Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007773.1 Hibiscus syriacus cultivar Beakdansim tig00110054_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: 557494
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:6671 original size:19 final size:21
Alignment explanation
Indices: 6634--6676 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
6624 TAACTTTTTC
6634 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
6654 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
6674 TTT
1 TTT
6677 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:6682 original size:19 final size:20
Alignment explanation
Indices: 6633--6682 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
6623 TTAACTTTTT
*
6633 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
6653 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
6672 CTTTTACCTTT
1 CTTTTACCTTT
6683 TCTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:10521 original size:16 final size:16
Alignment explanation
Indices: 10500--10532 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
10490 CAAGTGAGGA
10500 TTATTT-TCTTCTTATT
1 TTATTTATCTT-TTATT
10516 TTATTTATCTTTTATT
1 TTATTTATCTTTTATT
10532 T
1 T
10533 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTATCTTTTATT
Found at i:15958 original size:25 final size:22
Alignment explanation
Indices: 15922--15973 Score: 52
Period size: 22 Copynumber: 2.2 Consensus size: 22
15912 ATATATATAT
15922 ATATAAATAAATGTACATAAGAAAA
1 ATATAAATAAA--TACATAA-AAAA
*
15947 ATAT-AATAAAATACATGAAAAA
1 ATATAAAT-AAATACATAAAAAA
15969 ATATA
1 ATATA
15974 GCTAAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
22 8 0.33
23 6 0.25
24 3 0.12
25 7 0.29
ACGTcount: A:0.65, C:0.04, G:0.06, T:0.25
Consensus pattern (22 bp):
ATATAAATAAATACATAAAAAA
Found at i:15991 original size:27 final size:27
Alignment explanation
Indices: 15943--16026 Score: 80
Period size: 27 Copynumber: 3.0 Consensus size: 27
15933 TGTACATAAG
15943 AAAAATATAATA-AAATACATGAAAAAAT
1 AAAAATA-AATATAAATA-ATGAAAAAAT
* ** *
15971 ATAGCTAAATATAAATAATGAGAAAAT
1 AAAAATAAATATAAATAATGAAAAAAT
15998 AAAAATAAATATAATATAAATGAATAAAA
1 AAAAATAAATATAA-AT-AATGAA-AAAA
16027 GACAAAAATA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
27 24 0.55
28 11 0.25
29 5 0.11
30 4 0.09
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.24
Consensus pattern (27 bp):
AAAAATAAATATAAATAATGAAAAAAT
Found at i:16077 original size:20 final size:21
Alignment explanation
Indices: 16032--16075 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
16022 TAAAAGACAA
16032 AAATAGAGAAATATAGTAAAT
1 AAATAGAGAAATATAGTAAAT
*
16053 AAATAGA-AAATATAATTAAAT
1 AAATAGAGAAATAT-AGTAAAT
16074 AA
1 AA
16076 TAATAATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.25
Consensus pattern (21 bp):
AAATAGAGAAATATAGTAAAT
Found at i:16115 original size:24 final size:24
Alignment explanation
Indices: 16060--16131 Score: 69
Period size: 24 Copynumber: 2.9 Consensus size: 24
16050 AATAAATAGA
16060 AAATATA-AT-TAAATAATAATAAT
1 AAATATATATATAAA-AATAATAAT
16083 GATAGATATAGTATA-AAAAATAATAAT
1 -A-A-ATATA-TATATAAAAATAATAAT
*
16110 AAATATATATATAATAATAATA
1 AAATATATATATAAAAATAATA
16132 CAATGAAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
23 4 0.10
24 15 0.37
25 2 0.05
26 6 0.15
27 9 0.22
28 5 0.12
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATATATATATAAAAATAATAAT
Found at i:16199 original size:39 final size:35
Alignment explanation
Indices: 16154--16234 Score: 94
Period size: 39 Copynumber: 2.2 Consensus size: 35
16144 GCAAATATAC
*
16154 AAAATAAGAT-GAAATAATATAATAATAGTAATTATAATA
1 AAAATAAGATAGAAATAA-ATAA-AATA-TAA--AAAATA
16193 AAAATAA-ATAGAAATAAATAAAATATAAAAAATA
1 AAAATAAGATAGAAATAAATAAAATATAAAAAATA
16227 AAAATAAG
1 AAAATAAG
16235 CGTAACAGGT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
34 12 0.31
36 3 0.08
37 4 0.10
38 6 0.15
39 14 0.36
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (35 bp):
AAAATAAGATAGAAATAAATAAAATATAAAAAATA
Found at i:16229 original size:14 final size:14
Alignment explanation
Indices: 16192--16233 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
16182 TAATTATAAT
*
16192 AAAAAT-AAATAGA
1 AAAAATAAAATATA
16205 AATAAATAAAATATA
1 AA-AAATAAAATATA
16220 AAAAATAAAA-ATA
1 AAAAATAAAATATA
16233 A
1 A
16234 GCGTAACAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 6 0.23
14 12 0.46
15 8 0.31
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (14 bp):
AAAAATAAAATATA
Found at i:17265 original size:2 final size:2
Alignment explanation
Indices: 17246--17312 Score: 113
Period size: 2 Copynumber: 35.0 Consensus size: 2
17236 AATTATAATT
17246 TA TA -A TA T- TA TA TA -A 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
17285 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
17313 ATTTGGACGG
Statistics
Matches: 62, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
1 3 0.05
2 59 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:19789 original size:31 final size:31
Alignment explanation
Indices: 19748--19843 Score: 97
Period size: 31 Copynumber: 3.1 Consensus size: 31
19738 GGAATAATCT
* * *
19748 CTAACGTTATCAATCCGTTTGATTTTAGTCC
1 CTAACATTATCAATCCATTCGATTTTAGTCC
*
19779 CTAACATTATCGATCCATTCGATTTTAGTCC
1 CTAACATTATCAATCCATTCGATTTTAGTCC
* *
19810 CTCAATCA-TA-GACTCTCATTCGATTTTAGTCC
1 CT-AA-CATTATCAATC-CATTCGATTTTAGTCC
19842 CT
1 CT
19844 CAGCCATGTT
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
31 31 0.56
32 22 0.40
33 2 0.04
ACGTcount: A:0.24, C:0.26, G:0.10, T:0.40
Consensus pattern (31 bp):
CTAACATTATCAATCCATTCGATTTTAGTCC
Found at i:19835 original size:32 final size:31
Alignment explanation
Indices: 19768--19845 Score: 104
Period size: 32 Copynumber: 2.5 Consensus size: 31
19758 CAATCCGTTT
* * *
19768 GATTTTAGTCCCTAACATTATCGATCCATTC
1 GATTTTAGTCCCTCACATCATAGATCCATTC
19799 GATTTTAGTCCCTCA-ATCATAGACTCTCATTC
1 GATTTTAGTCCCTCACATCATAGA-TC-CATTC
19831 GATTTTAGTCCCTCA
1 GATTTTAGTCCCTCA
19846 GCCATGTTAG
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
30 6 0.14
31 16 0.38
32 20 0.48
ACGTcount: A:0.24, C:0.27, G:0.10, T:0.38
Consensus pattern (31 bp):
GATTTTAGTCCCTCACATCATAGATCCATTC
Found at i:22803 original size:11 final size:11
Alignment explanation
Indices: 22787--22822 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
22777 ATTGCCAGAG
*
22787 TTCTCTCTGGC
1 TTCTCTCTAGC
22798 TTCTCTCTAGC
1 TTCTCTCTAGC
*
22809 TTCCCTCTAGC
1 TTCTCTCTAGC
22820 TTC
1 TTC
22823 CCTCATCGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.06, C:0.39, G:0.11, T:0.44
Consensus pattern (11 bp):
TTCTCTCTAGC
Found at i:22823 original size:11 final size:11
Alignment explanation
Indices: 22791--22826 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
22781 CCAGAGTTCT
* *
22791 CTCTGGCTTCT
1 CTCTAGCTTCC
22802 CTCTAGCTTCC
1 CTCTAGCTTCC
22813 CTCTAGCTTCC
1 CTCTAGCTTCC
22824 CTC
1 CTC
22827 ATCGGAGGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.06, C:0.44, G:0.11, T:0.39
Consensus pattern (11 bp):
CTCTAGCTTCC
Found at i:23560 original size:3 final size:3
Alignment explanation
Indices: 23552--23593 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
23542 GGCATGTTTG
* * *
23552 TAA TAA TAA TAA TAT TAA TAA TAA TAT TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
23594 AAAAATGAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:23974 original size:120 final size:118
Alignment explanation
Indices: 23743--24468 Score: 382
Period size: 113 Copynumber: 6.3 Consensus size: 118
23733 ATTCTTCTCT
* * * * *
23743 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGGGGATGATATTGACCTATTTCCTTAT
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGGAGATGATACTAACCTATCTCATTAT
* *
23808 GTGATAGAGTCATTCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC
66 GTGATAGAATCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC
* * * *
23861 TTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTCTGGAAAAGCTGATGCTAATCTATCTCAT
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGG---AGATGATACTAACCTATCTCAT
* * *
23925 TCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTC
63 TATGTGATAGAATCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC
* * *
23981 TTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CTGGCA-ATG-T--TGATCC-A--TCA--
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGG-AGATGATACT-AACCTATCTCATT
* ** **
24036 A-ATGAT-GAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC
64 ATGTGATAGAA-TCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAA---CTTCTT-C
* * *
24094 TTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCA-ATG-T--TGATCC-A--TC
1 TTCTTCAGAT---GAGTTCTTCTCATTATGAACTTTCCGCTGG-AGATGATACT-AACCTATCTC
* ** **
24151 A--A-ATGATA-AATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC
61 ATTATGTGATAGAA-TCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC
* *
24206 TTCCTTGTTCAGATGAGTTCTTCTCATTATGAACTTT-CTCTGGA-A--A-AGCTGATCC-A--T
1 TT-C---TTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGGAGATGATA-CT-AACCTATCT
* * * * ** *
24263 CA--A-GTGATGGATTTGA-GTAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTC
60 CATTATGTGATAGA-ATCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC
*
24319 TTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTT-C-CTGGCA-ATG-T--TGATCC-A--T
1 TTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TTCCGCTGG-AGATGATACT-AACCTATCT
* ** **
24375 CA--A-ATGAT-GAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC
60 CATTATGTGATAGAA-TCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAA---CTTCTT-C
*
24435 TTCTTCAGATGAGTTCTTCTCATTATGAATTTTC
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTC
24469 TCTGGAAAAG
Statistics
Matches: 526, Mismatches: 42, Indels: 85
0.81 0.06 0.13
Matches are distributed among these distances:
