Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1115
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: 495024
ACGTcount: A:0.19, C:0.08, G:0.09, T:0.18
Warning! 230474 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:3377 original size:2 final size:2
Alignment explanation
Indices: 3370--3401 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3360 TATTATTTCA
3370 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3402 GTCTTCTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8334 original size:129 final size:128
Alignment explanation
Indices: 8100--8336 Score: 287
Period size: 129 Copynumber: 1.8 Consensus size: 128
8090 AACCAAGATT
* * *
8100 TAAGTTTTCCTTAGCTTTATTCAACAAACGATAAAACTTGTAGCATCGCCATTAGGTTTTTCAAA
1 TAAGTTTTCCTTAGCCTTATACAACAAACGATAAAACTTGTAGCATCGCCATTAAGTTTTTCAAA
* * ***
8165 TGTCACATTTGAATTGATGTCACTAGATTCAGTTGACATAGTAACAGATACACTGTCAGGATA
66 TGTCACATTTAAATTAATGTCACTAGATTCAGCAAACATAGTAACAGATACACTGTCAGGATA
* * * * *
8228 TAAGTTTTCCTTAGCCTTGTACAACAAATGATAAAAGTTTGTAGCTTCGCCGTTAAGTTCTTT-A
1 TAAGTTTTCCTTAGCCTTATACAACAAACGATAAAA-CTTGTAGCATCGCCATTAAGTT-TTTCA
* * * * *
8292 ATTGTCGCATTTAAATTAATGTTAGTAGATTTAGCAAACATAGTA
64 AATGTCACATTTAAATTAATGTCACTAGATTCAGCAAACATAGTA
8337 GTGGACACAT
Statistics
Matches: 89, Mismatches: 18, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
128 32 0.36
129 54 0.61
130 3 0.03
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (128 bp):
TAAGTTTTCCTTAGCCTTATACAACAAACGATAAAACTTGTAGCATCGCCATTAAGTTTTTCAAA
TGTCACATTTAAATTAATGTCACTAGATTCAGCAAACATAGTAACAGATACACTGTCAGGATA
Found at i:15839 original size:17 final size:17
Alignment explanation
Indices: 15813--15858 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
15803 ATTAAATTTT
*
15813 TTATAATTATTAGATAA
1 TTATATTTATTAGATAA
*
15830 TTATATTTATTAGGTAA
1 TTATATTTATTAGATAA
15847 -TATTATTTATTA
1 TTA-TATTTATTA
15859 AGTTCAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 2 0.08
17 24 0.92
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (17 bp):
TTATATTTATTAGATAA
Found at i:20184 original size:11 final size:10
Alignment explanation
Indices: 20158--20183 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
20148 GACTTATTTG
20158 AAAAAATACA
1 AAAAAATACA
20168 AAAAAATACA
1 AAAAAATACA
20178 AAAAAA
1 AAAAAA
20184 AGAGGTGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.85, C:0.08, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAATACA
Found at i:20695 original size:20 final size:20
Alignment explanation
Indices: 20670--20740 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
20660 TTTTACCCAG
20670 ATGTATCGATATATTTTTCA
1 ATGTATCGATATATTTTTCA
* * *
20690 ATGTATCGATATATGTATGA
1 ATGTATCGATATATTTTTCA
* * *
20710 ATGTATCGACACATTTTTTA
1 ATGTATCGATATATTTTTCA
20730 ATGTATCGATA
1 ATGTATCGATA
20741 CATTCTATTT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.44
Consensus pattern (20 bp):
ATGTATCGATATATTTTTCA
Found at i:21656 original size:21 final size:20
Alignment explanation
Indices: 21624--21671 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 20
21614 TCTAAACAAC
21624 CCATGTCCATGCATTTTAAG
1 CCATGTCCATGCATTTTAAG
21644 CCATGTACCATGCATTTTAA-
1 CCATGT-CCATGCATTTTAAG
21664 -CATGTCCA
1 CCATGTCCA
21672 ACATCTAGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 3 0.11
19 5 0.19
20 6 0.22
21 13 0.48
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.33
Consensus pattern (20 bp):
CCATGTCCATGCATTTTAAG
Found at i:25555 original size:2 final size:2
Alignment explanation
Indices: 25531--25577 Score: 55
Period size: 2 Copynumber: 25.0 Consensus size: 2
25521 TTTTTATTCT
* *
25531 TA TA TA TT TA T- TA TA TT TA -A TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25571 TA -A TA TA
1 TA TA TA TA
25578 GTAGAACAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
1 3 0.08
2 35 0.92
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:26801 original size:20 final size:19
Alignment explanation
Indices: 26763--26811 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
26753 TTTTTTTGTG
*
26763 TTTTTT-TATTTATCGTAT
1 TTTTTTATATTTATAGTAT
*
26781 TTATTTTATATTTATATTAT
1 TT-TTTTATATTTATAGTAT
26801 TTTTATTATAT
1 TTTT-TTATAT
26812 ATGTTTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 2 0.08
19 6 0.23
20 18 0.69
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTTTTATATTTATAGTAT
Found at i:26802 original size:16 final size:16
Alignment explanation
Indices: 26781--26813 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
26771 TTTATCGTAT
26781 TTATTTTATATT-TATA
1 TTATTTT-TATTATATA
26797 TTATTTTTATTATATA
1 TTATTTTTATTATATA
26813 T
1 T
26814 GTTTATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTTTATTATATA
Found at i:35203 original size:19 final size:19
Alignment explanation
Indices: 35179--35218 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
35169 TAATCAATTC
*
35179 AAAA-TTTAAGAATTTATAT
1 AAAATTTTAA-AATTTAAAT
35198 AAAATTTTAAAATTTAAAT
1 AAAATTTTAAAATTTAAAT
35217 AA
1 AA
35219 TTTATATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (19 bp):
AAAATTTTAAAATTTAAAT
Found at i:35240 original size:28 final size:27
Alignment explanation
Indices: 35182--35294 Score: 81
Period size: 27 Copynumber: 4.0 Consensus size: 27
35172 TCAATTCAAA
* *
35182 ATTTAAGA-ATTTATATAAAATTTTAAA-
1 ATTTAA-ATATTTATAT-AAATATAAAAT
35209 ATTTAAATAATTTATATAAATATAAAAT
1 ATTTAAAT-ATTTATATAAATATAAAAT
*
35237 ATTTTAAATATGATTATA-ACACTATAAAAT
1 A-TTTAAATAT--TTATATA-AATATAAAAT
* *
35267 ATATAAATA-TAATATAAATATATAAAT
1 ATTTAAATATTTATATAAATATA-AAAT
35294 A
1 A
35295 ATTATTTTTA
Statistics
Matches: 71, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
26 10 0.14
27 20 0.28
28 11 0.15
29 15 0.21
30 15 0.21
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (27 bp):
ATTTAAATATTTATATAAATATAAAAT
Found at i:39973 original size:19 final size:20
Alignment explanation
Indices: 39930--39979 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
39920 TATATCCAGA
* * *
39930 TGTATCGATATATTATGCTT
1 TGTATCGATACATGATGCAT
39950 TGTATCGATACATGAT-CAT
1 TGTATCGATACATGATGCAT
39969 TGTATCGATAC
1 TGTATCGATAC
39980 TTACACAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (20 bp):
TGTATCGATACATGATGCAT
Found at i:40050 original size:13 final size:13
Alignment explanation
Indices: 40032--40056 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40022 TACCACTGTT
40032 TGTATCGATACAA
1 TGTATCGATACAA
40045 TGTATCGATACA
1 TGTATCGATACA
40057 TGAAGAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:48024 original size:34 final size:34
Alignment explanation
Indices: 47984--48066 Score: 132
Period size: 34 Copynumber: 2.4 Consensus size: 34
47974 TTGGCATTAG
47984 ACAAAGGGGGAGAAATAAAAAGAATTTTTATAAC
1 ACAAAGGGGGAGAAATAAAAAGAATTTTTATAAC
* *
48018 ACAAAGGGGAAGAAATAAAAAGAATTTTTATAAT
1 ACAAAGGGGGAGAAATAAAAAGAATTTTTATAAC
48052 A-AAAGGGGGGAGAAA
1 ACAAA-GGGGGAGAAA
48067 ATCTTGAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
33 3 0.07
34 42 0.93
ACGTcount: A:0.54, C:0.04, G:0.24, T:0.18
Consensus pattern (34 bp):
ACAAAGGGGGAGAAATAAAAAGAATTTTTATAAC
Found at i:48671 original size:16 final size:16
Alignment explanation
Indices: 48650--48680 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
48640 TTTTGTTGAA
48650 TTTTTTT-ATTTTCTT
1 TTTTTTTGATTTTCTT
48665 TTTTTTTGATTTTCTT
1 TTTTTTTGATTTTCTT
48681 GAAATTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.06, C:0.06, G:0.03, T:0.84
Consensus pattern (16 bp):
TTTTTTTGATTTTCTT
Found at i:48691 original size:6 final size:6
Alignment explanation
Indices: 48682--48728 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
48672 GATTTTCTTG
* *
48682 AAATTA AAATTA AAATTG AAACT- -AATT- AAATTA AAATTA AAATTA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
48727 AA
1 AA
48729 GTCAAAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
4 3 0.08
5 4 0.11
6 29 0.81
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (6 bp):
AAATTA
Found at i:48986 original size:36 final size:35
Alignment explanation
Indices: 48909--49021 Score: 99
Period size: 33 Copynumber: 3.3 Consensus size: 35
48899 TTTAAAATGA
* ** *
48909 AAAAAACTCTTTTATTAAGGTTTCAA-TTTTAAAT
1 AAAAAACTCTTTCACCAAGGCTTCAACTTTTAAAT
*
48943 -GAAAACTCTTTCACCAAGGCTTCAACTTTTAAAGT
1 AAAAAACTCTTTCACCAAGGCTTCAACTTTTAAA-T
* * *
