Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold349
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: 1036866
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 6 of 6
Found at i:910493 original size:53 final size:51
Alignment explanation
Indices: 910426--910548 Score: 140
Period size: 51 Copynumber: 2.4 Consensus size: 51
910416 AAATAACGGG
* * * **
910426 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTGTTTTTTGGAAATAAAATTGGA
1 GTTGGAGTATCCCCGATTGTAG-AAAATTAGCG--TTTTGAAAATAAAATCAGA
*
910479 GTTGGAGTATCCCCGATTATAGAAAATTAGCGTTTTGAAAATAAAATCAGA
1 GTTGGAGTATCCCCGATTGTAGAAAATTAGCGTTTTGAAAATAAAATCAGA
* *
910530 GTGGGAATATCCCCGATTG
1 GTTGGAGTATCCCCGATTG
910549 CGGAGAATTG
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
51 32 0.53
53 27 0.45
54 1 0.02
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.32
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTAGAAAATTAGCGTTTTGAAAATAAAATCAGA
Found at i:912827 original size:20 final size:20
Alignment explanation
Indices: 912802--912848 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
912792 GCAAAGCAGA
912802 AAAAATGGCTCGAAGTGGTC
1 AAAAATGGCTCGAAGTGGTC
912822 AAAAATGGCTCGAAGTGGTC
1 AAAAATGGCTCGAAGTGGTC
912842 AAAAATG
1 AAAAATG
912849 CCTAAATGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.40, C:0.13, G:0.28, T:0.19
Consensus pattern (20 bp):
AAAAATGGCTCGAAGTGGTC
Found at i:912942 original size:13 final size:13
Alignment explanation
Indices: 912924--912949 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
912914 ACAAAGATCC
912924 ATGTATCGATACA
1 ATGTATCGATACA
912937 ATGTATCGATACA
1 ATGTATCGATACA
912950 TGGAATAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:913009 original size:13 final size:13
Alignment explanation
Indices: 912987--913076 Score: 63
Period size: 13 Copynumber: 6.0 Consensus size: 13
912977 GGCAGTAGCT
*
912987 TTGTAGCGATACA
1 TTGTATCGATACA
913000 TTGTATCGATACAACA
1 TTGTATCGAT---ACA
913016 CTTATGTATCGATACA
1 --T-TGTATCGATACA
913032 TTGTATCGATACAATA
1 TTGTATCGATAC---A
913048 TTTAAGTATCGATACA
1 -TT--GTATCGATACA
913064 TTGTATCGATACA
1 TTGTATCGATACA
913077 ACACTTATGT
Statistics
Matches: 64, Mismatches: 1, Indels: 24
0.72 0.01 0.27
Matches are distributed among these distances:
13 31 0.48
14 1 0.02
15 2 0.03
16 8 0.12
17 2 0.03
18 1 0.02
19 19 0.30
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:913025 original size:19 final size:18
Alignment explanation
Indices: 913001--913096 Score: 77
Period size: 19 Copynumber: 5.7 Consensus size: 18
912991 AGCGATACAT
913001 TGTATCGATACAACACTTA
1 TGTATCGATACAACA-TTA
913020 TGTATCGAT---ACA-T-
1 TGTATCGATACAACATTA
*
913033 TGTATCGATACAATATTTA
1 TGTATCGATACAACA-TTA
*
913052 AGTATCGAT---ACA-T-
1 TGTATCGATACAACATTA
913065 TGTATCGATACAACACTTA
1 TGTATCGATACAACA-TTA
913084 TGTATCGATACAA
1 TGTATCGATACAA
913097 ATCGCTGAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 24
0.69 0.04 0.27
Matches are distributed among these distances:
13 17 0.28
14 2 0.03
16 10 0.16
18 2 0.03
19 30 0.49
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAACATTA
Found at i:913034 original size:32 final size:32
Alignment explanation
Indices: 912988--913095 Score: 180
Period size: 32 Copynumber: 3.4 Consensus size: 32
912978 GCAGTAGCTT
*
912988 TGTAGCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
* *
913020 TGTATCGATACATTGTATCGATACAATATTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
*
913052 AGTATCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
913084 TGTATCGATACA
1 TGTATCGATACA
913096 AATCGCTGAA
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 69 1.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAACACTTA
Found at i:913165 original size:21 final size:22
Alignment explanation
Indices: 913139--913210 Score: 87
Period size: 21 Copynumber: 3.4 Consensus size: 22
913129 ACCTTTTATT
* *
913139 GATACATTTGTA-GAATGTATC
1 GATACATTTCTACAAATGTATC
*
913160 GATACA-TTCCACAAATGTATC
1 GATACATTTCTACAAATGTATC
*
913181 GATAC-CTTCTACAAATGTATC
1 GATACATTTCTACAAATGTATC
913202 GATACATTT
1 GATACATTT
913211 GGATAAAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
20 3 0.07
21 38 0.88
22 2 0.05
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (22 bp):
GATACATTTCTACAAATGTATC
Found at i:914125 original size:33 final size:33
Alignment explanation
Indices: 914083--914146 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
914073 TTTATAGTCG
* *
914083 TTTACCAAGTATCGATATAATGTATCGATACTT
1 TTTACCAAGTATCAATACAATGTATCGATACTT
*
914116 TTTACCAAGTATCAATACATTGTATCGATAC
1 TTTACCAAGTATCAATACAATGTATCGATAC
914147 AATGTCCCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (33 bp):
TTTACCAAGTATCAATACAATGTATCGATACTT
Found at i:914223 original size:20 final size:20
Alignment explanation
Indices: 914197--914251 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
914187 CTGCCAATTT
914197 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATTGAG
* *
914217 TATGTATCGAGACAA-TGAG
1 CATGTATCGATACAATTGAG
* *
914236 CATGTGTCAATACAAT
1 CATGTATCGATACAAT
914252 GTATGGATAC
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (20 bp):
CATGTATCGATACAATTGAG
Found at i:914240 original size:19 final size:20
Alignment explanation
Indices: 914197--914240 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
914187 CTGCCAATTT
*
914197 CATGTATCGATACAATTGAG
1 CATGTATCGAGACAATTGAG
*
914217 TATGTATCGAGACAA-TGAG
1 CATGTATCGAGACAATTGAG
914236 CATGT
1 CATGT
914241 GTCAATACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.30
Consensus pattern (20 bp):
CATGTATCGAGACAATTGAG
Found at i:917158 original size:48 final size:48
Alignment explanation
Indices: 917094--917190 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
917084 TATTCAAATA
*
917094 AATTATCAAAAGTGCAACTTGTCATTTCATGTGACCAAAAATAATCAT
1 AATTATCAAAAATGCAACTTGTCATTTCATGTGACCAAAAATAATCAT
917142 AATTATCAAAAATGCAACTTGTCATTTCATGTGACCAAAAATAATCAT
1 AATTATCAAAAATGCAACTTGTCATTTCATGTGACCAAAAATAATCAT
917190 A
1 A
917191 TTTGGCATTG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.31
Consensus pattern (48 bp):
AATTATCAAAAATGCAACTTGTCATTTCATGTGACCAAAAATAATCAT
Found at i:923142 original size:20 final size:20
Alignment explanation
Indices: 923116--923170 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 20
923106 CTGCTAATTT
923116 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATTGAG
*
923136 TATGTATCGATACAA-TGAG
1 CATGTATCGATACAATTGAG
*
923155 CATATATCGATACAAT
1 CATGTATCGATACAAT
923171 GAATCGATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAG
Found at i:924723 original size:66 final size:67
Alignment explanation
Indices: 924596--924741 Score: 276
Period size: 66 Copynumber: 2.2 Consensus size: 67
924586 ACATAAGGGT
*
924596 GAAGTCGACGATTGTAGTCTTATGTACTATTTTTGTCACTCTTCTTAATACAAATATAACTAATA
1 GAAGTCGACCATTGTAGTCTTATGTACTATTTTTGTCACTCTTCTTAATACAAATATAACTAATA
924661 GA
66 GA
924663 GAAGTCGACCATTGTAGTCTTATGTACTA-TTTTGTCACTCTTCTTAATACAAATATAACTAATA
1 GAAGTCGACCATTGTAGTCTTATGTACTATTTTTGTCACTCTTCTTAATACAAATATAACTAATA
924727 GA
66 GA
924729 GAAGTCGACCATT
1 GAAGTCGACCATT
924742 ATGGTTCCAT
Statistics
Matches: 78, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
66 50 0.64
67 28 0.36
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (67 bp):
GAAGTCGACCATTGTAGTCTTATGTACTATTTTTGTCACTCTTCTTAATACAAATATAACTAATA
GA
Found at i:926117 original size:15 final size:15
Alignment explanation
Indices: 926044--926122 Score: 65
Period size: 14 Copynumber: 5.4 Consensus size: 15
926034 GTTAGCATAA
* *
926044 TACTCTTTGACAAAAA
1 TACT-TTTGGCAAAAG
*
926060 TACTTTTGGC-ATAG
1 TACTTTTGGCAAAAG
* *
926074 TAC-ATTGGCAGAAG
1 TACTTTTGGCAAAAG
* *
926088 TAC-TTTGGTATAAG
1 TACTTTTGGCAAAAG
926102 TACTTTTGGCAAAAG
1 TACTTTTGGCAAAAG
926117 TACTTT
1 TACTTT
926123 GATATAGGTA
Statistics
Matches: 50, Mismatches: 11, Indels: 5
0.76 0.17 0.08
Matches are distributed among these distances:
13 5 0.10
14 21 0.42
15 20 0.40
16 4 0.08
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.37
Consensus pattern (15 bp):
TACTTTTGGCAAAAG
Found at i:926118 original size:29 final size:29
Alignment explanation
Indices: 926040--926134 Score: 88
Period size: 29 Copynumber: 3.3 Consensus size: 29
926030 CCTAGTTAGC
* * *
926040 ATAA-TACTCTTTGACAAAAATACTTTTGGC
1 ATAAGTACT-TTTGGCAAAAGTAC-TTTGGT
* *
926070 AT-AGTAC-ATTGGCAGAAGTACTTTGGT
1 ATAAGTACTTTTGGCAAAAGTACTTTGGT
*
926097 ATAAGTACTTTTGGCAAAAGTACTTTGAT
1 ATAAGTACTTTTGGCAAAAGTACTTTGGT
*
926126 ATAGGTACT
1 ATAAGTACT
926135 ACGATAGAGA
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
27 7 0.13
28 15 0.28
29 26 0.49
30 5 0.09
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.36
Consensus pattern (29 bp):
ATAAGTACTTTTGGCAAAAGTACTTTGGT
Found at i:926159 original size:14 final size:15
Alignment explanation
Indices: 926142--926178 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
926132 ACTACGATAG
926142 AGATACTTTGGCA-A
1 AGATACTTTGGCATA
*
926156 AGATACATTGGCATA
1 AGATACTTTGGCATA
926171 AG-TACTTT
1 AGATACTTT
926179 AGTAGAGGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 17 0.85
15 3 0.15
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (15 bp):
AGATACTTTGGCATA
Found at i:926226 original size:85 final size:84
Alignment explanation
Indices: 926059--926235 Score: 194
Period size: 85 Copynumber: 2.1 Consensus size: 84
926049 TTTGACAAAA
* * *
926059 ATACTTTTGGCATAGTACATTGGCAGAAGTACTTTGGTATAAGTACTTTTGGCAAAAGTACTTTG
1 ATAC-TTTGGCAAAGTACATTGGCAGAAGTACTTTAGTAGAAGTACTTTTGGCAAAAGTACTTTG
* *
926124 ATATAGGTACTACGATAGAG
65 ATAAAGATACTACGATAGAG
* * * * * *
926144 ATACTTTGGCAAAGATACATTGGCATAAGTACTTTAGTAGAGGTA-TTTTTGCACAAGTATTTTT
1 ATACTTTGGCAAAG-TACATTGGCAGAAGTACTTTAGTAGAAGTACTTTTGGCAAAAGTACTTTG
**
926208 AGTAAAGATACTTTGATAGAG
65 A-TAAAGATACTACGATAGAG
*
926229 GTACTTT
1 ATACTTT
926236 AACACATGTA
Statistics
Matches: 76, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
84 25 0.33
85 51 0.67
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (84 bp):
ATACTTTGGCAAAGTACATTGGCAGAAGTACTTTAGTAGAAGTACTTTTGGCAAAAGTACTTTGA
TAAAGATACTACGATAGAG
Found at i:926265 original size:29 final size:29
