Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005853.1 Hibiscus syriacus cultivar Beakdansim tig00013738_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: 876857
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 5
Found at i:527977 original size:11 final size:12
Alignment explanation
Indices: 527925--527974 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
527915 ATCAATCCAT
527925 ATTTTAAAATAA
1 ATTTTAAAATAA
** *
527937 A--TTAATCTAT
1 ATTTTAAAATAA
527947 ATTTTAAAATAA
1 ATTTTAAAATAA
*
527959 ATTTTAAAATAG
1 ATTTTAAAATAA
527971 ATTT
1 ATTT
527975 AAATGATTTT
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
10 7 0.24
12 22 0.76
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (12 bp):
ATTTTAAAATAA
Found at i:530529 original size:54 final size:53
Alignment explanation
Indices: 530471--531059 Score: 820
Period size: 54 Copynumber: 10.9 Consensus size: 53
530461 GGTGCACAAG
* * * * *
530471 TAGTGTCGTTACGGTCATTCATAAGCTCATTATGAATGTCGTGGGTTGCACACA
1 TAGTGTCGATACGGTCGTTCATAAACTTATTATGAAT-TCGTGGGTTGCACACT
* * * *
530525 TAGTGCCGCTACGGTTGTTCATAAACTTATTATGAATTTCTTGGGTTGCACACT
1 TAGTGTCGATACGGTCGTTCATAAACTTATTATGAA-TTCGTGGGTTGCACACT
530579 TAGTGTCGATACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTTGCACACT
1 TAGTGTCGATACGGTCGTTCATAAACTTATTATGAATTC-GTGGGTTGCACACT
530633 TAGTGTCGATACGGTCGTTCATAAACTTATTATGAATTACGTGGGTTGCACACT
1 TAGTGTCGATACGGTCGTTCATAAACTTATTATGAATT-CGTGGGTTGCACACT
* **
530687 TAGTGCCGATACACTCGTTCATAAACTTATTATGAATTTCGTGGGTTGCACACT
1 TAGTGTCGATACGGTCGTTCATAAACTTATTATGAA-TTCGTGGGTTGCACACT
*
530741 TAGTGTCGATACAGTCGTTCATAAACTTATTATGAATTCCGTGGGTTGCACACT
1 TAGTGTCGATACGGTCGTTCATAAACTTATTATGAATT-CGTGGGTTGCACACT
* **
530795 TAGTTTCGATACACTCGTTCATAAACTTATTATGAATTCCGTGGGTTGCACACT
1 TAGTGTCGATACGGTCGTTCATAAACTTATTATGAATT-CGTGGGTTGCACACT
* * *
530849 TAGTGTCGATACAGTCGTTCATAAACTTATTATGAATTCTGTGGGTTGAACACA
1 TAGTGTCGATACGGTCGTTCATAAACTTATTATGAATTC-GTGGGTTGCACACT
* * *
530903 TAGT-ACTGATACGATTGTTCATAAACTTATTATGAATTACGTGGGTTGCACACT
1 TAGTGTC-GATACGGTCGTTCATAAACTTATTATGAATT-CGTGGGTTGCACACT
* *
530957 TAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTTGCACACA
1 TAGTGTCGATACGGTCGTTCATAAACTTATTATGAATTC-GTGGGTTGCACACT
* * *
531011 TAATGCCGATACGGTCGTTCATAAACTTATTATGAATTTCGTGCGTTGC
1 TAGTGTCGATACGGTCGTTCATAAACTTATTATGAA-TTCGTGGGTTGC
531060 GCTCATAGTG
Statistics
Matches: 489, Mismatches: 35, Indels: 22
0.90 0.06 0.04
Matches are distributed among these distances:
53 8 0.02
54 472 0.97
55 9 0.02
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.36
Consensus pattern (53 bp):
TAGTGTCGATACGGTCGTTCATAAACTTATTATGAATTCGTGGGTTGCACACT
Found at i:530606 original size:27 final size:27
Alignment explanation
Indices: 530576--530661 Score: 70
Period size: 27 Copynumber: 3.2 Consensus size: 27
530566 TGGGTTGCAC
530576 ACTTAGTGTCGATACGGTCGTTCATAA
1 ACTTAGTGTCGATACGGTCGTTCATAA
* * * * * *
530603 ACTTATTAT-GAATTCTGTGGGTTGC--AC
1 ACTTAGTGTCG-ATACGGT-CGTT-CATAA
530630 ACTTAGTGTCGATACGGTCGTTCATAA
1 ACTTAGTGTCGATACGGTCGTTCATAA
530657 ACTTA
1 ACTTA
530662 TTATGAATTA
Statistics
Matches: 41, Mismatches: 12, Indels: 12
0.63 0.18 0.18
Matches are distributed among these distances:
25 1 0.02
26 4 0.10
27 31 0.76
28 4 0.10
29 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (27 bp):
ACTTAGTGTCGATACGGTCGTTCATAA
Found at i:530795 original size:27 final size:27
Alignment explanation
Indices: 530765--530850 Score: 65
Period size: 27 Copynumber: 3.2 Consensus size: 27
530755 TCGTTCATAA
530765 ACTTATTATGAATTCCGTGGGTTGCAC
1 ACTTATTATGAATTCCGTGGGTTGCAC
* * *
530792 ACTTAGTT-TCG-ATACAC-T-CGTT-CATAA
1 ACTTA-TTAT-GAATTC-CGTGGGTTGC--AC
530819 ACTTATTATGAATTCCGTGGGTTGCAC
1 ACTTATTATGAATTCCGTGGGTTGCAC
530846 ACTTA
1 ACTTA
530851 GTGTCGATAC
Statistics
Matches: 43, Mismatches: 6, Indels: 20
0.62 0.09 0.29
Matches are distributed among these distances:
25 1 0.02
26 7 0.16
27 27 0.63
28 7 0.16
29 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (27 bp):
ACTTATTATGAATTCCGTGGGTTGCAC
Found at i:532847 original size:24 final size:23
Alignment explanation
Indices: 532810--532873 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
532800 TTATTTTCGT
* *
532810 GAACATGTTCATTTATATATTCAC
1 GAACGTGTTCATTTA-ACATTCAC
* *
532834 GATCGTGTTCATTTAGCATTCAC
1 GAACGTGTTCATTTAACATTCAC
*
532857 GAACGTGTTTATTTAAC
1 GAACGTGTTCATTTAAC
532874 GTTTATGAAC
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
23 20 0.61
24 13 0.39
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (23 bp):
GAACGTGTTCATTTAACATTCAC
Found at i:534622 original size:66 final size:66
Alignment explanation
Indices: 534498--534622 Score: 169
Period size: 66 Copynumber: 1.9 Consensus size: 66
534488 CGGAGTACAT
* * * * * *
534498 GTGAACACCGGGAAAGGAAAGGCAGGGGGTGGCACCCATGTGAACGTTGGCGGCAAAGGAGTTGG
1 GTGAACACCGGGAAAGGAAAGCCAGGAGATGGCACCCATGTCAACGTCGGAGGCAAAGGAGTTGG
534563 A
66 A
* * *
534564 GTGAACACTGGGAAAGGAAAGCCAGGAGATGGCACTCATGTCAACGTCGGAGGTAAAGG
1 GTGAACACCGGGAAAGGAAAGCCAGGAGATGGCACCCATGTCAACGTCGGAGGCAAAGG
534623 TGGAGGAGTA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
66 50 1.00
ACGTcount: A:0.31, C:0.17, G:0.39, T:0.13
Consensus pattern (66 bp):
GTGAACACCGGGAAAGGAAAGCCAGGAGATGGCACCCATGTCAACGTCGGAGGCAAAGGAGTTGG
A
Found at i:536758 original size:20 final size:21
Alignment explanation
Indices: 536718--536759 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
536708 TGGATTATTT
* *
536718 AAAATTTTATTTTGACTAATA
1 AAAAATTTATTTTGACAAATA
536739 AAAAATTTATTTTGA-AAATA
1 AAAAATTTATTTTGACAAATA
536759 A
1 A
536760 TTATCCACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (21 bp):
AAAAATTTATTTTGACAAATA
Found at i:539062 original size:91 final size:91
Alignment explanation
Indices: 538907--539089 Score: 285
Period size: 91 Copynumber: 2.0 Consensus size: 91
538897 CCTAGAACAC
* *
538907 CCATGTGCCTTGCATATGACCAGCCTCCACGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCACGTGCCTTGCATGTGGATCATTTAGGCACCAAGATG
538972 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGTTCTCTCCCTATTCGGCCAAG
** * * * *
538998 CCATGTGTTTTGCATGTGATCAGCCCCCATGTGCCTTGCATGTGGTTCATTTAGGCACCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCACGTGCCTTGCATGTGGATCATTTAGGCACCAAGATG
*
539063 AAGAGTTCTCTCCTTATTCGGCCAAG
66 AAGAGTTCTCTCCCTATTCGGCCAAG
539089 C
1 C
539090 ATTAACTGCC
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
91 83 1.00
ACGTcount: A:0.20, C:0.28, G:0.23, T:0.29
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGACCAGCCCCCACGTGCCTTGCATGTGGATCATTTAGGCACCAAGATG
AAGAGTTCTCTCCCTATTCGGCCAAG
Found at i:539894 original size:28 final size:27
Alignment explanation
Indices: 539862--539919 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
539852 AAAAATCAGA
* * *
539862 AAAGAAATTGAAGCACTCCAAAAGAAAG
1 AAAGAAAATCAAGCACTCAAAAAG-AAG
*
539890 AAAGAAAATCTAGCACTCAAAAAGAAG
1 AAAGAAAATCAAGCACTCAAAAAGAAG
539917 AAA
1 AAA
539920 AACAAAGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 6 0.23
28 20 0.77
ACGTcount: A:0.60, C:0.14, G:0.16, T:0.10
Consensus pattern (27 bp):
AAAGAAAATCAAGCACTCAAAAAGAAG
Found at i:543445 original size:91 final size:91
Alignment explanation
Indices: 543285--543467 Score: 278
Period size: 91 Copynumber: 2.0 Consensus size: 91
543275 CCTAGAACAC
*
543285 CCATGTGCCTTGCATATGACCAGCCTCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATA
1 CCATGTGCCTTGCATATGACCAGCCTCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATA
543350 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGTTCTCTCCCTATTCGGCCAAG
** * * *
543376 CCATGTGTTTTGCATGTGATCAG-CTCCCATGTGCCTTGCATGTGGTTCATTTAGGCACCAAGAT
1 CCATGTGCCTTGCATATGACCAGCCT-CCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGAT
* *
543440 GAAGAGTTCTCTCCTTATTCGGCCAAG
65 AAAGAGTTCTCTCCCTATTCGGCCAAG
543467 C
1 C
543468 ATTAACTGCC
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
90 2 0.02
91 81 0.98
ACGTcount: A:0.21, C:0.27, G:0.22, T:0.30
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGACCAGCCTCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATA
AAGAGTTCTCTCCCTATTCGGCCAAG
Found at i:550066 original size:2 final size:2
Alignment explanation
Indices: 550001--550048 Score: 80
Period size: 2 Copynumber: 24.0 Consensus size: 2
549991 GGTACCTATT
550001 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TAC -C TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T-C TC TC TC
550043 TC TC TC
1 TC TC TC
550049 CCTCCTTCCG
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 42 0.95
3 1 0.02
ACGTcount: A:0.02, C:0.50, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:552163 original size:6 final size:6
Alignment explanation
Indices: 552152--552181 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
552142 CCAGCCCTTC
552152 CCATCT CCATCT CCATCT CCATCT CCATCT
1 CCATCT CCATCT CCATCT CCATCT CCATCT
552182 TTTGTTTCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.50, G:0.00, T:0.33
Consensus pattern (6 bp):
CCATCT
Found at i:558117 original size:15 final size:15
Alignment explanation
Indices: 558092--558127 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
558082 GTTAAGAAAG
*
558092 AAAACAAAATAAATA
1 AAAATAAAATAAATA
*
558107 ATAATAAAATAAATA
1 AAAATAAAATAAATA
558122 AAAATA
1 AAAATA
558128 TACAAAATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAATAAAATAAATA
Found at i:558134 original size:19 final size:19
Alignment explanation
Indices: 558098--558135 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
558088 AAAGAAAACA
*
558098 AAATAAATAATAATAAAAT
1 AAATAAATAATAACAAAAT
558117 AAATAAA-AATATACAAAAT
1 AAATAAATAATA-ACAAAAT
558136 TAGAAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (19 bp):
AAATAAATAATAACAAAAT
Found at i:565678 original size:2 final size:2
Alignment explanation
Indices: 565671--565713 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
565661 ATGGATTGCT
565671 TA TA TA TA -A TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
565713 T
1 T
565714 TTAGTATTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.03
2 36 0.92
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:565774 original size:2 final size:2
Alignment explanation
Indices: 565767--565797 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
565757 TCAATCTACA
565767 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
565798 AAATTTACGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:565980 original size:13 final size:12
Alignment explanation