108 3 0.01
109 42 0.08
111 4 0.01
112 89 0.17
113 123 0.23
114 5 0.01
115 7 0.01
116 110 0.21
117 7 0.01
118 34 0.06
120 101 0.19
121 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (118 bp):
TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGGAGATGATACTAACCTATCTCATTAT
GTGATAGAATCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC
Found at i:24286 original size:113 final size:113
Alignment explanation
Indices: 23942--24552 Score: 846
Period size: 113 Copynumber: 5.4 Consensus size: 113
23932 TAGAATTATG
** *
23942 CAAAAGGTTGAACAAGCTCTTCTCATTGTGAA---CTTCTT-CTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
24003 TTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAA
66 TTATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAA
24051 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTC
* *
24116 TCATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATAAATTCAAA
63 TCATTATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAA
*
24167 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTGTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * * ** *
24232 TTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
66 TTATGAACTCTTC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAA
*
24280 TAAAAGGTTGAACAAATTCTTCTCATTATGAA--T-TTCTT-CTTCTTCAGATGACGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTC
24341 TCATTATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAA
63 TCATTATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAA
24392 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * * * * ** *
24457 TTATGAA-TTTTCTCTGGAAAAGCTAATCCATCAAGTGATGGATTTGAG
66 TTATGAACTCTTC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAA
24505 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTT
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTT
24553 ATTATGAACT
Statistics
Matches: 449, Mismatches: 36, Indels: 30
0.87 0.07 0.06
Matches are distributed among these distances:
109 39 0.09
110 5 0.01
111 1 0.00
112 91 0.20
113 185 0.41
114 1 0.00
115 5 0.01
116 122 0.27
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (113 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAA
Found at i:24345 original size:225 final size:224
Alignment explanation
Indices: 23942--24546 Score: 957
Period size: 225 Copynumber: 2.7 Consensus size: 224
23932 TAGAATTATG
** *
23942 CAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTT-C--TTCAGATGAGTTCTTCTCAT
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTTTCAGATGAGTTCTTCTCAT
* * * * * * ** *
24004 TATGAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAAT
66 TATGAACT-TTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
24068 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACC
130 TCTTCTCATTATGAA--T-TTCTT-CTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACC
24133 TGGCAATGTTGATCCATCAAATGATAAATTCAAA
191 TGGCAATGTTGATCCATCAAATGATAAATTCAAA
24167 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTGTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTT-TTCAGATGAGTTCTTCTCA
*
24232 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGTAAAAGGTTGAACAAAT
65 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
*
24297 TCTTCTCATTATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTGGC
130 TCTTCTCATTATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGC
*
24362 AATGTTGATCCATCAAATGATGAATTCAAA
195 AATGTTGATCCATCAAATGATAAATTCAAA
24392 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTT-TTCAGATGAGTTCTTCTCA
* *
24457 TTATGAATTTTCTCTGGAAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
65 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
*
24522 TCTTCTCATTATGAACTTCTTCTTC
130 TCTTCTCATTATGAATTTCTTCTTC
24547 CTTCTTATTA
Statistics
Matches: 355, Mismatches: 20, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
225 260 0.73
226 6 0.02
227 1 0.00
228 2 0.01
229 86 0.24
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (224 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATT
CTTCTCATTATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCA
ATGTTGATCCATCAAATGATAAATTCAAA
Found at i:25472 original size:114 final size:114
Alignment explanation
Indices: 25309--25528 Score: 334
Period size: 114 Copynumber: 1.9 Consensus size: 114
25299 GATCATGCAG
* * * * * * *
25309 TTCATCTTTTAATTCCAATGATTGGTTCTTTGGTTCTTACCGAACCAGATCAGATGACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTCTTGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
25374 AAACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
66 AAACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
*
25423 TTCATCTTTCAAATCCAATGATTGATT-TTGGGGTTCATACCAAATCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGATTCTT-GGGTTCATACCAAACCAGATCAGATAACTCAAAG
* *
25487 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTTTACTA
65 AAAACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTA
25529 CGAGAACGTA
Statistics
Matches: 95, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
113 2 0.02
114 93 0.98
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGATTCTTGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
AAACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
Found at i:25854 original size:19 final size:17
Alignment explanation
Indices: 25826--25874 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
25816 AAAATAAAAG
*
25826 AATAAGTTGAATTTTCGAA
1 AATAAATTGAATTTTC--A
*
25845 AATAAATTGAA-TCTCA
1 AATAAATTGAATTTTCA
25861 AATAAATTGAATTT
1 AATAAATTGAATTT
25875 AGAGAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 12 0.46
17 1 0.04
18 3 0.12
19 10 0.38
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (17 bp):
AATAAATTGAATTTTCA
Found at i:26230 original size:1 final size:1
Alignment explanation
Indices: 26224--26271 Score: 51
Period size: 1 Copynumber: 48.0 Consensus size: 1
26214 CATCTTGACC
* * * * *
26224 TTTTTTTTTTCTTTTTTTCTTTTTTCTTTTTTTTTCTTTTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
26272 CTTCTTCAAG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (1 bp):
T
Found at i:26240 original size:8 final size:8
Alignment explanation
Indices: 26227--26277 Score: 75
Period size: 8 Copynumber: 6.2 Consensus size: 8
26217 CTTGACCTTT
26227 TTTTTTTC
1 TTTTTTTC
26235 TTTTTTTC
1 TTTTTTTC
*
26243 TTTTTTCTT
1 TTTTTT-TC
26252 TTTTTTTC
1 TTTTTTTC
26260 TTTTTTTC
1 TTTTTTTC
*
26268 TTTTCTTC
1 TTTTTTTC
26276 TT
1 TT
26278 CAAGCATAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
8 32 0.82
9 7 0.18
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTTTTTC
Found at i:26244 original size:25 final size:25
Alignment explanation
Indices: 26216--26269 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
26206 TGAGTTTTCA
26216 TCTTGACCT-TTTTTTTTTCTTTTTT
1 TCTT-ACCTCTTTTTTTTTCTTTTTT
***
26241 TCTTTTTTCTTTTTTTTTCTTTTTT
1 TCTTACCTCTTTTTTTTTCTTTTTT
26266 TCTT
1 TCTT
26270 TTCTTCTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 1 0.04
25 24 0.96
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.81
Consensus pattern (25 bp):
TCTTACCTCTTTTTTTTTCTTTTTT
Found at i:26270 original size:25 final size:26
Alignment explanation
Indices: 26225--26277 Score: 99
Period size: 25 Copynumber: 2.1 Consensus size: 26
26215 ATCTTGACCT
26225 TTTTTTTTTCTTTTTTTCTTTT-TTC
1 TTTTTTTTTCTTTTTTTCTTTTCTTC
26250 TTTTTTTTTCTTTTTTTCTTTTCTTC
1 TTTTTTTTTCTTTTTTTCTTTTCTTC
26276 TT
1 TT
26278 CAAGCATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 22 0.81
26 5 0.19
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (26 bp):
TTTTTTTTTCTTTTTTTCTTTTCTTC
Found at i:37683 original size:20 final size:20
Alignment explanation
Indices: 37589--37957 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
37579 GATTTTCCAT
* ** *
37589 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
37609 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
37629 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
37649 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
37669 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
37689 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
37709 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
37729 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
37749 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
37769 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
37789 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
37809 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
37829 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
37849 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
37869 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
37889 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
37909 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
37929 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
37949 AATCACAAC
1 AATCGCAAC
37958 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:38666 original size:24 final size:24
Alignment explanation
Indices: 38627--38673 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
38617 AAATTTGGTC
38627 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
38651 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
38674 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:41191 original size:19 final size:19
Alignment explanation
Indices: 41169--41475 Score: 342
Period size: 19 Copynumber: 17.4 Consensus size: 19
41159 CGGAAAATAC
*
41169 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
41188 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
41202 AATCGCAATGCGGAAATGAAA
1 AATCGCAATGC-GAAATG-AA
*
41223 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
41237 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
41256 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
