Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007923.1 Hibiscus syriacus cultivar Beakdansim tig00110328_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8415618
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 40
Found at i:834746 original size:12 final size:11
Alignment explanation
Indices: 834697--834751 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
834687 AAAATAAATA
834697 ATAAAATATTT
1 ATAAAATATTT
834708 -T-AAATATTT
1 ATAAAATATTT
* *
834717 TTAAAATGTTT
1 ATAAAATATTT
834728 A-ATAAATATTT
1 ATA-AAATATTT
834739 AGTAAAATATTT
1 A-TAAAATATTT
834751 A
1 A
834752 AAATATTCCA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
9 8 0.22
10 3 0.08
11 15 0.42
12 9 0.25
13 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (11 bp):
ATAAAATATTT
Found at i:836424 original size:29 final size:28
Alignment explanation
Indices: 836360--836440 Score: 119
Period size: 29 Copynumber: 2.9 Consensus size: 28
836350 CAAACTAAAT
*
836360 TGATGTCATTACTTACATCATTT-TTAA
1 TGATGTCATTGCTTACATCATTTATTAA
*
836387 AGATGTCATTGCTTACATCATTTAATTAA
1 TGATGTCATTGCTTACATCATTT-ATTAA
836416 TGATGTCATTGCTTACATCAATTTA
1 TGATGTCATTGCTTACATC-ATTTA
836441 GTTAGGTGAG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
27 21 0.44
29 23 0.48
30 4 0.08
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (28 bp):
TGATGTCATTGCTTACATCATTTATTAA
Found at i:841154 original size:29 final size:29
Alignment explanation
Indices: 841119--841200 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
841109 AAACTAAATT
*
841119 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
841148 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
841177 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
841201 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:857362 original size:44 final size:44
Alignment explanation
Indices: 857312--857444 Score: 248
Period size: 44 Copynumber: 3.0 Consensus size: 44
857302 ATGGGGTGAG
*
857312 TGGTCAACGGGTCAGGTATGCAGCCAATGGTCCAAGTAAGCATT
1 TGGTCAACGGGTCAGGTATGCAGCCAACGGTCCAAGTAAGCATT
857356 TGGTCAACGGGTCAGGTATGCAGCCAACGGTCCAAGTAAGCATT
1 TGGTCAACGGGTCAGGTATGCAGCCAACGGTCCAAGTAAGCATT
*
857400 TGGTCAACGGGTCAGGTATGCAGCCAACGGTTCAAGTAAGCATT
1 TGGTCAACGGGTCAGGTATGCAGCCAACGGTCCAAGTAAGCATT
857444 T
1 T
857445 AACTGTCCAA
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 87 1.00
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (44 bp):
TGGTCAACGGGTCAGGTATGCAGCCAACGGTCCAAGTAAGCATT
Found at i:857385 original size:20 final size:20
Alignment explanation
Indices: 857360--857429 Score: 61
Period size: 20 Copynumber: 3.3 Consensus size: 20
857350 AGCATTTGGT
857360 CAACGGGTCAGGTATGCAGC
1 CAACGGGTCAGGTATGCAGC
* * *
857380 CAAC-GGTCCAAGTAAGCATTTGGT
1 CAACGGGT-CAGGTATGCA----GC
857404 CAACGGGTCAGGTATGCAGC
1 CAACGGGTCAGGTATGCAGC
857424 CAACGG
1 CAACGG
857430 TTCAAGTAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
19 3 0.08
20 19 0.50
24 13 0.34
25 3 0.08
ACGTcount: A:0.27, C:0.24, G:0.31, T:0.17
Consensus pattern (20 bp):
CAACGGGTCAGGTATGCAGC
Found at i:857407 original size:24 final size:24
Alignment explanation
Indices: 857340--857409 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 24
857330 TGCAGCCAAT
857340 GGTCCAAGTAAGCATTTGGTCAAC
1 GGTCCAAGTAAGCATTTGGTCAAC
* * *
857364 GGGT-CAGGTATGCA----GCCAAC
1 -GGTCCAAGTAAGCATTTGGTCAAC
857384 GGTCCAAGTAAGCATTTGGTCAAC
1 GGTCCAAGTAAGCATTTGGTCAAC
857408 GG
1 GG
857410 GTCAGGTATG
Statistics
Matches: 34, Mismatches: 6, Indels: 11
0.67 0.12 0.22
Matches are distributed among these distances:
19 3 0.09
20 13 0.38
24 15 0.44
25 3 0.09
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.21
Consensus pattern (24 bp):
GGTCCAAGTAAGCATTTGGTCAAC
Found at i:857462 original size:32 final size:32
Alignment explanation
Indices: 857423--857492 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
857413 AGGTATGCAG
*
857423 CCAACGGTTCAAGTAAGCATTTAACTGTCCAA
1 CCAACGGTCCAAGTAAGCATTTAACTGTCCAA
857455 CCAACGGTCCAAGTAAGCATTTAACTGTCCAA
1 CCAACGGTCCAAGTAAGCATTTAACTGTCCAA
857487 CTCAAC
1 C-CAAC
857493 TTTCCATCAC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 32 0.89
33 4 0.11
ACGTcount: A:0.34, C:0.29, G:0.14, T:0.23
Consensus pattern (32 bp):
CCAACGGTCCAAGTAAGCATTTAACTGTCCAA
Found at i:860394 original size:15 final size:15
Alignment explanation
Indices: 860374--860405 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
860364 TTCATATGTT
860374 ATATTAATTAAAATA
1 ATATTAATTAAAATA
*
860389 ATATTAATTAAATTA
1 ATATTAATTAAAATA
860404 AT
1 AT
860406 TTTTTTAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATATTAATTAAAATA
Found at i:861728 original size:3 final size:3
Alignment explanation
Indices: 861720--861751 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
861710 TTTTCCCACC
*
861720 ATT ATT ATT ATT ATT ATT ATT ATT AAT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
861752 AAGATGAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:862060 original size:18 final size:19
Alignment explanation
Indices: 862037--862076 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
862027 ACGATTACCC
*
862037 TTTAAAAAATTTTAA-ATT
1 TTTAAAAAATTATAATATT
*
862055 TTTAAATAATTATAATATT
1 TTTAAAAAATTATAATATT
862074 TTT
1 TTT
862077 TTATATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTAAAAAATTATAATATT
Found at i:862890 original size:90 final size:90
Alignment explanation
Indices: 862789--862968 Score: 308
Period size: 90 Copynumber: 2.0 Consensus size: 90
862779 TAAACCAAAA
862789 AAATTATAAACA-TATACTATAAGGTAATTTTGTGTGTGTGAATTATCATTGAATCCGGTTGTTT
1 AAATTATAAACAGT-TACTATAAGGTAATTTTGTGTGTGTGAATTATCATTGAATCCGGTTGTTT
* *
862853 TTTGTCATTTAAACACACAAAAATGT
65 TTGGTCATTCAAACACACAAAAATGT
*
862879 AAATTATAAACAGTTACTATAGGGTAATTTTGTGTGTGTGAATTATCATTGAATCCGGTTGTTTT
1 AAATTATAAACAGTTACTATAAGGTAATTTTGTGTGTGTGAATTATCATTGAATCCGGTTGTTTT
*
862944 TGGTCATTCAAGCACACAAAAATGT
66 TGGTCATTCAAACACACAAAAATGT
862969 GGTGAACGGT
Statistics
Matches: 85, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
90 84 0.99
91 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.39
Consensus pattern (90 bp):
AAATTATAAACAGTTACTATAAGGTAATTTTGTGTGTGTGAATTATCATTGAATCCGGTTGTTTT
TGGTCATTCAAACACACAAAAATGT
Found at i:869803 original size:10 final size:10
Alignment explanation
Indices: 869790--869830 Score: 66
Period size: 10 Copynumber: 4.2 Consensus size: 10
869780 TTTATTTATT
*
869790 TTATTTTTAA
1 TTATTATTAA
869800 TTATTATTAA
1 TTATTATTAA
869810 TTATTATT-A
1 TTATTATTAA
869819 TTATTATTAA
1 TTATTATTAA
869829 TT
1 TT
869831 TTACATATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
9 9 0.31
10 20 0.69
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TTATTATTAA
Found at i:869803 original size:19 final size:19
Alignment explanation
Indices: 869765--869823 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
869755 GTCCGGGTCT
*
869765 TTTATATTTATTTTTTTTA
1 TTTATATTTATTTTTATTA
869784 TTTAT-TTTATTTTTAATTA
1 TTTATATTTATTTTT-ATTA
* *
869803 -TTATTAATTATTATTATTA
1 TTTA-TATTTATTTTTATTA
869822 TT
1 TT
869824 ATTAATTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
18 12 0.36
19 13 0.39
20 8 0.24
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTATATTTATTTTTATTA
Found at i:869807 original size:3 final size:3
Alignment explanation
Indices: 869785--869827 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
869775 TTTTTTTTAT
*
869785 TTA TT- TTA TTT TTAA TTA TTA TTAA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TT-A TTA TTA TTA TTA TTA TTA
869828 ATTTTACATA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 2 0.06
3 28 0.80
4 5 0.14
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:869839 original size:19 final size:19
Alignment explanation
Indices: 869799--869840 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
869789 TTTATTTTTA
*
869799 ATTATTATTAATTATTATT
1 ATTATTATTAATTATTAAT
869818 ATTATTATTAATT-TTACAT
1 ATTATTATTAATTATTA-AT
869837 ATTA
1 ATTA
869841 CATTTTTTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTATTATTAATTATTAAT
Found at i:872652 original size:16 final size:16
Alignment explanation
Indices: 872618--872660 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
872608 AACGTAGACC
*
872618 AAATTTTTGTCTTATA
1 AAATTTTTTTCTTATA
872634 AAATTATTTTTCTTA-A
1 AAATT-TTTTTCTTATA
872650 AAATTGTTTTT
1 AAATT-TTTTT
872661 AAAAGACGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.58
Consensus pattern (16 bp):
AAATTTTTTTCTTATA
Found at i:884431 original size:44 final size:43
Alignment explanation
Indices: 884382--884467 Score: 102
Period size: 43 Copynumber: 2.0 Consensus size: 43
884372 TGTCATCTAC
* * *
884382 CCTTAGACGACCAGACTC-TCCTCATCACGTAGGAGCCGTGTTAA
1 CCTTAGACAACCAG-C-CGTCCTCATCACGTAGGAACCGAGTTAA
* *
884426 CCTTAGATAATCAGCCGTCCTCATCACGTAGGAACCGAGTTA
1 CCTTAGACAACCAGCCGTCCTCATCACGTAGGAACCGAGTTA
884468 TCACCCTTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
42 1 0.03
43 24 0.67
44 11 0.31
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.23
Consensus pattern (43 bp):
CCTTAGACAACCAGCCGTCCTCATCACGTAGGAACCGAGTTAA
Found at i:884762 original size:14 final size:14
Alignment explanation
Indices: 884745--884774 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
884735 TGTCCGGGTC
884745 TTTTATATTTATTTT
1 TTTTAT-TTTATTTT
884760 TTTTATTTTATTTT
1 TTTTATTTTATTTT
884774 T
1 T
884775 AATTATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTATTTTATTTT
Found at i:884770 original size:20 final size:21
Alignment explanation
Indices: 884745--884785 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
884735 TGTCCGGGTC
*
884745 TTTTATATTT-ATTTTTTTTA
1 TTTTATATTTAATTATTTTTA
*
884765 TTTTATTTTTAATTATTTTTA
1 TTTTATATTTAATTATTTTTA