Indices: 565962--566024 Score: 54
Period size: 13 Copynumber: 4.9 Consensus size: 12
565952 GCTCAATGAA
565962 CGTCATAAATTAG
1 CGTCATAAATT-G
*
565975 CGTCATTAATGTG
1 CGTCATAAAT-TG
*
565988 TGTCATAAATGTG
1 CGTCATAAAT-TG
* *
566001 TGTCATAAATGCG
1 CGTCATAAAT-TG
566014 CGTCATAAATT
1 CGTCATAAATT
566025 TATGACGCAC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
13 42 0.98
14 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (12 bp):
CGTCATAAATTG
Found at i:565980 original size:85 final size:85
Alignment explanation
Indices: 565817--565980 Score: 197
Period size: 85 Copynumber: 1.9 Consensus size: 85
565807 AAATACAATC
* * * * *
565817 ATGATACACGAATGTGTGTCATCTTTTTTAATGACGTGTGCTTCAATGACACGCAATGTAAGTCA
1 ATGACACACAAATGTGTGTCATCTTATTTAATGACGGGGGCTTCAATGACACGCAATGTAAGTCA
* * *
565882 TACATGCGTGTCATATATTT
66 TAAATGAGCGTCATATATTT
* *
565902 ATGACACACAAATGTGTGTCATCTTAATTT-ATGACGGGGGCTTCAATGACGCTCAATG-AACGT
1 ATGACACACAAATGTGTGTCATCTT-ATTTAATGACGGGGGCTTCAATGACACGCAATGTAA-GT
*
565965 CATAAATTAGCGTCAT
64 CATAAATGAGCGTCAT
565981 TAATGTGTGT
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
84 2 0.03
85 61 0.92
86 3 0.05
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Consensus pattern (85 bp):
ATGACACACAAATGTGTGTCATCTTATTTAATGACGGGGGCTTCAATGACACGCAATGTAAGTCA
TAAATGAGCGTCATATATTT
Found at i:565992 original size:26 final size:25
Alignment explanation
Indices: 565962--566024 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
565952 GCTCAATGAA
* *
565962 CGTCATAAATTAGCGTCATTAATGTG
1 CGTCATAAATT-GCGTCATAAATGCG
* *
565988 TGTCATAAATGTGTGTCATAAATGCG
1 CGTCATAAAT-TGCGTCATAAATGCG
566014 CGTCATAAATT
1 CGTCATAAATT
566025 TATGACGCAC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
25 1 0.03
26 29 0.94
27 1 0.03
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (25 bp):
CGTCATAAATTGCGTCATAAATGCG
Found at i:566172 original size:21 final size:21
Alignment explanation
Indices: 566148--566219 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 21
566138 TTTTCTACTA
566148 GTGATGACTGGTTATCTGAGG
1 GTGATGACTGGTTATCTGAGG
* * * *
566169 GTGATAACACGGTTCCTACGTGATGA
1 GTGATGAC-TGGTT-AT-C-TGA-GG
566195 G-GATGACTGGTTATCTGAGG
1 GTGATGACTGGTTATCTGAGG
566215 GTGAT
1 GTGAT
566220 AACACGGTTC
Statistics
Matches: 37, Mismatches: 8, Indels: 12
0.65 0.14 0.21
Matches are distributed among these distances:
20 2 0.05
21 13 0.35
22 5 0.14
23 2 0.05
24 5 0.14
25 8 0.22
26 2 0.05
ACGTcount: A:0.22, C:0.12, G:0.35, T:0.31
Consensus pattern (21 bp):
GTGATGACTGGTTATCTGAGG
Found at i:566228 original size:22 final size:22
Alignment explanation
Indices: 566157--566228 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
566147 AGTGATGACT
566157 GGTTATCTGAGGGTGATAACAC
1 GGTTATCTGAGGGTGATAACAC
* * * *
566179 GGTTCCTACGTGATGAG-GATGAC-T
1 GGTT-AT-C-TGA-GGGTGATAACAC
566203 GGTTATCTGAGGGTGATAACAC
1 GGTTATCTGAGGGTGATAACAC
566225 GGTT
1 GGTT
566229 CCTACGTGAT
Statistics
Matches: 36, Mismatches: 8, Indels: 12
0.64 0.14 0.21
Matches are distributed among these distances:
20 2 0.06
21 8 0.22
22 9 0.25
23 2 0.06
24 5 0.14
25 8 0.22
26 2 0.06
ACGTcount: A:0.24, C:0.14, G:0.33, T:0.29
Consensus pattern (22 bp):
GGTTATCTGAGGGTGATAACAC
Found at i:566276 original size:93 final size:88
Alignment explanation
Indices: 566150--566334 Score: 253
Period size: 93 Copynumber: 2.0 Consensus size: 88
566140 TTCTACTAGT
* * *
566150 GATGACTGGTTATCTGAGGGTGATAACACGGTTCCTACGTGATGAGGATGACTGGTTATCTGAGG
1 GATGACTAGTTATCTAAGGGTGATAACACGGTTCCTACGTGATAAGGATGACTGGTTATCT-AGG
* *
566215 GTGATAACACGGTTCCTACGTGATGAG
65 GTG---ACACGATTCCTACGCGATGAG
* *
566242 GATGACTAGTTATCTAAAGGGTGATAACATGGTTCCTACGTTATAAGGATGACTGGTTATCTAGG
1 GATGACTAGTTATCT-AAGGGTGATAACACGGTTCCTACGTGATAAGGATGACTGGTTATCTAGG
*
566307 GTGACACGATTCCTATGCGATGAG
65 GTGACACGATTCCTACGCGATGAG
566331 GATG
1 GATG
566335 GATGGTCGGT
Statistics
Matches: 84, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
89 22 0.26
92 20 0.24
93 42 0.50
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.29
Consensus pattern (88 bp):
GATGACTAGTTATCTAAGGGTGATAACACGGTTCCTACGTGATAAGGATGACTGGTTATCTAGGG
TGACACGATTCCTACGCGATGAG
Found at i:566281 original size:47 final size:46
Alignment explanation
Indices: 566150--566334 Score: 261
Period size: 46 Copynumber: 4.1 Consensus size: 46
566140 TTCTACTAGT
566150 GATGACTGGTTATCTGAGGGTGATAACACGGTTCCTACGTGATGAG
1 GATGACTGGTTATCTGAGGGTGATAACACGGTTCCTACGTGATGAG
566196 GATGACTGGTTATCTGAGGGTGATAACACGGTTCCTACGTGATGAG
1 GATGACTGGTTATCTGAGGGTGATAACACGGTTCCTACGTGATGAG
* * * * *
566242 GATGACTAGTTATCTAAAGGGTGATAACATGGTTCCTACGTTATAAG
1 GATGACTGGTTATCT-GAGGGTGATAACACGGTTCCTACGTGATGAG
* * *
566289 GATGACTGGTTATCT-AGGGTG---ACACGATTCCTATGCGATGAG
1 GATGACTGGTTATCTGAGGGTGATAACACGGTTCCTACGTGATGAG
566331 GATG
1 GATG
566335 GATGGTCGGT
Statistics
Matches: 126, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
42 19 0.15
45 6 0.05
46 60 0.48
47 41 0.33
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.29
Consensus pattern (46 bp):
GATGACTGGTTATCTGAGGGTGATAACACGGTTCCTACGTGATGAG
Found at i:572926 original size:15 final size:15
Alignment explanation
Indices: 572882--572927 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
572872 GTTAAGAAAG
*
572882 AAAACAAA-ACAAAAC
1 AAAACAAATA-AAAAT
572897 AAAACAAATAAAAAT
1 AAAACAAATAAAAAT
*
572912 AAAATAAATAAAAAT
1 AAAACAAATAAAAAT
572927 A
1 A
572928 TAAAAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 27 0.96
16 1 0.04
ACGTcount: A:0.80, C:0.09, G:0.00, T:0.11
Consensus pattern (15 bp):
AAAACAAATAAAAAT
Found at i:578077 original size:15 final size:14
Alignment explanation
Indices: 578051--578081 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
578041 TATCTAGAAG
578051 CTTATTTCCTTCTT
1 CTTATTTCCTTCTT
578065 CTTATTCTCCTTCTT
1 CTTATT-TCCTTCTT
578080 CT
1 CT
578082 CCCCGTAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.06, C:0.32, G:0.00, T:0.61
Consensus pattern (14 bp):
CTTATTTCCTTCTT
Found at i:578678 original size:64 final size:63
Alignment explanation
Indices: 578558--578678 Score: 145
Period size: 64 Copynumber: 1.9 Consensus size: 63
578548 CACATTCAAA
* * *
578558 GTGCATCGATGCACCCTTTAAAGAATAAACATCGAATGCAATTAGTGCATCAATGCATAAGGC
1 GTGCATCGATGCACCCTTGAAACAATAAACATCGAATGCAATTAGTGCACCAATGCATAAGGC
* * * * *
578621 GTGCATCGATGCATTCCCTTGATACAA-AAACATCGAATGTATTTTGTGCACCGATGCA
1 GTGCATCGATGCA--CCCTTGAAACAATAAACATCGAATGCAATTAGTGCACCAATGCA
578679 CCATCGATGC
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
63 13 0.27
64 26 0.54
65 9 0.19
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.26
Consensus pattern (63 bp):
GTGCATCGATGCACCCTTGAAACAATAAACATCGAATGCAATTAGTGCACCAATGCATAAGGC
Found at i:579578 original size:23 final size:22
Alignment explanation
Indices: 579543--579616 Score: 87
Period size: 23 Copynumber: 3.3 Consensus size: 22
579533 TAAGGACATT
579543 ATTATA-TGGCACTACGGTGCA
1 ATTATACTGGCACTACGGTGCA
* *
579564 ATTATACTCGGCACTCCGGAGCA
1 ATTATACT-GGCACTACGGTGCA
* *
579587 ATTCTACGTGGCACTTCGGTGCA
1 ATTATAC-TGGCACTACGGTGCA
579610 ATTATAC
1 ATTATAC
579617 GAGCTGTGGT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
21 6 0.14
22 1 0.02
23 36 0.82
24 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (22 bp):
ATTATACTGGCACTACGGTGCA
Found at i:583663 original size:15 final size:14
Alignment explanation
Indices: 583637--583667 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
583627 TATCTAGAAG
583637 CTTATTTCCTTCTT
1 CTTATTTCCTTCTT
583651 CTTATTCTCCTTCTT
1 CTTATT-TCCTTCTT
583666 CT
1 CT
583668 CCCCGTAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.06, C:0.32, G:0.00, T:0.61
Consensus pattern (14 bp):
CTTATTTCCTTCTT
Found at i:585169 original size:23 final size:23
Alignment explanation
Indices: 585138--585203 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
585128 TATTATATGG
585138 CACTACGGTGCAATTATACGCGA
1 CACTACGGTGCAATTATACGCGA
* * * *
585161 CACTCCGGTGCAATTCTATGTGA
1 CACTACGGTGCAATTATACGCGA
*
585184 CACTTCGGTGCAATTATACG
1 CACTACGGTGCAATTATACG
585204 AGCTGTGGTG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (23 bp):
CACTACGGTGCAATTATACGCGA
Found at i:587686 original size:25 final size:25
Alignment explanation
Indices: 587654--587711 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
587644 AGACATATAT
*
587654 TTGCACTCGAAAATGTCTTGTAGTA
1 TTGCACTCGAAAATGTCGTGTAGTA
* *
587679 TTGCACTCGAAAGTGTCGTGTAGTG
1 TTGCACTCGAAAATGTCGTGTAGTA
587704 TTGCACTC
1 TTGCACTC
587712 AAAGTGCCTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.34
Consensus pattern (25 bp):
TTGCACTCGAAAATGTCGTGTAGTA
Found at i:587725 original size:24 final size:24
Alignment explanation
Indices: 587654--587725 Score: 74
Period size: 25 Copynumber: 2.9 Consensus size: 24
587644 AGACATATAT
* *
587654 TTGCACTCGAAAATGTCTTGTAGTA
1 TTGCACTCGAAAGTG-CCTGTAGTA
* *
587679 TTGCACTCGAAAGTGTCGTGTAGTG
1 TTGCACTCGAAAGTG-CCTGTAGTA
587704 TTGCACTC-AAAGTGCCTCGTAG
1 TTGCACTCGAAAGTGCCT-GTAG
587726 GATTCATACC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
23 2 0.05
24 10 0.24
25 30 0.71
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (24 bp):
TTGCACTCGAAAGTGCCTGTAGTA
Found at i:590027 original size:22 final size:23
Alignment explanation
Indices: 589984--590029 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
589974 TATGTTTGGG
* **
589984 TTGGTTTGGCAGGAATGTAAGAT
1 TTGGTTTGGAAGGAATAAAAGAT
590007 TTGGTTT-GAAGGAATAAAAGAT
1 TTGGTTTGGAAGGAATAAAAGAT
590029 T
1 T
590030 ATTGGAATGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.33, C:0.02, G:0.30, T:0.35
Consensus pattern (23 bp):
TTGGTTTGGAAGGAATAAAAGAT
Found at i:591080 original size:202 final size:199
Alignment explanation
Indices: 590665--591080 Score: 744
Period size: 202 Copynumber: 2.1 Consensus size: 199
590655 CCGTCTTTTT
*
590665 TATTTCAATTTTTGGTTTTTCAGTATAGTTCTTCGGATTTCCAATTTTATAACCACTAGATTAGT
1 TATTTCAATTTTTGGTTTTTCAGTATAATTCTTCGGATTTCCAATTTTATAACCACTAGATTAGT
590730 CGACTCTCAATTGAAATAGTTCGATTGATCGAATTAAGACCCTATTAACAACGAACCTAAAAGAA
66 CGACTCTCAATTGAAATAGTTCGATTGATCGAATTAAGACCCTATTAACAACGAACCTAAAAGAA
590795 CTTGCTCATCCGATTTTCCTATTTCAATGTTTGGTTTTGGTTTTGAAGTTGCTCACAACAATTCT
131 CTTGCTCATCCGATTTTCCTATTTCAATGTTTGGTTTTGGTTTTGAAGTTGCTCACAACAATTCT
590860 TCAA
196 TCAA
*
590864 TTTTATTTCAATTTTTGGTTTTTCAGTATAATTCTTCTGATTTCCAATTTTATAACCACTAGATT
1 ---TATTTCAATTTTTGGTTTTTCAGTATAATTCTTCGGATTTCCAATTTTATAACCACTAGATT
590929 AGTCGACTCTCAATTGAAATAGTTCGATTGATCGAATTAAAGACCCTATTAACAACGAACCTAAA
