Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr6
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: 44797108
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 921406 characters in sequence are not A, C, G, or T
File 92 of 144
Found at i:28067187 original size:38 final size:36
Alignment explanation
Indices: 28067124--28067206 Score: 130
Period size: 38 Copynumber: 2.2 Consensus size: 36
28067114 ATTACAAAAT
28067124 CATATCTTCTAAGATTACATATCATATCTAAGATTG
1 CATATCTTCTAAGATTACATATCATATCTAAGATTG
* *
28067160 CATATCATATCTAGGATTGCATATCATATCTAAGATTG
1 CATATC-T-TCTAAGATTACATATCATATCTAAGATTG
28067198 CATATCTTC
1 CATATCTTC
28067207 AAAAATTATG
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
36 8 0.19
37 2 0.05
38 33 0.77
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.39
Consensus pattern (36 bp):
CATATCTTCTAAGATTACATATCATATCTAAGATTG
Found at i:28067568 original size:44 final size:44
Alignment explanation
Indices: 28067520--28067733 Score: 107
Period size: 44 Copynumber: 4.9 Consensus size: 44
28067510 CTGTAACCAG
*
28067520 AGGGAGGTAAAATCAACCATCTTCGATCTACTCCACTACTGCTT
1 AGGGAGGTAAAATCAACCATCTTCAATCTACTCCACTACTGCTT
* * * ** *
28067564 AGGGAGATAAGATCTGAA--ATCTTCAATCTATTCCACTGTTGCCT
1 AGGGAGGTAAAATC--AACCATCTTCAATCTACTCCACTACTGCTT
* * * * *** * * **
28067608 AGGAAAGTAGAAT-TACTGGCTTCAATGTACTCCACTA-TAAACAC
1 AGGGAGGTAAAATCAACCATCTTCAATCTACTCCACTACT--GCTT
** * *
28067652 AGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTT
1 AGGGAGGTAAAATCAACCATCTTCAATCTACTCCACTACTGCTT
* * *
28067696 AGGGAGATAAGATCTGAA--ATCTTCAATCTATTCCACTA
1 AGGGAGGTAAAATC--AACCATCTTCAATCTACTCCACTA
28067734 TTGTCCAGGG
Statistics
Matches: 118, Mismatches: 42, Indels: 20
0.66 0.23 0.11
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 15 0.13
44 82 0.69
45 16 0.14
46 3 0.03
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.28
Consensus pattern (44 bp):
AGGGAGGTAAAATCAACCATCTTCAATCTACTCCACTACTGCTT
Found at i:28067672 original size:132 final size:132
Alignment explanation
Indices: 28067432--28068879 Score: 2264
Period size: 132 Copynumber: 11.0 Consensus size: 132
28067422 CTGCAACTGC
* * * ** * * * **
28067432 AGGGAGATAAGA-CTTACAATCTTTAACCTATTCCACTACTGACTAGG-GAGATAGGATTACTAA
1 AGGGAGATAAGATCTGA-AATCTTCAATCTATTCCACTGTTGCCTAGGAAAG-TAGAATTACTGG
* * * ** *
28067495 CTTCAATGTATTCCACTGTAACCAGAGGGAGGTAAAATCAACCATCTTCGATCTACTCCACTACT
64 CTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACT
28067560 GCTT
129 GCTT
28067564 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCTAGGAAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCTAGGAAAGTAGAATTACTGGCT
*
28067629 TCAATGTACTCCACTATAAACACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
66 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
28067694 TT
131 TT
* *
28067696 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTATTGTCC-AGGGAAGTAGAATTACTGGC
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTG-CCTAGGAAAGTAGAATTACTGGC
* * * *
28067760 TTCAATGTACTCCACTATAACCATAGGGAGGTAAAATTCGCCATCTCCGATATGCTCCACTACTG
65 TTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTG
28067825 CTT
130 CTT
*
28067828 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCTAGGAAAGAAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCTAGGAAAGTAGAATTACTGGCT
* * *
28067893 TCAATGTCCTCCACTATAACCACAGGGAGATAAAATCCGCCATCTTCGAGCTGCTCCACTACTGC
66 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
28067958 TT
131 TT
*
28067960 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCTAGGAAAGAAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCTAGGAAAGTAGAATTACTGGCT
* * *
28068025 TCAATGTCCTCCACTATAACCACAGGGAGATAAAATCCGCCATCTTCGAGCTGCTCCACTACTGC
66 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
28068090 TT
131 TT
*
28068092 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAAGGAAA-TAGAATTACTGGC
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTG-CCTAGGAAAGTAGAATTACTGGC
* * *
28068156 TTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCGTCATCTTCGATCTGCTCCACTACTG
65 TTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTG
28068221 CTT
130 CTT
* * * *
28068224 AGGGAGATAAGATCTGAAAATCTTCAATTTATTCCACTGTTGTGC-AGGGAAGTAGAATCACTGG
1 AGGGAGATAAGATCTG-AAATCTTCAATCTATTCCACTGTTG-CCTAGGAAAGTAGAATTACTGG
* *
28068288 CTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATTCGTCATCTTCGATCTGCTCCACTACT
64 CTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACT
28068353 GCTT
129 GCTT
* *
28068357 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTACCTAAGG-AAGTAAAATTACTGGC
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCT-AGGAAAGTAGAATTACTGGC
**
28068421 TTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTATACTACTG
65 TTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTG
28068486 CTT
130 CTT
* * *
28068489 AGGGAGATAAGATCTGAAAATCTTCAATTTATTCCACTGTTGTCC-AGGGAAGTAGAATCACTGG
1 AGGGAGATAAGATCTG-AAATCTTCAATCTATTCCACTGTTG-CCTAGGAAAGTAGAATTACTGG
*
28068553 CTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATTCGCCATCTTCGATCTGCTCCACTACT
64 CTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACT
28068618 GCTT
129 GCTT
* *
28068622 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCATTGTTGTCC-AGGGAAGTAGAATTACTGGC
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTG-CCTAGGAAAGTAGAATTACTGGC
28068686 TTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTG
65 TTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTG
28068751 CTT
130 CTT
* *
28068754 AAGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGAAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCTAGGAAAGTAGAATTACTGGCT
*
28068819 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATTCGCCATCTTCGATCTGCTCCACTA
66 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTA
28068880 TCAATGCAGG
Statistics
Matches: 1232, Mismatches: 71, Indels: 26
0.93 0.05 0.02
Matches are distributed among these distances:
131 5 0.00
132 968 0.79
133 257 0.21
134 2 0.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.28
Consensus pattern (132 bp):
AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCTAGGAAAGTAGAATTACTGGCT
TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
TT
Found at i:28067863 original size:44 final size:44
Alignment explanation
Indices: 28067814--28068128 Score: 119
Period size: 44 Copynumber: 7.2 Consensus size: 44
28067804 CTCCGATATG
28067814 CTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTA
* ** * * * * * *
28067858 TTCCACTGTTGCCTA-GGAAAGAAGAATTACTG---GCTTCAATGTC
1 CTCCACTACTGCTTAGGGAGATAAG-A-T-CTGAAATCTTCAATCTA
* ** * * ** * * *
28067901 CTCCACTA-TAACCACAGGGAGATAAAATCCGCCATCTTCGAGCTG
1 CTCCACTACT--GCTTAGGGAGATAAGATCTGAAATCTTCAATCTA
28067946 CTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTA
* ** * * * * * *
28067990 TTCCACTGTTGCCTA-GGAAAGAAGAATTACTG---GCTTCAATGTC
1 CTCCACTACTGCTTAGGGAGATAAG-A-T-CTGAAATCTTCAATCTA
* ** * * ** * * *
28068033 CTCCACTA-TAACCACAGGGAGATAAAATCCGCCATCTTCGAGCTG
1 CTCCACTACT--GCTTAGGGAGATAAGATCTGAAATCTTCAATCTA
28068078 CTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTA
*
28068122 TTCCACT
1 CTCCACT
28068129 GTTGTCCAAG
Statistics
Matches: 184, Mismatches: 67, Indels: 40
0.63 0.23 0.14
Matches are distributed among these distances:
42 6 0.03
43 44 0.24
44 84 0.46
45 42 0.23
46 8 0.04
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.27
Consensus pattern (44 bp):
CTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTA
Found at i:28068909 original size:45 final size:45
Alignment explanation
Indices: 28068860--28068991 Score: 110
Period size: 45 Copynumber: 3.0 Consensus size: 45
28068850 AAAATTCGCC
28068860 ATCTTCGATCTGCTCCACTATCAATGCAGGAAGGCAAGATCTACT
1 ATCTTCGATCTGCTCCACTATCAATGCAGGAAGGCAAGATCTACT
** * * * *
28068905 ATCTTTAACCTGCTCCACTA-CAA-ACGAGGAAGGCAAG-GCT-TT
1 ATCTTCGATCTGCTCCACTATCAATGC-AGGAAGGCAAGATCTACT
* * * * * * *
28068947 GTTTTCGATCTGCTTCGCTGTCGATGCAGGAAGACAAGATCTACT
1 ATCTTCGATCTGCTCCACTATCAATGCAGGAAGGCAAGATCTACT
28068992 CTTTCACTGA
Statistics
Matches: 63, Mismatches: 19, Indels: 10
0.68 0.21 0.11
Matches are distributed among these distances:
42 13 0.21
43 15 0.24
44 17 0.27
45 18 0.29
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (45 bp):
ATCTTCGATCTGCTCCACTATCAATGCAGGAAGGCAAGATCTACT
Found at i:28070236 original size:11 final size:11
Alignment explanation
Indices: 28070222--28070260 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
28070212 CAATTTTTCC
28070222 TTTTTTTTGTT
1 TTTTTTTTGTT
28070233 TTTTTTTTGTT
1 TTTTTTTTGTT
*
28070244 TTTTGTTTGTT
1 TTTTTTTTGTT
28070255 TTTTTT
1 TTTTTT
28070261 AATCTGAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (11 bp):
TTTTTTTTGTT
Found at i:28070245 original size:18 final size:19
Alignment explanation
Indices: 28070224--28070259 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
28070214 ATTTTTCCTT
28070224 TTTTTTGTTT-TTTTTTTG
1 TTTTTTGTTTGTTTTTTTG
28070242 TTTTTTGTTTGTTTTTTT
1 TTTTTTGTTTGTTTTTTT
28070260 TAATCTGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (19 bp):
TTTTTTGTTTGTTTTTTTG
Found at i:28074429 original size:98 final size:98
Alignment explanation
Indices: 28074257--28074450 Score: 325
Period size: 98 Copynumber: 2.0 Consensus size: 98
28074247 ACAATAAAAA
* *
28074257 TTTAAAAGAACATCCACTTATCCAATATTTAAGAAATCACACCCAATACGTTAGGGCACGATTCC
1 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
* *
28074322 TCTAGAATCCCAAACTCGGAATATTTTCTTTTC
66 TCTAAAATCCCAAACTCGGAATATTTCCTTTTC
* *
28074355 TTTAAAAGAACATCCACTTATTCAAGATTTAAGAAATCACACCCAATACGTTATGGCACAATTCC
1 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
*
28074420 TTTAAAATCCCAAACTCGGAATATTTCCTTT
66 TCTAAAATCCCAAACTCGGAATATTTCCTTT
28074451 ATTATTTAAA
Statistics
Matches: 89, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 89 1.00
ACGTcount: A:0.36, C:0.24, G:0.09, T:0.31
Consensus pattern (98 bp):
TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
TCTAAAATCCCAAACTCGGAATATTTCCTTTTC
Found at i:28074739 original size:9 final size:9
Alignment explanation
Indices: 28074725--28074749 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
28074715 TGCAAATGCT
28074725 ATAATAACA
1 ATAATAACA
28074734 ATAATAACA
1 ATAATAACA
28074743 ATAATAA
1 ATAATAA
28074750 ATACATCATC
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:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (9 bp):
ATAATAACA
Found at i:28075040 original size:34 final size:33
Alignment explanation
Indices: 28074984--28075049 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
28074974 AACACATAAT
*
28074984 ATACATATGAAAATAAAGAAAAAAATAATTATAC
1 ATACATATGAAAATAAAG-AAAAAATAAGTATAC
* *
28075018 ATACATATATAAAAT-AATAAAAAATAAGTATA
1 ATACATAT-GAAAATAAAGAAAAAATAAGTATA
28075050 TTTTAGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 13 0.46
34 10 0.36
35 5 0.18
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.26
Consensus pattern (33 bp):
ATACATATGAAAATAAAGAAAAAATAAGTATAC
Found at i:28075790 original size:23 final size:22
Alignment explanation
Indices: 28075747--28075804 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
28075737 AAAAGGTATC
* *
28075747 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
28075768 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
28075791 TACATATCATATCT
1 TACAAATCATATCT