884786 ATTATTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTATATTTAATTATTTTTA
Found at i:884780 original size:10 final size:10
Alignment explanation
Indices: 884767--884807 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
884757 TTTTTTTATT
*
884767 TTATTTTTAA
1 TTATTATTAA
*
884777 TTATTTTTAA
1 TTATTATTAA
884787 TTATTATT-A
1 TTATTATTAA
884796 TTATTATTAA
1 TTATTATTAA
884806 TT
1 TT
884808 TTACATATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
9 9 0.31
10 20 0.69
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTATTATTAA
Found at i:884780 original size:15 final size:14
Alignment explanation
Indices: 884747--884803 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 14
884737 TCCGGGTCTT
*
884747 TTATATTTATTTTTT
1 TTAT-TTTATTTTTA
884762 TTATTTTATTTTTAA
1 TTATTTTATTTTT-A
*
884777 TTATTTTTAATTATTA
1 TTA-TTTT-ATTTTTA
884793 TTATTATTATT
1 TTATT-TTATT
884804 AATTTTACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 9 0.25
15 12 0.33
16 10 0.28
17 5 0.14
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTATTTTATTTTTA
Found at i:884816 original size:19 final size:19
Alignment explanation
Indices: 884776--884817 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
884766 TTTATTTTTA
* *
884776 ATTATTTTTAATTATTATT
1 ATTATTATTAATTATTAAT
884795 ATTATTATTAATT-TTACAT
1 ATTATTATTAATTATTA-AT
884814 ATTA
1 ATTA
884818 CATTTTTTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTATTATTAATTATTAAT
Found at i:884817 original size:25 final size:26
Alignment explanation
Indices: 884762--884810 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
884752 TTTATTTTTT
* *
884762 TTATT-TTATTTTTAATTATTTTTAA
1 TTATTATTATTATTAATTAATTTTAA
884787 TTATTATTATTATT-ATTAATTTTA
1 TTATTATTATTATTAATTAATTTTA
884811 CATATTACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (26 bp):
TTATTATTATTATTAATTAATTTTAA
Found at i:887608 original size:16 final size:16
Alignment explanation
Indices: 887574--887616 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
887564 AACGTAGACC
*
887574 AAATTTTTGTCTTATA
1 AAATTTTTTTCTTATA
887590 AAATTATTTTTCTTA-A
1 AAATT-TTTTTCTTATA
887606 AAATTGTTTTT
1 AAATT-TTTTT
887617 AAAAGACGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.58
Consensus pattern (16 bp):
AAATTTTTTTCTTATA
Found at i:888260 original size:25 final size:25
Alignment explanation
Indices: 888214--888264 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 25
888204 AAAATATTTA
888214 TATTTTATATTGAATTTATTTTTATT
1 TATTTTATATTGAA-TTATTTTTATT
*
888240 TATTTT-TATTGGATTATTTTTATT
1 TATTTTATATTGAATTATTTTTATT
888264 T
1 T
888265 TACATTGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 12 0.50
25 6 0.25
26 6 0.25
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (25 bp):
TATTTTATATTGAATTATTTTTATT
Found at i:893503 original size:58 final size:59
Alignment explanation
Indices: 893441--893563 Score: 142
Period size: 59 Copynumber: 2.1 Consensus size: 59
893431 ACTTCAGGGT
* * * * **
893441 AAAGTACACAAATGGTCTCT-GATTATATAGTGTTATTTT-TTTAGTTTTTCAACTATTA
1 AAAGTACA-AAATGGTCTCTCGACTATAAAATGTTATTTTATTAAGTTACTCAACTATTA
* *
893499 AAAGTTATAAAATGGTCTCTCGACTATAAAATGTTATTTTATTAAGTTACTCGACTATTA
1 AAAG-TACAAAATGGTCTCTCGACTATAAAATGTTATTTTATTAAGTTACTCAACTATTA
893559 AAAGT
1 AAAGT
893564 TATAAAATAG
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
58 15 0.28
59 20 0.37
60 19 0.35
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (59 bp):
AAAGTACAAAATGGTCTCTCGACTATAAAATGTTATTTTATTAAGTTACTCAACTATTA
Found at i:893525 original size:29 final size:30
Alignment explanation
Indices: 893492--893586 Score: 81
Period size: 29 Copynumber: 3.2 Consensus size: 30
893482 TAGTTTTTCA
*
893492 ACTATTAAAAGTTATAAAAT-GGTCT-CTCG
1 ACTATTAAAAGTTATAAAATAAGT-TACTCG
** *
893521 ACTA-TAAAATGTTATTTTATTAAGTTACTCG
1 ACTATTAAAA-GTTA-TAAAATAAGTTACTCG
* *
893552 ACTATTAAAAGTTATAAAAT-AGTTATTCA
1 ACTATTAAAAGTTATAAAATAAGTTACTCG
893581 ACTATT
1 ACTATT
893587 TATATGTTAT
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
28 5 0.10
29 21 0.40
30 7 0.13
31 14 0.27
32 5 0.10
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (30 bp):
ACTATTAAAAGTTATAAAATAAGTTACTCG
Found at i:893562 original size:60 final size:58
Alignment explanation
Indices: 893450--893571 Score: 163
Period size: 60 Copynumber: 2.1 Consensus size: 58
893440 TAAAGTACAC
* * * * **
893450 AAATGGTCTCTGATTATATAGTGTTATTTTTTTAGTTTTTCAACTATTAAAAGTTATA
1 AAATGGTCTCTGACTATAAAATGTTATTTTTTAAGTTACTCAACTATTAAAAGTTATA
*
893508 AAATGGTCTCTCGACTATAAAATGTTATTTTATTAAGTTACTCGACTATTAAAAGTTATA
1 AAATGGTCTCT-GACTATAAAATGTTATTTT-TTAAGTTACTCAACTATTAAAAGTTATA
893568 AAAT
1 AAAT
893572 AGTTATTCAA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
58 11 0.20
59 16 0.29
60 28 0.51
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.44
Consensus pattern (58 bp):
AAATGGTCTCTGACTATAAAATGTTATTTTTTAAGTTACTCAACTATTAAAAGTTATA
Found at i:900011 original size:45 final size:45
Alignment explanation
Indices: 899947--900033 Score: 174
Period size: 45 Copynumber: 1.9 Consensus size: 45
899937 AATTAATTAC
899947 TATTGATGTGGCTGCCTGTTATCAATACATCATCAAAACGACGAT
1 TATTGATGTGGCTGCCTGTTATCAATACATCATCAAAACGACGAT
899992 TATTGATGTGGCTGCCTGTTATCAATACATCATCAAAACGAC
1 TATTGATGTGGCTGCCTGTTATCAATACATCATCAAAACGAC
900034 ACCGTTTTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (45 bp):
TATTGATGTGGCTGCCTGTTATCAATACATCATCAAAACGACGAT
Found at i:904965 original size:2 final size:2
Alignment explanation
Indices: 904958--904987 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
904948 AAATAAAATT
904958 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
904988 GAGGATCTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:909096 original size:20 final size:20
Alignment explanation
Indices: 909073--909143 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
909063 CACAGAATGT
909073 AAGATTACCAGTTGGAATAA
1 AAGATTACCAGTTGGAATAA
*
909093 AAGATTATCAGTTGGAATAA
1 AAGATTACCAGTTGGAATAA
*
909113 AAGATTACCAGTGGGAATAA
1 AAGATTACCAGTTGGAATAA
*
909133 AATATTACCAG
1 AAGATTACCAG
909144 GGAATATGAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (20 bp):
AAGATTACCAGTTGGAATAA
Found at i:914109 original size:16 final size:18
Alignment explanation
Indices: 914088--914131 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 18
914078 TTTAAAATAA
*
914088 AAATATTTAAAGTTA-T-
1 AAATATTTAAAATTATTC
914104 AAATA--TAAAATTATTC
1 AAATATTTAAAATTATTC
914120 AAATATTTAAAA
1 AAATATTTAAAA
914132 AAAATAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
14 7 0.30
15 1 0.04
16 10 0.43
18 5 0.22
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (18 bp):
AAATATTTAAAATTATTC
Found at i:914130 original size:24 final size:23
Alignment explanation
Indices: 914077--914135 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 23
914067 TTATTTAATT
*
914077 TTTTAAAATAAAAATATTTAAAG
1 TTTTAAAATAAAAATATTCAAAG
* *
914100 TTATAAATATAAAATTATTCAAA-
1 TTTTAAA-ATAAAAATATTCAAAG
914123 TATTTAAAA-AAAA
1 T-TTTAAAATAAAA
914136 TAAATATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
22 4 0.13
23 8 0.27
24 18 0.60
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (23 bp):
TTTTAAAATAAAAATATTCAAAG
Found at i:914427 original size:25 final size:25
Alignment explanation
Indices: 914371--914428 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
914361 GTATTTTTAC
** *
914371 TGGATTAATCGAGATTTACAAAATT
1 TGGATTAGCCGAGACTTACAAAATT
** *
914396 TAAATTAGCCGAGACTTACAAATTT
1 TGGATTAGCCGAGACTTACAAAATT
914421 TGGATTAG
1 TGGATTAG
914429 TTGAAATTTA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.34
Consensus pattern (25 bp):
TGGATTAGCCGAGACTTACAAAATT
Found at i:936077 original size:2 final size:2
Alignment explanation
Indices: 936070--936105 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
936060 GGAGATGTTA
936070 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
936106 ATCTACTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:936322 original size:2 final size:2
Alignment explanation
Indices: 936315--936339 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
936305 TGATCTTACC
936315 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 T
936340 TATGTGAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:941274 original size:15 final size:15
Alignment explanation
Indices: 941251--941292 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
941241 AAATTGAAGA
941251 AAAAT-AAATATATT
1 AAAATAAAATATATT
* *
941265 AAATTAAAATAAATT
1 AAAATAAAATATATT
941280 AAAATAAACATAT
1 AAAATAAA-ATAT
941293 GACATGACGT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 4 0.18
15 15 0.68
16 3 0.14
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (15 bp):
AAAATAAAATATATT
Found at i:942911 original size:6 final size:6
Alignment explanation
Indices: 942903--942954 Score: 95
Period size: 6 Copynumber: 8.7 Consensus size: 6
942893 TAGCGTAGGT
*
942903 TTGGGT TTGGGA TTGGGA TTGGGA TTGGGA TTGGGA TTGGGA TTGGGA
1 TTGGGA TTGGGA TTGGGA TTGGGA TTGGGA TTGGGA TTGGGA TTGGGA
942951 TTGG
1 TTGG
942955 AACGGTGCAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.13, C:0.00, G:0.50, T:0.37
Consensus pattern (6 bp):
TTGGGA
Found at i:944623 original size:22 final size:21
Alignment explanation
Indices: 944595--944666 Score: 67
Period size: 22 Copynumber: 3.4 Consensus size: 21
944585 TTGAAAATCG
*
944595 CGTTGCGATGGTCTACAGTTGT
1 CGTTGCGATAGTCTA-AGTTGT
** * *
944617 CGTTGCGATTTTCCAAATT-T
1 CGTTGCGATAGTCTAAGTTGT
944637 -GTTGCGATAGTCTATAGTTGT
1 CGTTGCGATAGTCTA-AGTTGT
944658 CGTTGCGAT
1 CGTTGCGAT
944667 TTTCCAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 11 0.28
20 4 0.10
21 4 0.10
22 20 0.51
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.40
Consensus pattern (21 bp):
CGTTGCGATAGTCTAAGTTGT
Found at i:944642 original size:19 final size:19