63 AGTCGACTCTCAATTGAAATAGTTCGATTGATCGAATT-AAGACCCTATTAACAACGAACCT-AA
590994 AAGAACTTGCTCATCCGATTTTTCCTATTTCAATGTTTGGTTTTGGTTTTGAAGTTGCTCACAAC
126 AAGAACTTGCTCATCCGA-TTTTCCTATTTCAATGTTTGGTTTTGGTTTTGAAGTTGCTCACAAC
591059 AATTCTTCAA
190 AATTCTTCAA
591069 -ATTTCCAATTTT
1 TATTT-CAATTTT
591081 AGACAGATGA
Statistics
Matches: 208, Mismatches: 2, Indels: 8
0.95 0.01 0.04
Matches are distributed among these distances:
201 4 0.02
202 105 0.50
203 23 0.11
204 20 0.10
205 56 0.27
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (199 bp):
TATTTCAATTTTTGGTTTTTCAGTATAATTCTTCGGATTTCCAATTTTATAACCACTAGATTAGT
CGACTCTCAATTGAAATAGTTCGATTGATCGAATTAAGACCCTATTAACAACGAACCTAAAAGAA
CTTGCTCATCCGATTTTCCTATTTCAATGTTTGGTTTTGGTTTTGAAGTTGCTCACAACAATTCT
TCAA
Found at i:599255 original size:24 final size:24
Alignment explanation
Indices: 599228--599278 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
599218 GTGTTATATA
599228 AATGTGAAATATTGTAGTGTGAAC
1 AATGTGAAATATTGTAGTGTGAAC
599252 AATGTGAAATATTGTAGTGTGAAC
1 AATGTGAAATATTGTAGTGTGAAC
599276 AAT
1 AAT
599279 ATGACAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.33
Consensus pattern (24 bp):
AATGTGAAATATTGTAGTGTGAAC
Found at i:599612 original size:32 final size:33
Alignment explanation
Indices: 599571--599696 Score: 131
Period size: 31 Copynumber: 4.0 Consensus size: 33
599561 AGGGTCGAGG
599571 GTTACCTATG-TCTTTCGAGACATATGGACAGT
1 GTTACCTATGTTCTTTCGAGACATATGGACAGT
*
599603 GTTACCTATG-TCCTTCG-GACATATGGACAG-
1 GTTACCTATGTTCTTTCGAGACATATGGACAGT
*** *
599633 GATTACCTATGTTCTAAGGA-ACATATGGACAAT
1 G-TTACCTATGTTCTTTCGAGACATATGGACAGT
* *
599666 -TTACCTATGTTCTTT-GGGACCTATGGACAGT
1 GTTACCTATGTTCTTTCGAGACATATGGACAGT
599697 TGCTGAGGTT
Statistics
Matches: 78, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
30 2 0.03
31 46 0.59
32 30 0.38
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.33
Consensus pattern (33 bp):
GTTACCTATGTTCTTTCGAGACATATGGACAGT
Found at i:600889 original size:20 final size:20
Alignment explanation
Indices: 600864--600908 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
600854 ATACAAGCCC
600864 TTACAAAAACATAAATAAAA
1 TTACAAAAACATAAATAAAA
600884 TTACAAAAACATAAATAAAA
1 TTACAAAAACATAAATAAAA
*
600904 ATACA
1 TTACA
600909 GACACTGCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.69, C:0.11, G:0.00, T:0.20
Consensus pattern (20 bp):
TTACAAAAACATAAATAAAA
Found at i:602357 original size:20 final size:20
Alignment explanation
Indices: 602332--602405 Score: 114
Period size: 20 Copynumber: 3.7 Consensus size: 20
602322 TGACCAACAA
602332 TTCGCAACGCGAATTCCAAT
1 TTCGCAACGCGAATTCCAAT
602352 TTCGCAACGCGAATTCCAAT
1 TTCGCAACGCGAATTCCAAT
* *
602372 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGA-ATTCCAAT
602392 TTCGCAACGCGAAT
1 TTCGCAACGCGAAT
602406 ATGTAAATCG
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.04
20 44 0.92
21 2 0.04
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (20 bp):
TTCGCAACGCGAATTCCAAT
Found at i:602416 original size:20 final size:21
Alignment explanation
Indices: 602392--602524 Score: 79
Period size: 20 Copynumber: 6.6 Consensus size: 21
602382 AGTTTCCAAT
602392 TTCGCAACGCGAATATGTAAA
1 TTCGCAACGCGAATATGTAAA
** * * **
602413 -TCGCATTGCGATTTTCCAAA
1 TTCGCAACGCGAATATGTAAA
602433 TTCGCAACGCGAA-A-G-ACAA
1 TTCGCAACGCGAATATGTA-AA
*
602452 TTCGCAACGCGAATTTGTAAA
1 TTCGCAACGCGAATATGTAAA
*
602473 -TCGCAACAC-AGA-A-GTCAAA
1 TTCGCAACGCGA-ATATGT-AAA
602492 TTCGCAACGCG-ATA-GTCAAA
1 TTCGCAACGCGAATATGT-AAA
*
602512 TTCGCAACACGAA
1 TTCGCAACGCGAA
602525 AGTCAAATGT
Statistics
Matches: 85, Mismatches: 16, Indels: 22
0.69 0.13 0.18
Matches are distributed among these distances:
18 3 0.04
19 20 0.24
20 48 0.56
21 13 0.15
22 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (21 bp):
TTCGCAACGCGAATATGTAAA
Found at i:602417 original size:40 final size:41
Alignment explanation
Indices: 602345--602445 Score: 107
Period size: 40 Copynumber: 2.5 Consensus size: 41
602335 GCAACGCGAA
*
602345 TTCCAATTTCGCAACGCGAATTCCAATTTCGCA-ACCCAGT
1 TTCCAATTTCGCAACGCGAATTCCAATATCGCATACCCAGT
** ** * *
602385 TTCCAATTTCGCAACGCGAATATGTAA-ATCGCATTGCGATT
1 TTCCAATTTCGCAACGCGAAT-TCCAATATCGCATACCCAGT
*
602426 TTCCAAATTCGCAACGCGAA
1 TTCCAATTTCGCAACGCGAA
602446 AGACAATTCG
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
40 26 0.51
41 25 0.49
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (41 bp):
TTCCAATTTCGCAACGCGAATTCCAATATCGCATACCCAGT
Found at i:602494 original size:40 final size:40
Alignment explanation
Indices: 602429--602532 Score: 126
Period size: 40 Copynumber: 2.6 Consensus size: 40
602419 TGCGATTTTC
* * *
602429 CAAATTCGCAACGCGAAAGAC-AATTCGCAACGCGAATTTGT
1 CAAATTCGCAACACGAAAGTCAAATTCGCAACGCG-A-TAGT
602470 -AAA-TCGCAACAC-AGAAGTCAAATTCGCAACGCGATAGT
1 CAAATTCGCAACACGA-AAGTCAAATTCGCAACGCGATAGT
602508 CAAATTCGCAACACGAAAGTCAAAT
1 CAAATTCGCAACACGAAAGTCAAAT
602533 GTTTTTACGC
Statistics
Matches: 55, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
38 4 0.07
39 16 0.29
40 34 0.62
41 1 0.02
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.17
Consensus pattern (40 bp):
CAAATTCGCAACACGAAAGTCAAATTCGCAACGCGATAGT
Found at i:602528 original size:20 final size:20
Alignment explanation
Indices: 602429--602532 Score: 108
Period size: 20 Copynumber: 5.2 Consensus size: 20
602419 TGCGATTTTC
*
602429 CAAATTCGCAACGCGAAAGA
1 CAAATTCGCAACGCGAAAGT
*
602449 C-AATTCGCAACGCGAATTTGT
1 CAAATTCGCAACGCGAA--AGT
*
602470 -AAA-TCGCAACAC-AGAAGT
1 CAAATTCGCAACGCGA-AAGT
*
602488 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
*
602508 CAAATTCGCAACACGAAAGT
1 CAAATTCGCAACGCGAAAGT
602528 CAAAT
1 CAAAT
602533 GTTTTTACGC
Statistics
Matches: 69, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
18 2 0.03
19 19 0.28
20 44 0.64
21 4 0.06
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.17
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:602687 original size:22 final size:22
Alignment explanation
Indices: 602662--602703 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
602652 GGCGACATCC
*
602662 GTCCCCATCTCCGACGAAATAA
1 GTCCCCATCTCCAACGAAATAA
*
602684 GTCCCCATTTCCAACGAAAT
1 GTCCCCATCTCCAACGAAAT
602704 TCGTCTATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.31, C:0.36, G:0.12, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCAACGAAATAA
Found at i:602932 original size:13 final size:13
Alignment explanation
Indices: 602914--602947 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
602904 GTTAGTATTG
602914 TTTTTGTTTTGTC
1 TTTTTGTTTTGTC
*
602927 TTTTTGTTTTTTC
1 TTTTTGTTTTGTC
602940 TTTTTGTT
1 TTTTTGTT
602948 AAAGAAACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.00, C:0.06, G:0.12, T:0.82
Consensus pattern (13 bp):
TTTTTGTTTTGTC
Found at i:605111 original size:21 final size:21
Alignment explanation
Indices: 605064--605155 Score: 66
Period size: 21 Copynumber: 4.6 Consensus size: 21
605054 GATGCACCTA
* ** *
605064 TCATCATTCAAGAGGTGCCTT
1 TCATCGTTCAAGAGGCCCCTC
*
605085 TTATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
*
605106 TCATCG---AAGAAG-CCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
605123 CCACCGTTGAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTC
605144 TCATCGTTCAAG
1 TCATCGTTCAAG
605156 TGGTCCCGCC
Statistics
Matches: 53, Mismatches: 14, Indels: 8
0.71 0.19 0.11
Matches are distributed among these distances:
17 9 0.17
18 5 0.09
20 5 0.09
21 34 0.64
ACGTcount: A:0.23, C:0.32, G:0.21, T:0.25
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:605412 original size:200 final size:196
Alignment explanation
Indices: 605073--605468 Score: 720
Period size: 200 Copynumber: 2.0 Consensus size: 196
605063 ATCATCATTC
605073 AAGAGGTGCCTTTTATCGTTCAAGAGGCCCCTCTCATCGAAGAAGCCCTCCCACCGTTGAAGAGG
1 AAGAGGTGCCTTTTATCGTTCAAGAGGCCCCTCTCATCGAAGAAGCCCTCCCACCGTTGAAGAGG
605138 CCCCTGTCATCGTTCAAGTGGTCCCGCCCGCCGTTCAAGAGCCCGATTCATTTGGTGTCATATGT
66 CCCCTGTCATCGTTCAAGTGGTCCCGCCCGCCGTTCAAGAGCCCGATTCATTTGGTGTCATATGT
*
605203 CGACATATTGATAAACCCCCTCCCGTGTCCGATATGATGGATGCGTGTTGGCTTTCGTATGAGTT
131 CGACATATTGATAAACCCCCTCCCGTATCCGATATGATGGATGCGTGTTGGCTTTCGTATGAGTT
605268 A
196 A
*
605269 AAGAGGTGCCTTTTATCGTTCAATAGGCCCCTCTCATCATCGAAGAAGCCGCTCCCACCGTTGAA
1 AAGAGGTGCCTTTTATCGTTCAAGAGG-CCC-CTC-TCATCGAAGAAGCC-CTCCCACCGTTGAA
*
605334 GAGGCCCCTGTCATCGTTCAAGTGGTCTCGCCCGCCGTTCAAGAGCCCGATTCATTTGGTGTCAT
62 GAGGCCCCTGTCATCGTTCAAGTGGTCCCGCCCGCCGTTCAAGAGCCCGATTCATTTGGTGTCAT
*
605399 ATGTTGACATATTGATAAACCCCCTCCCGTATCCGATATGATGGATGCGTGTTGGCTTTCGTATG
127 ATGTCGACATATTGATAAACCCCCTCCCGTATCCGATATGATGGATGCGTGTTGGCTTTCGTATG
605464 AGTTA
192 AGTTA
605469 CCGACCAGTA
Statistics
Matches: 192, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
196 26 0.14
197 3 0.02
198 3 0.02
199 14 0.07
200 146 0.76
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.28
Consensus pattern (196 bp):
AAGAGGTGCCTTTTATCGTTCAAGAGGCCCCTCTCATCGAAGAAGCCCTCCCACCGTTGAAGAGG
CCCCTGTCATCGTTCAAGTGGTCCCGCCCGCCGTTCAAGAGCCCGATTCATTTGGTGTCATATGT
CGACATATTGATAAACCCCCTCCCGTATCCGATATGATGGATGCGTGTTGGCTTTCGTATGAGTT
A
Found at i:606798 original size:14 final size:14
Alignment explanation
Indices: 606779--606818 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
606769 TTTTGATTAA
606779 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
** *
606793 TTGATTTGTTTAAT
1 TTGATTTGTAAAAG
606807 TTGATTTGTAAA
1 TTGATTTGTAAA
606819 TAAGAATTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:606830 original size:61 final size:62
Alignment explanation
Indices: 606729--606868 Score: 185
Period size: 66 Copynumber: 2.2 Consensus size: 62
606719 TTTTACATTG
*
606729 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTA-TTTT-TTGATTAATTGATTTGTA
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTCTTGATTAATTGATTTGTA
** * *
606789 AAAGTTGATTTGTTTAATTTGATTTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATTA--TTTTT-CTTGATTAATTGATTTGT
606854 A
62 A
606855 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
606869 GTTTCTAAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
60 17 0.25
61 17 0.25
64 4 0.06
66 31 0.45
ACGTcount: A:0.31, C:0.01, G:0.17, T:0.51
Consensus pattern (62 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTCTTGATTAATTGATTTGTA
Found at i:606953 original size:20 final size:20
Alignment explanation
Indices: 606928--606965 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
606918 GTTGAAGGTA
606928 CAAATTCACAACGCGAAACT
1 CAAATTCACAACGCGAAACT
* *
606948 CAAATTCGCAATGCGAAA