41275 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
41289 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
41308 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
41327 AATCG-AA-CCGACAT---
1 AATCGCAATGCGAAATGAA
*
41341 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
41360 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
41379 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
41398 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
41416 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
41430 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
41449 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
41468 AATCGCAA
1 AATCGCAA
41476 CGAGATAATC
Statistics
Matches: 248, Mismatches: 13, Indels: 54
0.79 0.04 0.17
Matches are distributed among these distances:
14 44 0.18
15 5 0.02
16 21 0.08
17 9 0.04
18 14 0.06
19 142 0.57
20 3 0.01
21 10 0.04
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:41263 original size:33 final size:33
Alignment explanation
Indices: 41169--41497 Score: 241
Period size: 33 Copynumber: 9.5 Consensus size: 33
41159 CGGAAAATAC
* *
41169 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAA
*
41202 AATCGCAATGCGGAAATGAAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATG-AAAATCGCAACGAGAA
41237 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
41275 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
* *
41308 AATCGCAATGCGAAATGAAAATCG-AACCGACAT
1 AATCGCAATGCGAAATGAAAATCGCAA-CGAGAA
*
41341 AATCGCAATGCGAAATTAAAATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGC-A-ACG--A-GAA
*
41379 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGA
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAGA--A
41416 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
41449 AATCGCAATGCGAAATGAAAATCGCAACGAGAT
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
41482 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
41498 TATAAACGCA
Statistics
Matches: 249, Mismatches: 16, Indels: 62
0.76 0.05 0.19
Matches are distributed among these distances:
32 12 0.05
33 100 0.40
34 17 0.07
35 42 0.17
36 11 0.04
37 15 0.06
38 52 0.21
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:41289 original size:52 final size:53
Alignment explanation
Indices: 41197--41475 Score: 342
Period size: 52 Copynumber: 5.2 Consensus size: 53
41187 AAATCCCAAC
*
41197 ATGAAAATCGCAATGCGGAAATGAAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATG-AAAATCGCAAGCGAGAAAATCGCAATGCGAA
*
41251 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
* * *
41303 ATGAAAATCGCAATGCGAAATGAAAATCG-AACCGACATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
* *
41355 ATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A-GAAAATCGCAATGCGAA
41412 ATG-AAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A-GAAAATCGCAATGCGAA
41463 ATGAAAATCGCAA
1 ATGAAAATCGCAA
41476 CGAGATAATC
Statistics
Matches: 210, Mismatches: 8, Indels: 16
0.90 0.03 0.07
Matches are distributed among these distances:
51 38 0.18
52 113 0.54
53 9 0.04
54 23 0.11
56 10 0.05
57 17 0.08
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (53 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
Found at i:41321 original size:71 final size:70
Alignment explanation
Indices: 41237--41475 Score: 351
Period size: 71 Copynumber: 3.4 Consensus size: 70
41227 GCAACGAGAG
*
41237 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATG-AAATCGCAACGAAAGAATCGCAATGCGA
41302 AATGAA
65 AATGAA
* * *
41308 AATCGCAATGCGAAATGAAAATCG-AA-CCGACAT--AATCGCAATGCGAAATTAAAATCGCAAT
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAA--CG-AA--AGAATCGCAAT
*
41369 ACGAAATGAA
61 GCGAAATGAA
41379 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAACGAAAGAATCGCAATGCGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAACGAAAGAATCGCAATGCGAA
41444 ATGAA
66 ATGAA
41449 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
41476 CGAGATAATC
Statistics
Matches: 150, Mismatches: 9, Indels: 19
0.84 0.05 0.11
Matches are distributed among these distances:
66 8 0.05
68 2 0.01
69 6 0.04
70 48 0.32
71 67 0.45
72 4 0.03
73 7 0.05
75 8 0.05
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (70 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAACGAAAGAATCGCAATGCGAA
ATGAA
Found at i:41613 original size:19 final size:19
Alignment explanation
Indices: 41504--41605 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
41494 AAATTATAAA
41504 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
41523 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
41543 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
41559 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
41576 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
41595 CGCATTGCGAT
1 CGCATTGCGAT
41606 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:41902 original size:14 final size:14
Alignment explanation
Indices: 41883--41972 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
41873 TTGAAATGAA
41883 AATCGCAACGAGAG
1 AATCGCAACGAGAG
41897 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
*
41914 ACAATCGCAACGATAG
1 --AATCGCAACGAGAG
*
41930 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
41949 AATCGCAACGAGAG
1 AATCGCAACGAGAG
41963 AATCGCAACG
1 AATCGCAACG
41973 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 28 0.45
15 1 0.02
16 8 0.13
17 7 0.11
18 1 0.02
19 17 0.27
ACGTcount: A:0.42, C:0.23, G:0.24, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:41920 original size:33 final size:33
Alignment explanation
Indices: 41875--41989 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
41865 TCTTTTGGTT
41875 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* * *
41908 GAGATGACAATCGCAACGATAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
41941 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
41974 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
41990 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:41921 original size:19 final size:19
Alignment explanation
Indices: 41878--41994 Score: 84
Period size: 19 Copynumber: 6.9 Consensus size: 19
41868 TTTGGTTGAA
41878 ATGAAAATCGCAA--CGAG
1 ATGAAAATCGCAACGCGAG
41895 A-G--AATCGCAACGCGAG
1 ATGAAAATCGCAACGCGAG
*
41911 ATGACAATCGCAA--C--G
1 ATGAAAATCGCAACGCGAG
* *
41926 AT-AGAATCGCAACGCGAA
1 ATGAAAATCGCAACGCGAG
41944 ATGAAAATCGCAA--CGAG
1 ATGAAAATCGCAACGCGAG
*
41961 A-G--AATCGCAACGCGAA
1 ATGAAAATCGCAACGCGAG
*
41977 ATGAAAATCGCAATGCGA
1 ATGAAAATCGCAACGCGA
41995 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 6, Indels: 28
0.70 0.05 0.25
Matches are distributed among these distances:
14 25 0.32
15 3 0.04
16 12 0.15
17 8 0.10
18 2 0.03
19 29 0.37
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.11
Consensus pattern (19 bp):
ATGAAAATCGCAACGCGAG
Found at i:42025 original size:14 final size:14
Alignment explanation
Indices: 42006--42060 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
41996 TTTGGTTTCG
42006 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
42020 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
42039 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
42053 CGTTGCGA
1 CGTTGCGA
42061 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:42071 original size:20 final size:20
Alignment explanation
Indices: 42046--42101 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
42036 TCGCGTTGCG
42046 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGACAGTC
***
42066 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGACAGTC
*
42086 ATTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGAC
42102 TCTTCTGCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.14, C:0.27, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTCTCTCGTTGCGACAGTC
Found at i:42222 original size:33 final size:33
Alignment explanation
Indices: 42180--42250 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
42170 AATACTAACT
*
42180 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
42213 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
42246 TGAAA
1 TGAAA
42251 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:42483 original size:22 final size:22
Alignment explanation
Indices: 42431--42485 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
42421 TGGTTGTGAG
**
42431 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
42453 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
42475 GGATTTCTTCG
1 GGATTTCTTCG
42486 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:42653 original size:20 final size:20
Alignment explanation
Indices: 42628--42821 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
42618 CTTTAAATAT
42628 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
42648 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
42670 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
42689 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
42709 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
42729 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
42749 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
42769 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
42789 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
42809 CGCGTTGCGATTT
1 CGCGTTGCGATTT
42822 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:42815 original size:60 final size:60
Alignment explanation
Indices: 42628--42821 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
42618 CTTTAAATAT
**
42628 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
42689 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
42749 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
42809 CGCGTTGCGATTT
1 CGCGTTGCGATTT