Alignment explanation
Indices: 944618--944685 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 19
944608 TACAGTTGTC
944618 GTTGCGATTTTCCAAATTT
1 GTTGCGATTTTCCAAATTT
** * *
944637 GTTGCGATAGTCTATAGTTGT
1 GTTGCGATTTTCCA-AATT-T
*
944658 CGTTGCGATTTTCCAAATTC
1 -GTTGCGATTTTCCAAATTT
944678 GTTGCGAT
1 GTTGCGAT
944686 AGTTAAAAAA
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
19 19 0.51
20 3 0.08
21 4 0.11
22 11 0.30
ACGTcount: A:0.19, C:0.16, G:0.22, T:0.43
Consensus pattern (19 bp):
GTTGCGATTTTCCAAATTT
Found at i:944650 original size:41 final size:41
Alignment explanation
Indices: 944595--944688 Score: 161
Period size: 41 Copynumber: 2.3 Consensus size: 41
944585 TTGAAAATCG
*
944595 CGTTGCGATGGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
* *
944636 TGTTGCGATAGTCTATAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
944677 CGTTGCGATAGT
1 CGTTGCGATAGT
944689 TAAAAAAAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.18, C:0.17, G:0.24, T:0.40
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
Found at i:945444 original size:19 final size:19
Alignment explanation
Indices: 945422--945491 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 19
945412 TTTTTAAACT
945422 ATCGCAACGAATTTAGAAA
1 ATCGCAACGAATTTAGAAA
* **
945441 ATCGCAACGATAACTGTAGACT
1 ATCGCAACG--AA-TTTAGAAA
* *
945463 ATCGCAACAAATTTGGAAA
1 ATCGCAACGAATTTAGAAA
945482 ATCGCAACGA
1 ATCGCAACGA
945492 CAACTGTAGA
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 22 0.56
20 2 0.05
21 2 0.05
22 13 0.33
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (19 bp):
ATCGCAACGAATTTAGAAA
Found at i:945466 original size:22 final size:21
Alignment explanation
Indices: 945419--945512 Score: 70
Period size: 22 Copynumber: 4.6 Consensus size: 21
945409 TTTTTTTTAA
*
945419 ACTATCGCAACG-AA-TTTAG
1 ACTATCGCAACGAAACTGTAG
**
945438 AAAATCGCAACGATAACTGTAG
1 ACTATCGCAACGA-AACTGTAG
* *
945460 ACTATCGCAAC-AAA-TTTGG
1 ACTATCGCAACGAAACTGTAG
**
945479 AAAATCGCAACGACAACTGTAG
1 ACTATCGCAACGA-AACTGTAG
*
945501 ACTATAGCAACG
1 ACTATCGCAACG
945513 CGATTGCGAA
Statistics
Matches: 55, Mismatches: 14, Indels: 9
0.71 0.18 0.12
Matches are distributed among these distances:
19 22 0.40
20 3 0.05
21 5 0.09
22 25 0.45
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.20
Consensus pattern (21 bp):
ACTATCGCAACGAAACTGTAG
Found at i:945476 original size:41 final size:41
Alignment explanation
Indices: 945419--945511 Score: 150
Period size: 41 Copynumber: 2.3 Consensus size: 41
945409 TTTTTTTTAA
* *
945419 ACTATCGCAACGAATTTAGAAAATCGCAACGATAACTGTAG
1 ACTATCGCAACAAATTTAGAAAATCGCAACGACAACTGTAG
*
945460 ACTATCGCAACAAATTTGGAAAATCGCAACGACAACTGTAG
1 ACTATCGCAACAAATTTAGAAAATCGCAACGACAACTGTAG
*
945501 ACTATAGCAAC
1 ACTATCGCAAC
945512 GCGATTGCGA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.20
Consensus pattern (41 bp):
ACTATCGCAACAAATTTAGAAAATCGCAACGACAACTGTAG
Found at i:945576 original size:20 final size:20
Alignment explanation
Indices: 945518--945586 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
945508 CAACGCGATT
*
945518 GCGAAATAGAAAATCGCAAC
1 GCGAAATGGAAAATCGCAAC
** ** *
945538 GCGATTTTCAACTATCGCAAC
1 GCGAAATGGAA-AATCGCAAC
945559 GCGAAATGGAAAATCGCAAC
1 GCGAAATGGAAAATCGCAAC
945579 GCGAAATG
1 GCGAAATG
945587 CAACACGAAT
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 23 0.61
21 15 0.39
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.16
Consensus pattern (20 bp):
GCGAAATGGAAAATCGCAAC
Found at i:947242 original size:20 final size:20
Alignment explanation
Indices: 947217--947261 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
947207 AAAAATAACT
* *
947217 TATTTTTTACACTACACAAA
1 TATTTTTTACAATACAAAAA
947237 TATTTTTTACAATACAAAAA
1 TATTTTTTACAATACAAAAA
947257 TATTT
1 TATTT
947262 ATTTTTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.44
Consensus pattern (20 bp):
TATTTTTTACAATACAAAAA
Found at i:949106 original size:12 final size:13
Alignment explanation
Indices: 949091--949124 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
949081 GTTTTTTGGC
949091 ATTTTTTTAA-TT
1 ATTTTTTTAATTT
949103 ATTTTTTTAATTT
1 ATTTTTTTAATTT
949116 ATCTTTTTT
1 AT-TTTTTT
949125 TCAAATGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 10 0.50
13 4 0.20
14 6 0.30
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTTTTTAATTT
Found at i:955618 original size:23 final size:23
Alignment explanation
Indices: 955588--955631 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
955578 CTTGTTTTCT
*
955588 CAATTAGACAATATATTATATGC
1 CAATTAGACAAGATATTATATGC
955611 CAATTAGACAAGATATTATAT
1 CAATTAGACAAGATATTATAT
955632 ACCATGCTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.34
Consensus pattern (23 bp):
CAATTAGACAAGATATTATATGC
Found at i:962842 original size:2 final size:2
Alignment explanation
Indices: 962835--962866 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
962825 ATAGTTTGCT
962835 GA GA GA GA GA GA GA GA GA GA GA GA GA -A GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
962867 GGCATAGATC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:968200 original size:14 final size:16
Alignment explanation
Indices: 968170--968201 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
968160 AATGACATAA
968170 AAAATGAAAATCAATG
1 AAAATGAAAATCAATG
968186 AAAA-GAAAA-CAATG
1 AAAATGAAAATCAATG
968200 AA
1 AA
968202 TTCAATGCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 5 0.31
16 4 0.25
ACGTcount: A:0.69, C:0.06, G:0.12, T:0.12
Consensus pattern (16 bp):
AAAATGAAAATCAATG
Found at i:978408 original size:21 final size:21
Alignment explanation
Indices: 978384--978424 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
978374 TTACTATGTC
* *
978384 AACATCATGAATTGTCACATT
1 AACATCATAAATTATCACATT
978405 AACATCATAAATTATCACAT
1 AACATCATAAATTATCACAT
978425 CGATACCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.32
Consensus pattern (21 bp):
AACATCATAAATTATCACATT
Found at i:986119 original size:39 final size:39
Alignment explanation
Indices: 986033--986137 Score: 147
Period size: 39 Copynumber: 2.7 Consensus size: 39
986023 ATACCAGAAG
*
986033 TTTAGTTTTTGTTTCATTTTAATATCCCACCGTTAAAAAC
1 TTTAGTTTTTGTTTCATTTTAGTA-CCCACCGTTAAAAAC
* * * **
986073 TTCAGTTTTTGATTCATTTTAGTACTCGTCGTTAAAAAC
1 TTTAGTTTTTGTTTCATTTTAGTACCCACCGTTAAAAAC
986112 TTTAGTTTTTGTTTCATTTTAGTACC
1 TTTAGTTTTTGTTTCATTTTAGTACC
986138 ATTCAAACTT
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
39 35 0.62
40 21 0.38
ACGTcount: A:0.24, C:0.15, G:0.10, T:0.50
Consensus pattern (39 bp):
TTTAGTTTTTGTTTCATTTTAGTACCCACCGTTAAAAAC
Found at i:986427 original size:2 final size:2
Alignment explanation
Indices: 986420--986453 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
986410 AAAACAAAGA
986420 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
986454 TTTGAAGCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:993070 original size:20 final size:22
Alignment explanation
Indices: 993032--993071 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
993022 GGGCAGCTAA
993032 TAAGAGATATGACAGCTTCACC
1 TAAGAGATATGACAGCTTCACC
993054 TAAGA-ATATGA-AGCTTCA
1 TAAGAGATATGACAGCTTCA
993072 ATCAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 6 0.33
22 5 0.28
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.25
Consensus pattern (22 bp):
TAAGAGATATGACAGCTTCACC
Found at i:993296 original size:71 final size:70
Alignment explanation
Indices: 993189--993681 Score: 514
Period size: 71 Copynumber: 7.0 Consensus size: 70
993179 TTTTAGAAGT
* * * *
993189 TTAGGTTCATATGATGATCTTTCTAAGTTTTCGTAACGCCTATATG-TTTTGGTGATCTTTTAAG
1 TTAGGATCATATGATGATCTTTCTAAGTTGTCGTAAC-CCTATGTGCTTTT-ATGATCTTTTAAG
*
993253 AAGTGGA
64 AAGTGAA
* * * * * * *
993260 TTAGGATTATATGATGATCTTTCTAAGTTTTTGTAACACGTATGTGCTTTAATGATCTTTTGAGG
1 TTAGGATCATATGATGATCTTTCTAAGTTGTCGTAAC-CCTATGTGCTTTTATGATCTTTTAAGA
* *
993325 CGTTAA
65 AGTGAA
* * * *
993331 TTAGGATTATATGACGATCTTTCTAAGTTGTCGTAACACTCATGTGCTTTTATGATCTTATAAGA
1 TTAGGATCATATGATGATCTTTCTAAGTTGTCGTAACCCT-ATGTGCTTTTATGATCTTTTAAGA
993396 AGTGAA
65 AGTGAA
* * * * * * * *
993402 TTAGGATCATATGATGTTCTTTCTATGTTGTGGTAATGCTTATGTGATTTGATGATCCTTTAAGA
1 TTAGGATCATATGATGATCTTTCTAAGTTGTCGTAA-CCCTATGTGCTTTTATGATCTTTTAAGA
*
993467 AGTAAA
65 AGTGAA
* * * *
993473 TTAGGATCATACGATGATCTTTCTATGTTGTCGTAACCCTCCTGTTCTTTTATGATCTTTTAAGA
1 TTAGGATCATATGATGATCTTTCTAAGTTGTCGTAACCCT-ATGTGCTTTTATGATCTTTTAAGA
993538 AGTGAA
65 AGTGAA
* * * *
993544 ATAGGATCATAT-ATTAATCTTTCTATGTTGTCGTAACACTCATGTGCTTTTATGATCTTTT-A-
1 TTAGGATCATATGA-TGATCTTTCTAAGTTGTCGTAACCCT-ATGTGCTTTTATGATCTTTTAAG
993606 AA-TGAA
64 AAGTGAA
* * *
993612 TTAGGATCATATGATGATCTTTTTAAGTTGTCGTAACACC--TGTGTTTTTATGATCTTTTAATA
1 TTAGGATCATATGATGATCTTTCTAAGTTGTCGTAAC-CCTATGTGCTTTTATGATCTTTTAAGA
993675 AGTGAA
65 AGTGAA
993681 T
1 T
993682 CTAGCACCCT
Statistics
Matches: 352, Mismatches: 60, Indels: 22
0.81 0.14 0.05
Matches are distributed among these distances:
66 18 0.05
67 1 0.00
68 37 0.11
69 9 0.03
70 5 0.01
71 278 0.79
72 4 0.01
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (70 bp):
TTAGGATCATATGATGATCTTTCTAAGTTGTCGTAACCCTATGTGCTTTTATGATCTTTTAAGAA
GTGAA
Found at i:1009763 original size:20 final size:19
Alignment explanation
Indices: 1009740--1009786 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1009730 CGATATAACA
*
1009740 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAAAC
*
1009760 GGTATCAAAATGATAAAAAC
1 GGTA-AAAAATGATAAAAAC
1009780 GGTAAAA
1 GGTAAAA
1009787 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAAAC
Found at i:1012120 original size:33 final size:33
Alignment explanation
Indices: 1012078--1012143 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1012068 AAATAGATGG
*