28075805 AAGATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:28075807 original size:19 final size:19
Alignment explanation
Indices: 28075760--28075838 Score: 77
Period size: 21 Copynumber: 3.8 Consensus size: 19
28075750 AAATTAAATC
*
28075760 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
28075780 TCTTCTAAGATTACATATCATA
1 ---TCTAAGATTACATATCATA
*
28075802 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
*
28075823 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
28075839 CTCAAAAATT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
19 14 0.28
21 18 0.36
22 7 0.14
23 11 0.22
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:28075820 original size:21 final size:21
Alignment explanation
Indices: 28075794--28075837 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
28075784 CTAAGATTAC
28075794 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
28075815 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
28075836 AT
1 AT
28075838 CCTCAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.39
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:28078550 original size:16 final size:16
Alignment explanation
Indices: 28078498--28078550 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
28078488 TTTTGGGAAA
*
28078498 AAAATAAAAATAAATT
1 AAAATAAAAATAAAAT
* *
28078514 AAAATAAAAATTTAAAC
1 AAAATAAAAA-TAAAAT
28078531 AAAAT-AAAATCAAAAT
1 AAAATAAAAAT-AAAAT
28078547 AAAA
1 AAAA
28078551 CCTACCCCCC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 1 0.03
16 21 0.70
17 8 0.27
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAATAAAAATAAAAT
Found at i:28081938 original size:101 final size:100
Alignment explanation
Indices: 28081826--28082051 Score: 278
Period size: 101 Copynumber: 2.2 Consensus size: 100
28081816 TGTGTGGCAC
* * * *
28081826 GTACTGTGTGTAGGCCACTATGTAAAAGTGAAAGTGAT-GGTCACGTGTGTAGTACTATGTGTAG
1 GTACTATGTGTAGGCTACTATGTAAAA--GAAAGT-ATCGATCACGTGTGTAGTACTATGTGCAG
*
28081890 GCTACTACATGTACCGGAATGAT-A-GGTCGCATGTGTA
63 GCTACTACATGTACCGG-ATGATAATGGTCACATGTGTA
** * *
28081927 GTACTATGTGTAGGCTACTATTTGTACCAGATAGTTTCGATCACGTGTGTAGTACTATGTGCAGG
1 GTACTATGTGTAGGCTACTA--TGTAAAAGAAAGTATCGATCACGTGTGTAGTACTATGTGCAGG
*
28081992 CTACTACATGTATCGGATGATAATGGTCACATGTGTA
64 CTACTACATGTACCGGATGATAATGGTCACATGTGTA
*
28082029 GTACTATGTGCAGGCTACTATGT
1 GTACTATGTGTAGGCTACTATGT
28082052 GAACCGAATA
Statistics
Matches: 109, Mismatches: 11, Indels: 11
0.83 0.08 0.08
Matches are distributed among these distances:
100 9 0.08
101 64 0.59
102 31 0.28
103 5 0.05
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (100 bp):
GTACTATGTGTAGGCTACTATGTAAAAGAAAGTATCGATCACGTGTGTAGTACTATGTGCAGGCT
ACTACATGTACCGGATGATAATGGTCACATGTGTA
Found at i:28081996 original size:51 final size:51
Alignment explanation
Indices: 28081862--28082048 Score: 211
Period size: 51 Copynumber: 3.7 Consensus size: 51
28081852 AGTGAAAGTG
* * *
28081862 ATGGTCACGTGTGTAGTACTATGTGTAGGCTACTACATGTACCGGA-A-TG
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACATGTACCGGATAGTA
* * ** *
28081911 ATAGGTCGCATGTGTAGTACTATGTGTAGGCTACTATTTGTACCAGATAGT-
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACATGTACCGGATAGTA
* * * *
28081962 TTCGATCACGTGTGTAGTACTATGTGCAGGCTACTACATGTATCGGAT-GATA
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACATGTACCGGATAG-TA
28082014 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
28082049 TGTGAACCGA
Statistics
Matches: 115, Mismatches: 18, Indels: 8
0.82 0.13 0.06
Matches are distributed among these distances:
49 2 0.02
50 40 0.35
51 71 0.62
52 2 0.02
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (51 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACATGTACCGGATAGTA
Found at i:28082110 original size:45 final size:45
Alignment explanation
Indices: 28082054--28082144 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
28082044 TACTATGTGA
* * *
28082054 ACCGAATATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
*
28082099 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGTTGAATCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
28082144 A
1 A
28082145 TCGAGTATCT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.34
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
Found at i:28087137 original size:36 final size:36
Alignment explanation
Indices: 28087090--28087188 Score: 135
Period size: 37 Copynumber: 2.7 Consensus size: 36
28087080 TGGTTTTTCG
*
28087090 CATTGGTCTGCAGATAATTCCCTTTGTAAATTCATC
1 CATTGGCCTGCAGATAATTCCCTTTGTAAATTCATC
**
28087126 CATTGGCCTGCAGATAATTACAATTTGTAAATTCATC
1 CATTGGCCTGCAGATAATT-CCCTTTGTAAATTCATC
* * *
28087163 TATTGGCTTGTAGATAATTCCCTTTG
1 CATTGGCCTGCAGATAATTCCCTTTG
28087189 ATGGTTCTCA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
36 23 0.43
37 31 0.57
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.39
Consensus pattern (36 bp):
CATTGGCCTGCAGATAATTCCCTTTGTAAATTCATC
Found at i:28091558 original size:48 final size:48
Alignment explanation
Indices: 28091490--28091683 Score: 244
Period size: 48 Copynumber: 4.0 Consensus size: 48
28091480 AATAGATTTC
* * * * * *
28091490 TCGGTGGCCTGCACACAGTCCGTACCACCTTTGTGTAATAACAGATTC
1 TCGGTGGCCTGCACATAGTCCGTGCCACCCTTGTATCATAACAGATTA
* * *
28091538 TCGGTGGCCTACACATAGTCCGTGCCACCCTTGTATCTTAACAGGTTA
1 TCGGTGGCCTGCACATAGTCCGTGCCACCCTTGTATCATAACAGATTA
* * *
28091586 TTGGTGGCCTGCACATAGTCTGTGCCACCCTTGTATCATAACAGAATA
1 TCGGTGGCCTGCACATAGTCCGTGCCACCCTTGTATCATAACAGATTA
* * * *
28091634 TCGATGGCCTGCACAAAGTCCGTGCCACCCTTGTGTCATAACAGAATA
1 TCGGTGGCCTGCACATAGTCCGTGCCACCCTTGTATCATAACAGATTA
28091682 TC
1 TC
28091684 AGTGTGCATA
Statistics
Matches: 126, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 126 1.00
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (48 bp):
TCGGTGGCCTGCACATAGTCCGTGCCACCCTTGTATCATAACAGATTA
Found at i:28093112 original size:21 final size:19
Alignment explanation
Indices: 28093086--28093138 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 19
28093076 TTGGAGCAGG
*
28093086 AATATCGATACTTTTAGGAA
1 AATATCGATACTTTCA-GAA
*
28093106 ATATATCGATACCTTCAGAA
1 A-ATATCGATACTTTCAGAA
28093126 AAGTATCGATACT
1 AA-TATCGATACT
28093139 GGATCGATAC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 1 0.04
20 14 0.50
21 13 0.46
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (19 bp):
AATATCGATACTTTCAGAA
Found at i:28098673 original size:15 final size:15
Alignment explanation
Indices: 28098648--28098682 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
28098638 GGATTGATGG
28098648 ATTAT-AGTTAGTAC
1 ATTATGAGTTAGTAC
28098662 ATTATGAGTTAGTAC
1 ATTATGAGTTAGTAC
28098677 ATTATG
1 ATTATG
28098683 TGTGAGCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (15 bp):
ATTATGAGTTAGTAC
Found at i:28104755 original size:49 final size:50
Alignment explanation
Indices: 28104687--28104788 Score: 134
Period size: 50 Copynumber: 2.1 Consensus size: 50
28104677 TCTTATAGAC
* ** *
28104687 AACATATGGAAAGAATT-AAACATTTTATATACTTTTCAAAAAGAATTAT
1 AACATATGGAAAGAATTAAAAAACGTTATATACTTTCCAAAAAGAATTAT
* * *
28104736 AACATATGGAAAGTATTAAAAAACGTTATATTCTTTCCAAAATGAATTAT
1 AACATATGGAAAGAATTAAAAAACGTTATATACTTTCCAAAAAGAATTAT
28104786 AAC
1 AAC
28104789 TACCATTTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
49 16 0.36
50 29 0.64
ACGTcount: A:0.48, C:0.10, G:0.09, T:0.33
Consensus pattern (50 bp):
AACATATGGAAAGAATTAAAAAACGTTATATACTTTCCAAAAAGAATTAT
Found at i:28111715 original size:49 final size:49
Alignment explanation
Indices: 28111655--28111756 Score: 134
Period size: 51 Copynumber: 2.1 Consensus size: 49
28111645 TCTTATAGAG
*
28111655 AACATAAGGAAAGAATT-AAACACGTTATATCCTTTCTAAAAAGAATTAT
1 AACATAAGGAAAGAATTAAAACACGTTATATCCTTTCCAAAAA-AATTAT
* * * *
28111704 AACATATGGAAAGTATTAAAAACATGTTATATTCTTTCCAAAAAAATTAT
1 AACATAAGGAAAGAATT-AAAACACGTTATATCCTTTCCAAAAAAATTAT
28111754 AAC
1 AAC
28111757 TACCATGTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
49 15 0.33
50 9 0.20
51 22 0.48
ACGTcount: A:0.49, C:0.12, G:0.09, T:0.30
Consensus pattern (49 bp):
AACATAAGGAAAGAATTAAAACACGTTATATCCTTTCCAAAAAAATTAT
Found at i:28117731 original size:24 final size:24
Alignment explanation
Indices: 28117695--28117755 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
28117685 GATGAGATAG
*
28117695 CGACC-TTTCATTGCTATCATTTT
1 CGACCTTTTCATTGATATCATTTT
*
28117718 CGACCTTTTCATTGATATCCTTTT
1 CGACCTTTTCATTGATATCATTTT
28117742 -GAACCTTTTCATTG
1 CG-ACCTTTTCATTG
28117756 TTTTAGGGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
23 6 0.18
24 28 0.82
ACGTcount: A:0.18, C:0.25, G:0.10, T:0.48
Consensus pattern (24 bp):
CGACCTTTTCATTGATATCATTTT
Found at i:28127305 original size:24 final size:24
Alignment explanation
Indices: 28127244--28127321 Score: 68
Period size: 25 Copynumber: 3.2 Consensus size: 24
28127234 GTACATGTAT
* * * *
28127244 GCTCATACGAGCTATGAATCGATAT
1 GCTCATACGAGCTGT-AAACGGTAA
* *
28127269 GCTCTTACTAGCTGTAAACGGTAA
1 GCTCATACGAGCTGTAAACGGTAA
28127293 GCTCATACGAGCTG-AATATCGGTAA
1 GCTCATACGAGCTGTAA-A-CGGTAA
28127318 GCTC
1 GCTC
28127322 TCTCGAGCTG
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
23 2 0.05
24 19 0.44
25 22 0.51
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
GCTCATACGAGCTGTAAACGGTAA
Found at i:28131124 original size:22 final size:22
Alignment explanation
Indices: 28131094--28131137 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
28131084 AAAATAAATC
* *
28131094 AAAATTAATCAAAATTTAATAT
1 AAAAGTAATCAAAATTCAATAT
*
28131116 AAAAGTAATTAAAATTCAATAT
1 AAAAGTAATCAAAATTCAATAT
28131138 GTTAATAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (22 bp):
AAAAGTAATCAAAATTCAATAT
Found at i:28132668 original size:21 final size:22
Alignment explanation
Indices: 28132644--28132687 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
28132634 ACAAACTATG
28132644 CTTATCAATACAT-TGCAT-AAT
1 CTTA-CAATACATATGCATCAAT
*
28132665 CTTAGAATACATATGCATCAAT
1 CTTACAATACATATGCATCAAT
28132687 C
1 C
28132688 CAACATGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 7 0.35
21 9 0.45
22 4 0.20
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (22 bp):
CTTACAATACATATGCATCAAT
Found at i:28132918 original size:31 final size:31
Alignment explanation
Indices: 28132846--28132918 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 31
28132836 GTTGTCCCAA
* * * *
28132846 CCCTTTTTCATAGCTCGATAGCCAAAGCTAT
1 CCCTTTTTCATTGCCCAATAGCCAAAACTAT
28132877 CCC-TTTTCATTGCCCAATAGCCAAAACTAT
1 CCCTTTTTCATTGCCCAATAGCCAAAACTAT
28132907 CCCTTTTTCATT
1 CCCTTTTTCATT
28132919 ATTTGATGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 26 0.70
31 11 0.30
ACGTcount: A:0.25, C:0.32, G:0.08, T:0.36
Consensus pattern (31 bp):
CCCTTTTTCATTGCCCAATAGCCAAAACTAT
Found at i:28132974 original size:30 final size:30
Alignment explanation
Indices: 28132940--28133006 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
28132930 GTCACCATCA
* **
28132940 CTTTTCATAATTTGATAGCTGAAGCTATCC
1 CTTTTCATAATTTGACAGCCAAAGCTATCC
28132970 CTTTTCATAATTTGACAGCCAAAGCTATCC
1 CTTTTCATAATTTGACAGCCAAAGCTATCC
28133000 CTTTTCA
1 CTTTTCA
28133007 CTCTCTGATG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.27, C:0.24, G:0.10, T:0.39
Consensus pattern (30 bp):
CTTTTCATAATTTGACAGCCAAAGCTATCC
Found at i:28133051 original size:29 final size:30
Alignment explanation
Indices: 28132996--28133065 Score: 108
