Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 3 of 171
Found at i:876793 original size:23 final size:23
Alignment explanation
Indices: 876746--876818 Score: 85
Period size: 24 Copynumber: 3.1 Consensus size: 23
876736 TTTAATATTG
* *
876746 TTTTTTTACTATTTTGGTTGCTAT
1 TTTTTTTACTATTTT-GATGTTAT
*
876770 TTTTTTTGCTATTTTGATGTTA-
1 TTTTTTTACTATTTTGATGTTAT
*
876792 TTTTTTTACTATTTTGATTGTTGT
1 TTTTTTTACTATTTTGA-TGTTAT
876816 TTT
1 TTT
876819 GTTGTTATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
22 16 0.38
23 9 0.21
24 17 0.40
ACGTcount: A:0.12, C:0.05, G:0.12, T:0.70
Consensus pattern (23 bp):
TTTTTTTACTATTTTGATGTTAT
Found at i:876796 original size:12 final size:12
Alignment explanation
Indices: 876755--876919 Score: 83
Period size: 12 Copynumber: 14.1 Consensus size: 12
876745 GTTTTTTTAC
* *
876755 TATTTTGGTTGC
1 TATTTTTGTTGT
* *
876767 TATTTTTTTTGC
1 TATTTTTGTTGT
*
876779 TA-TTTTGATGT
1 TATTTTTGTTGT
**
876790 TATTTTT-TTAC
1 TATTTTTGTTGT
876801 TA-TTTTGATTGT
1 TATTTTTG-TTGT
*
876813 T-GTTTTGTTGT
1 TATTTTTGTTGT
* *
876824 TATTTTTTTTAT
1 TATTTTTGTTGT
*
876836 TA-TTTTGGTGT
1 TATTTTTGTTGT
* *
876847 TGTTTTTATTGT
1 TATTTTTGTTGT
*
876859 TATTTTTGTTGC
1 TATTTTTGTTGT
*
876871 TATTTTT-TCTAT
1 TATTTTTGT-TGT
*
876883 TATTTTTGCTGT
1 TATTTTTGTTGT
* *
876895 T-GTTTTGATTAT
1 TATTTTTG-TTGT
*
876907 TATTTTGGTTGT
1 TATTTTTGTTGT
876919 T
1 T
876920 TGGATGTTAT
Statistics
Matches: 111, Mismatches: 32, Indels: 20
0.68 0.20 0.12
Matches are distributed among these distances:
10 4 0.04
11 29 0.26
12 74 0.67
13 4 0.04
ACGTcount: A:0.12, C:0.04, G:0.15, T:0.70
Consensus pattern (12 bp):
TATTTTTGTTGT
Found at i:876804 original size:34 final size:35
Alignment explanation
Indices: 876766--876842 Score: 93
Period size: 34 Copynumber: 2.2 Consensus size: 35
876756 ATTTTGGTTG
**
876766 CTATTTTTTTTGCTATTTTGATGTTA-TTTTTTTA
1 CTATTTTGATTGCTATTTTGATGTTATTTTTTTTA
* * *
876800 CTATTTTGATTGTTGTTTTGTTGTTATTTTTTTTA
1 CTATTTTGATTGCTATTTTGATGTTATTTTTTTTA
*
876835 TTATTTTG
1 CTATTTTG
876843 GTGTTGTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
34 21 0.58
35 15 0.42
ACGTcount: A:0.13, C:0.04, G:0.12, T:0.71
Consensus pattern (35 bp):
CTATTTTGATTGCTATTTTGATGTTATTTTTTTTA
Found at i:876827 original size:23 final size:23
Alignment explanation
Indices: 876754--876876 Score: 95
Period size: 23 Copynumber: 5.3 Consensus size: 23
876744 TGTTTTTTTA
* * *
876754 CTATTTTGGTTGCTATTTTTTTTG
1 CTATTTTGATTGTTA-TTTTGTTG
* *
876778 CTATTTTGA-TGTTATTTTTTTA
1 CTATTTTGATTGTTATTTTGTTG
*
876800 CTATTTTGATTGTTGTTTTGTTG
1 CTATTTTGATTGTTATTTTGTTG
* ** * *
876823 TTATTTTTTTTATTATTTTGGTG
1 CTATTTTGATTGTTATTTTGTTG
* * *
876846 TTGTTTTTATTGTTATTTTTGTTG
1 CTATTTTGATTGTTA-TTTTGTTG
876870 CTATTTT
1 CTATTTT
876877 TTCTATTATT
Statistics
Matches: 79, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
22 16 0.20
23 43 0.54
24 20 0.25
ACGTcount: A:0.11, C:0.04, G:0.15, T:0.70
Consensus pattern (23 bp):
CTATTTTGATTGTTATTTTGTTG
Found at i:876839 original size:46 final size:45
Alignment explanation
Indices: 876735--876889 Score: 123
Period size: 46 Copynumber: 3.4 Consensus size: 45
876725 TATATTGTTA
* * * *
876735 TTTTAATATTGTTTTTTTACTATTTTGGTTGCTATTTTTTTTGCTA-
1 TTTTTATATTATTTTTTTACTATTTTGATTG-T-TTTTTGTTGCTAT
* * *
876781 TTTTGATGTTATTTTTTTACTATTTTGATTGTTGTTTTGTTGTTAT
1 TTTTTATATTATTTTTTTACTATTTTGATTGTT-TTTTGTTGCTAT
* ** ** * *
876827 TTTTTTTATTATTTTGGTGTTGTTTTTATTGTTATTTTTGTTGCTAT
1 TTTTTATATTATTTTTTTACTATTTTGATTG-T-TTTTTGTTGCTAT
*
876874 TTTTTCTATTATTTTT
1 TTTTTATATTATTTTT
876890 GCTGTTGTTT
Statistics
Matches: 87, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
44 1 0.01
45 10 0.11
46 49 0.56
47 26 0.30
48 1 0.01
ACGTcount: A:0.13, C:0.04, G:0.12, T:0.71
Consensus pattern (45 bp):
TTTTTATATTATTTTTTTACTATTTTGATTGTTTTTTGTTGCTAT
Found at i:876848 original size:34 final size:36
Alignment explanation
Indices: 876781--876876 Score: 117
Period size: 35 Copynumber: 2.8 Consensus size: 36
876771 TTTTTTGCTA
* *
876781 TTTTGATGTTA-TTTTTTTACTATTTTGATTGTTG-
1 TTTTGTTGTTATTTTTTTTACTATTTTGAGTGTTGT
*
876815 TTTTGTTGTTATTTTTTTTATTATTTTG-GTGTTGT
1 TTTTGTTGTTATTTTTTTTACTATTTTGAGTGTTGT
* * *
876850 TTTTATTGTTATTTTTGTTGCTATTTT
1 TTTTGTTGTTATTTTTTTTACTATTTT
876877 TTCTATTATT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
34 15 0.28
35 38 0.72
ACGTcount: A:0.11, C:0.02, G:0.15, T:0.72
Consensus pattern (36 bp):
TTTTGTTGTTATTTTTTTTACTATTTTGAGTGTTGT
Found at i:876853 original size:24 final size:23
Alignment explanation
Indices: 876815--876915 Score: 89
Period size: 23 Copynumber: 4.3 Consensus size: 23
876805 TTGATTGTTG
* * *
876815 TTTTGTTGTTATTTTTTTTATTA
1 TTTTGGTGTTGTTTTTATTATTA
*
876838 TTTTGGTGTTGTTTTTATTGTTA
1 TTTTGGTGTTGTTTTTATTATTA
*
876861 TTTT--TGTTGCTATTTTTTCTATTA
1 TTTTGGTGTTG-T-TTTTAT-TATTA
* *
876885 TTTTTGCTGTTGTTTTGATTATTA
1 -TTTTGGTGTTGTTTTTATTATTA
876909 TTTTGGT
1 TTTTGGT
876916 TGTTTGGATG
Statistics
Matches: 63, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
21 5 0.08
22 1 0.02
23 34 0.54
24 9 0.14
25 8 0.13
26 1 0.02
27 5 0.08
ACGTcount: A:0.11, C:0.03, G:0.15, T:0.71
Consensus pattern (23 bp):
TTTTGGTGTTGTTTTTATTATTA
Found at i:876897 original size:48 final size:47
Alignment explanation
Indices: 876815--876917 Score: 143
Period size: 48 Copynumber: 2.2 Consensus size: 47
876805 TTGATTGTTG
* * * * *
876815 TTTTGTTGTTATTTTTTTTATTATTTTGGTGTTGTTTTTATTGTTAT
1 TTTTGTTGCTATTTTTTCTATTATTTTGCTGTTGTTTTGATTATTAT
876862 TTTTGTTGCTATTTTTTCTATTATTTTTGCTGTTGTTTTGATTATTAT
1 TTTTGTTGCTATTTTTTCTATTA-TTTTGCTGTTGTTTTGATTATTAT
*
876910 TTTGGTTG
1 TTTTGTTG
876918 TTTGGATGTT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
47 21 0.43
48 28 0.57
ACGTcount: A:0.11, C:0.03, G:0.16, T:0.71
Consensus pattern (47 bp):
TTTTGTTGCTATTTTTTCTATTATTTTGCTGTTGTTTTGATTATTAT
Found at i:876933 original size:21 final size:23
Alignment explanation
Indices: 876880--876933 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 23
876870 CTATTTTTTC
*
876880 TATTATTTTTGCTGTTGTTTTGAT
1 TATTATTTTTGC-GTTGTTTGGAT
876904 TATTA-TTTTG-GTTGTTTGGA-
1 TATTATTTTTGCGTTGTTTGGAT
*
876924 TGTTATTTTT
1 TATTATTTTT
876934 ATACATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 4 0.15
21 13 0.48
23 5 0.19
24 5 0.19
ACGTcount: A:0.13, C:0.02, G:0.19, T:0.67
Consensus pattern (23 bp):
TATTATTTTTGCGTTGTTTGGAT
Found at i:877712 original size:19 final size:20
Alignment explanation
Indices: 877688--877743 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
877678 AATTATCGAC
*
877688 TTAATTTTTATATTTT-AAT
1 TTAATTTATATATTTTGAAT
*
877707 TTAATTTATATTTTTTGAATT
1 TTAATTTATATATTTTGAA-T
*
877728 TTAAATTATAATATTT
1 TTAATTTAT-ATATTT
877744 AAAGTTTTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 14 0.47
20 2 0.07
21 9 0.30
22 5 0.17
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
TTAATTTATATATTTTGAAT
Found at i:878754 original size:12 final size:12
Alignment explanation
Indices: 878737--878761 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
878727 CACAAAGAAT
878737 AGGAAAACCATC
1 AGGAAAACCATC
878749 AGGAAAACCATC
1 AGGAAAACCATC
878761 A
1 A
878762 ATACAAAAAA
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:0.52, C:0.24, G:0.16, T:0.08
Consensus pattern (12 bp):
AGGAAAACCATC
Found at i:883947 original size:21 final size:20
Alignment explanation
Indices: 883932--883969 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
883922 GTTTTATCAC
883932 AATTTAATTT-TTTTTTAATA
1 AATTTAATTTATTTTTT-ATA
*
883952 TATTTAATTTATTTTTTA
1 AATTTAATTTATTTTTTA
883970 AAAAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
AATTTAATTTATTTTTTATA
Found at i:889964 original size:83 final size:83
Alignment explanation
Indices: 889803--890056 Score: 337
Period size: 84 Copynumber: 3.0 Consensus size: 83
889793 GTCAAAATTA
* * * * *
889803 TAATTCATGAAACTAGTCTTCATTTGTTTGACATTACAACATATATATTTCATTTAAATTGCAAT
1 TAATCCATGGAACTACTCTACATTTGTTTGACATTACTA-A-ATATATTTCATTTAAATTGCAAT
889868 TCAAATTAATACAATTTTGT
64 TCAAATTAATACAATTTTGT
* *
889888 TAATCCATGGTACTACTCTACATTTGTTTGACATTACTAAATATATTTCATTTAAATTGCAATTT
1 TAATCCATGGAACTACTCTACATTTGTTTGACATTACTAAATATATTTCATTTAAATTGCAATTC
* ** *
889953 AAATTTATACAAGCTTGC
66 AAATTAATACAATTTTGT
* * * *
889971 TAATCCATGGAACTATTGATACATTTGTTTGACATTACTAAATGTATTTCATTTAAATTGCAAAT