1012078 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
1012111 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1012144 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:1013972 original size:19 final size:19
Alignment explanation
Indices: 1013928--1013971 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1013918 AATGTCGAGT
1013928 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1013947 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
1013966 T-ATTTT
1 TAATTTT
1013972 TTATGTGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1014877 original size:199 final size:199
Alignment explanation
Indices: 1014051--1015862 Score: 3319
Period size: 199 Copynumber: 9.1 Consensus size: 199
1014041 TTAAGGGTCA
*
1014051 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1014115 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
1014180 TAATATGTAATTTTTTAATCTAACCGGTACAATTATA-CGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1014244 AATG
196 AATG
* * *
1014248 TGTCGACACTAATATAGTTTGTGTGGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1014313 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
1014377 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1014442 AATG
196 AATG
1014446 TGTCGACACT-A-ATAGTTTGTGTCGATATTTTTTT-CCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1014508 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
1014573 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1014638 AATG
196 AATG
*
1014642 TGTCGACACT-ATATAGTTTGTGTCGATATTTTTTTCCCATAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
1014706 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT-AT
66 AATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1014770 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
1014835 TAATG
195 TAATG
1014840 TGTCGACACTAATATAG-TTGTGTCGATATTTTTTTTCCCAGAATGAATTAAAAACAAGGTGCAC
1 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCCAGAATGAATTAAAAACAAGGTGCAC
*
1014904 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
65 CAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
1014969 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
1015034 TAATG
195 TAATG
1015039 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATT-AAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
1015103 AATAAAGTGTCGATCCATATTTAAAAAGTGTCGATCCC-AAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
1015167 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1015232 AATG
196 AATG
1015236 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
1015301 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 AATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1015366 GTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGG-TTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
1015429 TAATG
195 TAATG
1015434 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCCAGAATGAATTAAAAACAAGGTGCAC
1 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCCAGAATGAATTAAAAACAAGGTGCAC
*
1015499 CCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
65 CAATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
*
1015564 TGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAA
129 TGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAA
1015629 ATAATG
194 ATAATG
1015635 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAATTAAAAACAAGGTGCAC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATG-AATTAAAAACAAGGTGCAC
*
1015700 CAATAAAGTGTCGATCCATATTTAAAAAGTGTCGAT-CCAAAATCATCGAACCCAAAAGTATAAT
65 CAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
1015764 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAA
130 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
1015829 TAATG
195 TAATG
*
1015834 TGTCGACACTAATATATTTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
1015863 CTAATTTAAA
Statistics
Matches: 1577, Mismatches: 21, Indels: 32
0.97 0.01 0.02
Matches are distributed among these distances:
195 65 0.04
196 127 0.08
197 264 0.17
198 428 0.27
199 492 0.31
200 105 0.07
201 96 0.06
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (199 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
AATG
Found at i:1015024 original size:397 final size:398
Alignment explanation
Indices: 1014051--1015862 Score: 3319
Period size: 397 Copynumber: 4.6 Consensus size: 398
1014041 TTAAGGGTCA
*
1014051 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1014115 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
1014180 TAATATGTAATTTTTTAATCTAACCGGTACAATTATA-CGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
* *
1014244 AATGTGTCGACACTAATATAGTTTGTGTGGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTG
196 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
*
1014309 CATCAATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAATCATCGAACCCAAAAGTAT
261 CACCAATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAATCATCGAACCCAAAAGTAT
*
1014373 AATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
326 AATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
1014438 AAATAATG
391 AAATAATG
1014446 TGTCGACACT-A-ATAGTTTGTGTCGATATTTTTTT-CCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1014508 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
1014573 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
*
1014638 AATGTGTCGACACT-ATATAGTTTGTGTCGATATTTTTTTCCCATAATGAATTAAAAACAAGGTG
196 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
*
1014702 CACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
261 CACCAATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCC-AAATCATCGAACCCAAAAGTA
1014767 T-ATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTC
325 TAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTC
1014831 TAAATAATG
390 TAAATAATG
1014840 TGTCGACACTAATATAG-TTGTGTCGATATTTTTTTTCCCAGAATGAATTAAAAACAAGGTGCAC
1 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCCAGAATGAATTAAAAACAAGGTGCAC
*
1014904 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
65 CAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
1014969 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
1015034 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATT-AAAACAAGGT
195 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGT
*
1015098 GCACCAATAAAGTGTCGATCCATAT-TTAAAAAGTGTCGATCCCAAATCATCGAACCCAAAAGTA
260 GCACCAATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAATCATCGAACCCAAAAGTA
1015162 TAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTC
325 TAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTC
1015227 TAAATAATG
390 TAAATAATG
1015236 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
1015301 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 AATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1015366 GTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGG-TTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
1015429 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCCAGAATGAATTAAAAACAAGG
195 TAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCCAGAATGAATTAAAAACAAGG
*
1015494 TGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAG
259 TGCACCAATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCC-AAATCATCGAACCCAAAAG
*
1015559 TATAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAG
323 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAG
1015624 TCTAAATAATG
388 TCTAAATAATG
1015635 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAATTAAAAACAAGGTGCAC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATG-AATTAAAAACAAGGTGCAC
*
1015700 CAATAAAGTGTCGATCCATATTTAAAAAGTGTCGAT-CCAAAATCATCGAACCCAAAAGTATAAT
65 CAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
1015764 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAA
130 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
*
1015829 TAATGTGTCGACACTAATATATTTTGTGTCGATA
195 TAATGTGTCGACACTAATATAGTTTGTGTCGATA
1015863 CTAATTTAAA
Statistics
Matches: 1378, Mismatches: 21, Indels: 31
0.96 0.01 0.02
Matches are distributed among these distances:
393 223 0.16
394 139 0.10
395 121 0.09
396 224 0.16
397 302 0.22
398 93 0.07
399 182 0.13
400 94 0.07
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (398 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
CACCAATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAATCATCGAACCCAAAAGTAT
AATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
AAATAATG
Found at i:1017334 original size:18 final size:18
Alignment explanation
Indices: 1017311--1017378 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 18
1017301 TCGGTCGCGA
1017311 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* *
1017329 GAAGATGACGATGATGATGAT
1 GAAGATGA--A-GCTGACGAT
*
1017350 GATGACGATGAAGCTGGCGAT
1 GA--A-GATGAAGCTGACGAT
1017371 GAAGATGA
1 GAAGATGA
1017379 TGACGATGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
18 13 0.33
19 1 0.03
20 1 0.03
21 17 0.44
22 1 0.03
23 1 0.03
24 5 0.13
ACGTcount: A:0.37, C:0.09, G:0.35, T:0.19
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:1017335 original size:6 final size:6
Alignment explanation
Indices: 1017311--1017408 Score: 70
Period size: 6 Copynumber: 16.3 Consensus size: 6
1017301 TCGGTCGCGA
* * * * * *
1017311 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* ** * * * * *
1017359 GAAGCT GGCGAT GAAGAT GATGAC GATGAT GATGAT GATGAT GAAGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
1017407 GA
1 GA
1017409 TGATCCAAAC
Statistics
Matches: 74, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 74 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:1017346 original size:3 final size:3
Alignment explanation
Indices: 1017326--1017412 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