42822 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:42838 original size:21 final size:20
Alignment explanation
Indices: 42814--42890 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
42804 ATATTCGCGT
42814 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
42835 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
42855 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
42877 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
42891 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:42901 original size:20 final size:20
Alignment explanation
Indices: 42876--42927 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
42866 AAGAATCGCG
*
42876 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
42896 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
42916 TTGCGATTCTGG
1 TTGCGATTCTGG
42928 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:44797 original size:3 final size:3
Alignment explanation
Indices: 44789--44842 Score: 63
Period size: 3 Copynumber: 18.0 Consensus size: 3
44779 GACATGTTTG
* * * * *
44789 TAA TAA TAA TAA TAT TAA TAA AAA TAA TAT TAA TAA TAA TAT TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
44837 TAA TAA
1 TAA TAA
44843 AAAAAATGAA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:44809 original size:15 final size:15
Alignment explanation
Indices: 44789--44842 Score: 78
Period size: 15 Copynumber: 3.8 Consensus size: 15
44779 GACATGTTTG
44789 TAATAATAATAATAT
1 TAATAATAATAATAT
*
44804 TAATAAAAATAATAT
1 TAATAATAATAATAT
44819 TAATAATAAT-AT-T
1 TAATAATAATAATAT
44832 T-ATAATAATAA
1 TAATAATAATAA
44843 AAAAAATGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
12 8 0.22
13 3 0.08
14 2 0.06
15 23 0.64
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TAATAATAATAATAT
Found at i:45444 original size:2 final size:2
Alignment explanation
Indices: 45437--45461 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
45427 TTCACCGTTA
45437 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
45462 ATTTTGAAGA
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:65936 original size:21 final size:21
Alignment explanation
Indices: 65910--65966 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
65900 TTCTGGGCAG
*
65910 AGTGCATCGATGCATATTCAT
1 AGTGCACCGATGCATATTCAT
65931 AGTGCACCGATGCATATTCAT
1 AGTGCACCGATGCATATTCAT
65952 AGTGCACCGATGCAT
1 AGTGCACCGATGCAT
65967 CAAGGTTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (21 bp):
AGTGCACCGATGCATATTCAT
Found at i:67098 original size:31 final size:31
Alignment explanation
Indices: 67060--67155 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
67050 AGAGTCGAGG
67060 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTAGGTTCTTCGGGACCTATGGACA
*
67091 GTTTACCTAGGTTCTTCGGGACCTATAGACA
1 GTTTACCTAGGTTCTTCGGGACCTATGGACA
*
67122 GTTTACCTAGGTTCGTCGGGACCTATGGACA
1 GTTTACCTAGGTTCTTCGGGACCTATGGACA
67153 GTT
1 GTT
67156 GTCGAGGTTC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.32
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTCGGGACCTATGGACA
Found at i:67175 original size:30 final size:29
Alignment explanation
Indices: 67141--67204 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
67131 GGTTCGTCGG
*
67141 GACCTATGGACAGTTGTCGAGGTTCTTTAT
1 GACCTATGGACAGTT-ACGAGGTTCTTTAT
* * * *
67171 GACCTCTGGATAGTTACGGGGTTCTTTGT
1 GACCTATGGACAGTTACGAGGTTCTTTAT
67200 GACCT
1 GACCT
67205 CTGTATAGGA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 16 0.55
30 13 0.45
ACGTcount: A:0.17, C:0.19, G:0.28, T:0.36
Consensus pattern (29 bp):
GACCTATGGACAGTTACGAGGTTCTTTAT
Found at i:71290 original size:31 final size:31
Alignment explanation
Indices: 71248--71312 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
71238 AGAGTCGAGG
* * *
71248 GTTTACGTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTAGGTTCATCAGGACCTATGGACA
71279 GTTTACCTAGGTTCATCAGGACCTATGGACA
1 GTTTACCTAGGTTCATCAGGACCTATGGACA
71310 GTT
1 GTT
71313 GCCGAGGTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (31 bp):
GTTTACCTAGGTTCATCAGGACCTATGGACA
Found at i:71332 original size:30 final size:30
Alignment explanation
Indices: 71267--71366 Score: 94
Period size: 30 Copynumber: 3.3 Consensus size: 30
71257 GGTTCTTCGG
* * * *
71267 GACCTATGGACAGTTTACCTAGGTTCATCAG
1 GACCTATGGACAG-TTACCGAGGTTCTTTAT
*
71298 GACCTATGGACAGTTGCCGAGGTTCTTTAT
1 GACCTATGGACAGTTACCGAGGTTCTTTAT
* * * *
71328 GACCTCTGGATAGTTACCG-GGGTCTTTGT
1 GACCTATGGACAGTTACCGAGGTTCTTTAT
*
71357 GACCTCTGGA
1 GACCTATGGA
71367 TAGGTCATTC
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
29 18 0.31
30 28 0.47
31 13 0.22
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (30 bp):
GACCTATGGACAGTTACCGAGGTTCTTTAT
Found at i:71354 original size:29 final size:30
Alignment explanation
Indices: 71298--71369 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
71288 GGTTCATCAG
* * * *
71298 GACCTATGGACAGTTGCCGAGGTTCTTTAT
1 GACCTCTGGATAGTTACCGAGGGTCTTTAT
*
71328 GACCTCTGGATAGTTACCG-GGGTCTTTGT
1 GACCTCTGGATAGTTACCGAGGGTCTTTAT
71357 GACCTCTGGATAG
1 GACCTCTGGATAG
71370 GTCATTCGAG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 21 0.57
30 16 0.43
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGGTCTTTAT
Found at i:72266 original size:64 final size:63
Alignment explanation
Indices: 72194--72402 Score: 226
Period size: 65 Copynumber: 3.2 Consensus size: 63
72184 GTGCACCAAG
*
72194 TGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGAGTGCATCGATGCATGGCT
1 TGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATATCCTGAGTGCATCGATGCATGG-T
* * *
72258 TGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATAGAG
1 TGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATATCCTGAGTGCATCGATGCAT-G-G
72323 -
63 T
** * * * *
72323 AATGCATCGGTGCATGGAATGCATTCGATGTTTCAATTAAT-TCACT-AATGCATCGATGCATGG
1 TGTGCATCGATGCATGAAATGCATTCGATGTTTGAA--AATATC-CTGAGTGCATCGATGCATGG
72386 T
63 T
*
72387 TGATGCATCGGTGCAT
1 TG-TGCATCGATGCAT
72403 CACCTCAAAT
Statistics
Matches: 122, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
63 1 0.01
64 35 0.29
65 80 0.66
66 5 0.04
67 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (63 bp):
TGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATATCCTGAGTGCATCGATGCATGGT
Found at i:72344 original size:17 final size:19
Alignment explanation
Indices: 72306--72352 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
72296 ATATTCAGAG
72306 TGCATCGATGCATAGAGAA
1 TGCATCGATGCATAGAGAA
*
72325 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATAGAGAA
72342 TGCATTCGATG
1 TGCA-TCGATG
72353 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATAGAGAA
Found at i:77824 original size:22 final size:21
Alignment explanation
Indices: 77782--77821 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
77772 GAGTTTGTTT
*
77782 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
77803 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
77822 ACAGTTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:79832 original size:64 final size:64
Alignment explanation
Indices: 79779--79942 Score: 229
Period size: 65 Copynumber: 2.5 Consensus size: 64
79769 CGGTGCACCA
*
79779 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * **
79843 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * *
79908 AGAATGCATCGGTGCATGGAATGCATTCGATGTTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTT
79943 CAATTAATTC
Statistics
Matches: 86, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
64 32 0.37
65 54 0.63
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:79931 original size:17 final size:19
Alignment explanation
Indices: 79893--79939 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
79883 ATATTCAGAG
79893 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
79912 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
79929 TGCATTCGATG
1 TGCA-TCGATG
79940 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:79962 original size:65 final size:62
Alignment explanation
Indices: 79783--79989 Score: 204
Period size: 65 Copynumber: 3.2 Consensus size: 62
79773 GCACCAAGTG
* *
79783 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGC-CTGAGTGCATCGATGCATGGCTTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAT-TCACT-AGTGCATCGATGCATGG--AG
79847 -
62 A
* *
79847 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGAGA
1 TGCATCGATGCATGAAATGCATTCGATG-TTTG-AAA-ATTCACTAGTGCATCGATGCATGGAG-
79911 A
62 A
* * * * *
79912 TGCATCGGTGCATGGAATGCATTCGATGTTTCAATTAATTCACTAATGCATCGATGCATGGTTGA
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAA--AATTCACTAGTGCATCGATGCATGG-AGA
*
79977 TGCATCGGTGCAT
1 TGCATCGATGCAT
79990 CACCTCAAAT
Statistics
Matches: 122, Mismatches: 11, Indels: 19
0.80 0.07 0.12
Matches are distributed among these distances:
63 3 0.02
64 35 0.29
65 77 0.63
66 5 0.04
67 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.31
Consensus pattern (62 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAATTCACTAGTGCATCGATGCATGGAGA
Found at i:80179 original size:20 final size:21
Alignment explanation
Indices: 80156--80195 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
80146 GAATCGAATA
80156 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
80176 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
80196 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:82026 original size:37 final size:37
Alignment explanation
Indices: 81976--82047 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
81966 AAAACATTTC
* *
81976 TTAATTTCTTCAAGAAAACCATTAGCCTAAGTAATAT
1 TTAATTTCGTCAAGAAAACCATTAGACTAAGTAATAT
82013 TTAATTTCGTCAAGAAAACCATTAGACTAAGTAAT
1 TTAATTTCGTCAAGAAAACCATTAGACTAAGTAAT
82048 CTTTTCAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (37 bp):
TTAATTTCGTCAAGAAAACCATTAGACTAAGTAATAT
Found at i:86607 original size:16 final size:16