1 TAATCCATGGAACTACT-CTACATTTGTTTGACATTACTAAATATATTTCATTTAAATTGCAATT
*
890036 CAAATTGATACAATTTTGT
65 CAAATTAATACAATTTTGT
890055 TA
1 TA
890057 GATTTGACTT
Statistics
Matches: 147, Mismatches: 21, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
83 53 0.36
84 61 0.41
85 33 0.22
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (83 bp):
TAATCCATGGAACTACTCTACATTTGTTTGACATTACTAAATATATTTCATTTAAATTGCAATTC
AAATTAATACAATTTTGT
Found at i:891196 original size:21 final size:21
Alignment explanation
Indices: 891154--891196 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
891144 TAATAGTAAA
*
891154 TTTAAAAAAAATCTTAAAAAT
1 TTTAAAAAAAATCATAAAAAT
*
891175 TTTAAATAAAAAT-ATAAGAAT
1 TTTAAA-AAAAATCATAAAAAT
891196 T
1 T
891197 GAATATTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (21 bp):
TTTAAAAAAAATCATAAAAAT
Found at i:891234 original size:29 final size:28
Alignment explanation
Indices: 891171--891236 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 28
891161 AAAATCTTAA
*
891171 AAATTTT--AAATAAAAATATAAGAATT
1 AAATTTTCAAAATAAAAATATAAAAATT
* *
891197 GAATATTTCAAAATTAAAATATAAAAAATT
1 AAAT-TTTCAAAATAAAAATAT-AAAAATT
891227 AAATTTTCAA
1 AAATTTTCAA
891237 TTTCAAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
26 3 0.09
27 3 0.09
29 17 0.53
30 9 0.28
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (28 bp):
AAATTTTCAAAATAAAAATATAAAAATT
Found at i:895770 original size:19 final size:22
Alignment explanation
Indices: 895736--895780 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 22
895726 AATTGTATAA
*
895736 AATTTATATATAAATACTAA-T
1 AATTTATATATAAATAATAATT
895757 AATTT-TAT-TAAATAATAATT
1 AATTTATATATAAATAATAATT
895777 AATT
1 AATT
895781 ATAACTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 9 0.41
20 8 0.36
21 5 0.23
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
AATTTATATATAAATAATAATT
Found at i:904877 original size:18 final size:19
Alignment explanation
Indices: 904828--904877 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
904818 GATAATAAAA
*
904828 ATAATATACT-AAAGTTAT
1 ATAATAAACTAAAAGTTAT
* **
904846 AAAATAAAAAAAAAG-TAT
1 ATAATAAACTAAAAGTTAT
904864 ATAATAAACTAAAA
1 ATAATAAACTAAAA
904878 TGTAATGAAA
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.26
Consensus pattern (19 bp):
ATAATAAACTAAAAGTTAT
Found at i:905675 original size:31 final size:31
Alignment explanation
Indices: 905640--905749 Score: 82
Period size: 31 Copynumber: 3.5 Consensus size: 31
905630 AATATTTTTT
905640 ATCAATAAATCATAATTTGAGTTTTAAAATA
1 ATCAATAAATCATAATTTGAGTTTTAAAATA
* ** * * * *
905671 ATCAAAGTACAA--AT-ATTTAAGCCCTGATATTT
1 ATC-AA-TA-AATCATAATTTGAG-TTTTAAAATA
*
905703 ATCAATAAATTATAATTTGAGTTTTAAAATA
1 ATCAATAAATCATAATTTGAGTTTTAAAATA
*
905734 ATCAATACATCATAAT
1 ATCAATAAATCATAAT
905750 AGAAAAATAT
Statistics
Matches: 56, Mismatches: 16, Indels: 14
0.65 0.19 0.16
Matches are distributed among these distances:
29 2 0.04
30 2 0.04
31 31 0.55
32 17 0.30
33 2 0.04
34 2 0.04
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.37
Consensus pattern (31 bp):
ATCAATAAATCATAATTTGAGTTTTAAAATA
Found at i:905885 original size:24 final size:25
Alignment explanation
Indices: 905840--905892 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
905830 ATTACATAGA
*
905840 AATAAAATTAACAAAAATAAAACAC
1 AATAAAATTAACAAAAAGAAAACAC
* *
905865 AATAAATTTAAC-ACAAGAAAACAC
1 AATAAAATTAACAAAAAGAAAACAC
905889 AATA
1 AATA
905893 GCCCATCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.68, C:0.13, G:0.02, T:0.17
Consensus pattern (25 bp):
AATAAAATTAACAAAAAGAAAACAC
Found at i:906978 original size:3 final size:3
Alignment explanation
Indices: 906972--907028 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
906962 AAATAGATAG
906972 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
907020 ATT ATT ATT
1 ATT ATT ATT
907029 GTCAAGAAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:919182 original size:10 final size:11
Alignment explanation
Indices: 919144--919200 Score: 53
Period size: 11 Copynumber: 5.0 Consensus size: 11
919134 ATATATATAT
*
919144 TTATTTAAAAA
1 TTATATAAAAA
*
919155 TCATATAAAAAA
1 TTATAT-AAAAA
919167 CTT-TATTAAAAA
1 -TTATA-TAAAAA
919179 TTATATAAAAA
1 TTATATAAAAA
*
919190 TAATATAAAAA
1 TTATATAAAAA
919201 ATTTTAATAC
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 22 0.58
12 14 0.37
13 2 0.05
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (11 bp):
TTATATAAAAA
Found at i:919184 original size:24 final size:25
Alignment explanation
Indices: 919143--919189 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
919133 TATATATATA
919143 TTTATTTAAAAATCATATAAAAAAC
1 TTTATTTAAAAATCATATAAAAAAC
*
919168 TTTA-TTAAAAATTATATAAAAA
1 TTTATTTAAAAATCATATAAAAA
919190 TAATATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (25 bp):
TTTATTTAAAAATCATATAAAAAAC
Found at i:919189 original size:12 final size:12
Alignment explanation
Indices: 919150--919203 Score: 58
Period size: 12 Copynumber: 4.6 Consensus size: 12
919140 ATATTTATTT
*
919150 AAAAATCATATA
1 AAAAATTATATA
*
919162 AAAAACTT-TATT
1 AAAAA-TTATATA
919174 AAAAATTATAT-
1 AAAAATTATATA
*
919185 AAAAATAATATA
1 AAAAATTATATA
919197 AAAAATT
1 AAAAATT
919204 TTAATACGGG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
11 12 0.34
12 22 0.63
13 1 0.03
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAAATTATATA
Found at i:922849 original size:18 final size:18
Alignment explanation
Indices: 922815--922849 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
922805 ATTTCTTAAA
*
922815 TATGTTTACGTTGTTTAT
1 TATGTTTACGTTATTTAT
*
922833 TATGTTTAGGTTATTTA
1 TATGTTTACGTTATTTA
922850 GATTACCCAA
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:0.20, C:0.03, G:0.17, T:0.60
Consensus pattern (18 bp):
TATGTTTACGTTATTTAT
Found at i:938678 original size:26 final size:24
Alignment explanation
Indices: 938623--938672 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
938613 TCAACCAGAT
938623 TGATTTTTTAATAGTAGTAACAAA
1 TGATTTTTTAATAGTAGTAACAAA
938647 TG-TTTTTTAATAGTAGTAACAAA
1 TGATTTTTTAATAGTAGTAACAAA
938670 TGA
1 TGA
938673 AATTTTCAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 23 0.92
24 2 0.08
ACGTcount: A:0.40, C:0.04, G:0.14, T:0.42
Consensus pattern (24 bp):
TGATTTTTTAATAGTAGTAACAAA
Found at i:945887 original size:17 final size:17
Alignment explanation
Indices: 945865--945897 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
945855 GTTTGCTCTC
*
945865 TTTTTTTTTAGTTTTAG
1 TTTTTTTTTACTTTTAG
945882 TTTTTTTTTACTTTTA
1 TTTTTTTTTACTTTTA
945898 AAAATTATGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.03, G:0.06, T:0.79
Consensus pattern (17 bp):
TTTTTTTTTACTTTTAG
Found at i:950459 original size:17 final size:17
Alignment explanation
Indices: 950424--950457 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
950414 AAAGGAGATT
*
950424 ATTTTATAATTTATAAA
1 ATTTTATAATTAATAAA
950441 ATTTTA-AATTAATAAA
1 ATTTTATAATTAATAAA
950457 A
1 A
950458 ATAAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTTTATAATTAATAAA
Found at i:953329 original size:15 final size:14
Alignment explanation
Indices: 953309--953344 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
953299 TCTATGTATT
953309 ATATTGAATACCCAA
1 ATATTGAA-ACCCAA
953324 ATATTG-AACCCAA
1 ATATTGAAACCCAA
953337 ATATTGAA
1 ATATTGAA
953345 CTGATTCTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 12 0.60
14 2 0.10
15 6 0.30
ACGTcount: A:0.47, C:0.17, G:0.08, T:0.28
Consensus pattern (14 bp):
ATATTGAAACCCAA
Found at i:953711 original size:62 final size:62
Alignment explanation
Indices: 953614--953736 Score: 201
Period size: 62 Copynumber: 2.0 Consensus size: 62
953604 TCGATGATAA
953614 ATGGCTTTCTCTATTTACATTGTGTACATCAATCAAAAGCGTTCTTTCCCCTTCTCTTCTAT
1 ATGGCTTTCTCTATTTACATTGTGTACATCAATCAAAAGCGTTCTTTCCCCTTCTCTTCTAT
* * * * *
953676 ATGGCTTTTTCTATTTGCTTTGTGTGCATCAATCAAAAGCGTTCTTTCCCGTTCTCTTCTA
1 ATGGCTTTCTCTATTTACATTGTGTACATCAATCAAAAGCGTTCTTTCCCCTTCTCTTCTA
953737 CAATTTAATT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.19, C:0.24, G:0.12, T:0.45
Consensus pattern (62 bp):
ATGGCTTTCTCTATTTACATTGTGTACATCAATCAAAAGCGTTCTTTCCCCTTCTCTTCTAT
Found at i:953936 original size:31 final size:32
Alignment explanation