1 CAAATTCACAACGCGAAA
606966 TAAGCGTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.26, G:0.13, T:0.16
Consensus pattern (20 bp):
CAAATTCACAACGCGAAACT
Found at i:607028 original size:34 final size:34
Alignment explanation
Indices: 606990--607058 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 34
606980 GTCAAATTCA
606990 CAACGCGAT-TTTCAGT-TTGCGAATTTGACTTTCG
1 CAACGC-ATATTTC-GTGTTGCGAATTTGACTTTCG
*
607024 CAACGCTTATTTCGTGTTGCGAATTTGACTTTCG
1 CAACGCATATTTCGTGTTGCGAATTTGACTTTCG
607058 C
1 C
607059 GTTGATCGCA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 3 0.09
34 29 0.91
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.39
Consensus pattern (34 bp):
CAACGCATATTTCGTGTTGCGAATTTGACTTTCG
Found at i:607292 original size:39 final size:39
Alignment explanation
Indices: 607238--607320 Score: 148
Period size: 39 Copynumber: 2.1 Consensus size: 39
607228 TCAAGTTGTA
*
607238 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTGGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
607277 GATTTGGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTGGATTTCCTTTTGCTTGGCACCATATGAGATTTG
607316 GATTT
1 GATTT
607321 TGATGAGCAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.17, C:0.16, G:0.22, T:0.46
Consensus pattern (39 bp):
GATTTGGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:607657 original size:18 final size:18
Alignment explanation
Indices: 607634--607670 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
607624 CGAAATTTAT
607634 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
607652 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
607670 A
1 A
607671 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:607969 original size:23 final size:23
Alignment explanation
Indices: 607917--607970 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
607907 TGAATGAAAA
*
607917 TATACATACAATATAATCAAACC
1 TATACATACAACATAATCAAACC
* **
607940 TAAACATACATACATAA-CAAATT
1 TATACATACA-ACATAATCAAACC
607963 TATACATA
1 TATACATA
607971 ACAATGTTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.28
Consensus pattern (23 bp):
TATACATACAACATAATCAAACC
Found at i:608091 original size:25 final size:25
Alignment explanation
Indices: 608057--608106 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
608047 ATTATTTTTC
*
608057 CAAAAAATGTACCCATAACAATGTT
1 CAAAAAATGTACCCACAACAATGTT
* *
608082 CAAATAATGTACCCACAATAATGTT
1 CAAAAAATGTACCCACAACAATGTT
608107 TAATTGATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.46, C:0.20, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAAAAATGTACCCACAACAATGTT
Found at i:608568 original size:6 final size:6
Alignment explanation
Indices: 608559--608593 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
608549 GTGTGATTGG
**
608559 GATTTT GATTTT GATTTT GATTGC GATTTT GATTT
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATTT
608594 CCTTTTGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.17, C:0.03, G:0.20, T:0.60
Consensus pattern (6 bp):
GATTTT
Found at i:610875 original size:24 final size:24
Alignment explanation
Indices: 610841--610894 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
610831 CCATCACATC
610841 ATCAAAATCCGAGTATTAACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
* * *
610865 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
610889 ATCAAA
1 ATCAAA
610895 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:611812 original size:18 final size:19
Alignment explanation
Indices: 611791--611852 Score: 76
Period size: 18 Copynumber: 3.4 Consensus size: 19
611781 ACTAAAACCT
*
611791 GTTGCGAA-TT-AAATTCGC
1 GTTGCGAATTTGAAATTC-A
*
611809 GTTGTGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
611828 GTT-CGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
611846 GTTGCGA
1 GTTGCGA
611853 TTTACAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
18 24 0.63
19 8 0.21
20 6 0.16
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.37
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:611863 original size:19 final size:18
Alignment explanation
Indices: 611814--611863 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
611804 TTCGCGTTGT
*
611814 GAATTTGAAATTCAGTTC
1 GAATTTCAAATTCAGTTC
*
611832 GAATTTGAAATTCAGTTGC
1 GAATTTCAAATTCAGTT-C
611851 G-ATTTACAAATTC
1 GAATTT-CAAATTC
611864 GCGTTGCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 21 0.72
19 8 0.28
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (18 bp):
GAATTTCAAATTCAGTTC
Found at i:622682 original size:28 final size:30
Alignment explanation
Indices: 622650--622708 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
622640 ATATTATAAA
622650 AATTTA-AT-TTAAATTAAAAAATATATAT
1 AATTTATATATTAAATTAAAAAATATATAT
* * *
622678 AATTTATATATTTAATTTAAATATATATAT
1 AATTTATATATTAAATTAAAAAATATATAT
622708 A
1 A
622709 CCCAATCCGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 6 0.23
29 2 0.08
30 18 0.69
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
AATTTATATATTAAATTAAAAAATATATAT
Found at i:622688 original size:13 final size:13
Alignment explanation
Indices: 622670--622704 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
622660 AAATTAAAAA
622670 ATATATATAATTT
1 ATATATATAATTT
*
622683 ATATATTTAATTT
1 ATATATATAATTT
*
622696 AAATATATA
1 ATATATATA
622705 TATACCCAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
ATATATATAATTT
Found at i:626923 original size:35 final size:36
Alignment explanation
Indices: 626862--626936 Score: 107
Period size: 39 Copynumber: 2.0 Consensus size: 36
626852 ACGTAGAATC
*
626862 TACAAGAGAATGAATGAATGTCAAATACAGTCATTCAAA
1 TACAAGAGAATGAATGAA--T-AAATAAAGTCATTCAAA
626901 TACAAGAGAATGAATGAA-AAATAAAGTCATTCAAA
1 TACAAGAGAATGAATGAATAAATAAAGTCATTCAAA
626936 T
1 T
626937 CACCTAAGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
35 17 0.49
39 18 0.51
ACGTcount: A:0.52, C:0.11, G:0.15, T:0.23
Consensus pattern (36 bp):
TACAAGAGAATGAATGAATAAATAAAGTCATTCAAA
Found at i:629900 original size:31 final size:31
Alignment explanation
Indices: 629840--629900 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
629830 GGCTCCCTCA
*
629840 TCAAAACGACGTCGTTTTGATGCTCAAAAAC
1 TCAAAACGACGTCGTTTTGATGATCAAAAAC
* *
629871 TCAAAACGACGTCGTTTTGTTGATGAAAAA
1 TCAAAACGACGTCGTTTTGATGATCAAAAA
629901 AATATTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (31 bp):
TCAAAACGACGTCGTTTTGATGATCAAAAAC
Found at i:632355 original size:27 final size:25
Alignment explanation
Indices: 632317--632376 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 25
632307 ATGTTTTCCA
*
632317 ATTTTCAAAAAATTGAAAATAAAAAAT
1 ATTTTCAAAAAA--CAAAATAAAAAAT
* *
632344 ATTTTCTAAAAACAAAATAGAAAAT
1 ATTTTCAAAAAACAAAATAAAAAAT
632369 ATTTTCAA
1 ATTTTCAA
632377 GAACCAAACG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 18 0.62
27 11 0.38
ACGTcount: A:0.58, C:0.07, G:0.03, T:0.32
Consensus pattern (25 bp):
ATTTTCAAAAAACAAAATAAAAAAT
Found at i:633313 original size:27 final size:27
Alignment explanation
Indices: 633240--633354 Score: 81
Period size: 27 Copynumber: 4.1 Consensus size: 27
633230 TATATTAAGT
*
633240 TAAGAATAAAATATTTGTTTTCAATTTAAAA
1 TAAGAATAAAATA--T-TTTT-AAATTAAAA
* **
633271 TAA-AA-AAATTACATTTTTAAATTATGA
1 TAAGAATAAA--ATATTTTTAAATTAAAA
* *
633298 TCAGAATAAAATATTTTTAAGTTAAAA
1 TAAGAATAAAATATTTTTAAATTAAAA
* * *
633325 TAAGATTAAAATATTTTTAAGTTAAGA
1 TAAGAATAAAATATTTTTAAATTAAAA
633352 TAA
1 TAA
633355 AAAATATTAA
Statistics
Matches: 68, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
27 48 0.71
28 6 0.09
29 7 0.10
30 2 0.03
31 5 0.07
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (27 bp):
TAAGAATAAAATATTTTTAAATTAAAA
Found at i:633523 original size:28 final size:28
Alignment explanation
Indices: 633485--633538 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
633475 ATATTTCTAA
*
633485 AATTAAATTAATAATAAAATAGATTTTC
1 AATTAAATTAAGAATAAAATAGATTTTC
* *
633513 AATTAAGTTAAGAATAAAATATATTT
1 AATTAAATTAAGAATAAAATAGATTT
633539 AATAAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.39
Consensus pattern (28 bp):
AATTAAATTAAGAATAAAATAGATTTTC
Found at i:634808 original size:55 final size:54
Alignment explanation
Indices: 634727--635311 Score: 276
Period size: 55 Copynumber: 10.6 Consensus size: 54
634717 GCACCCGTAG
** * * * *
634727 TGCCAATACA-ATAATTCACCACCTCATTAAGAATTACGTGGGAATGCACACCCAA
1 TGCCAATACAGA-AATTCATAAACTCATTATGAATTACGTAGG-ATGCACACACAA
* * * * * * *
634782 TGTCAATACGGAAATTCATAATCTCATTATGAATTTCTTAGGTTGCACACACAG
1 TGCCAATACAGAAATTCATAAACTCATTATGAATTACGTAGGATGCACACACAA
* * * * *
634836 TGCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAG
1 TGCCAATACAGAAATTCATAAACTCATTATGAATTACGTAGGATGCACACACAA
* * * * * * ** *
634890 TACCAATACGGAAATTTATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
1 TGCCAATACAGAAATTCATAAACTCATTATGAATTACGTAG-GATGCACACACAA
* * * * * **
634945 TGCCCATAC-GAAAATTCATAAGCTTATTATGAATTTCTTAGTTTTGCACACACAA
1 TGCCAATACAG-AAATTCATAAACTCATTATGAATTACGTAG-GATGCACACACAA
** * * * * * * * **
635000 CACCCATACGGAAATTCATAAGCTTATTATGCATTTCTTAGTTTTGCACACACAA
1 TGCCAATACAGAAATTCATAAACTCATTATGAATTACGTAG-GATGCACACACAA
* * * *** ** *
635055 TGCCCATACGGAAATTCATAAACTTATTATGAATTTTTTAGTTTTTGCACACACAG
1 TGCCAATACAGAAATTCATAAACTCATTATGAATTACGTAG--GATGCACACACAA
* * * * * * ** *
635111 TGCCCATACGGAAATTCATAAATTTATTATGAATTTCTTAGTTTTGCTCACAC-A
1 TGCCAATACAGAAATTCATAAACTCATTATGAATTACGTAG-GATGCACACACAA
* * * * * * ** * *
635165 TAGCCCACACGGAAATTCATAAAACTTATTATGAATTTCTTAGTTTTGTACACACAG
1 T-GCCAATACAGAAATTCAT-AAACTCATTATGAATTACGTAG-GATGCACACACAA
* * * * * * ** *
635222 TGCCCATACGGAAATTCATAAACTTATTATGAGTTTCTTAGTTTTGCACACACAG
1 TGCCAATACAGAAATTCATAAACTCATTATGAATTACGTAG-GATGCACACACAA
* *
635277 TGCCCATACAGAAATTCATAAACTTATTATGAATT
1 TGCCAATACAGAAATTCATAAACTCATTATGAATT
635312 TATTAGGTTG
Statistics
Matches: 474, Mismatches: 48, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
54 99 0.21
55 272 0.57
56 102 0.22
57 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.34
Consensus pattern (54 bp):
TGCCAATACAGAAATTCATAAACTCATTATGAATTACGTAGGATGCACACACAA
Found at i:635148 original size:166 final size:163
Alignment explanation
Indices: 634787--635325 Score: 783
Period size: 166 Copynumber: 3.3 Consensus size: 163
634777 CCCAATGTCA
* * * * *
634787 ATACGGAAATTCATAATCTCATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACAGAAATT
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACA-AGCCCATACGGAAATT
* * * *