Period size: 29 Copynumber: 2.4 Consensus size: 30
28132986 AGCCAAAGCT
28132996 ATCCCTTTTCACTCTCTGATGCTCGTCACC
1 ATCCCTTTTCACTCTCTGATGCTCGTCACC
*
28133026 ATCCCTTTTC-CTCAT-TGATGGTCGTCACC
1 ATCCCTTTTCACTC-TCTGATGCTCGTCACC
28133055 ATCCCTTTTCA
1 ATCCCTTTTCA
28133066 TAATTCGATA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
29 26 0.70
30 11 0.30
ACGTcount: A:0.14, C:0.37, G:0.10, T:0.39
Consensus pattern (30 bp):
ATCCCTTTTCACTCTCTGATGCTCGTCACC
Found at i:28140033 original size:25 final size:25
Alignment explanation
Indices: 28139973--28140049 Score: 86
Period size: 25 Copynumber: 3.1 Consensus size: 25
28139963 TCAGGATTGA
28139973 TCATGTGAG-CATATAAATAGGAAGC
1 TCATGTGAGCCATAT-AATAGGAAGC
* * *
28139998 TC-TTTCAAGCCATATAATGGGAAGC
1 TCATGT-GAGCCATATAATAGGAAGC
*
28140023 TCATGTGAGCCATGTAATAGGAAGC
1 TCATGTGAGCCATATAATAGGAAGC
28140048 TC
1 TC
28140050 CGAAGAGACA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
24 2 0.05
25 33 0.79
26 7 0.17
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (25 bp):
TCATGTGAGCCATATAATAGGAAGC
Found at i:28140170 original size:27 final size:25
Alignment explanation
Indices: 28140134--28140184 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 25
28140124 AGAGAGCCAA
*
28140134 TTAATTGGGAAGCTCATGAAAGAGCCT
1 TTAATCGGGAAGCTC-TG-AAGAGCCT
28140161 TTAATCGGGAAGCTCTGAAGAGCC
1 TTAATCGGGAAGCTCTGAAGAGCC
28140185 ATATATCGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.30
26 2 0.09
27 14 0.61
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (25 bp):
TTAATCGGGAAGCTCTGAAGAGCCT
Found at i:28140192 original size:25 final size:25
Alignment explanation
Indices: 28140042--28140195 Score: 86
Period size: 25 Copynumber: 6.1 Consensus size: 25
28140032 CCATGTAATA
* * *
28140042 GGAAGCTCCGAAGAGACATTAAT-G
1 GGAAGCTCTGAAGAGCCAATAATCG
* *
28140066 GGAAGCTCTTACGAGCCAAT-ATCG
1 GGAAGCTCTGAAGAGCCAATAATCG
* * * *
28140090 GTAAGGT-TCAAGTGAGCCAAT-ATAG
1 GGAAGCTCTGAA--GAGCCAATAATCG
* *
28140115 GGAAGCCCT-AGAGAGCCAATTAATTG
1 GGAAGCTCTGA-AGAGCCAA-TAATCG
**
28140141 GGAAGCTCATGAAAGAGCCTTTAATCG
1 GGAAGCTC-TG-AAGAGCCAATAATCG
28140168 GGAAGCTCTGAAGAGCC-ATATATCG
1 GGAAGCTCTGAAGAGCCAATA-ATCG
28140193 GGA
1 GGA
28140196 CACTTATAAG
Statistics
Matches: 100, Mismatches: 19, Indels: 21
0.71 0.14 0.15
Matches are distributed among these distances:
23 4 0.04
24 30 0.30
25 31 0.31
26 14 0.14
27 14 0.14
28 6 0.06
29 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (25 bp):
GGAAGCTCTGAAGAGCCAATAATCG
Found at i:28142871 original size:21 final size:21
Alignment explanation
Indices: 28142846--28142920 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 21
28142836 GTTGTGGAGA
28142846 AGGAAGTTGCTACTGCAGAAG
1 AGGAAGTTGCTACTGCAGAAG
* *
28142867 AGGAAGTTGATGCTGCAGAAG
1 AGGAAGTTGCTACTGCAGAAG
* * * **
28142888 AGGTAGTTGGTGCTAAAGAAG
1 AGGAAGTTGCTACTGCAGAAG
*
28142909 AAGAAGTTGCTA
1 AGGAAGTTGCTA
28142921 AAAATGAAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.35, C:0.09, G:0.35, T:0.21
Consensus pattern (21 bp):
AGGAAGTTGCTACTGCAGAAG
Found at i:28149877 original size:23 final size:23
Alignment explanation
Indices: 28149851--28149936 Score: 72
Period size: 23 Copynumber: 3.8 Consensus size: 23
28149841 GTTGCCAAAG
28149851 AAAAGGGAATGATGAGTTGAAAT
1 AAAAGGGAATGATGAGTTGAAAT
* *
28149874 AAAAGGGAATGATTG-GTTACCAAAA
1 AAAAGGGAATGA-TGAGTT--GAAAT
* *
28149899 AAAATGAAAT-ATGA--TGAAAT
1 AAAAGGGAATGATGAGTTGAAAT
*
28149919 AAAAGGGAATAATGAGTT
1 AAAAGGGAATGATGAGTT
28149937 AAAAGATGTA
Statistics
Matches: 48, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
20 11 0.23
21 4 0.08
22 1 0.02
23 18 0.38
24 3 0.06
25 11 0.23
ACGTcount: A:0.51, C:0.02, G:0.24, T:0.22
Consensus pattern (23 bp):
AAAAGGGAATGATGAGTTGAAAT
Found at i:28154671 original size:33 final size:33
Alignment explanation
Indices: 28154634--28154699 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
28154624 AAAAAAGAAA
28154634 TAAAAATTTTAATGGGTTTAATGGTGGAATAGT
1 TAAAAATTTTAATGGGTTTAATGGTGGAATAGT
28154667 TAAAAATTTTAATGGGTTTAATGGTGGAATAGT
1 TAAAAATTTTAATGGGTTTAATGGTGGAATAGT
28154700 GGATTAAACG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.39
Consensus pattern (33 bp):
TAAAAATTTTAATGGGTTTAATGGTGGAATAGT
Found at i:28160310 original size:23 final size:23
Alignment explanation
Indices: 28160267--28160310 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
28160257 GAATAAAAAT
* *
28160267 AATTATATAATATATTTATTAAG
1 AATTATATAATAAATTAATTAAG
28160290 AATTCATATAA-AAATTAATTA
1 AATT-ATATAATAAATTAATTA
28160311 TTACTTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
AATTATATAATAAATTAATTAAG
Found at i:28180926 original size:40 final size:40
Alignment explanation
Indices: 28180889--28181113 Score: 253
Period size: 40 Copynumber: 5.7 Consensus size: 40
28180879 GCTACTCGTT
* *
28180889 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
28180929 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
28180969 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
28181009 TC-AATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGAA
1 -CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* ** * * * *
28181048 CAAATGCCTT-TGGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
28181089 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
28181114 CATCATTCGA
Statistics
Matches: 161, Mismatches: 17, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
38 3 0.02
39 29 0.18
40 116 0.72
41 13 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:28181073 original size:119 final size:120
Alignment explanation
Indices: 28180891--28181113 Score: 283
Period size: 119 Copynumber: 1.9 Consensus size: 120
28180881 TACTCGTTCA
* *
28180891 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGAACAAATGCCTTCGGGACTTAACCCGGAT
* *
28180956 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCATC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCATC
* * * **
28181011 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGAACAAATGCCTT-TGGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGAACAAATGCCTTCGGGA-CTTAACCCGG
* * *
28181073 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
28181114 CATCATTCGA
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
118 4 0.05
119 64 0.73
120 20 0.23
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGAACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCATC
Found at i:28182307 original size:56 final size:56
Alignment explanation
Indices: 28182240--28182415 Score: 343
Period size: 56 Copynumber: 3.1 Consensus size: 56
28182230 TATTAGTTTA
*
28182240 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
28182296 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
28182352 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
28182408 TTGCCCAT
1 TTGCCCAT
28182416 CATCCCTTGT
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 119 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:28184854 original size:40 final size:40
Alignment explanation
Indices: 28184806--28185153 Score: 624
Period size: 40 Copynumber: 8.7 Consensus size: 40
28184796 GCGAACACAT
* * *
28184806 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
28184846 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
28184886 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
28184926 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
28184966 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* **
28185006 TTGCCTTCGGGTCGTAGTTCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
28185046 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
28185086 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
28185126 TTGCCTTCGGGTCTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
28185154 TCCAATGCTC
Statistics
Matches: 295, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 295 1.00
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:28192315 original size:39 final size:39
Alignment explanation
Indices: 28192233--28192456 Score: 267
Period size: 39 Copynumber: 5.7 Consensus size: 39
28192223 GCTACTCGTT
* * *
28192233 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAT-TAGTAACTCGCA
* *
28192273 CAAACGCCTTCGGGACTTAACCCGGATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTAGTAACTCGCA
* *
28192312 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGA-TTAGTAACTCGCA
*
28192352 TC-AATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 -CAAATGCCTTCGGGACTTAGCCCGG-ATTAGTAACTCGCA
* *
28192391 CAAATGCCTTCGGG-CTTAGCCTGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-ATTAGTAACTCGCA
*
28192430 CAAATGCCTTC-GGATCTTAGTCCGGAT
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT
28192457 ATTGTCACTT
Statistics
Matches: 165, Mismatches: 13, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
38 3 0.02
39 105 0.64
40 56 0.34
41 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTAGTAACTCGCA
Found at i:28192449 original size:79 final size:79
Alignment explanation
Indices: 28192233--28192455 Score: 274
Period size: 79 Copynumber: 2.8 Consensus size: 79
28192223 GCTACTCGTT
* * * *
28192233 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTTGCACAAACGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACAAATGCCTTC-GGACTTAGCCCG
28192297 G-ATTAGTAACTCGCA
64 GAATTAGTAACTCGCA
* * *
28192312 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGTATC-AATGCCTTCGGGCTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA-CAAATGCCTTCGGACTTAGCCCGG
*
28192376 AATTAGTATCTCGCA
65 AATTAGTAACTCGCA
* * * *
28192391 CAAATGCCTTCGGG-CTTAGCCTGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGA-CTTAGCCCGG
28192455 A
65 A
28192456 TATTGTCACT
Statistics
Matches: 124, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
77 1 0.01
78 42 0.34
79 78 0.63
80 3 0.02
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGACTTAGCCCGGA
ATTAGTAACTCGCA
Found at i:28192456 original size:118 final size:119
Alignment explanation
Indices: 28192210--28192442 Score: 307
Period size: 118 Copynumber: 2.0 Consensus size: 119
28192200 CCTTCAGAAT
* * *
28192210 TTAA-CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTTGCA
1 TTAACCCGGATTTAG-TAACTCGTTCAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCA
28192273 CAAACGCCTTCGGGACTTAACCCGGATTAGTAACTCGCACAAATGCCTTCGGGAC
65 CAAACGCCTTCGGGACTTAACCCGGATTAGTAACTCGCACAAATGCCTTCGGGAC
* *
28192328 TTAACCCGGATTTAGTAACTCGTATC-AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGC
1 TTAACCCGGATTTAGTAACTCGT-TCAAATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGC
* * * *
28192390 ACAAATGCCTTCGGG-CTTAGCCTGGAATTAGTATCTCGCACAAATGCCTTCGG
64 ACAAACGCCTTCGGGACTTAACCCGG-ATTAGTAACTCGCACAAATGCCTTCGG
28192443 ATCTTAGTCC
Statistics
Matches: 101, Mismatches: 9, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
117 9 0.09
118 63 0.62
119 27 0.27
120 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (119 bp):
TTAACCCGGATTTAGTAACTCGTTCAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCAC
AAACGCCTTCGGGACTTAACCCGGATTAGTAACTCGCACAAATGCCTTCGGGAC
Found at i:28192510 original size:62 final size:62
Alignment explanation
Indices: 28192408--28192532 Score: 214
Period size: 62 Copynumber: 2.0 Consensus size: 62
28192398 CTTCGGGCTT
* * *
28192408 AGCCTGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGC
1 AGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGAATATGGTCACTTAGC
*
28192470 AGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGAATATGGTCATTTAGC
1 AGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGAATATGGTCACTTAGC
28192532 A
1 A
28192533 CAAAGCCTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.30
Consensus pattern (62 bp):
AGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGAATATGGTCACTTAGC
Found at i:28193749 original size:56 final size:56
Alignment explanation
Indices: 28193682--28193857 Score: 334
Period size: 56 Copynumber: 3.1 Consensus size: 56
28193672 TATTAGTTTA
*
28193682 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
*
28193738 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAAAATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
28193794 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
28193850 TTGCCCAT
1 TTGCCCAT
28193858 CATCCCTTGT
Statistics
Matches: 117, Mismatches: 3, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
56 117 1.00
ACGTcount: A:0.23, C:0.22, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:28196663 original size:50 final size:50
Alignment explanation
Indices: 28196565--28196670 Score: 149
Period size: 50 Copynumber: 2.1 Consensus size: 50
28196555 TATTGCGGTT
* * **
28196565 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCGTTGGTACCGAG
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATAGACACCGAG
* * *
28196615 ATGAGAGGTCCCCCGTAAGACTATGTCTGGGACATGGCATAGACACCGAT
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATAGACACCGAG
28196665 ATGAGA
1 ATGAGA
28196671 ACTTTCATGT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.27, C:0.22, G:0.31, T:0.20
Consensus pattern (50 bp):
ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATAGACACCGAG
Found at i:28207928 original size:39 final size:40
Alignment explanation
Indices: 28207833--28208094 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
28207823 TTGAATGATG
*
28207833 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
28207871 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
28207912 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
28207951 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
28207990 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
28208029 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
28208068 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
28208095 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:28221999 original size:16 final size:17
Alignment explanation
Indices: 28221978--28222009 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
28221968 TAATAATAAT
28221978 ACTTACCTTA-TATTTC
1 ACTTACCTTATTATTTC
28221994 ACTTACCTTATTATTT
1 ACTTACCTTATTATTT
28222010 GCTTACCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.25, C:0.22, G:0.00, T:0.53
Consensus pattern (17 bp):
ACTTACCTTATTATTTC
Found at i:28222649 original size:18 final size:18
Alignment explanation
Indices: 28222628--28222662 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28222618 TAGTTTTTTC
*
28222628 TTTCTCTCTTTTTTTCTT
1 TTTCTCTCTTTCTTTCTT
*
28222646 TTTCTTTCTTTCTTTCT
1 TTTCTCTCTTTCTTTCT
28222663 CCCCTGTTTC
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:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTCTCTCTTTCTTTCTT
Found at i:28222736 original size:19 final size:19
Alignment explanation
Indices: 28222708--28222744 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
28222698 CTGTTTCTTT
28222708 CTTTCGTTTATTTCATTTG
1 CTTTCGTTTATTTCATTTG
*
28222727 CTTTCTTTTATTTCATTT
1 CTTTCGTTTATTTCATTT
28222745 TATTTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.11, C:0.16, G:0.05, T:0.68
Consensus pattern (19 bp):
CTTTCGTTTATTTCATTTG
Found at i:28222755 original size:19 final size:19
Alignment explanation
Indices: 28222709--28222749 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
28222699 TGTTTCTTTC
* *
28222709 TTTCGTTTATTTCATTTGC
1 TTTCTTTTATTTCATTTGA
*
28222728 TTTCTTTTATTTCATTTTA
1 TTTCTTTTATTTCATTTGA
28222747 TTT
1 TTT
28222750 TATTTACTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.12, C:0.12, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTCTTTTATTTCATTTGA
Found at i:28228000 original size:196 final size:196
Alignment explanation
Indices: 28227666--28228252 Score: 985
Period size: 196 Copynumber: 3.0 Consensus size: 196
28227656 GGTGTTACAG
* * * *
28227666 TTAGCTTGTGTAAGCAGACTCATTTCATAGCTCAAGTGAGCAATGATGTAAAGGAAAAGGAAATG
1 TTAGCTTGTGTAAGCAGACTCATTTCACAGCTCGAGTGAGCAACGTTGTAAAGGAAAAGGAAATG
* * * * * *
28227731 TTACAACTATATGTTTAGCACACTTCGTGTGATCTTTCCCGCGTATCTGATGTTATTCTAAATGG
66 TTACGACTGTATGTTTAGCAGACTTCGTGTGAGCTTTCCCGCGTATCCGATGTCATTCTAAATGG
* * *
28227796 TTCAACGGGTATGAAAAAGAAATGAACGGTAAGTGTTCAAATAACTTATGTTGTGAATTTGTGAT
131 TTCAACGGGCATGAAAAGGAAATGAACGGTAAGTGTTCAAATAACTTATGTTGTGAATTTGTGAA
28227861 T
196 T
* *
28227862 TTAGCTTGTGTTAGCAGACTCATTTCGCAGCTCGAGTGAGCAACGTTGTAAAGGAAAAGGAAATG
1 TTAGCTTGTGTAAGCAGACTCATTTCACAGCTCGAGTGAGCAACGTTGTAAAGGAAAAGGAAATG
28227927 TTACGACTGTATGTTTAGCAGACTTCGTGTGAGCTTTCCCGCGTATCCGATGTCATTCTAAATGG
66 TTACGACTGTATGTTTAGCAGACTTCGTGTGAGCTTTCCCGCGTATCCGATGTCATTCTAAATGG
* *
28227992 TTCAACGGGCATGAAAAGGAAATCAACGGTAAGTGTTCAAATAACTTATGATGTGAATTTGTGAA
131 TTCAACGGGCATGAAAAGGAAATGAACGGTAAGTGTTCAAATAACTTATGTTGTGAATTTGTGAA
28228057 T
196 T
* *
28228058 TTAGCTTGGGTGAGCAGACTCATTTCACAGCTCGAGTGAGCAACGTTGTAAAGGAAAAGGAAATG
1 TTAGCTTGTGTAAGCAGACTCATTTCACAGCTCGAGTGAGCAACGTTGTAAAGGAAAAGGAAATG
28228123 TTACGACTGTATGTTTAGCAGACTTCGTGTGAGCTTTCCCGCGTATCCGATGTCATTCTAAATGG
66 TTACGACTGTATGTTTAGCAGACTTCGTGTGAGCTTTCCCGCGTATCCGATGTCATTCTAAATGG
* *
28228188 TTCAACGGGCATGAAAAGGAAATGAACGGTAAGTGTTTAAATAACTTATGTTGTGAATTTATGAA
131 TTCAACGGGCATGAAAAGGAAATGAACGGTAAGTGTTCAAATAACTTATGTTGTGAATTTGTGAA
28228253 AAGGAAGTTT
Statistics
Matches: 367, Mismatches: 24, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
196 367 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.31
Consensus pattern (196 bp):
TTAGCTTGTGTAAGCAGACTCATTTCACAGCTCGAGTGAGCAACGTTGTAAAGGAAAAGGAAATG
TTACGACTGTATGTTTAGCAGACTTCGTGTGAGCTTTCCCGCGTATCCGATGTCATTCTAAATGG
TTCAACGGGCATGAAAAGGAAATGAACGGTAAGTGTTCAAATAACTTATGTTGTGAATTTGTGAA
T
Found at i:28246385 original size:21 final size:21
Alignment explanation
Indices: 28246346--28246385 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
28246336 GGTAGAAACT
*
28246346 TTTCTGAAAATTCTGACATGG
1 TTTCTGAAAACTCTGACATGG
28246367 TTTCTGAAAAACTCT-ACAT
1 TTTCTG-AAAACTCTGACAT
28246386 CAACATCATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (21 bp):
TTTCTGAAAACTCTGACATGG
Found at i:28251440 original size:61 final size:61
Alignment explanation
Indices: 28251265--28251625 Score: 334
Period size: 61 Copynumber: 5.9 Consensus size: 61
28251255 TGATCCAACA
* * * * * *
28251265 AGTACTAGATATAAAGGATAACCTTTGTGGTACAGCTCTGGACAAGAAAGCCTTTGCGGTG
1 AGTACTAGATATAAAGGACAGCCTTTGTGGCACAACTCTAGACAAGAAAGCCTTTGTGGTG
* * * * * * *
28251326 AGTATTGGATATAAAGGA-AGCATTTGTGGCACAAATCTAGATAGGAAAGCCTTTGTGGCG
1 AGTACTAGATATAAAGGACAGCCTTTGTGGCACAACTCTAGACAAGAAAGCCTTTGTGGTG
* * * * * * *
28251386 AGTACTAGATATAAATGATAGCCCTTT-TGGCACAACTTTTGACAGGAAAACCTTTATGGTG
1 AGTACTAGATATAAAGGACAG-CCTTTGTGGCACAACTCTAGACAAGAAAGCCTTTGTGGTG
* * * *
28251447 AGTACT-GAATGTAAAGGACAGCCTTTGTGGGACAACTCTAGACAAGAAAGACTTTATGGTG
1 AGTACTAG-ATATAAAGGACAGCCTTTGTGGCACAACTCTAGACAAGAAAGCCTTTGTGGTG
* * * * * *
28251508 AGTACT-GAATGTAAAGGACAGTCTTTATGGCACAACTCTAGACATGAAAGCCTTTGTAGCG
1 AGTACTAG-ATATAAAGGACAGCCTTTGTGGCACAACTCTAGACAAGAAAGCCTTTGTGGTG
* * ** * * *
28251569 AGTACTAAATGTAAAGGACAATCTTTGTGGCAAAAATCAAGACAAGAAAGCCTTTGT
1 AGTACTAGATATAAAGGACAGCCTTTGTGGCACAACTCTAGACAAGAAAGCCTTTGT
28251626 TGTAACCTCT
Statistics
Matches: 248, Mismatches: 47, Indels: 10
0.81 0.15 0.03
Matches are distributed among these distances:
60 53 0.21
61 191 0.77
62 4 0.02
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (61 bp):
AGTACTAGATATAAAGGACAGCCTTTGTGGCACAACTCTAGACAAGAAAGCCTTTGTGGTG
Found at i:28256282 original size:38 final size:38
Alignment explanation
Indices: 28256218--28256292 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
28256208 AATCCGAGTT
*
28256218 TAAAGACCCGCTGACTATATGAAGAGATTATGTCCGGG
1 TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
* *
28256256 TAAAGACCCGATGGCTATGT-ACAGAGATTATGTCCGG
1 TAAAGACCCGATGACTATATGA-AGAGATTATGTCCGG
28256293 ATTAAAATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.24
Consensus pattern (38 bp):
TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
Found at i:28256405 original size:40 final size:40
Alignment explanation
Indices: 28256350--28256547 Score: 281
Period size: 40 Copynumber: 5.0 Consensus size: 40
28256340 CTCGACAATG
28256350 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
*
28256390 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
* *
28256430 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
* * * * *
28256470 ATCCGTGCTAA-ACCTCGAAGAGCATTCGTGCTGGTGTTAT
1 ATCCGGGCTAAGTCC-CGAAGAGCATTCATGCTAGTGATAT
* * *
28256510 ATCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGAT
28256548 GTGTATTCGG
Statistics
Matches: 141, Mismatches: 15, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
39 1 0.01
40 138 0.98
41 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
Found at i:28260036 original size:33 final size:33
Alignment explanation
Indices: 28259972--28260038 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
28259962 AATGGCCAAT
** * **
28259972 GTGATGAATGTGAACATGTGTATGTTTGATAAG
1 GTGATGAATGTGAACATGCATATATGAGATAAG
28260005 GTGATGAATGTGAACATGCATATATGAGATAAG
1 GTGATGAATGTGAACATGCATATATGAGATAAG
28260038 G
1 G
28260039 CCGAATGGCC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.31
Consensus pattern (33 bp):
GTGATGAATGTGAACATGCATATATGAGATAAG
Found at i:28260062 original size:47 final size:47
Alignment explanation
Indices: 28260005--28260131 Score: 157
Period size: 47 Copynumber: 2.7 Consensus size: 47
28259995 GTTTGATAAG
*
28260005 GTGATGAATGTGAACA-TGCATATATGAGATAAGGCCGAATGGCCAAT
1 GTGATAAATGTGAA-AGTGCATATATGAGATAAGGCCGAATGGCCAAT
* *
28260052 GTGATAAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAAT
1 GTGATAAATGTGAAAGTGCATATATGAGATAAGGCCGAATGGCCAAT
** * * * *
28260099 GTGATGGATGTGGAAGTGTATAAATGTGATAAG
1 GTGATAAATGTGAAAGTGCATATATGAGATAAG
28260132 ACCCGAAGGG
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
46 1 0.01
47 71 0.99
ACGTcount: A:0.35, C:0.08, G:0.30, T:0.27
Consensus pattern (47 bp):
GTGATAAATGTGAAAGTGCATATATGAGATAAGGCCGAATGGCCAAT
Found at i:28263902 original size:21 final size:21
Alignment explanation
Indices: 28263864--28263903 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
28263854 AAGAACAAGG
**
28263864 AAAATAAAAATATTTTAAAAT
1 AAAATAAAAATAAATTAAAAT
*
28263885 AAAATAAAACTAAATTAAA
1 AAAATAAAAATAAATTAAA
28263904 TCCTAAACTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAATAAAAATAAATTAAAAT
Found at i:28268636 original size:18 final size:17
Alignment explanation
Indices: 28268609--28268642 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
28268599 GCATTTTTGA
28268609 TAAATCATTGAAAATTT
1 TAAATCATTGAAAATTT
28268626 TAAATTCATTGAAAATT
1 TAAA-TCATTGAAAATT
28268643 AATAATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (17 bp):
TAAATCATTGAAAATTT
Found at i:28268805 original size:10 final size:10
Alignment explanation