48978 AAAAAACTC-CTCTACCAAGACTTCTAC-TTTAAAT
1 AAAAAACTCTTTC-ACCAAGGCTTCAACTTTTAAAT
49012 GAAAAAACTC
1 -AAAAAACTC
49022 CTCTATCGAG
Statistics
Matches: 65, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
33 20 0.31
34 8 0.12
35 18 0.28
36 19 0.29
ACGTcount: A:0.41, C:0.19, G:0.07, T:0.33
Consensus pattern (35 bp):
AAAAAACTCTTTCACCAAGGCTTCAACTTTTAAAT
Found at i:49017 original size:35 final size:35
Alignment explanation
Indices: 48955--49121 Score: 110
Period size: 35 Copynumber: 4.8 Consensus size: 35
48945 AAACTCTTTC
*
48955 ACCAAGGCTTCAACTTTTAAA-GTAAAAAACTCCTCT
1 ACCAAGGCTTCTAC-TTTAAATG-AAAAAACTCCTCT
*
48991 ACCAAGACTTCTACTTTAAATGAAAAAACTCCTCT
1 ACCAAGGCTTCTACTTTAAATGAAAAAACTCCTCT
* * * * *
49026 ATCGAGGTTTCTAATTTAAATTG-AAAAACT-CTCC
1 ACCAAGGCTTCTACTTTAAA-TGAAAAAACTCCTCT
*** * * *
49060 ATTGAGGCTT-TAACTTTGAATAAAAAAACTCCTCC
1 ACCAAGGCTTCT-ACTTTAAATGAAAAAACTCCTCT
* * *
49095 ATCGAGGCTT-TAACTTTACATGAAAAA
1 ACCAAGGCTTCT-ACTTTAAATGAAAAA
49122 CTCTTTCATT
Statistics
Matches: 109, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
33 2 0.02
34 24 0.22
35 68 0.62
36 15 0.14
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (35 bp):
ACCAAGGCTTCTACTTTAAATGAAAAAACTCCTCT
Found at i:49076 original size:69 final size:68
Alignment explanation
Indices: 48994--49170 Score: 200
Period size: 69 Copynumber: 2.6 Consensus size: 68
48984 CTCCTCTACC
* *
48994 AAGACTTCT-ACTTTAAATGAAAAAACTCCTCTATCGAGGTTTCTAA-TTTAAATTGAAAAACTC
1 AAGACTT-TAACTTTAAAT-AAAAAACTCCTCCATCGAGGCTT-TAACTTTAAA-TGAAAAACTC
49057 -TCCATT
62 TTCCATT
* * * * *
49063 GAGGCTTTAACTTTGAATAAAAAAACTCCTCCATCGAGGCTTTAACTTTACATGAAAAACTCTTT
1 AAGACTTTAACTTTAAAT-AAAAAACTCCTCCATCGAGGCTTTAACTTTAAATGAAAAACTCTTC
49128 CATT
65 CATT
49132 AAGACTTTAACTTTAAAATAAAAAAC-CCTTCCATCGAGG
1 AAGACTTTAACTTT-AAATAAAAAACTCC-TCCATCGAGG
49171 ATTCAACAAT
Statistics
Matches: 92, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
68 16 0.17
69 73 0.79
70 3 0.03
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (68 bp):
AAGACTTTAACTTTAAATAAAAAACTCCTCCATCGAGGCTTTAACTTTAAATGAAAAACTCTTCC
ATT
Found at i:49090 original size:34 final size:33
Alignment explanation
Indices: 49049--49157 Score: 112
Period size: 34 Copynumber: 3.2 Consensus size: 33
49039 ATTTAAATTG
49049 AAAAACTCTCCATTGAGGCTTTAACTTTGAATAA
1 AAAAACTCTCCATTGAGGCTTTAACTTT-AATAA
* *
49083 AAAAACTCCTCCATCGAGGCTTTAACTTTACAT-G
1 AAAAACT-CTCCATTGAGGCTTTAACTTTA-ATAA
* * * *
49117 AAAAACTCTTTCATTAAGACTTTAACTTTAAAATA
1 AAAAACTC-TCCATTGAGGCTTTAACTTTAATA-A
49152 AAAAAC
1 AAAAAC
49158 CCTTCCATCG
Statistics
Matches: 62, Mismatches: 8, Indels: 9
0.78 0.10 0.11
Matches are distributed among these distances:
33 2 0.03
34 32 0.52
35 28 0.45
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.31
Consensus pattern (33 bp):
AAAAACTCTCCATTGAGGCTTTAACTTTAATAA
Found at i:50884 original size:15 final size:16
Alignment explanation
Indices: 50846--50884 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
50836 TTTCATATCT
50846 TTTTTTTCATTTTCTCA
1 TTTTTTTCA-TTTCTCA
*
50863 ATTTTTTC-TTTCTCA
1 TTTTTTTCATTTCTCA
50878 TTTTTTT
1 TTTTTTT
50885 GTCATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 13 0.65
17 7 0.35
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTTTCATTTCTCA
Found at i:54948 original size:153 final size:154
Alignment explanation
Indices: 54483--54952 Score: 465
Period size: 156 Copynumber: 3.0 Consensus size: 154
54473 AAGTTCAAGG
* * *
54483 AAAATTATGAAAATACCCTTAGGAGATACTTTCGATGT-AAAA-GTACTTGAGACCCCT-AAAGT
1 AAAATTATGAAAATACCCTTAGGGGATACTTTCGATGTGAAAATG-ACCTGATA-CCCTAAAAG-
* * * * *
54545 ACTTAAAAAGGATTATAGATGGGATGAACCTATCTTAAATATCCACCTTTGGCATAAAAGCAGAC
63 ACTTTAAAAGGA-T-TAGATGGGATGAACCTATCCTAAATATCTACCTTTAGCATAAAAGTAGAC
** *
54610 TTGGTAATGACCTAGGACTCGATTCTAAA
126 CCGGTGATGACCTAGGACTCGATTCTAAA
* * * *
54639 AAAA-TATTAAAATACCCTTAGGGGATATCTTTAAC-AT-AG-AAGT-TCCTGATATCCCTAAAA
1 AAAATTATGAAAATACCCTTAGGGGATA-CTTT--CGATGTGAAAATGACCTGATA-CCCTAAAA
* * * * * *
54699 GACTTTAAAAGGATTACAAAATGGGATGAACCTATCCTAAATACCTACCATCAGCTTAAAAGTGG
62 GACTTTAAAAGGATT---AGATGGGATGAACCTATCCTAAATATCTACCTTTAGCATAAAAGTAG
* ** * *
54764 ATCCGGTGACAACCTAGGACTCAATTTTAAA
124 ACCCGGTGATGACCTAGGACTCGATTCTAAA
* *
54795 AAAATTATGAAAATACCCCTAGGGGATACTTTCGATGTGAAAATGCCCT-ATACCCTTAAAAGA-
1 AAAATTATGAAAATACCCTTAGGGGATACTTTCGATGTGAAAATGACCTGATACCC-TAAAAGAC
* *
54858 TTTAAAAGGATTAGATGGGATGAACTTATCCTAAATGTCTACCTTTAGCATAAAAGTAGACCCGG
65 TTTAAAAGGATTAGATGGGATGAACCTATCCTAAATATCTACCTTTAGCATAAAAGTAGACCCGG
* *
54923 TGATGACCTAGGACTTGGTTCTAAA
130 TGATGACCTAGGACTCGATTCTAAA
54948 AAAAT
1 AAAAT
54953 ACCCTAAAGG
Statistics
Matches: 252, Mismatches: 47, Indels: 33
0.76 0.14 0.10
Matches are distributed among these distances:
153 69 0.27
154 2 0.01
155 43 0.17
156 98 0.39
157 36 0.14
158 4 0.02
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (154 bp):
AAAATTATGAAAATACCCTTAGGGGATACTTTCGATGTGAAAATGACCTGATACCCTAAAAGACT
TTAAAAGGATTAGATGGGATGAACCTATCCTAAATATCTACCTTTAGCATAAAAGTAGACCCGGT
GATGACCTAGGACTCGATTCTAAA
Found at i:56852 original size:23 final size:22
Alignment explanation
Indices: 56826--56992 Score: 93
Period size: 23 Copynumber: 7.1 Consensus size: 22
56816 GTTTCTTTTT
56826 TTGCTGTTTGCTGCTGCTTTTGC
1 TTGCTGTTTGCTGCTG-TTTTGC
* * *
56849 TTGCTGTTTGTTGCTACTTTTTAC
1 TTGCTGTTTGCTGCT--GTTTTGC
* * *
56873 TTGCTATTTTCTTGCT-TGTTTCC
1 TTGCTGTTTGC-TGCTGT-TTTGC
**
56896 TTGCTGTCTTATTGCTTATTGTTTTGC
1 TTGCTG---T-TTGC-TGCTGTTTTGC
* * *
56923 TTTCTATTTGCTGTTGTTTTGC
1 TTGCTGTTTGCTGCTGTTTTGC
* * *
56945 TTACTGTGTGCTGTTGTTTTGC
1 TTGCTGTTTGCTGCTGTTTTGC
*
56967 TTGCTGTGTTGCTACTGTTTTGC
1 TTGCTGT-TTGCTGCTGTTTTGC
56990 TTG
1 TTG
56993 TTAAGTTGCT
Statistics
Matches: 112, Mismatches: 22, Indels: 20
0.73 0.14 0.13
Matches are distributed among these distances:
22 36 0.32
23 42 0.38
24 14 0.12
25 4 0.04
26 1 0.01
27 14 0.12
28 1 0.01
ACGTcount: A:0.05, C:0.17, G:0.21, T:0.57
Consensus pattern (22 bp):
TTGCTGTTTGCTGCTGTTTTGC
Found at i:56984 original size:26 final size:22
Alignment explanation
Indices: 56914--56991 Score: 93
Period size: 22 Copynumber: 3.5 Consensus size: 22
56904 TTATTGCTTA
* * *
56914 TTGTTTTGCTTTCTATTTGCTG
1 TTGTTTTGCTTACTGTGTGCTG
56936 TTGTTTTGCTTACTGTGTGCTG
1 TTGTTTTGCTTACTGTGTGCTG
* *
56958 TTGTTTTGCTTGCTGTGTTGCTA
1 TTGTTTTGCTTACTGTG-TGCTG
*
56981 CTGTTTTGCTT
1 TTGTTTTGCTT
56992 GTTAAGTTGC
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
22 35 0.71
23 14 0.29
ACGTcount: A:0.04, C:0.14, G:0.23, T:0.59
Consensus pattern (22 bp):
TTGTTTTGCTTACTGTGTGCTG
Found at i:57000 original size:23 final size:23
Alignment explanation
Indices: 56959--57011 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
56949 TGTGTGCTGT
**
56959 TGTTTTGCTTGCTGTGTTGCTAC
1 TGTTTTGCTTGCTAAGTTGCTAC
*
56982 TGTTTTGCTTGTTAAGTTGCTAC
1 TGTTTTGCTTGCTAAGTTGCTAC
57005 TGCTTTT
1 TG-TTTT
57012 TCCTTTCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.08, C:0.15, G:0.23, T:0.55
Consensus pattern (23 bp):
TGTTTTGCTTGCTAAGTTGCTAC
Found at i:69105 original size:19 final size:19
Alignment explanation
Indices: 69081--69121 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
69071 AATAATTTTT
69081 AAAAT-AAAATATAGATATA
1 AAAATAAAAATATA-ATATA
69100 AAAATAAAAAATATAATATA
1 AAAAT-AAAAATATAATATA
69120 AA
1 AA
69122 TATATGAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 7 0.35
21 8 0.40
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (19 bp):
AAAATAAAAATATAATATA
Found at i:77228 original size:15 final size:16
Alignment explanation
Indices: 77188--77230 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
77178 AATTTTCATG
*
77188 AATAATAAATATAAAAT
1 AATAAAAAAT-TAAAAT
77205 AATAAAAAATTAAAAT
1 AATAAAAAATTAAAAT
*
77221 TA-AAAAAATT
1 AATAAAAAATT
77231 GACCAACAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 8 0.33
16 7 0.29
17 9 0.38
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AATAAAAAATTAAAAT
Found at i:77504 original size:9 final size:9
Alignment explanation
Indices: 77489--77522 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
77479 AATTTATTCG
77489 AATATATTA
1 AATATATTA
*
77498 TATATATTA
1 AATATATTA
*
77507 AATATAATA
1 AATATATTA
77516 AATATAT
1 AATATAT
77523 ACAAATAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
AATATATTA
Found at i:79439 original size:20 final size:20