Indices: 953895--953967 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 32
953885 GCGAAACTTT
* *
953895 TTAAAAAAAAAAAACTT-AACAGTTTAGTTAC
1 TTAAATAAAAAAAACTTGAACAGTTTAGTAAC
*** *
953926 TTAAAT-AAAAACTTTTGAATAGTTTAGTAAC
1 TTAAATAAAAAAAACTTGAACAGTTTAGTAAC
953957 TTAAATAAAAA
1 TTAAATAAAAA
953968 CTTTTGAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
30 7 0.21
31 23 0.68
32 4 0.12
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (32 bp):
TTAAATAAAAAAAACTTGAACAGTTTAGTAAC
Found at i:953968 original size:31 final size:31
Alignment explanation
Indices: 953915--953980 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
953905 AAAACTTAAC
*
953915 AGTTTAGTTACTTAAATAAAAACTTTTGAAT
1 AGTTTAGTAACTTAAATAAAAACTTTTGAAT
953946 AGTTTAGTAACTTAAATAAAAACTTTTGAAT
1 AGTTTAGTAACTTAAATAAAAACTTTTGAAT
953977 AGTT
1 AGTT
953981 CAATGATCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.41
Consensus pattern (31 bp):
AGTTTAGTAACTTAAATAAAAACTTTTGAAT
Found at i:958662 original size:8 final size:8
Alignment explanation
Indices: 958651--958736 Score: 55
Period size: 10 Copynumber: 9.5 Consensus size: 8
958641 TTAAATTTAT
958651 AAAATATA
1 AAAATATA
958659 AAAATATTA
1 AAAATA-TA
958668 AATAATTATTA
1 AA-AA-TA-TA
958679 AAAATTATA
1 AAAA-TATA
*
958688 AAATTTTATA
1 AAA--ATATA
*
958698 AAAATGTAAA
1 AAAA--TATA
958708 AAAATATA
1 AAAATATA
*
958716 AAATATTTA
1 AAA-ATATA
958725 AAAATATA
1 AAAATATA
958733 AAAA
1 AAAA
958737 AATTATACAA
Statistics
Matches: 64, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
8 20 0.31
9 16 0.25
10 21 0.33
11 7 0.11
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (8 bp):
AAAATATA
Found at i:958699 original size:19 final size:20
Alignment explanation
Indices: 958655--958727 Score: 59
Period size: 19 Copynumber: 3.8 Consensus size: 20
958645 ATTTATAAAA
*
958655 TATAAAAA-TATTAAATAAT
1 TATAAAAATTATAAAATAAT
*
958674 TATTAAAAATTATAAAAT-TT
1 TA-TAAAAATTATAAAATAAT
958694 TATAAAAATGTA-AAAA-AA-
1 TATAAAAAT-TATAAAATAAT
958712 TATAAAATATT-TAAAA
1 TATAAAA-ATTATAAAA
958728 ATATAAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
18 12 0.27
19 15 0.33
20 11 0.24
21 7 0.16
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (20 bp):
TATAAAAATTATAAAATAAT
Found at i:958710 original size:10 final size:9
Alignment explanation
Indices: 958651--958765 Score: 54
Period size: 10 Copynumber: 12.1 Consensus size: 9
958641 TTAAATTTAT
958651 AAAATATAAA
1 AAAAT-TAAA
*
958661 AATATT-AA
1 AAAATTAAA
* *
958669 ATAATTATTA
1 AAAATTA-AA
958679 AAAATTATAA
1 AAAATTA-AA
** *
958689 AATTTTATA
1 AAAATTAAA
958698 AAAATGTAAA
1 AAAAT-TAAA
958708 AAAATATAAA
1 AAAAT-TAAA
* *
958718 ATATTTAAA
1 AAAATTAAA
*
958727 AATA-TAAA
1 AAAATTAAA
958735 AAAATTATACA
1 AAAATTA-A-A
*
958746 AAATGTTAAA
1 AAA-ATTAAA
958756 AAAATTAAA
1 AAAATTAAA
958765 A
1 A
958766 TTCATAATAA
Statistics
Matches: 77, Mismatches: 21, Indels: 15
0.68 0.19 0.13
Matches are distributed among these distances:
8 13 0.17
9 18 0.23
10 38 0.49
11 5 0.06
12 3 0.04
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (9 bp):
AAAATTAAA
Found at i:958710 original size:20 final size:19
Alignment explanation
Indices: 958651--958791 Score: 75
Period size: 18 Copynumber: 7.4 Consensus size: 19
958641 TTAAATTTAT
958651 AAAA-TATA-AAAATATTAA
1 AAAATTATATAAAA-ATTAA
* *
958669 ATAATTAT-TAAAAATTAT
1 AAAATTATATAAAAATTAA
*
958687 AAAATTTTATAAAAATGTAA
1 AAAATTATATAAAAAT-TAA
*
958707 AAAA--ATATAAAATATTTA
1 AAAATTATATAAAA-ATTAA
*
958725 AAAA-TATAAAAAAATTATA
1 AAAATTATATAAAAATTA-A
*
958744 CAAAATGT-TAAAAAAATT--
1 -AAAAT-TATATAAAAATTAA
*
958762 AAAATTCATAATAAAAGTATAA
1 AAAATT-AT-ATAAAAAT-TAA
958784 AAAATTAT
1 AAAATTAT
958792 CATATACCAT
Statistics
Matches: 96, Mismatches: 11, Indels: 29
0.71 0.08 0.21
Matches are distributed among these distances:
16 1 0.01
17 5 0.05
18 30 0.31
19 30 0.31
20 11 0.11
21 12 0.12
22 7 0.07
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (19 bp):
AAAATTATATAAAAATTAA
Found at i:958710 original size:29 final size:28
Alignment explanation
Indices: 958651--958765 Score: 103
Period size: 28 Copynumber: 4.0 Consensus size: 28
958641 TTAAATTTAT
* *
958651 AAAA-TATAAAAATATTA-AATAATTATTA
1 AAAATTAT-AAAATATTATAAAAATTA-AA
*
958679 AAAATTATAAAATTTTATAAAAATGTAAA
1 AAAATTATAAAATATTATAAAAAT-TAAA
958708 AAAA-TATAAAATATT-TAAAAATATAAA
1 AAAATTATAAAATATTATAAAAAT-TAAA
* *
958735 AAAATTATACAAAATGTTAAAAAAATTAAA
1 AAAATTAT--AAAATATTATAAAAATTAAA
958765 A
1 A
958766 TTCATAATAA
Statistics
Matches: 73, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
27 15 0.21
28 25 0.34
29 13 0.18
30 14 0.19
31 6 0.08
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (28 bp):
AAAATTATAAAATATTATAAAAATTAAA
Found at i:958756 original size:48 final size:49
Alignment explanation
Indices: 958658--958791 Score: 129
Period size: 49 Copynumber: 2.8 Consensus size: 49
958648 TATAAAATAT
* **
958658 AAAAATATTAAATAATTATTAAAAATTATAAAATTTTATAAAAATGTAA
1 AAAAATATAAAATAATTATTAAAAATTATAAAAAATTATAAAAATGTAA
958707 AAAAATATAAAAT-A-T-TTAAAAA-TATAAAAAAATTATACAAAATGTTAA
1 AAAAATATAAAATAATTATTAAAAATTAT-AAAAAATTATA-AAAATG-TAA
* * *
958755 AAAAAT-TAAAAT--TCATAATAAAAGTATAAAAAATTAT
1 AAAAATATAAAATAATTATTA-AAAATTATAAAAAATTAT
958792 CATATACCAT
Statistics
Matches: 73, Mismatches: 5, Indels: 14
0.79 0.05 0.15
Matches are distributed among these distances:
45 3 0.04
46 16 0.22
47 13 0.18
48 12 0.16
49 26 0.36
50 3 0.04
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.32
Consensus pattern (49 bp):
AAAAATATAAAATAATTATTAAAAATTATAAAAAATTATAAAAATGTAA
Found at i:964936 original size:33 final size:33
Alignment explanation
Indices: 964894--964994 Score: 186
Period size: 34 Copynumber: 3.1 Consensus size: 33
964884 TTATAAAAAG
964894 AAAGAAAAGAAAGAGAGGGAAAGAAGAATATAA
1 AAAGAAAAGAAAGAGAGGGAAAGAAGAATATAA
964927 AAAGAAAAGAAAGAGAGGGAAAGAAGAATATAAA
1 AAAGAAAAGAAAGAGAGGGAAAGAAGAATAT-AA
964961 AAAGAAAAGAAAGAGAGGGAAAGAAGAATA-AA
1 AAAGAAAAGAAAGAGAGGGAAAGAAGAATATAA
964993 AA
1 AA
964995 TCGAACATTG
Statistics
Matches: 67, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
32 4 0.06
33 31 0.46
34 32 0.48
ACGTcount: A:0.68, C:0.00, G:0.27, T:0.05
Consensus pattern (33 bp):
AAAGAAAAGAAAGAGAGGGAAAGAAGAATATAA
Found at i:964968 original size:34 final size:34
Alignment explanation
Indices: 964894--964994 Score: 188
Period size: 33 Copynumber: 3.0 Consensus size: 34
964884 TTATAAAAAG
964894 AAAGAAAAGAAAGAGAGGGAAAGAAGAATAT-AA
1 AAAGAAAAGAAAGAGAGGGAAAGAAGAATATAAA
964927 AAAGAAAAGAAAGAGAGGGAAAGAAGAATATAAA
1 AAAGAAAAGAAAGAGAGGGAAAGAAGAATATAAA
964961 AAAGAAAAGAAAGAGAGGGAAAGAAGAATA-AAA
1 AAAGAAAAGAAAGAGAGGGAAAGAAGAATATAAA
964994 A
1 A
964995 TCGAACATTG
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
33 35 0.52
34 32 0.48
ACGTcount: A:0.68, C:0.00, G:0.27, T:0.05
Consensus pattern (34 bp):
AAAGAAAAGAAAGAGAGGGAAAGAAGAATATAAA
Found at i:974905 original size:25 final size:24
Alignment explanation
Indices: 974860--974907 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
974850 TAAAAAAATA
974860 AATTATATAATACAAATATATTTC
1 AATTATATAATACAAATATATTTC
* *
974884 AATTATATCTATATAAATATATTT
1 AATTATAT-AATACAAATATATTT
974908 ATATTTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (24 bp):
AATTATATAATACAAATATATTTC
Found at i:976871 original size:17 final size:18
Alignment explanation
Indices: 976839--976872 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
976829 AAAAAAAATT
976839 AATTCAAAATATTTATAA
1 AATTCAAAATATTTATAA
*
976857 AATTCCAAA-ATTTATA
1 AATTCAAAATATTTATA
976873 TTTTTTTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTCAAAATATTTATAA
Found at i:976923 original size:20 final size:18
Alignment explanation
Indices: 976889--976941 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 18
976879 TGAAAAATTA
976889 TAAAAA-TTAAAAAAAGT
1 TAAAAATTTAAAAAAAGT
976906 TAAAGAATATATAAAAAAAGT
1 TAAA-AAT-T-TAAAAAAAGT
976927 TAAAAATTTAAAAAA
1 TAAAAATTTAAAAAA
976942 TTTCAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 4 0.12
18 9 0.28
19 1 0.03
20 4 0.12
21 14 0.44
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.25
Consensus pattern (18 bp):
TAAAAATTTAAAAAAAGT
Found at i:977384 original size:75 final size:75
Alignment explanation
Indices: 977290--977436 Score: 249
Period size: 75 Copynumber: 2.0 Consensus size: 75