Indices: 28268792--28268816 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
28268782 TTTCATTTTA
28268792 ATATTATCTT
1 ATATTATCTT
28268802 ATATTATCTT
1 ATATTATCTT
28268812 ATATT
1 ATATT
28268817 CAAATTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (10 bp):
ATATTATCTT
Found at i:28269302 original size:19 final size:19
Alignment explanation
Indices: 28269271--28269310 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
28269261 AAAAAGTAGC
28269271 TTATCATAATTTAAATAAA
1 TTATCATAATTTAAATAAA
*
28269290 TTAT-ATAAGTTTAAATCAA
1 TTATCATAA-TTTAAATAAA
28269309 TT
1 TT
28269311 TTTATGACTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (19 bp):
TTATCATAATTTAAATAAA
Found at i:28282986 original size:18 final size:18
Alignment explanation
Indices: 28282963--28282998 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
28282953 GAAAAGTATA
28282963 AAAATTTTGGAAAATAAG
1 AAAATTTTGGAAAATAAG
28282981 AAAATTTTGGAAAATAAG
1 AAAATTTTGGAAAATAAG
28282999 GTCACACGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.17, T:0.28
Consensus pattern (18 bp):
AAAATTTTGGAAAATAAG
Found at i:28289072 original size:44 final size:43
Alignment explanation
Indices: 28288891--28289392 Score: 238
Period size: 44 Copynumber: 11.7 Consensus size: 43
28288881 CTTTGGTCTA
* ** * * *
28288891 CTCCACTGTAACCTCAGGGAGATAAGA-C-CTAATGCGATCTA
1 CTCCACTGTAACTTCAGGGAGATAAGATCTCTGCTTCAATCTG
* * ** * * ** * *
28288932 CTCTATTGTAACTTCAAAGAGATAAAATCTTTTATTTTAATCCG
1 CTCCACTGTAACTTCAGGGAGATAAGATC-TCTGCTTCAATCTG
* * *
28288976 CTCCATTGTAACTTCAGGGAGAT-AGGT-TAGTGTCTTCAATCTG
1 CTCCACTGTAACTTCAGGGAGATAAGATCT-CTG-CTTCAATCTG
** *
28289019 CTCTGCTGTAATTTCAGGGAGATAAGATCTCTGGCTTCAATCTG
1 CTCCACTGTAACTTCAGGGAGATAAGATCTCT-GCTTCAATCTG
* * * * *
28289063 CTCCACTGTAACATCAGGGAGATAAGATCTGAAATTCTTCGATCTA
1 CTCCACTGTAACTTCAGGGAGATAAGATCT---CTGCTTCAATCTG
* * * * *
28289109 CTCCACTGTAACCTCAGGGAGATAAGA-C-CTGATGCGATCTA
1 CTCCACTGTAACTTCAGGGAGATAAGATCTCTGCTTCAATCTG
* * * ** * *
28289150 CTCTACTGTAACTTCAGAGAGATAAGATCTTTTATTTTAATCTA
1 CTCCACTGTAACTTCAGGGAGATAAGATC-TCTGCTTCAATCTG
* * **
28289194 CTCCACTATAACTTCAGGGAGATAGGAT-AGTGCTTCAATCTG
1 CTCCACTGTAACTTCAGGGAGATAAGATCTCTGCTTCAATCTG
* * * * * *
28289236 CTCCGCTGTAA-TCTCAGGGAGATAAGA-GT-TGATGCGATCTA
1 CTCCACTGTAACT-TCAGGGAGATAAGATCTCTGCTTCAATCTG
* * * * ** * *
28289277 CTCTACTGTAACTTCAGAGAGATACGATCTTTTATTTTAATCCG
1 CTCCACTGTAACTTCAGGGAGATAAGATC-TCTGCTTCAATCTG
* *
28289321 CTCTACTGTAA-TCTCAAGGAGATAAGAT-TACTAGCTTCAATCTG
1 CTCCACTGTAACT-TCAGGGAGATAAGATCT-CT-GCTTCAATCTG
**
28289365 CTCTGCTGTAA-TCTCAGGGAGATAAGAT
1 CTCCACTGTAACT-TCAGGGAGATAAGAT
28289393 TCACCATTTC
Statistics
Matches: 347, Mismatches: 91, Indels: 43
0.72 0.19 0.09
Matches are distributed among these distances:
41 85 0.24
42 35 0.10
43 31 0.09
44 158 0.46
45 3 0.01
46 34 0.10
47 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.32
Consensus pattern (43 bp):
CTCCACTGTAACTTCAGGGAGATAAGATCTCTGCTTCAATCTG
Found at i:28289098 original size:218 final size:217
Alignment explanation
Indices: 28288708--28289262 Score: 702
Period size: 218 Copynumber: 2.5 Consensus size: 217
28288698 AGTCTGATGA
* * * * * ** * * * *
28288708 GATCTGCTCTACTGCAACTTCAGAGGGATAAGATCCATCATTTTGATCCGCTCCACTACAACTTC
1 GATCTACTCTACTGTAACTTCAAAGAGATAAAATCTTTTATTTTAATCCACTCCACTATAACTTC
* * ** * * * **
28288773 AGGGAAATAAGATTTTTGGCTTCTATCTGCTCCGCTGTAATCTCAGGGAAATAAGAT-TGGTATC
66 AGGGAGATAGGA-TAGT-GCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT-CTGGC
* * * * * * *
28288837 CTCGATCTGCTCCACTACT-GC-TTAGGGAGATAAGATCTGAAATTCTTTGGTCTACTCCACTGT
128 TTCAATCTGCTCCACT-GTAACATCAGGGAGATAAGATCTGAAATTCTTCGATCTACTCCACTGT
28288900 AACCTCAGGGAGATAAGACCTAATGC
192 AACCTCAGGGAGATAAGACCTAATGC
* * * *
28288926 GATCTACTCTATTGTAACTTCAAAGAGATAAAATCTTTTATTTTAATCCGCTCCATTGTAACTTC
1 GATCTACTCTACTGTAACTTCAAAGAGATAAAATCTTTTATTTTAATCCACTCCACTATAACTTC
* * *
28288991 AGGGAGATAGGTTAGTGTCTTCAATCTGCTCTGCTGTAATTTCAGGGAGATAAGATCTCTGGCTT
66 AGGGAGATAGGATAGTG-CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTT
28289056 CAATCTGCTCCACTGTAACATCAGGGAGATAAGATCTGAAATTCTTCGATCTACTCCACTGTAAC
130 CAATCTGCTCCACTGTAACATCAGGGAGATAAGATCTGAAATTCTTCGATCTACTCCACTGTAAC
*
28289121 CTCAGGGAGATAAGACCTGATGC
195 CTCAGGGAGATAAGACCTAATGC
* * *
28289144 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCTTTTATTTTAATCTACTCCACTATAACTTC
1 GATCTACTCTACTGTAACTTCAAAGAGATAAAATCTTTTATTTTAATCCACTCCACTATAACTTC
28289209 AGGGAGATAGGATAGTGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
66 AGGGAGATAGGATAGTGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
28289263 GTTGATGCGA
Statistics
Matches: 290, Mismatches: 43, Indels: 9
0.85 0.13 0.03
Matches are distributed among these distances:
216 2 0.01
217 88 0.30
218 200 0.69
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (217 bp):
GATCTACTCTACTGTAACTTCAAAGAGATAAAATCTTTTATTTTAATCCACTCCACTATAACTTC
AGGGAGATAGGATAGTGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTC
AATCTGCTCCACTGTAACATCAGGGAGATAAGATCTGAAATTCTTCGATCTACTCCACTGTAACC
TCAGGGAGATAAGACCTAATGC
Found at i:28289166 original size:131 final size:127
Alignment explanation
Indices: 28289014--28289391 Score: 362
Period size: 127 Copynumber: 2.9 Consensus size: 127
28289004 AGTGTCTTCA
* * * * * * *
28289014 ATCTGCTCTGCTGTAATTTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACATCA
1 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCTCTGACTTCAATCTACTCCACTATAACATCA
* *
28289079 GGGAGATAAGATCTGAAATTCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGC
66 GGGAGATAAGA--T--AATGCTTCAATCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGC
28289144 G
127 G
* * * * *
28289145 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCTTTTATTTTAATCTACTCCACTATAACTTCA
1 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCTCTGACTTCAATCTACTCCACTATAACATCA
* * * * * **
28289210 GGGAGATAGGATAGTGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGAGTTGATGCG
66 GGGAGATAAGATAATGCTTCAATCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCG
* * * * * ** * *
28289272 ATCTACTCTACTGTAACTTCAGAGAGATACGATCTTTTATTTTAATCCGCTCTACTGTAATC-TC
1 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCTCTGACTTCAATCTACTCCACTATAA-CATC
* * * ** *
28289336 AAGGAGATAAGATTACTAGCTTCAATCTGCTCTGCTGTAATCTCAGGGAGATAAGA
65 AGGGAGATAAGA-TAAT-GCTTCAATCTACTCCACTGTAACCTCAGGGAGATAAGA
28289392 TTCACCATTT
Statistics
Matches: 214, Mismatches: 30, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
127 109 0.51
128 4 0.02
129 38 0.18
131 63 0.29
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (127 bp):
ATCTACTCTACTGTAACTTCAGAGAGATAAGATCTCTGACTTCAATCTACTCCACTATAACATCA
GGGAGATAAGATAATGCTTCAATCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCG
Found at i:28289289 original size:127 final size:129
Alignment explanation
Indices: 28289099--28289391 Score: 421
Period size: 127 Copynumber: 2.3 Consensus size: 129
28289089 ATCTGAAATT
* * * *
28289099 CTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTT
1 CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTT
* * * *
28289164 CAGAGAGATAAGATCTTTTATTTTAATCTACTCCACTATAA-CTTCAGGGAGATAGGA-TAGT-G
66 CAGAGAGATAAGATCTTTTATTTTAATCCACTCCACTATAATC-TCAAGGAGATAAGATTACTAG
**
28289226 CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGAGTTGATGCGATCTACTCTACTGTAACTT
1 CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTT
* * * *
28289291 CAGAGAGATACGATCTTTTATTTTAATCCGCTCTACTGTAATCTCAAGGAGATAAGATTACTAG
66 CAGAGAGATAAGATCTTTTATTTTAATCCACTCCACTATAATCTCAAGGAGATAAGATTACTAG
*
28289355 CTTCAATCTGCTCTGCTGTAATCTCAGGGAGATAAGA
1 CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
28289392 TTCACCATTT
Statistics
Matches: 148, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
127 107 0.72
128 4 0.03
129 37 0.25
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (129 bp):
CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTT
CAGAGAGATAAGATCTTTTATTTTAATCCACTCCACTATAATCTCAAGGAGATAAGATTACTAG
Found at i:28289554 original size:132 final size:132
Alignment explanation
Indices: 28289380--28289879 Score: 735
Period size: 131 Copynumber: 3.8 Consensus size: 132
28289370 CTGTAATCTC
* * * * * *
28289380 AGGG-AGATAAGATTCACCAT-TTCCGAT-TAGCTCCACTATTGCTTAGGGGGATAAGATCTGTA
1 AGGGAAGATAAGATTCGCCGTCTT-CGATCT-GCTCCGCTACTGCTTAGGGAGACAAGATCTGTA
* *
28289442 ATTTCCAACCTACTCCACTGTTGACCAGGGACATAGGACTTGTGGCTTAAATCTGTTTCCATACT
64 ATTTCCAACCTACTCCACTGCTGACCAGGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTACT
28289507 CCTG
129 CCTG
*
28289511 AGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAAT
1 AGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAAT
* * *
28289576 TTCCAATCTACTCCACTGCTGACTAGGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCT
66 TTCCAACCTACTCCACTGCTGACCAGGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCC
28289641 TG
131 TG
* *
28289643 -GGGAAGATAAGATTCGCCGTCTTCGATTTGCTCCGCTACTGCTTAGGGAGACAAGATCTATAAT
1 AGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAAT
* * *
28289707 TTTCAACCTACTCCATTGCTGACCAGGGACATAGGAAAC-T-TGGCTTAAATTTGTTTCCCTACT
66 TTCCAACCTACTCCACTGCTGACCAGGGACATAGG--ACTTGTGGCTTAAATCTGTTTCCCTACT
28289770 CCT-
129 CCTG
* * *
28289773 AGGGAAGATAAGATTTGCCGTCTTCGATCTACTCCGCTACTGCTTAGGGAGACAAGATTTGTAAT
1 AGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAAT
28289838 TTCCAACCTACTCCACTGCTGACCAGGGACATAGGACTTGTG
66 TTCCAACCTACTCCACTGCTGACCAGGGACATAGGACTTGTG
28289880 ATTTCACCGA
Statistics
Matches: 335, Mismatches: 26, Indels: 16
0.89 0.07 0.04
Matches are distributed among these distances:
129 2 0.01
130 1 0.00
131 214 0.64
132 113 0.34
133 5 0.01
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.30
Consensus pattern (132 bp):
AGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAAT
TTCCAACCTACTCCACTGCTGACCAGGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCC
TG
Found at i:28292101 original size:6 final size:6
Alignment explanation
Indices: 28292077--28292125 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
28292067 TTTTTCTCTC
* **
28292077 ATTTTC ATTTTG ACCTTG ATTTTG ATTTTG ATTTTTG ATTTTTG ATTTT
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG A-TTTTG A-TTTTG ATTTT
28292126 TTGAGCTCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
6 24 0.65
7 13 0.35
ACGTcount: A:0.16, C:0.06, G:0.12, T:0.65
Consensus pattern (6 bp):
ATTTTG
Found at i:28292129 original size:8 final size:7
Alignment explanation
Indices: 28292092--28292126 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
28292082 CATTTTGACC
28292092 TTGA-TT
1 TTGATTT
28292098 TTGA-TT
1 TTGATTT
28292104 TTGATTT
1 TTGATTT
28292111 TTGATTT
1 TTGATTT
28292118 TTGATTT
1 TTGATTT
28292125 TT
1 TT
28292127 TGAGCTCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 10 0.36
7 18 0.64
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.71
Consensus pattern (7 bp):
TTGATTT
Found at i:28303227 original size:26 final size:25
Alignment explanation
Indices: 28303174--28303236 Score: 99
Period size: 26 Copynumber: 2.5 Consensus size: 25
28303164 ACATATTTTC
*
28303174 TCAAAATTTTACCAGGGTAAAATTA
1 TCAAAATTTTACCAGGGTAAAATCA
*
28303199 TCAAAATTTTATCGAGGGTAAAATCA
1 TCAAAATTTTA-CCAGGGTAAAATCA
28303225 TCAAAATTTTAC
1 TCAAAATTTTAC
28303237 TAAGGGCTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 12 0.34
26 23 0.66