Alignment explanation
Indices: 79392--79439 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
79382 AATTTTTTAA
*
79392 TATTATTAATATTTTGTACTT
1 TATTA-TAATACTTTGTACTT
79413 TATTATAATACTTT-TACTT
1 TATTATAATACTTTGTACTT
79432 TATATATA
1 TAT-TATA
79440 TATATATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 8 0.32
20 12 0.48
21 5 0.20
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.58
Consensus pattern (20 bp):
TATTATAATACTTTGTACTT
Found at i:80789 original size:2 final size:2
Alignment explanation
Indices: 80782--80844 Score: 60
Period size: 2 Copynumber: 33.0 Consensus size: 2
80772 GAATTAAGAG
* * * * *
80782 AT AT AT AT AT AT AT AT AT TT AT TT AT TT AT A- AT -T GT -T AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
80821 AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
80845 GTTGAATTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
1 3 0.06
2 47 0.94
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (2 bp):
AT
Found at i:82673 original size:16 final size:16
Alignment explanation
Indices: 82652--82700 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
82642 TTAATATTTT
82652 AATTTAATAAAAAATA
1 AATTTAATAAAAAATA
* *
82668 AATTTAA-AAATAAGTT
1 AATTTAATAAA-AAATA
82684 AATATTAATAAAAAATA
1 AAT-TTAATAAAAAATA
82701 TATTAATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
15 3 0.12
16 13 0.50
17 7 0.27
18 3 0.12
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (16 bp):
AATTTAATAAAAAATA
Found at i:82705 original size:15 final size:16
Alignment explanation
Indices: 82685--82717 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
82675 AAATAAGTTA
82685 ATATTAA-TAAAAAAT
1 ATATTAATTAAAAAAT
*
82700 ATATTAATTATAAAAT
1 ATATTAATTAAAAAAT
82716 AT
1 AT
82718 TTACGTAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATATTAATTAAAAAAT
Found at i:84389 original size:18 final size:19
Alignment explanation
Indices: 84356--84392 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
84346 GACGAACAAA
*
84356 TGAGATATCAATAAAAACG
1 TGAGATATCAAAAAAAACG
84375 TGAGAT-TCAAAAAAAACG
1 TGAGATATCAAAAAAAACG
84393 AAGTAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.54, C:0.11, G:0.16, T:0.19
Consensus pattern (19 bp):
TGAGATATCAAAAAAAACG
Found at i:86292 original size:18 final size:15
Alignment explanation
Indices: 86256--86284 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
86246 ATTTTTATGA
86256 TTTAATATATATATC
1 TTTAATATATATATC
86271 TTTAAT-TATATATC
1 TTTAATATATATATC
86285 ATCCTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTAATATATATATC
Found at i:86862 original size:13 final size:13
Alignment explanation
Indices: 86844--86873 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
86834 ACAGCTTTTA
86844 TATTTTTTTAATT
1 TATTTTTTTAATT
*
86857 TATTTTTTTACTT
1 TATTTTTTTAATT
86870 TATT
1 TATT
86874 ATATTATTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (13 bp):
TATTTTTTTAATT
Found at i:87227 original size:16 final size:16
Alignment explanation
Indices: 87203--87245 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
87193 TTTGGGTCAG
*
87203 TCTCGGGTTCGGGTTC
1 TCTCAGGTTCGGGTTC
*
87219 TCTCAGGTTCAGGTTC
1 TCTCAGGTTCGGGTTC
*
87235 TTTCAGGTTCG
1 TCTCAGGTTCG
87246 AATTCTTTCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.07, C:0.23, G:0.30, T:0.40
Consensus pattern (16 bp):
TCTCAGGTTCGGGTTC
Found at i:91856 original size:20 final size:21
Alignment explanation
Indices: 91823--91863 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
91813 ATAGTATATA
91823 TATATATATAGATGATTTGTT
1 TATATATATAGATGATTTGTT
91844 TATATAT-TAGATGATTTGTT
1 TATATATATAGATGATTTGTT
91864 AAGGAAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.54
Consensus pattern (21 bp):
TATATATATAGATGATTTGTT
Found at i:93935 original size:23 final size:25
Alignment explanation
Indices: 93884--93936 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
93874 GAAAAGAGAT
93884 TTTTATAAAATTTTTGAGAAAAATA
1 TTTTATAAAATTTTTGAGAAAAATA
*
93909 -TTTA-AAAA-TTTTG-TAAAAATCA
1 TTTTATAAAATTTTTGAGAAAAAT-A
93931 TTTTAT
1 TTTTAT
93937 GGGCCAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
21 6 0.25
22 6 0.25
23 8 0.33
24 4 0.17
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (25 bp):
TTTTATAAAATTTTTGAGAAAAATA
Found at i:104957 original size:46 final size:45
Alignment explanation
Indices: 104908--105089 Score: 231
Period size: 46 Copynumber: 4.0 Consensus size: 45
104898 ATTAAAATAT
* *
104908 TTTTATTTTTAATTAAAATAAATTAATTAAAAGATAAATAAAAAA
1 TTTTATCTCTAATTAAAATAAATTAATTAAAAGATAAATAAAAAA
* * * *
104953 TTTTTACCTCTAATTAAATTAAATTAATTAAGATATAAATGAAAAAA
1 -TTTTATCTCTAATTAAAATAAATTAATTAAAAGATAAAT-AAAAAA
* * *
105000 TCTTATCTCTAATTAAATTAAATTAATTAACAGATAAATAAAAAA
1 TTTTATCTCTAATTAAAATAAATTAATTAAAAGATAAATAAAAAA
* *
105045 TTTTATCTTTAATTAAAATAAATTAATTAAGAA-ACAAATAAAAAA
1 TTTTATCTCTAATTAAAATAAATTAATTAA-AAGATAAATAAAAAA
105090 ATAAGTTTTT
Statistics
Matches: 119, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
45 44 0.37
46 69 0.58
47 6 0.05
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (45 bp):
TTTTATCTCTAATTAAAATAAATTAATTAAAAGATAAATAAAAAA
Found at i:105090 original size:91 final size:92
Alignment explanation
Indices: 104917--105091 Score: 271
Period size: 91 Copynumber: 1.9 Consensus size: 92
104907 TTTTTATTTT
*
104917 TAATTAAAATAAATTAATTAAAAGATAAATAAAAAATTTTTACCTCTAATTAAATTAAATTAATT
1 TAATTAAAATAAATTAATTAAAAGATAAATAAAAAATTTTTACCTCTAATTAAAATAAATTAATT
* * *
104982 AAGATATAAATGAAAAAATCTTATCTC
66 AAGAAACAAATAAAAAAATCTTATCTC
* * * *
105009 TAATTAAATTAAATTAATTAACAGATAAATAAAAAA-TTTTATCTTTAATTAAAATAAATTAATT
1 TAATTAAAATAAATTAATTAAAAGATAAATAAAAAATTTTTACCTCTAATTAAAATAAATTAATT
105073 AAGAAACAAATAAAAAAAT
66 AAGAAACAAATAAAAAAAT
105092 AAGTTTTTTA
Statistics
Matches: 75, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
91 41 0.55
92 34 0.45
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (92 bp):
TAATTAAAATAAATTAATTAAAAGATAAATAAAAAATTTTTACCTCTAATTAAAATAAATTAATT
AAGAAACAAATAAAAAAATCTTATCTC
Found at i:106179 original size:21 final size:20
Alignment explanation
Indices: 106151--106220 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 20
106141 AAACCATTAA
106151 TATT-TTATCAGAATAACTT
1 TATTATTATCAGAATAACTT
*
106170 TATTAATTATCAGTATTAA---
1 TATT-ATTATCAG-AATAACTT
106189 TATT-TTATCAGAATAACTT
1 TATTATTATCAGAATAACTT
106208 TATTGATTATCAG
1 TATT-ATTATCAG
106221 TATAGATCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
16 4 0.10
17 7 0.17
19 12 0.29
21 14 0.34
22 4 0.10
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (20 bp):
TATTATTATCAGAATAACTT
Found at i:106188 original size:38 final size:38
Alignment explanation
Indices: 106146--106223 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
106136 TTTACAAACC
106146 ATTAATATTTTATCAGAATAACTTTATTAATTATCAGT
1 ATTAATATTTTATCAGAATAACTTTATTAATTATCAGT
*
106184 ATTAATATTTTATCAGAATAACTTTATTGATTATCAGT
1 ATTAATATTTTATCAGAATAACTTTATTAATTATCAGT
106222 AT
1 AT
106224 AGATCTTTTG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.47
Consensus pattern (38 bp):
ATTAATATTTTATCAGAATAACTTTATTAATTATCAGT
Found at i:106273 original size:5 final size:5
Alignment explanation
Indices: 106242--106270 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
106232 TGCACGGACA
106242 ATTTT ATTTT ATTTT ATTTT ATTTT -TTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
106271 TTTGGTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
ATTTT
Found at i:107055 original size:2 final size:2
Alignment explanation
Indices: 107048--107102 Score: 80
Period size: 2 Copynumber: 29.0 Consensus size: 2
107038 GAATTAGGAA
*
107048 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT -T GT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
107087 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
107103 GTTGAATTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 3 0.06
2 47 0.94
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:107145 original size:26 final size:27
Alignment explanation
Indices: 107100--107150 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
107090 TATATATATA
* * *
107100 TATGTTGAATTTTATTTATTTAAATAG
1 TATGTAGAAATTTATTTATTAAAATAG
107127 TATGTAGAAATTT-TTTATTAAAAT
1 TATGTAGAAATTTATTTATTAAAAT
107151 TTTTATTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 10 0.48