Alignment explanation
Indices: 926227--926335 Score: 85
Period size: 29 Copynumber: 3.8 Consensus size: 29
926217 ACTTTGATAG
*
926227 AGGTACTTTAACACATGTACTTTTGGCAT
1 AGGTACTTTAACACAGGTACTTTTGGCAT
* ** *
926256 AGGTATTTTAGTAAAGGTAC-TTTGGCAT
1 AGGTACTTTAACACAGGTACTTTTGGCAT
*** * * *
926284 TTATATTTTAACATAGGTACTTTTGACAT
1 AGGTACTTTAACACAGGTACTTTTGGCAT
* * *
926313 AAGTACTTTGACACAAGTACTTT
1 AGGTACTTTAACACAGGTACTTT
926336 GACACAAGTA
Statistics
Matches: 60, Mismatches: 19, Indels: 2
0.74 0.23 0.02
Matches are distributed among these distances:
28 22 0.37
29 38 0.63
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (29 bp):
AGGTACTTTAACACAGGTACTTTTGGCAT
Found at i:926324 original size:14 final size:14
Alignment explanation
Indices: 926294--926363 Score: 95
Period size: 14 Copynumber: 4.9 Consensus size: 14
926284 TTATATTTTA
*
926294 ACATAGGTACTTTTG
1 ACATAAGTAC-TTTG
926309 ACATAAGTACTTTG
1 ACATAAGTACTTTG
*
926323 ACACAAGTACTTTG
1 ACATAAGTACTTTG
* *
926337 ACACAAGTACTTCG
1 ACATAAGTACTTTG
926351 ACATAAGTACTTT
1 ACATAAGTACTTT
926364 ATTATTGGCA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
14 41 0.82
15 9 0.18
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (14 bp):
ACATAAGTACTTTG
Found at i:928595 original size:60 final size:61
Alignment explanation
Indices: 928515--928629 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 61
928505 ATGTATTTTA
*
928515 AATTATTAAGCATTACTTTTAATGAAAAAATTTCAATAATACTCTTT-TAAAATATTAAATT
1 AATTATTAAACATTACTTTTAATGAAAAAATTTCAATAATA-TCTTTCTAAAATATTAAATT
* ** *
928576 AATT-TTAAACATTATTTTTAATGAAAATTTTTCAATAATATTTTTCTAAAATAT
1 AATTATTAAACATTACTTTTAATGAAAAAATTTCAATAATATCTTTCTAAAATAT
928630 ACTTTTGTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 4 0.08
60 40 0.83
61 4 0.08
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (61 bp):
AATTATTAAACATTACTTTTAATGAAAAAATTTCAATAATATCTTTCTAAAATATTAAATT
Found at i:928715 original size:25 final size:24
Alignment explanation
Indices: 928687--928759 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 24
928677 TTATATATAA
928687 TATATTAAAACTATTTTTAATATGC
1 TATATTAAAA-TATTTTTAATATGC
* * **
928712 TATATTGAAATAATTTTAAT-TTT
1 TATATTAAAATATTTTTAATATGC
928735 TAATATTAAATATTATTTTTAATAT
1 T-ATATTAAA-A-TATTTTTAATAT
928760 ATGTTTTAGC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
23 2 0.05
24 16 0.42
25 10 0.26
26 9 0.24
27 1 0.03
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (24 bp):
TATATTAAAATATTTTTAATATGC
Found at i:929748 original size:4 final size:4
Alignment explanation
Indices: 929739--929765 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
929729 GTATATAATA
929739 TTCT TTCT TTCT TTCT TTCT TTCT TTC
1 TTCT TTCT TTCT TTCT TTCT TTCT TTC
929766 CATTAGGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TTCT
Found at i:931460 original size:1 final size:1
Alignment explanation
Indices: 931456--931480 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
931446 TTTTTTTTTT
931456 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
931481 AGGACACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:933135 original size:22 final size:22
Alignment explanation
Indices: 933095--933136 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
933085 TATTTAAATA
*
933095 TAAATATAATAATATAATTTTT
1 TAAATATAATAATAAAATTTTT
933117 TAAATAT-ATAATTAAAATTT
1 TAAATATAATAA-TAAAATTT
933137 AAAATAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TAAATATAATAATAAAATTTTT
Found at i:937719 original size:71 final size:75
Alignment explanation
Indices: 937603--937800 Score: 188
Period size: 71 Copynumber: 2.6 Consensus size: 75
937593 TTAGTGCCAT
** * * * * *
937603 GTCATCCAACCATCATCTGCCATGTGTCCCTACTGCCATATCATCACCCCAATCAGCCTAA-TC-
1 GTCATCCAACCATCATCCACCAAGTGTCCTTACTACCACATCATCACCCCAATCAGCCCAATTCT
937666 A-A-CACCAC
66 ACAGCACCAC
* * * ** * *
937674 GTCATCCAATCATCATCCCCCAAGTGTCTTTACTACCACATCATCAAGCTAGTCAGCCCAATTGT
1 GTCATCCAACCATCATCCACCAAGTGTCCTTACTACCACATCATCACCCCAATCAGCCCAA-T-T
937739 CTAGTCAGCACCAC
64 CTA--CAGCACCAC
* *
937753 GTTATCCAACCATCATCCACCACGTGTCCTTACTACCACATCATCACC
1 GTCATCCAACCATCATCCACCAAGTGTCCTTACTACCACATCATCACC
937801 TAGTCAGCCC
Statistics
Matches: 99, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
71 48 0.48
74 2 0.02
75 1 0.01
78 1 0.01
79 47 0.47
ACGTcount: A:0.28, C:0.39, G:0.09, T:0.24
Consensus pattern (75 bp):
GTCATCCAACCATCATCCACCAAGTGTCCTTACTACCACATCATCACCCCAATCAGCCCAATTCT
ACAGCACCAC
Found at i:937760 original size:79 final size:78
Alignment explanation
Indices: 937668--937823 Score: 231
Period size: 79 Copynumber: 2.0 Consensus size: 78
937658 GCCTAATCAA
* * * *
937668 CACCACGTCATCCAATCATCATCCCCCAAGTGTCTTTACTACCACATCATCAAGCTAGTCAGCCC
1 CACCACGTCATCCAACCATCATCCACCAAGTGTCCTTACTACCACATCATC-ACCTAGTCAGCCC
*
937733 AATTGTCTAGTCAG
65 AATTGTCCAGTCAG
* * *
937747 CACCACGTTATCCAACCATCATCCACCACGTGTCCTTACTACCACATCATCACCTAGTCAGCCCG
1 CACCACGTCATCCAACCATCATCCACCAAGTGTCCTTACTACCACATCATCACCTAGTCAGCCCA
937812 ATTGTCCAGTCA
66 ATTGTCCAGTCA
937824 TTACCATGTC
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
78 23 0.33
79 46 0.67
ACGTcount: A:0.27, C:0.38, G:0.11, T:0.24
Consensus pattern (78 bp):
CACCACGTCATCCAACCATCATCCACCAAGTGTCCTTACTACCACATCATCACCTAGTCAGCCCA
ATTGTCCAGTCAG
Found at i:937854 original size:78 final size:78
Alignment explanation
Indices: 937668--937884 Score: 213
Period size: 78 Copynumber: 2.8 Consensus size: 78
937658 GCCTAATCAA
* * * * * * *
937668 CACCACGTCATCCAATCATCATCCCCCAAGTGTCTTTACTACCACATCATCAAGCTAGTCAGCCC
1 CACCACGTCAGCCAACCAGCATCCACCACGTGTCCTTACTACCACATCATC-ACCTAGTCAGCCC
*
937733 AATTGTCTAGTCAG
65 AATTGTCCAGTCAG
* * * *
937747 CACCACGTTATCCAACCATCATCCACCACGTGTCCTTACTACCACATCATCACCTAGTCAGCCCG
1 CACCACGTCAGCCAACCAGCATCCACCACGTGTCCTTACTACCACATCATCACCTAGTCAGCCCA
*
937812 ATTGTCCAGTCAT
66 ATTGTCCAGTCAG
* * * ** * * *
937825 TACCATGTCAGCCAACTAGCA-CGTGCCACGTGTTCGTACTGCCACATCATCACC-AGTCAG
1 CACCACGTCAGCCAACCAGCATC-CACCACGTGTCCTTACTACCACATCATCACCTAGTCAG
937885 TATTCTTTTC
Statistics
Matches: 117, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
77 7 0.06
78 64 0.55
79 46 0.39
ACGTcount: A:0.26, C:0.37, G:0.13, T:0.24
Consensus pattern (78 bp):
CACCACGTCAGCCAACCAGCATCCACCACGTGTCCTTACTACCACATCATCACCTAGTCAGCCCA
ATTGTCCAGTCAG
Found at i:943324 original size:13 final size:13
Alignment explanation
Indices: 943306--943332 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
943296 AAATTTCCCA
943306 AATGTATCGATAC
1 AATGTATCGATAC
943319 AATGTATCGATAC
1 AATGTATCGATAC
943332 A
1 A
943333 TTGAGTAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:943394 original size:13 final size:13
Alignment explanation
Indices: 943376--943427 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
943366 AGCTTCGTAG
943376 CGATACATTGTAT
1 CGATACATTGTAT
943389 CGATACAACATTTGTGTAT
1 CGAT---ACA-TT--GTAT
943408 CGATACATTGTAT
1 CGATACATTGTAT
943421 CGATACA
1 CGATACA
943428 ACACTTGTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 15 0.45
15 2 0.06
16 6 0.18
17 2 0.06
19 8 0.24
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:943417 original size:32 final size:32
Alignment explanation
Indices: 943376--943446 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
943366 AGCTTCGTAG
*
943376 CGATACATTGTATCGATACAACATTTGTGTAT
1 CGATACATTGTATCGATACAACACTTGTGTAT
943408 CGATACATTGTATCGATACAACACTTGTGTAT
1 CGATACATTGTATCGATACAACACTTGTGTAT
943440 CGATACA
1 CGATACA
943447 ATTACTGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTGTGTAT
Found at i:943461 original size:21 final size:19
Alignment explanation
Indices: 943383--943468 Score: 78
Period size: 19 Copynumber: 4.7 Consensus size: 19
943373 TAGCGATACA
943383 TTGTATCGATACAACA-TT
1 TTGTATCGATACAACACTT
943401 TGTGTATCGAT---ACA---
1 T-TGTATCGATACAACACTT
943415 TTGTATCGATACAACACTT
1 TTGTATCGATACAACACTT
* *
943434 GTGTATCGATACAATTACTGT
1 TTGTATCGATACAA-CACT-T
943455 TTGTATCGATACAA
1 TTGTATCGATACAA
943469 ATTGTTGAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
13 9 0.16
14 1 0.02
16 6 0.11
18 1 0.02
19 22 0.39
20 3 0.05
21 14 0.25
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACAACACTT
Found at i:952005 original size:19 final size:19
Alignment explanation
Indices: 951981--952021 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
951971 ATTACTTTAA
*
951981 AATAATATAAACTTTTATT
1 AATAATATAAACTTATATT
*
952000 AATAATATAATCTTATATT
1 AATAATATAAACTTATATT
952019 AAT
1 AAT
952022 TTTTAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
AATAATATAAACTTATATT
Found at i:952352 original size:27 final size:28
Alignment explanation
Indices: 952295--952362 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 28
952285 AAAATAGTAG
* * *
952295 TATTTTGATAATTTATTTTAAATTAACAA
1 TATTTTAAT-ATTTATTTAAAAATAACAA
952324 TATTTTAATATTTATTTAAAAATAA-AA
1 TATTTTAATATTTATTTAAAAATAACAA
952351 TATAGTTTAATA
1 TAT--TTTAATA
952363 AATGTGCTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.15
28 14 0.41
29 15 0.44
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (28 bp):
TATTTTAATATTTATTTAAAAATAACAA
Found at i:953127 original size:47 final size:47
Alignment explanation
Indices: 953071--953169 Score: 128
Period size: 47 Copynumber: 2.1 Consensus size: 47
953061 TTTAAATAGG
* * * * *
953071 TAAAATTATAAA-TTCTTTTTATAAATAATTTATAATTTTTGCACGAA
1 TAAAGTTATAAACTT-TTTTCAAAAACAATTTATAACTTTTGCACGAA
*
953118 TAAAGTTATAAACTTTTTTCAAAAACAATTTATAACTTTTGTACGAA
1 TAAAGTTATAAACTTTTTTCAAAAACAATTTATAACTTTTGCACGAA
953165 TAAAG
1 TAAAG
953170 CTACAAACCA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
47 43 0.96
48 2 0.04
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.42
Consensus pattern (47 bp):
TAAAGTTATAAACTTTTTTCAAAAACAATTTATAACTTTTGCACGAA
Found at i:953404 original size:21 final size:20
Alignment explanation
Indices: 953380--953424 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
953370 ACAGCAAAAA
*
953380 ATTATCACAAAGATTTATTT
1 ATTACCACAAAGATTTATTT
*
953400 CATTACCACAAATATTTATTT
1 -ATTACCACAAAGATTTATTT
953421 ATTA
1 ATTA
953425 AATAAACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.40, C:0.13, G:0.02, T:0.44
Consensus pattern (20 bp):