634852 CATAAACTTATTATGAATTTCTTAG-GTTGCACACACAGTACCAATACGGAAATTTATAAACTTA
65 CATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGGAAATTCATAAACTTA
634916 TTATGAATTTCTTAGTTTTGCACACACAGTGCCC
130 TTATGAATTTCTTAGTTTTGCACACACAGTGCCC
* * * *
634950 ATACGAAAATTCATAAGCTTATTATGAATTTCTTAGTTTTGCACACACAACACCCATACGGAAAT
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAG-GTTGCACACACAA-GCCCATACGGAAAT
* * *
635015 TCATAAGCTTATTATGCATTTCTTAGTTTTGCACACACAATGCCCATACGGAAATTCATAAACTT
64 TCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGGAAATTCATAAACTT
*
635080 ATTATGAATTTTTTAGTTTTTGCACACACAGTGCCC
129 ATTATGAATTTCTTAG-TTTTGCACACACAGTGCCC
* * * *
635116 ATACGGAAATTCATAAATTTATTATGAATTTCTTAGTTTTGCTCACACATAGCCCACACGGAAAT
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAG-GTTGCACACACA-AGCCCATACGGAAAT
*
635181 TCATAAAACTTATTATGAATTTCTTAGTTTTGTACACACAGTGCCCATACGGAAATTCATAAACT
64 TCAT-AAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGGAAATTCATAAACT
*
635246 TATTATGAGTTTCTTAGTTTTGCACACACAGTGCCC
128 TATTATGAATTTCTTAGTTTTGCACACACAGTGCCC
* *
635282 ATACAGAAATTCATAAACTTATTATGAATTTATTAGGTTGCACA
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACA
635326 TATAGTGTCA
Statistics
Matches: 337, Mismatches: 33, Indels: 10
0.89 0.09 0.03
Matches are distributed among these distances:
163 33 0.10
164 46 0.14
165 54 0.16
166 132 0.39
167 72 0.21
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (163 bp):
ATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAAGCCCATACGGAAATTC
ATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGGAAATTCATAAACTTAT
TATGAATTTCTTAGTTTTGCACACACAGTGCCC
Found at i:635163 original size:111 final size:110
Alignment explanation
Indices: 634787--635325 Score: 789
Period size: 111 Copynumber: 4.9 Consensus size: 110
634777 CCCAATGTCA
* * * * *
634787 ATACGGAAATTCATAATCTCATTATGAATTTCTTAG-GTTGCACACACAGTGCCAATACAGAAAT
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGGAAAT
* *
634851 TCATAAACTTATTATGAATTTCTTAG-GTTGCACACACAGTACCA
66 TCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTACCC
* *
634895 ATACGGAAATTTATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGAAAAT
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGGAAAT
* **
634960 TCATAAGCTTATTATGAATTTCTTAGTTTTGCACACACAACACCC
66 TCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTACCC
* * *
635005 ATACGGAAATTCATAAGCTTATTATGCATTTCTTAGTTTTGCACACACAATGCCCATACGGAAAT
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGGAAAT
* *
635070 TCATAAACTTATTATGAATTTTTTAGTTTTTGCACACACAGTGCCC
66 TCATAAACTTATTATGAATTTCTTAG-TTTTGCACACACAGTACCC
* * *
635116 ATACGGAAATTCATAAATTTATTATGAATTTCTTAGTTTTGCTCACACA-TAGCCCACACGGAAA
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGT-GCCCATACGGAAA
* *
635180 TTCATAAAACTTATTATGAATTTCTTAGTTTTGTACACACAGTGCCC
65 TTCAT-AAACTTATTATGAATTTCTTAGTTTTGCACACACAGTACCC
* *
635227 ATACGGAAATTCATAAACTTATTATGAGTTTCTTAGTTTTGCACACACAGTGCCCATACAGAAAT
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGGAAAT
* *
635292 TCATAAACTTATTATGAATTTATTAG-GTTGCACA
66 TCATAAACTTATTATGAATTTCTTAGTTTTGCACA
635326 TATAGTGTCA
Statistics
Matches: 388, Mismatches: 37, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
108 33 0.09
109 55 0.14
110 120 0.31
111 158 0.41
112 22 0.06
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (110 bp):
ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGGAAAT
TCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTACCC
Found at i:638999 original size:6 final size:5
Alignment explanation
Indices: 638974--639157 Score: 113
Period size: 5 Copynumber: 37.2 Consensus size: 5
638964 TAAAATAGTA
* *
638974 AATA- AATAT AATAT AATAT AACTAT AA-CT AATAT AATAT -A-AT ACTAT
1 AATAT AATAT AATAT AATAT AA-TAT AATAT AATAT AATAT AATAT AATAT
* * *
639021 AATATT AAT-T AACAT AATATAT AATAT AA-AGT -ATAAT AATAT ACTTT
1 AATA-T AATAT AATAT -A-ATAT AATAT AATA-T AAT-AT AATAT AATAT
* *
639068 AATAT -ATAT ATATGT AATAT -ATAT AATAT -GTAT AATAT ATATAT AATAT
1 AATAT AATAT A-ATAT AATAT AATAT AATAT AATAT AATAT A-ATAT AATAT
* *
639117 TATA- ATATAT AATAT ATATAT TATAT AATAT -ATAT AATAT A
1 AATAT A-ATAT AATAT A-ATAT AATAT AATAT AATAT AATAT A
639158 TATTATCCTG
Statistics
Matches: 140, Mismatches: 18, Indels: 43
0.70 0.09 0.21
Matches are distributed among these distances:
3 2 0.01
4 28 0.20
5 79 0.56
6 28 0.20
7 3 0.02
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.42
Consensus pattern (5 bp):
AATAT
Found at i:639007 original size:15 final size:13
Alignment explanation
Indices: 638978--639157 Score: 138
Period size: 14 Copynumber: 13.5 Consensus size: 13
638968 ATAGTAAATA
638978 AATATAATATAAT
1 AATATAATATAAT
*
638991 -ATA-ACTATAACT
1 AATATAATATAA-T
639003 AATATAATATAAT
1 AATATAATATAAT
*
639016 ACTATAATATTAATT
1 AATATAATA-TAA-T
*
639031 AACATAATAT-AT
1 AATATAATATAAT
639043 AATATAAAGTATAAT
1 AATAT-AA-TATAAT
* *
639058 AATATACTTTAAT
1 AATATAATATAAT
*
639071 ATATATATATGTAAT
1 A-ATATA-ATATAAT
*
639086 ATATATAATATGTAT
1 A-ATATAATAT-AAT
639101 AATATATATATAAT
1 AATATA-ATATAAT
*
639115 ATTATAATAT-AT
1 AATATAATATAAT
639127 AATAT-ATAT-AT
1 AATATAATATAAT
*
639138 TATATAATATATAT
1 AATATAATATA-AT
639152 AATATA
1 AATATA
639158 TATTATCCTG
Statistics
Matches: 135, Mismatches: 17, Indels: 29
0.75 0.09 0.16
Matches are distributed among these distances:
11 16 0.12
12 19 0.14
13 25 0.19
14 41 0.30
15 34 0.25
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (13 bp):
AATATAATATAAT
Found at i:639007 original size:20 final size:19
Alignment explanation
Indices: 638981--639157 Score: 108
Period size: 19 Copynumber: 9.4 Consensus size: 19
638971 GTAAATAAAT
638981 ATAATATAATATAACTATA
1 ATAATATAATATAACTATA
639000 ACTAATATAATATAA-TACT-
1 A-TAATATAATATAACTA-TA
639019 ATAATATTAAT-TAAC-ATA
1 ATAATA-TAATATAACTATA
*
639037 AT-ATATAATATAAAGTATA
1 ATAATATAATAT-AACTATA
* *
639056 ATAATATACTTTAA-TATA
1 ATAATATAATATAACTATA
*
639074 TATATATGTAATAT-A-TATA
1 -ATA-ATATAATATAACTATA
*
639093 ATATGTATAATATATA-TATA
1 ATA-ATATAATATA-ACTATA
* *
639113 ATATTATAATATATAATAT-
1 ATAATATAATATA-ACTATA
*
639132 AT-ATATTATATAA-TATA
1 ATAATATAATATAACTATA
639149 TATAATATA
1 -ATAATATA
639158 TATTATCCTG
Statistics
Matches: 129, Mismatches: 12, Indels: 34
0.74 0.07 0.19
Matches are distributed among these distances:
16 7 0.05
17 6 0.05
18 38 0.29
19 40 0.31
20 38 0.29
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (19 bp):
ATAATATAATATAACTATA
Found at i:639076 original size:2 final size:2
Alignment explanation
Indices: 639069--639160 Score: 96
Period size: 2 Copynumber: 51.0 Consensus size: 2
639059 ATATACTTTA
* *
639069 AT AT AT AT AT AT GT A- AT AT AT AT A- AT AT GT AT A- 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
639108 AT AT A- AT AT -T AT A- AT AT AT A- AT AT AT AT AT -T AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
639144 AT AT AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
639161 TATCCTGGAT
Statistics
Matches: 76, Mismatches: 4, Indels: 20
0.76 0.04 0.20
Matches are distributed among these distances:
1 10 0.13
2 66 0.87
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:639089 original size:9 final size:9
Alignment explanation
Indices: 638974--639160 Score: 126
Period size: 9 Copynumber: 21.0 Consensus size: 9
638964 TAAAATAGTA
*
638974 AATAAATAT
1 AATATATAT
638983 AATATAATAT
1 AATAT-ATAT
638993 AACTATA-ACT
1 AA-TATATA-T
639003 AATATAATAT
1 AATAT-ATAT
*
639013 AATA-CTAT
1 AATATATAT
639021 AATAT-TA-
1 AATATATAT
* *
639028 ATTA-ACAT
1 AATATATAT
639036 AATATATA-
1 AATATATAT
*
639044 ATATAAAGTAT
1 A-ATATA-TAT
639055 AATA-ATAT
1 AATATATAT
* *
639063 ACTTTAATAT
1 AATAT-ATAT
*
639073 ATATATATGT
1 A-ATATATAT
639083 AATATATAT
1 AATATATAT
*
639092 AATATGTAT
1 AATATATAT
639101 AATATATAT
1 AATATATAT
639110 -ATA-ATAT
1 AATATATAT
*
639117 TATAATATAT
1 AAT-ATATAT
639127 AATATATAT
1 AATATATAT
639136 -AT-TATAT
1 AATATATAT
639143 AATATATAT
1 AATATATAT
639152 AATATATAT
1 AATATATAT
639161 TATCCTGGAT
Statistics
Matches: 142, Mismatches: 16, Indels: 40
0.72 0.08 0.20
Matches are distributed among these distances:
7 13 0.09
8 27 0.19
9 59 0.42
10 36 0.25
11 7 0.05
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (9 bp):
AATATATAT
Found at i:639769 original size:98 final size:98
Alignment explanation
Indices: 639599--639786 Score: 322
Period size: 98 Copynumber: 1.9 Consensus size: 98
639589 CTTTGTCTTT
*
639599 AAGTTGAAATTAATCTCAAAATCTGCACTGGAATGTGGCTCCTCGTTGTCGAGTTATAATCAACC
1 AAGTTGAAATTAATCTCAAAATATGCACTGGAATGTGGCTCCTCGTTGTCGAGTTATAATCAACC
639664 TTAGTCTTCTTCTTGGCTTAAAGACATCGGTTG
66 TTAGTCTTCTTCTTGGCTTAAAGACATCGGTTG
* * *
639697 AAGTTGAAATTAATCTCGAAATATGCACTGGAATGTGGCTCCTTGTTGTCGAGTTATAGTCAACC
1 AAGTTGAAATTAATCTCAAAATATGCACTGGAATGTGGCTCCTCGTTGTCGAGTTATAATCAACC
* *
639762 TTGGTCTTCTTTTTGGCTTAAAGAC
66 TTAGTCTTCTTCTTGGCTTAAAGAC
639787 CTCAGTTTAA
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 84 1.00
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (98 bp):
AAGTTGAAATTAATCTCAAAATATGCACTGGAATGTGGCTCCTCGTTGTCGAGTTATAATCAACC
TTAGTCTTCTTCTTGGCTTAAAGACATCGGTTG
Found at i:640091 original size:201 final size:200
Alignment explanation
Indices: 639757--640288 Score: 701
Period size: 201 Copynumber: 2.6 Consensus size: 200
639747 GAGTTATAGT
* * * ** *
639757 CAACCTTGGTCTTCTTTTTGGCTTAAAGACCTCAGTTTAAAATTCAATTGGAAAGTAGTTCCTCA
1 CAACCTAGGTCTTCTTCTTGGCTTAAAGACCTCAGTTTAAAATTCAACTAAAAAGTAGTTCCTCG
* * * * * * *
639822 CTACTACCATGCAGTCGATACGCCCTTGAGCTAACTGGAATCAAACTCGAAAGTTTTTGTTTACA
66 CTGCTACCATGTAGTTGATACGCCCTCGAGCTAA-TGGAATCGAACTCGAAAGTTTTCGTTGACA
* **
639887 TACAACTTTTCTCGACTTAAGTTATGTTGTAAATTAGGCTGGGAGATAGTTCCTTGTTGCTAAAT
130 TACAACTTTTCTCGACTTAAGCTATGTTGTAAATTAGGCTAAGAGATAGTTCCTTGTTGCTAAAT
639952 CGCAAC
195 CGCAAC
* * *
639958 CAACCTAGGTCTTCTTCTTGGCTTAAAGACCTC-GTTTTGAATTTCAACTAAAAATTAGTTCCTC
1 CAACCTAGGTCTTCTTCTTGGCTTAAAGACCTCAG-TTTAAAATTCAACTAAAAAGTAGTTCCTC
* * *
640022 GCTGCTACCATGT-GATTGATACGCCCTCGAGCTGAATGTAATCGAACTTGAAAGTTTTCATTGA
65 GCTGCTACCATGTAG-TTGATACGCCCTCGAGCT-AATGGAATCGAACTCGAAAGTTTTCGTTGA
** *
640086 CATACAACTTTTCTCGACTTAAGCTATGTTGTAAATTAGGCTAAGAGATAGTTTTTTTTTGCTAA
128 CATACAACTTTTCTCGACTTAAGCTATGTTGTAAATTAGGCTAAGAGATAGTTCCTTGTTGCTAA
*
640151 ATCGCAGC
193 ATCGCAAC
** * *
640159 CAATATAGGTCTTCTTCTTGGTTTAAAGACCTCAGTTTAAAATTCAAC-AGAAAAGTAGTTCTTC
1 CAACCTAGGTCTTCTTCTTGGCTTAAAGACCTCAGTTTAAAATTCAACTA-AAAAGTAGTTCCTC
* *
640223 GCTGCTACCATATAGTTGATACGCCCTCGAGCTAAATGGAATTGAACTCGAAAGTTTTCGTTGAC