1017316 TGAAGCTGAC
* * * * * ** *
1017326 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
1017374 GAT GAT GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1017413 CCAAACAATA
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.36, C:0.06, G:0.34, T:0.24
Consensus pattern (3 bp):
GAT
Found at i:1017373 original size:42 final size:42
Alignment explanation
Indices: 1017314--1017404 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
1017304 GTCGCGAGAA
*
1017314 GATGAAGCTGACGATGAAGATGACGATGATGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
* * *
1017356 GATGAAGCTGGCGATGAAGATGATGACGATGATGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
1017398 GATGAAG
1 GATGAAG
1017405 ATGATGATCC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.22
Consensus pattern (42 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
Found at i:1017412 original size:18 final size:18
Alignment explanation
Indices: 1017311--1017408 Score: 88
Period size: 18 Copynumber: 5.4 Consensus size: 18
1017301 TCGGTCGCGA
* *
1017311 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGATGAT
*
1017329 GAAGATGACGATGATGAT
1 GAAGATGAAGATGATGAT
* * * *
1017347 GATGATGACGATGAAGCT
1 GAAGATGAAGATGATGAT
** *
1017365 GGCGATGAAGATGATGAC
1 GAAGATGAAGATGATGAT
* *
1017383 GATGATGATGATGATGAT
1 GAAGATGAAGATGATGAT
1017401 GAAGATGA
1 GAAGATGA
1017409 TGATCCAAAC
Statistics
Matches: 63, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 63 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (18 bp):
GAAGATGAAGATGATGAT
Found at i:1019147 original size:179 final size:183
Alignment explanation
Indices: 1018840--1019678 Score: 1458
Period size: 179 Copynumber: 4.7 Consensus size: 183
1018830 CACTTTCAAT
**
1018840 ATTATAATAAAATAGATAA-TTTGTAATATAACCGGTATAAATATACCGGTCTTATG-GCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
1018903 GGTCTACAA-CTATATCGACAC-TTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
1018966 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTT-ACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTAACATCGGAACCCATA
* *
1019018 A-T-TAATGTAATAGATAA-TTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCCAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
1019080 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
1019145 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTA-ACATCGGAACCCATA
*
1019199 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
1019264 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTA-TTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
1019328 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTA-ACATCGGAACCCATA
*
1019382 ATTATAATGTAATAGATAATTTTGTAATATAACC-GTAT-AA-ATACC-GTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
1019443 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAG-AA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
1019507 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTA-ACATCGGAACCCATA
*
1019561 ATTATAATGTAATAGATAATTTTGT-A-ATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
*
1019624 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
1019679 CCATTTAAAA
Statistics
Matches: 636, Mismatches: 12, Indels: 23
0.95 0.02 0.03
Matches are distributed among these distances:
176 49 0.08
177 22 0.03
178 18 0.03
179 219 0.34
180 29 0.05
181 86 0.14
182 5 0.01
183 124 0.19
184 84 0.13
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (183 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTAACATCGGAACCCATA
Found at i:1019515 original size:362 final size:362
Alignment explanation
Indices: 1018840--1019678 Score: 1466
Period size: 362 Copynumber: 2.3 Consensus size: 362
1018830 CACTTTCAAT
**
1018840 ATTATAATAAAATAGATAA-TTTGTAATATAACCGGTATAAATATACCGGTCTTATGGCGAATAG
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGGCGAATAG
1018904 GTCTACAA-CTATATCGACAC-TTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
66 GTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
1018967 ATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACATCGGAACCCATAATTAATGTAATAGA
131 ATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACATCGGAACCCATAATTAATGTAATAGA
*
1019032 TAATTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCCAATAGGTCTACAACCTATATC
196 TAATTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCCAATAGGTCTACAACCTATATC
1019097 GACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACAATT
261 GACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACAATT
1019162 TAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
326 TAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
1019199 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATG-GCGAATA
1019264 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTA-TTTATGTCCATATTGGAAGAAA
65 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
1019328 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTA
130 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTT--ACATCGGAACCCATAA-T-TAATGTA
* *
1019393 ATAGATAATTTTGTAATATAACC-GTAT-AA-ATACC-GTCTTATGCGCGAATAGGTCTACAACC
191 ATAGATAA-TTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCCAATAGGTCTACAACC
1019454 TATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAG-AAAATGTGTCGAT
255 TATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGAT
*
1019518 ACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
320 ACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
*
1019561 ATTATAATGTAATAGATAATTTTGT-A-ATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATG-GCGAATA
*
1019624 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATA
65 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
1019679 CCATTTAAAA
Statistics
Matches: 461, Mismatches: 9, Indels: 18
0.94 0.02 0.04
Matches are distributed among these distances:
359 17 0.04
360 113 0.25
361 29 0.06
362 151 0.33
363 94 0.20
364 21 0.05
365 3 0.01
366 19 0.04
367 14 0.03
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (362 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGGCGAATAG
GTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
ATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACATCGGAACCCATAATTAATGTAATAGA
TAATTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCCAATAGGTCTACAACCTATATC
GACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACAATT
TAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:1022229 original size:22 final size:23
Alignment explanation
Indices: 1022199--1022259 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
1022189 ATAGGTAAAC
*
1022199 ATATGATGTAATAGGTAGC-CCT
1 ATATAATGTAATAGGTAGCGCCT
* **
1022221 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCCT
1022244 ATATAATGT-ATAGGTA
1 ATATAATGTAATAGGTA
1022260 ATGGTTATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 24 0.71
23 10 0.29
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCCT
Found at i:1022267 original size:22 final size:23
Alignment explanation
Indices: 1022220--1022269 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
1022210 TAGGTAGCCC
*
1022220 TATATAATGTAATAGGTATCGTT
1 TATATAATGTAATAGGTATCGGT
1022243 TATATAATGT-ATAGGTAAT-GGT
1 TATATAATGTAATAGGT-ATCGGT
1022265 TATAT
1 TATAT
1022270 TGTAAAGTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 13 0.52
23 12 0.48
ACGTcount: A:0.36, C:0.02, G:0.18, T:0.44
Consensus pattern (23 bp):
TATATAATGTAATAGGTATCGGT
Found at i:1023091 original size:21 final size:23
Alignment explanation
Indices: 1023055--1023096 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
1023045 TGGTAGGCCC
1023055 TTATATAATGTAATAGGTATCGT
1 TTATATAATGTAATAGGTATCGT
1023078 TTATAT-ATGT-ATAGGTATC
1 TTATATAATGTAATAGGTATC
1023097 TATCTCACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 9 0.47
22 4 0.21
23 6 0.32
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.45
Consensus pattern (23 bp):
TTATATAATGTAATAGGTATCGT
Found at i:1023316 original size:18 final size:18
Alignment explanation
Indices: 1023295--1023329 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1023285 GTAATTGGAG
1023295 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
1023313 TTTGAGTTTGAATTTCA
1 TTTGAATTTAAATTTCA
1023330 TATATATTTC
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:0.31, C:0.06, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:1046206 original size:20 final size:21
Alignment explanation
Indices: 1046166--1046210 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1046156 TGAGTTGATT
*
1046166 AAAATGGTTTTAAAGTATTTA
1 AAAATAGTTTTAAAGTATTTA
*
1046187 AAAATAGTTTTAAAG-CTTTA
1 AAAATAGTTTTAAAGTATTTA
1046207 AAAA
1 AAAA
1046211 CATGAAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (21 bp):
AAAATAGTTTTAAAGTATTTA
Found at i:1053129 original size:8 final size:7
Alignment explanation
Indices: 1053116--1053180 Score: 64
Period size: 7 Copynumber: 9.4 Consensus size: 7
1053106 AATAAGAAGC
1053116 AAAAAAGG
1 AAAAAA-G
1053124 AAAAAAG
1 AAAAAAG
1053131 --AAAAG
1 AAAAAAG
*
1053136 AAAAAAA
1 AAAAAAG
*
1053143 AAAAAAC
1 AAAAAAG
1053150 AAAAAAGG
1 AAAAAA-G
1053158 AAAAAA-
1 AAAAAAG
*
1053164 ACAAAAG
1 AAAAAAG
1053171 AAAAAAG
1 AAAAAAG
1053178 AAA
1 AAA
1053181 GAACAAAGAT
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
5 5 0.10
6 5 0.10
7 26 0.54
8 12 0.25
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:1053140 original size:13 final size:13
Alignment explanation
Indices: 1053118--1053174 Score: 55
Period size: 13 Copynumber: 4.3 Consensus size: 13
1053108 TAAGAAGCAA
*
1053118 AAAAGGAAAAAAG
1 AAAAGAAAAAAAG
1053131 AAAAGAAAAAAA-
1 AAAAGAAAAAAAG
*
1053143 AAAAAACAAAAAAGG
1 AAAAGA-AAAAAA-G
1053158 AAAA-AAACAAAAG
1 AAAAGAAA-AAAAG
1053171 AAAA
1 AAAA
1053175 AAGAAAGAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