ATTACCACAAAGATTTATTT
Found at i:955053 original size:2 final size:2
Alignment explanation
Indices: 955046--955080 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
955036 TTAAGACATA
955046 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
955081 TCCCTATGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:955589 original size:20 final size:20
Alignment explanation
Indices: 955564--955634 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
955554 ACCCAGATGC
*
955564 ATCGATACATTTTTCAATAT
1 ATCGATACATTTTTCAATGT
* * *
955584 ATCGATACATGTATGAATGT
1 ATCGATACATTTTTCAATGT
* *
955604 ATCGATATATTCTTCAATGT
1 ATCGATACATTTTTCAATGT
955624 ATCGATACATT
1 ATCGATACATT
955635 ATATCTTTTT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (20 bp):
ATCGATACATTTTTCAATGT
Found at i:960889 original size:20 final size:20
Alignment explanation
Indices: 960866--960938 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
960856 ACAATTCAAA
960866 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
960886 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
960907 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
960927 GTATCGATACAT
1 GTATCGATACAT
960939 AAAAAAAGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:960917 original size:41 final size:42
Alignment explanation
Indices: 960866--960960 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
960856 ACAATTCAAA
*
960866 GTATCGATACATGTTGCAATGTATCGATACAT-GAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
960907 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
960949 GTATCGATACAT
1 GTATCGATACAT
960961 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 32 0.62
42 20 0.38
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (42 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
Found at i:961017 original size:13 final size:13
Alignment explanation
Indices: 960999--961024 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
960989 TACAGCAAGT
960999 ATGTATCGATACA
1 ATGTATCGATACA
961012 ATGTATCGATACA
1 ATGTATCGATACA
961025 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:965106 original size:15 final size:15
Alignment explanation
Indices: 965086--965116 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
965076 TAAAAATGTC
*
965086 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
965101 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
965116 C
1 C
965117 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:967214 original size:13 final size:13
Alignment explanation
Indices: 967196--967234 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
967186 ACATTTTTCC
967196 TTGTATCGATACA
1 TTGTATCGATACA
967209 TTGTATCGATACA
1 TTGTATCGATACA
*
967222 CTGTATCGATACA
1 TTGTATCGATACA
967235 GGGTGTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:969098 original size:36 final size:36
Alignment explanation
Indices: 969027--969126 Score: 186
Period size: 36 Copynumber: 2.8 Consensus size: 36
969017 AATTTTGATA
969027 TGAATTACTTGATTAAGGGGGAGA--TTTTTTTTTT
1 TGAATTACTTGATTAAGGGGGAGATTTTTTTTTTTT
969061 TGAATTACTTGATTAAGGGGGAGATTTTTTTTTTTT
1 TGAATTACTTGATTAAGGGGGAGATTTTTTTTTTTT
969097 TGAATTACTTGATTAAGGGGGAGATTTTTT
1 TGAATTACTTGATTAAGGGGGAGATTTTTT
969127 AATAAACGGG
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
34 24 0.38
36 40 0.62
ACGTcount: A:0.24, C:0.03, G:0.24, T:0.49
Consensus pattern (36 bp):
TGAATTACTTGATTAAGGGGGAGATTTTTTTTTTTT
Found at i:969770 original size:20 final size:20
Alignment explanation
Indices: 969747--969819 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
969737 ACAATTCAAA
969747 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
969767 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
969788 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
969808 GTATCGATACAT
1 GTATCGATACAT
969820 AAAAAAAGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:969798 original size:41 final size:42
Alignment explanation
Indices: 969747--969841 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
969737 ACAATTCAAA
*
969747 GTATCGATACATGTTGCAATGTATCGATACAT-GAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
969788 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
969830 GTATCGATACAT
1 GTATCGATACAT
969842 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 32 0.62
42 20 0.38
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (42 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
Found at i:969898 original size:13 final size:13
Alignment explanation
Indices: 969880--969905 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
969870 TACAGCAAGT
969880 ATGTATCGATACA
1 ATGTATCGATACA
969893 ATGTATCGATACA
1 ATGTATCGATACA
969906 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:972477 original size:13 final size:13
Alignment explanation
Indices: 972459--972483 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
972449 CATAAAATGT
972459 TGTATCGATACAA
1 TGTATCGATACAA
972472 TGTATCGATACA
1 TGTATCGATACA
972484 TATTTTTTGT
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:972499 original size:32 final size:33
Alignment explanation
Indices: 972439--972504 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
972429 TTCAACGATT
972439 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
** *
972472 TGTATCGATACAT-ATTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
972504 T
1 T
972505 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:972563 original size:13 final size:13
Alignment explanation
Indices: 972545--972569 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
972535 ATTACTCAAA
972545 TGTATCGATACAT
1 TGTATCGATACAT
972558 TGTATCGATACA
1 TGTATCGATACA
972570 GTGATCTTTG
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:972671 original size:52 final size:53
Alignment explanation
Indices: 972577--972707 Score: 205
Period size: 52 Copynumber: 2.5 Consensus size: 53
972567 ACAGTGATCT
* *
972577 TTGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAA
1 TTGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATTAAA
972628 TTGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATTAAA
1 TTGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATTAAA
* *
972681 -TGTATCGATACATGCAAGCAACTTTTC
1 TTGTATCGATACATGCAGGCAAATTTTC
972708 ATATTTCGGG
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
51 20 0.27
52 48 0.65
53 6 0.08
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (53 bp):
TTGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATTAAA
Found at i:983318 original size:12 final size:12
Alignment explanation
Indices: 983301--983371 Score: 63
Period size: 13 Copynumber: 5.8 Consensus size: 12
983291 CGTCCTTTAC
983301 ACAAAAAAAAAA
1 ACAAAAAAAAAA
983313 ACAAAAAAAAAAA
1 AC-AAAAAAAAAA
983326 ACAAAACAAAAAA
1 ACAAAA-AAAAAA
**
983339 A-AATGAAAAAA
1 ACAAAAAAAAAA
* *
983350 CCAAGAAAAAATA
1 ACAA-AAAAAAAA
*
983363 GCAAAAAAA
1 ACAAAAAAA
983372 GAGAAAAGGG
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
11 6 0.12
12 15 0.31
13 27 0.56
ACGTcount: A:0.83, C:0.10, G:0.04, T:0.03
Consensus pattern (12 bp):
ACAAAAAAAAAA
Found at i:983321 original size:13 final size:13
Alignment explanation
Indices: 983303--983340 Score: 67
Period size: 13 Copynumber: 2.8 Consensus size: 13
983293 TCCTTTACAC
983303 AAAAAAAAAAACA
1 AAAAAAAAAAACA
983316 AAAAAAAAAAACA
1 AAAAAAAAAAACA
983329 AAACAAAAAAAA
1 AAA-AAAAAAAA
983341 ATGAAAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 16 0.67
14 8 0.33
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAACA
Found at i:983326 original size:18 final size:18
Alignment explanation
Indices: 983303--983360 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
983293 TCCTTTACAC
983303 AAAAAAAAAAACAAAAAA
1 AAAAAAAAAAACAAAAAA
*
983321 AAAAAACAAAACAAAAAA
1 AAAAAAAAAAACAAAAAA
* *
983339 AAATGAAAAAACCAAGAAAA
1 AAA-AAAAAAAACAA-AAAA
983359 AA
1 AA
983361 TAGCAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
18 20 0.59
19 8 0.24
20 6 0.18
ACGTcount: A:0.86, C:0.09, G:0.03, T:0.02
Consensus pattern (18 bp):
AAAAAAAAAAACAAAAAA
Found at i:983360 original size:1 final size:1
Alignment explanation
Indices: 983303--983341 Score: 51
Period size: 1 Copynumber: 39.0 Consensus size: 1
983293 TCCTTTACAC
* * *
983303 AAAAAAAAAAACAAAAAAAAAAAACAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
983342 TGAAAAAACC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:984722 original size:28 final size:27
Alignment explanation
Indices: 984593--985782 Score: 1371
Period size: 28 Copynumber: 42.2 Consensus size: 27
984583 AATGTTCATC
**
984593 CCTTTCAAAGCCCATGAGTCAGTGGCA
1 CCTTTCAAAGCCCACAAGTCAGTGGCA
* *
984620 CCATTTTCAAAGCCCATATGTCAGTGGCA
1 CC--TTTCAAAGCCCACAAGTCAGTGGCA
*
984649 CTCTTTTCAAAACCCACAAGTCAGTGGCA
1 C-C-TTTCAAAGCCCACAAGTCAGTGGCA
*
984678 CTCTTTTCAAAGCCCACAAGTTAGTGGCA
1 C-C-TTTCAAAGCCCACAAGTCAGTGGCA
984707 TCCTTTCAAAGCCCACAAGTCAGTGGCA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
984735 CTCTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CTTTCAAAGCCCACAAGTCAGTGGCA
984763 TCCTTTCAAAGCCCACAAGTCAGTGGCA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
**
984791 CTCTTTCAAAGCCCATGAGTCAGTGGCA
1 C-CTTTCAAAGCCCACAAGTCAGTGGCA
* *
984819 CTATTTTCAAAGCCCACATGTCAGTGGCA
1 C--CTTTCAAAGCCCACAAGTCAGTGGCA
*
984848 CCCTTTTCAAAACCCACAAGTCAGTGGCA
1 -CC-TTTCAAAGCCCACAAGTCAGTGGCA
*
984877 CTCTTTTCAAAGCCCACAAGTTAGTGGCA
1 C-C-TTTCAAAGCCCACAAGTCAGTGGCA
*
984906 TCCTTTCAAAGCCCACAAGTTAGTGGCA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
984934 CTCTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CTTTCAAAGCCCACAAGTCAGTGGCA
*
984962 TCCTTTCAAAGCCCATAAGTCAGTGGCA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
*
984990 CTCTTTCAAAGCCCACAAGTCAGTGGTA
1 C-CTTTCAAAGCCCACAAGTCAGTGGCA
*
985018 CCTTTTC-AAGCTCACAAGTCAGTGGCA
1 CC-TTTCAAAGCCCACAAGTCAGTGGCA
985045 CTCTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CTTTCAAAGCCCACAAGTCAGTGGCA
985073 CCTTTTC-AAGCCCACAAGTCAGTGGCA
1 CC-TTTCAAAGCCCACAAGTCAGTGGCA
*
985100 CTCTTTTCAAAGCCCACAAGTTAGTGGCA
1 C-C-TTTCAAAGCCCACAAGTCAGTGGCA