977280 CTTTACATAA
* *
977290 CATAGCGTTTCAGTAAATTTATGCTTCTAGATGAAATTAAGGCTAGCCGTCTTGCTTGTCCCTCA
1 CATAACGTTTCAGTAAATTTATGCTTCTAGATGAAATTAAGGCTAGCCATCTTGCTTGTCCCTCA
977355 TCCAAGAAAG
66 TCCAAGAAAG
* * *
977365 CATAACGTTTCAGTAAATTTATGTTTGTAGATGAAATTAAGGCTAGCCATCTTGCTTGTCCCTCC
1 CATAACGTTTCAGTAAATTTATGCTTCTAGATGAAATTAAGGCTAGCCATCTTGCTTGTCCCTCA
977430 TCCAAGA
66 TCCAAGA
977437 TTGCCCTATA
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (75 bp):
CATAACGTTTCAGTAAATTTATGCTTCTAGATGAAATTAAGGCTAGCCATCTTGCTTGTCCCTCA
TCCAAGAAAG
Found at i:991400 original size:21 final size:20
Alignment explanation
Indices: 991357--991397 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
991347 AAAACTAAAA
991357 AACAATTTCTTTTAACTTTTT
1 AACAATTTCTTTT-ACTTTTT
991378 AACAATTTCTATTT-CTTTTT
1 AACAATTTCT-TTTACTTTTT
991398 TAATTATCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 10 0.53
22 3 0.16
ACGTcount: A:0.27, C:0.15, G:0.00, T:0.59
Consensus pattern (20 bp):
AACAATTTCTTTTACTTTTT
Found at i:995534 original size:14 final size:13
Alignment explanation
Indices: 995493--995535 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
995483 ATAATAATAT
995493 TTATTATTTTTAAA
1 TTATTATTTTT-AA
* *
995507 TAATAATTTTTAA
1 TTATTATTTTTAA
995520 TTATTAGTTTTTAA
1 TTATTA-TTTTTAA
995534 TT
1 TT
995536 GAGTTGGAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 6 0.25
14 18 0.75
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (13 bp):
TTATTATTTTTAA
Found at i:999244 original size:21 final size:21
Alignment explanation
Indices: 999220--999259 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
999210 AGAGGATGAC
*
999220 GACGATGATGATGATGATGGG
1 GACGAAGATGATGATGATGGG
999241 GACGAAGATGATGATGATG
1 GACGAAGATGATGATGATG
999260 ACGATGATGG
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:0.40, T:0.23
Consensus pattern (21 bp):
GACGAAGATGATGATGATGGG
Found at i:999295 original size:15 final size:15
Alignment explanation
Indices: 999271--999305 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
999261 CGATGATGGT
*
999271 GAGGATGAAGAAGAG
1 GAGGACGAAGAAGAG
*
999286 GAGGACGAAGAAGAT
1 GAGGACGAAGAAGAG
999301 GAGGA
1 GAGGA
999306 TGATGAGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.46, C:0.03, G:0.46, T:0.06
Consensus pattern (15 bp):
GAGGACGAAGAAGAG
Found at i:1023078 original size:18 final size:17
Alignment explanation
Indices: 1023055--1023095 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
1023045 AGGTATCAAA
1023055 ATAAATAAAATAAAAAGT
1 ATAAATAAAA-AAAAAGT
*
1023073 ATAAAT-ATAAAAAAGT
1 ATAAATAAAAAAAAAGT
1023089 ATAAATA
1 ATAAATA
1023096 TCTAGATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 13 0.62
17 2 0.10
18 6 0.29
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (17 bp):
ATAAATAAAAAAAAAGT
Found at i:1023087 original size:16 final size:16
Alignment explanation
Indices: 1023066--1023096 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1023056 TAAATAAAAT
1023066 AAAAAGTATAAATATA
1 AAAAAGTATAAATATA
1023082 AAAAAGTATAAATAT
1 AAAAAGTATAAATAT
1023097 CTAGATTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (16 bp):
AAAAAGTATAAATATA
Found at i:1025888 original size:19 final size:18
Alignment explanation
Indices: 1025850--1025901 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 18
1025840 ATGTTTTGAT
*
1025850 TTTAATTTTTGTTACTTG
1 TTTAATTTTTTTTACTTG
1025868 TTTAATTTTTTTTA-TTG
1 TTTAATTTTTTTTACTTG
1025885 TGTTAATATTTTTTTAC
1 T-TTAAT-TTTTTTTAC
1025902 AATAATTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 4 0.13
18 18 0.60
19 8 0.27
ACGTcount: A:0.19, C:0.04, G:0.08, T:0.69
Consensus pattern (18 bp):
TTTAATTTTTTTTACTTG
Found at i:1032571 original size:23 final size:22
Alignment explanation
Indices: 1032541--1032585 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
1032531 AATTAGATCT
1032541 GAATTTTAAAATTTCAAAAATA
1 GAATTTTAAAATTTCAAAAATA
* *
1032563 GAATATTTAAATTTTTAAAAATA
1 GAAT-TTTAAAATTTCAAAAATA
1032586 TAAATATAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (22 bp):
GAATTTTAAAATTTCAAAAATA
Found at i:1033668 original size:22 final size:22
Alignment explanation
Indices: 1033640--1033717 Score: 77
Period size: 22 Copynumber: 3.4 Consensus size: 22
1033630 TGTTGAAATT
1033640 TATTTTAAATATATAA-TATTA
1 TATTTTAAATATATAATTATTA
* *
1033661 TATGTTTAAATTTATAATTGTTA
1 TAT-TTTAAATATATAATTATTA
*
1033684 TATTTTAAATTATATATTTAAATTA
1 TATTTTAAA-TATATAATT--ATTA
*
1033709 AATTTTAAA
1 TATTTTAAA
1033718 ATAAGTAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
21 3 0.07
22 18 0.39
23 14 0.30
25 11 0.24
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (22 bp):
TATTTTAAATATATAATTATTA
Found at i:1033705 original size:13 final size:12
Alignment explanation
Indices: 1033681--1033717 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
1033671 TTTATAATTG
1033681 TTATATTTTAAA
1 TTATATTTTAAA
1033693 TTATATATTTAAA
1 TTATAT-TTTAAA
*
1033706 TTAAATTTTAAA
1 TTATATTTTAAA
1033718 ATAAGTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TTATATTTTAAA
Found at i:1047053 original size:16 final size:16
Alignment explanation
Indices: 1047018--1047070 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
1047008 TTTCTTGAAT
1047018 TTAAT-TTATAATTAA
1 TTAATATTATAATTAA
1047033 TTAATATTATAATATAA
1 TTAATATTATAAT-TAA
* *
1047050 -TAATATAAATAATTAT
1 TTAATAT-TATAATTAA
1047066 TTAAT
1 TTAAT
1047071 TAGTATTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 5 0.16
16 15 0.47
17 12 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTAATATTATAATTAA
Found at i:1047993 original size:37 final size:38
Alignment explanation
Indices: 1047943--1048035 Score: 100
Period size: 37 Copynumber: 2.4 Consensus size: 38
1047933 CGGATAGATT
*
1047943 CGATGAGGTACTGGGTACCACTTTA-CTTCG-ACTAGGC
1 CGATGAGGCACTGGGTACCACTTTATCTTCGAACTA-GC
* ** *
1047980 CGATGAGACACTGGGTGTCACTTTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTACCACTTTA-T-CTTCGAACTAGC
1048020 CGATGAGGCACTGGGT
1 CGATGAGGCACTGGGT
1048036 GCCATTCTGG
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
37 21 0.46
40 21 0.46
41 4 0.09
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.28
Consensus pattern (38 bp):
CGATGAGGCACTGGGTACCACTTTATCTTCGAACTAGC
Found at i:1064914 original size:8 final size:8
Alignment explanation
Indices: 1064901--1064934 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
1064891 CATGTGTGTA
1064901 TATATATG
1 TATATATG
*
1064909 TATATATA
1 TATATATG
*
1064917 CATATATG
1 TATATATG
1064925 TATATATG
1 TATATATG
1064933 TA
1 TA
1064935 AAAAAATGGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (8 bp):
TATATATG
Found at i:1067151 original size:28 final size:27
Alignment explanation
Indices: 1067111--1067258 Score: 88
Period size: 28 Copynumber: 5.2 Consensus size: 27
1067101 GAACTTAACA
1067111 TTTTTTTCTAATTTGGTACTTAAACTT
1 TTTTTTTCTAATTTGGTACTTAAACTT
* * *
1067138 TTTTTTGTCTAATTTGTTTCTCAAACTT
1 TTTTTT-TCTAATTTGGTACTTAAACTT
*
1067166 GATATTTTTT-TAAAGTTGGTACTTAAA-TT
1 --T-TTTTTTCT-AATTTGGTACTTAAACTT
** *
1067195 TTTTGGGATCTAATTTGGTACTTGAACTT
1 TTTT--TTTCTAATTTGGTACTTAAACTT
* *
1067224 GACTCTTTTTCCTAATTTGGTACCT-AA-TT
1 ---T-TTTTTTCTAATTTGGTACTTAAACTT
1067253 TTTTTT
1 TTTTTT
1067259 AATATTATTT
Statistics
Matches: 93, Mismatches: 15, Indels: 28
0.68 0.11 0.21
Matches are distributed among these distances:
25 5 0.05
26 4 0.04
27 7 0.08
28 32 0.34
29 8 0.09
30 15 0.16
31 18 0.19
32 1 0.01
33 3 0.03
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.55
Consensus pattern (27 bp):
TTTTTTTCTAATTTGGTACTTAAACTT
Found at i:1067165 original size:59 final size:59
Alignment explanation
Indices: 1067102--1067258 Score: 160
Period size: 58 Copynumber: 2.7 Consensus size: 59
1067092 TTGATAGCTG
* * *
1067102 AACTTAACATTTTTTTCTAATTTGGTACTTAAACTTTTTTTTG-TCTAATTTGTTTCTCA
1 AACTTGACATTTTTTTCTAATTTGGTACTTAAA-TTTTTTTTGATCTAATTTGGTACTCA
* * * ** **
1067161 AACTTGATATTTTTTT-AAAGTTGGTACTTAAATTTTTTGGGATCTAATTTGGTACTTG
1 AACTTGACATTTTTTTCTAATTTGGTACTTAAATTTTTTTTGATCTAATTTGGTACTCA
* *
1067219 AACTTGAC-TCTTTTTCCTAATTTGGTACCT-AATTTTTTTT
1 AACTTGACAT-TTTTTTCTAATTTGGTACTTAAATTTTTTTT
1067259 AATATTATTT
Statistics
Matches: 78, Mismatches: 17, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
57 8 0.10
58 46 0.59