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (25 bp):
TCAAAATTTTACCAGGGTAAAATCA
Found at i:28303248 original size:26 final size:26
Alignment explanation
Indices: 28303174--28303247 Score: 89
Period size: 26 Copynumber: 2.8 Consensus size: 26
28303164 ACATATTTTC
* *
28303174 TCAAAATTTTAC-CAGGGTAAAATTA
1 TCAAAATTTTACTAAGGGTAAAATCA
*
28303199 TCAAAATTTTA-TCGAGGGTAAAATCA
1 TCAAAATTTTACT-AAGGGTAAAATCA
28303225 TCAAAATTTTACTAAGGGCTAAA
1 TCAAAATTTTACTAAGGG-TAAA
28303248 TAGGGATTTG
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
25 11 0.26
26 26 0.62
27 5 0.12
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (26 bp):
TCAAAATTTTACTAAGGGTAAAATCA
Found at i:28304293 original size:105 final size:105
Alignment explanation
Indices: 28304086--28304285 Score: 303
Period size: 105 Copynumber: 1.9 Consensus size: 105
28304076 AACTAGAAAG
* * * *
28304086 ACAATCGATTTAAATAGAAAGACAATCAATTCAAAAGAAGCAATTTTCCAACCATTTCTACAAAT
1 ACAATCGATTCAAACAGAAAGACAATCAATTCAAAAGAAGCAACTTTCCAACCATTTCCACAAAT
28304151 ACATCAATAACAATAAGGAATCAATTCTAACAAAAAAAAA
66 ACATCAATAACAATAAGGAATCAATTCTAACAAAAAAAAA
** *
28304191 ACAATCGATTCAAACAGAAAGACAATTGATTCAAAGGAAGCAACTTTCCAA-CATTTTCCACAAA
1 ACAATCGATTCAAACAGAAAGACAATCAATTCAAAAGAAGCAACTTTCCAACCA-TTTCCACAAA
* *
28304255 TACATCAATAACAATAATGAATCGATTCTAA
65 TACATCAATAACAATAAGGAATCAATTCTAA
28304286 TAGAAAAACG
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
104 2 0.02
105 83 0.98
ACGTcount: A:0.50, C:0.18, G:0.08, T:0.23
Consensus pattern (105 bp):
ACAATCGATTCAAACAGAAAGACAATCAATTCAAAAGAAGCAACTTTCCAACCATTTCCACAAAT
ACATCAATAACAATAAGGAATCAATTCTAACAAAAAAAAA
Found at i:28308898 original size:12 final size:12
Alignment explanation
Indices: 28308881--28308905 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28308871 TTCATCATAT
28308881 TCAATTTATCAA
1 TCAATTTATCAA
28308893 TCAATTTATCAA
1 TCAATTTATCAA
28308905 T
1 T
28308906 TCTTTACGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (12 bp):
TCAATTTATCAA
Found at i:28314258 original size:15 final size:16
Alignment explanation
Indices: 28314232--28314262 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
28314222 TTAATATTTT
28314232 AATAATAAATTTTAAA
1 AATAATAAATTTTAAA
28314248 AATAA-AAATTTTAAA
1 AATAATAAATTTTAAA
28314263 TAAATATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AATAATAAATTTTAAA
Found at i:28314321 original size:15 final size:15
Alignment explanation
Indices: 28314301--28314357 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
28314291 ATTCAATATT
28314301 AATATTTTAATAATA
1 AATATTTTAATAATA
*
28314316 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
28314335 AATATATTAATAATA
1 AATATTTTAATAATA
*
28314350 AATGTTTT
1 AATATTTT
28314358 TAGTATAAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:28316102 original size:106 final size:106
Alignment explanation
Indices: 28315940--28316152 Score: 408
Period size: 106 Copynumber: 2.0 Consensus size: 106
28315930 TGGCAAGAAG
28315940 AAGGTTGAAGATGACTCCCACAATCAAAAGATTGTTAAAACAACTTCTAAAGAAAACTCAAGAGA
1 AAGGTTGAAGATGACTCCCACAATCAAAAGATTGTTAAAACAACTTCTAAAGAAAACTCAAGAGA
*
28316005 GAAATCTTGGAGAAAACTCAAAGAAAATTCTGCTCTCTCAA
66 AAAATCTTGGAGAAAACTCAAAGAAAATTCTGCTCTCTCAA
*
28316046 AAGGTTGAAGATGGCTCCCACAATCAAAAGATTGTTAAAACAACTTCTAAAGAAAACTCAAGAGA
1 AAGGTTGAAGATGACTCCCACAATCAAAAGATTGTTAAAACAACTTCTAAAGAAAACTCAAGAGA
28316111 AAAATCTTGGAGAAAACTCAAAGAAAATTCTGCTCTCTCAA
66 AAAATCTTGGAGAAAACTCAAAGAAAATTCTGCTCTCTCAA
28316152 A
1 A
28316153 TCTGAAATTT
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 105 1.00
ACGTcount: A:0.46, C:0.18, G:0.15, T:0.22
Consensus pattern (106 bp):
AAGGTTGAAGATGACTCCCACAATCAAAAGATTGTTAAAACAACTTCTAAAGAAAACTCAAGAGA
AAAATCTTGGAGAAAACTCAAAGAAAATTCTGCTCTCTCAA
Found at i:28322400 original size:21 final size:20
Alignment explanation
Indices: 28322361--28322401 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
28322351 CTCACATGCC
* *
28322361 AAAGTGAAAAATTGATTTTT
1 AAAGTGAAAAAGTAATTTTT
28322381 AAAGTGAAAAAGTAATTTTT
1 AAAGTGAAAAAGTAATTTTT
28322401 A
1 A
28322402 TGGCCATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.37
Consensus pattern (20 bp):
AAAGTGAAAAAGTAATTTTT
Found at i:28322515 original size:47 final size:47
Alignment explanation
Indices: 28322453--28322602 Score: 237
Period size: 47 Copynumber: 3.2 Consensus size: 47
28322443 AAGAAGTGAC
** * *
28322453 AGTTTATCTATAAAAGTGTTGGCTTGTCCACAATATTATAAAGTGGT
1 AGTTTATCTGCAAAAGTGGTGGCTTGTCCACAATATTATTAAGTGGT
*
28322500 AGTTTATCTGCAAAAGTGGTGGCTTGTCCACAATTTTATTAAGTGGT
1 AGTTTATCTGCAAAAGTGGTGGCTTGTCCACAATATTATTAAGTGGT
* *
28322547 AGTTTATATGCAAAAGTGGTGGCTTGTCCACAATATTATTAAGTGGC
1 AGTTTATCTGCAAAAGTGGTGGCTTGTCCACAATATTATTAAGTGGT
28322594 AGTTTATCT
1 AGTTTATCT
28322603 ACATTATTAT
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 94 1.00
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (47 bp):
AGTTTATCTGCAAAAGTGGTGGCTTGTCCACAATATTATTAAGTGGT
Found at i:28325641 original size:41 final size:41
Alignment explanation
Indices: 28325553--28325648 Score: 111
Period size: 41 Copynumber: 2.3 Consensus size: 41
28325543 TACAAACTTT
* * * **
28325553 ACGTCTAGCAGGCTTGATGCCGGTGAAATAATTCAGATTTT
1 ACGTCTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTAC
* * *
28325594 ACGTCTAGCAGGCTTAATGCCGGTGATACATTTCGGACTAC
1 ACGTCTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTAC
*
28325635 AGGTCTAGCAGGCT
1 ACGTCTAGCAGGCT
28325649 AAAAGCCAGT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (41 bp):
ACGTCTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTAC
Found at i:28330029 original size:63 final size:63
Alignment explanation
Indices: 28329930--28330048 Score: 229
Period size: 63 Copynumber: 1.9 Consensus size: 63
28329920 AAAACGATAG
28329930 TGATGTGATCCGGCCCAGGTTAATCGAGTCGTTTCACAAAGTTGCCCGATCATCGATACCAAA
1 TGATGTGATCCGGCCCAGGTTAATCGAGTCGTTTCACAAAGTTGCCCGATCATCGATACCAAA
*
28329993 TGATGTGATCCGGCCCAGGTTAATCGAGTCGTTTCACAAAGTTGCCCGATCGTCGA
1 TGATGTGATCCGGCCCAGGTTAATCGAGTCGTTTCACAAAGTTGCCCGATCATCGA
28330049 CGAGAAGTTC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.26
Consensus pattern (63 bp):
TGATGTGATCCGGCCCAGGTTAATCGAGTCGTTTCACAAAGTTGCCCGATCATCGATACCAAA
Found at i:28342789 original size:27 final size:28
Alignment explanation
Indices: 28342732--28342790 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
28342722 TTAGGTTGCT
* * * *
28342732 CCATGAAGGCATTTCTTTTTAGATATAG
1 CCATGAAGACATTCCTTTTAAGAGATAG
*
28342760 CCATGAAGAC-TTCCTTTTAAGAGATTG
1 CCATGAAGACATTCCTTTTAAGAGATAG
28342787 CCAT
1 CCAT
28342791 AGAGAGTTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 17 0.65
28 9 0.35
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.36
Consensus pattern (28 bp):
CCATGAAGACATTCCTTTTAAGAGATAG
Found at i:28342905 original size:61 final size:61
Alignment explanation
Indices: 28342838--28343014 Score: 187
Period size: 61 Copynumber: 2.9 Consensus size: 61
28342828 TTCATTTTAA
* * * *
28342838 AGATTTGCCATAAAGGCTATCCTTTACATCTAGTACTCGCCACATAGGCTTTCCTGTCCAG
1 AGATTTGCCATAAAGGTTATCCTTTACATCCAGTACTCACCACAAAGGCTTTCCTGTCCAG
* * * * *
28342899 AGATTTGCCACAAAGGTTGTGCTTTACATCCATTACTCACCACAAAGGCTTTCCTGTCTAG
1 AGATTTGCCATAAAGGTTATCCTTTACATCCAGTACTCACCACAAAGGCTTTCCTGTCCAG
** * * * *
28342960 ATTTTTTCCATGAAGGTTTTCCTTTACATCCA-TGACT-ATGCACAAAGGCTTTCCT
1 AGATTTGCCATAAAGGTTATCCTTTACATCCAGT-ACTCA-CCACAAAGGCTTTCCT
28343015 AGACTCACAC
Statistics
Matches: 97, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
60 2 0.02
61 95 0.98
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (61 bp):
AGATTTGCCATAAAGGTTATCCTTTACATCCAGTACTCACCACAAAGGCTTTCCTGTCCAG
Found at i:28343196 original size:53 final size:54
Alignment explanation
Indices: 28343095--28343197 Score: 145
Period size: 53 Copynumber: 1.9 Consensus size: 54
28343085 TTCCTTAATT
* ***
28343095 TTCCCTATATGATGCGATAACCCACCAGTTACGATCTTACATGGTATGGTATTC
1 TTCCCTATATGATGCCATAACCCACCAGTTACGATCTTACACAATATGGTATTC
* *
28343149 TTCCC-ATATGATGCCATAATCCACCAGTTACGGTCTTACACAATATGGT
1 TTCCCTATATGATGCCATAACCCACCAGTTACGATCTTACACAATATGGT
28343198 CTTCCATTGC
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
53 38 0.88
54 5 0.12
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (54 bp):
TTCCCTATATGATGCCATAACCCACCAGTTACGATCTTACACAATATGGTATTC
Found at i:28349863 original size:75 final size:75
Alignment explanation
Indices: 28349777--28350081 Score: 601
Period size: 75 Copynumber: 4.1 Consensus size: 75
28349767 GGAAAGCTAG
28349777 ATTGGTTTGGTACATTTTGATGCCTTACCAAGTTATGTGATTTTGGTTACTTGATGTGCTTATTT
1 ATTGGTTTGGTACATTTTGATGCCTTACCAAGTTATGTGATTTTGGTTACTTGATGTGCTTATTT
28349842 TCAAGGTTAT
66 TCAAGGTTAT
28349852 ATTGGTTTGGTACATTTTGATGCCTTACCAAGTTATGTGATTTTGGTTACTTGATGTGCTTATTT
1 ATTGGTTTGGTACATTTTGATGCCTTACCAAGTTATGTGATTTTGGTTACTTGATGTGCTTATTT
28349917 TCAAGGTTAT
66 TCAAGGTTAT
28349927 ATTGGTTTGGTACATTTTGATGCCTTACCAAGTTATGTGATTTTGGTTACTTGATGTGCTTATTT
1 ATTGGTTTGGTACATTTTGATGCCTTACCAAGTTATGTGATTTTGGTTACTTGATGTGCTTATTT
28349992 TCAAGGTTAT
66 TCAAGGTTAT
*
28350002 ATTGGTTTGGTACATTTTGATGCCTTACCAAGTTATGTGATTTTGGTTACTTGATGTGCTTGTTT
1 ATTGGTTTGGTACATTTTGATGCCTTACCAAGTTATGTGATTTTGGTTACTTGATGTGCTTATTT
28350067 TCAAGGTTAT
66 TCAAGGTTAT
28350077 ATTGG
1 ATTGG
28350082 CATGTTGATA
Statistics
Matches: 229, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 229 1.00
ACGTcount: A:0.20, C:0.10, G:0.22, T:0.48
Consensus pattern (75 bp):
ATTGGTTTGGTACATTTTGATGCCTTACCAAGTTATGTGATTTTGGTTACTTGATGTGCTTATTT
TCAAGGTTAT
Found at i:28354198 original size:36 final size:36
Alignment explanation
Indices: 28354151--28354225 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
28354141 ATGCCTAGGG
28354151 CACAGGCTATCACACGGCCTGGGGCACGGGCTGCGA
1 CACAGGCTATCACACGGCCTGGGGCACGGGCTGCGA
*
28354187 CACAGGCTATCACACGGCCTGGGGCGCGGGCTGCGA
1 CACAGGCTATCACACGGCCTGGGGCACGGGCTGCGA
28354223 CAC
1 CAC
28354226 GGCCGTGTGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.19, C:0.35, G:0.36, T:0.11
Consensus pattern (36 bp):
CACAGGCTATCACACGGCCTGGGGCACGGGCTGCGA
Found at i:28355150 original size:28 final size:28
Alignment explanation
Indices: 28355043--28355165 Score: 103
Period size: 27 Copynumber: 4.5 Consensus size: 28
28355033 TCTAGAAATT
*
28355043 GCCACGAAGGTTTTCCTTT--CAGCGTCTC
1 GCCACAAAGGTTTTCCTTTAACAG-GT-TC
**
28355071 GCCACAAAGG-CGTCCTTTAGA-AGGTTC
1 GCCACAAAGGTTTTCCTTTA-ACAGGTTC
* ** *
28355098 ACCACAAAGG-CATCCTTTAAAAGGTTC
1 GCCACAAAGGTTTTCCTTTAACAGGTTC
*
28355125 GCCACAAAGGTTTTCCTTTAACAGGTTT
1 GCCACAAAGGTTTTCCTTTAACAGGTTC
*
28355153 ACCACAAAGGTTT
1 GCCACAAAGGTTT
28355166 CCGTTTCCAA
Statistics
Matches: 79, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
26 1 0.01
27 40 0.51
28 36 0.46
29 2 0.03
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.28
Consensus pattern (28 bp):
GCCACAAAGGTTTTCCTTTAACAGGTTC
Found at i:28356088 original size:56 final size:56
Alignment explanation
Indices: 28355211--28356069 Score: 1709
Period size: 56 Copynumber: 15.3 Consensus size: 56
28355201 ACAAAGTTCG
28355211 CCACAAAGGCTTACCTTTCCATTATTTTTCCACAAAGGTTGTATGTTAATAGGTTTT
1 CCAC-AAGGCTTACCTTTCCATTATTTTTCCACAAAGGTTGTATGTTAATAGGTTTT
28355268 CCACAAGGCTTACCTTTCCATTATTTTTCCACAAAGGTTGTATGTTAATAGGTTTT
1 CCACAAGGCTTACCTTTCCATTATTTTTCCACAAAGGTTGTATGTTAATAGGTTTT
28355324 CCACAAGGCTTACCTTTCCATTATTTTTCCACAAAGGTTGTATGTTAATAGGTTTT
1 CCACAAGGCTTACCTTTCCATTATTTTTCCACAAAGGTTGTATGTTAATAGGTTTT