985129 TCCTTTCAAAGCCCACAAGTCAGTGGCA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
985157 CTCTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CTTTCAAAGCCCACAAGTCAGTGGCA
* *
985185 TCCTTTTAAAGCCCACAAGTCAATGGCA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
* *
985213 CTCTTTCAAAGCCCACAAGTTAGTGGTA
1 C-CTTTCAAAGCCCACAAGTCAGTGGCA
985241 CCTTTTC-AAGCCCACAAGTCAGTGGCA
1 CC-TTTCAAAGCCCACAAGTCAGTGGCA
*
985268 CTCTTTCAAAGCCCACAAGTTAGTGGCA
1 C-CTTTCAAAGCCCACAAGTCAGTGGCA
*
985296 TCCTTTCAAAGCCCACAAGTAAGTGGCA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
985324 CTCTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CTTTCAAAGCCCACAAGTCAGTGGCA
** *
985352 CCTTTTTAAGCCCACAAGTCAGTGGTA
1 CCTTTCAAAGCCCACAAGTCAGTGGCA
985379 CCTTTTC-AAGCCCACAAGTCAGTGGCA
1 CC-TTTCAAAGCCCACAAGTCAGTGGCA
985406 CTCTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CTTTCAAAGCCCACAAGTCAGTGGCA
* * *
985434 TCTTTTCAAAGCCCACGAGTTAGTGGCA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
**
985462 CCCTTTTGAAGCCCACAAGTCAGTGGCA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
* * * * *
985490 CCCTTGCGAAGCCCATAATTCAGTGGTA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
* *
985518 CTATTTCAAAGCCCACAAGTCAGTGACA
1 C-CTTTCAAAGCCCACAAGTCAGTGGCA
*
985546 CCCTTTCAAAGCCCACACAAGTTAGTGGCA
1 -CCTTTCAAAG-CC-CACAAGTCAGTGGCA
* *
985576 CTCCTTTTAGAGCCCACAAGTCAGTGGCA
1 --CCTTTCAAAGCCCACAAGTCAGTGGCA
*
985605 CCCTTTCGAAGCCCACAAGTCAGTGGCA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
* * * * *
985633 CCCTTGCGAAGCCTACAATTTAGTGGCA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
*
985661 CTCTTTTAAAGCCCACAAGTCAGTGGCA
1 C-CTTTCAAAGCCCACAAGTCAGTGGCA
*
985689 CCCTTTCAAAGCCCACAAGTTAGTGGCA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
* **
985717 CCCTTTTAAAGCCCACGCAAGTCAGTAACA
1 -CCTTTCAAAGCCCA--CAAGTCAGTGGCA
*
985747 CTCTTTTCAAAGCCCACACGTGTCAGTGGCA
1 C-C-TTTCAAAGCCCACA--AGTCAGTGGCA
*
985778 ACTTT
1 CCTTT
985783 TTTCGAAGCC
Statistics
Matches: 1018, Mismatches: 98, Indels: 92
0.84 0.08 0.08
Matches are distributed among these distances:
27 130 0.13
28 634 0.62
29 195 0.19
30 32 0.03
31 27 0.03
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (27 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:986404 original size:20 final size:20
Alignment explanation
Indices: 986376--986450 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
986366 TTTTACCTAG
986376 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
986396 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
986416 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
986436 ATGTATCGATACATT
1 ATGTATCGATACATT
986451 ATGTCTTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:986436 original size:40 final size:39
Alignment explanation
Indices: 986376--986453 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
986366 TTTTACCTAG
*
986376 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTTCAATATATCGATACAT-TATGA
* *
986416 ATGTATCGATATATTCTTCAATGTATCGATACATTATG
1 ATGTATCGATACATTCTTCAATATATCGATACATTATG
986454 TCTTTTTACC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTTCAATATATCGATACATTATGA
Found at i:987386 original size:22 final size:22
Alignment explanation
Indices: 987360--987410 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
987350 AGCCTTTGAC
987360 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
987382 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
987404 CATGCAT
1 CATGCAT
987411 CTTTAACATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.59
Consensus pattern (22 bp):
CATGCATTTTTTTATTATGTTT
Found at i:990011 original size:15 final size:15
Alignment explanation
Indices: 989990--990033 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
989980 AAATAAAAAA
989990 AATGAAAAGAGAGAAG
1 AATGAAAAGAGA-AAG
*
990006 AA-GAAAAAAGAAAG
1 AATGAAAAGAGAAAG
*
990020 AATGAAAAGGGAAA
1 AATGAAAAGAGAAA
990034 AGAAATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 5 0.21
15 17 0.71
16 2 0.08
ACGTcount: A:0.68, C:0.00, G:0.27, T:0.05
Consensus pattern (15 bp):
AATGAAAAGAGAAAG
Found at i:990140 original size:17 final size:17
Alignment explanation
Indices: 990118--990181 Score: 60
Period size: 17 Copynumber: 3.7 Consensus size: 17
990108 TTTAGGAATT
*
990118 AAATTTATTTTTTTTAA
1 AAATTAATTTTTTTTAA
*
990135 AAATTTAA-TTTTGTTAGA
1 AAA-TTAATTTTTTTTA-A
*
990153 AAATAAATTATTTTTT-A
1 AAATTAATT-TTTTTTAA
990170 AAATTAATTTTT
1 AAATTAATTTTT
990182 CAAAAATATT
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
16 3 0.08
17 22 0.58
18 8 0.21
19 5 0.13
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
AAATTAATTTTTTTTAA
Found at i:991676 original size:20 final size:21
Alignment explanation
Indices: 991634--991681 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
991624 ATTCAAACAA
*
991634 AAATGATTTAAATATTAAAAT
1 AAATAATTTAAATATTAAAAT
*
991655 AAATAATTTTAATATT-AAAT
1 AAATAATTTAAATATTAAAAT
*
991675 AAGTAAT
1 AAATAAT
991682 AAATATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (21 bp):
AAATAATTTAAATATTAAAAT
Found at i:991691 original size:16 final size:16
Alignment explanation
Indices: 991672--991702 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
991662 TTTAATATTA
*
991672 AATAAGTAATAAATAT
1 AATAAATAATAAATAT
991688 AATAAATAATAAATA
1 AATAAATAATAAATA
991703 AAAATATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (16 bp):
AATAAATAATAAATAT
Found at i:992781 original size:64 final size:64
Alignment explanation
Indices: 992675--992800 Score: 234
Period size: 64 Copynumber: 2.0 Consensus size: 64
992665 TGTTTGTATG
* *
992675 AAACTTATAGCTGTGGCTTGGATATCAGCTAAGGAAATAAAATATTAACAGTGTTAATAGTTAC
1 AAACATATAGCTGTGGCTTGAATATCAGCTAAGGAAATAAAATATTAACAGTGTTAATAGTTAC
992739 AAACATATAGCTGTGGCTTGAATATCAGCTAAGGAAATAAAATATTAACAGTGTTAATAGTT
1 AAACATATAGCTGTGGCTTGAATATCAGCTAAGGAAATAAAATATTAACAGTGTTAATAGTT
992801 TATAAAGTTT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.31
Consensus pattern (64 bp):
AAACATATAGCTGTGGCTTGAATATCAGCTAAGGAAATAAAATATTAACAGTGTTAATAGTTAC
Found at i:994657 original size:19 final size:19
Alignment explanation
Indices: 994633--994670 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
994623 GATATGTTGT
994633 TTTGAAATATTTTTCTAGA
1 TTTGAAATATTTTTCTAGA
994652 TTTGAAATATTTTTCTAGA
1 TTTGAAATATTTTTCTAGA
994671 ATACTATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTGAAATATTTTTCTAGA
Found at i:996141 original size:2 final size:2
Alignment explanation
Indices: 996134--996204 Score: 117
Period size: 2 Copynumber: 36.0 Consensus size: 2
996124 TTTGAACTTC
996134 AT AT AT AT AT 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 AT AT AT AT AT
**
996176 AT AT AT AT GC AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
996205 TTAAAGGTTT
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
1 1 0.02
2 63 0.98
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:996368 original size:20 final size:19
Alignment explanation
Indices: 996339--996378 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
996329 GTTTTAAAAA
996339 AATTTGAATATAAATTAAAT
1 AATTTGAATATAAA-TAAAT
* *
996359 AATTTTAATATCAATAAAT
1 AATTTGAATATAAATAAAT
996378 A
1 A
996379 TTAAATATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (19 bp):
AATTTGAATATAAATAAAT
Found at i:997452 original size:12 final size:12
Alignment explanation
Indices: 997413--997455 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
997403 TTCCTGTGCT
*
997413 TATTTTTTTTCA
1 TATTTTTTTTTA
*
997425 TATTTAATTATTTA
1 TATTT--TTTTTTA
997439 TATTTTTTTTTA
1 TATTTTTTTTTA
997451 TATTT
1 TATTT
997456 CACCCACAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 16 0.62
14 10 0.38
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (12 bp):
TATTTTTTTTTA
Found at i:999546 original size:79 final size:77
Alignment explanation
Indices: 999437--999723 Score: 303
Period size: 79 Copynumber: 3.7 Consensus size: 77
999427 TCTCTTGGAG
* * *
999437 ATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATCGATGTTTTAGAAATAAAATCGAGGTTGGA
1 ATAACGGGGTTGGAGTATTCCCAATGGTGAAAAATCGATATTTTAGAAATAAAA-CGAGGTTGGA
999502 GTATCCTCTCGAAA
65 GTATCC-CTCGAAA
* * * * *
999516 ATAACGGGGTTGGAGTATTCCCAATGGTGAAAAATCAATATTTCAGAAA-AAAAAGGGAGCTGGA
1 ATAACGGGGTTGGAGTATTCCCAATGGTGAAAAATCGATATTTTAGAAATAAAACGAG-GTTGGA
*
999580 GTGTCCCCTCGAAA
65 GTAT-CCCTCGAAA
* *
999594 ATAATGGGGTTGGAGTA-TCCTCAATTGTGAAAAATC-AGTATTTTAGAAATAAAACTGAGGTTG
1 ATAACGGGGTTGGAGTATTCC-CAATGGTGAAAAATCGA-TATTTTAGAAATAAAAC-GAGGTTG
999657 GAGTATCCCTTCGAAA
63 GAGTATCCC-TCGAAA
* * * * * * *
999673 ATAATGAGATTAGAGTATTCTCGATGGT-AGAAAATCGATGTTTTAGAAATA
1 ATAACGGGGTTGGAGTATTCCCAATGGTGA-AAAATCGATATTTTAGAAATA
999724 TATCGTAATG
Statistics
Matches: 175, Mismatches: 23, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
77 6 0.03
78 63 0.36
79 101 0.58
80 5 0.03
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (77 bp):
ATAACGGGGTTGGAGTATTCCCAATGGTGAAAAATCGATATTTTAGAAATAAAACGAGGTTGGAG
TATCCCTCGAAA
Found at i:1003070 original size:25 final size:27
Alignment explanation
Indices: 1003036--1003104 Score: 81
Period size: 25 Copynumber: 2.6 Consensus size: 27
1003026 TTTATTTTGA
* *
1003036 TTTTAGTTTTTTGATTTGA-TGA-TTT
1 TTTTAATTTTTTGATTTCATTGATTTT
*
1003061 TTTTATTTTTTTGA-TTCATTGATTTT
1 TTTTAATTTTTTGATTTCATTGATTTT
1003087 TTTTGAATTTTTTGATTT
1 TTTT-AATTTTTTGATTT
1003105 TTCATTCTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
24 3 0.08
25 16 0.43
26 7 0.19
27 9 0.24
28 2 0.05
ACGTcount: A:0.16, C:0.01, G:0.12, T:0.71
Consensus pattern (27 bp):
TTTTAATTTTTTGATTTCATTGATTTT
Found at i:1003089 original size:18 final size:19
Alignment explanation
Indices: 1003066--1003106 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1003056 GATTTTTTTA
1003066 TTTTTTTG-ATTCATTGAT
1 TTTTTTTGAATTCATTGAT
**
1003084 TTTTTTTGAATTTTTTGAT
1 TTTTTTTGAATTCATTGAT
1003103 TTTT
1 TTTT
1003107 CATTCTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.15, C:0.02, G:0.10, T:0.73
Consensus pattern (19 bp):
TTTTTTTGAATTCATTGAT
Found at i:1003104 original size:8 final size:8
Alignment explanation
Indices: 1003006--1003106 Score: 52
Period size: 8 Copynumber: 12.8 Consensus size: 8