59 24 0.31
ACGTcount: A:0.24, C:0.12, G:0.11, T:0.54
Consensus pattern (59 bp):
AACTTGACATTTTTTTCTAATTTGGTACTTAAATTTTTTTTGATCTAATTTGGTACTCA
Found at i:1075820 original size:17 final size:17
Alignment explanation
Indices: 1075798--1075835 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1075788 AAAAAAAAAA
1075798 TATTATTACACAAACAT
1 TATTATTACACAAACAT
1075815 TATTATTACACAAACAT
1 TATTATTACACAAACAT
1075832 TATT
1 TATT
1075836 CTCCAAGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (17 bp):
TATTATTACACAAACAT
Found at i:1076515 original size:17 final size:17
Alignment explanation
Indices: 1076495--1076530 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1076485 CCAACAACAT
1076495 GAAATGATGAATTCATG
1 GAAATGATGAATTCATG
1076512 GAAATGATGAATTCATG
1 GAAATGATGAATTCATG
1076529 GA
1 GA
1076531 TATGGATGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.28
Consensus pattern (17 bp):
GAAATGATGAATTCATG
Found at i:1080288 original size:8 final size:8
Alignment explanation
Indices: 1080275--1080309 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
1080265 AAATGTATTT
1080275 ATTATATA
1 ATTATATA
1080283 ATTATATA
1 ATTATATA
1080291 ATTATATA
1 ATTATATA
**
1080299 AAAATATA
1 ATTATATA
1080307 ATT
1 ATT
1080310 TCAATATTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
ATTATATA
Found at i:1085423 original size:15 final size:16
Alignment explanation
Indices: 1085405--1085435 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1085395 TTAAAAGTTA
1085405 AAAATT-AAAAAAAAT
1 AAAATTGAAAAAAAAT
1085420 AAAATTGAAAAAAAAT
1 AAAATTGAAAAAAAAT
1085436 GGAGTTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (16 bp):
AAAATTGAAAAAAAAT
Found at i:1090875 original size:4 final size:4
Alignment explanation
Indices: 1090866--1090897 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
1090856 ACTTGATTCG
1090866 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1090898 TTCTTATTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:1097037 original size:3 final size:3
Alignment explanation
Indices: 1097029--1097053 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1097019 TCCTCTTTTC
1097029 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
1097054 GAAGATTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:1099004 original size:1 final size:1
Alignment explanation
Indices: 1098998--1099024 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1098988 TTGCAAAGCA
1098998 GGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGG
1099025 AGGGATTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:1101513 original size:77 final size:77
Alignment explanation
Indices: 1101386--1101543 Score: 316
Period size: 77 Copynumber: 2.1 Consensus size: 77
1101376 AACGTGTAAA
1101386 AGAGTTTAAATGCTATAAAGTTTTTCTAATCTCATGTCATGATATCATTAGGGTCGGTATAATCT
1 AGAGTTTAAATGCTATAAAGTTTTTCTAATCTCATGTCATGATATCATTAGGGTCGGTATAATCT
1101451 TGGTGTAACTTT
66 TGGTGTAACTTT
1101463 AGAGTTTAAATGCTATAAAGTTTTTCTAATCTCATGTCATGATATCATTAGGGTCGGTATAATCT
1 AGAGTTTAAATGCTATAAAGTTTTTCTAATCTCATGTCATGATATCATTAGGGTCGGTATAATCT
1101528 TGGTGTAACTTT
66 TGGTGTAACTTT
1101540 AGAG
1 AGAG
1101544 AAGCTAAGAA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 81 1.00
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.41
Consensus pattern (77 bp):
AGAGTTTAAATGCTATAAAGTTTTTCTAATCTCATGTCATGATATCATTAGGGTCGGTATAATCT
TGGTGTAACTTT
Found at i:1108432 original size:19 final size:19
Alignment explanation
Indices: 1108395--1108432 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1108385 ATCTTACCCA
*
1108395 GAAAAATAAAGAAATAAAG
1 GAAAAATAAAGAAAGAAAG
*
1108414 GAAAAATAAAGATAGAAAG
1 GAAAAATAAAGAAAGAAAG
1108433 CGGACGAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.11
Consensus pattern (19 bp):
GAAAAATAAAGAAAGAAAG
Found at i:1110258 original size:20 final size:18
Alignment explanation
Indices: 1110230--1110284 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 18
1110220 AAATAAGTAT
1110230 AAATAATTTATTAATATATTA
1 AAAT-ATTTA-TAATA-ATTA
1110251 AAATATTTATAATAATTTA
1 AAATATTTATAATAA-TTA
*
1110270 AATATAATTATAATA
1 AA-ATATTTATAATA
1110285 CAAAAATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
18 1 0.03
19 10 0.32
20 16 0.52
21 4 0.13
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AAATATTTATAATAATTA
Found at i:1111648 original size:6 final size:6
Alignment explanation
Indices: 1111637--1111663 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1111627 TGAAACAATA
1111637 TCACAT TCACAT TCACAT TCACAT TCA
1 TCACAT TCACAT TCACAT TCACAT TCA
1111664 ACTTCATTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (6 bp):
TCACAT
Found at i:1117003 original size:14 final size:14
Alignment explanation
Indices: 1116984--1117012 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1116974 TTGTAATATT
1116984 TGTAATTATCTAGG
1 TGTAATTATCTAGG
1116998 TGTAATTATCTAGG
1 TGTAATTATCTAGG
1117012 T
1 T
1117013 TGTTTTAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.45
Consensus pattern (14 bp):
TGTAATTATCTAGG
Found at i:1124020 original size:5 final size:5
Alignment explanation
Indices: 1124010--1124043 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
1124000 CAGTTTGACT
1124010 ATCAA ATCAA ATCAA ATCAA ATCAA ATCAA ATCA
1 ATCAA ATCAA ATCAA ATCAA ATCAA ATCAA ATCA
1124044 TATCTATAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.59, C:0.21, G:0.00, T:0.21
Consensus pattern (5 bp):
ATCAA
Found at i:1124294 original size:21 final size:18
Alignment explanation
Indices: 1124280--1124315 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1124270 CAAAGCTTGG
1124280 ACCCACTTCACCAAATGTT
1 ACCCACTTCACCAAA-GTT
*
1124299 ACCTACTTCACCAAAGT
1 ACCCACTTCACCAAAGT
1124316 ATATTTATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 2 0.12
19 14 0.88
ACGTcount: A:0.33, C:0.36, G:0.06, T:0.25
Consensus pattern (18 bp):
ACCCACTTCACCAAAGTT
Found at i:1128022 original size:42 final size:42
Alignment explanation
Indices: 1127975--1128058 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
1127965 AAAAGGAGTT
* *
1127975 GTTTATGAGTGTTATTT-AGGAATAAAATTATATTTGGGTTTA
1 GTTTATGAGTGTT-TTTGAAGAATAAAATTATATTTGAGTTTA
*
1128017 GTTTATGAGTGTTTTTGAAGAATGAAATTATATTTGAGTTTA
1 GTTTATGAGTGTTTTTGAAGAATAAAATTATATTTGAGTTTA
1128059 AAAATATTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 3 0.08
42 35 0.92
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (42 bp):
GTTTATGAGTGTTTTTGAAGAATAAAATTATATTTGAGTTTA
Found at i:1131005 original size:22 final size:23
Alignment explanation
Indices: 1130965--1131007 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1130955 AACGCTTCTT
*
1130965 TTTTTAGAATTATACAAATAAAA
1 TTTTTAGAATAATACAAATAAAA
*
1130988 TTTTTA-AATAATATAAATAA
1 TTTTTAGAATAATACAAATAA
1131008 TTCTGATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TTTTTAGAATAATACAAATAAAA
Found at i:1131159 original size:21 final size:22
Alignment explanation
Indices: 1131117--1131159 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
1131107 AATCTCTCCT
* *
1131117 TTTTTATATTTAAATTTTAAAA
1 TTTTTATATTTAAATCTCAAAA
*
1131139 TTTTT-TATTTACATCTCAAAA
1 TTTTTATATTTAAATCTCAAAA
1131160 ATCACATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTTATATTTAAATCTCAAAA
Found at i:1132921 original size:18 final size:17
Alignment explanation
Indices: 1132863--1132921 Score: 50
Period size: 18 Copynumber: 3.4 Consensus size: 17
1132853 CTCTTACTCA
1132863 TATTTGTATTTTT-ATTT
1 TATTT-TATTTTTAATTT
* *
1132880 CATTTTA-TTTTAAGCTT
1 TATTTTATTTTTAA-TTT
1132897 TACTTTTATTTTTAATTAT
1 TA-TTTTATTTTTAATT-T
1132916 TATTTT
1 TATTTT
1132922 TAACATATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
15 4 0.12
16 3 0.09
17 7 0.21
18 10 0.30
19 9 0.27
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.69
Consensus pattern (17 bp):
TATTTTATTTTTAATTT
Found at i:1133052 original size:13 final size:13
Alignment explanation
Indices: 1133034--1133058 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1133024 TTTCAAGTTT
1133034 TTTTTAATTAATG
1 TTTTTAATTAATG
1133047 TTTTTAATTAAT
1 TTTTTAATTAAT
1133059 AAATATATTA
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:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATG
Found at i:1134961 original size:30 final size:29
Alignment explanation
