 Score: 196
Period size: 78 Copynumber: 2.0 Consensus size: 79
24874 TTTTCAAAAT
* * *
24884 TATATAGTTTTCAAAAATGTTTTTTAAAACTATATATTATAAGTTTTCAAAATGATTTCAAAACT
1 TATATAGTTTTCAAAAATGTTTTTTAAAAATATATATTATAAGTTTTAAAAATGATTTCAAAACC
24949 ATATAATATATATA
66 ATATAATATATATA
* *
24963 TATATATGTTTTC-AAAATGTTTCTTTTTAAAAAT-TATATT-T-A-TTTTAAAAATGTTTTTAA
1 TATATA-GTTTTCAAAAATG--T-TTTTTAAAAATATATATTATAAGTTTTAAAAATGATTTCAA
25023 AACCATATAATATATAT
62 AACCATATAATATATAT
25040 TTTCAAAAAC
Statistics
Matches: 68, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
78 31 0.46
79 13 0.19
80 7 0.10
81 7 0.10
82 10 0.15
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.47
Consensus pattern (79 bp):
TATATAGTTTTCAAAAATGTTTTTTAAAAATATATATTATAAGTTTTAAAAATGATTTCAAAACC
ATATAATATATATA
Found at i:25671 original size:20 final size:20
Alignment explanation
Indices: 25646--25696 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
25636 ATCCTATTCC
*
25646 CTGGTAATTTTTTATTCACA
1 CTGGTAATCTTTTATTCACA
*
25666 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTTTATTCACA
25686 CTGGTAATCTT
1 CTGGTAATCTT
25697 ACATTCCGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.20, G:0.12, T:0.47
Consensus pattern (20 bp):
CTGGTAATCTTTTATTCACA
Found at i:25702 original size:20 final size:20
Alignment explanation
Indices: 25659--25703 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
25649 GTAATTTTTT
* **
25659 ATTCACACTGGTAATCTTTT
1 ATTCCCACTGGTAATCTTAC
25679 ATTCCCACTGGTAATCTTAC
1 ATTCCCACTGGTAATCTTAC
25699 ATTCC
1 ATTCC
25704 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.27, G:0.09, T:0.40
Consensus pattern (20 bp):
ATTCCCACTGGTAATCTTAC
Found at i:26524 original size:18 final size:18
Alignment explanation
Indices: 26501--26537 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
26491 CAAAACAATG
26501 CTTATTGCTTATACTTTT
1 CTTATTGCTTATACTTTT
26519 CTTATTGCTTATACTTTT
1 CTTATTGCTTATACTTTT
26537 C
1 C
26538 ATAAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.19, G:0.05, T:0.59
Consensus pattern (18 bp):
CTTATTGCTTATACTTTT
Found at i:26549 original size:2 final size:2
Alignment explanation
Indices: 26542--26571 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
26532 CTTTTCATAA
26542 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
26572 TGCAAACTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36872 original size:17 final size:16
Alignment explanation
Indices: 36846--36889 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
36836 CTTTCCGTCA
* *
36846 ATAAGATTTTTATTTT
1 ATAAGGTTTTTATCTT
36862 CATAAGGTTTTTATCTT
1 -ATAAGGTTTTTATCTT
36879 AGTAAGGTTTT
1 A-TAAGGTTTT
36890 AACGAGACAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 1 0.04
17 23 0.96
ACGTcount: A:0.27, C:0.05, G:0.14, T:0.55
Consensus pattern (16 bp):
ATAAGGTTTTTATCTT
Found at i:41155 original size:18 final size:18
Alignment explanation
Indices: 41121--41155 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41111 TACAGACACG
* *
41121 AACCTCAACCTTTCACCA
1 AACCTCAACCCTACACCA
41139 AACCTCAACCCTACACC
1 AACCTCAACCCTACACC
41156 TCTCAAAACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.49, G:0.00, T:0.17
Consensus pattern (18 bp):
AACCTCAACCCTACACCA
Found at i:41495 original size:16 final size:16
Alignment explanation
Indices: 41474--41513 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
41464 GGATTTTAGA
41474 CTCTGGTTGTGGATTT
1 CTCTGGTTGTGGATTT
41490 CTCTGGTTGTGGATTT
1 CTCTGGTTGTGGATTT
41506 CTCTGGTT
1 CTCTGGTT
41514 TCGTCGTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.05, C:0.15, G:0.30, T:0.50
Consensus pattern (16 bp):
CTCTGGTTGTGGATTT
Found at i:42606 original size:54 final size:54
Alignment explanation
Indices: 42474--42738 Score: 295
Period size: 54 Copynumber: 4.9 Consensus size: 54
42464 TTTTCAACAT
* **
42474 CGGGTTCGCTCCCTATCGCTTCAGGGA-ACATAGAACTCGAATAATCTTCTGCTAA
1 CGGGTTCGCTCCCTCTTTCTTCAGGGAGA-ATAGAACTCGAA-AATCTTCTGCTAA
* *
42529 CGGGTTCGCTCCCTATTGT-TTCAGGGAGTATAGAACTC-AAGAATCTTCTGCTAA
1 CGGGTTCGCTCCCTCTT-TCTTCAGGGAGAATAGAACTCGAA-AATCTTCTGCTAA
* * * * *
42583 CCGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAACATCTTCTTCAAA
1 CGGGTTCGCTCCCTCTTTCTTCAGGGAGAATAGAACTCGAAAATCTTCTGCTAA
* * * * *
42637 TGAGTTCGCTCCCTCTTTCTTCAGGGAGAATAGAACTCGAATATCTTCTTCAAA
1 CGGGTTCGCTCCCTCTTTCTTCAGGGAGAATAGAACTCGAAAATCTTCTGCTAA
* * *
42691 CGGGTTTGCTCCCTCTCTC-TCTAGGGAGAATAGAACTCGAATATCTTC
1 CGGGTTCGCTCCCTCTTTCTTC-AGGGAGAATAGAACTCGAAAATCTTC
42739 AACAATCGTG
Statistics
Matches: 187, Mismatches: 18, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
53 3 0.02
54 149 0.80
55 35 0.19
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (54 bp):
CGGGTTCGCTCCCTCTTTCTTCAGGGAGAATAGAACTCGAAAATCTTCTGCTAA
Found at i:42755 original size:54 final size:53
Alignment explanation
Indices: 42492--42768 Score: 244
Period size: 54 Copynumber: 5.1 Consensus size: 53
42482 CTCCCTATCG
* * *
42492 CTTCAGGGA-ACATAGAACTCGAATAATCTTCTGCTAA-CGGGTTCGCTCCCTATTGT
1 CTTCAGGGAGA-ATAGAACTCGAAT-ATCTTCTTC-AATCGAGTT-GCTCCCTCTT-T
* * * *
42548 -TTCAGGGAGTATAGAACTC-AAGAATCTTCTGCTAACCG-GTTCGCTCCCTCTTT
1 CTTCAGGGAGAATAGAACTCGAA-TATCTTCTTC-AATCGAGTT-GCTCCCTCTTT
* *
42601 CTTCAGGGAGTATAGAACTCGAACATCTTCTTCAAAT-GAGTTCGCTCCCTCTTT
1 CTTCAGGGAGAATAGAACTCGAATATCTTCTTC-AATCGAGTT-GCTCCCTCTTT
* * *
42655 CTTCAGGGAGAATAGAACTCGAATATCTTCTTCAAACGGGTTTGCTCCCTCTCT
1 CTTCAGGGAGAATAGAACTCGAATATCTTCTTCAATCGAG-TTGCTCCCTCTTT
** * *
42709 C-TCTAGGGAGAATAGAACTCGAATATCTTCAACAATCGTGTCTGCTCCCTATTT
1 CTTC-AGGGAGAATAGAACTCGAATATCTTCTTCAATCGAGT-TGCTCCCTCTTT
42763 CTTCAG
1 CTTCAG
42769 AGAGTATAAG
Statistics
Matches: 192, Mismatches: 18, Indels: 24
0.82 0.08 0.10
Matches are distributed among these distances:
53 7 0.04
54 160 0.83
55 25 0.13
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (53 bp):
CTTCAGGGAGAATAGAACTCGAATATCTTCTTCAATCGAGTTGCTCCCTCTTT
Found at i:42756 original size:108 final size:108
Alignment explanation
Indices: 42476--42768 Score: 292
Period size: 108 Copynumber: 2.7 Consensus size: 108
42466 TTCAACATCG
* * * ** * * *
42476 GGTTCGCTCCCTATCGCTTCAGGGA-ACATAGAACTCGAATAATCTTCTGCTAACGGGTTCGCTC