1002996 TTTCATCATC
*
1003006 ATTTTTTT
1 ATTTTTTG
1003014 ATTTTATT-
1 ATTTT-TTG
1003022 ATTTTTT-
1 ATTTTTTG
1003029 A--TTTTG
1 ATTTTTTG
*
1003035 A-TTTTAG
1 ATTTTTTG
1003042 -TTTTTTG
1 ATTTTTTG
**
1003049 ATTTGATG
1 ATTTTTTG
*
1003057 ATTTTTTT
1 ATTTTTTG
1003065 ATTTTTTTG
1 A-TTTTTTG
**
1003074 ATTCATTG
1 ATTTTTTG
1003082 ATTTTTTTTG
1 A--TTTTTTG
1003092 AATTTTTTG
1 -ATTTTTTG
1003101 ATTTTT
1 ATTTTT
1003107 CATTCTTATA
Statistics
Matches: 72, Mismatches: 12, Indels: 18
0.71 0.12 0.18
Matches are distributed among these distances:
5 4 0.06
6 1 0.01
7 12 0.17
8 33 0.46
9 16 0.22
10 5 0.07
11 1 0.01
ACGTcount: A:0.17, C:0.01, G:0.09, T:0.73
Consensus pattern (8 bp):
ATTTTTTG
Found at i:1004095 original size:61 final size:61
Alignment explanation
Indices: 1004010--1004234 Score: 190
Period size: 61 Copynumber: 3.7 Consensus size: 61
1004000 GAGAAGAGTG
* * ** * *
1004010 CCAATGTGCTGATTTAAGATCAGCGACATTAAACTTAAAGATGAGAAGAATGATAAAGGTA
1 CCAATATGCTGATTCAAGGCCAGCGACATTGAACTTAAAGATGAGAAAAATGATAAAGGTA
* * * ** * *
1004071 TCGATATGCTGATTCAAGGCCAGCGATATTGGGCTTTAAAGA--AAAAAAATTTGA-AAA-GTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGAAC-TTAAAGATGAGAAAAA--TGATAAAGGTA
* * * * *
1004131 CCAATATGTTGATTCAA-GCCAACGACATTGAGCTTGAAGATGAGAAAAATGATACAGGTA
1 CCAATATGCTGATTCAAGGCCAGCGACATTGAACTTAAAGATGAGAAAAATGATAAAGGTA
* * * *
1004191 CCAATATACTAATTCAAGGCCAGCGATATTGGACTTAAAGATGA
1 CCAATATGCTGATTCAAGGCCAGCGACATTGAACTTAAAGATGA
1004235 TAAAGGTGCC
Statistics
Matches: 125, Mismatches: 31, Indels: 16
0.73 0.18 0.09
Matches are distributed among these distances:
58 9 0.07
59 15 0.12
60 43 0.34
61 48 0.38
62 10 0.08
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (61 bp):
CCAATATGCTGATTCAAGGCCAGCGACATTGAACTTAAAGATGAGAAAAATGATAAAGGTA
Found at i:1004174 original size:120 final size:120
Alignment explanation
Indices: 1004006--1004231 Score: 301
Period size: 120 Copynumber: 1.9 Consensus size: 120
1003996 GGATGAGAAG
* * * * *
1004006 AGTGCCAATGTGCTGATTTAAGATCAGCGACATTAAACTTAAAGATGAGAAGAATGATAAAGGTA
1 AGTGCCAATATGCTGATTCAAGACCAACGACATTAAACTTAAAGATGAGAAAAATGATAAAGGTA
* * * * *
1004071 TCGATATGCTGATTCAAGGCCAGCGATATTGGGCTTTAAAGAAAAAAAATTTGAAA
66 CCAATATACTAATTCAAGGCCAGCGATATTGGAC-TTAAAGAAAAAAAATTTGAAA
* * * * *
1004127 AGTGCCAATATGTTGATTCAAG-CCAACGACATTGAGCTTGAAGATGAGAAAAATGATACAGGTA
1 AGTGCCAATATGCTGATTCAAGACCAACGACATTAAACTTAAAGATGAGAAAAATGATAAAGGTA
1004191 CCAATATACTAATTCAAGGCCAGCGATATTGGACTTAAAGA
66 CCAATATACTAATTCAAGGCCAGCGATATTGGACTTAAAGA
1004232 TGATAAAGGT
Statistics
Matches: 90, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
119 7 0.08
120 64 0.71
121 19 0.21
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.25
Consensus pattern (120 bp):
AGTGCCAATATGCTGATTCAAGACCAACGACATTAAACTTAAAGATGAGAAAAATGATAAAGGTA
CCAATATACTAATTCAAGGCCAGCGATATTGGACTTAAAGAAAAAAAATTTGAAA
Found at i:1004262 original size:52 final size:52
Alignment explanation
Indices: 1004179--1004283 Score: 147
Period size: 52 Copynumber: 2.0 Consensus size: 52
1004169 GATGAGAAAA
* * **
1004179 ATGATACAGGTACCAATATACTAATTCAAGGCCAGCGATATTGGACTTAAAG
1 ATGATAAAGGTACCAATATACTAATTCAAGGCCAGCAATATCAGACTTAAAG
* * *
1004231 ATGATAAAGGTGCCAATATACTGATTTAAGGCCAGCAATATCAGACTTAAAG
1 ATGATAAAGGTACCAATATACTAATTCAAGGCCAGCAATATCAGACTTAAAG
1004283 A
1 A
1004284 AAAAAATTTA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (52 bp):
ATGATAAAGGTACCAATATACTAATTCAAGGCCAGCAATATCAGACTTAAAG
Found at i:1004576 original size:29 final size:28
Alignment explanation
Indices: 1004360--1004748 Score: 297
Period size: 29 Copynumber: 13.4 Consensus size: 28
1004350 TCGACTTGTA
*
1004360 TGGGCTTTAAAAGGGTTG-CAATCGACTTG
1 TGGGCTTTAAAAGGG-TGCCACT-GACTTG
*
1004389 T---CTTTAAAAGGGTTGCCAC-CAGCTGTG
1 TGGGCTTTAAAAGGG-TGCCACTGA-CT-TG
**
1004416 TGGGCTTTAAAAAGAAATGCCA-TCGACTTG
1 TGGGCTTT-AAAAG-GGTGCCACT-GACTTG
* * * * *
1004446 CATGAGCTTTTGAAAGGGTTCCCACCGACTTA
1 --TGGGC-TTTAAAAGGG-TGCCACTGACTTG
* *
1004478 TGGGCTTTCCAAAGGGTGCCACCGACTTG
1 TGGGCTTT-AAAAGGGTGCCACTGACTTG
** * * * *
1004507 TAAGCTATGAAAGGATGCCATTGA-TTCG
1 TGGGCTTTAAAAGGGTGCCACTGACTT-G
* * * *
1004535 TGGGCTTTGAAAGGATGCCATTGAATTTG
1 TGGGCTTTAAAAGGGTGCCACTG-ACTTG
* * *
1004564 TGGGCTTTAAAAGGGTGTCACTGGCTCG
1 TGGGCTTTAAAAGGGTGCCACTGACTTG
1004592 TGGGCTTTGAAAAGGGTGCCACTGACTTG
1 TGGGCTTT-AAAAGGGTGCCACTGACTTG
1004621 TGGGCTTTTAAAAGGGTGCCACTGACTTG
1 TGGGC-TTTAAAAGGGTGCCACTGACTTG
*
1004650 TGGGCTTTGAAAAGGGTGCCACTGACTTA
1 TGGGCTTT-AAAAGGGTGCCACTGACTTG
*
1004679 TGGGCTTTAAAAGGGTGCCACTAACTTG
1 TGGGCTTTAAAAGGGTGCCACTGACTTG
* *
1004707 TGGGCTTTTGAAAGGATGCCACTGACTTG
1 TGGGC-TTTAAAAGGGTGCCACTGACTTG
1004736 TGGGCTTTTAAAA
1 TGGGC-TTTAAAA
1004749 TGATGCCATT
Statistics
Matches: 294, Mismatches: 43, Indels: 46
0.77 0.11 0.12
Matches are distributed among these distances:
25 1 0.00
26 16 0.05
27 7 0.02
28 69 0.23
29 147 0.50
30 21 0.07
31 12 0.04
32 18 0.06
33 3 0.01
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (28 bp):
TGGGCTTTAAAAGGGTGCCACTGACTTG
Found at i:1004634 original size:58 final size:56
Alignment explanation
Indices: 1004478--1005564 Score: 664
Period size: 57 Copynumber: 19.4 Consensus size: 56
1004468 CACCGACTTA
* * * ** * * * * *
1004478 TGGGCTTTCCAAAGGGTGCCACCGACTTGTAAGCTATGAAAGGATGCCATTGATTCG
1 TGGGCTTT-GAAAGGATGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTCG
* * * *
1004535 TGGGCTTTGAAAGGATGCCATTGAATTTGTGGGCTTTAAAAGGGTGTCACTGGCTCG
1 TGGGCTTTGAAAGGATGCCACTG-ACTTGTGGGCTTTAAAAGGGTGCCACTGACTCG
* *
1004592 TGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTAAAAGGGTGCCACTGACTTG
1 TGGGCTTTG-AAAGGATGCCACTGACTTGTGGGC-TTTAAAAGGGTGCCACTGACTCG
* * * *
1004650 TGGGCTTTGAAAAGGGTGCCACTGACTTATGGGCTTTAAAAGGGTGCCACTAACTTG
1 TGGGCTTTG-AAAGGATGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTCG
* * *
1004707 TGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTTAAAATGATGCCATTGA---G
1 TGGGC-TTTGAAAGGATGCCACTGACTTGTGGGC-TTTAAAAGGGTGCCACTGACTCG
* * ** * * ** * * *
1004762 AGGG--ATGCCA--CTG--ACT--CATG-GGCTTTGAAAGGGATGCCACTGACTCG
1 TGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTCG
* * * * * * *
1004809 TGAGCTTTGAAAAG-TGCCACTGACTTAT-GGCTTTAAAAGAGTGACACTAACTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTCG
* * * * ** * *
1004863 GGGGCTTTAAAAGG-TGCCACTAATTTGTGGGCTTTAAAAATGTGTCACTGACTTATGGCTTT
1 TGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGAC---T--C--G
* * * * * * * *
1004925 TGAAAGG-ATTGAAAGGATGCTATTGACTTGTAGGCTTTGAAAGGGTGTCATTGACTTG
1 TG---GGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTCG
* * * * ** *
1004983 TGGGCTTTTGAAAGGGTGCAACTAACTTGTAGGCTTTAAAAGGGTATCACTGACTTG
1 TGGGC-TTTGAAAGGATGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTCG
* * * * * * *
1005040 TGGGCTTTGAAAAGGGTGCCACTGGCTTATGGGCTTTGAAAATGGTTCCATTGACTTG
1 TGGGCTTTG-AAAGGATGCCACTGACTTGTGGGCTTT-AAAAGGGTGCCACTGACTCG
* ** ** * *
1005098 TGGGCATTTGAAAGGGTATCACTGACTTGTGGGCTTTAAAAGGGTATCACTCACTTG
1 TGGGC-TTTGAAAGGATGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTCG
* * * * * *
1005155 TGGGCTTTATAAAGGGTGCCACTAACTTATGGGCTTTTGAAAGGGTGCCACTGACTTG
1 TGGGCTTT-GAAAGGATGCCACTGACTTGTGGGC-TTTAAAAGGGTGCCACTGACTCG
* * * * **
1005213 TGGGC-TTGAAAAGGGTGTCACTCATTTGTGGGCTTTGAAAAGGGTGCCACTGACTTA
1 TGGGCTTTG-AAAGGATGCCACTGACTTGTGGGCTTT-AAAAGGGTGCCACTGACTCG
* * * * * **
1005270 TGGCCTTTGATAAGAATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGATTTA
1 TGGGCTTTGA-AAGGATGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTCG
* * * * *
1005327 TGGGCTTTAAAAGGATACCACTGACTCGTGGGCTTTTGAAATGGTGCCACTGACTCG
1 TGGGCTTTGAAAGGATGCCACTGACTTGTGGGC-TTTAAAAGGGTGCCACTGACTCG
* * * ** * *
1005384 TGGACTTTTGAAATGATGCCACTAACTCATGGGCTTTGAAAGGGATGCCACTGACTCA
1 TGGGC-TTTGAAAGGATGCCACTGACTTGTGGGCTTTAAAAGGG-TGCCACTGACTCG
* * *
1005442 TGGGCTTTGAAAGGGATGCCACCGACTTGTGGGCTTT-------TG--AATGGCTCG
1 TGGGCTTTGAAA-GGATGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTCG
* * *
1005490 TGGGCTTTGAAAAGG-TGCCACTGACTTGTGAGCTTTAAAA-GGTGCCATTGACTTG
1 TGGGCTTTG-AAAGGATGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTCG
1005545 TGGGCTTTGAAAGGATGCCA
1 TGGGCTTTGAAAGGATGCCA
1005565 TTAACTCATG
Statistics
Matches: 810, Mismatches: 166, Indels: 110
0.75 0.15 0.10
Matches are distributed among these distances:
44 15 0.02
45 2 0.00
46 3 0.00
47 22 0.03
48 20 0.02
49 6 0.01
50 6 0.01
52 6 0.01
53 2 0.00
54 45 0.06
55 45 0.06
56 41 0.05
57 316 0.39
58 237 0.29
59 4 0.00
62 2 0.00
64 7 0.01
65 31 0.04
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (56 bp):
TGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTCG
Found at i:1004756 original size:29 final size:29
Alignment explanation
Indices: 1004451--1004748 Score: 300
Period size: 29 Copynumber: 10.3 Consensus size: 29
1004441 ACTTGCATGA
* * * *
1004451 GCTTTTGAAAGGGTTCCCACCGACTTATGG
1 GCTTTTAAAAGGG-TGCCACTGACTTGTGG
** * **
1004481 GCTTTCCAAAGGGTGCCACCGACTTGTAA
1 GCTTTTAAAAGGGTGCCACTGACTTGTGG
* * * *
1004510 GC-TATGAAAGGATGCCATTGA-TTCGTGG
1 GCTTTTAAAAGGGTGCCACTGACTT-GTGG
* * * *
1004538 GC-TTTGAAAGGATGCCATTGAATTTGTGG
1 GCTTTTAAAAGGGTGCCACTG-ACTTGTGG
* * *
1004567 GC-TTTAAAAGGGTGTCACTGGCTCGTGG
1 GCTTTTAAAAGGGTGCCACTGACTTGTGG
*
1004595 GCTTTGAAAAGGGTGCCACTGACTTGTGG
1 GCTTTTAAAAGGGTGCCACTGACTTGTGG
1004624 GCTTTTAAAAGGGTGCCACTGACTTGTGG
1 GCTTTTAAAAGGGTGCCACTGACTTGTGG
* *
1004653 GCTTTGAAAAGGGTGCCACTGACTTATGG
1 GCTTTTAAAAGGGTGCCACTGACTTGTGG
*
1004682 GC-TTTAAAAGGGTGCCACTAACTTGTGG
1 GCTTTTAAAAGGGTGCCACTGACTTGTGG
* *
1004710 GCTTTTGAAAGGATGCCACTGACTTGTGG
1 GCTTTTAAAAGGGTGCCACTGACTTGTGG
1004739 GCTTTTAAAA
1 GCTTTTAAAA
1004749 TGATGCCATT
Statistics
Matches: 227, Mismatches: 36, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
27 2 0.01
28 66 0.29
29 146 0.64
30 13 0.06
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.30
Consensus pattern (29 bp):
GCTTTTAAAAGGGTGCCACTGACTTGTGG
Found at i:1004756 original size:86 final size:86
Alignment explanation
Indices: 1004451--1005570 Score: 468
Period size: 86 Copynumber: 12.9 Consensus size: 86
1004441 ACTTGCATGA
* * * * ** * ** * *
1004451 GCTTTTGAAAGGGTTCCCACCGACTTATGGGCTTTCCAAAGGGTGCCACCGACTTGTAAGCTATG