28355380 CCACAAGGCTTACCTTTCCATTATTTTTCCACAAAGGTTGTATGTTAATAGGTTTT
1 CCACAAGGCTTACCTTTCCATTATTTTTCCACAAAGGTTGTATGTTAATAGGTTTT
28355436 CCACAAGGCTTACCTTTCCATTATTTTTCCACAAAGGTTGTATGTTAATAGGTTTT
1 CCACAAGGCTTACCTTTCCATTATTTTTCCACAAAGGTTGTATGTTAATAGGTTTT
28355492 CCACAAGGCTTACCTTTCCATTATTTTTCCACAAAGGTTGTATGTTAATAGGTTTT
1 CCACAAGGCTTACCTTTCCATTATTTTTCCACAAAGGTTGTATGTTAATAGGTTTT
28355548 CCACAAGGCTTACCTTTCCATTATTTTTCCACAAAGGTTGTATGTTAATAGGTTTT
1 CCACAAGGCTTACCTTTCCATTATTTTTCCACAAAGGTTGTATGTTAATAGGTTTT
28355604 CCACAAGGCTTACCTTTCCATTATTTTTCCACAAAGGTTGTATGTTAATAGGTTTT
1 CCACAAGGCTTACCTTTCCATTATTTTTCCACAAAGGTTGTATGTTAATAGGTTTT
28355660 CCACAAGGCTTACCTTTCCATTATTTTTCCACAAAGGTTGTATGTTAATAGGTTTT
1 CCACAAGGCTTACCTTTCCATTATTTTTCCACAAAGGTTGTATGTTAATAGGTTTT
28355716 CCACAAGGCTTACCTTTCCATTATTTTTCCACAAAGGTTGTATGTTAATAGGTTTT
1 CCACAAGGCTTACCTTTCCATTATTTTTCCACAAAGGTTGTATGTTAATAGGTTTT
28355772 CCACAAGGCTTACCTTTCCATTATTTTTCCACAAAGGTTGTATGTTAATAGGTTTT
1 CCACAAGGCTTACCTTTCCATTATTTTTCCACAAAGGTTGTATGTTAATAGGTTTT
28355828 CCACAAGGCTTACCTTTCCATTATTTTTCCACAAAGGTTGTATGTTAATAGGTTTT
1 CCACAAGGCTTACCTTTCCATTATTTTTCCACAAAGGTTGTATGTTAATAGGTTTT
28355884 CCACAAGGCTTACCTTTCCATTATTTTTCCACAAAGGTTGTATGTTAATAGGTTTT
1 CCACAAGGCTTACCTTTCCATTATTTTTCCACAAAGGTTGTATGTTAATAGGTTTT
28355940 CCACAAGGCTTACCTTTCCATTATTTTTCCACAAAGGTTGTATGTTAATAGGTTTT
1 CCACAAGGCTTACCTTTCCATTATTTTTCCACAAAGGTTGTATGTTAATAGGTTTT
28355996 CCACAAGGCTTACCTTTCCATTATTTTTCCACAAAGGTTGTATGTTAATAGGTTTT
1 CCACAAGGCTTACCTTTCCATTATTTTTCCACAAAGGTTGTATGTTAATAGGTTTT
28356052 CCACAAGGCTTACCTTTC
1 CCACAAGGCTTACCTTTC
28356070 TACAGTTTTG
Statistics
Matches: 802, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
56 798 1.00
57 4 0.00
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (56 bp):
CCACAAGGCTTACCTTTCCATTATTTTTCCACAAAGGTTGTATGTTAATAGGTTTT
Found at i:28357562 original size:45 final size:45
Alignment explanation
Indices: 28357513--28357680 Score: 192
Period size: 45 Copynumber: 3.7 Consensus size: 45
28357503 AGTCTAGAAA
* * *
28357513 CGAGTAAGGCCATAACTGAAAGACGTTATTGCATCACGATTCTAT
1 CGAGTAAGACCATAACTGAAAGACGTTATGGCATCACAATTCTAT
* *
28357558 CGAGTAAGACCATAACTGAAAGACGTTATGGAATCACAATTTTAT
1 CGAGTAAGACCATAACTGAAAGACGTTATGGCATCACAATTCTAT
* * * * * *
28357603 CGAGTAAGACCATAGCTGAAAGAGGCTATGGCATCACAAATCAAA
1 CGAGTAAGACCATAACTGAAAGACGTTATGGCATCACAATTCTAT
* * ** *
28357648 CGAATAATACCATAGTTGAAAGACGCTATGGCA
1 CGAGTAAGACCATAACTGAAAGACGTTATGGCA
28357681 ACATGACGGA
Statistics
Matches: 106, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 106 1.00
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (45 bp):
CGAGTAAGACCATAACTGAAAGACGTTATGGCATCACAATTCTAT
Found at i:28357783 original size:91 final size:92
Alignment explanation
Indices: 28357649--28357817 Score: 223
Period size: 91 Copynumber: 1.8 Consensus size: 92
28357639 CAAATCAAAC
* * * **
28357649 GAATAATACCATAGTTGAAAGACGCTATGGCAACATGACGGAAAATGGATAAGACCACAGTTGAA
1 GAATAAGACCATAGTTGAAAGACACTATGGCAACAAGACGGAAAATAAATAAGACCACAGTTGAA
*
28357714 AGACACTATGGCAACACGATGGAAAAT
66 AGACACCATGGCAACACGATGGAAAAT
* ** * **
28357741 GAATAAGACCATGGTTGAAAGACACTATGGCGGCAAG-TGGAAAATAAATAAGACCATGGTTGAA
1 GAATAAGACCATAGTTGAAAGACACTATGGCAACAAGACGGAAAATAAATAAGACCACAGTTGAA
28357805 AGACACCATGGCA
66 AGACACCATGGCA
28357818 CCCTCCGATC
Statistics
Matches: 65, Mismatches: 12, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
91 34 0.52
92 31 0.48
ACGTcount: A:0.43, C:0.16, G:0.24, T:0.17
Consensus pattern (92 bp):
GAATAAGACCATAGTTGAAAGACACTATGGCAACAAGACGGAAAATAAATAAGACCACAGTTGAA
AGACACCATGGCAACACGATGGAAAAT
Found at i:28357797 original size:45 final size:46
Alignment explanation
Indices: 28357607--28357817 Score: 214
Period size: 46 Copynumber: 4.6 Consensus size: 46
28357597 TTTTATCGAG
* ** * *
28357607 TAAGACCATAGCTGAAAGAGGCTATGGCATCACAA-AT--CAAACGAA
1 TAAGACCATAGTTGAAAGACACTATGGCA--ACAAGATGGAAAATGAA
* * * * *
28357652 TAATACCATAGTTGAAAGACGCTATGGCAACATGACGGAAAATGGA
1 TAAGACCATAGTTGAAAGACACTATGGCAACAAGATGGAAAATGAA
* *
28357698 TAAGACCACAGTTGAAAGACACTATGGCAACACGATGGAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCAACAAGATGGAAAATGAA
* ** *
28357744 TAAGACCATGGTTGAAAGACACTATGGCGGCAAG-TGGAAAATAAA
1 TAAGACCATAGTTGAAAGACACTATGGCAACAAGATGGAAAATGAA
* *
28357789 TAAGACCATGGTTGAAAGACACCATGGCA
1 TAAGACCATAGTTGAAAGACACTATGGCA
28357818 CCCTCCGATC
Statistics
Matches: 141, Mismatches: 22, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
43 3 0.02
44 1 0.01
45 63 0.45
46 74 0.52
ACGTcount: A:0.43, C:0.17, G:0.23, T:0.17
Consensus pattern (46 bp):
TAAGACCATAGTTGAAAGACACTATGGCAACAAGATGGAAAATGAA
Found at i:28359843 original size:21 final size:21
Alignment explanation
Indices: 28359817--28359857 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28359807 TTGTGTACTT
*
28359817 ATTCAT-GACATAGGTAAATTC
1 ATTCATAG-CATAAGTAAATTC
28359838 ATTCATAGCATAAGTAAATT
1 ATTCATAGCATAAGTAAATT
28359858 TCTCACATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (21 bp):
ATTCATAGCATAAGTAAATTC
Found at i:28370899 original size:18 final size:18
Alignment explanation
Indices: 28370877--28370940 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 18
28370867 GAGGACACTA
28370877 TTGCTGAGAAGGAAGTTG
1 TTGCTGAGAAGGAAGTTG
*
28370895 ATGCTGTAGAAGAAGAAGTTG
1 TTGCTG-AGAAG--GAAGTTG
*
28370916 TTGCAG-GAGAGGAAGTTG
1 TTGCTGAGA-AGGAAGTTG
28370934 TTGCTGA
1 TTGCTGA
28370941 AGAAAAAGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
18 17 0.46
19 7 0.19
20 2 0.05
21 11 0.30
ACGTcount: A:0.30, C:0.06, G:0.38, T:0.27
Consensus pattern (18 bp):
TTGCTGAGAAGGAAGTTG
Found at i:28370930 original size:21 final size:21
Alignment explanation
Indices: 28370883--28370930 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
28370873 ACTATTGCTG
* *
28370883 AGAAGGAAGTTGATGCTGTAGA
1 AGAA-GAAGTTGATGCAGGAGA
*
28370905 AGAAGAAGTTGTTGCAGGAGA
1 AGAAGAAGTTGATGCAGGAGA
*
28370926 GGAAG
1 AGAAG
28370931 TTGTTGCTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.38, C:0.04, G:0.40, T:0.19
Consensus pattern (21 bp):
AGAAGAAGTTGATGCAGGAGA
Found at i:28370949 original size:18 final size:18
Alignment explanation
Indices: 28370902--28370951 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
28370892 TTGATGCTGT
28370902 AGAAGAAGAAGTTGTTGC
1 AGAAGAAGAAGTTGTTGC
* *
28370920 AGGAGAGGAAGTTGTTGC
1 AGAAGAAGAAGTTGTTGC
* *
28370938 TGAAGAAAAAGTTG
1 AGAAGAAGAAGTTG
28370952 CTAAAAATGA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.38, C:0.04, G:0.36, T:0.22
Consensus pattern (18 bp):
AGAAGAAGAAGTTGTTGC
Found at i:28373630 original size:29 final size:29
Alignment explanation
Indices: 28373598--28373653 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
28373588 TCTATATAAC
28373598 AGAGATCACCAG-AAAGGCTTCCTTTTAAA
1 AGAGATCACC-GCAAAGGCTTCCTTTTAAA
*
28373627 AGAGATCGCCGCAAAGGCTTCCTTTTA
1 AGAGATCACCGCAAAGGCTTCCTTTTA
28373654 GAGATAACCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 1 0.04
29 24 0.96
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (29 bp):
AGAGATCACCGCAAAGGCTTCCTTTTAAA
Found at i:28385643 original size:19 final size:20
Alignment explanation
Indices: 28385560--28385654 Score: 81
Period size: 19 Copynumber: 4.8 Consensus size: 20
28385550 TGTATAATTA
*
28385560 TACCCCTGATTGCACTTAC-G
1 TACCCCTGATCGCACTT-CGG
* * *
28385580 TGCCCTTG-TCGTACTTCGG
1 TACCCCTGATCGCACTTCGG
*
28385599 TACCCCTGATCACACTTAC-G
1 TACCCCTGATCGCACTT-CGG
* *
28385619 TGCCCCT-ATCGTACTTCGG
1 TACCCCTGATCGCACTTCGG
28385638 TACCCCTGATCGCACTT
1 TACCCCTGATCGCACTT
28385655 ACGTTTTCAT
Statistics
Matches: 57, Mismatches: 13, Indels: 10
0.71 0.16 0.12
Matches are distributed among these distances:
18 2 0.04
19 27 0.47
20 27 0.47
21 1 0.02
ACGTcount: A:0.16, C:0.37, G:0.17, T:0.31
Consensus pattern (20 bp):
TACCCCTGATCGCACTTCGG
Found at i:28385726 original size:39 final size:39
Alignment explanation
Indices: 28385560--28385739 Score: 200
Period size: 39 Copynumber: 4.6 Consensus size: 39
28385550 TGTATAATTA
* * *
28385560 TACCCCTGATTGCACTTACGTGCCCTTGTCGTACTTCGG
1 TACCCCTGATAGCACTTACGTGCCCCTATCGTACTTCGG
28385599 TACCCCTGATCA-CACTTACGTGCCCCTATCGTACTTCGG
1 TACCCCTGAT-AGCACTTACGTGCCCCTATCGTACTTCGG
* *** * * ** *
28385638 TACCCCTGATCGCACTTACGTTTTCATGTTATACTTTGG
1 TACCCCTGATAGCACTTACGTGCCCCTATCGTACTTCGG
*
28385677 TACCCCTGATAGCACTTACGTGCCCCTATTGTACTTCGG
1 TACCCCTGATAGCACTTACGTGCCCCTATCGTACTTCGG
* * *
28385716 TACTCTTGATAGCACTTTCGTGCC
1 TACCCCTGATAGCACTTACGTGCC
28385740 ATGGTTACAT
Statistics
Matches: 116, Mismatches: 23, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
39 116 1.00
ACGTcount: A:0.17, C:0.32, G:0.17, T:0.34
Consensus pattern (39 bp):
TACCCCTGATAGCACTTACGTGCCCCTATCGTACTTCGG
Found at i:28386408 original size:27 final size:27
Alignment explanation
Indices: 28386374--28386425 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
28386364 TTGTGATTAG
*
28386374 TATTTGGCTAAATTGAGTACATGGTAT
1 TATTTGGCCAAATTGAGTACATGGTAT
28386401 TATTTGGCCAAATTGAGTACATGGT
1 TATTTGGCCAAATTGAGTACATGGT
28386426 TACATGTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.38
Consensus pattern (27 bp):
TATTTGGCCAAATTGAGTACATGGTAT
Found at i:28400701 original size:25 final size:25
Alignment explanation
Indices: 28400630--28400702 Score: 92
Period size: 25 Copynumber: 2.9 Consensus size: 25
28400620 GATAATTCCT
* *
28400630 CACAAAGGTTTTCTAGAGAAGTCAC
1 CACAAAGGCTTTCTAGAGAATTCAC
* * * *
28400655 CACAATGGCTTTCCAAAAAATTCAC
1 CACAAAGGCTTTCTAGAGAATTCAC
28400680 CACAAAGGCTTTCTAGAGAATTC
1 CACAAAGGCTTTCTAGAGAATTC
28400703 TCGAGTTTAT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (25 bp):
CACAAAGGCTTTCTAGAGAATTCAC
Found at i:28424713 original size:29 final size:29
Alignment explanation
Indices: 28424643--28424714 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
28424633 GTATGGAAAG
* *
28424643 AGAAAGTCCACCAAGGACTAGTTCGACCAT
1 AGAAA-TCAACCAAAGACTAGTTCGACCAT
* * *
28424673 AGAAGTCCACCAAAGACTAGTTCGACCGT
1 AGAAATCAACCAAAGACTAGTTCGACCAT
* *
28424702 GGAAATTAACCAA
1 AGAAATCAACCAA
28424715 GAAAAGTATG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
29 31 0.89
30 4 0.11
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.17
Consensus pattern (29 bp):
AGAAATCAACCAAAGACTAGTTCGACCAT
Found at i:28425959 original size:26 final size:26
Alignment explanation
Indices: 28425906--28425955 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
28425896 TAAAAATAAA
* *
28425906 AAATTTGAAATAATTACTGAAACTAG
1 AAATTTGAAACAATTACTCAAACTAG
*
28425932 AAATTTGAAACAATT-CTCTAACTA
1 AAATTTGAAACAATTACTCAAACTA
28425956 AGAAGATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (26 bp):
AAATTTGAAACAATTACTCAAACTAG
Found at i:28426069 original size:20 final size:21
Alignment explanation
Indices: 28426046--28426128 Score: 73
Period size: 20 Copynumber: 4.0 Consensus size: 21
28426036 AATAAATATG
28426046 AAATAGATTTAAATCGATTG-
1 AAATAGATTTAAATCGATTGT
* * *
28426066 AAATAAACTTAAATTGATTGT
1 AAATAGATTTAAATCGATTGT
* * *
28426087 AACT-GATTTTGAATTGATTGT
1 AAATAGA-TTTAAATCGATTGT
*
28426108 AACTA-ATTTAAATCGATTGT
1 AAATAGATTTAAATCGATTGT
28426128 A
1 A
28426129 GCACATTTGA
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
20 31 0.61
21 20 0.39
ACGTcount: A:0.41, C:0.06, G:0.13, T:0.40
Consensus pattern (21 bp):
AAATAGATTTAAATCGATTGT
Found at i:28426102 original size:21 final size:21
Alignment explanation