1 GGTTCGCTCCCTCTCTCTTCAGGGAGA-ATAGAACTCGAA-CATCTTCAACAAATGAGTTCGCTC
* *
42540 CCTATTGT-TTCAGGGAGTATAGAACTCAAGAATCTTCTGCTAACC
64 CCTATT-TCTTCAGGGAGAATAGAACTCAAGAATCTTCTGCAAACC
* * **
42585 GGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAACATCTTCTTCAAATGAGTTCGCTCCC
1 GGTTCGCTCCCTCTCTCTTCAGGGAGAATAGAACTCGAACATCTTCAACAAATGAGTTCGCTCCC
* * * *
42650 TCTTTCTTCAGGGAGAATAGAACTCGAA-TATCTTCTTCAAACG
66 TATTTCTTCAGGGAGAATAGAACTC-AAGAATCTTCTGCAAACC
* * *
42693 GGTTTGCTCCCTCTCTC-TCTAGGGAGAATAGAACTCGAATATCTTCAAC-AAT-CGTGTCTGCT
1 GGTTCGCTCCCTCTCTCTTC-AGGGAGAATAGAACTCGAACATCTTCAACAAATGAGT-TC-GCT
42755 CCCTATTTCTTCAG
63 CCCTATTTCTTCAG
42769 AGAGTATAAG
Statistics
Matches: 155, Mismatches: 23, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
106 2 0.01
107 8 0.05
108 109 0.70
109 36 0.23
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (108 bp):
GGTTCGCTCCCTCTCTCTTCAGGGAGAATAGAACTCGAACATCTTCAACAAATGAGTTCGCTCCC
TATTTCTTCAGGGAGAATAGAACTCAAGAATCTTCTGCAAACC
Found at i:42758 original size:162 final size:163
Alignment explanation
Indices: 42477--42776 Score: 369
Period size: 162 Copynumber: 1.8 Consensus size: 163
42467 TCAACATCGG
*
42477 GTTCGCTCCCTATCGCTTCAGGGAACATAGAACTCGAATAATCTTCTGCTAACGGGTTCGCTCCC
1 GTTCGCTCCCTATCGCTTCAGGGAACATAGAACTCGAATAATCTTCTGCAAACGGGTTCGCTCCC
* * * ** *
42542 TATTGTTTCAGGGAGTATAGAACTCAAGAATCTTCTGCTAACCGGTTCGCTCCCTCTTTCTTCAG
66 TATTCTCTCAGGGAGAATAGAACTCAAGAATCTTCAACTAACCGGTTCGCTCCCTATTTCTTCAG
*
42607 GGAGTATAGAACTCGAACATCTTCTTCAAATGA
131 AGAGTATAGAACTCGAACATCTTCTTCAAATGA
* ** * *
42640 GTTCGCTCCCTCTTTCTTCAGGGAGA-ATAGAACTCGAAT-ATCTTCTTCAAACGGGTTTGCTCC
1 GTTCGCTCCCTATCGCTTCAGGGA-ACATAGAACTCGAATAATCTTCTGCAAACGGGTTCGCTCC
* * *
42703 CT-CTCTCTCTAGGGAGAATAGAACTCGAA-TATCTTCAAC-AATC-GTGTCTGCTCCCTATTTC
65 CTATTCTCTC-AGGGAGAATAGAACTC-AAGAATCTTCAACTAACCGGT-TC-GCTCCCTATTTC
42764 TTCAGAGAGTATA
126 TTCAGAGAGTATA
42777 AGACCCAAAC
Statistics
Matches: 116, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
160 2 0.02
161 9 0.08
162 68 0.59
163 36 0.31
164 1 0.01
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (163 bp):
GTTCGCTCCCTATCGCTTCAGGGAACATAGAACTCGAATAATCTTCTGCAAACGGGTTCGCTCCC
TATTCTCTCAGGGAGAATAGAACTCAAGAATCTTCAACTAACCGGTTCGCTCCCTATTTCTTCAG
AGAGTATAGAACTCGAACATCTTCTTCAAATGA
Found at i:42796 original size:55 final size:55
Alignment explanation
Indices: 42725--43022 Score: 436
Period size: 55 Copynumber: 5.4 Consensus size: 55
42715 GGAGAATAGA
* * * *
42725 ACTCGAA-TATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * ** * *
42779 ACCCAAACAATCTTCAACAAATCTTGTCTGCTCCCTATTCCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAAC-GATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
*
42835 ACTCGAACAATCTTCAATGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* *
42890 ACCCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGGGAGTATAAG
1 ACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* *
42945 ACTCGAACAATCTTCAACGATCGCCTCTTCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
43000 ACTCGAACAATCTTCAACGATCG
1 ACTCGAACAATCTTCAACGATCG
43023 TTGGGAAACC
Statistics
Matches: 222, Mismatches: 20, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
54 5 0.02
55 167 0.75
56 50 0.23
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (55 bp):
ACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
Found at i:44022 original size:8 final size:8
Alignment explanation
Indices: 44009--44073 Score: 70
Period size: 8 Copynumber: 8.9 Consensus size: 8
43999 TCTTGAACCC
44009 TCATTTTT
1 TCATTTTT
44017 TCATTTTT
1 TCATTTTT
**
44025 T--TTCAT
1 TCATTTTT
44031 TCATTTTT
1 TCATTTTT
44039 T-ATTTTT
1 TCATTTTT
44046 T-ATTTTT
1 TCATTTTT
44053 T-A-TTTT
1 TCATTTTT
44059 TCATTTTT
1 TCATTTTT
44067 TCATTTT
1 TCATTTT
44074 CACTCATTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
6 9 0.18
7 16 0.33
8 24 0.49
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (8 bp):
TCATTTTT
Found at i:44043 original size:7 final size:7
Alignment explanation
Indices: 44011--44073 Score: 65
Period size: 7 Copynumber: 8.7 Consensus size: 7
44001 TTGAACCCTC
44011 ATTTTTT
1 ATTTTTT
44018 CATTTTTT
1 -ATTTTTT
* *
44026 -TTCATTC
1 ATT-TTTT
44033 ATTTTTT
1 ATTTTTT
44040 ATTTTTT
1 ATTTTTT
44047 ATTTTTT
1 ATTTTTT
*
44054 ATTTTTC
1 ATTTTTT
44061 ATTTTTT
1 ATTTTTT
44068 CATTTT
1 -ATTTT
44074 CACTCATTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
6 2 0.04
7 30 0.65
8 14 0.30
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (7 bp):
ATTTTTT
Found at i:44045 original size:28 final size:27
Alignment explanation
Indices: 44013--44102 Score: 85
Period size: 28 Copynumber: 3.2 Consensus size: 27
44003 GAACCCTCAT
44013 TTTTTCATTTTTTTTCATTCATTTTTTA
1 TTTTTCATTTTTTTTC-TTCATTTTTTA
* *
44041 TTTTTTATTTTTTATTTTTCATTTTTTCA
1 TTTTTCATTTTTT-TTCTTCATTTTTT-A
* *
44070 -TTTTCACTCATTTTTTCTTCCTTTTTT-
1 TTTTTCA-T-TTTTTTTCTTCATTTTTTA
44097 TTTTTC
1 TTTTTC
44103 TTCAAGCAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
28 32 0.63
29 15 0.29
30 4 0.08
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (27 bp):
TTTTTCATTTTTTTTCTTCATTTTTTA
Found at i:44075 original size:14 final size:14
Alignment explanation
Indices: 44013--44073 Score: 79
Period size: 14 Copynumber: 4.3 Consensus size: 14
44003 GAACCCTCAT
44013 TTTTTCATTTTTT-
1 TTTTTCATTTTTTA
*
44026 TTCATTCATTTTTTA
1 TT-TTTCATTTTTTA
*
44041 TTTTTTATTTTTTA
1 TTTTTCATTTTTTA
44055 TTTTTCATTTTTTCA
1 TTTTTCATTTTTT-A
44070 TTTT
1 TTTT
44074 CACTCATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
13 2 0.05
14 32 0.78
15 7 0.17
ACGTcount: A:0.13, C:0.08, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTCATTTTTTA
Found at i:55235 original size:175 final size:182
Alignment explanation
Indices: 54871--55235 Score: 537
Period size: 175 Copynumber: 2.0 Consensus size: 182
54861 TGACTCTCTA
**
54871 AAGGTCCCCAGTGGAGTCGCCAAGCTGTCGAAACGATTTTTAAACGGGGCGTGGGGGAGCGAGAT
1 AAGGTCCCCAGCAGAGTCGCCAAGCTGTCGAAACGATTTTTAAAC---GCGTGGGGGAGCGAGAT
* *
54936 TTTGAAAACCGCATCATTTTTAATTATTCTCTTTTCAATTGAACTTTTAATTAAAAACAATGTGA
63 TTTGAAAACCGCATCATTTTTAATTATTCTCTTTACAATTGAACTTTCAATTAAAAACAATGTGA
* *