27 11 0.52
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (27 bp):
TATGTAGAAATTTATTTATTAAAATAG
Found at i:110802 original size:20 final size:21
Alignment explanation
Indices: 110769--110809 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
110759 TATATATATA
110769 TATATATATAGATGATTTGTT
1 TATATATATAGATGATTTGTT
110790 TATATAT-TAGATGATTTGTT
1 TATATATATAGATGATTTGTT
110810 AAGGAAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.54
Consensus pattern (21 bp):
TATATATATAGATGATTTGTT
Found at i:111038 original size:18 final size:18
Alignment explanation
Indices: 111017--111060 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
111007 TATTAATTAA
111017 TAAAATAATATTATATTT
1 TAAAATAATATTATATTT
* *
111035 TAAAAATAATTTTTTATTT
1 T-AAAATAATATTATATTT
*
111054 TTAAATA
1 TAAAATA
111061 TTTTAAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TAAAATAATATTATATTT
Found at i:111058 original size:20 final size:19
Alignment explanation
Indices: 111018--111054 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
111008 ATTAATTAAT
111018 AAAATAATATTATATTTTA
1 AAAATAATATTATATTTTA
* *
111037 AAAATAATTTTTTATTTT
1 AAAATAATATTATATTTT
111055 TAAATATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AAAATAATATTATATTTTA
Found at i:112880 original size:23 final size:25
Alignment explanation
Indices: 112829--112881 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
112819 GAAAAGGGAT
112829 TTTTATAAAATTTTTGAGAAAAATA
1 TTTTATAAAATTTTTGAGAAAAATA
*
112854 -TTTA-AAAA-TTTTG-TAAAAATCA
1 TTTTATAAAATTTTTGAGAAAAAT-A
112876 TTTTAT
1 TTTTAT
112882 GGGCCAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
21 6 0.25
22 6 0.25
23 8 0.33
24 4 0.17
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (25 bp):
TTTTATAAAATTTTTGAGAAAAATA
Found at i:123870 original size:15 final size:15
Alignment explanation
Indices: 123850--123879 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
123840 ATTTTTATTT
*
123850 TTAATTAAAATATAA
1 TTAATTAAAAGATAA
123865 TTAATTAAAAGATAA
1 TTAATTAAAAGATAA
123880 ATAAAAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (15 bp):
TTAATTAAAAGATAA
Found at i:123914 original size:42 final size:40
Alignment explanation
Indices: 123863--123998 Score: 164
Period size: 42 Copynumber: 3.2 Consensus size: 40
123853 ATTAAAATAT
*
123863 AATTAATTAAAAGATAAATAAAAAATTTTTACCTCTAATTA
1 AATTAATTAAAAGATAAATAAAAAA-TTTTATCTCTAATTA
* *
123904 AATTAAATTAAGAGATAAATGAAAAAATCTTATCTCTAAAATTA
1 AATT-AATTAAAAGATAAAT-AAAAAATTTTATCTCT--AATTA
* *
123948 AATTAATTAACAGATAAATAAAAAATTTTATCTTTAATTAA
1 AATTAATTAAAAGATAAATAAAAAATTTTATCTCTAATT-A
*
123989 AATAAATTAA
1 AATTAATTAA
123999 TTAAGAAACA
Statistics
Matches: 83, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
40 4 0.05
41 14 0.17
42 36 0.43
43 20 0.24
44 9 0.11
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.35
Consensus pattern (40 bp):
AATTAATTAAAAGATAAATAAAAAATTTTATCTCTAATTA
Found at i:125100 original size:21 final size:20
Alignment explanation
Indices: 125072--125141 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 20
125062 AAACCATTAA
125072 TATT-TTATCAGAATAACTT
1 TATTATTATCAGAATAACTT
*
125091 TATTAATTATCAGTATTAA---
1 TATT-ATTATCAG-AATAACTT
125110 TATT-TTATCAGAATAACTT
1 TATTATTATCAGAATAACTT
125129 TATTGATTATCAG
1 TATT-ATTATCAG
125142 TATAGATCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
16 4 0.10
17 7 0.17
19 12 0.29
21 14 0.34
22 4 0.10
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (20 bp):
TATTATTATCAGAATAACTT
Found at i:125109 original size:38 final size:38
Alignment explanation
Indices: 125067--125144 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
125057 TTTACAAACC
125067 ATTAATATTTTATCAGAATAACTTTATTAATTATCAGT
1 ATTAATATTTTATCAGAATAACTTTATTAATTATCAGT
*
125105 ATTAATATTTTATCAGAATAACTTTATTGATTATCAGT
1 ATTAATATTTTATCAGAATAACTTTATTAATTATCAGT
125143 AT
1 AT
125145 AGATCTTTTG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.47
Consensus pattern (38 bp):
ATTAATATTTTATCAGAATAACTTTATTAATTATCAGT
Found at i:125194 original size:5 final size:5
Alignment explanation
Indices: 125163--125191 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
125153 TGCACGGACA
125163 ATTTT ATTTT ATTTT ATTTT ATTTT -TTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
125192 TTTGGTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
ATTTT
Found at i:125978 original size:2 final size:2
Alignment explanation
Indices: 125971--126025 Score: 80
Period size: 2 Copynumber: 29.0 Consensus size: 2
125961 GAATTAGGAA
*
125971 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT -T GT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
126010 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
126026 GTTGAATTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 3 0.06
2 47 0.94
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:126068 original size:26 final size:27
Alignment explanation
Indices: 126023--126073 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
126013 TATATATATA
* * *
126023 TATGTTGAATTTTATTTATTTAAATAG
1 TATGTAGAAATTTATTTATTAAAATAG
126050 TATGTAGAAATTT-TTTATTAAAAT
1 TATGTAGAAATTTATTTATTAAAAT
126074 TTTTATTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 10 0.48
27 11 0.52
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (27 bp):
TATGTAGAAATTTATTTATTAAAATAG
Found at i:129722 original size:20 final size:21
Alignment explanation
Indices: 129689--129729 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
129679 TATATATATA
129689 TATATATATAGATGATTTGTT
1 TATATATATAGATGATTTGTT
129710 TATATAT-TAGATGATTTGTT
1 TATATATATAGATGATTTGTT
129730 AGGAAATGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.54
Consensus pattern (21 bp):
TATATATATAGATGATTTGTT
Found at i:129954 original size:18 final size:18
Alignment explanation
Indices: 129933--129976 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
129923 TATTAATTAA
129933 TAAAATAATATTATATTT
1 TAAAATAATATTATATTT
* *
129951 TAAAAATAATTTTTTATTT
1 T-AAAATAATATTATATTT
*
129970 TTAAATA
1 TAAAATA
129977 TTTTAAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TAAAATAATATTATATTT
Found at i:129974 original size:20 final size:19
Alignment explanation
Indices: 129934--129970 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
129924 ATTAATTAAT
129934 AAAATAATATTATATTTTA
1 AAAATAATATTATATTTTA
* *
129953 AAAATAATTTTTTATTTT
1 AAAATAATATTATATTTT
129971 TAAATATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AAAATAATATTATATTTTA
Found at i:131797 original size:23 final size:25
Alignment explanation
Indices: 131746--131798 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
131736 GAAAAGGGAT
131746 TTTTATAAAATTTTTGAGAAAAATA
1 TTTTATAAAATTTTTGAGAAAAATA
*
131771 -TTTA-AAAA-TTTTG-TAAAAATCA
1 TTTTATAAAATTTTTGAGAAAAAT-A
131793 TTTTAT
1 TTTTAT
131799 GGGCCAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
21 6 0.25
22 6 0.25
23 8 0.33
24 4 0.17
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (25 bp):
TTTTATAAAATTTTTGAGAAAAATA
Found at i:142753 original size:41 final size:40
Alignment explanation
Indices: 142706--142789 Score: 132
Period size: 41 Copynumber: 2.1 Consensus size: 40
142696 ATTTTTAATT
*
142706 AAATTAAATTAATTAAAATATAAATCAAGAAATTTTATCTC
1 AAATTAAATTAATTAAAATATAAATCAAGAAATCTTATC-C
* *
142747 AAATTAAATTAATTAAGATATAAATGAAGAAATCTTATCC
1 AAATTAAATTAATTAAAATATAAATCAAGAAATCTTATCC
142787 AAA
1 AAA
142790 AGATTACAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 4 0.10
41 36 0.90
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (40 bp):
AAATTAAATTAATTAAAATATAAATCAAGAAATCTTATCC
Found at i:142816 original size:117 final size:119
Alignment explanation
Indices: 142687--142907 Score: 340
Period size: 117 Copynumber: 1.8 Consensus size: 119
142677 ATTCTTTGAG
* * *
142687 AATATTTTTATTTTTAATTAAATTAAATTAATTAAAATATAAATCAAGAAA-TTTTA-TC-TCAA
1 AATATTTTTATTTTTAATTAAAATAAATTAATTAAAAGATAAAT-AAAAAATTTTTACTCATCAA
*
142749 ATTAAATTAATTAAGATATAAATGAAGAAATCTTATCCAAAAGATTACAAATTAA
65 ATTAAATTAATTAAGATATAAATGAAAAAATCTTATCCAAAAGATTACAAATTAA
*
142804 AATATTTTTATTTTTAATTAAAATAAATTAATTAAAAGATAAATAAAAAATTTTTACCTCTAATT
1 AATATTTTTATTTTTAATTAAAATAAATTAATTAAAAGATAAATAAAAAATTTTTA-CTC--ATC
142869 AAATTAAATTAATTAAGATATAAATGAAAAAATCTTATC
63 AAATTAAATTAATTAAGATATAAATGAAAAAATCTTATC
142908 TCTAATTAAA