Indices: 28426077--28426116 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
28426067 AATAAACTTA
*
28426077 AATTGATTGTAACTGATTTTG
1 AATTGATTGTAACTAATTTTG
28426098 AATTGATTGTAACTAATTT
1 AATTGATTGTAACTAATTT
28426117 AAATCGATTG
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:0.33, C:0.05, G:0.15, T:0.47
Consensus pattern (21 bp):
AATTGATTGTAACTAATTTTG
Found at i:28427444 original size:25 final size:24
Alignment explanation
Indices: 28427415--28427468 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 24
28427405 AATTGCTTAA
28427415 AATAAATTTTTTTACTATCTAAATT
1 AATAAA-TTTTTTACTATCTAAATT
28427440 AAT-AA--TTTTACTATCTAAATT
1 AATAAATTTTTTACTATCTAAATT
28427461 AATAAATT
1 AATAAATT
28427469 GAATGAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
21 19 0.73
22 2 0.08
24 2 0.08
25 3 0.12
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (24 bp):
AATAAATTTTTTACTATCTAAATT
Found at i:28427448 original size:21 final size:21
Alignment explanation
Indices: 28427424--28427465 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
28427414 AAATAAATTT
28427424 TTTTACTATCTAAATTAATAA
1 TTTTACTATCTAAATTAATAA
28427445 TTTTACTATCTAAATTAATAA
1 TTTTACTATCTAAATTAATAA
28427466 ATTGAATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTTACTATCTAAATTAATAA
Found at i:28429989 original size:28 final size:29
Alignment explanation
Indices: 28429943--28429998 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
28429933 CGGTATGGTA
* * *
28429943 TGGGTCTTAGCCTATTACAGTAA-CAGTG
1 TGGGCCTTAGCCCAATACAGTAATCAGTG
28429971 TGGGCCTTAGCCCAATACAGTAATCAGT
1 TGGGCCTTAGCCCAATACAGTAATCAGT
28429999 ACAATGTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (29 bp):
TGGGCCTTAGCCCAATACAGTAATCAGTG
Found at i:28430162 original size:26 final size:26
Alignment explanation
Indices: 28430098--28430177 Score: 79
Period size: 26 Copynumber: 3.1 Consensus size: 26
28430088 AACAACACAC
* *
28430098 CAATATCGCAGCAAAGCTGTCAGTAA
1 CAATAACGCAGCAAAGCTGCCAGTAA
* * *
28430124 TAATGACGTAGCAAAGCTGCCAGTAA
1 CAATAACGCAGCAAAGCTGCCAGTAA
** * *
28430150 CGCTAACGCAGCAAGGTTGCCAGTAA
1 CAATAACGCAGCAAAGCTGCCAGTAA
28430176 CA
1 CA
28430178 TTATATGTGG
Statistics
Matches: 41, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.36, C:0.24, G:0.23, T:0.17
Consensus pattern (26 bp):
CAATAACGCAGCAAAGCTGCCAGTAA
Found at i:28430394 original size:27 final size:27
Alignment explanation
Indices: 28430345--28430625 Score: 334
Period size: 27 Copynumber: 10.4 Consensus size: 27
28430335 GGGTATAACA
*
28430345 GTCA-TTTACCCTAT-GGGGGTATTTCG
1 GTCATTTTACCCT-TCGAGGGTATTTCG
* * * *
28430371 GTTATTTTACCCTTCGACGATATTTTG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * *
28430398 GTCATTTTAACCATCGGGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
*
28430425 GTCATTTTACCCTTCGAGGGTATTTTG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * * *
28430452 TTCATTTTACCTTTTGAGGGTATTTCA
1 GTCATTTTACCCTTCGAGGGTATTTCG
* *
28430479 GTCATTTTACCTATTAG-GGGTATTTCG
1 GTCATTTTACC-CTTCGAGGGTATTTCG
* *
28430506 GTCATTTTACCCTTCTAGGGTATTTCA
1 GTCATTTTACCCTTCGAGGGTATTTCG
28430533 GTCATTTTACCCTTCGAGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * *
28430560 ATCATTTTACCCTTCGACGGTAGTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
*
28430587 GTCATTTTACCCTTCGACGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
28430614 GTCATTTTACCC
1 GTCATTTTACCC
28430626 ACGAATTGCA
Statistics
Matches: 215, Mismatches: 36, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
26 6 0.03
27 206 0.96
28 3 0.01
ACGTcount: A:0.17, C:0.21, G:0.20, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCTTCGAGGGTATTTCG
Found at i:28437377 original size:27 final size:29
Alignment explanation
Indices: 28437325--28437382 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 29
28437315 TATCGGTATG
* *
28437325 GTGTGGGCCTTAGCCCATTACCGTAA-CA
1 GTGTGGGCCTTAGCCCAATACAGTAATCA
*
28437353 GTGTGGG-CTTAGTCCAATACAGTAATCA
1 GTGTGGGCCTTAGCCCAATACAGTAATCA
28437381 GT
1 GT
28437383 ACAATGCAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 15 0.58
28 11 0.42
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (29 bp):
GTGTGGGCCTTAGCCCAATACAGTAATCA
Found at i:28437715 original size:27 final size:27
Alignment explanation
Indices: 28437682--28438026 Score: 347
Period size: 27 Copynumber: 12.8 Consensus size: 27
28437672 TACTCTATGG
* *
28437682 GGGTATTTCGGTCATATTACCCTTTTA
1 GGGTATTTCGGTCATTTTACCCTTTGA
* ** * *
28437709 GGATATTTTAGTTATTTTACCCTTCGA
1 GGGTATTTCGGTCATTTTACCCTTTGA
* * *
28437736 GGGTATTTTGGTCATTTTACCC-GTCA
1 GGGTATTTCGGTCATTTTACCCTTTGA
*
28437762 GAGGTATTGCGGTCATTTTACCCTTTGA
1 G-GGTATTTCGGTCATTTTACCCTTTGA
* * * *
28437790 GGTTATTTCAGTCATTTTACCCATTGG
1 GGGTATTTCGGTCATTTTACCCTTTGA
* * * *
28437817 GGGCATTTCAGTCATTTTACTCTTCGA
1 GGGTATTTCGGTCATTTTACCCTTTGA
* * *
28437844 GGGTATTTCGATCATTTTACCCATCG-
1 GGGTATTTCGGTCATTTTACCCTTTGA
** *
28437870 GGGATATTTCATTCATTTTACCCTTCGA
1 GGG-TATTTCGGTCATTTTACCCTTTGA
*
28437898 GGGTATTTTGGTCATTTTACCC-TTGA
1 GGGTATTTCGGTCATTTTACCCTTTGA
* * * *
28437924 GGGTATTTTGATTATTTTACTCTTTGA
1 GGGTATTTCGGTCATTTTACCCTTTGA
*
28437951 GGGTATTTTGGTCATTTTACCCTTTGA
1 GGGTATTTCGGTCATTTTACCCTTTGA
*
28437978 GGGTATTTCGGTCATTTTA-CGTTTCGA
1 GGGTATTTCGGTCATTTTACCCTTT-GA
28438005 GGGTATTTCGGTCATTTTACCC
1 GGGTATTTCGGTCATTTTACCC
28438027 ACGAAACGCA
Statistics
Matches: 262, Mismatches: 49, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
26 31 0.12
27 224 0.85
28 7 0.03
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.44
Consensus pattern (27 bp):
GGGTATTTCGGTCATTTTACCCTTTGA
Found at i:28441023 original size:18 final size:18
Alignment explanation
Indices: 28440996--28441030 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28440986 TCATTCTCCT
28440996 TTCCTCCCCCTTCTTTTC
1 TTCCTCCCCCTTCTTTTC
*
28441014 TTCCTTCCCCTTCTTTT
1 TTCCTCCCCCTTCTTTT
28441031 AACCTTAGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (18 bp):
TTCCTCCCCCTTCTTTTC
Found at i:28441448 original size:52 final size:52
Alignment explanation
Indices: 28441332--28441436 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
28441322 ATCGATTTTC
28441332 TCTTTCCCTTATATTTTTTATTTTTTATTTATCTTGTTATTTCGAGTGTTGT
1 TCTTTCCCTTATATTTTTTATTTTTTATTTATCTTGTTATTTCGAGTGTTGT
*
28441384 NCTTTCCCTTATATTTTTTATTTTTTATTTATCTTGTTATTTCGAGTGTTGT
1 TCTTTCCCTTATATTTTTTATTTTTTATTTATCTTGTTATTTCGAGTGTTGT
28441436 T
1 T
28441437 TTTTTTCTTA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.13, C:0.11, G:0.10, T:0.65
Consensus pattern (52 bp):
TCTTTCCCTTATATTTTTTATTTTTTATTTATCTTGTTATTTCGAGTGTTGT
Found at i:28442885 original size:53 final size:53
Alignment explanation
Indices: 28442784--28442886 Score: 127
Period size: 53 Copynumber: 1.9 Consensus size: 53
28442774 ACATTAAACA
* * * *
28442784 TGGGGAATAATGTGTAAGACTATAGCTCGACTATGGAAATATAAAGAGTCTGG
1 TGGGGAATAATGTGTAAGACCATAGCTCAAATATGGAAACATAAAGAGTCTGG
* * *
28442837 TGGGGTATAATTTGTAAGACCATAGCTCAAATAT-GACAACATAGAGAGTC
1 TGGGGAATAATGTGTAAGACCATAGCTCAAATATGGA-AACATAAAGAGTC
28442887 CGCCAAGACA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
52 2 0.05
53 40 0.95
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.26
Consensus pattern (53 bp):
TGGGGAATAATGTGTAAGACCATAGCTCAAATATGGAAACATAAAGAGTCTGG
Found at i:28442930 original size:120 final size:120
Alignment explanation
Indices: 28442717--28443075 Score: 610
Period size: 120 Copynumber: 3.0 Consensus size: 120
28442707 TGGGCTGTAA
* * * * * * * *
28442717 TGGGGAATAATGTGAAAGACCATAGCTCGACTATGGCAACATAGAGAGTCCGCTAGGACATTAAA
1 TGGGGTATAATTTGTAAGACCATAGCTCAAATATGACAACATAGAGAGTCCGCCAAGACATTAAA
28442782 CATGGGGAATAATGTGTAAGACTATAGCTCGACTATGGAAATATAAAGAGTCTGG
66 CATGGGGAATAATGTGTAAGACTATAGCTCGACTATGGAAATATAAAGAGTCTGG
28442837 TGGGGTATAATTTGTAAGACCATAGCTCAAATATGACAACATAGAGAGTCCGCCAAGACATTAAA
1 TGGGGTATAATTTGTAAGACCATAGCTCAAATATGACAACATAGAGAGTCCGCCAAGACATTAAA
28442902 CATGGGGAATAATGTGTAAGACTATAGCTCGACTATGGAAATATAAAGAGTCTGG
66 CATGGGGAATAATGTGTAAGACTATAGCTCGACTATGGAAATATAAAGAGTCTGG
28442957 TGGGGTATAATTTGTAAGACCATAGCTCAAATATGACAACATAGAGAGTCCGCCAAGACATTAAA
1 TGGGGTATAATTTGTAAGACCATAGCTCAAATATGACAACATAGAGAGTCCGCCAAGACATTAAA
** * *
28443022 CATGGGGAATAATGTGTAAGACCGTAGCTCGACTATGGAAACATAGAGAGTCTG
66 CATGGGGAATAATGTGTAAGACTATAGCTCGACTATGGAAATATAAAGAGTCTG
28443076 CCATGACATT
Statistics
Matches: 227, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 227 1.00
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (120 bp):
TGGGGTATAATTTGTAAGACCATAGCTCAAATATGACAACATAGAGAGTCCGCCAAGACATTAAA
CATGGGGAATAATGTGTAAGACTATAGCTCGACTATGGAAATATAAAGAGTCTGG
Found at i:28443005 original size:53 final size:53
Alignment explanation
Indices: 28442904--28443006 Score: 127
Period size: 53 Copynumber: 1.9 Consensus size: 53
28442894 ACATTAAACA
* * * *
28442904 TGGGGAATAATGTGTAAGACTATAGCTCGACTATGGAAATATAAAGAGTCTGG
1 TGGGGAATAATGTGTAAGACCATAGCTCAAATATGGAAACATAAAGAGTCTGG
* * *
28442957 TGGGGTATAATTTGTAAGACCATAGCTCAAATAT-GACAACATAGAGAGTC
1 TGGGGAATAATGTGTAAGACCATAGCTCAAATATGGA-AACATAAAGAGTC
28443007 CGCCAAGACA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
52 2 0.05
53 40 0.95
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.26
Consensus pattern (53 bp):
TGGGGAATAATGTGTAAGACCATAGCTCAAATATGGAAACATAAAGAGTCTGG
Found at i:28443065 original size:67 final size:68
Alignment explanation
Indices: 28442957--28443125 Score: 243
Period size: 67 Copynumber: 2.5 Consensus size: 68
28442947 AAGAGTCTGG
* * * *
28442957 TGGGGTATAATTTGTAAGACCATAGCTCAAATAT-GACAACATAGAGAGTCCGCCAAGACATTAA
1 TGGGGAATAATGTGTAAGACCATAGCTCGACTATGGACAACATAGAGAGTCCGCCAAGACATTAA
28443021 ACA
66 ACA
* * *
28443024 TGGGGAATAATGTGTAAGACCGTAGCTCGACTATGGA-AACATAGAGAGTCTGCCATGACATTAA
1 TGGGGAATAATGTGTAAGACCATAGCTCGACTATGGACAACATAGAGAGTCCGCCAAGACATTAA
28443088 ACA
66 ACA
* *
28443091 TGGGGCATGATGTGTAAGACCATAGCTCGACTATG
1 TGGGGAATAATGTGTAAGACCATAGCTCGACTATG
28443126 ATAGCATAAA
Statistics
Matches: 91, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
67 89 0.98
68 2 0.02
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (68 bp):
TGGGGAATAATGTGTAAGACCATAGCTCGACTATGGACAACATAGAGAGTCCGCCAAGACATTAA
ACA
Found at i:28444959 original size:22 final size:23
Alignment explanation
Indices: 28444915--28444985 Score: 81
Period size: 23 Copynumber: 3.1 Consensus size: 23
28444905 AGGGTGTTAT
28444915 AAAATACACCACAAAAGCATCAC
1 AAAATACACCACAAAAGCATCAC
* *
28444938 AAAATACATCAC-AAGGCATCAC
1 AAAATACACCACAAAAGCATCAC
* * * *
28444960 ATAATACGCCACAAATGCTTCAC
1 AAAATACACCACAAAAGCATCAC
28444983 AAA
1 AAA
28444986 TAACTTTCCT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
22 18 0.46
23 21 0.54
ACGTcount: A:0.51, C:0.28, G:0.07, T:0.14
Consensus pattern (23 bp):
AAAATACACCACAAAAGCATCAC
Found at i:28444987 original size:22 final size:22
Alignment explanation
Indices: 28444916--28444987 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
28444906 GGGTGTTATA
28444916 AAATACACCACAAAAGCATCAC
1 AAATACACCACAAAAGCATCAC
* *
28444938 AAAATACATCAC-AAGGCATCAC
1 -AAATACACCACAAAAGCATCAC
* * *
28444960 ATAATACGCCACAAATGCTTCAC
1 A-AATACACCACAAAAGCATCAC
28444983 AAATA
1 AAATA
28444988 ACTTTCCTCA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
21 1 0.02
22 21 0.51
23 19 0.46
ACGTcount: A:0.50, C:0.28, G:0.07, T:0.15
Consensus pattern (22 bp):
AAATACACCACAAAAGCATCAC
Done.