55001 TTTTTAGAAAACTTCTCGTTTCGAAAATTTGGAAATTCCTTTACGATAAAAACAT
128 TTTTTAGAAAACCTCTCGTTTCGAAAATTTGGAAATTCCGTTACGATAAAAACAT
55056 AAGGTCCCCAGCAGAGTCGCCAAGCTGTCGAAACGATTTTTAAAC-CGT-GGGG-G-G-GA-TTT
1 AAGGTCCCCAGCAGAGTCGCCAAGCTGTCGAAACGATTTTTAAACGCGTGGGGGAGCGAGATTTT
* * * * *
55115 GGAAACCGCGTCATTTTTAATTGTTCTCTTTACGATTTAA-TTTCAATTAAAAACAATGTGATTT
66 GAAAACCGCATCATTTTTAATTATTCTCTTTACAATTGAACTTTCAATTAAAAACAATGTGATTT
* *
55179 TTAGAAAACCTCTCGTTTCGAAAATTTGGAAATTCCGTTACGGTAAAAATAT
131 TTAGAAAACCTCTCGTTTCGAAAATTTGGAAATTCCGTTACGATAAAAACAT
55231 AAGGT
1 AAGGT
55236 TCGAGGAGTC
Statistics
Matches: 167, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
175 76 0.46
176 37 0.22
177 2 0.01
178 1 0.01
179 1 0.01
180 4 0.02
181 3 0.02
185 43 0.26
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (182 bp):
AAGGTCCCCAGCAGAGTCGCCAAGCTGTCGAAACGATTTTTAAACGCGTGGGGGAGCGAGATTTT
GAAAACCGCATCATTTTTAATTATTCTCTTTACAATTGAACTTTCAATTAAAAACAATGTGATTT
TTAGAAAACCTCTCGTTTCGAAAATTTGGAAATTCCGTTACGATAAAAACAT
Found at i:56953 original size:18 final size:18
Alignment explanation
Indices: 56919--56953 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
56909 TACAGACACG
* *
56919 AACCTCAACCTTTCACCA
1 AACCTCAACCCTACACCA
56937 AACCTCAACCCTACACC
1 AACCTCAACCCTACACC
56954 TCTCAAAACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.49, G:0.00, T:0.17
Consensus pattern (18 bp):
AACCTCAACCCTACACCA
Found at i:57292 original size:16 final size:16
Alignment explanation
Indices: 57271--57310 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
57261 GGATTTTAGA
57271 CTCTGGTTGTGGATTT
1 CTCTGGTTGTGGATTT
57287 CTCTGGTTGTGGATTT
1 CTCTGGTTGTGGATTT
57303 CTCTGGTT
1 CTCTGGTT
57311 TCGTCGTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.05, C:0.15, G:0.30, T:0.50
Consensus pattern (16 bp):
CTCTGGTTGTGGATTT
Found at i:59971 original size:20 final size:20
Alignment explanation
Indices: 59942--59979 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
59932 AACACAACTA
*
59942 TTCACTAAGCGAATTTCGTT
1 TTCACAAAGCGAATTTCGTT
59962 TTCACAAAGCGAATTTCG
1 TTCACAAAGCGAATTTCG
59980 CAAATCGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (20 bp):
TTCACAAAGCGAATTTCGTT
Found at i:60497 original size:20 final size:20
Alignment explanation
Indices: 60472--60509 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
60462 ATTCGATTTG
*
60472 CGAAATTTGCGTTGCGAAAA
1 CGAAATTCGCGTTGCGAAAA
60492 CGAAATTCGCGTTGCGAA
1 CGAAATTCGCGTTGCGAA
60510 TAGTTGTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (20 bp):
CGAAATTCGCGTTGCGAAAA
Found at i:61048 original size:21 final size:21
Alignment explanation
Indices: 61024--61063 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
61014 ATTCGAATAT
*
61024 TTGATTTTGTTTAAGGAATCC
1 TTGATTTTGCTTAAGGAATCC
61045 TTGATTTTGCTTAAGGAAT
1 TTGATTTTGCTTAAGGAAT
61064 ATAGTGTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.07, G:0.20, T:0.47
Consensus pattern (21 bp):
TTGATTTTGCTTAAGGAATCC
Found at i:61554 original size:16 final size:16
Alignment explanation
Indices: 61530--61577 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
61520 ATTAGTTAAA
*
61530 AATTTAAATATAATTT
1 AATTAAAATATAATTT
61546 AATTAAAATATAATATT
1 AATTAAAATATAAT-TT
* *
61563 TATAAAAAT-TAATTT
1 AATTAAAATATAATTT
61578 TTTAGTAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 2 0.07
16 17 0.61
17 9 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AATTAAAATATAATTT
Found at i:63009 original size:48 final size:49
Alignment explanation
Indices: 62946--63044 Score: 173
Period size: 48 Copynumber: 2.0 Consensus size: 49
62936 GGATTAAATG
*
62946 TATAATTATACGTTTAGTACTTTATAATTTAATA-TTTATAAATTAATT
1 TATAATTATACGTTTAATACTTTATAATTTAATATTTTATAAATTAATT
*
62994 TATAATTATATGTTTAATACTTTATAATTTAATATTTTATAAATTAATT
1 TATAATTATACGTTTAATACTTTATAATTTAATATTTTATAAATTAATT
63043 TA
1 TA
63045 ATGATACTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
48 32 0.67
49 16 0.33
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (49 bp):
TATAATTATACGTTTAATACTTTATAATTTAATATTTTATAAATTAATT
Found at i:63040 original size:15 final size:15
Alignment explanation
Indices: 62966--63041 Score: 64
Period size: 15 Copynumber: 4.9 Consensus size: 15
62956 CGTTTAGTAC
62966 TTTATAATTTAATA-
1 TTTATAATTTAATAT
*
62980 TTTATAAATTAATTTAT
1 TTTATAATTTAA--TAT
* * *
62997 AATTATATGTTTAATAC
1 -TTTATA-ATTTAATAT
63014 TTTATAATTTAATAT
1 TTTATAATTTAATAT
*
63029 TTTATAAATTAAT
1 TTTATAATTTAAT
63042 TTAATGATAC
Statistics
Matches: 48, Mismatches: 9, Indels: 9
0.73 0.14 0.14
Matches are distributed among these distances:
14 11 0.23
15 19 0.40
16 7 0.15
17 2 0.04
18 5 0.10
19 4 0.08
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (15 bp):
TTTATAATTTAATAT
Found at i:63178 original size:11 final size:12
Alignment explanation
Indices: 63155--63185 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
63145 ACTCAATATT
63155 AAAACATTAAAA
1 AAAACATTAAAA
63167 AAAACATTAAAA
1 AAAACATTAAAA
63179 AAAACAT
1 AAAACAT
63186 CCCAAAGGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.74, C:0.10, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAACATTAAAA
Found at i:64626 original size:19 final size:18
Alignment explanation
Indices: 64572--64627 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 18
64562 CAAACCGGTA
*
64572 TGACCCGTTGACTTTGACC
1 TGACCCATTGACTTTGA-C
*
64591 T-ACCCATTGATCGTTGAC
1 TGACCCATTGA-CTTTGAC
64609 TAGACCCATTGACTTTGAC
1 T-GACCCATTGACTTTGAC
64628 ATTTTACTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 10 0.32
19 12 0.39
20 9 0.29
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.32
Consensus pattern (18 bp):
TGACCCATTGACTTTGAC
Found at i:66374 original size:14 final size:14
Alignment explanation
Indices: 66333--66375 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
66323 TGAGATCTAG
* *
66333 TTTCTGATTATTGG
1 TTTCTGATTTTTGA
*
66347 TTTCTGATATTTGA
1 TTTCTGATTTTTGA
66361 TTTCTGATTTTTGA
1 TTTCTGATTTTTGA
66375 T
1 T
66376 ATTAATGTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.16, C:0.07, G:0.16, T:0.60
Consensus pattern (14 bp):
TTTCTGATTTTTGA
Found at i:66805 original size:31 final size:31