Alignment explanation
Indices: 86583--86614 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
86573 TATATTATAA
86583 CCAACAATCAAAACTG
1 CCAACAATCAAAACTG
*
86599 CCAATAATCAAAACTG
1 CCAACAATCAAAACTG
86615 AAAAATTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.28, G:0.06, T:0.16
Consensus pattern (16 bp):
CCAACAATCAAAACTG
Found at i:87920 original size:2 final size:2
Alignment explanation
Indices: 87913--87947 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
87903 CTTAATTGAT
*
87913 TA TA TA TA TA TA TA TA TA TA TC TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
87948 GAGTATTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:90658 original size:2 final size:2
Alignment explanation
Indices: 90651--90675 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
90641 CTTTTAAAAC
90651 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
90676 CCCCATCCGT
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:90809 original size:35 final size:35
Alignment explanation
Indices: 90733--90809 Score: 111
Period size: 35 Copynumber: 2.2 Consensus size: 35
90723 CCCTGTCACA
*
90733 TCCAA-TAAGGCCCTGAGCACACAGCCGAGGAACC
1 TCCAAGTAAGGCCCTGAGCACACAGCCAAGGAACC
***
90767 AGTAAGTAAGGCCCTGAGCACACAGCCAAGGAACC
1 TCCAAGTAAGGCCCTGAGCACACAGCCAAGGAACC
90802 TCCAAGTA
1 TCCAAGTA
90810 TTCTTCCTCC
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
34 2 0.06
35 33 0.94
ACGTcount: A:0.35, C:0.31, G:0.23, T:0.10
Consensus pattern (35 bp):
TCCAAGTAAGGCCCTGAGCACACAGCCAAGGAACC
Found at i:90900 original size:24 final size:24
Alignment explanation
Indices: 90890--91024 Score: 193
Period size: 24 Copynumber: 5.7 Consensus size: 24
90880 CATAATTCAC
* * *
90890 GTCAAGTATCATATCAAAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
* *
90914 GTC-AGTATCAGATCAAAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
90937 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
*
90961 GT-AAGATATCATATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
90985 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
91009 GTCAAGTATCAGATCA
1 GTCAAGTATCAGATCA
91025 AAAATCAAAT
Statistics
Matches: 103, Mismatches: 5, Indels: 6
0.90 0.04 0.05
Matches are distributed among these distances:
23 25 0.24
24 75 0.73
25 3 0.03
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:93471 original size:13 final size:13
Alignment explanation
Indices: 93449--93518 Score: 72
Period size: 13 Copynumber: 5.3 Consensus size: 13
93439 GCCGGTCAAC
*
93449 GGTCAACGGGTGG
1 GGTCAACGGGTCG
*
93462 GGTCAGCGGGT--
1 GGTCAACGGGTCG
*
93473 GGTCAGCGGGTCG
1 GGTCAACGGGTCG
93486 GGTCAACGGGTCGGG
1 GGTCAACGGGTC--G
93501 TGGTCAACGGGTCG
1 -GGTCAACGGGTCG
93515 GGTC
1 GGTC
93519 GGTTGTGACC
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
11 11 0.22
13 25 0.50
14 1 0.02
15 1 0.02
16 12 0.24
ACGTcount: A:0.11, C:0.20, G:0.51, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:93482 original size:24 final size:24
Alignment explanation
Indices: 93449--93496 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
93439 GCCGGTCAAC
* *
93449 GGTCAACGGGTGGGGTCAGCGGGT
1 GGTCAACGGGTCGGGTCAACGGGT
*
93473 GGTCAGCGGGTCGGGTCAACGGGT
1 GGTCAACGGGTCGGGTCAACGGGT
93497 CGGGTGGTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.12, C:0.19, G:0.52, T:0.17
Consensus pattern (24 bp):
GGTCAACGGGTCGGGTCAACGGGT
Found at i:93505 original size:16 final size:16
Alignment explanation
Indices: 93468--93517 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
93458 GTGGGGTCAG
*
93468 CGGGTGGTCAGCGGGT
1 CGGGTGGTCAACGGGT
93484 C--G-GGTCAACGGGT
1 CGGGTGGTCAACGGGT
93497 CGGGTGGTCAACGGGT
1 CGGGTGGTCAACGGGT
93513 CGGGT
1 CGGGT
93518 CGGTTGTGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 11 0.37
14 1 0.03
15 1 0.03
16 17 0.57
ACGTcount: A:0.10, C:0.20, G:0.52, T:0.18
Consensus pattern (16 bp):
CGGGTGGTCAACGGGT
Found at i:96076 original size:30 final size:28
Alignment explanation
Indices: 96031--96089 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 28
96021 TAATTCCCAT
96031 GATGGATGGTTTAAGAGGAAGGGTAAAC
1 GATGGATGGTTTAAGAGGAAGGGTAAAC
96059 GATGGATGGTTTTTAAGAGGAAGGGTAAAC
1 GATGGATGG--TTTAAGAGGAAGGGTAAAC
96089 G
1 G
96090 TGGTAGTATG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 9 0.31
30 20 0.69
ACGTcount: A:0.34, C:0.03, G:0.39, T:0.24
Consensus pattern (28 bp):
GATGGATGGTTTAAGAGGAAGGGTAAAC
Found at i:98403 original size:134 final size:137
Alignment explanation
Indices: 98132--98405 Score: 493
Period size: 134 Copynumber: 2.0 Consensus size: 137
98122 GTACAATTTG
98132 TATGATGCACAAGAAAAACACAAAAACAAACTAGCTGCTCGATTTCGGCTCCAGCTTGTAAGCAT
1 TATGATGCACAAGAAAAACACAAAAACAAACTAGCTGCTCGATTTCGGCTCCAGCTTGTAAGCAT
*
98197 TGCAATGACAACGTGAGCATATGGTGAAAGTTCATTTTTTCATGGAAGGACAATTTATAAATGCA
66 TGCAAGGACAACGTGAGCATATGGTGAAAGTTCATTTTTTCATGGAAGGACAATTTATAAATGCA
98262 TATGTTT
131 TATGTTT
98269 TATGATGCACAAGAAAAACAC-AAAACAAACTAGCTGCTCGATTTTCGGCTCCAGCTTGTAA-CA
1 TATGATGCACAAGAAAAACACAAAAACAAACTAGCTGCTCGA-TTTCGGCTCCAGCTTGTAAGCA
*
98332 TTGCAAGGACAATGTGAGCATAT-G-GAAAGTTCATTTTTTCATGGAAGGACAATTTATAAATGC
65 TTGCAAGGACAACGTGAGCATATGGTGAAAGTTCATTTTTTCATGGAAGGACAATTTATAAATGC
98395 ATATGTTT
130 ATATGTTT
98403 TAT
1 TAT
98406 TTTAAGAAAT
Statistics
Matches: 134, Mismatches: 2, Indels: 5
0.95 0.01 0.04
Matches are distributed among these distances:
134 50 0.37
135 1 0.01
136 43 0.32
137 40 0.30
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (137 bp):
TATGATGCACAAGAAAAACACAAAAACAAACTAGCTGCTCGATTTCGGCTCCAGCTTGTAAGCAT
TGCAAGGACAACGTGAGCATATGGTGAAAGTTCATTTTTTCATGGAAGGACAATTTATAAATGCA
TATGTTT
Found at i:99273 original size:55 final size:55
Alignment explanation
Indices: 99210--99324 Score: 167
Period size: 55 Copynumber: 2.1 Consensus size: 55
99200 GTAATTTACA
* *
99210 TGCAATGGAAAATGAATATCATCATCTTAATGTCTAATTAACGAAACAATCAACC
1 TGCAATGGAAAATGAATATCATCATCTTAATATCTAATTAACAAAACAATCAACC
* * * * *
99265 TGCAATGGAAAATGACTATCATTATCTTAATATTTAATTAACAAAACACTCAACG
1 TGCAATGGAAAATGAATATCATCATCTTAATATCTAATTAACAAAACAATCAACC
99320 TGCAA
1 TGCAA
99325 ATAATAAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.29
Consensus pattern (55 bp):
TGCAATGGAAAATGAATATCATCATCTTAATATCTAATTAACAAAACAATCAACC
Found at i:111645 original size:20 final size:20
Alignment explanation
Indices: 111620--111686 Score: 125
Period size: 20 Copynumber: 3.4 Consensus size: 20
111610 ATACTAATAG
111620 GAGTATCGATACCAAGGGTA
1 GAGTATCGATACCAAGGGTA
111640 GAGTATCGATACCAAGGGTA
1 GAGTATCGATACCAAGGGTA
*
111660 GAGTATCAATACCAAGGGTA
1 GAGTATCGATACCAAGGGTA
111680 GAGTATC
1 GAGTATC
111687 AATAATCCCT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.36, C:0.15, G:0.28, T:0.21
Consensus pattern (20 bp):
GAGTATCGATACCAAGGGTA
Found at i:114278 original size:6 final size:6
Alignment explanation
Indices: 114267--114293 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
114257 AGAGATAATA
114267 TATATT TATATT TATATT TATATT TAT
1 TATATT TATATT TATATT TATATT TAT
114294 GTCGTTCTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATATT
Found at i:119278 original size:2 final size:2
Alignment explanation
Indices: 119271--119298 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
119261 AATTATTAGT
119271 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
119299 ATAATAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:131097 original size:22 final size:22
Alignment explanation
Indices: 131069--131123 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
131059 ATCTACATGC
131069 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
131091 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
131113 TTCAAAGATGA
1 TTCAAAGATGA
131124 AAGCTTTATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:132082 original size:127 final size:127
Alignment explanation
Indices: 131838--132121 Score: 446
Period size: 127 Copynumber: 2.2 Consensus size: 127
131828 GTCAATCATT
*
131838 TTCAGTCTTCACAAAAAGAGTAGTGAAGCAAGAACAAGATCAAAATTCGCTCTCCACGGAAGAGT
1 TTCAGCCTTCACAAAAAGAGTAGTGAAGCAAGAACAAGATCAAAATTCGCTCTCCACGGAAGAGT
131903 AGTGGAAAGGATTTTTCAGCAAAGTATGAAGCCTTCACGAGAAAGTAATGGAGTAATGAAAA
66 AGTGGAAAGGATTTTTCAGCAAAGTATGAAGCCTTCACGAGAAAGTAATGGAGTAATGAAAA
* * * *
131965 TTCATCCTTCACAAAAAAAGTAGTGAAGCAAGAACAAGATTAAAATTCGCTCTCCATGGAAGAGT
1 TTCAGCCTTCACAAAAAGAGTAGTGAAGCAAGAACAAGATCAAAATTCGCTCTCCACGGAAGAGT
* * * *
132030 AGTGGAATGGATTTTTCAGCAAAGTATGAAGCCTTCATGAGAGAG-AAGTGGAGTAATGTAAA
66 AGTGGAAAGGATTTTTCAGCAAAGTATGAAGCCTTCACGAGAAAGTAA-TGGAGTAATGAAAA
* *
132092 TTCAGCCTTCAC-AGAAGAGTAGTGGAGCAA
1 TTCAGCCTTCACAAAAAGAGTAGTGAAGCAA
132122 ATCATTTGCA
Statistics
Matches: 143, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
126 17 0.12
127 126 0.88
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.23
Consensus pattern (127 bp):
TTCAGCCTTCACAAAAAGAGTAGTGAAGCAAGAACAAGATCAAAATTCGCTCTCCACGGAAGAGT
AGTGGAAAGGATTTTTCAGCAAAGTATGAAGCCTTCACGAGAAAGTAATGGAGTAATGAAAA
Found at i:141065 original size:13 final size:14
Alignment explanation
Indices: 141047--141076 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
141037 CACACATAAA
141047 AAATGT-AAAATGC
1 AAATGTAAAAATGC
141060 AAATGTAAAAATGC
1 AAATGTAAAAATGC
141074 AAA
1 AAA
141077 ATGTGTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.60, C:0.07, G:0.13, T:0.20
Consensus pattern (14 bp):
AAATGTAAAAATGC
Found at i:141612 original size:17 final size:17
Alignment explanation
Indices: 141590--141625 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
141580 CAACATCTCT
*
141590 ATGTCATAATGATGCAA
1 ATGTCATAAGGATGCAA
*
141607 ATGTCATGAGGATGCAA
1 ATGTCATAAGGATGCAA
141624 AT
1 AT
141626 TCAAGAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (17 bp):
ATGTCATAAGGATGCAA
Found at i:144370 original size:2 final size:2
Alignment explanation