Statistics
Matches: 93, Mismatches: 5, Indels: 7
0.89 0.05 0.07
Matches are distributed among these distances:
116 5 0.05
117 47 0.51
119 2 0.02
122 39 0.42
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.39
Consensus pattern (119 bp):
AATATTTTTATTTTTAATTAAAATAAATTAATTAAAAGATAAATAAAAAATTTTTACTCATCAAA
TTAAATTAATTAAGATATAAATGAAAAAATCTTATCCAAAAGATTACAAATTAA
Found at i:142858 original size:46 final size:45
Alignment explanation
Indices: 142809--142990 Score: 231
Period size: 46 Copynumber: 4.0 Consensus size: 45
142799 ATTAAAATAT
* *
142809 TTTTATTTTTAATTAAAATAAATTAATTAAAAGATAAATAAAAAA
1 TTTTATCTCTAATTAAAATAAATTAATTAAAAGATAAATAAAAAA
* * * *
142854 TTTTTACCTCTAATTAAATTAAATTAATTAAGATATAAATGAAAAAA
1 -TTTTATCTCTAATTAAAATAAATTAATTAAAAGATAAAT-AAAAAA
* * *
142901 TCTTATCTCTAATTAAATTAAATTAATTAACAGATAAATAAAAAA
1 TTTTATCTCTAATTAAAATAAATTAATTAAAAGATAAATAAAAAA
* *
142946 TTTTATCTTTAATTAAAATAAATTAATTAAGAA-ACAAATAAAAAA
1 TTTTATCTCTAATTAAAATAAATTAATTAA-AAGATAAATAAAAAA
142991 ATAAGTTTTT
Statistics
Matches: 119, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
45 44 0.37
46 69 0.58
47 6 0.05
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (45 bp):
TTTTATCTCTAATTAAAATAAATTAATTAAAAGATAAATAAAAAA
Found at i:142991 original size:91 final size:92
Alignment explanation
Indices: 142818--142992 Score: 271
Period size: 91 Copynumber: 1.9 Consensus size: 92
142808 TTTTTATTTT
*
142818 TAATTAAAATAAATTAATTAAAAGATAAATAAAAAATTTTTACCTCTAATTAAATTAAATTAATT
1 TAATTAAAATAAATTAATTAAAAGATAAATAAAAAATTTTTACCTCTAATTAAAATAAATTAATT
* * *
142883 AAGATATAAATGAAAAAATCTTATCTC
66 AAGAAACAAATAAAAAAATCTTATCTC
* * * *
142910 TAATTAAATTAAATTAATTAACAGATAAATAAAAAA-TTTTATCTTTAATTAAAATAAATTAATT
1 TAATTAAAATAAATTAATTAAAAGATAAATAAAAAATTTTTACCTCTAATTAAAATAAATTAATT
142974 AAGAAACAAATAAAAAAAT
66 AAGAAACAAATAAAAAAAT
142993 AAGTTTTTTA
Statistics
Matches: 75, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
91 41 0.55
92 34 0.45
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (92 bp):
TAATTAAAATAAATTAATTAAAAGATAAATAAAAAATTTTTACCTCTAATTAAAATAAATTAATT
AAGAAACAAATAAAAAAATCTTATCTC
Found at i:144081 original size:21 final size:20
Alignment explanation
Indices: 144053--144122 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 20
144043 AAACCATTAA
144053 TATT-TTATCAGAATAACTT
1 TATTATTATCAGAATAACTT
*
144072 TATTAATTATCAGTATTAA---
1 TATT-ATTATCAG-AATAACTT
144091 TATT-TTATCAGAATAACTT
1 TATTATTATCAGAATAACTT
144110 TATTGATTATCAG
1 TATT-ATTATCAG
144123 TATAGATCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
16 4 0.10
17 7 0.17
19 12 0.29
21 14 0.34
22 4 0.10
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (20 bp):
TATTATTATCAGAATAACTT
Found at i:144090 original size:38 final size:38
Alignment explanation
Indices: 144048--144125 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
144038 TTTACAAACC
144048 ATTAATATTTTATCAGAATAACTTTATTAATTATCAGT
1 ATTAATATTTTATCAGAATAACTTTATTAATTATCAGT
*
144086 ATTAATATTTTATCAGAATAACTTTATTGATTATCAGT
1 ATTAATATTTTATCAGAATAACTTTATTAATTATCAGT
144124 AT
1 AT
144126 AGATCTTTTG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.47
Consensus pattern (38 bp):
ATTAATATTTTATCAGAATAACTTTATTAATTATCAGT
Found at i:144174 original size:5 final size:5
Alignment explanation
Indices: 144144--144172 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
144134 TGCACGGACA
144144 ATTTT ATTTT ATTTT ATTTT ATTTT -TTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
144173 TTGGTTTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
ATTTT
Found at i:144956 original size:2 final size:2
Alignment explanation
Indices: 144949--145003 Score: 80
Period size: 2 Copynumber: 29.0 Consensus size: 2
144939 GAATTAGGAA
*
144949 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT -T GT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
144988 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
145004 GTTGAATTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 3 0.06
2 47 0.94
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:145046 original size:26 final size:27
Alignment explanation
Indices: 145001--145051 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
144991 TATATATATA
* * *
145001 TATGTTGAATTTTATTTATTTAAATAG
1 TATGTAGAAATTTATTTATTAAAATAG
145028 TATGTAGAAATTT-TTTATTAAAAT
1 TATGTAGAAATTTATTTATTAAAAT
145052 TTTTATTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 10 0.48
27 11 0.52
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (27 bp):
TATGTAGAAATTTATTTATTAAAATAG
Found at i:148665 original size:2 final size:2
Alignment explanation
Indices: 148658--148688 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
148648 CTCATAATAG
148658 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
148689 TCATCTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:152147 original size:52 final size:51
Alignment explanation
Indices: 152008--152156 Score: 208
Period size: 52 Copynumber: 2.9 Consensus size: 51
151998 CGAAATATGA
152008 AAATTTGCTTGCATGTATCGATACATTGAATAATGTATCGATACATCTGGGC
1 AAATTTGCTTGCATGTATCGATACATTG-ATAATGTATCGATACATCTGGGC
* * * * *
152060 AAATTTGCCTGTATGTATCGATATATTTTATAATGTATCAATACATCTGGGC
1 AAATTTGCTTGCATGTATCGATACA-TTGATAATGTATCGATACATCTGGGC
**
152112 AAATTTGCTTGCATGTATCGATACAAAGATCAATGTATCGATACA
1 AAATTTGCTTGCATGTATCGATACATTGAT-AATGTATCGATACA
152157 ATGTATCGAT
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
51 2 0.02
52 79 0.95
53 2 0.02
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Consensus pattern (51 bp):
AAATTTGCTTGCATGTATCGATACATTGATAATGTATCGATACATCTGGGC
Found at i:152160 original size:13 final size:13
Alignment explanation
Indices: 152142--152169 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
152132 ATACAAAGAT
152142 CAATGTATCGATA
1 CAATGTATCGATA
152155 CAATGTATCGATA
1 CAATGTATCGATA
152168 CA
1 CA
152170 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:152249 original size:13 final size:13
Alignment explanation
Indices: 152231--152255 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
152221 ACAAAAAATA
152231 TGTATCGATACAT
1 TGTATCGATACAT
152244 TGTATCGATACA
1 TGTATCGATACA
152256 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:152251 original size:32 final size:33
Alignment explanation
Indices: 152210--152275 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
152200 AGTAGCTTAA
152210 ATTGTATCGATACAA-AAAATATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
***
152242 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
152275 A
1 A
152276 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAACAAAATATGTATCGATAC
Found at i:152569 original size:22 final size:21
Alignment explanation
Indices: 152544--152600 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 21
152534 AAGTGTCTAC
152544 AACATTTAAATTAAAATTAATT
1 AACATTTAAATTAAAA-TAATT
*
152566 AACA-ATAAA-TAAAA-AATT
1 AACATTTAAATTAAAATAATT
*
152584 TAC-TTTAAATATAAAAT
1 AACATTTAAAT-TAAAAT
152601 CACATATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 9
0.70 0.08 0.22
Matches are distributed among these distances:
18 10 0.36
20 10 0.36
21 4 0.14
22 4 0.14
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (21 bp):
AACATTTAAATTAAAATAATT
Found at i:154325 original size:17 final size:17
Alignment explanation
Indices: 154305--154338 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
154295 AAATGTGATT
154305 AATATAAAAATAATATA
1 AATATAAAAATAATATA
* *
154322 AATATAATATTAATATA
1 AATATAAAAATAATATA
154339 TAAATATCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AATATAAAAATAATATA
Found at i:154351 original size:28 final size:28
Alignment explanation
Indices: 154302--154367 Score: 66
Period size: 28 Copynumber: 2.4 Consensus size: 28
154292 AATAAATGTG
154302 ATTAATATAAAAATAATAT-AAATATAAT
1 ATTAATATAAAAATAATATAAAAT-TAAT
* *
154330 ATTAATATATAAAT-ATCTTAAAATTAAT
1 ATTAATATAAAAATAAT-ATAAAATTAAT
*
154358 A-TAACATAAA
1 ATTAATATAAA
154368 TTATTAACGC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
27 9 0.28
28 19 0.59
29 4 0.12
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (28 bp):
ATTAATATAAAAATAATATAAAATTAAT
Found at i:156862 original size:30 final size:31
Alignment explanation
Indices: 156823--156891 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 31
156813 TGAGGCTATA