12 5 0.13
13 24 0.63
14 5 0.13
15 4 0.11
ACGTcount: A:0.84, C:0.04, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAAAG
Found at i:1053141 original size:14 final size:13
Alignment explanation
Indices: 1053124--1053176 Score: 63
Period size: 13 Copynumber: 4.0 Consensus size: 13
1053114 GCAAAAAAGG
1053124 AAAAAAGAAAAGAA
1 AAAAAAGAAAA-AA
1053138 AAAAAA-AAAAACA
1 AAAAAAGAAAAA-A
*
1053151 AAAAAGGAAAAAA
1 AAAAAAGAAAAAA
*
1053164 ACAAAAGAAAAAA
1 AAAAAAGAAAAAA
1053177 GAAAGAACAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
12 1 0.03
13 22 0.65
14 11 0.32
ACGTcount: A:0.87, C:0.04, G:0.09, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAA
Found at i:1053158 original size:34 final size:35
Alignment explanation
Indices: 1053115--1053187 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 35
1053105 CAATAAGAAG
*
1053115 CAAAAAAGG-AAAAAAGAAAAGAAAAAAAAAAAAA
1 CAAAAAAGGAAAAAAACAAAAGAAAAAAAAAAAAA
* *
1053149 CAAAAAAGGAAAAAAACAAAAGAAAAAAGAAAGAA
1 CAAAAAAGGAAAAAAACAAAAGAAAAAAAAAAAAA
1053184 CAAA
1 CAAA
1053188 GATCAAAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
34 9 0.26
35 26 0.74
ACGTcount: A:0.82, C:0.05, G:0.12, T:0.00
Consensus pattern (35 bp):
CAAAAAAGGAAAAAAACAAAAGAAAAAAAAAAAAA
Found at i:1053175 original size:13 final size:12
Alignment explanation
Indices: 1053116--1053176 Score: 63
Period size: 11 Copynumber: 5.2 Consensus size: 12
1053106 AATAAGAAGC
*
1053116 AAAAAAGGAAAA
1 AAAAAAAGAAAA
*
1053128 AAGAAAAG-AAA
1 AAAAAAAGAAAA
*
1053139 AAAAAAA-AAAC
1 AAAAAAAGAAAA
*
1053150 AAAAAAGGAAAA
1 AAAAAAAGAAAA
1053162 AAACAAAAGAAAA
1 AAA-AAAAGAAAA
1053175 AA
1 AA
1053177 GAAAGAACAA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
11 17 0.44
12 12 0.31
13 10 0.26
ACGTcount: A:0.85, C:0.03, G:0.11, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAA
Found at i:1053177 original size:21 final size:21
Alignment explanation
Indices: 1053131--1053180 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1053121 AGGAAAAAAG
1053131 AAAAGAAAAAAAAAAAAACAA
1 AAAAGAAAAAAAAAAAAACAA
* * *
1053152 AAAAGGAAAAAAACAAAAGAA
1 AAAAGAAAAAAAAAAAAACAA
1053173 AAAAGAAA
1 AAAAGAAA
1053181 GAACAAAGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.86, C:0.04, G:0.10, T:0.00
Consensus pattern (21 bp):
AAAAGAAAAAAAAAAAAACAA
Found at i:1053180 original size:20 final size:20
Alignment explanation
Indices: 1053126--1053201 Score: 70
Period size: 19 Copynumber: 3.8 Consensus size: 20
1053116 AAAAAAGGAA
1053126 AAAAGAAAAGAA-AAAAAAA-
1 AAAAGAAAA-AAGAAAAAAAC
*
1053145 AAAACAAAAAAGGAAAAAAAC
1 AAAAGAAAAAA-GAAAAAAAC
*
1053166 AAAAGAAAAAAG-AAAGAAC
1 AAAAGAAAAAAGAAAAAAAC
1053185 -AAAGATCAAAAAGAAAA
1 AAAAGA--AAAAAGAAAA
1053202 GGGGACAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
18 7 0.15
19 14 0.29
20 14 0.29
21 13 0.27
ACGTcount: A:0.82, C:0.05, G:0.12, T:0.01
Consensus pattern (20 bp):
AAAAGAAAAAAGAAAAAAAC
Found at i:1053188 original size:11 final size:11
Alignment explanation
Indices: 1053116--1053189 Score: 55
Period size: 11 Copynumber: 6.7 Consensus size: 11
1053106 AATAAGAAGC
*
1053116 AAAAAAGGAAAA
1 AAAAAA-GAAAG
1053128 AAGAAAAGAAA-
1 AA-AAAAGAAAG
* *
1053139 AAAAAAAAAAC
1 AAAAAAGAAAG
1053150 AAAAAAGGAAA-
1 AAAAAA-GAAAG
*
1053161 AAAACA-AAAG
1 AAAAAAGAAAG
1053171 AAAAAAGAAAG
1 AAAAAAGAAAG
*
1053182 AACAAAGA
1 AAAAAAGA
1053190 TCAAAAAGAA
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
9 3 0.06
10 12 0.23
11 24 0.46
12 9 0.17
13 4 0.08
ACGTcount: A:0.82, C:0.04, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:1053830 original size:22 final size:22
Alignment explanation
Indices: 1053799--1053847 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
1053789 CCCCATCAAT
*
1053799 CCTTTGAGCATCAAATACCAAA
1 CCTTTAAGCATCAAATACCAAA
*
1053821 CCTTTAAGCATCAAATGCCAAA
1 CCTTTAAGCATCAAATACCAAA
1053843 CCTTT
1 CCTTT
1053848 GACCAAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.37, C:0.29, G:0.08, T:0.27
Consensus pattern (22 bp):
CCTTTAAGCATCAAATACCAAA
Found at i:1055505 original size:43 final size:42
Alignment explanation
Indices: 1055444--1055592 Score: 115
Period size: 43 Copynumber: 3.5 Consensus size: 42
1055434 CAGAGCCAAT
*
1055444 TTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAG
1 TTCAACTTCACGACGAAGGATATTGGACTCAAGACAA-GCAAG
*** ** * *
1055487 TTCAACTTCACGACGAAGGACCGCTGGTTGTCAATA-AA-CAAC
1 TTCAACTTCACGACGAAGGA-TATTGG-ACTCAAGACAAGCAAG
* * *
1055529 TTCCCAATTTCA-TAGCGAAGGATATTGGACTCCAGACAATGCAAG
1 TT--CAACTTCACGA-CGAAGGATATTGGACTCAAGACAA-GCAAG
1055574 TTCAACTTCACGACGAAGG
1 TTCAACTTCACGACGAAGG
1055593 GACCGCTGGT
Statistics
Matches: 77, Mismatches: 20, Indels: 18
0.67 0.17 0.16
Matches are distributed among these distances:
42 9 0.12
43 38 0.49
44 20 0.26
45 10 0.13
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.21
Consensus pattern (42 bp):
TTCAACTTCACGACGAAGGATATTGGACTCAAGACAAGCAAG
Found at i:1055734 original size:106 final size:106
Alignment explanation
Indices: 1055544--1055984 Score: 661
Period size: 106 Copynumber: 4.2 Consensus size: 106
1055534 AATTTCATAG
*
1055544 CGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
1 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
* *
1055609 TAAACAACTTCCCAATTTTAGAGCCAATTTCAACTTCAC-A
66 CAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACGA
* *
1055649 TCGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCA
1 -CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* *
1055714 ACAAACAACTTCTCAATTTTAGAGCCAATTTCAACTTCACGA
65 ACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACGA
*
1055756 CGAAGGATATTGGACTCCAGACAACGGAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
1 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
*
1055821 CAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCAC-A
66 CAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACGA
* * * * * *
1055861 GCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAAGGACGGCTGTTTGTCA
1 -CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* * ** *
1055926 ATAAACAATTTCCCGGTTCCAGAGCCAATTTCAACTTCACGA
65 ACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACGA
*
1055968 CGGAGGATATTGGACTC
1 CGAAGGATATTGGACTC
1055985 GGAACAATAC
Statistics
Matches: 309, Mismatches: 23, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
105 1 0.00
106 306 0.99
107 2 0.01
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.23
Consensus pattern (106 bp):
CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
CAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACGA
Found at i:1056915 original size:3 final size:3
Alignment explanation
Indices: 1056909--1056943 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
1056899 TGTTGTTTAT
* *
1056909 TTA TTA TTA TTA TTA TTA TTA TTT TTA TTT TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1056944 TTTGTAGGCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (3 bp):
TTA
Found at i:1056944 original size:6 final size:6
Alignment explanation
Indices: 1056908--1056946 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
1056898 TTGTTGTTTA
* * *
1056908 TTTATT ATTATT ATTATT ATTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTT
1056947 GTAGGCCCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTATT
Found at i:1056944 original size:12 final size:12
Alignment explanation
Indices: 1056908--1056946 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
1056898 TTGTTGTTTA
1056908 TTTATTATTATT
1 TTTATTATTATT
*
1056920 ATTATTATTATT
1 TTTATTATTATT
*
1056932 TTTATTTTTATT
1 TTTATTATTATT
1056944 TTT
1 TTT
1056947 GTAGGCCCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTATTATTATT
Found at i:1058165 original size:11 final size:10
Alignment explanation
Indices: 1058136--1058163 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1058126 ATTCATTTTT
1058136 TATTTTTTAA
1 TATTTTTTAA
1058146 TATTTTTTAA
1 TATTTTTTAA
1058156 TATTTTTT
1 TATTTTTT
1058164 TATTTTCCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (10 bp):
TATTTTTTAA
Found at i:1058872 original size:45 final size:45
Alignment explanation
Indices: 1058808--1059014 Score: 353
Period size: 45 Copynumber: 4.6 Consensus size: 45
1058798 TGGAATGGTT
*
1058808 TAATGAAGTTATTAAAATGTTATATATTTTGTTAATAGAAAAGTC
1 TAATGAAGTTATTAAAATGTTATATATTTTGTTAATAGAATAGTC
*
1058853 TAATGAAGTTATTAAAATGTTATATATTTTGTTAATATAATAGTC
1 TAATGAAGTTATTAAAATGTTATATATTTTGTTAATAGAATAGTC
1058898 TAATGAAGTTATTAAAATGTTATATATTTTGTTAATAGAATAGTC
1 TAATGAAGTTATTAAAATGTTATATATTTTGTTAATAGAATAGTC
* *
1058943 TAATGAAGGTATT-AAATGTTATATATTTTGTTAATATAATAGTC
1 TAATGAAGTTATTAAAATGTTATATATTTTGTTAATAGAATAGTC
*
1058987 TAATGAAGTTATTAAAAATGTGATATAT
1 TAATGAAGTTATT-AAAATGTTATATAT
1059015 AAATATTTTG
Statistics
Matches: 153, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
44 42 0.27
45 99 0.65
46 12 0.08
ACGTcount: A:0.41, C:0.02, G:0.13, T:0.44
Consensus pattern (45 bp):
TAATGAAGTTATTAAAATGTTATATATTTTGTTAATAGAATAGTC
Found at i:1065724 original size:4 final size:4
Alignment explanation
Indices: 1065715--1065741 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1065705 GTTTAATTTA
1065715 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1065742 ATTTAAAGGA
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:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:1065767 original size:29 final size:29
Alignment explanation
Indices: 1065731--1065789 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
1065721 ATAAATAAAT
1065731 AAATAAA-TAAAATTTAAAGGATCAAATTG
1 AAATAAATTAAAATTT-AAGGATCAAATTG
*
1065760 AAATAAATTAAAATTTATGGATCAAATTG
1 AAATAAATTAAAATTTAAGGATCAAATTG
1065789 A
1 A
1065790 TGTTAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.56, C:0.03, G:0.10, T:0.31