Indices: 144363--144397 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
144353 ATTATTTTAC
144363 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 A
144398 GTCACTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:144475 original size:38 final size:37
Alignment explanation
Indices: 144424--144970 Score: 345
Period size: 38 Copynumber: 14.1 Consensus size: 37
144414 TGGAGTTTTA
*
144424 TTTTTGAAACATTTTTAAAATATATATATAATATATAG
1 TTTTTGAAACATTTTTGAAA-ATATATATAATATATAG
*
144462 TTTTTGAAACA-TTTT-AAAAAATATATAATATATAG
1 TTTTTGAAACATTTTTGAAAATATATATAATATATAG
144497 TTTTTGAAACATTTTTTTTGAAAATATATATAATATATAG
1 TTTTTGAAACA---TTTTTGAAAATATATATAATATATAG
*
144537 TTTTTGGAACATTTTTTGAAAATATATATAATATATAG
1 TTTTTGAAACA-TTTTTGAAAATATATATAATATATAG
144575 -TTTTGAAAACATTTTTGAAAATATATATATAATATATAG
1 TTTTTG-AAACATTTTTG-AAA-ATATATATAATATATAG
* **
144614 TTTTGGAAAACATTTTTCGAAAACGTATATAATATATAG
1 TTTTTG-AAACATTTTT-GAAAATATATATAATATATAG
* *
144653 -TTTTGAAAAACTTTTTTTTGGAAATATATATAATATATAG
1 TTTTTG--AAAC--ATTTTTGAAAATATATATAATATATAG
* * *
144693 -TTTTGAAA-ACGTTTTGAAAAAAAAAATATATATATATA-
1 TTTTTGAAACA-TTTTTG--AAAATATATATA-ATATATAG
* * * * *
144731 TATAT-AATATATAGTTTAGAAAACATTTTTTAAAACATATATATAATATA-
1 TTTTTGAA-ACAT--TTTTG-AAA-A-----T---ATATATA-AT-ATATAG
* * *
144781 TAGTTTTGAAAATATTTTTGAAAATATATATAATATATAG
1 T-TTTTG--AAACATTTTTGAAAATATATATAATATATAG
* *
144821 TTTTGGAAAACATTTATTGAAAATACATATAATATATAG
1 TTTTTG-AAACATTT-TTGAAAATATATATAATATATAG
* *
144860 -TTTTGAAAACA-TTTTGAATATATATATAATACATAG
1 TTTTTG-AAACATTTTTGAAAATATATATAATATATAG
*
144896 -TTTTGAAAACGTTTTTG-AAA-ATATATAAT-T-TAG
1 TTTTTG-AAACATTTTTGAAAATATATATAATATATAG
* * ***
144929 AATTTAGAATTTTTTTTGAAAATATATATAATATAT-G
1 -TTTTTGAAACATTTTTGAAAATATATATAATATATAG
144966 TTTTT
1 TTTTT
144971 TAAAAAATAC
Statistics
Matches: 419, Mismatches: 45, Indels: 92
0.75 0.08 0.17
Matches are distributed among these distances:
33 3 0.01
34 8 0.02
35 43 0.10
36 52 0.12
37 24 0.06
38 82 0.20
39 80 0.19
40 78 0.19
41 17 0.04
44 1 0.00
49 10 0.02
50 9 0.02
51 6 0.01
53 4 0.01
54 2 0.00
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (37 bp):
TTTTTGAAACATTTTTGAAAATATATATAATATATAG
Found at i:144486 original size:37 final size:38
Alignment explanation
Indices: 144424--144975 Score: 383
Period size: 39 Copynumber: 14.3 Consensus size: 38
144414 TGGAGTTTTA
*
144424 TTTTTG-AAACATTTTTAAAATATATATATAATATATAG
1 TTTTTGAAAACATTTTTGAAA-ATATATATAATATATAG
*
144462 TTTTTG-AAACA-TTTT-AAAAAATATATAATATATAG
1 TTTTTGAAAACATTTTTGAAAATATATATAATATATAG
144497 TTTTTG-AAACATTTTTTTTGAAAATATATATAATATATAG
1 TTTTTGAAAACA---TTTTTGAAAATATATATAATATATAG
*
144537 TTTTTG-GAACATTTTTTGAAAATATATATAATATATAG
1 TTTTTGAAAACA-TTTTTGAAAATATATATAATATATAG
144575 -TTTTGAAAACATTTTTGAAAATATATATATAATATATAG
1 TTTTTGAAAACATTTTTG-AAA-ATATATATAATATATAG
* **
144614 TTTTGGAAAACATTTTTCGAAAACGTATATAATATATAG
1 TTTTTGAAAACATTTTT-GAAAATATATATAATATATAG
* *
144653 -TTTTGAAAAACTTTTTTTTGGAAATATATATAATATATAG
1 TTTTTG-AAAAC--ATTTTTGAAAATATATATAATATATAG
* * *
144693 -TTTTGAAAAC-GTTTTGAAAAAAAAAATATATATATATA-
1 TTTTTGAAAACATTTTTG--AAAATATATATA-ATATATAG
* * * * * *
144731 TATAT-AATATATAGTTTAGAAAACATTTTTTAAAACATATATATAATATA-
1 TTTTTGAA-A-ACATTTTTG-AAA-A-----T---ATATATA-AT-ATATAG
* * *
144781 TAGTTTTGAAAATATTTTTGAAAATATATATAATATATAG
1 T-TTTTG-AAAACATTTTTGAAAATATATATAATATATAG
* *
144821 TTTTGGAAAACATTTATTGAAAATACATATAATATATAG
1 TTTTTGAAAACATTT-TTGAAAATATATATAATATATAG
* *
144860 -TTTTGAAAACA-TTTTGAATATATATATAATACATAG
1 TTTTTGAAAACATTTTTGAAAATATATATAATATATAG
*
144896 -TTTTGAAAACGTTTTTG-AAA-ATATATAAT-T-TAG
1 TTTTTGAAAACATTTTTGAAAATATATATAATATATAG
** ***
144929 AATTT-AGAATTTTTTTTGAAAATATATATAATATAT-G
1 TTTTTGA-AAACATTTTTGAAAATATATATAATATATAG
*
144966 TTTTTTAAAA
1 TTTTTGAAAA
144976 AATACAGTTT
Statistics
Matches: 425, Mismatches: 46, Indels: 87
0.76 0.08 0.16
Matches are distributed among these distances:
33 4 0.01
34 11 0.03
35 39 0.09
36 49 0.12
37 29 0.07
38 80 0.19
39 85 0.20
40 78 0.18
41 18 0.04
44 1 0.00
49 10 0.02
50 9 0.02
51 9 0.02
52 1 0.00
53 2 0.00
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (38 bp):
TTTTTGAAAACATTTTTGAAAATATATATAATATATAG
Found at i:144843 original size:131 final size:130
Alignment explanation
Indices: 144595--144831 Score: 365
Period size: 131 Copynumber: 1.8 Consensus size: 130
144585 ATTTTTGAAA
* *
144595 ATATATATATAATATATAGTTTTGGAAAACATTTTTCGAAAACGTATATAATATATAGTTTTGAA
1 ATATATATATAATATATAGTTTTAGAAAACATTTTTCGAAAACATATATAATATATAGTTTTGAA
* *
144660 AAACTTTTTTTTGGAAATATATATAATATATAGTTTTGAAAACGTTTTGAAAAAAAAAATATATA
66 AAAC-TATTTTTGAAAATATATATAATATATAGTTTTGAAAACGTTTTGAAAAAAAAAATATATA
144725 T
130 T
*
144726 ATATATATATAATATATAG-TTTAGAAAACATTTTT-TAAAACATATATATAATATATAGTTTTG
1 ATATATATATAATATATAGTTTTAGAAAACATTTTTCGAAAAC--ATATATAATATATAGTTTTG
144789 -AAAA-TATTTTTGAAAATATATATAATATATAGTTTTGGAAAAC
64 AAAAACTATTTTTGAAAATATATATAATATATAGTTTT-GAAAAC
144832 ATTTATTGAA
Statistics
Matches: 98, Mismatches: 5, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
128 30 0.31
129 11 0.11
130 19 0.19
131 38 0.39
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.42
Consensus pattern (130 bp):
ATATATATATAATATATAGTTTTAGAAAACATTTTTCGAAAACATATATAATATATAGTTTTGAA
AAACTATTTTTGAAAATATATATAATATATAGTTTTGAAAACGTTTTGAAAAAAAAAATATATAT
Found at i:145034 original size:17 final size:16
Alignment explanation
Indices: 144983--145058 Score: 53
Period size: 19 Copynumber: 4.3 Consensus size: 16
144973 AAAAATACAG
144983 TTTTATTTACATTATATTT
1 TTTTATTT--ATT-TATTT
*
145002 TTTTATTTATTCATTT
1 TTTTATTTATTTATTT
*
145018 TGTTTATTTCTTTATTT
1 T-TTTATTTATTTATTT
* *
145035 TAATTCTATTTTTTTCTTT
1 T--TT-TATTTATTTATTT
145054 TTTTA
1 TTTTA
145059 AGGTTCAATA
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
16 7 0.15
17 19 0.40
18 2 0.04
19 20 0.42
ACGTcount: A:0.18, C:0.07, G:0.01, T:0.74
Consensus pattern (16 bp):
TTTTATTTATTTATTT
Found at i:145799 original size:31 final size:30
Alignment explanation
Indices: 145761--145846 Score: 88
Period size: 29 Copynumber: 2.9 Consensus size: 30
145751 CGTCCCCAAC
*
145761 AGGTCGCCATGCATTCCCCAAC-ACCCCTACA
1 AGGTCGCCATGCACTCCCCAACGA--CCTACA
* * *
145792 AGGTCGCCAAGTACT-CCCAGCGACCTACA
1 AGGTCGCCATGCACTCCCCAACGACCTACA
*
145821 AGGTCGCCATGCACT-CCCAGCGACCT
1 AGGTCGCCATGCACTCCCCAACGACCT
145847 TGTAGGTCGC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
29 30 0.62
30 5 0.10
31 13 0.27
ACGTcount: A:0.24, C:0.42, G:0.19, T:0.15
Consensus pattern (30 bp):
AGGTCGCCATGCACTCCCCAACGACCTACA
Found at i:145823 original size:29 final size:29
Alignment explanation
Indices: 145786--145903 Score: 130
Period size: 29 Copynumber: 4.1 Consensus size: 29
145776 CCCCAACACC
* *
145786 CCTACAAGGTCGCCAAGTACTCCCAGCGA
1 CCTACAAGGTCGCCAAGCAATCCCAGCGA
* *
145815 CCTACAAGGTCGCCATGCACTCCCAGCGA
1 CCTACAAGGTCGCCAAGCAATCCCAGCGA
*** *
145844 CCTTGTAGGTCGCCAAGCAATCCCGGCGA
1 CCTACAAGGTCGCCAAGCAATCCCAGCGA
**
145873 CCTTGTAA-GTCGCCAAGCAATCCCAGCGA
1 CC-TACAAGGTCGCCAAGCAATCCCAGCGA
145902 CC
1 CC
145904 AAGCCTCGAC
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
29 74 0.97
30 2 0.03
ACGTcount: A:0.25, C:0.38, G:0.22, T:0.15
Consensus pattern (29 bp):
CCTACAAGGTCGCCAAGCAATCCCAGCGA
Found at i:145873 original size:58 final size:58
Alignment explanation
Indices: 145792--145903 Score: 145
Period size: 58 Copynumber: 1.9 Consensus size: 58
145782 CACCCCTACA
* * * *
145792 AGGTCGCCAAGTACTCCCAGCGACC-TACAAGGTCGCCATGCACTCCCAGCGACCTTGT
1 AGGTCGCCAAGCAATCCCAGCGACCTTACAA-GTCGCCAAGCAATCCCAGCGACCTTGT
* **
145850 AGGTCGCCAAGCAATCCCGGCGACCTTGTAAGTCGCCAAGCAATCCCAGCGACC
1 AGGTCGCCAAGCAATCCCAGCGACCTTACAAGTCGCCAAGCAATCCCAGCGACC
145904 AAGCCTCGAC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
58 43 0.93
59 3 0.07
ACGTcount: A:0.24, C:0.38, G:0.23, T:0.15
Consensus pattern (58 bp):
AGGTCGCCAAGCAATCCCAGCGACCTTACAAGTCGCCAAGCAATCCCAGCGACCTTGT
Found at i:145963 original size:32 final size:32
Alignment explanation
Indices: 145922--145986 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
145912 ACTTAACCCT
145922 GCTCCCTCGTGCATGGGTTGCATCCATAGCTG
1 GCTCCCTCGTGCATGGGTTGCATCCATAGCTG
145954 GCTCCCTCGTGCATGGGTTGCATCCATAGCTG
1 GCTCCCTCGTGCATGGGTTGCATCCATAGCTG
145986 G
1 G
145987 GAGATTCCTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.12, C:0.31, G:0.29, T:0.28
Consensus pattern (32 bp):
GCTCCCTCGTGCATGGGTTGCATCCATAGCTG
Found at i:146002 original size:23 final size:23
Alignment explanation
Indices: 145972--146015 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
145962 GTGCATGGGT
145972 TGCATCCATAGCTGGGAGATTCC
1 TGCATCCATAGCTGGGAGATTCC
145995 TGCATCCATAGCTGGGAGATT
1 TGCATCCATAGCTGGGAGATT
146016 GTAGCCAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (23 bp):
TGCATCCATAGCTGGGAGATTCC
Found at i:146490 original size:28 final size:30
Alignment explanation
Indices: 146446--146507 Score: 101
Period size: 28 Copynumber: 2.1 Consensus size: 30
146436 AATTTAGTTA
*
146446 ATTAGTTTGTTAGTTTAAG-T-TATATTAT
1 ATTAGTTTGTTAATTTAAGTTATATATTAT
146474 ATTAGTTTGTTAATTTAAGTTATATATTAT
1 ATTAGTTTGTTAATTTAAGTTATATATTAT
146504 ATTA
1 ATTA
146508 TATAAAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 18 0.58
29 1 0.03
30 12 0.39
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.56
Consensus pattern (30 bp):
ATTAGTTTGTTAATTTAAGTTATATATTAT
Found at i:146496 original size:23 final size:23
Alignment explanation
Indices: 146436--146498 Score: 58
Period size: 28 Copynumber: 2.6 Consensus size: 23
146426 GTAAAACTAA
146436 AATTT-AGTTA-ATTAGTTTGTT
1 AATTTAAGTTATATTAGTTTGTT
*
146457 AGTTTAAGTTATATTATATTAGTTTGTT
1 AATTTAAG-----TTATATTAGTTTGTT
146485 AATTTAAGTTATAT
1 AATTTAAGTTATAT
146499 ATTATATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
21 4 0.12
22 2 0.06
23 6 0.18
27 3 0.09
28 18 0.55