65 GCTGCTACCATGTAGTTGATACGCCCTCGAGCT-AATGGAATCGAACTCGAAAGTTTTCGTTGAC
640288 A
129 A
640289 AATAACCCTT
Statistics
Matches: 286, Mismatches: 39, Indels: 12
0.85 0.12 0.04
Matches are distributed among these distances:
200 3 0.01
201 279 0.98
202 4 0.01
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34
Consensus pattern (200 bp):
CAACCTAGGTCTTCTTCTTGGCTTAAAGACCTCAGTTTAAAATTCAACTAAAAAGTAGTTCCTCG
CTGCTACCATGTAGTTGATACGCCCTCGAGCTAATGGAATCGAACTCGAAAGTTTTCGTTGACAT
ACAACTTTTCTCGACTTAAGCTATGTTGTAAATTAGGCTAAGAGATAGTTCCTTGTTGCTAAATC
GCAAC
Found at i:642335 original size:24 final size:24
Alignment explanation
Indices: 642277--642370 Score: 109
Period size: 24 Copynumber: 4.0 Consensus size: 24
642267 GGTTCTACAC
* *
642277 GGTCCTTCGGGACATA-TCTATGT
1 GGTCCTTCGGGACAAATTCTACGT
* *
642300 GGTCATTTGGGACAAATTCTACGT
1 GGTCCTTCGGGACAAATTCTACGT
* * *
642324 TGTCCTTCGGGATAAATTCTACGC
1 GGTCCTTCGGGACAAATTCTACGT
*
642348 GGTCCTTCGGGACGAATTCTACG
1 GGTCCTTCGGGACAAATTCTACG
642371 CAGTCATTAG
Statistics
Matches: 58, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
23 13 0.22
24 45 0.78
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.32
Consensus pattern (24 bp):
GGTCCTTCGGGACAAATTCTACGT
Found at i:643995 original size:27 final size:27
Alignment explanation
Indices: 643965--644022 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
643955 ATCAAGGCTC
* *
643965 GCATTCTCATTGTTTCTCTTCGATGTG
1 GCATTCCCATTGTTTCTCTTCGATATG
643992 GCATTCCCATTGTTTCTCTTCGATATG
1 GCATTCCCATTGTTTCTCTTCGATATG
644019 GCAT
1 GCAT
644023 CCTGAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.45
Consensus pattern (27 bp):
GCATTCCCATTGTTTCTCTTCGATATG
Found at i:646680 original size:216 final size:217
Alignment explanation
Indices: 646306--646744 Score: 871
Period size: 216 Copynumber: 2.0 Consensus size: 217
646296 TCATGTTGGT
646306 GGTGACGGTGCGACCTACGGATGTCGGAATCATGAAGAATATCAATAATAGGGTTTATGAAGCTT
1 GGTGACGGTGCGACCTACGGATGTCGGAATCATGAAGAATATCAATAATAGGGTTTATGAAGCTT
646371 CAAAGGGCCACCCACAACGATCGATGGTGGTTTACAGTGAATAACCATAAGGTTTTTGGTAAAGG
66 CAAAGGGCCACCCACAACGATCGATGGTGGTTTACAGTGAATAACCATAAGGTTTTTGGTAAAGG
646436 ATGGTGGGGAACGTTTTGGTGCTGGCAGTGCACGCCACTATTGAGAAATGACGACAGAAGAAGAA
131 ATGGTGGGGAACGTTTTGGTGCTGGCAGTGCACGCCACTATTGAGAAATGACGACAGAAGAAGAA
646501 GAATGAATGAAGAGTTTAAC-G
196 GAATGAATGAAGAGTTTAACGG
646522 GGTGACGGTGCGACCTACGGATGTCGGAATCATGAAGAATATCAATAATAGGGTTTATGAAGCTT
1 GGTGACGGTGCGACCTACGGATGTCGGAATCATGAAGAATATCAATAATAGGGTTTATGAAGCTT
646587 CAAAGGGCCACCCACAACGATCGATGGTGGTTTACAGTGAATAACCATAAGGTTTTTGGTAAAGG
66 CAAAGGGCCACCCACAACGATCGATGGTGGTTTACAGTGAATAACCATAAGGTTTTTGGTAAAGG
646652 ATGGTGGGGAACGTTTTGGTGCTGGCAGTGCACGCCACTATTGAGAAATGACGACAGAAGAAGAA
131 ATGGTGGGGAACGTTTTGGTGCTGGCAGTGCACGCCACTATTGAGAAATGACGACAGAAGAAGAA
646717 GAATGAATGAAGAGTTTAACGG
196 GAATGAATGAAGAGTTTAACGG
646739 GGTGAC
1 GGTGAC
646745 CAAAATACAA
Statistics
Matches: 222, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
216 215 0.97
217 7 0.03
ACGTcount: A:0.32, C:0.15, G:0.30, T:0.23
Consensus pattern (217 bp):
GGTGACGGTGCGACCTACGGATGTCGGAATCATGAAGAATATCAATAATAGGGTTTATGAAGCTT
CAAAGGGCCACCCACAACGATCGATGGTGGTTTACAGTGAATAACCATAAGGTTTTTGGTAAAGG
ATGGTGGGGAACGTTTTGGTGCTGGCAGTGCACGCCACTATTGAGAAATGACGACAGAAGAAGAA
GAATGAATGAAGAGTTTAACGG
Found at i:647589 original size:23 final size:23
Alignment explanation
Indices: 647563--647610 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
647553 TTTGATATAT
647563 TTCTTATTGAAGTTT-AAAACTAA
1 TTCTTATTGAAGTTTGAAAA-TAA
*
647586 TTCTTATTTAAGTTTGAAAATAA
1 TTCTTATTGAAGTTTGAAAATAA
647609 TT
1 TT
647611 TAGGTATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (23 bp):
TTCTTATTGAAGTTTGAAAATAA
Found at i:650748 original size:28 final size:30
Alignment explanation
Indices: 650662--650763 Score: 127
Period size: 31 Copynumber: 3.4 Consensus size: 30
650652 TTCATTTGCA
* *
650662 TACCTTAAGTATTTTTTTGGTCAAAATAAG
1 TACCTAAAGTATTTTTTTGGTCAAAATAGG
* *
650692 TATCTAAAGTTATTTTTTTGGTCCAAATAGG
1 TACCTAAAG-TATTTTTTTGGTCAAAATAGG
*
650723 TACCTAAAGTA-TTTTAT-GTCAAAATAGG
1 TACCTAAAGTATTTTTTTGGTCAAAATAGG
*
650751 TACCTAAACTATT
1 TACCTAAAGTATT
650764 CAAACTTTTT
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
28 20 0.32
29 6 0.10
30 9 0.15
31 27 0.44
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (30 bp):
TACCTAAAGTATTTTTTTGGTCAAAATAGG
Found at i:650877 original size:30 final size:30
Alignment explanation
Indices: 650843--650948 Score: 126
Period size: 30 Copynumber: 3.6 Consensus size: 30
650833 AAAAAAATTG
*
650843 AATACTTTAGGTACCTATTTTGACCAAAAA
1 AATACTTTAGGTACTTATTTTGACCAAAAA
* * *
650873 AATACTTTAAGTACTTATTTTAACTAAAAA
1 AATACTTTAGGTACTTATTTTGACCAAAAA
* *
650903 GATAACTTTAGATACTTATTTTGA-C-AAAA
1 AAT-ACTTTAGGTACTTATTTTGACCAAAAA
*
650932 AATACTTTAGATACTTA
1 AATACTTTAGGTACTTA
650949 AATGAAAAAG
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 14 0.22
29 6 0.09
30 28 0.43
31 17 0.26
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (30 bp):
AATACTTTAGGTACTTATTTTGACCAAAAA
Found at i:650970 original size:59 final size:58
Alignment explanation
Indices: 650812--650981 Score: 141
Period size: 59 Copynumber: 2.8 Consensus size: 58
650802 GGCATTAATT
* * * * *
650812 AAATACTTTAGGTACTTAGATAAAAAAATTGAATACTTTAGGTACCTATTTTGACCAAAA
1 AAATACTTTAGATACTTAAAT-AAAAAATAG-ATACTTTAGATACTTATTTTGACCAAAA
**
650872 AAATACTTTA-AGTACTTATTTTAACTAAAA-AGATAACTTTAGATACTTATTTTGA-C-AAA
1 AAATACTTTAGA-TACTTA-AATAA--AAAATAGAT-ACTTTAGATACTTATTTTGACCAAAA
* *
650931 AAATACTTTAGATACTTAAATGAAAAAGATAGTATACTTTAGTTATTTATT
1 AAATACTTTAGATACTTAAAT-AAAAA-ATAG-ATACTTTAGATACTTATT
650982 ATATAATCCT
Statistics
Matches: 90, Mismatches: 10, Indels: 21
0.74 0.08 0.17
Matches are distributed among these distances:
57 3 0.03
58 2 0.02
59 37 0.41
60 24 0.27
61 20 0.22
62 4 0.04
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (58 bp):
AAATACTTTAGATACTTAAATAAAAAATAGATACTTTAGATACTTATTTTGACCAAAA
Found at i:651011 original size:17 final size:19
Alignment explanation
Indices: 650983--651017 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
650973 TTATTTATTA
650983 TATAATCCTTTAT-TTTAC
1 TATAATCCTTTATGTTTAC
651001 TATAA-CCTTTATGTTTA
1 TATAATCCTTTATGTTTA
651018 TAATAGTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.29, C:0.14, G:0.03, T:0.54
Consensus pattern (19 bp):
TATAATCCTTTATGTTTAC
Found at i:652433 original size:49 final size:50
Alignment explanation
Indices: 652373--652495 Score: 162
Period size: 49 Copynumber: 2.5 Consensus size: 50
652363 TGTTTTAATT
* *
652373 TATCCTTGTAATTTATTTTTCCT-ATTAAATGGATAATTAGAGGTTGATG
1 TATCCTCGTAATTTATTTTTCCTCATTAAATGGATAATTACAGGTTGATG
* *
652422 TATCCTCGTAATTTA-TTTTACTCATTAAATGGATGATTACAGGTTGATG
1 TATCCTCGTAATTTATTTTTCCTCATTAAATGGATAATTACAGGTTGATG
* * *
652471 TATCATCATAATCTATTTTT-CTCAT
1 TATCCTCGTAATTTATTTTTCCTCAT
652496 AAAAAGATAA
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
48 6 0.09
49 55 0.85
50 4 0.06
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.46
Consensus pattern (50 bp):
TATCCTCGTAATTTATTTTTCCTCATTAAATGGATAATTACAGGTTGATG
Found at i:655293 original size:18 final size:18
Alignment explanation
Indices: 655270--655314 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
655260 GTCTAGTTTA
655270 TAAAATTGATTAATTAAC
1 TAAAATTGATTAATTAAC
655288 TAAAATTGATTAATTAAC
1 TAAAATTGATTAATTAAC
*
655306 TGAAATTGA
1 TAAAATTGA
655315 CTTGACATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (18 bp):
TAAAATTGATTAATTAAC
Found at i:662500 original size:21 final size:22
Alignment explanation
Indices: 662474--662515 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
662464 ACTATATGAT
662474 ATGAACAATACC-TGAACAGTA
1 ATGAACAATACCGTGAACAGTA
662495 ATGAACAATACCGTGAACAGT
1 ATGAACAATACCGTGAACAGT
662516 GAAAAATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.45, C:0.19, G:0.17, T:0.19
Consensus pattern (22 bp):
ATGAACAATACCGTGAACAGTA
Found at i:663689 original size:20 final size:20
Alignment explanation
Indices: 663653--663690 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
663643 ATCCTATTCC
**
663653 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
663673 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
663691 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:663870 original size:31 final size:31
Alignment explanation
Indices: 663835--663936 Score: 91
Period size: 31 Copynumber: 3.3 Consensus size: 31
663825 CCGAATAACC
*
663835 TAGGTAAATTGTCCATATGTTCCTTAGAACA
1 TAGGTAAATTGTCCATATGTTCCCTAGAACA
* * * * *
663866 TAGGTATACTGTCTATATG-TCCCGAAAGACA
1 TAGGTAAATTGTCCATATGTTCCCTAGA-ACA
*
663897 TAGGT-AATTCAGTCCATATGTTCCGTAGAACA
1 TAGGTAAATT--GTCCATATGTTCCCTAGAACA
*
663929 TAGATAAA
1 TAGGTAAA
663937 CCCTCGACTC
Statistics
Matches: 53, Mismatches: 13, Indels: 8
0.72 0.18 0.11
Matches are distributed among these distances:
30 7 0.13
31 24 0.45
32 15 0.28
33 7 0.13
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (31 bp):
TAGGTAAATTGTCCATATGTTCCCTAGAACA
Found at i:663929 original size:63 final size:62
Alignment explanation
Indices: 663811--663931 Score: 165
Period size: 62 Copynumber: 1.9 Consensus size: 62
663801 AACCTCGGCA
* *
663811 ACTGTCCATAGGTCCCGAATAACCTAGGTAAATTGTCCATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATAGGTCCCGAATAACATAGGTAAATTGTCCATATGTTCCGTAGAACATAGGTAT
* *
663873 ACTGTCTATATGTCCCGAA-AGACATAGGT-AATTCAGTCCATATGTTCCGTAGAACATAG
1 ACTGTCCATAGGTCCCGAATA-ACATAGGTAAATT--GTCCATATGTTCCGTAGAACATAG
663932 ATAAACCCTC
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
61 5 0.10
62 24 0.46
63 23 0.44
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (62 bp):
ACTGTCCATAGGTCCCGAATAACATAGGTAAATTGTCCATATGTTCCGTAGAACATAGGTAT
Found at i:663930 original size:32 final size:31
Alignment explanation
Indices: 663845--663931 Score: 95
Period size: 32 Copynumber: 2.8 Consensus size: 31
663835 TAGGTAAATT
* *
663845 GTCCATATGTTCCTTAGAACATAGGTATACT
1 GTCCATATGTTCCGTAGAACATAGGTATACA
* * * *
663876 GTCTATATGTCCCG-AAAGACATAGGTAATTCA
1 GTCCATATGTTCCGTAGA-ACATAGGT-ATACA
663908 GTCCATATGTTCCGTAGAACATAG
1 GTCCATATGTTCCGTAGAACATAG
663932 ATAAACCCTC
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
30 2 0.05
31 19 0.43
32 21 0.48
33 2 0.05
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (31 bp):
GTCCATATGTTCCGTAGAACATAGGTATACA
Found at i:664209 original size:22 final size:22
Alignment explanation
Indices: 664168--664209 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
664158 ATTTATCTCA
*