*
156823 GGAATTGAGAAAGTTGTCAATGAAGAAG-TG
1 GGAAGTGAGAAAGTTGTCAATGAAGAAGTTG
* * *
156853 GGAAGTGAGAAGGTTGTTAATGAGGAAGTTG
1 GGAAGTGAGAAAGTTGTCAATGAAGAAGTTG
156884 GGAAGTGA
1 GGAAGTGA
156892 TCGGATAGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 24 0.71
31 10 0.29
ACGTcount: A:0.36, C:0.01, G:0.39, T:0.23
Consensus pattern (31 bp):
GGAAGTGAGAAAGTTGTCAATGAAGAAGTTG
Found at i:391456 original size:107 final size:107
Alignment explanation
Indices: 391310--391565 Score: 273
Period size: 110 Copynumber: 2.4 Consensus size: 107
391300 AATAAAATTG
* * * * *
391310 TGAAAATATTTAGAAATAAAGAGAAAATTTGAATTTTTTTATGGAGAATGGGTTTAGAGTATTCC
1 TGAAAATATTTAGGAACAAAGAGTAAATTTGAGTTTTTTTATGAAGAATGGGTTTAGAGTATTCC
**
391375 TTCAAAGTAGTAGGGTTGGAGTTTGCCCAAAGTCGAACATTA
66 TTCAAAGTAGTAGGGTTAAAGTTTGCCCAAAGTCGAACATTA
* * * * * *
391417 TGACAATATTTAGGAACAAAAAGTAAATTTGAGTATTTTTTTTTTTAAGATTGGGTTTGGAGTAT
1 TGAAAATATTTAGGAACAAAGAGTAAATTTGAG---TTTTTTTATGAAGAATGGGTTTAGAGTAT
** * * * * * *
391482 TCCTTCGGAGTAGTGGGGTTAAAGTTTTCCTAAAGTTGTAGATTA
63 TCCTTCAAAGTAGTAGGGTTAAAGTTTGCCCAAAGTCGAACATTA
*
391527 TGAAAATATTTAAGAAC--AGAGTAAATTTGAGTTTTTTTA
1 TGAAAATATTTAGGAACAAAGAGTAAATTTGAGTTTTTTTA
391566 AAGAACAAGG
Statistics
Matches: 121, Mismatches: 25, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
105 7 0.06
107 27 0.22
108 13 0.11
110 74 0.61
ACGTcount: A:0.34, C:0.06, G:0.21, T:0.38
Consensus pattern (107 bp):
TGAAAATATTTAGGAACAAAGAGTAAATTTGAGTTTTTTTATGAAGAATGGGTTTAGAGTATTCC
TTCAAAGTAGTAGGGTTAAAGTTTGCCCAAAGTCGAACATTA
Found at i:397637 original size:75 final size:75
Alignment explanation
Indices: 397469--397638 Score: 184
Period size: 75 Copynumber: 2.3 Consensus size: 75
397459 TGCCTATTTG
* * * * *
397469 ACCTCAATAGTTCTAGTTATCTTTCCTTAACATATTAACAAGTAACCTAAGTTACCACGTAAATA
1 ACCTCAATAGATCTAATTATCTTTCCTCAACATATAAACAAGTAACCTAAGTTACCACGAAAATA
*
397534 TGCTCATTCA
66 TACTCATTCA
* * * ** *
397544 ACCTCACTAGGTCCAATTATCTTTACC-CAACATATAAATGAGTAACGCTAAGTTATCAC-AAAA
1 ACCTCAATAGATCTAATTATCTTT-CCTCAACATATAAACAAGTAAC-CTAAGTTACCACGAAAA
397607 GTATACTCATTCA
64 -TATACTCATTCA
397620 ACCTCAATA-ATCTAATTAT
1 ACCTCAATAGATCTAATTAT
397639 ATTTTCAACA
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
75 46 0.59
76 32 0.41
ACGTcount: A:0.37, C:0.23, G:0.08, T:0.32
Consensus pattern (75 bp):
ACCTCAATAGATCTAATTATCTTTCCTCAACATATAAACAAGTAACCTAAGTTACCACGAAAATA
TACTCATTCA
Found at i:405264 original size:20 final size:20
Alignment explanation
Indices: 405239--405277 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
405229 TATAAAAAAT
*
405239 AATAATTTAATAAATATAAA
1 AATAATCTAATAAATATAAA
405259 AATAATCTAATAAATATAA
1 AATAATCTAATAAATATAA
405278 TTAACAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (20 bp):
AATAATCTAATAAATATAAA
Found at i:406419 original size:56 final size:58
Alignment explanation
Indices: 406352--406465 Score: 178
Period size: 60 Copynumber: 2.0 Consensus size: 58
406342 AAATGAAATA
*
406352 TTTAAAATTT-A-AAAATTAAATTTAAAATAATTAAATGCATGATTCATTATAATTGT
1 TTTAAAATTTAACAAAATTAAATATAAAATAATTAAATGCATGATTCATTATAATTGT
*
406408 TTTAAAATTTAAATCAAAATTAAATATAAAATAATTAAATGTATGATTCATTATAATT
1 TTTAAAATTT-AA-CAAAATTAAATATAAAATAATTAAATGCATGATTCATTATAATT
406466 ATTTAAGGTG
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
56 10 0.19
58 1 0.02
60 41 0.79
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (58 bp):
TTTAAAATTTAACAAAATTAAATATAAAATAATTAAATGCATGATTCATTATAATTGT
Found at i:408375 original size:21 final size:21
Alignment explanation
Indices: 408351--408391 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
408341 AAATAAATTG
408351 ATTTTAATTTAAAATTTAATA
1 ATTTTAATTTAAAATTTAATA
* *
408372 ATTTTAATTTGAATTTTAAT
1 ATTTTAATTTAAAATTTAAT
408392 TTGACAACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTTTAATTTAAAATTTAATA
Found at i:408386 original size:12 final size:12
Alignment explanation
Indices: 408351--408395 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
408341 AAATAAATTG
*
408351 ATTTTAATTTAA
1 ATTTTAATTTGA
*
408363 AATTTAA--T-A
1 ATTTTAATTTGA
408372 ATTTTAATTTGA
1 ATTTTAATTTGA
408384 ATTTTAATTTGA
1 ATTTTAATTTGA
408396 CAACTTGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
9 7 0.25
10 1 0.04
11 1 0.04
12 19 0.68
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (12 bp):
ATTTTAATTTGA
Found at i:412892 original size:2 final size:2
Alignment explanation
Indices: 412887--412925 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
412877 TATATGTGTG
*
412887 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
412926 TATCAAGAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:414596 original size:3 final size:3
Alignment explanation
Indices: 414588--414629 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
414578 TATAATCTTA
*
414588 ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
414630 GAAGAGTGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:415973 original size:52 final size:52
Alignment explanation
Indices: 415893--415993 Score: 141
Period size: 52 Copynumber: 1.9 Consensus size: 52
415883 TGAAATCCTT
* * * *
415893 ATATTCTTGTTTATGTTAACTAATACTAAATCCATTTAATAATGAATAACCC
1 ATATTCTTCTTTATATTAACTAACACTAAATCCAATTAATAATGAATAACCC
*
415945 ATATTCTTCTTTATATTAA-TCAACACTAAATCTAATTAATAATGAATAA
1 ATATTCTTCTTTATATTAACT-AACACTAAATCCAATTAATAATGAATAA
415994 AAAAAATTAC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
51 1 0.02
52 42 0.98
ACGTcount: A:0.42, C:0.14, G:0.04, T:0.41
Consensus pattern (52 bp):
ATATTCTTCTTTATATTAACTAACACTAAATCCAATTAATAATGAATAACCC
Found at i:416453 original size:6 final size:6
Alignment explanation
Indices: 416432--416482 Score: 59
Period size: 6 Copynumber: 8.3 Consensus size: 6
416422 TAAAATAAGA
* *
416432 TTAACTT TTATATT TTTATT TTTATT TTAATT TTAATT TTAA-T TTAATT
1 TTAA-TT TTA-ATT TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT
416481 TT
1 TT
416483 GAGATAATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
5 5 0.12
6 27 0.68
7 7 0.17
8 1 0.03
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (6 bp):
TTAATT
Found at i:416471 original size:17 final size:17
Alignment explanation
Indices: 416445--416482 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
416435 ACTTTTATAT
* *
416445 TTTTATTTTTATTTTAA
1 TTTTAATTTTAATTTAA
416462 TTTTAATTTTAATTTAA
1 TTTTAATTTTAATTTAA
416479 TTTT
1 TTTT
416483 GAGATAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTAATTTTAATTTAA
Found at i:416709 original size:5 final size:5
Alignment explanation
Indices: 416699--416734 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
416689 ATGTTTCTTG
*
416699 TTATA TTATA TTATA TTACA TTATA TTATA TTATA T
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA T
416735 ATAGTTTAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (5 bp):
TTATA
Found at i:417195 original size:19 final size:20
Alignment explanation
Indices: 417168--417207 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
417158 CGATTTAATC
*
417168 AGTTTTTTTAATTTT-TTCA
1 AGTTATTTTAATTTTGTTCA
*
417187 AGTTATTTTTATTTTGTTCA
1 AGTTATTTTAATTTTGTTCA
417207 A
1 A
417208 TTCACATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.23, C:0.05, G:0.07, T:0.65
Consensus pattern (20 bp):
AGTTATTTTAATTTTGTTCA
Found at i:417197 original size:20 final size:19
Alignment explanation
Indices: 417168--417207 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
417158 CGATTTAATC
417168 AGTTTTTTTAATTTT-TTCA
1 AGTTTTTTT-ATTTTGTTCA
417187 AGTTATTTTTATTTTGTTCA
1 AGTT-TTTTTATTTTGTTCA
417207 A
1 A
417208 TTCACATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.23, C:0.05, G:0.07, T:0.65
Consensus pattern (19 bp):
AGTTTTTTTATTTTGTTCA
Found at i:417289 original size:22 final size:22
Alignment explanation
Indices: 417264--417323 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
417254 TTAATTGGGT
*
417264 TTTTAGTTTAAATTTAGATGGA
1 TTTTAGTTTAAATTTAAATGGA
* * *
417286 TTTTTGTTTAGATTTAAATGGG
1 TTTTAGTTTAAATTTAAATGGA
*
417308 TTTAAGTTTAAATTTA
1 TTTTAGTTTAAATTTA
417324 TATTTTATTA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (22 bp):
TTTTAGTTTAAATTTAAATGGA
Found at i:417489 original size:18 final size:18
Alignment explanation
Indices: 417463--417498 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
417453 GAATTAACCA
*
417463 AACCGATTTAATCGATTT