Alignment explanation
Indices: 66770--66870 Score: 98
Period size: 31 Copynumber: 3.2 Consensus size: 31
66760 CCTAAGGTGA
*
66770 CCCTTAGTAGGCTCTTAGGACCCAAGGTAAT
1 CCCTTAGTAGGCTCTTAGGCCCCAAGGTAAT
* *
66801 CCCTTGGGTAGGAT-TTAAGGCCCCAAGGT-AT
1 CCCTT-AGTAGGCTCTT-AGGCCCCAAGGTAAT
* * * *
66832 TCCTTGGATAGGCTCTAAGGCCCCAAGGTATT
1 CCCTTAG-TAGGCTCTTAGGCCCCAAGGTAAT
66864 CCCTTAG
1 CCCTTAG
66871 GTTGGTTTCT
Statistics
Matches: 56, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
30 2 0.04
31 30 0.54
32 24 0.43
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.27
Consensus pattern (31 bp):
CCCTTAGTAGGCTCTTAGGCCCCAAGGTAAT
Found at i:66826 original size:32 final size:32
Alignment explanation
Indices: 66790--66868 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 32
66780 GCTCTTAGGA
* *
66790 CCCAAGGTAATCCCTTGGGTAGGATTTAAGGC
1 CCCAAGGTAATCCCTTGGATAGGATCTAAGGC
* *
66822 CCCAAGGT-ATTCCTTGGATAGGCTCTAAGGC
1 CCCAAGGTAATCCCTTGGATAGGATCTAAGGC
*
66853 CCCAAGGTATTCCCTT
1 CCCAAGGTAATCCCTT
66869 AGGTTGGTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
31 27 0.68
32 13 0.32
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.27
Consensus pattern (32 bp):
CCCAAGGTAATCCCTTGGATAGGATCTAAGGC
Found at i:74188 original size:2 final size:2
Alignment explanation
Indices: 74183--74209 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
74173 TATTTTTTCC
74183 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
74210 TATTTTACCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:78066 original size:13 final size:13
Alignment explanation
Indices: 78066--78100 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
78056 CCGTTGACCC
78066 GACCCGACCCATT
1 GACCCGACCCATT
* *
78079 TACCCGACCCGTT
1 GACCCGACCCATT
78092 GACCCGACC
1 GACCCGACC
78101 TGACCCGTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.20, C:0.49, G:0.17, T:0.14
Consensus pattern (13 bp):
GACCCGACCCATT
Found at i:78067 original size:18 final size:18
Alignment explanation
Indices: 78044--78120 Score: 83
Period size: 18 Copynumber: 4.6 Consensus size: 18
78034 ACCGGTCACA
78044 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
78062 ACCCGACCCGACCCATT-
1 ACCCGACCCGACCCGTTG
*
78079 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
* *
78093 ACCCGACCTGACCCGTTA
1 ACCCGACCCGACCCGTTG
78111 ACCCGACCCG
1 ACCCGACCCG
78121 TTGACCGTTG
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
13 11 0.23
18 36 0.77
ACGTcount: A:0.19, C:0.49, G:0.18, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:78087 original size:31 final size:31
Alignment explanation
Indices: 78049--78126 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
78039 TCACAACCCG
*
78049 ACCCGACCCGTTGACCCGACCCGACCCATTT
1 ACCCGACCCGTTGACCCGACCCGACCCATTA
* *
78080 ACCCGACCCGTTGACCCGACCTGACCCGTTA
1 ACCCGACCCGTTGACCCGACCCGACCCATTA
78111 ACCCGACCCGTTGACC
1 ACCCGACCCGTTGACC
78127 GTTGACCCGT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.19, C:0.47, G:0.18, T:0.15
Consensus pattern (31 bp):
ACCCGACCCGTTGACCCGACCCGACCCATTA
Found at i:78141 original size:14 final size:15
Alignment explanation
Indices: 78115--78148 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
78105 CCGTTAACCC
78115 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
78130 GACCCG-TGACCGTT
1 GACCCGTTGACCGTT
78144 G-CCCG
1 GACCCG
78149 GAGTTGACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.21
14 9 0.47
15 6 0.32
ACGTcount: A:0.12, C:0.38, G:0.29, T:0.21
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:79471 original size:18 final size:18
Alignment explanation
Indices: 79445--79480 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
79435 TCGAAAGGAC
*
79445 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
79463 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
79481 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:80651 original size:23 final size:23
Alignment explanation
Indices: 80625--80707 Score: 96
Period size: 23 Copynumber: 3.6 Consensus size: 23
80615 TCCGACTTGA
* *
80625 ATTCTGTTATGATCCTGACCTGG
1 ATTCTGATATGATCATGACCTGG
* *
80648 ATTCTGATCTGAT-ATTGACATGG
1 ATTCTGATATGATCA-TGACCTGG
*
80671 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGAT-CATGACCTGG
80695 ATTCTGATATGAT
1 ATTCTGATATGAT
80708 ACTTGACTTG
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
23 31 0.61
24 19 0.37
25 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (23 bp):
ATTCTGATATGATCATGACCTGG
Found at i:80695 original size:24 final size:24
Alignment explanation
Indices: 80640--80714 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
80630 GTTATGATCC
80640 TGACCTGGATTCTGATCTGATA-T
1 TGACCTGGATTCTGATCTGATACT
* *
80663 TGACATGGATTCTGATCTGATACA
1 TGACCTGGATTCTGATCTGATACT
*
80687 TGACCTGGATTCTGATATGATACT
1 TGACCTGGATTCTGATCTGATACT
80711 TGAC
1 TGAC
80715 TTGAATTATG
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 21 0.46
24 25 0.54
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.36
Consensus pattern (24 bp):
TGACCTGGATTCTGATCTGATACT
Found at i:82937 original size:13 final size:13
Alignment explanation
Indices: 82938--82967 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
82928 CCGTTGACCC
82938 GACCCGACCCGTT
1 GACCCGACCCGTT
82951 GACCCGACCCGTT
1 GACCCGACCCGTT
82964 GACC
1 GACC
82968 GTTGACCCGT
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:0.17, C:0.47, G:0.23, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:82937 original size:31 final size:31
Alignment explanation
Indices: 82902--82967 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
82892 GTCACAACCC
*
82902 GACCCGACCAGACCCATTTACCCGACCCGTT
1 GACCCGACCAGACCCATTGACCCGACCCGTT
* *
82933 GACCCGACCCGACCCGTTGACCCGACCCGTT
1 GACCCGACCAGACCCATTGACCCGACCCGTT
82964 GACC
1 GACC
82968 GTTGACCCGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.20, C:0.47, G:0.20, T:0.14
Consensus pattern (31 bp):
GACCCGACCAGACCCATTGACCCGACCCGTT
Found at i:82942 original size:18 final size:18
Alignment explanation
Indices: 82921--82961 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
82911 AGACCCATTT
82921 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