1 GCTTTTGAAA-GGATGCCACTGACTTGTGGGCTTTTAAAAGGGTGCCACTGACTTGTGGGCTTTA
* * *
1004516 AAAGGATGCCATTGA-TTCGTGG
65 AAAGGGTGCCACTAACTT-GTGG
* * * * *
1004538 GC-TTTGAAAGGATGCCATTGAATTTGTGGGC-TTTAAAAGGGTGTCACTGGCTCGTGGGCTTTG
1 GCTTTTGAAAGGATGCCACTG-ACTTGTGGGCTTTTAAAAGGGTGCCACTGACTTGTGGGCTTT-
*
1004601 AAAAGGGTGCCACTGACTTGTGG
64 AAAAGGGTGCCACTAACTTGTGG
* * * *
1004624 GCTTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTATGGGCTTTAA
1 GCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTTAAAAGGGTGCCACTGACTTGTGGGCTTTAA
1004689 AAGGGTGCCACTAACTTGTGG
66 AAGGGTGCCACTAACTTGTGG
* * * ** *
1004710 GCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTTAAAATGATGCCATTGA-GAG-GGATGCCAC
1 GCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTTAAAAGGGTGCCACTGACTTGTGG--G-C-T
* ** * ** *** *
1004773 TGACTCATGG-G-CTTTGAAAGGGATGCC
62 TTA-AAAGGGTGCCACT-AACTTG-TG-G
* * * ** ** ** * ** ** * * * *
1004800 ACTGACTCGTGAGCTTTGAAAAGTGCCAC-TGACTTATGGCTTTAAAAGAGTGACACTAACTTGG
1 GCT--TTTGAAAG-GATG-CCACTG--ACTTG---TGGGCTTTTAAAAGGGTGCCACTGACTTGT
*
1004864 GGGCTTTAAAA-GGTGCCACTAATTTGTGG
57 GGGCTTTAAAAGGGTGCCACTAACTTGTGG
** * * * * *
1004893 GCTTTAAAAATG-TGTCACTGACTTAT-GGCTTTTGAAAGGATTGAAAGGATGCTATTGACTTGT
1 GCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTT-AAA--A--G---GG-TGCCACTGACTTGT
* * * * *
1004956 AGGCTTTGAAAGGGTGTCATTGACTTGTGG
57 GGGCTTTAAAAGGGTGCCACTAACTTGTGG
* * * * **
1004986 GCTTTTGAAAGGGTGCAACTAACTTGTAGGC-TTTAAAAGGGTATCACTGACTTGTGGGCTTTGA
1 GCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTTAAAAGGGTGCCACTGACTTGTGGGCTTT-A
** *
1005050 AAAGGGTGCCACTGGCTTATGG
65 AAAGGGTGCCACTAACTTGTGG
* * * * **
1005072 GC-TTTGAAAATGG-TTCCATTGACTTGTGGGCATTTGAAAGGGTATCACTGACTTGTGGGCTTT
1 GCTTTTG-AAA-GGATGCCACTGACTTGTGGGCTTTTAAAAGGGTGCCACTGACTTGTGGGCTTT
** *
1005135 AAAAGGGTATCACTCACTTGTGG
64 AAAAGGGTGCCACTAACTTGTGG
* * * * *
1005158 GCTTTAT-AAAGGGTGCCACTAACTTATGGGCTTTTGAAAGGGTGCCACTGACTTGTGGGCTTGA
1 GCTTT-TGAAAGGATGCCACTGACTTGTGGGCTTTTAAAAGGGTGCCACTGACTTGTGGGCTTTA
* * *
1005222 AAAGGGTGTCACTCATTTGTGG
65 AAAGGGTGCCACTAACTTGTGG
* * * * * ** *
1005244 GC-TTTGAAAAGGGTGCCACTGACTTATGGCCTTTGATAAGAATGCCACTGACTTGTGGGCTTTG
1 GCTTTTG-AAAGGATGCCACTGACTTGTGGGCTTTTAAAAGGGTGCCACTGACTTGTGGGCTTTA
* * * *
1005308 AAAGGATGCCACTGATTTATGG
65 AAAGGGTGCCACTAACTTGTGG
* * * * * * * *
1005330 GC-TTTAAAAGGATACCACTGACTCGTGGGCTTTTGAAATGGTGCCACTGACTCGTGGACTTTTG
1 GCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTTAAAAGGGTGCCACTGACTTGTGGGC-TTTA
* * **
1005394 AAATGATGCCACTAACTCATGG
65 AAAGGGTGCCACTAACTTGTGG
** * *
1005416 GC-TTTGAAAGGGATGCCACTGACTCATGGGC-TTTGAAAGGGATGCCACCGACTTGTGGGCTTT
1 GCTTTTGAAA-GGATGCCACTGACTTGTGGGCTTTTAAAAGGG-TGCCACTGACTTGTGGGCTTT
** *
1005479 TGAA---TG--GCT--C--GTGG
64 AAAAGGGTGCCACTAACTTGTGG
* * *
1005493 GC-TTTGAAAAGG-TGCCACTGACTTGTGAGC-TTTAAAA-GGTGCCATTGACTTGTGGGCTTTG
1 GCTTTTG-AAAGGATGCCACTGACTTGTGGGCTTTTAAAAGGGTGCCACTGACTTGTGGGCTTTA
* *
1005554 AAAGGATGCCATTAACT
65 AAAGGGTGCCACTAACT
1005571 CATGAGCTTT
Statistics
Matches: 776, Mismatches: 197, Indels: 125
0.71 0.18 0.11
Matches are distributed among these distances:
74 21 0.03
75 2 0.00
76 21 0.03
77 13 0.02
78 3 0.00
79 2 0.00
81 3 0.00
83 6 0.01
84 7 0.01
85 93 0.12
86 355 0.46
87 117 0.15
88 11 0.01
89 8 0.01
90 2 0.00
91 4 0.01
92 22 0.03
93 30 0.04
94 20 0.03
95 10 0.01
96 6 0.01
97 1 0.00
98 16 0.02
99 1 0.00
100 2 0.00
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (86 bp):
GCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTTAAAAGGGTGCCACTGACTTGTGGGCTTTAA
AAGGGTGCCACTAACTTGTGG
Found at i:1004799 original size:29 final size:28
Alignment explanation
Indices: 1004757--1005478 Score: 554
Period size: 29 Copynumber: 25.1 Consensus size: 28
1004747 AATGATGCCA
* **
1004757 TTGAGAGGGATGCCACTGACTCATGGGCT
1 TTGAAAGGG-TGCCACTGACTTGTGGGCT
* *
1004786 TTGAAAGGGATGCCACTGACTCGTGAGCT
1 TTGAAAGGG-TGCCACTGACTTGTGGGCT
* *
1004815 TTGAAA-AGTGCCACTGACTTAT-GGCT
1 TTGAAAGGGTGCCACTGACTTGTGGGCT
* * * * *
1004841 TTAAAAGAGTGACACTAACTTGGGGGCT
1 TTGAAAGGGTGCCACTGACTTGTGGGCT
* * *
1004869 TT-AAAAGGTGCCACTAATTTGTGGGCT
1 TTGAAAGGGTGCCACTGACTTGTGGGCT
* ** * *
1004896 TTAAAAATGTGTCACTGACTTAT-GGCTT
1 TTGAAAGGGTGCCACTGACTTGTGGGC-T
* * *
1004924 TTGAAAGGATTGAAAGGATGCTATTGACTTGTAGGCT
1 TTG-AA--A--G---GG-TGCCACTGACTTGTGGGCT
* *
1004961 TTGAAAGGGTGTCATTGACTTGTGGGCTT
1 TTGAAAGGGTGCCACTGACTTGTGGGC-T
* * *
1004990 TTGAAAGGGTGCAACTAACTTGTAGGCT
1 TTGAAAGGGTGCCACTGACTTGTGGGCT
* **
1005018 TTAAAAGGGTATCACTGACTTGTGGGCT
1 TTGAAAGGGTGCCACTGACTTGTGGGCT
* *
1005046 TTGAAAAGGGTGCCACTGGCTTATGGGCT
1 TTG-AAAGGGTGCCACTGACTTGTGGGCT
* * *
1005075 TTGAAAATGGTTCCATTGACTTGTGGGCAT
1 TTG-AAAGGGTGCCACTGACTTGTGGGC-T
**
1005105 TTGAAAGGGTATCACTGACTTGTGGGCT
1 TTGAAAGGGTGCCACTGACTTGTGGGCT
* ** *
1005133 TTAAAAGGGTATCACTCACTTGTGGGCT
1 TTGAAAGGGTGCCACTGACTTGTGGGCT
* * *
1005161 TTATAAAGGGTGCCACTAACTTATGGGCTT
1 TT-GAAAGGGTGCCACTGACTTGTGGGC-T
1005191 TTGAAAGGGTGCCACTGACTTGTGGGC-
1 TTGAAAGGGTGCCACTGACTTGTGGGCT
* * *
1005218 TTGAAAAGGGTGTCACTCATTTGTGGGCT
1 TTG-AAAGGGTGCCACTGACTTGTGGGCT
* *
1005247 TTGAAAAGGGTGCCACTGACTTATGGCCT
1 TTG-AAAGGGTGCCACTGACTTGTGGGCT
**
1005276 TTGATAAGAATGCCACTGACTTGTGGGCT
1 TTGA-AAGGGTGCCACTGACTTGTGGGCT
* * *
1005305 TTGAAAGGATGCCACTGATTTATGGGCT
1 TTGAAAGGGTGCCACTGACTTGTGGGCT
* * * *
1005333 TTAAAAGGATACCACTGACTCGTGGGCTT
1 TTGAAAGGGTGCCACTGACTTGTGGGC-T
* * *
1005362 TTGAAATGGTGCCACTGACTCGTGGACTT
1 TTGAAAGGGTGCCACTGACTTGTGGGC-T
* * * **
1005391 TTGAAATGATGCCACTAACTCATGGGCT
1 TTGAAAGGGTGCCACTGACTTGTGGGCT
**
1005419 TTGAAAGGGATGCCACTGACTCATGGGCT
1 TTGAAAGGG-TGCCACTGACTTGTGGGCT
*
1005448 TTGAAAGGGATGCCACCGACTTGTGGGCT
1 TTGAAAGGG-TGCCACTGACTTGTGGGCT
1005477 TT
1 TT
1005479 TGAATGGCTC
Statistics
Matches: 567, Mismatches: 102, Indels: 48
0.79 0.14 0.07
Matches are distributed among these distances:
26 8 0.01
27 52 0.09
28 167 0.29
29 310 0.55
30 7 0.01
31 1 0.00
32 1 0.00
34 1 0.00
36 3 0.01
37 14 0.02
38 3 0.01
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (28 bp):
TTGAAAGGGTGCCACTGACTTGTGGGCT
Found at i:1004851 original size:27 final size:27
Alignment explanation
Indices: 1004767--1004924 Score: 115
Period size: 27 Copynumber: 5.7 Consensus size: 27
1004757 TTGAGAGGGA
* * *
1004767 TGCCACTGACTCATGGGCTTTGAAAGGG
1 TGCCACTGACTTAT-GGCTTTAAAAGAG
** *
1004795 ATGCCACTGACTCGTGAGCTTTGAAA-AG
1 -TGCCACTGACTTATG-GCTTTAAAAGAG
1004823 TGCCACTGACTTATGGCTTTAAAAGAG
1 TGCCACTGACTTATGGCTTTAAAAGAG
* * **
1004850 TGACACTAACTTGGGGGCTTTAAAAG-G
1 TGCCACTGACTT-ATGGCTTTAAAAGAG
* * *
1004877 TGCCACTAATTTGTGGGCTTTAAAA-ATG
1 TGCCACTGACTTAT-GGCTTTAAAAGA-G
*
1004905 TGTCACTGACTTATGGCTTT
1 TGCCACTGACTTATGGCTTT
1004925 TGAAAGGATT
Statistics
Matches: 107, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
26 9 0.08
27 52 0.49
28 24 0.22
29 22 0.21
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.30
Consensus pattern (27 bp):
TGCCACTGACTTATGGCTTTAAAAGAG
Found at i:1004881 original size:54 final size:56
Alignment explanation
Indices: 1004767--1004901 Score: 141
Period size: 54 Copynumber: 2.4 Consensus size: 56
1004757 TTGAGAGGGA
* * * * * *
1004767 TGCCACTGACTCATGGGCTTTGAAAGGGATGCCACTGACTCGTGAGCTTTGAAAAG
1 TGCCACTGACTTATGGGCTTTAAAAGAGATGACACTAACTCGGGAGCTTTGAAAAG
* *
1004823 TGCCACTGACTTAT-GGCTTTAAAAGAG-TGACACTAACTTGGGGGCTTT-AAAAGG
1 TGCCACTGACTTATGGGCTTTAAAAGAGATGACACTAACTCGGGAGCTTTGAAAA-G
* * *
1004877 TGCCACTAATTTGTGGGCTTTAAAA
1 TGCCACTGACTTATGGGCTTTAAAA
1004902 ATGTGTCACT
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
53 4 0.06
54 28 0.42
55 21 0.32
56 13 0.20
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (56 bp):
TGCCACTGACTTATGGGCTTTAAAAGAGATGACACTAACTCGGGAGCTTTGAAAAG
Found at i:1005525 original size:76 final size:75
Alignment explanation
Indices: 1005413--1005552 Score: 192
Period size: 74 Copynumber: 1.9 Consensus size: 75
1005403 CACTAACTCA
* * *
1005413 TGGGCTTTGAAAGGGATGCCACTGACTCATGGGCTTTGAAAGGGATGCCACCGACTTGTGGGCTT
1 TGGGCTTTGAAAAGGATGCCACTGACTCATGAGCTTT-AAAAGG-TGCCACCGACTTGTGGGCTT
1005478 TTGAATGGCTCG
64 TTGAATGGCTCG
** **
1005490 TGGGCTTTGAAAAGG-TGCCACTGACTTGTGAGCTTTAAAAGGTGCCATTGACTTGTGGGCTTT
1 TGGGCTTTGAAAAGGATGCCACTGACTCATGAGCTTTAAAAGGTGCCACCGACTTGTGGGCTTT
1005553 GAAAGGATGC
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
74 19 0.34
75 5 0.09
76 18 0.32
77 14 0.25
ACGTcount: A:0.20, C:0.18, G:0.32, T:0.30
Consensus pattern (75 bp):
TGGGCTTTGAAAAGGATGCCACTGACTCATGAGCTTTAAAAGGTGCCACCGACTTGTGGGCTTTT
GAATGGCTCG
Found at i:1005532 original size:27 final size:28
Alignment explanation
Indices: 1005493--1005587 Score: 122
Period size: 27 Copynumber: 3.4 Consensus size: 28
1005483 TGGCTCGTGG
*
1005493 GCTTTGAAAAGGTGCCACTGACTTGTGA
1 GCTTTGAAAAGGTGCCATTGACTTGTGA
*
1005521 GCTTT-AAAAGGTGCCATTGACTTGTGG
1 GCTTTGAAAAGGTGCCATTGACTTGTGA
* **
1005548 GCTTTG-AAAGGATGCCATTAACTCATGA
1 GCTTTGAAAAGG-TGCCATTGACTTGTGA
1005576 GCTTTGAAAAGG
1 GCTTTGAAAAGG
1005588 AAAAAGATTT
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
27 30 0.52
28 23 0.40
29 5 0.09
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.29
Consensus pattern (28 bp):
GCTTTGAAAAGGTGCCATTGACTTGTGA
Found at i:1006759 original size:21 final size:20
Alignment explanation
Indices: 1006733--1006814 Score: 67
Period size: 21 Copynumber: 3.9 Consensus size: 20
1006723 CATGTCCTTG
1006733 TTTTTTGATTTTGTTGTTCCT
1 TTTTTTGATTTTGTT-TTCCT
1006754 TTTTTT-ATTTTGCTTTTTCACT
1 TTTTTTGATTTTG--TTTTC-CT
* * *
1006776 TTTTTTGTTTTTCTTTTCAT
1 TTTTTTGATTTTGTTTTCCT
*
1006796 TTTTTATGCTTTTGATTTT
1 TTTTT-TGATTTTG-TTTT
1006815 GACTTTTTCG
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
20 12 0.24
21 20 0.40
22 14 0.28
23 4 0.08
ACGTcount: A:0.07, C:0.10, G:0.09, T:0.74
Consensus pattern (20 bp):
TTTTTTGATTTTGTTTTCCT
Found at i:1006777 original size:22 final size:22
Alignment explanation
Indices: 1006733--1006800 Score: 72
Period size: 20 Copynumber: 3.3 Consensus size: 22
1006723 CATGTCCTTG
* *
1006733 TTTTTTGATTTTG-TTGTTC-C
1 TTTTTTTATTTTGCTTTTTCAC
1006753 TTTTTTTATTTTGCTTTTTCAC
1 TTTTTTTATTTTGCTTTTTCAC
* *
1006775 TTTTTTTGTTTTTC-TTTTCA-
1 TTTTTTTATTTTGCTTTTTCAC
1006795 TTTTTT
1 TTTTTT