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.56
Consensus pattern (23 bp):
AATTTAAGTTATATTAGTTTGTT
Found at i:146845 original size:20 final size:21
Alignment explanation
Indices: 146801--146845 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
146791 AAATATTGTG
**
146801 TTTAAAAATATTTAGTGTTGT
1 TTTAAAAATATTTAGTGTTAA
*
146822 TTTAAAAATATTTTGT-TTAA
1 TTTAAAAATATTTAGTGTTAA
146842 TTTA
1 TTTA
146846 TATTATATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTAAAAATATTTAGTGTTAA
Found at i:149983 original size:10 final size:10
Alignment explanation
Indices: 149968--150001 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
149958 TTAGTAATAA
149968 TATATGTATT
1 TATATGTATT
*
149978 TATATGAATT
1 TATATGTATT
*
149988 TCTATGTATT
1 TATATGTATT
149998 TATA
1 TATA
150002 AGATTTAGTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.32, C:0.03, G:0.09, T:0.56
Consensus pattern (10 bp):
TATATGTATT
Found at i:150061 original size:49 final size:49
Alignment explanation
Indices: 150007--150715 Score: 790
Period size: 49 Copynumber: 13.3 Consensus size: 49
149997 TTATAAGATT
* *
150007 TAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTT--T-A-ATGAT--T--TGA
*
150065 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTT--T-A-ATG--ATT--TGA
150125 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
*
150176 TAGTAATAATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
* *
150225 TAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGATAGTAATGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTT--T-A-ATGAT--T--TGA
150283 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
*
150334 TAGTAATGATTAGTAATAATAAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
*
150383 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTT--T-A-ATG--ATT--TGA
*
150441 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGG
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
150492 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
*
150541 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTT--T-A-ATG--ATT--TGA
150599 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
* *
150650 TAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
*
150698 TATTAATGATTTAGTAAT
1 TAGTAATGA-TTAGTAAT
150716 GATTTGATAG
Statistics
Matches: 594, Mismatches: 19, Indels: 83
0.85 0.03 0.12
Matches are distributed among these distances:
48 34 0.06
49 274 0.46
50 9 0.02
51 11 0.02
52 3 0.01
53 13 0.02
54 8 0.01
55 10 0.02
56 11 0.02
57 4 0.01
58 9 0.02
59 12 0.02
60 194 0.33
62 2 0.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (49 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
Found at i:150080 original size:21 final size:21
Alignment explanation
Indices: 150003--150143 Score: 68
Period size: 21 Copynumber: 7.0 Consensus size: 21
149993 GTATTTATAA
150003 GATTTAGTAATGATTAGTAAT
1 GATTTAGTAATGATTAGTAAT
* * *
150024 GA--T-GAAATTATTATTAAT
1 GATTTAGTAATGATTAGTAAT
* *
150042 -ATTTAATGATTTGA-TAGTAAT
1 GATTTAGT-A-ATGATTAGTAAT
150063 GATTTAGTAATGATTAGTAAT
1 GATTTAGTAATGATTAGTAAT
* * * *
150084 -A-AT-GAAATTATTATTAAT
1 GATTTAGTAATGATTAGTAAT
* * *
150102 -ATTTAATGATTTGA-TATTAAT
1 GATTTAGT-A-ATGATTAGTAAT
150123 GATTTAGTAATGATTAGTAAT
1 GATTTAGTAATGATTAGTAAT
150144 AATGAAATTA
Statistics
Matches: 85, Mismatches: 22, Indels: 26
0.64 0.17 0.20
Matches are distributed among these distances:
17 1 0.01
18 25 0.29
19 4 0.05
20 7 0.08
21 32 0.38
22 16 0.19
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.45
Consensus pattern (21 bp):
GATTTAGTAATGATTAGTAAT
Found at i:150181 original size:109 final size:108
Alignment explanation
Indices: 150067--150666 Score: 718
Period size: 109 Copynumber: 5.6 Consensus size: 108
150057 AGTAATGATT
150067 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA-TTAGTA
*
150132 ATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
65 ATGATTAGTAATAATAAAATTATTATTAATTTTTAATGATTTGA
* *
150176 TAGTAATAATTAGTAATAATGAAATTATTATTAAT-TTT--T-A-ATG--ATT--TGA-TAGTAA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTAGTAA
*
150231 TGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGA
66 TGATTAGTAATAATAAAATTATTATTAATTTTTAATGATTTGA
* * * * * * *
150274 TAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTA-TTAAT-TTTTAATGATT--TGA-
1 TAGTAATGA-TTAGTAAT-AAT-GAAATTAT--TATTAATATTTAATGATTTGAT-ATTAATGAT
150334 TAGTAATGATTAGTAATAATAAAATTATTATTAATTTTTAATGATTTGA
60 TAGTAATGATTAGTAATAATAAAATTATTATTAATTTTTAATGATTTGA
150383 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA-TTAGTA
* *
150448 ATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGG
65 ATGATTAGTAATAATAAAATTATTATTAATTTTTAATGATTTGA
* *
150492 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTAGTAA
* * ** * * *
150557 T-AAT-G-AA-ATTATTATTAATATTTAATGATTTGAT-ATTAATGA
66 TGATTAGTAATAATAAAATTATTA-TTAAT-TTTTAATGATT--TGA
* *
150599 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGT
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTAGT
150664 AAT
64 AAT
150667 AATAATTTAT
Statistics
Matches: 433, Mismatches: 34, Indels: 48
0.84 0.07 0.09
Matches are distributed among these distances:
98 55 0.13
99 8 0.02
100 5 0.01
101 6 0.01
102 3 0.01
103 7 0.02
104 16 0.04
105 20 0.05
106 19 0.04
107 9 0.02
108 19 0.04
109 266 0.61
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (108 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTAGTAA
TGATTAGTAATAATAAAATTATTATTAATTTTTAATGATTTGA
Found at i:150295 original size:158 final size:158
Alignment explanation
Indices: 150067--150715 Score: 1210
Period size: 158 Copynumber: 4.1 Consensus size: 158
150057 AGTAATGATT
150067 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
*
150132 ATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATAATTAGTAATAATG
66 ATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATG
150197 AAATTATTATTAATTTTTAATGATTTGA
131 AAATTATTATTAATTTTTAATGATTTGA
* *
150225 TAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
*
150290 ATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATA
66 ATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATG
150355 AAATTATTATTAATTTTTAATGATTTGA
131 AAATTATTATTAATTTTTAATGATTTGA
150383 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
*
150448 ATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGGTAGTAATGATTAGTAATAATG
66 ATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATG
150513 AAATTATTATTAATTTTTAATGATTTGA
131 AAATTATTATTAATTTTTAATGATTTGA
150541 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
150606 ATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAAT-
66 ATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATG
* *
150670 AATTTATTATTAATATTTAATGATTTGA
131 AAATTATTATTAATTTTTAATGATTTGA
*
150698 TATTAATGATTTAGTAAT
1 TAGTAATGA-TTAGTAAT
150716 GATTTGATAG
Statistics
Matches: 478, Mismatches: 12, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
157 34 0.07
158 444 0.93
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (158 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
ATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATG
AAATTATTATTAATTTTTAATGATTTGA
Found at i:150693 original size:48 final size:49
Alignment explanation
Indices: 150601--150715 Score: 187
Period size: 48 Copynumber: 2.3 Consensus size: 49
150591 ATTAATGATT
*
150601 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
*
150650 TAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
*
150698 TATTAATGATTTAGTAAT
1 TAGTAATGA-TTAGTAAT
150716 GATTTGATAG
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
48 34 0.55
49 28 0.45
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (49 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
Found at i:150703 original size:14 final size:14
Alignment explanation
Indices: 150687--150734 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
150677 TATTAATATT
*
150687 TAATGATTTGATAT
1 TAATGATTTGATAG
150701 TAATGA-TT--TAG
1 TAATGATTTGATAG
150712 TAATGATTTGATAG
1 TAATGATTTGATAG
150726 TAATGATTT
1 TAATGATTT
150735 ATGACTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 8 0.27
12 2 0.07
13 2 0.07
14 18 0.60
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:150731 original size:109 final size:108
Alignment explanation
Indices: 150383--150719 Score: 484
Period size: 109 Copynumber: 3.1 Consensus size: 108
150373 AATGATTTGA
* *
150383 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA-TTAGTA
* * * * * * * * *
150448 ATGATTAGTAATAATGAA-A-TT-ATTA-TTAATTTTTAATGATTT
65 ATAATAAATTATTATTAATATTTAATGATTTGA-TATTAATGA-TT
150490 GGTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGT
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGT
150555 AATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATT
64 AATAAT-AAATTATTATTAATATTTAATGATTTGATATTAATGATT
150601 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAA
*
150666 TAATAATTTATTATTAATATTTAATGATTTGATATTAATGATT
66 TAATAAATTATTATTAATATTTAATGATTTGATATTAATGATT
150709 TAGTAATGATT
1 TAGTAATGATT
150720 TGATAGTAAT
Statistics
Matches: 211, Mismatches: 12, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
108 59 0.28
109 133 0.63
110 1 0.00
111 4 0.02
112 11 0.05
113 3 0.01
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (108 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAA
TAATAAATTATTATTAATATTTAATGATTTGATATTAATGATT
Found at i:153320 original size:22 final size:21
Alignment explanation
Indices: 153282--153322 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
153272 TTTATGTATA
*
153282 ATATAACTTAAACTAACAATC
1 ATATAACCTAAACTAACAATC
*
153303 ATATAACCCTAAATTAACAA
1 ATATAA-CCTAAACTAACAA
153323 ACTAATTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.54, C:0.20, G:0.00, T:0.27
Consensus pattern (21 bp):
ATATAACCTAAACTAACAATC
Found at i:153505 original size:26 final size:26