82939 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
82957 ACCCG
1 ACCCG
82962 TTGACCGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.17, C:0.51, G:0.22, T:0.10
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:82982 original size:14 final size:15
Alignment explanation
Indices: 82943--82988 Score: 62
Period size: 13 Copynumber: 3.3 Consensus size: 15
82933 GACCCGACCC
*
82943 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
82956 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
82971 GACCCG-TGACCGTT
1 GACCCGTTGACCGTT
82985 GACC
1 GACC
82989 GGAGTTGACC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 12 0.40
14 12 0.40
15 6 0.20
ACGTcount: A:0.15, C:0.39, G:0.26, T:0.20
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:82983 original size:21 final size:20
Alignment explanation
Indices: 82928--82989 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 20
82918 TTTACCCGAC
82928 CCGTTGACCCGACCC---GA
1 CCGTTGACCCGACCCGTTGA
82945 CCCGTTGACCCGACCCGTTGA
1 -CCGTTGACCCGACCCGTTGA
82966 CCGTTGACCCGTGA-CCGTTGA
1 CCGTTGACCC--GACCCGTTGA
82987 CCG
1 CCG
82990 GAGTTGACCA
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
18 15 0.38
20 10 0.26
21 12 0.31
22 2 0.05
ACGTcount: A:0.15, C:0.42, G:0.26, T:0.18
Consensus pattern (20 bp):
CCGTTGACCCGACCCGTTGA
Found at i:84306 original size:18 final size:18
Alignment explanation
Indices: 84280--84315 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
84270 TCGAAAGGAC
*
84280 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
84298 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
84316 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:85486 original size:23 final size:23
Alignment explanation
Indices: 85460--85542 Score: 96
Period size: 23 Copynumber: 3.6 Consensus size: 23
85450 TCCGACTTGA
* *
85460 ATTCTGTTATGATCCTGACCTGG
1 ATTCTGATATGATCATGACCTGG
* *
85483 ATTCTGATCTGAT-ATTGACATGG
1 ATTCTGATATGATCA-TGACCTGG
*
85506 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGAT-CATGACCTGG
85530 ATTCTGATATGAT
1 ATTCTGATATGAT
85543 ACTTGACTTG
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
23 31 0.61
24 19 0.37
25 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (23 bp):
ATTCTGATATGATCATGACCTGG
Found at i:85530 original size:24 final size:24
Alignment explanation
Indices: 85475--85549 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
85465 GTTATGATCC
85475 TGACCTGGATTCTGATCTGATA-T
1 TGACCTGGATTCTGATCTGATACT
* *
85498 TGACATGGATTCTGATCTGATACA
1 TGACCTGGATTCTGATCTGATACT
*
85522 TGACCTGGATTCTGATATGATACT
1 TGACCTGGATTCTGATCTGATACT
85546 TGAC
1 TGAC
85550 TTGAATTATG
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 21 0.46
24 25 0.54
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.36
Consensus pattern (24 bp):
TGACCTGGATTCTGATCTGATACT
Found at i:94662 original size:2 final size:2
Alignment explanation
Indices: 94655--94683 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
94645 ATGGTCACCA
94655 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 A
94684 GTAGTTACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:95060 original size:4 final size:4
Alignment explanation
Indices: 95051--95076 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
95041 CTATATAGAA
95051 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
95077 TAAGATGACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:98007 original size:31 final size:31
Alignment explanation
Indices: 97969--98032 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
97959 TTCAGGTGAC
* *
97969 CCTTGGGTAGGCTCTTAGTCCCCAAGGTATT
1 CCTTGGGTAGGCTCTAAGGCCCCAAGGTATT
*
98000 CCTTGGGTAGGCTCTAAGGCTCCAAGGTATT
1 CCTTGGGTAGGCTCTAAGGCCCCAAGGTATT
98031 CC
1 CC
98033 CTTAGGTTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.30
Consensus pattern (31 bp):
CCTTGGGTAGGCTCTAAGGCCCCAAGGTATT
Found at i:100773 original size:293 final size:292
Alignment explanation
Indices: 100215--100801 Score: 1117
Period size: 293 Copynumber: 2.0 Consensus size: 292
100205 TGCTTCAATC
100215 ATACATGAACATGGTGGATAGTTTATCTAGGTAGCTCCGAAGAGGTTACAAAACTTATGGAAAGA
1 ATACATGAACATGGTGGATAGTTTATCTAGGTAGCTCCGAAGAGGTTACAAAACTTATGGAAAGA
100280 GTTGAGGCTACATTCATCAAACACTTTGCAAACTCGAACCGCAGCAAAGGAATGAATATTTTAAG
66 GTTGAGGCTACATTCATCAAACACTTTGCAAACTCGAACCGCAGCAAAGGAATGAATATTTTAAG
100345 ACCAAAAACTAGGAAACAAAGACATACAACACATTTTATACTGGTAGAGCTTTGAATTTCATACA
131 ACCAAAAACTAGGAAACAAAGACATACAACACATTTTATACTGGTAGAGCTTTGAATTTCATACA
100410 CATAAGCAATTCATTTTTGAAAGATATAACTCTGCAATTCTTGAATATTTTATCAGGTTTCTTTG
196 CATAAGCAATTCATTTTTGAAAGATATAACTCTGCAATTCTTGAATATTTTATCAGGTTTCTTTG
100475 CTGGATGCGGATTTGCTCTCGTAATAGCTCTT
261 CTGGATGCGGATTTGCTCTCGTAATAGCTCTT
100507 ATACATGAACATGGTGGATAGTTCTTATCTAGGTAGCTCCGAAGAGGTTACAAAACTTATGGAAA
1 ATACATGAACATGGTGGATAG-T-TTATCTAGGTAGCTCCGAAGAGGTTACAAAACTTATGGAAA
100572 GAGTTGAGGCTACATTCATCAAACACTTTGCAAACTCGAACCGCAGCAAAGG-ATGAATA-TTTA
64 GAGTTGAGGCTACATTCATCAAACACTTTGCAAACTCGAACCGCAGCAAAGGAATGAATATTTTA
100635 AGACCAAAAACTAGGAAACAAAGACATACAACAACATTTTATACTGGTAGAGCTTTGAATTTCAT
129 AGACCAAAAACTAGGAAACAAAGACATACAAC-ACATTTTATACTGGTAGAGCTTTGAATTTCAT
100700 ACACATAAGCAATTCATTTTTTGAAAGATA-AACTCTGCAATTCTTGAATATTTTATCAGGTTTC
193 ACACATAAGCAATTCA-TTTTTGAAAGATATAACTCTGCAATTCTTGAATATTTTATCAGGTTTC
100764 TTTGCTGGATGCGGATTTGCTCTCGTAATAGCTCTT
257 TTTGCTGGATGCGGATTTGCTCTCGTAATAGCTCTT
100800 AT
1 AT
100802 TTTGATCATT
Statistics
Matches: 291, Mismatches: 0, Indels: 7
0.98 0.00 0.02
Matches are distributed among these distances:
292 57 0.20
293 128 0.44
294 106 0.36
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (292 bp):
ATACATGAACATGGTGGATAGTTTATCTAGGTAGCTCCGAAGAGGTTACAAAACTTATGGAAAGA
GTTGAGGCTACATTCATCAAACACTTTGCAAACTCGAACCGCAGCAAAGGAATGAATATTTTAAG
ACCAAAAACTAGGAAACAAAGACATACAACACATTTTATACTGGTAGAGCTTTGAATTTCATACA
CATAAGCAATTCATTTTTGAAAGATATAACTCTGCAATTCTTGAATATTTTATCAGGTTTCTTTG
CTGGATGCGGATTTGCTCTCGTAATAGCTCTT
Found at i:101223 original size:55 final size:55
Alignment explanation
Indices: 101139--101250 Score: 224
Period size: 55 Copynumber: 2.0 Consensus size: 55
101129 TAAGTTTTGG