1006801 ATGCTTTTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.43
21 11 0.26
22 13 0.31
ACGTcount: A:0.06, C:0.10, G:0.07, T:0.76
Consensus pattern (22 bp):
TTTTTTTATTTTGCTTTTTCAC
Found at i:1012077 original size:14 final size:15
Alignment explanation
Indices: 1012058--1012090 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1012048 TTATTTTTTA
*
1012058 TTTTGATTTTA-GAT
1 TTTTGATTTGATGAT
1012072 TTTTGATTTGATGAT
1 TTTTGATTTGATGAT
1012087 TTTT
1 TTTT
1012091 TTTATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.18, C:0.00, G:0.15, T:0.67
Consensus pattern (15 bp):
TTTTGATTTGATGAT
Found at i:1015551 original size:13 final size:13
Alignment explanation
Indices: 1015533--1015558 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1015523 CAATTTTTTG
1015533 TGTATCGATACAT
1 TGTATCGATACAT
1015546 TGTATCGATACAT
1 TGTATCGATACAT
1015559 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1018394 original size:17 final size:17
Alignment explanation
Indices: 1018374--1018408 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1018364 AAATATCACT
1018374 TATTGTTTATATATTGC
1 TATTGTTTATATATTGC
1018391 TATTGTTTATATATTGC
1 TATTGTTTATATATTGC
1018408 T
1 T
1018409 TTTTAAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.06, G:0.11, T:0.60
Consensus pattern (17 bp):
TATTGTTTATATATTGC
Found at i:1019766 original size:20 final size:20
Alignment explanation
Indices: 1019741--1019787 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1019731 AAGATTATCA
1019741 AATCAATCTAATTAATAGAT
1 AATCAATCTAATTAATAGAT
* *
1019761 AATCAATCTAATTAGTAGGT
1 AATCAATCTAATTAATAGAT
1019781 AATCAAT
1 AATCAAT
1019788 TGAAGCATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.34
Consensus pattern (20 bp):
AATCAATCTAATTAATAGAT
Found at i:1020324 original size:30 final size:30
Alignment explanation
Indices: 1020288--1020347 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1020278 AATAACTACA
**
1020288 TAATTTAATTATAA-AATAAATAAATAAAAC
1 TAATTTAAAAATAACAA-AAATAAATAAAAC
1020318 TAATTTAAAAATAACTAAAAATAAATAAAA
1 TAATTTAAAAATAAC-AAAAATAAATAAAA
1020348 TATAAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 12 0.46
31 12 0.46
32 2 0.08
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (30 bp):
TAATTTAAAAATAACAAAAATAAATAAAAC
Found at i:1020331 original size:21 final size:20
Alignment explanation
Indices: 1020305--1020360 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
1020295 ATTATAAAAT
* *
1020305 AAATAAATAAAACTAATTTAA
1 AAATAAATAAAAATAA-ATAA
*
1020326 AAATAACTAAAAATAAATAA
1 AAATAAATAAAAATAAATAA
1020346 AATATAAATAAAAAT
1 AA-ATAAATAAAAAT
1020361 TTTTAAGACA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 5 0.17
21 25 0.83
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (20 bp):
AAATAAATAAAAATAAATAA
Found at i:1020338 original size:10 final size:10
Alignment explanation
Indices: 1020305--1020360 Score: 67
Period size: 10 Copynumber: 5.4 Consensus size: 10
1020295 ATTATAAAAT
1020305 AAATAAATAA
1 AAATAAATAA
* *
1020315 AACTAATTTAA
1 AAATAA-ATAA
*
1020326 AAATAACTAA
1 AAATAAATAA
1020336 AAATAAATAA
1 AAATAAATAA
1020346 AATATAAATAA
1 AA-ATAAATAA
1020357 AAAT
1 AAAT
1020361 TTTTAAGACA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
10 21 0.54
11 18 0.46
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (10 bp):
AAATAAATAA
Found at i:1020338 original size:11 final size:11
Alignment explanation
Indices: 1020305--1020359 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 11
1020295 ATTATAAAAT
1020305 AAATAAAT-AA
1 AAATAAATAAA
* * *
1020315 AACTAATTTAA
1 AAATAAATAAA
*
1020326 AAATAACT-AA
1 AAATAAATAAA
1020336 AAATAAATAAA
1 AAATAAATAAA
*
1020347 ATATAAATAAA
1 AAATAAATAAA
1020358 AA
1 AA
1020360 TTTTTAAGAC
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
10 15 0.42
11 21 0.58
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.24
Consensus pattern (11 bp):
AAATAAATAAA
Found at i:1020785 original size:16 final size:16
Alignment explanation
Indices: 1020764--1020806 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
1020754 TTAAAAAATC
*
1020764 CAAACTTGAAATAGCT
1 CAAACTCGAAATAGCT
1020780 CAAACTCGAAATAGCT
1 CAAACTCGAAATAGCT
*
1020796 CAAACCCGAAA
1 CAAACTCGAAA
1020807 GAAACCGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.47, C:0.26, G:0.12, T:0.16
Consensus pattern (16 bp):
CAAACTCGAAATAGCT
Found at i:1021073 original size:22 final size:22
Alignment explanation
Indices: 1021048--1021091 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1021038 AAATAATAAT
1021048 TTATCAAAAAGTGAATTATATC
1 TTATCAAAAAGTGAATTATATC
1021070 TTATCAAAAAGTGAATTATATC
1 TTATCAAAAAGTGAATTATATC
1021092 ATGAGCTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (22 bp):
TTATCAAAAAGTGAATTATATC
Found at i:1022398 original size:201 final size:200
Alignment explanation
Indices: 1022053--1022453 Score: 694
Period size: 201 Copynumber: 2.0 Consensus size: 200
1022043 TATTAAAATC
* *
1022053 TTTAATTAATAATTTAATAAAAATGTAAACAAATATAACTTACTCTCATGCCTTGAGAAATTTTT
1 TTTAATTAATAATTTAATAAAAATGTAAACAAATATAACTTACTCTCATGCCTTGACAAATTTCT
* *
1022118 CTTTGACTATTTCTTTCAGCATCACTAGATGAAGCAAGTTGATGCTCCCCAAATTTATTTCGATA
66 CTTTGACTATTTCTTTCAACATCACTAGATGAAACAAGTTGATGCTCCCCAAATTTATTTCGATA
*
1022183 CTTTTCAAAAAGCTTCTTCATTTGTTCAAAAATACCTACCCAGTTATTTTCATATTGTGAACCCA
131 CTTTTCAAAAAGCTTCTT-ATTTGTTCAAAAATACCTACCCACTTATTTTCATATTGTGAACCCA
1022248 ATTGTA
195 ATTGTA
* *
1022254 TTTAATTAATAATTTAATAAAAATGTAAACAAATATAACTTATTCTCATTCCTTGACAAATTTCT
1 TTTAATTAATAATTTAATAAAAATGTAAACAAATATAACTTACTCTCATGCCTTGACAAATTTCT
*
1022319 CTTTGACTATTTCTTTCAACATCACTAGATGAAACAAGTTGATGCTCCCCAAATTTATTTTGATA
66 CTTTGACTATTTCTTTCAACATCACTAGATGAAACAAGTTGATGCTCCCCAAATTTATTTCGATA
* * *
1022384 CTTTTTAAAAAGCTTCTTATTTGTTCAAAAATACCTATCCACTTATTTTCATATTGTGGACCCAA
131 CTTTTCAAAAAGCTTCTTATTTGTTCAAAAATACCTACCCACTTATTTTCATATTGTGAACCCAA
1022449 TTGTA
196 TTGTA
1022454 AAAAGATATA
Statistics
Matches: 189, Mismatches: 11, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
200 49 0.26
201 140 0.74
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.40
Consensus pattern (200 bp):
TTTAATTAATAATTTAATAAAAATGTAAACAAATATAACTTACTCTCATGCCTTGACAAATTTCT
CTTTGACTATTTCTTTCAACATCACTAGATGAAACAAGTTGATGCTCCCCAAATTTATTTCGATA
CTTTTCAAAAAGCTTCTTATTTGTTCAAAAATACCTACCCACTTATTTTCATATTGTGAACCCAA
TTGTA
Found at i:1026215 original size:20 final size:20
Alignment explanation
Indices: 1026189--1026241 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1026179 ATTTGCCTGC
1026189 ATGTATCGATACAAAGA-TCA
1 ATGTATCGATACAAAGAGT-A
* *
1026209 GTGTATCGATACAATGAGTA
1 ATGTATCGATACAAAGAGTA
1026229 ATGTATCGATACA
1 ATGTATCGATACA
1026242 TTTTCTTGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (20 bp):
ATGTATCGATACAAAGAGTA
Found at i:1026286 original size:19 final size:19
Alignment explanation
Indices: 1026262--1026326 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
1026252 AGTAGCTTCA
1026262 TATGTATCGATACAGCACT
1 TATGTATCGATACAGCACT
1026281 TATGTATCGAT--A-CA--
1 TATGTATCGATACAGCACT
1026295 T-TGTATCGATACAGCACT
1 TATGTATCGATACAGCACT
1026313 TATGTATCGATACA
1 TATGTATCGATACA
1026327 AATCATTGAC
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
13 9 0.22
14 1 0.03
15 1 0.03
16 4 0.10
17 1 0.03
18 1 0.03
19 23 0.57
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Consensus pattern (19 bp):
TATGTATCGATACAGCACT
Found at i:1026301 original size:13 final size:13
Alignment explanation
Indices: 1026283--1026307 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1026273 ACAGCACTTA
1026283 TGTATCGATACAT
1 TGTATCGATACAT
1026296 TGTATCGATACA
1 TGTATCGATACA
1026308 GCACTTATGT
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:1026305 original size:32 final size:32
Alignment explanation
Indices: 1026264--1026326 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
1026254 TAGCTTCATA
1026264 TGTATCGATACAGCACTTATGTATCGATACAT
1 TGTATCGATACAGCACTTATGTATCGATACAT
1026296 TGTATCGATACAGCACTTATGTATCGATACA
1 TGTATCGATACAGCACTTATGTATCGATACA
1026327 AATCATTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (32 bp):
TGTATCGATACAGCACTTATGTATCGATACAT
Found at i:1028057 original size:28 final size:27
Alignment explanation
Indices: 1027996--1028077 Score: 87
Period size: 28 Copynumber: 3.0 Consensus size: 27
1027986 TTTTGGAGAT
*
1027996 AATAACGGGGTTGGAGTGTTCCCTC-A-A
1 AATAACGGGGTTGGAGT-ATCCC-CGATA
1028023 AAGTAACGGGGTTGGAGTATCCCCGATGA
1 AA-TAACGGGGTTGGAGTATCCCCGAT-A
* *
1028052 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGGGGTTGGAGTATCCCCGAT
1028078 TGTGAAAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
26 1 0.02
27 7 0.15
28 37 0.77
29 3 0.06
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.24
Consensus pattern (27 bp):
AATAACGGGGTTGGAGTATCCCCGATA
Found at i:1028121 original size:52 final size:52
Alignment explanation
Indices: 1028060--1028343 Score: 165
Period size: 52 Copynumber: 5.4 Consensus size: 52
1028050 GAAATAACGA
* ** * *
1028060 GGTTGGAGTATCCTCGATTGTGA-AAAATTGGTATTTTTGGAAATAAAA-TCGG
1 GGTTGGAGTATCCCCGATTGAAAGAAAATTGGT-GTTTTGAAAATAAAACT-GG
*
1028112 TGTTGGAGTATCCCCGATTGAAAGAAAATTGGTGTTTTGAAAATAAAACTGG
1 GGTTGGAGTATCCCCGATTGAAAGAAAATTGGTGTTTTGAAAATAAAACTGG
* * ** * ** ** *
1028164 GGTTGGAGTATCCCC--TCAGAAATAACGGGGTTGGAGTATCCCCGATGAT-TAAC-GG
1 GGTTGGAGTATCCCCGAT-TGAAAGAA---AATTGGTGT-T--TTGAAAATAAAACTGG
* *
1028219 GGTTGGAGTGTCCCCGATTGTAAAG-AAATTGGTGTTTTTTGGAAATAAAA-TCGG
1 GGTTGGAGTATCCCCGATTG-AAAGAAAATTGGTG--TTTTGAAAATAAAACT-GG
* * *
1028273 AGTTGGAGTATCCCCGATT-ATAGAAAATTAGTGTTTTGAAAATAAAA-TCGG
1 GGTTGGAGTATCCCCGATTGAAAGAAAATTGGTGTTTTGAAAATAAAACT-GG
* *
1028324 AGTTGGAATATCCCCGATTG
1 GGTTGGAGTATCCCCGATTG
1028344 TGGAGAATTG
Statistics
Matches: 178, Mismatches: 35, Indels: 38
0.71 0.14 0.15
Matches are distributed among these distances:
50 1 0.01
51 41 0.23
52 54 0.30
53 25 0.14
54 26 0.15
55 18 0.10
56 5 0.03
57 8 0.04
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.31
Consensus pattern (52 bp):
GGTTGGAGTATCCCCGATTGAAAGAAAATTGGTGTTTTGAAAATAAAACTGG
Found at i:1028170 original size:160 final size:159
Alignment explanation
Indices: 1027974--1028338 Score: 502