1 AACCAATTTAATCGATTT
417481 AACCAATTTAATCGATTT
1 AACCAATTTAATCGATTT
417499 TTCAATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.39
Consensus pattern (18 bp):
AACCAATTTAATCGATTT
Found at i:418045 original size:12 final size:12
Alignment explanation
Indices: 418030--418084 Score: 60
Period size: 12 Copynumber: 4.5 Consensus size: 12
418020 AAATTTAAAA
418030 ATTTATTTTATT
1 ATTTATTTTATT
*
418042 ATTTATTATATT
1 ATTTATTTTATT
418054 ATTAATATTTTATT
1 ATT--TATTTTATT
418068 -TTTATTTTTATT
1 ATTTA-TTTTATT
418080 -TTTAT
1 ATTTAT
418085 ATATTTTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
11 3 0.08
12 25 0.66
13 2 0.05
14 8 0.21
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
ATTTATTTTATT
Found at i:418062 original size:26 final size:27
Alignment explanation
Indices: 418033--418093 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
418023 TTTAAAAATT
418033 TATTTTATTATTTA-TTATATTATTA-A
1 TATTTTATT-TTTATTTATATTATTATA
* *
418059 TATTTTATTTTTATTTTTATTTTTATA
1 TATTTTATTTTTATTTATATTATTATA
418086 TATTTTAT
1 TATTTTAT
418094 AATTAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
25 4 0.13
26 18 0.58
27 9 0.29
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (27 bp):
TATTTTATTTTTATTTATATTATTATA
Found at i:418134 original size:26 final size:27
Alignment explanation
Indices: 418088--418140 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
418078 TTTTTATATA
*
418088 TTTTATAATTAAATTTAAA-TTAAATT
1 TTTTATAATTAAATATAAATTTAAATT
*
418114 TTTTATTATTAAATA-ATAATTTAAATT
1 TTTTATAATTAAATATA-AATTTAAATT
418141 AAATTAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 1 0.04
26 15 0.65
27 7 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TTTTATAATTAAATATAAATTTAAATT
Found at i:418353 original size:4 final size:4
Alignment explanation
Indices: 418346--418382 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
418336 TTTTTTTCTT
418346 TTTA TTTA TTTA TTTA TTTA -TTA -TTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
418383 GCTGAATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 6 0.19
4 26 0.81
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:418679 original size:25 final size:25
Alignment explanation
Indices: 418645--418720 Score: 77
Period size: 25 Copynumber: 3.1 Consensus size: 25
418635 AAAAAGTACA
*
418645 TATTTTATTAT-TGTTAGATAAATTT
1 TATTTTATTATAT-TTAAATAAATTT
418670 TATTTTATTATATTTAAATAAATTT
1 TATTTTATTATATTTAAATAAATTT
** *
418695 T-TAAT-TTATATCTAAATAAAATTT
1 TATTTTATTATATTTAAAT-AAATTT
418719 TA
1 TA
418721 ACATAAAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
23 11 0.25
24 9 0.20
25 23 0.52
26 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (25 bp):
TATTTTATTATATTTAAATAAATTT
Found at i:418710 original size:23 final size:23
Alignment explanation
Indices: 418677--418721 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
418667 TTTTATTTTA
* *
418677 TTATATTTAAATAAATTTTTAAT
1 TTATATCTAAATAAAATTTTAAT
418700 TTATATCTAAATAAAATTTTAA
1 TTATATCTAAATAAAATTTTAA
418722 CATAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
TTATATCTAAATAAAATTTTAAT
Found at i:420186 original size:15 final size:15
Alignment explanation
Indices: 420145--420178 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
420135 TTATTTTAAT
420145 AATTAA-TAATAAAA
1 AATTAATTAATAAAA
420159 AATTAATTAATAAAA
1 AATTAATTAATAAAA
420174 AATTA
1 AATTA
420179 TTTTATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AATTAATTAATAAAA
Found at i:420782 original size:15 final size:15
Alignment explanation
Indices: 420762--420792 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
420752 AACAACTAAT
420762 AAATATGTTAATGTA
1 AAATATGTTAATGTA
420777 AAATATGTTAATGTA
1 AAATATGTTAATGTA
420792 A
1 A
420793 TAGACATACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (15 bp):
AAATATGTTAATGTA
Found at i:421761 original size:71 final size:70
Alignment explanation
Indices: 421641--421783 Score: 216
Period size: 71 Copynumber: 2.0 Consensus size: 70
421631 TTTAATTCTT
* * *
421641 AAATAAATATATCACCGCTACCTAATTCTTCTAACATGCGCTGACGCCATGCTCAATAAGTTCAT
1 AAATAAATATATCACCGCTACCTAACTCTTCTAACATGCGCTGACGCCATGCTCAAAAAATTCAT
421706 AAACC
66 AAACC
* *
421711 AAATAAATAATATCACCGCTACCTAACTCTTCTAATAT-CTGCTGATGCCATGCTCAAAAAATTC
1 AAATAAAT-ATATCACCGCTACCTAACTCTTCTAACATGC-GCTGACGCCATGCTCAAAAAATTC
421775 ATAAACC
64 ATAAACC
421782 AA
1 AA
421784 TCTTATACAC
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
70 9 0.14
71 57 0.86
ACGTcount: A:0.38, C:0.26, G:0.08, T:0.27
Consensus pattern (70 bp):
AAATAAATATATCACCGCTACCTAACTCTTCTAACATGCGCTGACGCCATGCTCAAAAAATTCAT
AAACC
Found at i:428043 original size:2 final size:2
Alignment explanation
Indices: 428036--428064 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
428026 GACAGTACTT
428036 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
428065 GGTGGCGAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:428089 original size:33 final size:33
Alignment explanation
Indices: 428047--428112 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
428037 AGAGAGAGAG
428047 AGAGAGAGAGAGAGAGAGGGTGGCGAGGGGTTC
1 AGAGAGAGAGAGAGAGAGGGTGGCGAGGGGTTC
428080 AGAGAGAGAGAGAGAGAGGGTGGCGAGGGGTTC
1 AGAGAGAGAGAGAGAGAGGGTGGCGAGGGGTTC
428113 GGTGTGGTTG
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:0.30, C:0.06, G:0.55, T:0.09
Consensus pattern (33 bp):
AGAGAGAGAGAGAGAGAGGGTGGCGAGGGGTTC
Found at i:428518 original size:41 final size:41
Alignment explanation
Indices: 428473--428573 Score: 166
Period size: 41 Copynumber: 2.5 Consensus size: 41
428463 TTTTTTATTA
*
428473 AAAAATATTTCATATTAAACATGAATTACCATCTAAAAAAT
1 AAAAATATTTTATATTAAACATGAATTACCATCTAAAAAAT
* *
428514 AAAAATATTTTATATTAAACATGAATTATCATTTAAAAAAT
1 AAAAATATTTTATATTAAACATGAATTACCATCTAAAAAAT
*
428555 AAAATTATTTTATATTAAA
1 AAAAATATTTTATATTAAA
428574 TCTCAAATTA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (41 bp):
AAAAATATTTTATATTAAACATGAATTACCATCTAAAAAAT
Found at i:428574 original size:20 final size:20
Alignment explanation
Indices: 428510--428574 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
428500 ACCATCTAAA
*
428510 AAATAAAAATATTTTATATT
1 AAATAAAATTATTTTATATT
* * *
428530 AAACATGAATTATCATTTA-A-A
1 AAATA-AAATTAT--TTTATATT
428551 AAATAAAATTATTTTATATT
1 AAATAAAATTATTTTATATT
428571 AAAT
1 AAAT
428575 CTCAAATTAT
Statistics
Matches: 33, Mismatches: 7, Indels: 10
0.66 0.14 0.20
Matches are distributed among these distances:
18 4 0.12
19 1 0.03
20 14 0.42
21 9 0.27
22 1 0.03
23 4 0.12
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.42
Consensus pattern (20 bp):
AAATAAAATTATTTTATATT
Found at i:428594 original size:41 final size:41
Alignment explanation
Indices: 428473--428607 Score: 159
Period size: 41 Copynumber: 3.3 Consensus size: 41
428463 TTTTTTATTA
* * * *
428473 AAAAATATTTCATATTAAACATGAATTACCATCTAAAAAAT
1 AAAAATATTTTATATTAAACATAAATTATCATTTAAAAAAT
*
428514 AAAAATATTTTATATTAAACATGAATTATCATTTAAAAAAT
1 AAAAATATTTTATATTAAACATAAATTATCATTTAAAAAAT
* *
428555 AAAATTATTTTATATTAAATC-TCAAATTATTATTT-AAAAAT
1 AAAAATATTTTATATTAAA-CAT-AAATTATCATTTAAAAAAT
428596 AATAAA-ATTTTA
1 AA-AAATATTTTA
428608 AAAAATATTC
Statistics
Matches: 84, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
41 71 0.85
42 13 0.15
ACGTcount: A:0.53, C:0.07, G:0.01, T:0.39
Consensus pattern (41 bp):
AAAAATATTTTATATTAAACATAAATTATCATTTAAAAAAT
Found at i:428603 original size:22 final size:22
Alignment explanation
Indices: 428537--428604 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
428527 ATTAAACATG
*
428537 AATTATCATTT-AAAA-AATAA
1 AATTATTATTTAAAAATAATAA
* * *
428557 AATTATT-TTATATTAAAT-CTCA
1 AATTATTATT-TA-AAAATAATAA
428579 AATTATTATTTAAAAATAATAA
1 AATTATTATTTAAAAATAATAA
428601 AATT
1 AATT
428605 TTAAAAAATA
Statistics
Matches: 35, Mismatches: 7, Indels: 10
0.67 0.13 0.19
Matches are distributed among these distances:
19 2 0.06
20 7 0.20
21 4 0.11
22 20 0.57
23 2 0.06
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (22 bp):
AATTATTATTTAAAAATAATAA
Found at i:428610 original size:52 final size:51
Alignment explanation
Indices: 428554--429067 Score: 397
Period size: 52 Copynumber: 9.8 Consensus size: 51
428544 ATTTAAAAAA
*
428554 TAAAATTATTTTATATTAAATCTCAAATTATTATTTAAAAATAATAAAATTT
1 TAAAA-TATTTTATATTAAATCTCAAATTACTATTTAAAAATAATAAAATTT
* *