101139 CCTTGCAGTAATGGCACTTGCTAGTGTGCTCTCTAATCTTGATATGGAGATGGAT
1 CCTTGCAGTAATGGCACTTGCTAGTGTGCTCTCTAATCTTGATATGGAGATGGAT
101194 CCTTGCAGTAATGGCACTTGCTAGTGTGCTCTCTAATCTTGATATGGAGATGGAT
1 CCTTGCAGTAATGGCACTTGCTAGTGTGCTCTCTAATCTTGATATGGAGATGGAT
101249 CC
1 CC
101251 CAAAACTATG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (55 bp):
CCTTGCAGTAATGGCACTTGCTAGTGTGCTCTCTAATCTTGATATGGAGATGGAT
Found at i:108588 original size:50 final size:50
Alignment explanation
Indices: 108508--108607 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
108498 ATTAATCAAC
*
108508 ATACATCACCAAATTGATCTTTATCAAAACATTGTCATGTCAAAATTATT
1 ATACATCACCAAATTGATCTTTATCAAAACATTATCATGTCAAAATTATT
*
108558 ATACATCACCAAATTGATCTTTATCCAAACATTATCATGTCAAAATTATT
1 ATACATCACCAAATTGATCTTTATCAAAACATTATCATGTCAAAATTATT
108608 TATATGCATT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.40, C:0.19, G:0.05, T:0.36
Consensus pattern (50 bp):
ATACATCACCAAATTGATCTTTATCAAAACATTATCATGTCAAAATTATT
Found at i:109261 original size:27 final size:27
Alignment explanation
Indices: 109223--109274 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
109213 GCAACAAGGT
109223 CAAGGATAGTACCACTGTCCACATTTA
1 CAAGGATAGTACCACTGTCCACATTTA
109250 CAAGGATAGTACCACTGTCCACATT
1 CAAGGATAGTACCACTGTCCACATT
109275 GGTCCGACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (27 bp):
CAAGGATAGTACCACTGTCCACATTTA
Found at i:113710 original size:123 final size:123
Alignment explanation
Indices: 113519--113808 Score: 313
Period size: 124 Copynumber: 2.3 Consensus size: 123
113509 TATAACGGCG
* * * * * *
113519 TTTAAATCCCAAACGCCACAAAATGATAACATTAGCGGCGA--TTTCTATAATTTCCGCTATAGC
1 TTTAAAT-ACAAAAGCCACAAAATGA-AACATTAGCGGC-ATTTTTCTAGAAATGCCACTATAGC
* *
113582 CTCGTCTTTTGTGACAATTTTT-AAACAAACA-CTGCAAAAGGTCAGTGTATTAG-TGGCATT
63 CTCGTCTTTTGTGACAATTTTTAAAACAAACATC-GCAAAAGGTCAATGCATT-GTTGGCATT
*
113642 TTTAAATACAAAAGCCACAAAATAGAAACATTAGCGGTATTTTTCTAGAAATGCCACTATAGCCT
1 TTTAAATACAAAAGCCACAAAAT-GAAACATTAGCGGCATTTTTCTAGAAATGCCACTATAGCCT
* ** * * *
113707 CGTCTTTTGTGGCTTTTTTTAAAACAAATATCGCAATAGGTCAATGCATTGTTGGCGTT
65 CGTCTTTTGTGACAATTTTTAAAACAAACATCGCAAAAGGTCAATGCATTGTTGGCATT
* *
113766 TTTAAATACAAACA-CCATAAAATGGTAACATTAGCGGCATTTT
1 TTTAAATACAAA-AGCCACAAAAT-GAAACATTAGCGGCATTTT
113809 CCCAGTAACA
Statistics
Matches: 141, Mismatches: 19, Indels: 13
0.82 0.11 0.08
Matches are distributed among these distances:
121 1 0.01
122 25 0.18
123 47 0.33
124 66 0.47
125 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.32
Consensus pattern (123 bp):
TTTAAATACAAAAGCCACAAAATGAAACATTAGCGGCATTTTTCTAGAAATGCCACTATAGCCTC
GTCTTTTGTGACAATTTTTAAAACAAACATCGCAAAAGGTCAATGCATTGTTGGCATT
Found at i:113796 original size:124 final size:123
Alignment explanation
Indices: 113575--113896 Score: 335
Period size: 124 Copynumber: 2.6 Consensus size: 123
113565 ATAATTTCCG
* * * * * *
113575 CTATAGCCTCGTCTTTTGTGACAATTTTTAAACAAACA-CTGCAAAAGGTCAGTGTATTAGTGGC
1 CTATAGCCTCGTCTTTTGTGGCATTTTTTAAACAAATATC-GCAATAGGTCAATGCATTAGTGGC
* * * **
113639 ATTTTTAAATACAAAAGCCACAAAATAGAAACATTAGCGGTATTTTTCTAGAAATGCCA
65 ATTTTTAAATACAAAAGCCACAAAATAGAAACATTAGCGGCATTTTCCCAGAAACACCA
*
113698 CTATAGCCTCGTCTTTTGTGGCTTTTTTTAAAACAAATATCGCAATAGGTCAATGCATT-GTTGG
1 CTATAGCCTCGTCTTTTGTGGCATTTTTT-AAACAAATATCGCAATAGGTCAATGCATTAG-TGG
* * * * * *
113762 CGTTTTTAAATACAAACA-CCATAAAATGGTAACATTAGCGGCATTTTCCCAGTAACACCG
64 CATTTTTAAATACAAA-AGCCACAAAATAGAAACATTAGCGGCATTTTCCCAGAAACACCA
* ** * * * * * * *
113822 TTATATACTCATCTTTTGTGGCGTTTTTTAAACAAATGTCGAAATAGGTCAGTACATTAGTGGTA
1 CTATAGCCTCGTCTTTTGTGGCATTTTTTAAACAAATATCGCAATAGGTCAATGCATTAGTGGCA
113887 TTTTTAAATA
66 TTTTTAAATA
113897 TAAACATCGC
Statistics
Matches: 165, Mismatches: 29, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
123 65 0.39
124 98 0.59
125 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (123 bp):
CTATAGCCTCGTCTTTTGTGGCATTTTTTAAACAAATATCGCAATAGGTCAATGCATTAGTGGCA
TTTTTAAATACAAAAGCCACAAAATAGAAACATTAGCGGCATTTTCCCAGAAACACCA
Found at i:116300 original size:17 final size:18
Alignment explanation
Indices: 116269--116302 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
116259 AATAAAAATT
*
116269 ATAAAAATCTATTGAAAA
1 ATAAAAATATATTGAAAA
116287 ATAAAAATAT-TTGAAA
1 ATAAAAATATATTGAAA
116303 TTTAAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (18 bp):
ATAAAAATATATTGAAAA
Found at i:121158 original size:22 final size:22
Alignment explanation
Indices: 121119--121166 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
121109 TTTTAACTAA
*
121119 TTTATAATTATATGTTTAGTAC-
1 TTTATAATTATATATTTA-TACG
121141 TTTATAATT-TATAATTTATACG
1 TTTATAATTATAT-ATTTATACG
121163 TTTA
1 TTTA
121167 GCATTTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.56
Consensus pattern (22 bp):
TTTATAATTATATATTTATACG
Found at i:121166 original size:30 final size:29
Alignment explanation
Indices: 121116--121177 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 29
121106 GATTTTTAAC
* *
121116 TAATTTATAATTATATGTTTAGTACTTTA
1 TAATTTATAATTATACGTTTAGCACTTTA
*
121145 TAATTTATAATTTATACGTTTAGCATTTTA
1 TAATTTATAA-TTATACGTTTAGCACTTTA
121175 TAA
1 TAA
121178 ATTAATTTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 10 0.34
30 19 0.66
ACGTcount: A:0.35, C:0.05, G:0.06, T:0.53
Consensus pattern (29 bp):
TAATTTATAATTATACGTTTAGCACTTTA
Found at i:121253 original size:2 final size:2
Alignment explanation
Indices: 121246--121290 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
121236 CATCATCCTT
121246 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
121288 TA T
1 TA T
121291 TAAATAATCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:122211 original size:499 final size:500
Alignment explanation
Indices: 121272--122226 Score: 1840
Period size: 499 Copynumber: 1.9 Consensus size: 500
121262 TATATATATA
121272 TATATATATATATATATATTAAATAATCTGGATGATTACAATGTAACATCTGTTCATAATTTTTT
1 TATATATATATATATATATTAAATAATCTGGATGATTACAATGTAACATCTGTTCATAATTTTTT
*
121337 AACTCTTGATAATAAATATACTATTAAGACCACTCTATAGATTATCTTATCTATATATTTATATT
66 AACTCTTGATAATAAATATACTATTAAGACCACTCAATAGATTATCTTATCTATATATTTATATT
121402 ATGCAGATGATTGAGTTTGTATTATAAGGTTTAATCAGAAAAAAAATAAAATCTTTTGAATGAAA