Consensus pattern (29 bp):
AAATAAATTAAAATTTAAGGATCAAATTG
Found at i:1066962 original size:17 final size:17
Alignment explanation
Indices: 1066940--1066981 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1066930 GATTGGACAG
1066940 AAAAAAATAA-GAATAAT
1 AAAAAAA-AATGAATAAT
*
1066957 AAAAAAAAATTAATAAT
1 AAAAAAAAATGAATAAT
1066974 AAAAAAAA
1 AAAAAAAA
1066982 TAAACAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 2 0.09
17 21 0.91
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (17 bp):
AAAAAAAAATGAATAAT
Found at i:1066965 original size:20 final size:19
Alignment explanation
Indices: 1066940--1066981 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1066930 GATTGGACAG
1066940 AAAAAAATAAGAATAATAAA
1 AAAAAAATAAGAATAA-AAA
* *
1066960 AAAAAATTAATAATAAAAA
1 AAAAAAATAAGAATAAAAA
1066979 AAA
1 AAA
1066982 TAAACAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (19 bp):
AAAAAAATAAGAATAAAAA
Found at i:1066970 original size:14 final size:14
Alignment explanation
Indices: 1066953--1066994 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
1066943 AAAATAAGAA
1066953 TAATAAAAAAAAAT
1 TAATAAAAAAAAAT
*
1066967 TAATAATAAAAAAAA
1 TAATAA-AAAAAAAT
*
1066982 TAA-ACAAAAAAAT
1 TAATAAAAAAAAAT
1066995 AAAATATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 7 0.29
14 7 0.29
15 10 0.42
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (14 bp):
TAATAAAAAAAAAT
Found at i:1066983 original size:26 final size:26
Alignment explanation
Indices: 1066943--1067000 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
1066933 TGGACAGAAA
* * *
1066943 AAAATAAGAATAATAAA-AAAAAATT
1 AAAATAAAAAAAATAAACAAAAAAAT
1066968 AATAATAAAAAAAATAAACAAAAAAAT
1 AA-AATAAAAAAAATAAACAAAAAAAT
1066995 AAAATA
1 AAAATA
1067001 TTAATATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 2 0.07
26 17 0.61
27 9 0.32
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (26 bp):
AAAATAAAAAAAATAAACAAAAAAAT
Found at i:1066993 original size:16 final size:16
Alignment explanation
Indices: 1066957--1067000 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
1066947 TAAGAATAAT
* *
1066957 AAAAAAAAATTAATAA
1 AAAAAAAAATAAACAA
*
1066973 TAAAAAAAATAAACAA
1 AAAAAAAAATAAACAA
1066989 AAAAATAAAATA
1 AAAAA-AAAATA
1067001 TTAATATAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 17 0.74
17 6 0.26
ACGTcount: A:0.82, C:0.02, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAAAAAAATAAACAA
Found at i:1067096 original size:36 final size:36
Alignment explanation
Indices: 1067032--1067266 Score: 230
Period size: 35 Copynumber: 6.8 Consensus size: 36
1067022 TCAAAAAATT
*
1067032 TGTTTTCAAAAAACCATTTTTAAAAACTATATATTACA
1 TGTTTTC-AAAAACCA-TTTTAAAAACTATATATTATA
*
1067070 TGTTTTCAAAAACCATTTTAAAAACTATATACTATA
1 TGTTTTCAAAAACCATTTTAAAAACTATATATTATA
*
1067106 TGTTTTCAAAAA-TATTTTAAAAACTATATATTATA
1 TGTTTTCAAAAACCATTTTAAAAACTATATATTATA
*
1067141 TGTTTTCAAAAA-C----T--ATACTATATA-TATA
1 TGTTTTCAAAAACCATTTTAAAAACTATATATTATA
*
1067169 ----TTCAAAAA-TATTTTAAAAACTATATATTATA
1 TGTTTTCAAAAACCATTTTAAAAACTATATATTATA
* *
1067200 TGTTTTCAAAAA-TATGTTTTCAAAACTATATATTATA
1 TGTTTTCAAAAACCA--TTTTAAAAACTATATATTATA
* *
1067237 TGTTTTCCAAAACCGATTTAAAAAAACTAT
1 TGTTTTCAAAAACC-ATTT-TAAAAACTAT
1067267 GTTGAACTAT
Statistics
Matches: 168, Mismatches: 13, Indels: 32
0.79 0.06 0.15
Matches are distributed among these distances:
24 8 0.05
28 5 0.03
29 9 0.05
30 9 0.05
31 5 0.03
35 43 0.26
36 31 0.18
37 42 0.25
38 15 0.09
39 1 0.01
ACGTcount: A:0.45, C:0.11, G:0.03, T:0.41
Consensus pattern (36 bp):
TGTTTTCAAAAACCATTTTAAAAACTATATATTATA
Found at i:1067130 original size:35 final size:35
Alignment explanation
Indices: 1067049--1067248 Score: 235
Period size: 35 Copynumber: 5.9 Consensus size: 35
1067039 AAAAAACCAT
* *
1067049 TTTTAAAAACTATATATTACATGTTTTCAAAAACCA
1 TTTTAAAAACTATATATTATATGTTTTCAAAAA-TA
*
1067085 TTTTAAAAACTATATACTATATGTTTTCAAAAATA
1 TTTTAAAAACTATATATTATATGTTTTCAAAAATA
1067120 TTTTAAAAACTATATATTATATGTTTTCAAAAACTA
1 TTTTAAAAACTATATATTATATGTTTTCAAAAA-TA
1067156 ---T----ACTATATA-TATA----TTCAAAAATA
1 TTTTAAAAACTATATATTATATGTTTTCAAAAATA
1067179 TTTTAAAAACTATATATTATATGTTTTCAAAAATA
1 TTTTAAAAACTATATATTATATGTTTTCAAAAATA
* *
1067214 TGTTTTCAAAACTATATATTATATGTTTTCCAAAA
1 --TTTTAAAAACTATATATTATATGTTTTCAAAAA
1067249 CCGATTTAAA
Statistics
Matches: 143, Mismatches: 6, Indels: 29
0.80 0.03 0.16
Matches are distributed among these distances:
23 2 0.01
24 8 0.06
26 1 0.01
28 4 0.03
29 8 0.06
30 8 0.06
31 4 0.03
33 1 0.01
35 43 0.30
36 33 0.23
37 31 0.22
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.43
Consensus pattern (35 bp):
TTTTAAAAACTATATATTATATGTTTTCAAAAATA
Found at i:1067155 original size:24 final size:24
Alignment explanation
Indices: 1067117--1067176 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
1067107 GTTTTCAAAA
1067117 ATATTTT-AAAAACTATA-TATTAT
1 ATATTTTCAAAAACTATACTA-TAT
*
1067140 ATGTTTTCAAAAACTATACTATAT
1 ATATTTTCAAAAACTATACTATAT
*
1067164 ATATATTCAAAAA
1 ATATTTTCAAAAA
1067177 TATTTTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.19
24 24 0.75
25 2 0.06
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (24 bp):
ATATTTTCAAAAACTATACTATAT
Found at i:1067156 original size:59 final size:59
Alignment explanation
Indices: 1067085--1067211 Score: 213
Period size: 59 Copynumber: 2.2 Consensus size: 59
1067075 TCAAAAACCA
* *
1067085 TTTT-AAAAACTATA-TACTATATGTTTTCAAAAATATTTTAAAAACTATATATTATATG
1 TTTTCAAAAACTATACTA-TATATATATTCAAAAATATTTTAAAAACTATATATTATATG
1067143 TTTTCAAAAACTATACTATATATATATTCAAAAATATTTTAAAAACTATATATTATATG
1 TTTTCAAAAACTATACTATATATATATTCAAAAATATTTTAAAAACTATATATTATATG
1067202 TTTTCAAAAA
1 TTTTCAAAAA
1067212 TATGTTTTCA
Statistics
Matches: 65, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
58 4 0.06
59 59 0.91
60 2 0.03
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.43
Consensus pattern (59 bp):
TTTTCAAAAACTATACTATATATATATTCAAAAATATTTTAAAAACTATATATTATATG
Found at i:1067216 original size:14 final size:14
Alignment explanation
Indices: 1067197--1067224 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1067187 ACTATATATT
1067197 ATATGTTTTCAAAA
1 ATATGTTTTCAAAA
1067211 ATATGTTTTCAAAA
1 ATATGTTTTCAAAA
1067225 CTATATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
ATATGTTTTCAAAA
Found at i:1067225 original size:37 final size:37
Alignment explanation
Indices: 1067138--1067248 Score: 147
Period size: 37 Copynumber: 3.0 Consensus size: 37
1067128 ACTATATATT
* *
1067138 ATATGTTTTCAAAAACTATACTA-TATATATATTCAAAA
1 ATATGTTTTC-AAAACTATA-TATTATATGTTTTCAAAA
*
1067176 ATA--TTTTAAAAACTATATATTATATGTTTTCAAAA
1 ATATGTTTTCAAAACTATATATTATATGTTTTCAAAA
*
1067211 ATATGTTTTCAAAACTATATATTATATGTTTTCCAAA
1 ATATGTTTTCAAAACTATATATTATATGTTTTCAAAA
1067248 A
1 A
1067249 CCGATTTAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 7
0.84 0.06 0.09
Matches are distributed among these distances:
34 2 0.03
35 25 0.38
36 4 0.06
37 31 0.48
38 3 0.05
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (37 bp):
ATATGTTTTCAAAACTATATATTATATGTTTTCAAAA
Found at i:1067328 original size:34 final size:30
Alignment explanation
Indices: 1067290--1067358 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 30
1067280 TTGATATAAC
1067290 AATTTAAGGCAAAACGGATTTTGGACTTGAATTG
1 AATTTAA--CAAAA-GGATTTTGGACTT-AATTG
* *
1067324 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAAGGATTTTGGACTTAATTG
1067353 AATTTA
1 AATTTA
1067359 TTCAAAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 10 0.31
30 11 0.34
31 5 0.16
33 1 0.03
34 5 0.16
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.39
Consensus pattern (30 bp):
AATTTAACAAAAGGATTTTGGACTTAATTG
Found at i:1067464 original size:21 final size:21
Alignment explanation
Indices: 1067438--1067557 Score: 156
Period size: 21 Copynumber: 5.7 Consensus size: 21
1067428 AAGGTGTCAA
1067438 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
1067459 AGTGCATCCATGCACCCCTAC
1 AGTGCATCCATGCACCCCTGC
1067480 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
1067501 AGTGCATCCATGCA--CTTGCAC
1 AGTGCATCCATGCACCCCTG--C
* *
1067522 TAGTGCATCGATGCA-CCATGC
1 -AGTGCATCCATGCACCCCTGC
1067543 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
1067558 TCAAACACTG
Statistics
Matches: 88, Mismatches: 6, Indels: 10
0.85 0.06 0.10
Matches are distributed among these distances:
19 3 0.03
20 13 0.15
21 56 0.64
22 13 0.15
23 3 0.03
ACGTcount: A:0.23, C:0.38, G:0.19, T:0.21
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:1067497 original size:42 final size:43
Alignment explanation
Indices: 1067438--1067559 Score: 178
Period size: 42 Copynumber: 2.9 Consensus size: 43
1067428 AAGGTGTCAA
1067438 AGTGCATCCATGCACCCCTGCAGTGCATCCATGCAC-CCCTAC-
1 AGTGCATCCATGCACCCCTGCAGTGCATCCATGCACTCCC-ACT
**
1067480 AGTGCATCCATGCACCCCTGCAGTGCATCCATGCACTTGCACT
1 AGTGCATCCATGCACCCCTGCAGTGCATCCATGCACTCCCACT
* *
1067523 AGTGCATCGATGCA-CCATGCAGTGCATCCATGCACTC
1 AGTGCATCCATGCACCCCTGCAGTGCATCCATGCACTC
1067560 AAACACTGAA
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
42 59 0.81
43 14 0.19
ACGTcount: A:0.22, C:0.38, G:0.19, T:0.21
Consensus pattern (43 bp):
AGTGCATCCATGCACCCCTGCAGTGCATCCATGCACTCCCACT
Found at i:1067622 original size:21 final size:21
Alignment explanation
Indices: 1067578--1067723 Score: 190
Period size: 21 Copynumber: 7.0 Consensus size: 21
1067568 AATGCAATTA
***
1067578 GTGCATCGATGCATC-CTTCT
1 GTGCATCGATGCATCAAGGCT
1067598 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCAAGGCT
*
1067619 GTGCATCGATGCATCAAGGTT
1 GTGCATCGATGCATCAAGGCT
1067640 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCAAGGCT
1067661 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCAAGGCT
* **
1067682 GTGCATCAATGCATC-CTGCT
1 GTGCATCGATGCATCAAGGCT
*