Alignment explanation
Indices: 153465--153522 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
153455 CCCTTTCTTT
*
153465 CTTTC-TCGGCTGCAATTTCTTCGCC
1 CTTTCTTCGGCTGCAATCTCTTCGCC
* *
153490 CTTTCTTCTGCTGCAATCTCTTCTCC
1 CTTTCTTCGGCTGCAATCTCTTCGCC
153516 CTTTCTT
1 CTTTCTT
153523 TCTTTTATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 5 0.17
26 24 0.83
ACGTcount: A:0.07, C:0.36, G:0.10, T:0.47
Consensus pattern (26 bp):
CTTTCTTCGGCTGCAATCTCTTCGCC
Found at i:153855 original size:29 final size:29
Alignment explanation
Indices: 153772--153860 Score: 115
Period size: 29 Copynumber: 3.1 Consensus size: 29
153762 CGTGAAGCTT
* * ***
153772 GGTCGCCGGGATTGCTTGGCGACCTACAA
1 GGTCGCTGGGAGTGCTTGGCGACCTTGTA
*
153801 GGTCGCTGGGAGTGCATGGCGACCTTGTA
1 GGTCGCTGGGAGTGCTTGGCGACCTTGTA
*
153830 GGTCGTTGGGAGTGCTTGGCGACCTTGTA
1 GGTCGCTGGGAGTGCTTGGCGACCTTGTA
153859 GG
1 GG
153861 GGTGTTGGGG
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.13, C:0.21, G:0.40, T:0.25
Consensus pattern (29 bp):
GGTCGCTGGGAGTGCTTGGCGACCTTGTA
Found at i:153884 original size:31 final size:29
Alignment explanation
Indices: 153800--153885 Score: 84
Period size: 29 Copynumber: 2.9 Consensus size: 29
153790 GCGACCTACA
* * *
153800 AGGTCGCTGGGAGTGCATGGCGACCTTGT
1 AGGTCGTTGGGAATACATGGCGACCTTGT
* * *
153829 AGGTCGTTGGGAGTGCTTGGCGACCTTGT
1 AGGTCGTTGGGAATACATGGCGACCTTGT
153858 AGGGGT-GTTGGGGAATACATGGCGACCT
1 A--GGTCGTT-GGGAATACATGGCGACCT
153886 GTTGGGGACG
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
29 28 0.57
30 3 0.06
31 18 0.37
ACGTcount: A:0.15, C:0.17, G:0.42, T:0.26
Consensus pattern (29 bp):
AGGTCGTTGGGAATACATGGCGACCTTGT
Found at i:153891 original size:22 final size:23
Alignment explanation
Indices: 153863--153917 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
153853 CTTGTAGGGG
153863 TGTTGGGGA-ATACATGGCGACC
1 TGTTGGGGACATACATGGCGACC
* *
153885 TGTTGGGGACGTGCATGGCGACC
1 TGTTGGGGACATACATGGCGACC
153908 TGTTGGGGAC
1 TGTTGGGGAC
153918 GTGCATGTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 9 0.30
23 21 0.70
ACGTcount: A:0.16, C:0.18, G:0.42, T:0.24
Consensus pattern (23 bp):
TGTTGGGGACATACATGGCGACC
Found at i:153905 original size:23 final size:23
Alignment explanation
Indices: 153875--153924 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
153865 TTGGGGAATA
153875 CATGGCGACCTGTTGGGGACGTG
1 CATGGCGACCTGTTGGGGACGTG
153898 CATGGCGACCTGTTGGGGACGTG
1 CATGGCGACCTGTTGGGGACGTG
153921 CATG
1 CATG
153925 TGCCATGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.14, C:0.22, G:0.42, T:0.22
Consensus pattern (23 bp):
CATGGCGACCTGTTGGGGACGTG
Found at i:154110 original size:2 final size:2
Alignment explanation
Indices: 154099--154151 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
154089 GAGTTTAGCC
154099 TA TA -A 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
154140 TA TA TA TA TA TA
1 TA TA TA TA TA TA
154152 ATCACCAATC
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:154195 original size:15 final size:16
Alignment explanation
Indices: 154168--154202 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
154158 AATCTAATAA
154168 AATAATAAAAATAAAT
1 AATAATAAAAATAAAT
154184 AATAAT-AAAATAAAT
1 AATAATAAAAATAAAT
154199 AATA
1 AATA
154203 GAATAGTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AATAATAAAAATAAAT
Found at i:154567 original size:2 final size:2
Alignment explanation
Indices: 154560--154591 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
154550 TCATGTAGAT
154560 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
154592 ATCACCAATC
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):
TA
Found at i:154635 original size:29 final size:30
Alignment explanation
Indices: 154603--154667 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
154593 TCACCAATCT
*
154603 AATAAAATTA-TAAAAATAAAT-AATAATAA
1 AATAAAATAACTAAAAA-AAATAAATAATAA
*
154632 AAT-AAATAACTAAACAAAATAAATAATAA
1 AATAAAATAACTAAAAAAAATAAATAATAA
154661 AATAAAA
1 AATAAAA
154668 CTGAAATCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 9 0.29
29 19 0.61
30 3 0.10
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (30 bp):
AATAAAATAACTAAAAAAAATAAATAATAA
Found at i:155447 original size:26 final size:26
Alignment explanation
Indices: 155399--155450 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
155389 AGGAGGAAGA
*
155399 GGAGGAGGAAGGGGCAAGTAGAAGGC
1 GGAGGAGGAAGGGGCAAGCAGAAGGC
* *
155425 GGAGGAGGAAGGGGGAGGCAGAAGGC
1 GGAGGAGGAAGGGGCAAGCAGAAGGC
155451 CAGATTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.33, C:0.08, G:0.58, T:0.02
Consensus pattern (26 bp):
GGAGGAGGAAGGGGCAAGCAGAAGGC
Found at i:161241 original size:31 final size:32
Alignment explanation
Indices: 161198--161262 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
161188 AATTGTTGAC
161198 GTGACATATGCCAC-AT-TACAAAAGTAATGAT
1 GTGACATATGCCACAATATAC-AAAGTAATGAT
*
161229 GTGACATGTGCCACAATATACAAAGTAATGAT
1 GTGACATATGCCACAATATACAAAGTAATGAT
161261 GT
1 GT
161263 AATATATGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
31 13 0.42
32 15 0.48
33 3 0.10
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.26
Consensus pattern (32 bp):
GTGACATATGCCACAATATACAAAGTAATGAT
Found at i:161259 original size:32 final size:31
Alignment explanation
Indices: 161198--161276 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 31
161188 AATTGTTGAC
161198 GTGACATATGCCACATTACAAAAGTAATGAT
1 GTGACATATGCCACATTACAAAAGTAATGAT
*
161229 GTGACATGTGCCACAATATAC-AAAGTAATGAT
1 GTGACATATGCCAC-AT-TACAAAAGTAATGAT
* * *
161261 GTAATATATGTCACAT
1 GTGACATATGCCACAT
161277 CATCTAAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 15 0.37
32 23 0.56
33 3 0.07
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (31 bp):
GTGACATATGCCACATTACAAAAGTAATGAT
Found at i:161356 original size:35 final size:32
Alignment explanation
Indices: 161273--161359 Score: 147
Period size: 32 Copynumber: 2.7 Consensus size: 32
161263 AATATATGTC
* * *
161273 ACATCATCTAAAATGATTATGTGTAATGCGTT
1 ACATCATCCAATATGATGATGTGTAATGCGTT
161305 ACATCATCCAATATGATGATGTGTAATGCGTT
1 ACATCATCCAATATGATGATGTGTAATGCGTT
161337 ACATCATCCAATATGATGATGTG
1 ACATCATCCAATATGATGATGTG
161360 CATATGTTAC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Consensus pattern (32 bp):
ACATCATCCAATATGATGATGTGTAATGCGTT
Found at i:164144 original size:20 final size:20
Alignment explanation
Indices: 164119--164161 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
164109 TCTAAGAGCT
164119 CATTTAGGACCATATAGATG
1 CATTTAGGACCATATAGATG
* *
164139 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
164159 CAT
1 CAT
164162 GTGGTGGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.33
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:165181 original size:22 final size:22
Alignment explanation
Indices: 165156--165197 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
165146 CAATTCATTT
165156 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
165178 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
165198 ACAACACACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:167186 original size:21 final size:21
Alignment explanation
Indices: 167146--167187 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
167136 TCAGTGAACA
* *
167146 TTACCAAGGTACTTCATCCTC
1 TTACCAAGGTAATCCATCCTC
*
167167 TTACCAAGGTAATCCTTCCTC
1 TTACCAAGGTAATCCATCCTC
167188 ATCTTCTACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.33, G:0.10, T:0.33
Consensus pattern (21 bp):
TTACCAAGGTAATCCATCCTC
Found at i:169830 original size:22 final size:22
Alignment explanation
Indices: 169805--169846 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
169795 CAATTCATTT
169805 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
169827 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
169847 CCAACACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:171402 original size:23 final size:23
Alignment explanation
Indices: 171356--171402 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
171346 CACAATTTAA
* * *
171356 TTTGCCATGACATTTTCATCTGC
1 TTTGCCACGACATATCCATCTGC
*
171379 TTTGCCACGACATATCCATTTGC
1 TTTGCCACGACATATCCATCTGC
171402 T
1 T
171403 ACCATACCAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.19, C:0.28, G:0.13, T:0.40
Consensus pattern (23 bp):
TTTGCCACGACATATCCATCTGC
Found at i:177478 original size:12 final size:13
Alignment explanation
Indices: 177451--177481 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
177441 TTCTTATTTG
177451 CTTTACTTTTTCA
1 CTTTACTTTTTCA
177464 CTTTACTTTTT-A
1 CTTTACTTTTTCA
177476 CTTTAC
1 CTTTAC
177482 CTTCTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.61
Consensus pattern (13 bp):
CTTTACTTTTTCA
Found at i:184951 original size:45 final size:45
Alignment explanation
Indices: 184895--184999 Score: 185
Period size: 45 Copynumber: 2.3 Consensus size: 45
184885 ATCCGTATAC
184895 TTAATTTCTATAGAAGCCACTTTGA-CTCAATACCCGAATACTTGA
1 TTAATTTCTATAGAAGCCACTTT-ATCTCAATACCCGAATACTTGA
*
184940 TTAATTTCTATAGAAGCCACTTTATCTCGATACCCGAATACTTGA
1 TTAATTTCTATAGAAGCCACTTTATCTCAATACCCGAATACTTGA
184985 TTAATTTCTATAGAA
1 TTAATTTCTATAGAA
185000 ACCTAAGAGA
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
44 1 0.02
45 57 0.98
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.36
Consensus pattern (45 bp):
TTAATTTCTATAGAAGCCACTTTATCTCAATACCCGAATACTTGA
Found at i:188302 original size:18 final size:17
Alignment explanation
Indices: 188248--188296 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
188238 TTGGACCCTT
* *
188248 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
188266 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
188284 AGTGCATTCGATG
1 AGTGCA-TCGATG
188297 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Done.