131 ATGCAGATGATTGAGTTTGTATTATAAGGTTTAATCAGAAAAAAAATAAAATCTTTTGAATGAAA
121467 AATGATATTATAAACTTATACTTTTTATATTTTATGAAATTTTTAAATAATTAAATTAAAAATCA
196 AATGATATTATAAACTTATACTTTTTATATTTTATGAAATTTTTAAATAATTAAATTAAAAATCA
*
121532 AAATTAGTAAATTTTTTAGGATCAAACTCGAAATTAATAAAAGATTATATAAGTTTTTATCGATT
261 AAATTAGTAAATTTTTTAGGATCAAACTCGAAATTAATAAAAGATTATATAAATTTTTATCGATT
**
121597 GATTTATAATTATTTGTTAAATAAAATTTTATAATAATTTACTAATATTAAATATTTTCTTTTAT
326 GATCGATAATTATTTGTTAAATAAAATTTTATAATAATTTACTAATATTAAATATTTTCTTTTAT
121662 CTATATTATAAATGTGACTCGGTTTAATTAGTTTTAGTGTGATAGAAGTAAAGCGATAATTTTTT
391 CTATATTATAAATGTGACTCGGTTTAATTAGTTTTAGTGTGATAGAAGTAAAGCGATAATTTTTT
121727 TAACGGTACTCATCTGTACTCGTTGAGCGTGACATCATCATCCTT
456 TAACGGTACTCATCTGTACTCGTTGAGCGTGACATCATCATCCTT
121772 TATATATATATATATATATTAAATAATCTGGATGATTACAATGTAACATCTGTTCATAATTTTTT
1 TATATATATATATATATATTAAATAATCTGGATGATTACAATGTAACATCTGTTCATAATTTTTT
121837 AACTCTTGATAATAAATATACTATTAAGACCACTCAATAGATTATCTTATCTATATATTTATATT
66 AACTCTTGATAATAAATATACTATTAAGACCACTCAATAGATTATCTTATCTATATATTTATATT
121902 ATGCAGATGATTGAGTTTGTATTATAAGGTTTAATCAG-AAAAAAATAAAATCTTTTGAATGAAA
131 ATGCAGATGATTGAGTTTGTATTATAAGGTTTAATCAGAAAAAAAATAAAATCTTTTGAATGAAA
*
121966 AATGATATTATAAACTTATACTTTTTATATTTTATGAAATTTTTAAATAATTTAATTAAAAATCA
196 AATGATATTATAAACTTATACTTTTTATATTTTATGAAATTTTTAAATAATTAAATTAAAAATCA
122031 AAATTAGTAAATTTTTTAGGATCAAACTCGAAATTAATAAAAGATTATATAAATTTTTATCGATT
261 AAATTAGTAAATTTTTTAGGATCAAACTCGAAATTAATAAAAGATTATATAAATTTTTATCGATT
*
122096 GATCGATAATTATTTGTTAAATAAAATTTTATGATAATTTACTAATATTAAATATTTTCTTTTAT
326 GATCGATAATTATTTGTTAAATAAAATTTTATAATAATTTACTAATATTAAATATTTTCTTTTAT
*
122161 CTATATTATAAATGTGACTCGGTTTAATTAGTTTTAGTGTGATAGAAGTAAAGCGATAGTTTTTT
391 CTATATTATAAATGTGACTCGGTTTAATTAGTTTTAGTGTGATAGAAGTAAAGCGATAATTTTTT
122226 T
456 T
122227 CACATGCAAA
Statistics
Matches: 448, Mismatches: 7, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
499 281 0.63
500 167 0.37
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (500 bp):
TATATATATATATATATATTAAATAATCTGGATGATTACAATGTAACATCTGTTCATAATTTTTT
AACTCTTGATAATAAATATACTATTAAGACCACTCAATAGATTATCTTATCTATATATTTATATT
ATGCAGATGATTGAGTTTGTATTATAAGGTTTAATCAGAAAAAAAATAAAATCTTTTGAATGAAA
AATGATATTATAAACTTATACTTTTTATATTTTATGAAATTTTTAAATAATTAAATTAAAAATCA
AAATTAGTAAATTTTTTAGGATCAAACTCGAAATTAATAAAAGATTATATAAATTTTTATCGATT
GATCGATAATTATTTGTTAAATAAAATTTTATAATAATTTACTAATATTAAATATTTTCTTTTAT
CTATATTATAAATGTGACTCGGTTTAATTAGTTTTAGTGTGATAGAAGTAAAGCGATAATTTTTT
TAACGGTACTCATCTGTACTCGTTGAGCGTGACATCATCATCCTT
Found at i:122421 original size:40 final size:40
Alignment explanation
Indices: 122377--122469 Score: 98
Period size: 40 Copynumber: 2.3 Consensus size: 40
122367 AACTATAATT
* *
122377 TCGTAACAC-AGTTTCCAAATTTGCAACGCGAATATGTAAA
1 TCGTAACACGAATATCCAAA-TTGCAACGCGAATATGTAAA
* ** *
122417 TCGTAACGCGAATATGTAAATTGCAACGCGAATTTGTAAA
1 TCGTAACACGAATATCCAAATTGCAACGCGAATATGTAAA
* *
122457 TCGCAACTCGAAT
1 TCGTAACACGAAT
122470 TTGTAAATCG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 38 0.86
41 6 0.14
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (40 bp):
TCGTAACACGAATATCCAAATTGCAACGCGAATATGTAAA
Found at i:122426 original size:20 final size:20
Alignment explanation
Indices: 122399--122483 Score: 125
Period size: 20 Copynumber: 4.2 Consensus size: 20
122389 TTCCAAATTT
122399 GCAACGCGAATATGTAAATC
1 GCAACGCGAATATGTAAATC
* *
122419 GTAACGCGAATATGTAAATT
1 GCAACGCGAATATGTAAATC
*
122439 GCAACGCGAATTTGTAAATC
1 GCAACGCGAATATGTAAATC
* *
122459 GCAACTCGAATTTGTAAATC
1 GCAACGCGAATATGTAAATC
122479 GCAAC
1 GCAAC
122484 ACATAAGTCA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (20 bp):
GCAACGCGAATATGTAAATC
Found at i:122500 original size:20 final size:20
Alignment explanation
Indices: 122477--122519 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
122467 AATTTGTAAA
122477 TCGCAACACATAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
122497 TCGCAACACATAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
122517 TCG
1 TCG
122520 TAAAGCTTTC
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:0.42, C:0.26, G:0.12, T:0.21
Consensus pattern (20 bp):
TCGCAACACATAAGTCAAAT
Found at i:123048 original size:20 final size:20
Alignment explanation
Indices: 123025--123067 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
123015 AAACTTAAAT
123025 TCGTAACACGAAAATGAAAA
1 TCGTAACACGAAAATGAAAA
*
123045 TCGTAACGCGAAAATGAAAA
1 TCGTAACACGAAAATGAAAA
123065 TCG
1 TCG
123068 CAACGCGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.16, G:0.19, T:0.16
Consensus pattern (20 bp):
TCGTAACACGAAAATGAAAA
Found at i:123072 original size:20 final size:20
Alignment explanation
Indices: 123033--123075 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
123023 ATTCGTAACA
*
123033 CGAAAATGAAAATCGTAACG
1 CGAAAATGAAAATCGCAACG
123053 CGAAAATGAAAATCGCAACG
1 CGAAAATGAAAATCGCAACG
123073 CGA
1 CGA
123076 TTTTAGTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.19, G:0.21, T:0.12
Consensus pattern (20 bp):
CGAAAATGAAAATCGCAACG
Found at i:123131 original size:20 final size:20
Alignment explanation
Indices: 123072--123134 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
123062 AAATCGCAAC
*
123072 GCGATTTT-AGTTTCGTGTT
1 GCGATTTTCATTTTCGTGTT
**
123091 GCGATTTTCATTTTCACGTT
1 GCGATTTTCATTTTCGTGTT
*
123111 GCGATTTTCATTTTTGTGTT
1 GCGATTTTCATTTTCGTGTT
123131 GCGA
1 GCGA
123135 ATTTAAGTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 8 0.22
20 29 0.78
ACGTcount: A:0.13, C:0.14, G:0.22, T:0.51
Consensus pattern (20 bp):
GCGATTTTCATTTTCGTGTT
Found at i:124905 original size:21 final size:22
Alignment explanation
Indices: 124881--124936 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
124871 AGGTACAGTC
124881 TTTACGCGGTGAGGAA-GATGT
1 TTTACGCGGTGAGGAATGATGT
* * *
124902 TTTACGCGATGA-CAATGGTGT
1 TTTACGCGGTGAGGAATGATGT
*
124923 TTTACGTGGTGAGG
1 TTTACGCGGTGAGG
124937 TATCTACTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.21, C:0.11, G:0.36, T:0.32
Consensus pattern (22 bp):
TTTACGCGGTGAGGAATGATGT
Found at i:125276 original size:21 final size:21
Alignment explanation