1067702 GTGCATCCATGCA-CGAAGGCT
1 GTGCATCGATGCATC-AAGGCT
1067723 G
1 G
1067724 CAACGTCTAT
Statistics
Matches: 112, Mismatches: 11, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
19 1 0.01
20 30 0.27
21 81 0.72
ACGTcount: A:0.22, C:0.25, G:0.27, T:0.26
Consensus pattern (21 bp):
GTGCATCGATGCATCAAGGCT
Found at i:1067846 original size:21 final size:21
Alignment explanation
Indices: 1067817--1067856 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1067807 TTTGAGTAGA
1067817 AAAATCATCCCTAAACGGCTCC
1 AAAATCATCCC-AAACGGCTCC
*
1067839 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCAAACGGCT
1067857 ATATACAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 6 0.35
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCAAACGGCTCC
Found at i:1068418 original size:39 final size:39
Alignment explanation
Indices: 1068375--1068483 Score: 114
Period size: 37 Copynumber: 2.8 Consensus size: 39
1068365 AAATCCCAAC
* * *
1068375 AAACTATATATTATATACGTTTTCAAAAATATGTTTTCA
1 AAACTATATATTATATACATTTTCAAAAACATGCTTTCA
* *
1068414 AAACTATATA-T-TATACATTTTCAAAAGCGTGCTTTCA
1 AAACTATATATTATATACATTTTCAAAAACATGCTTTCA
* *
1068451 AAACCATATATATATATATATATATTCAAAAAC
1 AAA-C-TATATAT-TATATACATTTTCAAAAAC
1068484 CGTTTTTTAA
Statistics
Matches: 57, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
37 24 0.42
38 2 0.04
39 16 0.28
41 1 0.02
42 14 0.25
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.39
Consensus pattern (39 bp):
AAACTATATATTATATACATTTTCAAAAACATGCTTTCA
Found at i:1068540 original size:39 final size:38
Alignment explanation
Indices: 1068497--1068584 Score: 124
Period size: 39 Copynumber: 2.3 Consensus size: 38
1068487 TTTTTAAAAA
1068497 AAAAACTATATATTATAT-GCTTTCAAAAAACTATTTTC
1 AAAAACTATATATTATATAGCTTTCAAAAAA-TATTTTC
* **
1068535 TAAAAATTATATATTATATATTTTTCAAAAAATATTTTC
1 -AAAAACTATATATTATATAGCTTTCAAAAAATATTTTC
1068574 AAAAACTATAT
1 AAAAACTATAT
1068585 TATATTATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
38 10 0.23
39 24 0.55
40 10 0.23
ACGTcount: A:0.48, C:0.09, G:0.01, T:0.42
Consensus pattern (38 bp):
AAAAACTATATATTATATAGCTTTCAAAAAATATTTTC
Found at i:1068597 original size:124 final size:123
Alignment explanation
Indices: 1068375--1068602 Score: 273
Period size: 124 Copynumber: 1.8 Consensus size: 123
1068365 AAATCCCAAC
* *
1068375 AAACTATATATTATATACGTTTTCAAAAATATGTTTTCAAAACTATATATTATACATTTTCAAAA
1 AAACTATATATTATATA-GCTTTCAAAAATATGTTTTAAAAACTATATATTATACATTTTCAAAA
** *
1068440 GCGTGCTTTCAAAACCATATATATATATATATATATTCAAAAACCGTTTTTTAAAAAAA
65 GAATACTTTCAAAACCATATATATATATATATATATTCAAAAACCGTTTTTTAAAAAAA
* *
1068499 AAACTATATATTATAT-GCTTTCAAAAAACTAT-TTTCTAAAAATTATATATTATATATTTTTCA
1 AAACTATATATTATATAGCTTTC-AAAAA-TATGTTT-TAAAAACTATATATTATACA-TTTTCA
* *
1068562 AAA-AATATTTTCAAAAACTATATTATATTATTATATATATA
62 AAAGAATACTTTC-AAAACCATA-TATA-TA-TATATATATA
1068603 CTAAATAAAA
Statistics
Matches: 87, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
122 5 0.06
123 8 0.09
124 41 0.47
125 17 0.20
126 4 0.05
127 2 0.02
128 10 0.11
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (123 bp):
AAACTATATATTATATAGCTTTCAAAAATATGTTTTAAAAACTATATATTATACATTTTCAAAAG
AATACTTTCAAAACCATATATATATATATATATATTCAAAAACCGTTTTTTAAAAAAA
Found at i:1070000 original size:21 final size:22
Alignment explanation
Indices: 1069976--1070121 Score: 119
Period size: 21 Copynumber: 6.9 Consensus size: 22
1069966 GATTCGCAAC
1069976 GCGATT-TTCCAAATTCGCGTT
1 GCGATTATTCCAAATTCGCGTT
*
1069997 GCGATTTATTCCAAGTT--CGTT
1 GCGA-TTATTCCAAATTCGCGTT
* * *
1070018 GCGA-TAGTCGAAGTTCGCGTT
1 GCGATTATTCCAAATTCGCGTT
*
1070039 ACGATTTATTCCAAATT--CGTT
1 GCGA-TTATTCCAAATTCGCGTT
1070060 GCGATTTATTCCAAATTCGCGTT
1 GCGA-TTATTCCAAATTCGCGTT
* * *
1070083 GCGA-TAGTCGAAGTTCGCGTT
1 GCGATTATTCCAAATTCGCGTT
* *
1070104 GCGA-TAGTCCAAAATCGC
1 GCGATTATTCCAAATTCGC
1070122 AACGACTGGT
Statistics
Matches: 103, Mismatches: 14, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
19 9 0.09
21 68 0.66
22 2 0.02
23 24 0.23
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (22 bp):
GCGATTATTCCAAATTCGCGTT
Found at i:1070035 original size:42 final size:42
Alignment explanation
Indices: 1069983--1070121 Score: 156
Period size: 42 Copynumber: 3.3 Consensus size: 42
1069973 AACGCGATTT
1069983 TCCAAATTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAG
1 TCCAAATTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAG
* * * * *
1070025 TCGAAGTTCGCGTTACGATTTATTCCAAATTCGTTGCGATTTAT
1 TCCAAATTCGCGTTGCGATTTATTCCAAGTTCGTTGCGA--TAG
* *
1070069 TCCAAATTCGCGTTGCGA--TAGTCGAAGTTCGCGTTGCGATAG
1 TCCAAATTCGCGTTGCGATTTATTCCAAGTT--CGTTGCGATAG
*
1070111 TCCAAAATCGC
1 TCCAAATTCGC
1070122 AACGACTGGT
Statistics
Matches: 80, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
42 55 0.69
44 25 0.31
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.34
Consensus pattern (42 bp):
TCCAAATTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAG
Found at i:1070089 original size:65 final size:64
Alignment explanation
Indices: 1069982--1070108 Score: 202
Period size: 65 Copynumber: 2.0 Consensus size: 64
1069972 CAACGCGATT
*
1069982 TTCCAAATTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTACGATTTA
1 TTCCAAATTC-CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTACGATTTA
*
1070047 TTCCAAATT-CGTTGCGATTTATTCCAAATTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGAT
1 TTCCAAATTCCGTTGCGATTTATTCCAAATT--CGTTGCGATAGTCGAAGTTCGCGTTACGAT
1070109 AGTCCAAAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
63 20 0.34
65 38 0.66
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.36
Consensus pattern (64 bp):
TTCCAAATTCCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTACGATTTA
Found at i:1071000 original size:21 final size:19
Alignment explanation
Indices: 1070974--1071024 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
1070964 ATTTTGGACT
*
1070974 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTAG-A-AA
1070995 ATCGCAACGCGAATTTAGAAA
1 ATCGCAA--CGAATTTAGAAA
1071016 ATCGCAACG
1 ATCGCAACG
1071025 CGAACTTCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 2 0.07
21 16 0.59
22 1 0.04
23 8 0.30
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.20
Consensus pattern (19 bp):
ATCGCAACGAATTTAGAAA
Found at i:1071025 original size:21 final size:20
Alignment explanation
Indices: 1070993--1071089 Score: 86
Period size: 21 Copynumber: 4.7 Consensus size: 20
1070983 AATTTGGAAT
1070993 AAATCGCAACGCGAATTTAGA
1 AAATCGCAACGCGAATTT-GA
*
1071014 AAATCGCAACGCGAACTTCGA
1 AAATCGCAACGCGAA-TTTGA
**
1071035 CTATCGCAACGCGAACTTTGA
1 AAATCGCAACGCGAA-TTTGA
** * * *
1071056 TTATCGCAATGCGAATATGT
1 AAATCGCAACGCGAATTTGA
*
1071076 AAATCGCAATGCGA
1 AAATCGCAACGCGA
1071090 TAGTCGAAGT
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
20 15 0.23
21 48 0.74
22 2 0.03
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.22
Consensus pattern (20 bp):
AAATCGCAACGCGAATTTGA
Found at i:1072146 original size:34 final size:34
Alignment explanation
Indices: 1072106--1072174 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
1072096 CACATTTTCA
* *
1072106 ACTTTTAATCTCAACTATCACTTAACACTGATTC
1 ACTTTTAATCTCAACTATCACTCAACACTAATTC
1072140 ACTTTTAATCTCAACTATCACTCAACACTAATTC
1 ACTTTTAATCTCAACTATCACTCAACACTAATTC
1072174 A
1 A
1072175 ATGGTCCTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.35, C:0.28, G:0.01, T:0.36
Consensus pattern (34 bp):
ACTTTTAATCTCAACTATCACTCAACACTAATTC
Found at i:1072318 original size:21 final size:21
Alignment explanation
Indices: 1072285--1072339 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
1072275 GAATGGTTTC
*
1072285 CAAAGTTGACATCTTTATAAA
1 CAAAGCTGACATCTTTATAAA
*
1072306 CAAAGCTGGCATCTTTATAAA
1 CAAAGCTGACATCTTTATAAA
1072327 CAAAGCTTGACAT
1 CAAAGC-TGACAT
1072340 AAGCCAAACC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 25 0.83
22 5 0.17
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (21 bp):
CAAAGCTGACATCTTTATAAA
Found at i:1074898 original size:7 final size:7
Alignment explanation
Indices: 1074886--1074927 Score: 66
Period size: 7 Copynumber: 5.9 Consensus size: 7
1074876 GTATTATTTT
1074886 TTAAAAA
1 TTAAAAA
1074893 TTAAAAA
1 TTAAAAA
1074900 TTAAAAA
1 TTAAAAA
1074907 TTATAAAA
1 TTA-AAAA
*
1074915 TTAAATA
1 TTAAAAA
1074922 TTAAAA
1 TTAAAA
1074928 TAAAACAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
7 25 0.78
8 7 0.22
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (7 bp):
TTAAAAA
Found at i:1084044 original size:20 final size:20
Alignment explanation
Indices: 1083999--1084044 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
1083989 GACCAACAAA
*
1083999 ATCGCAATGCGATCGCTAAT
1 ATCGCAACGCGATCGCTAAT
* *
1084019 -TCGCAACGCGATCTCTATT
1 ATCGCAACGCGATCGCTAAT
1084038 ATCGCAA
1 ATCGCAA
1084045 ATTCGCGTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATCGCTAAT
Found at i:1084148 original size:20 final size:21
Alignment explanation
Indices: 1084123--1084215 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
1084113 TTTTCCCAAT
*
1084123 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1084143 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
1084164 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1084184 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1084205 TCGCAATGCGA
1 TCGCAATGCGA
1084216 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1084168 original size:41 final size:41
Alignment explanation
Indices: 1084123--1084215 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
1084113 TTTTCCCAAT
1084123 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1084164 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1084205 TCGCAATGCGA
1 TCGCAATGCGA
1084216 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Done.