664168 TCATAACATGTATCACATATGT
1 TCATAACATGTAACACATATGT
* *
664190 TCATATCATGTAACATATAT
1 TCATAACATGTAACACATAT
664210 CACATGTGCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.38
Consensus pattern (22 bp):
TCATAACATGTAACACATATGT
Found at i:664642 original size:20 final size:20
Alignment explanation
Indices: 664617--664672 Score: 94
Period size: 22 Copynumber: 2.7 Consensus size: 20
664607 TGCAATTCCC
664617 ATGCATCGATGCACTCCTTA
1 ATGCATCGATGCACTCCTTA
664637 ATGCATCGATGTGCACTCCTTA
1 ATGCATCGA--TGCACTCCTTA
664659 ATGCATCGATGCAC
1 ATGCATCGATGCAC
664673 CTTCAACTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.41
22 20 0.59
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.29
Consensus pattern (20 bp):
ATGCATCGATGCACTCCTTA
Found at i:665203 original size:3 final size:3
Alignment explanation
Indices: 665195--665225 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
665185 TCTCGTACAT
665195 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
665226 TAGAGAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:667150 original size:6 final size:6
Alignment explanation
Indices: 667139--667203 Score: 130
Period size: 6 Copynumber: 10.8 Consensus size: 6
667129 TTCCCTCTAT
667139 GGGATA GGGATA GGGATA GGGATA GGGATA GGGATA GGGATA GGGATA
1 GGGATA GGGATA GGGATA GGGATA GGGATA GGGATA GGGATA GGGATA
667187 GGGATA GGGATA GGGAT
1 GGGATA GGGATA GGGAT
667204 TCTTTCTTCT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.32, C:0.00, G:0.51, T:0.17
Consensus pattern (6 bp):
GGGATA
Found at i:671156 original size:37 final size:37
Alignment explanation
Indices: 671115--671215 Score: 139
Period size: 37 Copynumber: 2.7 Consensus size: 37
671105 TTCGTCCTAT
* * * *
671115 TAGGATTCAAATTCCTAAAAATAGGATAGAATTTTGC
1 TAGGATTCAAACTCCTAAAAATAAGATAGAATTCTAC
*
671152 TAGGATTCAAACTCCTAAAAATAAGATAGAGTTCTAC
1 TAGGATTCAAACTCCTAAAAATAAGATAGAATTCTAC
* *
671189 TATGATTTAAACTCCTAAAAATAAGAT
1 TAGGATTCAAACTCCTAAAAATAAGAT
671216 CCACAAGCAC
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.31
Consensus pattern (37 bp):
TAGGATTCAAACTCCTAAAAATAAGATAGAATTCTAC
Found at i:671757 original size:2 final size:2
Alignment explanation
Indices: 671752--671804 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
671742 TATTTTTTTA
671752 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
671794 AT AT AT AT AT A
1 AT AT AT AT AT A
671805 CTTTTTTTAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:676595 original size:29 final size:28
Alignment explanation
Indices: 676563--676627 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
676553 AATCAAGAAC
*
676563 AAAAAAGAAA-AGAAGCAAAAAAACAAAGA
1 AAAAAAGAAACAAAAG--AAAAAACAAAGA
*
676592 AAAAAGAGAAACAAAAGAAAAAAGAAAGA
1 AAAAA-AGAAACAAAAGAAAAAACAAAGA
676621 ACAAAAA
1 A-AAAAA
676628 TCAAAAAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
29 18 0.58
30 9 0.29
31 4 0.13
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (28 bp):
AAAAAAGAAACAAAAGAAAAAACAAAGA
Found at i:676606 original size:25 final size:26
Alignment explanation
Indices: 676560--676638 Score: 78
Period size: 25 Copynumber: 3.1 Consensus size: 26
676550 TCCAATCAAG
*
676560 AACAAA-AAAGAAAAGAAGCAAAA-A
1 AACAAAGAAAGAAAAGAAACAAAAGA
676584 AACAAAGAAA-AAAGAGAAACAAAAGA
1 AACAAAGAAAGAAA-AGAAACAAAAGA
676610 AA-AAAGAAAGAACAA-AAATCAAAAAGA
1 AACAAAGAAAGAA-AAGAAA-C-AAAAGA
676637 AA
1 AA
676639 AAGGGACAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 11
0.80 0.02 0.19
Matches are distributed among these distances:
24 9 0.19
25 22 0.47
26 7 0.15
27 9 0.19
ACGTcount: A:0.78, C:0.08, G:0.13, T:0.01
Consensus pattern (26 bp):
AACAAAGAAAGAAAAGAAACAAAAGA
Found at i:676610 original size:18 final size:18
Alignment explanation
Indices: 676565--676640 Score: 73
Period size: 18 Copynumber: 3.9 Consensus size: 18
676555 TCAAGAACAA
*
676565 AAAAGAAAAGAAGCAAAAAA
1 AAAAGAAAA-AAG-AAAAAC
*
676585 ACAAAGAAAAAAGAGAAAC
1 A-AAAGAAAAAAGAAAAAC
676604 AAAAGAAAAAAGAAAGAAC
1 AAAAGAAAAAAGAAA-AAC
676623 AAAA-ATCAAAAAGAAAAA
1 AAAAGA--AAAAAGAAAAA
676641 GGGACAAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
18 14 0.29
19 14 0.29
20 13 0.27
21 8 0.16
ACGTcount: A:0.79, C:0.07, G:0.13, T:0.01
Consensus pattern (18 bp):
AAAAGAAAAAAGAAAAAC
Found at i:676613 original size:30 final size:31
Alignment explanation
Indices: 676557--676627 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
676547 AGATCCAATC
*
676557 AAGAACAAAAAAGAAAAGAAGCAAAAAAACA
1 AAGAACAAAAAAGAAAAAAAGCAAAAAAACA
* *
676588 AAGAA-AAAAGAGAAACAAAAG--AAAAAAGA
1 AAGAACAAAAAAGAAA-AAAAGCAAAAAAACA
676617 AAGAACAAAAA
1 AAGAACAAAAA
676628 TCAAAAAGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
29 12 0.35
30 13 0.38
31 9 0.26
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (31 bp):
AAGAACAAAAAAGAAAAAAAGCAAAAAAACA
Found at i:676627 original size:20 final size:19
Alignment explanation
Indices: 676564--676640 Score: 77
Period size: 20 Copynumber: 3.9 Consensus size: 19
676554 ATCAAGAACA
676564 AAAAAGAAAAGAAGCAAAAA-
1 AAAAAGAAAA-AAG-AAAAAC
*
676584 AACAAAGAAAAAAGAGAAAC
1 AA-AAAGAAAAAAGAAAAAC
676604 -AAAAGAAAAAAGAAAGAAC
1 AAAAAGAAAAAAGAAA-AAC
**
676623 AAAAATCAAAAAGAAAAA
1 AAAAAGAAAAAAGAAAAA
676641 GGGACAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
18 13 0.27
19 10 0.20
20 18 0.37
21 8 0.16
ACGTcount: A:0.79, C:0.06, G:0.13, T:0.01
Consensus pattern (19 bp):
AAAAAGAAAAAAGAAAAAC
Found at i:678375 original size:106 final size:106
Alignment explanation
Indices: 678248--678976 Score: 1221
Period size: 106 Copynumber: 6.9 Consensus size: 106
678238 GTGCCACTTG
* * * * *
678248 AGACAACACAA-TTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTT
678312 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
*
678353 AGACAACGCAATTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTT
* * *
678418 CAGAGCCAATTTTAACTTCACAACGAAGGATATTGGACTCT
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
678459 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTC-CTAATT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC-AATT
*
678523 TCAGAGCCAATTTCAACTTCACAGCGAATGATATTGGACTCC
65 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* * *
678565 AGACAACGCAAATTCAACTTCATGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTT
*
678630 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* *
678671 AGATAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTT
* * *
678736 CAAAGCCAATTTCAACTTCACAGTGAAGGATATTGGACTCA
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* *
678777 AGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTT
678842 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
*
678883 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTT
678948 CAGAGCCAATTTCAACTTCAC-GACGAAGG
66 CAGAGCCAATTTCAACTTCACAG-CGAAGG
678977 GACCGCTGGT
Statistics
Matches: 583, Mismatches: 37, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
105 12 0.02
106 570 0.98
107 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTT
CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
Found at i:679091 original size:266 final size:269
Alignment explanation
Indices: 678683--679242 Score: 842
Period size: 266 Copynumber: 2.1 Consensus size: 269
678673 ATAACGCAAG
* *
678683 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCTCAATTTCAAAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCACAATTT-AAAG---ATTT
*** *
678748 CAACTTCACAGTGAAGGATATTGGACTCAAGACAACGTAAGTTCAACTTCACGACGAAGGGACCG
62 CAACAAAACA--GAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
678813 CTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
125 CTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
678878 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
190 ACTCAAGACAACGAAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
678943 AATTTCAGAGCCAAT
255 AATTTCAGAGCCAAT
*
678958 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCACAATTT-TAG-TTGTCAA
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCACAATTTAAAGATT-TCAA
* * *
679021 -AAAACA-AAGGATGTTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGT
65 CAAAACAGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* *
679084 TGTCAATAAACAATTTCCCAATTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
130 TGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
* *
679149 AGACAACGAAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAATAAACAACTTCCCAATTT
195 AGACAACGAAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
*
679214 CAGAGTCAAT
260 CAGAGCCAAT
*
679224 TTTAACTTCAC-AGCGAAGG
1 TTCAACTTCACGA-CGAAGG
679243 ATATTGGACT
Statistics
Matches: 264, Mismatches: 19, Indels: 13
0.89 0.06 0.04
Matches are distributed among these distances:
265 1 0.00
266 201 0.76
269 5 0.02
270 4 0.02
273 2 0.01
275 51 0.19
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (269 bp):
TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCACAATTTAAAGATTTCAAC
AAAACAGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTT
GTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAA
GACAACGAAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
AGAGCCAAT
Found at i:679108 original size:372 final size:374
Alignment explanation
Indices: 678577--679344 Score: 1245
Period size: 372 Copynumber: 2.0 Consensus size: 374
678567 ACAACGCAAA
* *
678577 TTCAACTTCATGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCACAATTT-AGAG---ATTT
* * *
678642 CAACTTCACAACGAAGGATATTGGACTCCAGATAACGCAAGTTCAACTTCACGACGAAGGGACCG
62 CAA---CAAAACAAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
* *
678707 CTGGTTGTCAATAAACAATTTCTCAATTTCAAAGCCAATTTCAACTTCACAGTGAAGGATATTGG
124 CTGGTTGTCAATAAACAATTTCCCAATTTCAAAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
678772 ACTCAAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
189 ACTCAAGACAACGAAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
678837 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
254 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACT
* * *
678902 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
319 TCACGACAAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTCCAGAGCCAAT
* *
678958 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCACAATTT-TAG-TTGTCAA
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCACAATTTAGAGATT-TCAA
* *
679021 -AAAACAAAGGATGTTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTT
65 CAAAACAAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTT
* *
679085 GTCAATAAACAATTTCCCAATTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAA
130 GTCAATAAACAATTTCCCAATTTCAAAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAA
*
679150 GACAACGAAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAATAAACAACTTCCCAATTTC
195 GACAACGAAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTC
* *
679215 AGAGTCAATTTTAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGA
260 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGA
*
679280 CAAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTCCAGAGCCAAT
325 CAAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTCCAGAGCCAAT
679330 TTCAACTTCACGACG
1 TTCAACTTCACGACG
679345 GAGGATATTA
Statistics
Matches: 364, Mismatches: 22, Indels: 11
0.92 0.06 0.03
Matches are distributed among these distances:
372 306 0.84
375 2 0.01
376 4 0.01
379 2 0.01
381 50 0.14
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (374 bp):
TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCACAATTTAGAGATTTCAAC
AAAACAAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
TCAATAAACAATTTCCCAATTTCAAAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAG
ACAACGAAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCA
GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGAC
AAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTCCAGAGCCAAT
Found at i:679212 original size:106 final size:106
Alignment explanation
Indices: 679027--679359 Score: 542
Period size: 106 Copynumber: 3.1 Consensus size: 106
679017 TCAAAAAACA
* * *
679027 AAGGATGTTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAATA
1 AAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATA
*
679092 AACAATTTCCCAATTTCAGAGTCAATTTCAACTTCACAGCG
66 AACAACTTCCCAATTTCAGAGTCAATTTCAACTTCACAGCG
* *
679133 AAGGATATTGGACTCAAGACAACGAAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAATA
1 AAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATA
*
679198 AACAACTTCCCAATTTCAGAGTCAATTTTAACTTCACAGCG
66 AACAACTTCCCAATTTCAGAGTCAATTTCAACTTCACAGCG
*
679239 AAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAATA
1 AAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATA
* *
679304 AACAACTTCCCAATTCCAGAGCCAATTTCAACTTCAC-GACG
66 AACAACTTCCCAATTTCAGAGTCAATTTCAACTTCACAG-CG
* *
679345 GAGGATATTAGACTC
1 AAGGATATTGGACTC
679360 GGAACAATGC
Statistics
Matches: 211, Mismatches: 15, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
105 1 0.00
106 210 1.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.23
Consensus pattern (106 bp):
AAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATA
AACAACTTCCCAATTTCAGAGTCAATTTCAACTTCACAGCG
Found at i:680143 original size:37 final size:37
Alignment explanation
Indices: 680090--680194 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
680080 CCTTTTCATC
680090 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
680127 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
680164 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
680195 CCACAAACAC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:681030 original size:2 final size:2
Alignment explanation
Indices: 681023--681051 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
681013 TTTACTCATT
681023 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
681052 TTTCATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:681091 original size:16 final size:16
Alignment explanation
Indices: 681072--681112 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
681062 TATTAATTTA
*
681072 TTTATTTATTTTTCCT
1 TTTATTTATTTTTACT
681088 TTTATTT-TTTTTACT
1 TTTATTTATTTTTACT
681103 TATT-TTTATT
1 T-TTATTTATT
681113 CTTCATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTATTTATTTTTACT
Found at i:681100 original size:25 final size:26
Alignment explanation
Indices: 681072--681132 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
681062 TATTAATTTA
*
681072 TTTATTTATTTTTCCTT-TT-ATTTTT
1 TTTATTTATTTTT-ATTCTTCATTTTT
*
681097 TTTACTTATTTTTATTCTTCATTTTT
1 TTTATTTATTTTTATTCTTCATTTTT
*
681123 TTCATTTATT
1 TTTATTTATT
681133 CATTTTTTCC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 2 0.07
25 14 0.47
26 14 0.47
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (26 bp):
TTTATTTATTTTTATTCTTCATTTTT
Found at i:683031 original size:5 final size:5
Alignment explanation
Indices: 683016--683046 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
683006 TTGCCGGGGA
683016 AACCAC AACCC AACCC AACCC AACCC AACCC
1 AACC-C AACCC AACCC AACCC AACCC AACCC
683047 CGACACTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.84
6 4 0.16
ACGTcount: A:0.42, C:0.58, G:0.00, T:0.00
Consensus pattern (5 bp):
AACCC
Found at i:686754 original size:24 final size:24
Alignment explanation
Indices: 686722--686777 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
686712 CTATTCTTTC
686722 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
686746 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
686770 GCTTCAAT
1 GCTTCAAT
686778 CGAACTTCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:687058 original size:20 final size:20
Alignment explanation
Indices: 687035--687073 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
687025 CTCGGTTTTC
687035 CCGGTT-TTTAGCCGGTTCTT
1 CCGGTTCTTTA-CCGGTTCTT
687055 CCGGTTCTTTACCGGTTCT
1 CCGGTTCTTTACCGGTTCT
687074 GTGCTAATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.05, C:0.28, G:0.23, T:0.44
Consensus pattern (20 bp):
CCGGTTCTTTACCGGTTCTT
Found at i:689042 original size:2 final size:2
Alignment explanation
Indices: 688995--689024 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
688985 ATTTAATTCA
688995 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
689025 CAATTGAATA
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):
AT
Found at i:689095 original size:4 final size:4
Alignment explanation
Indices: 689086--689110 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
689076 TTTTATGTAA
689086 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
689111 ATTATTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:690072 original size:18 final size:18
Alignment explanation
Indices: 690049--690085 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
690039 AAGAATTTGG
690049 GGTATAATTCTTGAGGGA
1 GGTATAATTCTTGAGGGA
690067 GGTATAATTCTTGAGGGA
1 GGTATAATTCTTGAGGGA
690085 G
1 G
690086 TTGTAAGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.05, G:0.35, T:0.32
Consensus pattern (18 bp):
GGTATAATTCTTGAGGGA
Found at i:696098 original size:14 final size:14
Alignment explanation
Indices: 696062--696119 Score: 59
Period size: 14 Copynumber: 4.3 Consensus size: 14
696052 CTTGATTTAC
696062 ATATATTTATAAAT
1 ATATATTTATAAAT
*
696076 CTATA--TATACAAT
1 ATATATTTATA-AAT
*
696089 -TATATTTATATAT
1 ATATATTTATAAAT
*
696102 ATATATTTATACAT
1 ATATATTTATAAAT
696116 ATAT
1 ATAT
696120 TACTTATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
12 8 0.22
13 5 0.14
14 24 0.65
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (14 bp):
ATATATTTATAAAT
Found at i:696104 original size:12 final size:12
Alignment explanation
Indices: 696059--696120 Score: 52
Period size: 12 Copynumber: 4.8 Consensus size: 12
696049 AAACTTGATT
696059 TACATATATTTA
1 TACATATATTTA
* * *
696071 TAAATCTATATA
1 TACATATATTTA
696083 TACAATTATATTTATA
1 TAC-A-TATA-TT-TA
*
696099 TATATATATTTA
1 TACATATATTTA
696111 TACATATATT
1 TACATATATT
696121 ACTTATTTTC
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
12 22 0.58
13 3 0.08
14 7 0.18
15 2 0.05
16 4 0.11
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (12 bp):
TACATATATTTA
Found at i:700466 original size:21 final size:21
Alignment explanation
Indices: 700410--700466 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
700400 ATGCTCGGAG
*
700410 GGAACCGATTCCCCAATAGGA
1 GGAACCGATTCCCCCATAGGA
700431 GGAACCGATTCCCCCATAGGA
1 GGAACCGATTCCCCCATAGGA
700452 GGAACCGATTCCCCC
1 GGAACCGATTCCCCC
700467 TAAACAGTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.28, C:0.35, G:0.23, T:0.14
Consensus pattern (21 bp):
GGAACCGATTCCCCCATAGGA
Found at i:700499 original size:95 final size:95
Alignment explanation
Indices: 700334--700540 Score: 272
Period size: 95 Copynumber: 2.2 Consensus size: 95
700324 TTACTCAGAG
* ** *
700334 GGAACCGATTCCCCCCCATAGGAGGAACCGAGTCCCCCTGAATGGTTTGGCTCCGAGATTTCCAG
1 GGAACCGATT--CCCCCATAGGAGGAACCGAGTCCCCCTAAACAGTTTGGCTCCGAGAATTCCAG
*
700399 AATGCTCGGAGGGAACCGAT-TCCCCAATAGGA
64 AATGCTCGGAGGGAACCGATCCCCCCAA-AGGA
* * * *
700431 GGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTTTGTTCCGAGAATTCCAGTA
1 GGAACCGATTCCCCCATAGGAGGAACCGAGTCCCCCTAAACAGTTTGGCTCCGAGAATTCCAGAA
* *
700496 TGCTCGGAGGGAACCGATCCCCCCCAAGGG
66 TGCTCGGAGGGAACCGATCCCCCCAAAGGA
*
700526 GGTACCGATTCCCCC
1 GGAACCGATTCCCCC
700541 CTTGTGCAAC
Statistics
Matches: 97, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
95 82 0.85
96 5 0.05
97 10 0.10
ACGTcount: A:0.24, C:0.32, G:0.25, T:0.19
Consensus pattern (95 bp):
GGAACCGATTCCCCCATAGGAGGAACCGAGTCCCCCTAAACAGTTTGGCTCCGAGAATTCCAGAA
TGCTCGGAGGGAACCGATCCCCCCAAAGGA
Found at i:706293 original size:20 final size:19
Alignment explanation
Indices: 706268--706327 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 19
706258 TTTTGGTGCA
*
706268 GAGGGAATCGATCTCCCCCT
1 GAGGGAACCGAT-TCCCCCT
706288 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCC--T
706309 GAAGGGGAACCGATTCCCC
1 G-A-GGGAACCGATTCCCC
706328 ACACAGGGGA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
19 6 0.17
20 11 0.31
21 2 0.06
22 1 0.03
23 15 0.43
ACGTcount: A:0.22, C:0.33, G:0.27, T:0.18
Consensus pattern (19 bp):
GAGGGAACCGATTCCCCCT
Found at i:709087 original size:75 final size:75
Alignment explanation
Indices: 708930--709137 Score: 265
Period size: 75 Copynumber: 2.8 Consensus size: 75
708920 CAAAGCCAAA
* * * * **
708930 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTACCCCCTGAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
708995 TTGGCTCCGAG
65 TTGGCTCCGAG
*
709006 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
* * *
709071 TTGTTCTGAG
66 TGGCTCCGAG
* * * *
709081 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCTAAAGG-GGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCC-ATAGGAGGAACCGATTCCCCCCT
709138 TGTGCAACGG
Statistics
Matches: 116, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
75 86 0.74
76 30 0.26
ACGTcount: A:0.25, C:0.30, G:0.24, T:0.22
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TGGCTCCGAG
Done.