Period size: 160 Copynumber: 2.3 Consensus size: 159
1027964 TTTCCCGATG
* * * * * *
1027974 AGAAATTTAATGTTTTGGAGATAATAACGGGGTTGGAGTGTTCCCTCA-AAAGTAACGGGGTTGG
1 AGAAAATTAGTGTTTTGAAAATAA-AACGGGGTTGGAGTATCCCCTCAGAAA-TAACGGGGTTGG
* *
1028038 AGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGTGAA-AAATTGGT-ATTTTTGGA
64 AGTATCCCCGATG-AATAACGAGGTTGGAGTATCCCCGATTGTAAAGAAATTGGTGATTTTTGGA
*
1028101 AATAAAATCGGTGTTGGAGTATCCCCGATTGAA
128 AATAAAATCGGAGTTGGAGTATCCCCGATT-AA
*
1028134 AGAAAATTGGTGTTTTGAAAATAAAACTGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGA
1 AGAAAATTAGTGTTTTGAAAATAAAAC-GGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGA
* * * *
1028199 GTATCCCCGATGATTAACGGGGTTGGAGTGTCCCCGATTGTAAAGAAATTGGTGTTTTTTGGAAA
65 GTATCCCCGATGAATAACGAGGTTGGAGTATCCCCGATTGTAAAGAAATTGGTGATTTTTGGAAA
*
1028264 TAAAATCGGAGTTGGAGTATCCCCGATTAT
130 TAAAATCGGAGTTGGAGTATCCCCGATTAA
* *
1028294 AGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCC
1 AGAAAATTAGTGTTTTGAAAATAAAA-CGGGGTTGGAGTATCCCC
1028339 GATTGTGGAG
Statistics
Matches: 182, Mismatches: 18, Indels: 10
0.87 0.09 0.05
Matches are distributed among these distances:
159 30 0.16
160 111 0.61
161 41 0.23
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (159 bp):
AGAAAATTAGTGTTTTGAAAATAAAACGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAG
TATCCCCGATGAATAACGAGGTTGGAGTATCCCCGATTGTAAAGAAATTGGTGATTTTTGGAAAT
AAAATCGGAGTTGGAGTATCCCCGATTAA
Found at i:1028224 original size:27 final size:28
Alignment explanation
Indices: 1028162--1028236 Score: 100
Period size: 27 Copynumber: 2.7 Consensus size: 28
1028152 AAATAAAACT
*
1028162 GGGGTTGGAGTATCCCCTCA-GAAATAAC
1 GGGGTTGGAGTATCCCC-GATGAAATAAC
*
1028190 GGGGTTGGAGTATCCCCGATG-ATTAAC
1 GGGGTTGGAGTATCCCCGATGAAATAAC
*
1028217 GGGGTTGGAGTGTCCCCGAT
1 GGGGTTGGAGTATCCCCGAT
1028237 TGTAAAGAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.58
28 18 0.42
ACGTcount: A:0.21, C:0.20, G:0.35, T:0.24
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCCGATGAAATAAC
Found at i:1028323 original size:51 final size:53
Alignment explanation
Indices: 1028220--1028342 Score: 169
Period size: 51 Copynumber: 2.3 Consensus size: 53
1028210 GATTAACGGG
* * * *
1028220 GTTGGAGTGTCCCCGATTGTAAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATAAAGAAATTAGTG-TTTTTGAAAATAAAATCGGA
*
1028274 GTTGGAGTATCCCCGATTATAGA-AAATTAGTG-TTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATAAAGAAATTAGTGTTTTTGAAAATAAAATCGGA
*
1028325 GTTGGAATATCCCCGATT
1 GTTGGAGTATCCCCGATT
1028343 GTGGAGAATT
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
51 35 0.56
53 8 0.13
54 20 0.32
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (53 bp):
GTTGGAGTATCCCCGATTATAAAGAAATTAGTGTTTTTGAAAATAAAATCGGA
Found at i:1030728 original size:13 final size:13
Alignment explanation
Indices: 1030710--1030735 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1030700 ACAAAGATCC
1030710 ATGTATCGATACA
1 ATGTATCGATACA
1030723 ATGTATCGATACA
1 ATGTATCGATACA
1030736 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1030731 original size:33 final size:33
Alignment explanation
Indices: 1030689--1030755 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1030679 AAAATTTCCA
***
1030689 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1030722 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1030755 A
1 A
1030756 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1030815 original size:13 final size:13
Alignment explanation
Indices: 1030797--1030821 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1030787 ACAATACTTA
1030797 TGTATCGATACAT
1 TGTATCGATACAT
1030810 TGTATCGATACA
1 TGTATCGATACA
1030822 AAATTTATGT
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:1030820 original size:32 final size:32
Alignment explanation
Indices: 1030778--1030838 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
1030768 TAGCTAATTA
* *
1030778 TGTATTGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
*
1030810 TGTATCGATACAAAATTTATGTATCGATA
1 TGTATCGATACAAAACTTATGTATCGATA
1030839 TAAATTGTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.39
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1030834 original size:19 final size:17
Alignment explanation
Indices: 1030773--1030844 Score: 62
Period size: 19 Copynumber: 4.2 Consensus size: 17
1030763 GGCAGTAGCT
*
1030773 AATTATGTATTGATACA
1 AATTATGTATCGATACA
1030790 ATACTTATGTATCGATAC-
1 A-A-TTATGTATCGATACA
1030808 -A-T-TGTATCGATACAA
1 AATTATGTATCGATAC-A
*
1030823 AATTTATGTATCGATATA
1 AA-TTATGTATCGATACA
1030841 AATT
1 AATT
1030845 GTTGAATTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 16
0.71 0.03 0.25
Matches are distributed among these distances:
13 11 0.24
14 1 0.02
16 2 0.04
17 3 0.07
18 5 0.11
19 23 0.51
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.40
Consensus pattern (17 bp):
AATTATGTATCGATACA
Found at i:1030918 original size:21 final size:20
Alignment explanation
Indices: 1030882--1030931 Score: 84
Period size: 21 Copynumber: 2.5 Consensus size: 20
1030872 GGACCTTGTG
1030882 TCGATACA-TCACAAATGTA
1 TCGATACATTCACAAATGTA
1030901 TCGATACATTCTACAAATGTA
1 TCGATACATTC-ACAAATGTA
1030922 TCGATACATT
1 TCGATACATT
1030932 TGAATTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 8 0.28
20 2 0.07
21 19 0.66
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (20 bp):
TCGATACATTCACAAATGTA
Found at i:1031850 original size:27 final size:27
Alignment explanation
Indices: 1031710--1031850 Score: 65
Period size: 28 Copynumber: 5.1 Consensus size: 27
1031700 TGTGGGCTTT
*
1031710 GAAAGGCGTCCTGCTCTTTGAGGACT-
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
** * * * *
1031736 GAAAGGTG-CCACCAACTTGTGTGGGCTT
1 GAAAGGTGTCCTGC-TCTT-TGAGGACTG
*
1031764 TAAGAGGTGTCCTGCTCTTTGAGGACTG
1 GAA-AGGTGTCCTGCTCTTTGAGGACTG
* ** * * * *
1031792 GAAA-ATG-CCACCAACTTGTGTGGGCTTT
1 GAAAGGTGTCCTGC-TCTT-TGAGGAC-TG
1031820 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
1031847 GAAA
1 GAAA
1031851 ATGCCACCAA
Statistics
Matches: 77, Mismatches: 28, Indels: 19
0.62 0.23 0.15
Matches are distributed among these distances:
25 6 0.08
26 15 0.19
27 17 0.22
28 20 0.26
29 13 0.17
30 6 0.08
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (27 bp):
GAAAGGTGTCCTGCTCTTTGAGGACTG
Found at i:1031958 original size:59 final size:58
Alignment explanation
Indices: 1031663--1032198 Score: 663
Period size: 59 Copynumber: 9.3 Consensus size: 58
1031653 ATAAAGTGTA
* * *
1031663 TCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT---G-AAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAGAAAAGGCG
*
1031718 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAG---AGGTG
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAGAAAAGGCG
** *
1031773 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT---G-AAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAGAAAAGGCG
** *
1031828 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT---G-AAAGGGG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAGAAAAGGCG
1031883 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAA-AGAAAAGGCG
*
1031942 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAA-AGAAAAGGCG
* *
1032001 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGAAAAAGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAA-AGAAAAGGCG
* *
1032060 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGAAAAAGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAA-AGAAAAGGCG
* ** * *
1032119 TCATGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGGGGGCTTTTAAAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGC-TTT-AAA-GAAAAGGCG
*
1032181 TCCTGCTCTCTGAGGACT
1 TCCTGCTCTTTGAGGACT
1032199 AAAAAGCGGA
Statistics
Matches: 443, Mismatches: 23, Indels: 23
0.91 0.05 0.05
Matches are distributed among these distances:
53 1 0.00
54 26 0.06
55 167 0.38
56 1 0.00
57 1 0.00
58 1 0.00
59 195 0.44
60 22 0.05
61 4 0.01
62 25 0.06
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (58 bp):
TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAGAAAAGGCG
Found at i:1033204 original size:12 final size:12
Alignment explanation
Indices: 1033187--1033213 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1033177 TCTCTTTTTC
1033187 TTTGTTTTGTTT
1 TTTGTTTTGTTT
1033199 TTTGTTTTGTTT
1 TTTGTTTTGTTT
1033211 TTT
1 TTT
1033214 CCTTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (12 bp):
TTTGTTTTGTTT
Found at i:1033207 original size:17 final size:16
Alignment explanation
Indices: 1033181--1033241 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 16
1033171 CTTTTCTCTC
*
1033181 TTTTTCTTTGTTTTGT
1 TTTTTTTTTGTTTTGT
1033197 TTTTTGTTTTGTTTT-T
1 TTTTT-TTTTGTTTTGT
*
1033213 TCCTTTTTTTTCTTTTGCT
1 T--TTTTTTTTGTTTTG-T
1033232 TTTTTTTTTG
1 TTTTTTTTTG
1033242 AAGAGAATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
16 7 0.19
17 24 0.65
18 4 0.11
19 2 0.05
ACGTcount: A:0.00, C:0.08, G:0.10, T:0.82
Consensus pattern (16 bp):
TTTTTTTTTGTTTTGT
Found at i:1033228 original size:15 final size:15
Alignment explanation
Indices: 1033163--1033238 Score: 66
Period size: 15 Copynumber: 5.1 Consensus size: 15
1033153 CTTAAGCAGG
*
1033163 TTCTTTTTCTTTTCT
1 TTCTTTTTCTTTTTT
* *
1033178 CTCTTTTTCTTTGTT
1 TTCTTTTTCTTTTTT
* *
1033193 TTGTTTTT-TGTTTTG
1 TTCTTTTTCT-TTTTT
*
1033208 TT-TTTTCCTTTTTT
1 TTCTTTTTCTTTTTT
*
1033222 TTCTTTTGCTTTTTT
1 TTCTTTTTCTTTTTT
1033237 TT
1 TT
1033239 TTGAAGAGAA
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
14 11 0.23
15 37 0.77
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (15 bp):
TTCTTTTTCTTTTTT
Found at i:1033234 original size:12 final size:12
Alignment explanation
Indices: 1033191--1033241 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
1033181 TTTTTCTTTG
*
1033191 TTTTGTTTTTTG
1 TTTTGTTTTTTC
1033203 TTTTGTTTTTTC
1 TTTTGTTTTTTC
*
1033215 -CTT-TTTTTTC
1 TTTTGTTTTTTC
1033225 TTTTGCTTTTTT-
1 TTTTG-TTTTTTC
1033237 TTTTG
1 TTTTG
1033242 AAGAGAATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
10 7 0.21
11 4 0.12
12 16 0.48
13 6 0.18
ACGTcount: A:0.00, C:0.08, G:0.10, T:0.82
Consensus pattern (12 bp):
TTTTGTTTTTTC
Done.