Indices: 1134891--1134963 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 29
1134881 TTGATTGCTA
*
1134891 TTTTTACTGTTTTGGTTTTTTTAACTGTT
1 TTTTTACTGTTTTGGTTGTTTTAACTGTT
* * *
1134920 TTAGTTGCTGTTTTGATGTTGTTTT-AGTGTT
1 TT-TTTACTGTTTTG--GTTGTTTTAACTGTT
1134951 TTTTTACTGTTTT
1 TTTTTACTGTTTT
1134964 AGTGTTATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
29 2 0.06
30 19 0.54
31 7 0.20
32 7 0.20
ACGTcount: A:0.10, C:0.05, G:0.18, T:0.67
Consensus pattern (29 bp):
TTTTTACTGTTTTGGTTGTTTTAACTGTT
Found at i:1134974 original size:21 final size:21
Alignment explanation
Indices: 1134856--1134975 Score: 83
Period size: 21 Copynumber: 5.9 Consensus size: 21
1134846 ATTATATTGT
1134856 TGTTTT-GATGTTATTTTTTAC
1 TGTTTTAG-TGTTATTTTTTAC
* *
1134877 TGTTTTGATTGCTA-TTTTTAC
1 TGTTTT-AGTGTTATTTTTTAC
*
1134898 TGTTTT-G-GTT-TTTTTAAC
1 TGTTTTAGTGTTATTTTTTAC
* * * **
1134916 TGTTTTAGTTGCTGTTTTGATGT
1 TGTTTTAG-TGTTATTTT-TTAC
1134939 TGTTTTAGTG-T-TTTTTTAC
1 TGTTTTAGTGTTATTTTTTAC
1134958 TGTTTTAGTGTTATTTTT
1 TGTTTTAGTGTTATTTTT
1134976 ATTGTTATTT
Statistics
Matches: 76, Mismatches: 13, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
18 14 0.18
19 12 0.16
20 5 0.07
21 27 0.36
22 10 0.13
23 8 0.11
ACGTcount: A:0.12, C:0.05, G:0.17, T:0.66
Consensus pattern (21 bp):
TGTTTTAGTGTTATTTTTTAC
Found at i:1134992 original size:12 final size:11
Alignment explanation
Indices: 1134966--1135042 Score: 50
Period size: 12 Copynumber: 6.8 Consensus size: 11
1134956 ACTGTTTTAG
*
1134966 TGTTATTTTTAT
1 TGTTA-TTTTGT
1134978 TGTTATTTGTGT
1 TGTTATTT-TGT
1134990 TG-T-TTTTGT
1 TGTTATTTTGT
* * *
1134999 TTTTGTTTTGC
1 TGTTATTTTGT
1135010 TGTTATTTTTGT
1 TGTTA-TTTTGT
* *
1135022 TGCTGTTTTGAT
1 TGTTATTTTG-T
1135034 TGTTATTTT
1 TGTTATTTT
1135043 TTTATTTGGA
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
9 4 0.08
10 4 0.08
11 17 0.34
12 25 0.50
ACGTcount: A:0.08, C:0.03, G:0.18, T:0.71
Consensus pattern (11 bp):
TGTTATTTTGT
Found at i:1135037 original size:44 final size:43
Alignment explanation
Indices: 1134958--1135045 Score: 99
Period size: 44 Copynumber: 2.0 Consensus size: 43
1134948 GTTTTTTTAC
* *
1134958 TGTTTTAGTGTTATTTTTATTGTTATTTGTGTTGTTTTTGTTTT
1 TGTTTTAGTGTTATTTTTATTGCTATTTGTGTTGTTATT-TTTT
* *
1135002 TGTTTT-GCTGTTATTTTTGTTGCTGTTT-TGATTGTTATTTTTT
1 TGTTTTAG-TGTTATTTTTATTGCTATTTGTG-TTGTTATTTTTT
1135045 T
1 T
1135046 ATTTGGATGC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
43 8 0.21
44 30 0.79
ACGTcount: A:0.08, C:0.02, G:0.18, T:0.72
Consensus pattern (43 bp):
TGTTTTAGTGTTATTTTTATTGCTATTTGTGTTGTTATTTTTT
Found at i:1135048 original size:32 final size:33
Alignment explanation
Indices: 1134918--1135049 Score: 80
Period size: 35 Copynumber: 4.1 Consensus size: 33
1134908 TTTTTAACTG
* * * *
1134918 TTTTAGTTGCTGTTTTGA-TGTT-GTTTTAGTG
1 TTTTTGTTGCTGTTTTGATTGTTATTTTTATTA
* * *
1134949 TTTTT-TTACTGTTTT-AGTGTTATTTTTATTG
1 TTTTTGTTGCTGTTTTGATTGTTATTTTTATTA
* * * *
1134980 TTATTTG-TGTTGTTTTTG-TTTTTGTTTTGCTGTTA
1 TT-TTTGTTGCTG-TTTTGATTGTTATTTT--TATTA
1135015 TTTTTGTTGCTGTTTTGATTGTTATTTTT-TTA
1 TTTTTGTTGCTGTTTTGATTGTTATTTTTATTA
1135047 TTT
1 TTT
1135050 GGATGCTATT
Statistics
Matches: 77, Mismatches: 14, Indels: 19
0.70 0.13 0.17
Matches are distributed among these distances:
29 1 0.01
30 13 0.17
31 13 0.17
32 12 0.16
33 12 0.16
34 9 0.12
35 17 0.22
ACGTcount: A:0.09, C:0.03, G:0.18, T:0.70
Consensus pattern (33 bp):
TTTTTGTTGCTGTTTTGATTGTTATTTTTATTA
Found at i:1136193 original size:24 final size:24
Alignment explanation
Indices: 1136165--1136235 Score: 79
Period size: 24 Copynumber: 2.9 Consensus size: 24
1136155 CGAAGTACTT
*
1136165 AACAGAAGCGCATAAGTGCTGGGA
1 AACAGAAGCACATAAGTGCTGGGA
* *
1136189 AACAGAAGCACGTAAGTGTTGGGA
1 AACAGAAGCACATAAGTGCTGGGA
* *
1136213 AACAGTAGGCACACACAGTGCTG
1 AACAG-AAGCACATA-AGTGCTG
1136236 AACAAAAGCT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
24 26 0.68
25 6 0.16
26 6 0.16
ACGTcount: A:0.37, C:0.18, G:0.31, T:0.14
Consensus pattern (24 bp):
AACAGAAGCACATAAGTGCTGGGA
Found at i:1136249 original size:22 final size:22
Alignment explanation
Indices: 1136221--1136305 Score: 107
Period size: 22 Copynumber: 3.9 Consensus size: 22
1136211 GAAACAGTAG
1136221 GCACACACAGTGCTGAACAAAA
1 GCACACACAGTGCTGAACAAAA
* * * *
1136243 GCTCACATAATGTTGAACAAAA
1 GCACACACAGTGCTGAACAAAA
*
1136265 GCACACACAGTGCTGAACAGAA
1 GCACACACAGTGCTGAACAAAA
* *
1136287 GCACACATAGTGCTAAACA
1 GCACACACAGTGCTGAACA
1136306 GTAGGCGCAC
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.44, C:0.25, G:0.18, T:0.14
Consensus pattern (22 bp):
GCACACACAGTGCTGAACAAAA
Found at i:1148293 original size:30 final size:31
Alignment explanation
Indices: 1148257--1148339 Score: 116
Period size: 30 Copynumber: 2.7 Consensus size: 31
1148247 TTTTATTCAA
* *
1148257 AAAAAAATTATGTTTAGGATAAAATTGAT-C
1 AAAAAAATTATATTTAGGGTAAAATTGATCC
* *
1148287 AAAAAAATTATATTTAGGGT-AATTTGGTCC
1 AAAAAAATTATATTTAGGGTAAAATTGATCC
1148317 AAAAAAATTATATTTAGGGTAAA
1 AAAAAAATTATATTTAGGGTAAA
1148340 CTACATTGGT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
29 6 0.13
30 39 0.83
31 2 0.04
ACGTcount: A:0.48, C:0.04, G:0.14, T:0.34
Consensus pattern (31 bp):
AAAAAAATTATATTTAGGGTAAAATTGATCC
Found at i:1152390 original size:62 final size:62
Alignment explanation
Indices: 1152223--1152394 Score: 238
Period size: 62 Copynumber: 2.8 Consensus size: 62
1152213 CCAAGTCAAA
** * * *
1152223 TTTGTATTTGAAGCACTGTTATGGTAAGTTACATTACATTCTCAAGGATAATTAGATATGGT
1 TTTGTATTTGAAGCACTGTTATGGTAAGACACATTACATTCTTAAGGATAAGTAGAGATGGT
* *
1152285 TTTGTATTTGAAGTACTGTTATGGTAA-AGCACATTATATTCTTAAGGATAAGTAGAGATGGT
1 TTTGTATTTGAAGCACTGTTATGGTAAGA-CACATTACATTCTTAAGGATAAGTAGAGATGGT
* * *
1152347 TTTGTATTTAAAGCACTGTTATGGTAAGACAGATTACAATCTTAAGGA
1 TTTGTATTTGAAGCACTGTTATGGTAAGACACATTACATTCTTAAGGA
1152395 GAGAATGTGG
Statistics
Matches: 96, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
62 95 0.99
63 1 0.01
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38
Consensus pattern (62 bp):
TTTGTATTTGAAGCACTGTTATGGTAAGACACATTACATTCTTAAGGATAAGTAGAGATGGT
Found at i:1156348 original size:4 final size:4
Alignment explanation
Indices: 1156339--1156369 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
1156329 CAAGTGAACT
1156339 TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
1156370 AACAATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:1156902 original size:18 final size:18
Alignment explanation
Indices: 1156870--1156904 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1156860 AAATGAAATG
1156870 AATTATATTTTTATTTAT
1 AATTATATTTTTATTTAT
1156888 AATTA-ATTTTATATTTA
1 AATTATATTTT-TATTTA
1156905 GTGATGCTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
AATTATATTTTTATTTAT
Found at i:1172238 original size:3 final size:3
Alignment explanation
Indices: 1172230--1172260 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1172220 TTTTCCCTTA
1172230 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1172261 AGCATCCCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:1176457 original size:15 final size:15
Alignment explanation
Indices: 1176439--1176472 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1176429 AAATTAATTT
*
1176439 TTAAAAAATAAAATA
1 TTAAAAAATAAAAAA
*
1176454 TTAAAATATAAAAAA
1 TTAAAAAATAAAAAA
1176469 TTAA
1 TTAA
1176473 CTATTGTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
TTAAAAAATAAAAAA
Found at i:1179652 original size:2 final size:2
Alignment explanation
Indices: 1179645--1179694 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1179635 AATCAGTGCA
1179645 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1179687 CT CT CT CT
1 CT CT CT CT
1179695 TTTTTGTTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1198388 original size:58 final size:60
Alignment explanation
Indices: 1198274--1198407 Score: 182
Period size: 60 Copynumber: 2.3 Consensus size: 60
1198264 ATTATATAAA
* *
1198274 TATTTAAAGTTAAAAGGTTAAAATATATAATATGGAAAAAAATAAAAAAAAAGAAATGTT
1 TATTTAAAGTTAAAAAGTTAAAATATATAATATGGAAAAAAATAAAAAAAAAGAAATATT
* * *
1198334 TATTTAAAGTTAAAAAGTTAAAATATATGATAT-GAAAAAAA-ATAAAAAAGGAAATATT
1 TATTTAAAGTTAAAAAGTTAAAATATATAATATGGAAAAAAATAAAAAAAAAGAAATATT
* * *
1198392 TTTTTAATGTTCAAAA
1 TATTTAAAGTTAAAAA
1198408 TTGGATGGGG