Indices: 125249--125343 Score: 122
Period size: 21 Copynumber: 4.6 Consensus size: 21
125239 ATTCACCTGT
*
125249 CATCGTTCAAGAGACCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
* * *
125270 TATCGTTCAAGAGGCTCCTCT
1 CATCGTTCAAGAGGCCCCTCC
125291 CATCGTTCAAGAGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
*
125312 CACCG-T-AAGAGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
*
125331 CACCGTTCAAGAG
1 CATCGTTCAAGAG
125344 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
19 18 0.28
20 2 0.03
21 44 0.69
ACGTcount: A:0.22, C:0.39, G:0.19, T:0.20
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTCC
Found at i:125323 original size:19 final size:19
Alignment explanation
Indices: 125299--125336 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
125289 CTCATCGTTC
125299 AAGAGGCCCCTCCCACCGT
1 AAGAGGCCCCTCCCACCGT
125318 AAGAGGCCCCTCCCACCGT
1 AAGAGGCCCCTCCCACCGT
125337 TCAAGAGCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.47, G:0.21, T:0.11
Consensus pattern (19 bp):
AAGAGGCCCCTCCCACCGT
Found at i:125338 original size:40 final size:42
Alignment explanation
Indices: 125252--125343 Score: 116
Period size: 40 Copynumber: 2.2 Consensus size: 42
125242 CACCTGTCAT
* * * * *
125252 CGTTCAAGAGACCCCTCCTATCGTTCAAGAGGCTCCTCTCAT
1 CGTTCAAGAGACCCCTCCCACCGTTCAAGAGGCCCCTCCCAC
*
125294 CGTTCAAGAGGCCCCTCCCACCG-T-AAGAGGCCCCTCCCAC
1 CGTTCAAGAGACCCCTCCCACCGTTCAAGAGGCCCCTCCCAC
125334 CGTTCAAGAG
1 CGTTCAAGAG
125344 CCCGATTCAC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
40 23 0.52
41 1 0.02
42 20 0.45
ACGTcount: A:0.22, C:0.39, G:0.20, T:0.20
Consensus pattern (42 bp):
CGTTCAAGAGACCCCTCCCACCGTTCAAGAGGCCCCTCCCAC
Found at i:126241 original size:21 final size:21
Alignment explanation
Indices: 126215--126257 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
126205 CAAGAAGCCA
126215 AATAAGTTAAAAGTTACAATG
1 AATAAGTTAAAAGTTACAATG
126236 AATAAGTTAAAAGTTACAATG
1 AATAAGTTAAAAGTTACAATG
126257 A
1 A
126258 TGAGAGACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.53, C:0.05, G:0.14, T:0.28
Consensus pattern (21 bp):
AATAAGTTAAAAGTTACAATG
Found at i:126876 original size:20 final size:20
Alignment explanation
Indices: 126851--126889 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
126841 GCACACTTTC
126851 GCAACGCGAAAATCAAATTT
1 GCAACGCGAAAATCAAATTT
*
126871 GCAACGCGAAAGTCAAATT
1 GCAACGCGAAAATCAAATT
126890 CGCGTTGCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.18
Consensus pattern (20 bp):
GCAACGCGAAAATCAAATTT
Found at i:126931 original size:20 final size:20
Alignment explanation
Indices: 126903--126946 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
126893 GTTGCGGTTA
*
126903 TTGCGAAAGTCAAATTCGAG
1 TTGCAAAAGTCAAATTCGAG
*
126923 TTGCAAAAGTCAAATTCGCG
1 TTGCAAAAGTCAAATTCGAG
126943 TTGC
1 TTGC
126947 GATTGTTACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (20 bp):
TTGCAAAAGTCAAATTCGAG
Found at i:126975 original size:49 final size:49
Alignment explanation
Indices: 126879--126975 Score: 142
Period size: 49 Copynumber: 2.0 Consensus size: 49
126869 TTGCAACGCG
* * *
126879 AAAGTCAAATTCGCGTTGCGGTTATTGCGAAAGTCAAATTCGAGTTGCA
1 AAAGTCAAATTCGCGTTGCGATTATTACGAAAGTCAAATTCCAGTTGCA
*
126928 AAAGTCAAATTCGCGTTGCGATTGTTACGAAAGTCAAA-TCCACGTTGC
1 AAAGTCAAATTCGCGTTGCGATTATTACGAAAGTCAAATTCCA-GTTGC
126976 GATTGTTGCA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
48 3 0.07
49 40 0.93
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (49 bp):
AAAGTCAAATTCGCGTTGCGATTATTACGAAAGTCAAATTCCAGTTGCA
Found at i:129511 original size:24 final size:24
Alignment explanation
Indices: 129477--129530 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
129467 CTGAAACATC
129477 ATCAAAATCCGAGTATTAACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
* * *
129501 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
129525 ATCAAA
1 ATCAAA
129531 TTTCGAATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:130513 original size:40 final size:40
Alignment explanation
Indices: 130450--130527 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
130440 TGCGAAATTT
* *
130450 AAATTCGTGTTGCAAATTCGAAAAT-TCAGTTGCGAAAACA
1 AAATTCGGGTTGCAAATTAGAAAATCT-AGTTGCGAAAACA
* * *
130490 AAATTCGGGTTGCGATTTAGAAAATCTTGTTGCGAAAA
1 AAATTCGGGTTGCAAATTAGAAAATCTAGTTGCGAAAA
130528 GGAAATTTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 31 0.97
41 1 0.03
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (40 bp):
AAATTCGGGTTGCAAATTAGAAAATCTAGTTGCGAAAACA
Found at i:130573 original size:20 final size:20
Alignment explanation
Indices: 130545--130604 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
130535 TGTTTTACGA
130545 AAAAGAAATTCGCGTTGCGAG
1 AAAA-AAATTCGCGTTGCGAG
130566 AAAAAAATTCGCGTTGCGAG
1 AAAAAAATTCGCGTTGCGAG
*
130586 AAAAAAATTCGCATTGCGA
1 AAAAAAATTCGCGTTGCGA
130605 TTGCAAAAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 34 0.89
21 4 0.11
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (20 bp):
AAAAAAATTCGCGTTGCGAG
Found at i:131409 original size:15 final size:15
Alignment explanation
Indices: 131391--131426 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
131381 GTATCATTAA
*
131391 ATTAATTTATAAAAT
1 ATTAAATTATAAAAT
*
131406 ATTAAATTATAAAGT
1 ATTAAATTATAAAAT
131421 ATTAAA
1 ATTAAA
131427 CGTATAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
ATTAAATTATAAAAT
Found at i:131733 original size:9 final size:9
Alignment explanation
Indices: 131719--131743 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
131709 GGTCCTAACT
131719 TTTAATTAA
1 TTTAATTAA
131728 TTTAATTAA
1 TTTAATTAA
131737 TTTAATT
1 TTTAATT
131744 TAATCCTCAA
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TTTAATTAA
Found at i:133173 original size:22 final size:22
Alignment explanation
Indices: 133145--133196 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
133135 AAATATATGT
* *
133145 TATTTTAATTAAATTATATTTA
1 TATTTTAACTAAATTATAATTA
*
133167 TATTTTAACTAATTTATAATTA
1 TATTTTAACTAAATTATAATTA
133189 TATGTTTA
1 TAT-TTTA
133197 GTACTTTGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (22 bp):
TATTTTAACTAAATTATAATTA
Done.