428606 TAAAAAATATTCTATATTAAATCTCAAAATTACCATTTAAAACAATAATAAAAATTT
1 T--AAAATATTTTATATTAAATCTC-AAATTACTATTT-AAA-AATAAT-AAAATTT
* * * * * *
428663 AAAAAAATAGTTTATACTAACTC-CAGATTACTATTT-AAAATAAGAAAAATTTT
1 --TAAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAA-TAAAA-TTT
* *
428716 TAAAATATTTTATACTAAA-CTCCATATTACTATTTAAAAATAATAAAAATTT
1 TAAAATATTTTATATTAAATCT-CAAATTACTATTTAAAAATAAT-AAAATTT
* * * ** * **
428768 TAAAAAATTTTTAATATCAAATTTTGAATTATTA-TCCAAAATAATAATAATTT
1 TAAAATA-TTTT-ATATTAAATCTCAAATTACTATTTAAAAATAATAA-AATTT
* ** *
428821 TAAAATATTTTATATTAAATTTTGAATTAGTATTT-AAAATAATAAAATTT
1 TAAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAATAAAATTT
* * *
428871 AAAAAATATTTTA-ATTTAAATATCGAATTACTATTTAAAAATAATAAAAATTT
1 -TAAAATATTTTATA-TTAAATCTCAAATTACTATTTAAAAATAAT-AAAATTT
* * *
428924 TAAAATATTTTATATTAAATTTAAAATTATTATTTAAAAAT-A-AAAA---
1 TAAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAATAAAATTT
* * *
428970 -AATATATTTTATATTAAATCTCGAATTACTATTTAAAAGATAATAAAA-AT
1 TAAAATATTTTATATTAAATCTCAAATTACTATTTAAAA-ATAATAAAATTT
* *
429020 TAATATGTATGTATTTTATATTAAATCTTAAATTATTATTTAAAAATA
1 TAA-A---A--TATTTTATATTAAATCTCAAATTACTATTTAAAAATA
429068 TTTTATATGA
Statistics
Matches: 378, Mismatches: 48, Indels: 68
0.77 0.10 0.14
Matches are distributed among these distances:
45 33 0.09
46 2 0.01
47 1 0.00
48 4 0.01
49 4 0.01
50 7 0.02
51 77 0.20
52 80 0.21
53 65 0.17
54 26 0.07
55 15 0.04
56 10 0.03
57 54 0.14
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (51 bp):
TAAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAATAAAATTT
Found at i:428721 original size:108 final size:106
Alignment explanation
Indices: 428580--428775 Score: 261
Period size: 108 Copynumber: 1.8 Consensus size: 106
428570 TAAATCTCAA
* * *
428580 ATTATTATTTAAAAATAATAAAATTTTAAAAAATATTCTATATTAAATCTCAAAATTACCATTTA
1 ATTACTATTTAAAAATAAAAAAATTTTAAAAAATATTCTATACTAAA-CTCAAAATTACCATTT-
428645 AAACAATAATAAAAATTTAAAAAAATAGTTTATACTAACTCCAG
64 AAA-AATAATAAAAATTTAAAAAAATAGTTTATACTAACTCCAG
* * * * *
428689 ATTACTATTT-AAAATAAGAAAAATTTT-TAAAATATTTTATACTAAACTCCATATTACTATTTA
1 ATTACTATTTAAAAATAA-AAAAATTTTAAAAAATATTCTATACTAAACTCAAAATTACCATTTA
*
428752 AAAATAATAAAAATTTTAAAAAAT
65 AAAATAATAAAAATTTAAAAAAAT
428776 TTTTAATATC
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
105 21 0.27
106 3 0.04
107 13 0.17
108 23 0.30
109 17 0.22
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.37
Consensus pattern (106 bp):
ATTACTATTTAAAAATAAAAAAATTTTAAAAAATATTCTATACTAAACTCAAAATTACCATTTAA
AAATAATAAAAATTTAAAAAAATAGTTTATACTAACTCCAG
Found at i:428964 original size:21 final size:20
Alignment explanation
Indices: 428914--428964 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 20
428904 TTTAAAAATA
428914 ATAAAAATTTTAAAATATTTT
1 ATAAAAA-TTTAAAATATTTT
*
428935 ATATTAAATTTAAAATTATTATT
1 ATA-AAAATTTAAAA-TATT-TT
428958 -TAAAAAT
1 ATAAAAAT
428965 AAAAAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 14 0.56
22 9 0.36
23 2 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATAAAAATTTAAAATATTTT
Found at i:429100 original size:35 final size:35
Alignment explanation
Indices: 429031--429099 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
429021 AATATGTATG
*
429031 TATTTTATATTAAATCTTAAATTATTATTTAAAAA
1 TATTTTATATGAAATCTTAAATTATTATTTAAAAA
* *
429066 TATTTTATATGAAATCTTGATTTATT-TTTAAAAA
1 TATTTTATATGAAATCTTAAATTATTATTTAAAAA
429100 AATAACAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
34 8 0.26
35 23 0.74
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (35 bp):
TATTTTATATGAAATCTTAAATTATTATTTAAAAA
Found at i:429248 original size:51 final size:50
Alignment explanation
Indices: 429061--429445 Score: 243
Period size: 51 Copynumber: 7.6 Consensus size: 50
429051 ATTATTATTT
* * * * * * *
429061 AAAAATATTTTATATGAAATCTTGATTTATTTTTAAAAAAATAACAAAATAA
1 AAAAATATTTTATATTAAATC-TAAATTATTTTTTAAATAATTA-AAAATTA
* * * *
429113 AAAATATATTTTATATTAAATTTTAAATTACTATTTAAATAATAATAATAAATTTT
1 AAAA-ATATTTTATATTAAA-TCTAAATTATTTTTTAAATAAT--TAA-AAA-TTA
** *
429169 AAAAATATTTCGTATTAAATCTCAAATTATTTTTTAAATATTTAAAAATTA
1 AAAAATATTTTATATTAAATCT-AAATTATTTTTTAAATAATTAAAAATTA
* ** *
429220 AAAAATATTTTATAATAAATCTAGAATTAATATTTAAAAATAATAAAAAATT-
1 AAAAATATTTTATATTAAATCTA-AATT-AT-TTTTTAAATAATTAAAAATTA
* * * * *
429272 -AAAATATGTTATATCAAATCCTAAATTACTTTTTAAAAAAATAAAAA-T-
1 AAAAATATTTTATATTAAAT-CTAAATTATTTTTTAAATAATTAAAAATTA
* ** * * * *
429320 AGAAATAGTTTTACCTTAAATCTATTATTACTATTGAAA-AATT-----TTA
1 AAAAATA-TTTTATATTAAATCTA-AATTATTTTTTAAATAATTAAAAATTA
* *
429366 AAAAATATTTTATATTAAATCTCAAATTATTTTTTAAA-AAATAAAGATTA
1 AAAAATATTTTATATTAAATCT-AAATTATTTTTTAAATAATTAAAAATTA
429416 AAAAATTATTTTATATTAAATCTATAATTA
1 AAAAA-TATTTTATATTAAATCTA-AATTA
429446 CTATTTGTCG
Statistics
Matches: 258, Mismatches: 51, Indels: 49
0.72 0.14 0.14
Matches are distributed among these distances:
45 27 0.10
46 7 0.03
48 1 0.00
49 24 0.09
50 31 0.12
51 67 0.26
52 12 0.05
53 47 0.18
54 4 0.02
55 33 0.13
56 5 0.02
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (50 bp):
AAAAATATTTTATATTAAATCTAAATTATTTTTTAAATAATTAAAAATTA
Found at i:429393 original size:95 final size:96
Alignment explanation
Indices: 429272--429450 Score: 231
Period size: 96 Copynumber: 1.9 Consensus size: 96
429262 ATAAAAAATT
*
429272 AAAATATGTTATATCAAATCCTAAATTACTTTTTAAAAAAATAAA-AAT-AGAAA-TAGTTTTAC
1 AAAATATGTTATATCAAATCCTAAATTA-TTTTTAAAAAAATAAAGAATAAAAAATTA-TTTTAC
* *
429334 CTTAAATCTATTATTACTATTGAAAAATTTTAA
64 ATTAAATCTATAATTACTATTGAAAAATTTTAA
* * * * *
429367 AAAATATTTTATATTAAAT-CTCAAATTATTTTTTAAAAAATAAAGATTAAAAAATTATTTTATA
1 AAAATATGTTATATCAAATCCT-AAATTATTTTTAAAAAAATAAAGAATAAAAAATTATTTTACA
429431 TTAAATCTATAATTACTATT
65 TTAAATCTATAATTACTATT
429451 TGTCGTAACG
Statistics
Matches: 72, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
94 17 0.24
95 25 0.35
96 28 0.39
97 2 0.03
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.42
Consensus pattern (96 bp):
AAAATATGTTATATCAAATCCTAAATTATTTTTAAAAAAATAAAGAATAAAAAATTATTTTACAT
TAAATCTATAATTACTATTGAAAAATTTTAA
Found at i:431665 original size:21 final size:22
Alignment explanation
Indices: 431641--431681 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
431631 AACATGTCAT
431641 AAATGCATGAAGCAT-AGCTCA
1 AAATGCATGAAGCATGAGCTCA
*
431662 AAATGCATGAATCATGAGCT
1 AAATGCATGAAGCATGAGCT
431682 GTTAACATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (22 bp):
AAATGCATGAAGCATGAGCTCA
Found at i:432604 original size:52 final size:52
Alignment explanation
Indices: 432526--432654 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
432516 CGAAATATGA
432526 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
432578 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
432630 AAATTTGCCTGCATGTATTGATACA
1 AAATTTGCCTGCATGTATCGATACA
432655 ATGTATCGAT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:432744 original size:19 final size:18
Alignment explanation
Indices: 432720--432784 Score: 77
Period size: 19 Copynumber: 3.8 Consensus size: 18
432710 AACTGTACAT
432720 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAA-TTA
432739 TGTATCGATAC---A-T-
1 TGTATCGATACAAAATTA
432752 TGTATCGATACAACAATTA
1 TGTATCGATACAA-AATTA
432771 TGTATCGATACAAA
1 TGTATCGATACAAA
432785 TCGTTGAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
16 1 0.03
17 1 0.03
18 2 0.05
19 24 0.60
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.32
Consensus pattern (18 bp):
TGTATCGATACAAAATTA
Found at i:432756 original size:32 final size:32
Alignment explanation
Indices: 432715--432782 Score: 120
Period size: 32 Copynumber: 2.1 Consensus size: 32
432705 TTCGTAACTG
432715 TACATTGTATCGATACAA-AACTTATGTATCGA
1 TACATTGTATCGATACAACAA-TTATGTATCGA
432747 TACATTGTATCGATACAACAATTATGTATCGA
1 TACATTGTATCGATACAACAATTATGTATCGA
432779 TACA
1 TACA
432783 AATCGTTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
32 33 0.94
33 2 0.06
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (32 bp):
TACATTGTATCGATACAACAATTATGTATCGA
Found at i:432757 original size:13 final size:13
Alignment explanation
Indices: 432739--432763 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
432729 ACAAAACTTA
432739 TGTATCGATACAT
1 TGTATCGATACAT
432752 TGTATCGATACA
1 TGTATCGATACA
432764 ACAATTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Done.