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
58 27 0.41
59 8 0.12
60 31 0.47
ACGTcount: A:0.57, C:0.01, G:0.10, T:0.31
Consensus pattern (60 bp):
TATTTAAAGTTAAAAAGTTAAAATATATAATATGGAAAAAAATAAAAAAAAAGAAATATT
Found at i:1199608 original size:53 final size:53
Alignment explanation
Indices: 1199493--1199608 Score: 162
Period size: 53 Copynumber: 2.2 Consensus size: 53
1199483 TATATATTAT
*
1199493 ATAAATATTTAAAGTTAAAAAGTTAAAATATGTAATATGAAAAAATAAAAAAA
1 ATAAATATTTAAAGTTAAAAAGTTAAAATATATAATATGAAAAAATAAAAAAA
** * * *
1199546 ATATTTATTTAAAGTTTAAAAGTTAAAATATATGATATGAAAAAA-ATAAAAA
1 ATAAATATTTAAAGTTAAAAAGTTAAAATATATAATATGAAAAAATAAAAAAA
1199598 ATGAAATATTT
1 AT-AAATATTT
1199609 TTTTAATGTT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
52 8 0.15
53 46 0.85
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (53 bp):
ATAAATATTTAAAGTTAAAAAGTTAAAATATATAATATGAAAAAATAAAAAAA
Found at i:1215865 original size:2 final size:2
Alignment explanation
Indices: 1215858--1215886 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1215848 TCTTAGCTTT
1215858 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 T
1215887 GGTCTTAGGT
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1220116 original size:14 final size:14
Alignment explanation
Indices: 1220082--1220119 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1220072 TTTTAAAAAC
1220082 ATATTTATA-ATTG
1 ATATTTATATATTG
*
1220095 ATATTTTATATATTT
1 ATA-TTTATATATTG
1220110 ATATTTATAT
1 ATATTTATAT
1220120 TTATTATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 3 0.14
14 13 0.59
15 6 0.27
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (14 bp):
ATATTTATATATTG
Found at i:1221451 original size:31 final size:30
Alignment explanation
Indices: 1221413--1221472 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
1221403 TTTGTATACT
*
1221413 TACATCAAA-TAAAATTTTTTGTATTAAATTA
1 TACATCAAACCAAAA-TTTTTGTA-TAAATTA
1221444 TACATCAAACCAAAATTTTTGTATAAATT
1 TACATCAAACCAAAATTTTTGTATAAATT
1221473 TAATATTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 6 0.22
31 17 0.63
32 4 0.15
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (30 bp):
TACATCAAACCAAAATTTTTGTATAAATTA
Found at i:1223692 original size:30 final size:31
Alignment explanation
Indices: 1223656--1223721 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 31
1223646 GTTTATATTT
1223656 CAGTCCCTCAACTTTGAAAA-TGTGACAAAA
1 CAGTCCCTCAACTTTGAAAACTGTGACAAAA
* *
1223686 CAGTCCCTTAACTTTTAAAACTGTGACAAAA
1 CAGTCCCTCAACTTTGAAAACTGTGACAAAA
1223717 CAGTC
1 CAGTC
1223722 TTTTTCTGTC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
30 18 0.55
31 15 0.45
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (31 bp):
CAGTCCCTCAACTTTGAAAACTGTGACAAAA
Found at i:1225426 original size:23 final size:23
Alignment explanation
Indices: 1225400--1225565 Score: 150
Period size: 23 Copynumber: 7.4 Consensus size: 23
1225390 AGTGCTGGGC
1225400 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
1225423 AACAGAGAGTACACAAA--G-T-
1 AACAGAGAGCACACAAAGTGCTA
*
1225442 -AC--TGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
1225462 ATCAGAGAGCACACGAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* * *
1225485 ATCGGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACAAAGTGCT-A
* *
1225509 TAACAGAGAGCACGA-GACGTGCTA
1 -AACAGAGAGCAC-ACAAAGTGCTA
*
1225533 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
1225556 ATCAGAGAGC
1 AACAGAGAGC
1225566 GCGCTAGTGT
Statistics
Matches: 114, Mismatches: 18, Indels: 22
0.74 0.12 0.14
Matches are distributed among these distances:
16 10 0.09
18 3 0.03
19 1 0.01
20 1 0.01
21 2 0.02
22 1 0.01
23 78 0.68
24 2 0.02
25 15 0.13
26 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.11
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:1225460 original size:39 final size:39
Alignment explanation
Indices: 1225406--1225480 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
1225396 GGGCAACAGA
*
1225406 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
* *
1225445 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT
1225481 GCTAATCGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
Found at i:1225519 original size:48 final size:46
Alignment explanation
Indices: 1225445--1225565 Score: 172
Period size: 48 Copynumber: 2.6 Consensus size: 46
1225435 ACAAAGTACT
* * *
1225445 GAGCACACAAAGTGCTAATCAGAGAGCAC-ACGAAGTGCTAATCGGA
1 GAGCACACACAGTGCTAATCAGAGAGCACGA-GAAGTGCTAAACAGA
*
1225491 GAGCACACACAGTGCTAATAACAGAGAGCACGAGACGTGCTAAACAGA
1 GAGCACACACAGTGCTAAT--CAGAGAGCACGAGAAGTGCTAAACAGA
1225539 GAGCACACACAGTGCTAATCAGAGAGC
1 GAGCACACACAGTGCTAATCAGAGAGC
1225566 GCGCTAGTGT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
46 26 0.38
48 41 0.60
49 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.12
Consensus pattern (46 bp):
GAGCACACACAGTGCTAATCAGAGAGCACGAGAAGTGCTAAACAGA
Found at i:1228455 original size:16 final size:17
Alignment explanation
Indices: 1228425--1228457 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1228415 CTATTAGATC
*
1228425 TTTTATAATTTATAAAA
1 TTTTATAATTGATAAAA
1228442 TTTTA-AATTGATAAAA
1 TTTTATAATTGATAAAA
1228458 AAAATTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TTTTATAATTGATAAAA
Found at i:1228558 original size:26 final size:28
Alignment explanation
Indices: 1228503--1228561 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 28
1228493 AAAGACTATT
*
1228503 AAAATAATAAAATTATAATTTTTTCATA
1 AAAATAATAAAATTATAATTTTATCATA
* *
1228531 AAAAT-ATATAATT-TAATTTTATCCTA
1 AAAATAATAAAATTATAATTTTATCATA
1228557 AAAAT
1 AAAAT
1228562 TATTTTTTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 16 0.57
27 7 0.25
28 5 0.18
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (28 bp):
AAAATAATAAAATTATAATTTTATCATA
Found at i:1230385 original size:15 final size:17
Alignment explanation
Indices: 1230365--1230398 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
1230355 GTTTATCCAC
1230365 ATTTTAAAA-AT-TTAT
1 ATTTTAAAAGATATTAT
1230380 ATTTTAAAAGATATTAT
1 ATTTTAAAAGATATTAT
1230397 AT
1 AT
1230399 AGTATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 2 0.12
17 6 0.35
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
ATTTTAAAAGATATTAT
Found at i:1230918 original size:88 final size:85
Alignment explanation
Indices: 1230756--1230999 Score: 235
Period size: 87 Copynumber: 2.8 Consensus size: 85
1230746 TTGAGGATGT
* * * * * * *
1230756 AAAAAACCTTCAAACTTTTTCAAAAAA-CAATTGAACCCCTGTTTTTATGTTACACTTACTTGAA
1 AAAAAACC-TCAAAC-TTATCAAAAAAGCAATT-AAGCCCTG-TTTTATTTTGCACTCAATTGGA
*
1230820 TACTTGAACTTTCAAAATGCAT-A
62 TACTTAAACTTTCAAAATGCATCA
1230843 AAAAAATCCTCAAACTTCATCAAAAAAGCAATTAAGCCTCTGCTTTTATTTTGCACTCAATTGGA
1 AAAAAA-CCTCAAACTT-ATCAAAAAAGCAATTAAGCC-CTG-TTTTATTTTGCACTCAATTGGA
* *
1230908 TATTTAAACTTTCAAAATTCATCA
62 TACTTAAACTTTCAAAATGCATCA
* * *
1230932 AAAAAGCCCTCAAACTTA-AAAAAAAGCACAATTAAGCCCTTGATTT-TTTTGCACTCAATTGGA
1 AAAAA-ACCTCAAACTTATCAAAAAAG--CAATTAAGCCC-TGTTTTATTTTGCACTCAATTGGA
1230995 TACTT
62 TACTT
1231000 GAATCACTCC
Statistics
Matches: 133, Mismatches: 15, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
86 2 0.02
87 52 0.39
88 51 0.38
89 28 0.21
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (85 bp):
AAAAAACCTCAAACTTATCAAAAAAGCAATTAAGCCCTGTTTTATTTTGCACTCAATTGGATACT
TAAACTTTCAAAATGCATCA
Found at i:1231115 original size:20 final size:20
Alignment explanation
Indices: 1231092--1231155 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
1231082 TTTTGATGCA
*
1231092 TTTTATAAATTTTTTCTAAT
1 TTTTATAAATTTTTTATAAT
* *
1231112 TTTTATTAAA-ATTTAATAAT
1 TTTTA-TAAATTTTTTATAAT
**
1231132 TTTTATTGATTTTTTATAAT
1 TTTTATAAATTTTTTATAAT
1231152 TTTT
1 TTTT
1231156 TTGTCACATG
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
19 2 0.06
20 29 0.83
21 4 0.11
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTTATAAATTTTTTATAAT
Found at i:1237287 original size:27 final size:27
Alignment explanation
Indices: 1237245--1237300 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
1237235 GTGAAGTTAC
1237245 AAGGTCTTATAGCATAATAAACCCAAA
1 AAGGTCTTATAGCATAATAAACCCAAA
1237272 AAGGTCTTAT-GACATAATAAACCCAAA
1 AAGGTCTTATAG-CATAATAAACCCAAA
1237299 AA
1 AA
1237301 TAATTCCGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 1 0.04
27 27 0.96
ACGTcount: A:0.50, C:0.18, G:0.11, T:0.21
Consensus pattern (27 bp):
AAGGTCTTATAGCATAATAAACCCAAA
Found at i:1240880 original size:14 final size:15
Alignment explanation
Indices: 1240861--1240889 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1240851 ATAAAATTAT
1240861 AAAATAT-TTTTTAA
1 AAAATATATTTTTAA
1240875 AAAATATATTTTTAA
1 AAAATATATTTTTAA
1240890 TATTTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAAATATATTTTTAA
Found at i:1256838 original size:1 final size:1
Alignment explanation
Indices: 1256832--1256858 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1256822 CGATACCTTT
1256832 GGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGG
1256859 TTGCAGTCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:1271887 original size:23 final size:23
Alignment explanation
Indices: 1271860--1271904 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1271850 TAATTATATT
1271860 TAATAAAAATATATAAATAAAAG
1 TAATAAAAATATATAAATAAAAG
* * *
1271883 TAATAAAATTTTATAGATAAAA
1 TAATAAAAATATATAAATAAAA
1271905 TTTGATGGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (23 bp):
TAATAAAAATATATAAATAAAAG
Found at i:1273452 original size:23 final size:23
Alignment explanation
Indices: 1273378--1273591 Score: 151
Period size: 23 Copynumber: 9.5 Consensus size: 23
1273368 TAAACGGAAC
* * *
1273378 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
1273400 GAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
1273422 GGGCAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
*
1273448 AAACAGAGAGTACACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
*
1273468 --AC--TGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
1273487 AATCAGAGAGCACACGAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
1273510 AATCGGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
1273533 AATAACAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
*
1273558 AAACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
1273581 AATCAGAGAGC
1 AAACAGAGAGC
1273592 GCGCTAGTGT
Statistics
Matches: 151, Mismatches: 25, Indels: 31
0.73 0.12 0.15
Matches are distributed among these distances:
16 10 0.07
18 3 0.02
19 1 0.01
20 1 0.01
21 2 0.01
22 18 0.12
23 78 0.52
24 2 0.01
25 28 0.19
26 8 0.05
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:1273486 original size:39 final size:39
Alignment explanation
Indices: 1273432--1273506 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
1273422 GGGCAACAGA
*
1273432 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
* *
1273471 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT
1273507 GCTAATCGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
Found at i:1273545 original size:48 final size:46
Alignment explanation
Indices: 1273471--1273591 Score: 172
Period size: 48 Copynumber: 2.6 Consensus size: 46
1273461 ACAAAGTACT
* * *
1273471 GAGCACACAAAGTGCTAATCAGAGAGCAC-ACGAAGTGCTAATCGGA
1 GAGCACACACAGTGCTAATCAGAGAGCACGA-GAAGTGCTAAACAGA
*
1273517 GAGCACACACAGTGCTAATAACAGAGAGCACGAGACGTGCTAAACAGA
1 GAGCACACACAGTGCTAAT--CAGAGAGCACGAGAAGTGCTAAACAGA
1273565 GAGCACACACAGTGCTAATCAGAGAGC
1 GAGCACACACAGTGCTAATCAGAGAGC
1273592 GCGCTAGTGT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
46 26 0.38
48 41 0.60
49 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.12
Consensus pattern (46 bp):
GAGCACACACAGTGCTAATCAGAGAGCACGAGAAGTGCTAAACAGA
Found at i:1275489 original size:18 final size:19
Alignment explanation
Indices: 1275446--1275491 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
1275436 TATCATTAAT
*
1275446 AATTCAATTTTAATATAAA
1 AATTCAATATTAATATAAA
* *
1275465 TATTCAATATTATTA-AAA
1 AATTCAATATTAATATAAA
1275483 AATTCAATA
1 AATTCAATA
1275492 CTATAGATAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTCAATATTAATATAAA
Found at i:1276046 original size:22 final size:21
Alignment explanation
Indices: 1276011--1276094 Score: 78
Period size: 22 Copynumber: 3.8 Consensus size: 21
1276001 TATATTGTTG
* *
1276011 TTTTGGTGCTGTTTTTTACTA
1 TTTTGTTGTTGTTTTTTACTA
1276032 TTTTGATTGTTGTTTTTTACTA
1 TTTTG-TTGTTGTTTTTTACTA
* * *
1276054 TTTTTGTGCTATTTTTTTTTACTG
1 -TTTTGT--TGTTGTTTTTTACTA
*
1276078 TTTTGTTGTTGCTTTTT
1 TTTTGTTGTTGTTTTTT
1276095 GTTGTTATTT
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
21 13 0.25
22 15 0.29
23 11 0.22
24 12 0.24
ACGTcount: A:0.08, C:0.07, G:0.15, T:0.69
Consensus pattern (21 bp):
TTTTGTTGTTGTTTTTTACTA
Found at i:1276093 original size:23 final size:23
Alignment explanation
Indices: 1276017--1276112 Score: 65
Period size: 24 Copynumber: 4.0 Consensus size: 23
1276007 GTTGTTTTGG
1276017 TGCTGTTTTTTACTATTTTGATTGT
1 TGCT-TTTTTTACTATTTTG-TTGT
1276042 TG--TTTTTTACTATTTT-TGTGCT
1 TGCTTTTTTTACTATTTTGT-TG-T
* *
1276064 AT-TTTTTTTTACTGTTTTGTTGT
1 -TGCTTTTTTTACTATTTTGTTGT
**
1276087 TGCTTTTTGTTGTTATTTTGATTGT
1 TGCTTTTT-TTACTATTTTG-TTGT
1276112 T
1 T
1276113 TTTGTTGCTA
Statistics
Matches: 57, Mismatches: 5, Indels: 18
0.71 0.06 0.22
Matches are distributed among these distances:
20 1 0.02
21 2 0.04
22 16 0.28
23 7 0.12
24 23 0.40
25 8 0.14
ACGTcount: A:0.09, C:0.06, G:0.16, T:0.69
Consensus pattern (23 bp):
TGCTTTTTTTACTATTTTGTTGT
Found at i:1276100 original size:21 final size:21
Alignment explanation
Indices: 1276090--1276146 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
1276080 TTGTTGTTGC
1276090 TTTTTGTTGTTATTTTGATTG
1 TTTTTGTTGTTATTTTGATTG
* *
1276111 TTTTTGTTGCTATTTTTATT-
1 TTTTTGTTGTTATTTTGATTG
*
1276131 ATTTTGTTGTTATTTT
1 TTTTTGTTGTTATTTT
1276147 TGCTGCTGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.11, C:0.02, G:0.14, T:0.74
Consensus pattern (21 bp):
TTTTTGTTGTTATTTTGATTG
Found at i:1276105 original size:12 final size:12
Alignment explanation
Indices: 1276052--1276177 Score: 60
Period size: 11 Copynumber: 11.1 Consensus size: 12
1276042 TGTTTTTTAC
*
1276052 TATTTTTG-TGC
1 TATTTTTGTTGT
1276063 TATTTTT-TT-T
1 TATTTTTGTTGT
1276073 TACTGTTTTGTTGT
1 TA-T-TTTTGTTGT
*
1276087 TGCTTTTTGTTGT
1 T-ATTTTTGTTGT
1276100 TA-TTTTGATTG-
1 TATTTTTG-TTGT
*
1276111 --TTTTTGTTGC
1 TATTTTTGTTGT
*
1276121 TA--TTT-TTAT
1 TATTTTTGTTGT
1276130 TA-TTTTGTTGT
1 TATTTTTGTTGT
* *
1276141 TATTTTTGCTGC
1 TATTTTTGTTGT
*
1276153 T-GTTTTGATTGT
1 TATTTTTG-TTGT
1276165 TATTTTTGTTGT
1 TATTTTTGTTGT
1276177 T
1 T
1276178 TGGATGTTAT
Statistics
Matches: 87, Mismatches: 12, Indels: 31
0.67 0.09 0.24
Matches are distributed among these distances:
9 7 0.08
10 13 0.15
11 24 0.28
12 23 0.26
13 17 0.20
14 3 0.03
ACGTcount: A:0.09, C:0.05, G:0.17, T:0.70
Consensus pattern (12 bp):
TATTTTTGTTGT
Found at i:1276165 original size:24 final size:21
Alignment explanation
Indices: 1276091--1276191 Score: 86
Period size: 20 Copynumber: 4.8 Consensus size: 21
1276081 TGTTGTTGCT
1276091 TTTTG-TTGTTA-TTTTGATTG
1 TTTTGATTGTTATTTTTG-TTG
* * *
1276111 TTTTTG-TTGCTATTTTTATTA
1 -TTTTGATTGTTATTTTTGTTG
1276132 TTTTG-TTGTTATTTTTGCTGCTG
1 TTTTGATTGTTATTTTTG-T--TG
1276155 TTTTGATTGTTATTTTTGTTG
1 TTTTGATTGTTATTTTTGTTG
*
1276176 TTTGGA-TGTTATTTTT
1 TTTTGATTGTTATTTTT
1276192 ATGCGTTTTT
Statistics
Matches: 68, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
20 25 0.37
21 20 0.29
22 4 0.06
23 7 0.10
24 12 0.18
ACGTcount: A:0.10, C:0.03, G:0.18, T:0.69
Consensus pattern (21 bp):
TTTTGATTGTTATTTTTGTTG
Found at i:1276199 original size:21 final size:22
Alignment explanation
Indices: 1276137--1276199 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 22
1276127 TATTATTTTG
* *
1276137 TTGTTATTTTTGCTGCTGTTTTGA
1 TTGTTATTTTT-ATGC-GTTTGGA
* *
1276161 TTGTTATTTTTGT-TGTTTGGA
1 TTGTTATTTTTATGCGTTTGGA
1276182 -TGTTATTTTTATGCGTTT
1 TTGTTATTTTTATGCGTTT
1276200 TTATTATTGT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
20 11 0.33
21 10 0.30
23 1 0.03
24 11 0.33
ACGTcount: A:0.10, C:0.05, G:0.21, T:0.65
Consensus pattern (22 bp):
TTGTTATTTTTATGCGTTTGGA
Found at i:1292012 original size:10 final size:10
Alignment explanation
Indices: 1291997--1292026 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1291987 TTATACAATG
1291997 TGGTACCGGT
1 TGGTACCGGT
1292007 TGGTACCGGT
1 TGGTACCGGT
*
1292017 TGGTAACGGT
1 TGGTACCGGT
1292027 GTTAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.13, C:0.17, G:0.40, T:0.30
Consensus pattern (10 bp):
TGGTACCGGT
Done.